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CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background One aim of the in silico characterization of proteins is to identify all residue-positions, which are crucial for function or structure. Several sequence-based algorithms exist, which predict functionally important sites. However, with respect to sequence information, many functionally and structurally important sites are hard to distinguish and consequently a large number of incorrectly predicted functional sites have to be expected. This is why we were interested to design a new classifier that differentiates between functionally and structurally important sites and to assess its performance on representative datasets. Results We have implemented CLIPS-1D, which predicts a role in catalysis, ligand-binding, or protein structure for residue-positions in a mutually exclusive manner. By analyzing a multiple sequence alignment, the algorithm scores conservation as well as abundance of residues at individual sites and their local neighborhood and categorizes by means of a multiclass support vector machine. A cross-validation confirmed that residue-positions involved in catalysis were identified with state-of-the-art quality; the mean MCC-value was 0.34. For structurally important sites, prediction quality was considerably higher (mean MCC = 0.67. For ligand-binding sites, prediction quality was lower (mean MCC = 0.12, because binding sites and structurally important residue-positions share conservation and abundance values, which makes their separation difficult. We show that classification success varies for residues in a class-specific manner. This is why our algorithm computes residue-specific p-values, which allow for the statistical assessment of each individual prediction. CLIPS-1D is available as a Web service at http://www-bioinf.uni-regensburg.de/. Conclusions CLIPS-1D is a classifier, whose prediction quality has been determined separately for catalytic sites, ligand-binding sites, and structurally important sites. It generates hypotheses about residue-positions important for a set of homologous proteins and focuses on conservation and abundance signals. Thus, the algorithm can be applied in cases where function cannot be transferred from well-characterized proteins by means of sequence comparison.

Janda Jan-Oliver

2012-04-01

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PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences.  

Science.gov (United States)

Annotation of any newly determined protein sequence depends on the pairwise sequence identity with known sequences. However, for the twilight zone sequences which have only 15-25% identity, the pair-wise comparison methods are inadequate and the annotation becomes a challenging task. Such sequences can be annotated by using methods that recognize their fold. Bowie et al. described a 3D1D profile method in which the amino acid sequences that fold into a known 3D structure are identified by their compatibility to that known 3D structure. We have improved the above method by using the predicted secondary structure information and employ it for fold recognition from the twilight zone sequences. In our Protein Secondary Structure 3D1D (PSS-3D1D) method, a score (w) for the predicted secondary structure of the query sequence is included in finding the compatibility of the query sequence to the known fold 3D structures. In the benchmarks, the PSS-3D1D method shows a maximum of 21% improvement in predicting correctly the ? + ? class of folds from the sequences with twilight zone level of identity, when compared with the 3D1D profile method. Hence, the PSS-3D1D method could offer more clues than the 3D1D method for the annotation of twilight zone sequences. The web based PSS-3D1D method is freely available in the PredictFold server at http://bioinfo.bdu.ac.in/servers/ . PMID:22160493

Ganesan, K; Parthasarathy, S

2011-12-01

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Two new 1D coordination polymers: syntheses, structures and properties  

Directory of Open Access Journals (Sweden)

Full Text Available Two new coordination polymers, namely, [Zn(bi(Cl2]n (1 and [Cu(L2(bib(H2O2]n (2 (bi = 4,4'-bis(2-methylimidazol-1-ylmethylbiphenyl; L = 4-(2-(4-(methoxycarbonylphenoxyethoxybenzoic acid and bib = 2,3-bis(4-pyridylbutane, are synthesized and characterized. Both of 1 and 2 have 1D covalent chains, which show different conformally chain feature. 2D supremolecular rhombic and rectangle motifs are observed in 1 and 2, respectively. The O–H···O and C–H···Cl hydrogen-bonding interactions play a significant role in promoting the diversity of structural patterns. DOI: http://dx.doi.org/10.4314/bcse.v28i3.11

J. Wu

2014-09-01

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Spin asymmetry A1d and the spin-dependent structure function g1d of the deuteron at low values of x and Q2  

Science.gov (United States)

We present a precise measurement of the deuteron longitudinal spin asymmetry A1d and of the deuteron spin-dependent structure function g1d at Q2 < 1 (GeV / c) 2 and 4 ×10-5 < x < 2.5 ×10-2 based on the data collected by the COMPASS experiment at CERN during the years 2002 and 2003. The statistical precision is tenfold better than that of the previous measurement in this region. The measured A1d and g1d are found to be consistent with zero in the whole range of x.

Alexakhin, V. Yu.; Alexandrov, Yu.; Alexeev, G. D.; Amoroso, A.; Bade?ek, B.; Balestra, F.; Ball, J.; Baum, G.; Bedfer, Y.; Bernet, C.; Bertini, R.; Birsa, R.; Bisplinghoff, J.; Bordalo, P.; Bradamante, F.; Bravar, A.; Bressan, A.; Brona, G.; Burtin, E.; Bussa, M. P.; Chapiro, A.; Cicuttin, A.; Colantoni, M.; Costa, S.; Crespo, M. L.; D'Hose, N.; Dalla Torre, S.; Dasgupta, S. S.; de Masi, R.; Denisov, O. Yu.; Dhara, L.; Diaz Kavka, V.; Dinkelbach, A. M.; Donskov, S. V.; Dorofeev, V. A.; Doshita, N.; Duic, V.; Dünnweber, W.; Eversheim, P. D.; Eyrich, W.; Fabro, M.; Faessler, M.; Falaleev, V.; Ferrero, A.; Ferrero, L.; Finger, M.; Finger, M.; Fischer, H.; Franz, J.; Friedrich, J. M.; Frolov, V.; Garfagnini, R.; Gautheron, F.; Gavrichtchouk, O. P.; Gerassimov, S.; Geyer, R.; Giorgi, M.; Gobbo, B.; Goertz, S.; Gorin, A. M.; Grajek, O. A.; Grasso, A.; Grube, B.; Hannappel, J.; von Harrach, D.; Hasegawa, T.; Heckmann, J.; Hedicke, S.; Heinsius, F. H.; Hermann, R.; Heß, C.; Hinterberger, F.; von Hodenberg, M.; Horikawa, N.; Horikawa, S.; Ilgner, C.; Ioukaev, A. I.; Ishimoto, S.; Ivanov, O.; Iwata, T.; Jahn, R.; Janata, A.; Joosten, R.; Jouravlev, N. I.; Kabuß, E.; Kang, D.; Ketzer, B.; Khaustov, G. V.; Khokhlov, Yu. A.; Khomutov, N. V.; Kisselev, Yu.; Klein, F.; Koblitz, S.; Koivuniemi, J. H.; Kolosov, V. N.; Komissarov, E. V.; Kondo, K.; Königsmann, K.; Konorov, I.; Konstantinov, V. F.; Korentchenko, A. S.; Korzenev, A.; Kotzinian, A. M.; Koutchinski, N. A.; Kravchuk, N. P.; Kroumchtein, Z. V.; Kuhn, R.; Kunne, F.; Kurek, K.; Ladygin, M. E.; Lamanna, M.; Le Goff, J. M.; Lichtenstadt, J.; Liska, T.; Ludwig, I.; Maggiora, A.; Maggiora, M.; Magnon, A.; Mallot, G. K.; Marchand, C.; Marroncle, J.; Martin, A.; Marzec, J.; Matsuda, T.; Maximov, A. N.; Meyer, W.; Mielech, A.; Mikhailov, Yu. V.; Moinester, M. A.; Nähle, O.; Nassalski, J.; Neliba, S.; Neyret, D. P.; Nikolaenko, V. I.; Nozdrin, A. A.; Obraztsov, V. F.; Olshevsky, A. G.; Ostrick, M.; Padee, A.; Pagano, P.; Panebianco, S.; Panzieri, D.; Paul, S.; Peshekhonov, D. V.; Peshekhonov, V. D.; Piragino, G.; Platchkov, S.; Pochodzalla, J.; Polyakov, V. A.; Popov, A. A.; Pretz, J.; Procureur, S.; Quintans, C.; Ramos, S.; Reicherz, G.; Rozhdestvensky, A. M.; Rondio, E.; Sadovski, A. B.; Samoylenko, V. D.; Sandacz, A.; Sapozhnikov, M. G.; Savin, I. A.; Schiavon, P.; Schill, C.; Schmitt, L.; Shevchenko, O. Yu.; Shishkin, A. A.; Siebert, H.-W.; Sinha, L.; Sissakian, A. N.; Slunecka, M.; Smirnov, G. I.; Sozzi, F.; Sugonyaev, V. P.; Srnka, A.; Stinzing, F.; Stolarski, M.; Sulc, M.; Sulej, R.; Takabayashi, N.; Tchalishev, V. V.; Tessarotto, F.; Teufel, A.; Tkatchev, L. G.; Virius, M.; Vlassov, N. V.; Webb, R.; Weise, E.; Weitzel, Q.; Windmolders, R.; Wirth, S.; Wi?licki, W.; Zaremba, K.; Zhao, J.; Ziegler, R.; Zvyagin, A.; Compass Collaboration

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Spin asymmetry A1d and the spin-dependent structure function g1d of the deuteron at low values of x and Q  

Science.gov (United States)

We present a precise measurement of the deuteron longitudinal spin asymmetry A1d and of the deuteron spin-dependent structure function g1d at Q<1 GeV and 4×101d and g1d are found to be consistent with zero in the whole range of x.

Compass Collaboration; Alexakhin, V. Yu.; Alexandrov, Yu.; Alexeev, G. D.; Amoroso, A.; Bade?ek, B.; Balestra, F.; Ball, J.; Baum, G.; Bedfer, Y.; Bernet, C.; Bertini, R.; Birsa, R.; Bisplinghoff, J.; Bordalo, P.; Bradamante, F.; Bravar, A.; Bressan, A.; Brona, G.; Burtin, E.; Bussa, M. P.; Chapiro, A.; Cicuttin, A.; Colantoni, M.; Costa, S.; Crespo, M. L.; D'Hose, N.; Dalla Torre, S.; Dasgupta, S. S.; de Masi, R.; Denisov, O. Yu.; Dhara, L.; Diaz Kavka, V.; Dinkelbach, A. M.; Donskov, S. V.; Dorofeev, V. A.; Doshita, N.; Duic, V.; Dünnweber, W.; Eversheim, P. D.; Eyrich, W.; Fabro, M.; Faessler, M.; Falaleev, V.; Ferrero, A.; Ferrero, L.; Finger, M.; Finger, M.; Fischer, H.; Franz, J.; Friedrich, J. M.; Frolov, V.; Garfagnini, R.; Gautheron, F.; Gavrichtchouk, O. P.; Gerassimov, S.; Geyer, R.; Giorgi, M.; Gobbo, B.; Goertz, S.; Gorin, A. M.; Grajek, O. A.; Grasso, A.; Grube, B.; Hannappel, J.; von Harrach, D.; Hasegawa, T.; Heckmann, J.; Hedicke, S.; Heinsius, F. H.; Hermann, R.; Heß, C.; Hinterberger, F.; von Hodenberg, M.; Horikawa, N.; Horikawa, S.; Ilgner, C.; Ioukaev, A. I.; Ishimoto, S.; Ivanov, O.; Iwata, T.; Jahn, R.; Janata, A.; Joosten, R.; Jouravlev, N. I.; Kabuß, E.; Kang, D.; Ketzer, B.; Khaustov, G. V.; Khokhlov, Yu. A.; Khomutov, N. V.; Kisselev, Yu.; Klein, F.; Koblitz, S.; Koivuniemi, J. H.; Kolosov, V. N.; Komissarov, E. V.; Kondo, K.; Königsmann, K.; Konorov, I.; Konstantinov, V. F.; Korentchenko, A. S.; Korzenev, A.; Kotzinian, A. M.; Koutchinski, N. A.; Kravchuk, N. P.; Kroumchtein, Z. V.; Kuhn, R.; Kunne, F.; Kurek, K.; Ladygin, M. E.; Lamanna, M.; Le Goff, J. M.; Lichtenstadt, J.; Liska, T.; Ludwig, I.; Maggiora, A.; Maggiora, M.; Magnon, A.; Mallot, G. K.; Marchand, C.; Marroncle, J.; Martin, A.; Marzec, J.; Matsuda, T.; Maximov, A. N.; Meyer, W.; Mielech, A.; Mikhailov, Yu. V.; Moinester, M. A.; Nähle, O.; Nassalski, J.; Neliba, S.; Neyret, D. P.; Nikolaenko, V. I.; Nozdrin, A. A.; Obraztsov, V. F.; Olshevsky, A. G.; Ostrick, M.; Padee, A.; Pagano, P.; Panebianco, S.; Panzieri, D.; Paul, S.; Peshekhonov, D. V.; Peshekhonov, V. D.; Piragino, G.; Platchkov, S.; Pochodzalla, J.; Polyakov, V. A.; Popov, A. A.; Pretz, J.; Procureur, S.; Quintans, C.; Ramos, S.; Reicherz, G.; Rozhdestvensky, A. M.; Rondio, E.; Sadovski, A. B.; Samoylenko, V. D.; Sandacz, A.; Sapozhnikov, M. G.; Savin, I. A.; Schiavon, P.; Schill, C.; Schmitt, L.; Shevchenko, O. Yu.; Shishkin, A. A.; Siebert, H.-W.; Sinha, L.; Sissakian, A. N.; Slunecka, M.; Smirnov, G. I.; Sozzi, F.; Sugonyaev, V. P.; Srnka, A.; Stinzing, F.; Stolarski, M.; Sulc, M.; Sulej, R.; Takabayashi, N.; Tchalishev, V. V.; Tessarotto, F.; Teufel, A.; Tkatchev, L. G.; Virius, M.; Vlassov, N. V.; Webb, R.; Weise, E.; Weitzel, Q.; Windmolders, R.; Wirth, S.; Wi?licki, W.; Zaremba, K.; Zhao, J.; Ziegler, R.; Zvyagin, A.

2007-04-01

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[Chemical structural features and anti-complementary activity of polysaccharide HPS1-D from Hedysarum polybotrys].  

Science.gov (United States)

HPS1-D, an active polysaccharide,was isolated and purified from Hedysarum polybotrys. HPS1-D was obtained after treated with Savage method and H2O2, and purified with DEAE-cellulose 52 and Sephadex G-100 gel filtration chromatography. Then physicochemical property analysis, GC, methylation, partial acid hydrolysis, and NMR method were used to study chemical structural of HPS1-D. The conformation was primarily analyzed with GPC-MALLS method and Congo red reaction. The anti-complementary activity of HPS1-D was evaluated with the hemolysis assay. HPS1-D was a heteropolysaccharide and consisted of D-glucose, L-arabinose, (7.2:1.3). HPS1-D proved to be a neutral sugar, with 1, 4-and 1, 4, 6-alpha-D-glucopyranosyl residues in backbone ,and 1, 5-and 1, 3, 5-alpha-L-arabinofuranosyl residues in branches. HPS1-D has a random coil state conformation with monodisperse mass distribution in 0.9% NaCl solution. And HPS1-D had triple-helix conformation in concentrate of NaOH solution. Anti-complementary activity of HPS1-D was closed to its positive control heparin. PMID:24754175

Yang, Tao; Guo, Long; Li, Can; Yang, Ying-Lai; Feng, Shi-Lan

2014-01-01

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Structure and Catalytic Mechanism of Human Steroid 5-Reductase (AKR1D1)  

Energy Technology Data Exchange (ETDEWEB)

Human steroid 5{beta}-reductase (aldo-keto reductase (AKR) 1D1) catalyzes reduction of {Delta}{sup 4}-ene double bonds in steroid hormones and bile acid precursors. We have reported the structures of an AKR1D1-NADP{sup +} binary complex, and AKR1D1-NADP{sup +}-cortisone, AKR1D1-NADP{sup +}-progesterone and AKR1D1-NADP{sup +}-testosterone ternary complexes at high resolutions. Recently, structures of AKR1D1-NADP{sup +}-5{beta}-dihydroprogesterone complexes showed that the product is bound unproductively. Two quite different mechanisms of steroid double bond reduction have since been proposed. However, site-directed mutagenesis supports only one mechanism. In this mechanism, the 4-pro-R hydride is transferred from the re-face of the nicotinamide ring to C5 of the steroid substrate. E120, a unique substitution in the AKR catalytic tetrad, permits a deeper penetration of the steroid substrate into the active site to promote optimal reactant positioning. It participates with Y58 to create a 'superacidic' oxyanion hole for polarization of the C3 ketone. A role for K87 in the proton relay proposed using the AKR1D1-NADP{sup +}-5{beta}-dihydroprogesterone structure is not supported.

Costanzo, L.; Drury, J; Christianson, D; Penning, T

2009-01-01

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Structural resistance of chemically modified 1-D nanostructured titanates in inorganic acid environment  

International Nuclear Information System (INIS)

Sodium containing one-dimensional nanostructured layered titanates (1-D NSLT) were produced both from commercial anatase powder and Brazilian natural rutile mineral sands by alkali hydrothermal process. The 1-D NSLT were chemically modified with proton, cobalt or iron via ionic exchange and all products were additionally submitted to intensive inorganic acid aging (pH = 0.5) for 28 days. The morphology and crystal structure transformations of chemically modified 1-D NSLT were followed by transmission electron microscopy, powder X-ray diffraction, selected area electron diffraction and energy dispersive spectroscopy. It was found that the original sodium rich 1-D NSLT and cobalt substituted 1-D NSLT were completely converted to rutile nanoparticles, while the protonated form was transformed in a 70%-30% (by weight) anatase-rutile nanoparticles mixture, very similar to that of the well-known TiO2-photocatalyst P25 (Degussa). The iron substituted 1-D NSLT presented better acid resistance as 13% of the original structure and morphology remained, the rest being converted in rutile. A significant amount of remaining 1-D NSLT was also observed after the acid treatment of the product obtained from rutile sand. The results showed that phase transformation of NSLT into titanium dioxide polymorph in inorganic acid conditions were controllable by varying the exchanged cations. Finally, the possibility to transform, through acid aging, 1-D NSLT obtained from Brazilian natural rutile sand into TiO2-polymorphs was demonstrated for the first time to the best of authors' knowledge, opening path for producing TiO2-nanoproducts with different morphologies through a simple process and from a low cost precursor.

9

Structural resistance of chemically modified 1-D nanostructured titanates in inorganic acid environment  

Energy Technology Data Exchange (ETDEWEB)

Sodium containing one-dimensional nanostructured layered titanates (1-D NSLT) were produced both from commercial anatase powder and Brazilian natural rutile mineral sands by alkali hydrothermal process. The 1-D NSLT were chemically modified with proton, cobalt or iron via ionic exchange and all products were additionally submitted to intensive inorganic acid aging (pH = 0.5) for 28 days. The morphology and crystal structure transformations of chemically modified 1-D NSLT were followed by transmission electron microscopy, powder X-ray diffraction, selected area electron diffraction and energy dispersive spectroscopy. It was found that the original sodium rich 1-D NSLT and cobalt substituted 1-D NSLT were completely converted to rutile nanoparticles, while the protonated form was transformed in a 70%-30% (by weight) anatase-rutile nanoparticles mixture, very similar to that of the well-known TiO{sub 2}-photocatalyst P25 (Degussa). The iron substituted 1-D NSLT presented better acid resistance as 13% of the original structure and morphology remained, the rest being converted in rutile. A significant amount of remaining 1-D NSLT was also observed after the acid treatment of the product obtained from rutile sand. The results showed that phase transformation of NSLT into titanium dioxide polymorph in inorganic acid conditions were controllable by varying the exchanged cations. Finally, the possibility to transform, through acid aging, 1-D NSLT obtained from Brazilian natural rutile sand into TiO{sub 2}-polymorphs was demonstrated for the first time to the best of authors' knowledge, opening path for producing TiO{sub 2}-nanoproducts with different morphologies through a simple process and from a low cost precursor.

Marinkovic, Bojan A., E-mail: bojan@puc-rio.br [Departamento de Engenharia de Materiais, Pontificia Universidade Catolica de Rio de Janeiro-PUC-Rio, Rua Marques de Sao Vicente 225, Gavea, RJ (Brazil); Fredholm, Yann C. [Nanogavea-Nanotecnologia Sustentavel Ltda, Av. Padre Leonel Franca 150, Gavea, RJ (Brazil); Morgado, Edisson [PETROBRAS S.A./CENPES, Research and Development Centre, Av. Horacio Macedo, 950, Cidade Universitaria, 21941-915, Rio de Janeiro, RJ (Brazil); Jardim, Paula M.; Rizzo, Fernando [Departamento de Engenharia de Materiais, Pontificia Universidade Catolica de Rio de Janeiro-PUC-Rio, Rua Marques de Sao Vicente 225, Gavea, RJ (Brazil)

2010-10-15

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The deuteron spin-dependent structure function g1d and its first moment  

Science.gov (United States)

We present a measurement of the deuteron spin-dependent structure function g1d based on the data collected by the COMPASS experiment at CERN during the years 2002 2004. The data provide an accurate evaluation for ?1d, the first moment of g1d(x), and for the matrix element of the singlet axial current, a. The results of QCD fits in the next to leading order (NLO) on all g deep inelastic scattering data are also presented. They provide two solutions with the gluon spin distribution function ?G positive or negative, which describe the data equally well. In both cases, at Q=3GeV the first moment of ?G(x) is found to be of the order of 0.2 0.3 in absolute value.

Compass Collaboration; Alexakhin, V. Yu.; Alexandrov, Yu.; Alexeev, G. D.; Alexeev, M.; Amoroso, A.; Bade?ek, B.; Balestra, F.; Ball, J.; Barth, J.; Baum, G.; Becker, M.; Bedfer, Y.; Bernet, C.; Bertini, R.; Bettinelli, M.; Birsa, R.; Bisplinghoff, J.; Bordalo, P.; Bradamante, F.; Bressan, A.; Brona, G.; Burtin, E.; Bussa, M. P.; Bytchkov, V. N.; Chapiro, A.; Cicuttin, A.; Colantoni, M.; Colavita, A. A.; Costa, S.; Crespo, M. L.; D'Hose, N.; Dalla Torre, S.; Das, S.; Dasgupta, S. S.; de Masi, R.; Dedek, N.; Demchenko, D.; Denisov, O. Yu.; Dhara, L.; Diaz, V.; Dinkelbach, A. M.; Donskov, S. V.; Dorofeev, V. A.; Doshita, N.; Duic, V.; Dünnweber, W.; Efremov, A.; Eversheim, P. D.; Eyrich, W.; Faessler, M.; Fauland, P.; Ferrero, A.; Ferrero, L.; Finger, M.; Finger, M.; Fischer, H.; Franz, J.; Friedrich, J. M.; Frolov, V.; Garfagnini, R.; Gautheron, F.; Gavrichtchouk, O. P.; Gerassimov, S.; Geyer, R.; Giorgi, M.; Gobbo, B.; Goertz, S.; Gorin, A. M.; Grajek, O. A.; Grasso, A.; Grube, B.; Guskov, A.; Haas, F.; Hannappel, J.; von Harrach, D.; Hasegawa, T.; Hedicke, S.; Heinsius, F. H.; Hermann, R.; Heß, C.; Hinterberger, F.; von Hodenberg, M.; Horikawa, N.; Horikawa, S.; Horn, I.; Ilgner, C.; Ioukaev, A. I.; Ivanchin, I.; Ivanov, O.; Iwata, T.; Jahn, R.; Janata, A.; Joosten, R.; Jouravlev, N. I.; Kabuß, E.; Kang, D.; Ketzer, B.; Khaustov, G. V.; Khokhlov, Yu. A.; Kisselev, Yu.; Klein, F.; Klimaszewski, K.; Koblitz, S.; Koivuniemi, J. H.; Kolosov, V. N.; Komissarov, E. V.; Kondo, K.; Königsmann, K.; Konorov, I.; Konstantinov, V. F.; Korentchenko, A. S.; Korzenev, A.; Kotzinian, A. M.; Koutchinski, N. A.; Kouznetsov, O.; Kowalik, K.; Kramer, D.; Kravchuk, N. P.; Krivokhizhin, G. V.; Kroumchtein, Z. V.; Kubart, J.; Kuhn, R.; Kukhtin, V.; Kunne, F.; Kurek, K.; Ladygin, M. E.; Lamanna, M.; Le Goff, J. M.; Leberig, M.; Lednev, A. A.; Lehmann, A.; Lichtenstadt, J.; Liska, T.; Ludwig, I.; Maggiora, A.; Maggiora, M.; Magnon, A.; Mallot, G. K.; Marchand, C.; Marroncle, J.; Martin, A.; Marzec, J.; Masek, L.; Massmann, F.; Matsuda, T.; Matthiä, D.; Maximov, A. N.; Meyer, W.; Mielech, A.; Mikhailov, Yu. V.; Moinester, M. A.; Nagel, T.; Nähle, O.; Nassalski, J.; Neliba, S.; Neyret, D. P.; Nikolaenko, V. I.; Nikolaev, K.; Nozdrin, A. A.; Obraztsov, V. F.; Olshevsky, A. G.; Ostrick, M.; Padee, A.; Pagano, P.; Panebianco, S.; Panzieri, D.; Paul, S.; Peshekhonov, D. V.; Peshekhonov, V. D.; Piragino, G.; Platchkov, S.; Pochodzalla, J.; Polak, J.; Polyakov, V. A.; Pontecorvo, G.; Popov, A. A.; Pretz, J.; Procureur, S.; Quintans, C.; Ramos, S.; Reicherz, G.; Rondio, E.; Rozhdestvensky, A. M.; Ryabchikov, D.; Samoylenko, V. D.; Sandacz, A.; Santos, H.; Sapozhnikov, M. G.; Savin, I. A.; Schiavon, P.; Schill, C.; Schmitt, L.; Schroeder, W.; Seeharsch, D.; Seimetz, M.; Setter, D.; Shevchenko, O. Yu.; Siebert, H.-W.; Silva, L.; Sinha, L.; Sissakian, A. N.; Slunecka, M.; Smirnov, G. I.; Sozzi, F.; Srnka, A.; Stinzing, F.; Stolarski, M.; Sugonyaev, V. P.; Sulc, M.; Sulej, R.; Tchalishev, V. V.; Tessaro, S.; Tessarotto, F.; Teufel, A.; Tkatchev, L. G.; Trippel, S.; Venugopal, G.; Virius, M.; Vlassov, N. V.; Webb, R.; Weise, E.; Weitzel, Q.; Windmolders, R.; Wi?licki, W.; Zaremba, K.; Zavertyaev, M.; Zemlyanichkina, E.; Zhao, J.; Ziegler, R.; Zvyagin, A.

2007-03-01

11

HERMES Precision Results on g1p, g1d and g1n and the First Measurement of the Tensor Structure Function b1d  

CERN Document Server

Final HERMES results on the proton, deuteron and neutron structure function g1 are presented in the kinematic range 0.0021structure function b1d are presented.

Riedl, C; Akopov, Z; Amarian, M; Ammosov, V V; Andrus, A; Aschenauer, E C; Augustyniak, W; Avakian, R; Avetisian, A; Avetissian, E; Bailey, P; Baturin, V; Baumgarten, C; Beckmann, M; Belostotskii, S; Bernreuther, S; Bianchi, N; Blok, H P; Böttcher, Helmut B; Borisov, A; Bouwhuis, M; Brack, J; Brüll, A; Bryzgalov, V V; Capitani, G P; Chiang, H C; Ciullo, G; Contalbrigo, M; Dalpiaz, P F; De Leo, R; De Nardo, L; De Sanctis, E; Devitsin, E G; Di Nezza, P; Düren, M; Ehrenfried, M; Elalaoui-Moulay, A; Elbakian, G M; Ellinghaus, F; Elschenbroich, U; Ely, J; Fabbri, R; Fantoni, A; Feshchenko, A; Felawka, L; Fox, B; Franz, J; Frullani, S; Gärber, Y; Gapienko, G; Gapienko, V; Garibaldi, F; Garrow, K; Garutti, E; Gaskell, D; Gavrilov, G E; Karibian, V; Graw, G; Grebenyuk, O; Greeniaus, L G; Hafidi, K; Hartig, M; Hasch, D; Heesbeen, D; Henoch, M; Hertenberger, R; Hesselink, W H A; Hillenbrand, A; Hoek, M; Holler, Y; Hommez, B; Iarygin, G; Ivanilov, A; Izotov, A; Jackson, H E; Jgoun, A; Kaiser, R; Kinney, E; Kiselev, A; Königsmann, K C; Kopytin, M; Korotkov, V A; Kozlov, V; Krauss, B; Krivokhizhin, V G; Lagamba, L; Lapikas, L; Laziev, A; Lenisa, P; Liebing, P; Lindemann, T; Lipka, K; Lorenzon, W; Lü, J; Maiheu, B; Makins, N C R; Marianski, B; Marukyan, H O; Masoli, F; Mexner, V; Meyners, N; Miklukho, O; Miller, C A; Miyachi, Y; Muccifora, V; Nagaitsev, A; Nappi, E; Naryshkin, Yu; Nass, A; Negodaev, M A; Nowak, Wolf-Dieter; Oganessyan, K; Ohsuga, H; Orlandi, G; Pickert, N; Potashov, S Yu; Potterveld, D H; Raithel, M; Reggiani, D; Reimer, P E; Reischl, A; Reolon, A R; Rith, K; Airapetian, A; Rosner, G; Rostomyan, A; Rubacek, L; Ryckbosch, D; Salomatin, Yu I; Sanjiev, I; Savin, I; Scarlett, C; Schäfer, A; Schill, C; Schnell, G; Schüler, K P; Schwind, A; Seele, J; Seidl, R; Seitz, B; Shanidze, R G; Shearer, C; Shibata, T A; Shutov, V B; Simani, M C; Sinram, K; Stancari, M D; Statera, M; Steffens, E; Steijger, J J M; Stewart, J; Stösslein, U; Tait, P; Tanaka, H; Taroian, S P; Tchuiko, B; Terkulov, A R; Tkabladze, A V; Trzcinski, A; Tytgat, M; Vandenbroucke, A; Van der Nat, P B; van der Steenhoven, G; Vetterli, Martin C; Vikhrov, V; Vincter, M G; Visser, J; Vogel, C; Vogt, M; Volmer, J; Weiskopf, C; Wendland, J; Wilbert, J; Ybeles-Smit, G V; Yen, S; Zihlmann, B; Zohrabyan, H G; Zupranski, P; Riedl, Caroline

2005-01-01

12

Non-linear Finite-Frequency Waveform Inversion for 1-D Structures  

Science.gov (United States)

One-dimensional velocity models are representative of regional tectonic units. They are important in determining the locations and focal mechanisms of earthquakes, and provide initial models for tomographic studies. We develop a new approach to the non-linear inversion of finite-frequency traveltimes and amplitudes for 1-D models. Frequency-dependent traveltime and amplitude anomalies are measured by cross-correlation of three-component synthetic and recorded waveforms windowed around body and surface waves. Sensitivity kernels to parameters involved in the 1-D model, such as P- and S-wave speeds and depths of seismic discontinuities, are computed numerically by perturbing the reference model and measuring the resulting traveltime and amplitude perturbations, thus avoiding the invocation of Born approximation. An iterative inversion is carried out with updates of traveltime and amplitude measurements and sensitivity kernels following each iteration. We apply this new approach to the inversion of 1D structures around the source region of the May 12, 2008, Wenchuan earthquake. Numerous moderate aftershocks (Mw=5-6) and densely deployed broadband stations provide plenty of records for obtaining 1-D models along a variety of source-receiver path, revealing lateral structural variations in both the Tibetan Plateau and Sichuan Basin.

Wan, K.; Ni, S.; Zhao, L.

2010-12-01

13

The Dynamic Structure Factor of the 1D Bose Gas near the Tonks-Girardeau Limit  

CERN Document Server

While the 1D Bose gas appears to exhibit superfluid response under certain conditions, it fails the Landau criterion according to the elementary excitation spectrum calculated by Lieb. The apparent riddle is solved by calculating the dynamic structure factor of the Lieb-Liniger 1D Bose gas. A pseudopotential Hamiltonian in the fermionic representation is used to derive a Hartree-Fock operator, which turns out to be well-behaved and local. The Random-Phase approximation for the dynamic structure factor based on this derivation is calculated analytically and is expected to be valid at least up to first order in $1/\\gamma$, where $\\gamma$ is the dimensionless interaction strength of the model. The dynamic structure factor in this approximation clearly indicates a crossover behavior from the non-superfluid Tonks to the superfluid weakly-interacting regime, which should be observable by Bragg scattering in current experiments.

Brand, J; Brand, Joachim; Cherny, Alexander Yu.

2004-01-01

14

Structurally unstable regular dynamics in 1D piecewise smooth maps, and circle maps  

International Nuclear Information System (INIS)

Highlights: ? A discontinuous 1D map with two discontinuity points is considered. ? Dynamic behaviors are either periodic or quasiperiodic. ? Dynamics are always structurally unstable. ? Any small perturbation in one of the parameters leads to different dynamics. - Abstract: In this work we consider a simple system of piecewise linear discontinuous 1D map with two discontinuity points: X? = aX if ?X? z, where a and b can take any real value, and may have several applications. We show that its dynamic behaviors are those of a linear rotation: either periodic or quasiperiodic, and always structurally unstable. A generalization to piecewise monotone functions X? = F(X) if ?X? z is also given, proving the conditions leading to a homeomorphism of the circle.

15

1D vs 2D crystal architecture of hybrid inorganic-organic structures with benzidine dication  

Science.gov (United States)

A series of a dozen novel inorganic-organic hybrid salts of benzidine dication containing complex inorganic anions such as metal halides have been prepared and structurally characterized. Crystal structures obtained have either linear 1D or layered 2D architectures created by aromatic benzidine moieties aggregated in stacks or sheets. A small number of structures with polymerized inorganic layers of the perovskite-like type is associated with a relatively high 2D density of charge caused by close packing of organic cations with charge compensated by inorganic complex moieties. Also the dual nature of the benzidine cations helps in formation of stacks of molecules instead of layers. Another feature discussed is an inherent tendency to form twins caused by the way of packing of molecules in some of the presented crystals.

Dobrzycki, Lukasz; Wo?niak, Krzysztof

2009-03-01

16

Role of potential structure in the collisional excitation of metastable O(1D) atoms  

International Nuclear Information System (INIS)

This paper considers the collisional excitation of O(1D) modeled by the crossing of two valence 1 3?g curves dissociating to O(3P)+O(3P) [V11(R)] and O(3P)+O(1D) [V22(R)] which in turn are further crossed by the 3?g Rydberg curve dissociating to O(3P)+O(5S) [V33(R)]. The role of structure in the potential curves and coupling matrix elements is quantitatively probed by the first-order functional-sensitivity densities ? ln?12(E)/? lnVij(R) of the excitation cross section ?12(E) obtained from close-coupling calculations. The results reveal that, in spite of the well-separated nature of the crossing between the two valence curves from their crossings with the Rydberg potential curve, the excitation cross section ?12 displays considerable sensitivity to the Rydberg curve V33(R) at all energies in the range 3.0--9.0 eV. For relative collisional energies corresponding to the higher closely spaced vibrational energy levels of the Rydberg state, the excitation cross section is found to be much more sensitive to the Rydberg state than to the two valence states themselves

17

Hydrothermal synthesis and structural characterization of two 1-D and 2-D Dawson-based phosphotungstates  

International Nuclear Information System (INIS)

Two new Dawson-based phosphotungstates (H2en)0.5H[Cu(en)2(H2O)]2{[Cu(en)2](?1-P2W17CuO61)}.8H2O (1) (en=ethylenediamine) and [4,4'-H2bpy]2{[Cu(4,4'-bpy)3][Cu(4,4'-bpy)4(H2O)2]2[Cu(4,4'-bpy)] [?-P2W18O62]2}.6H2O (2) (4,4'-bpy=4,4'-bipyridine) have been hydrothermally synthesized and structurally characterized. 1 crystallizes in the triclinic space group P-1 with a=11.7626(17), b=13.246(2), c=29.350(5) A, ?=87.355(5), ?=79.583(5), ?=66.993(3)o, V=4138.3(11) A3, Z=2, GOF=1.089, R1=0.0563 and wR2=0.1505, whereas 2 belongs to the orthorhombic space group Iba2 with a=22.277(8), b=47.04(2), c=22.153(8) A, V=23215(17) A3, Z=4, GOF=1.051, R1=0.0627 and wR2=0.1477. 1 consists of a 1-D linear chain structure constructed from monocopperII-substituted Dawson polyoxoanions, while 2 represents the first 2-D sheet-like structure with a (4,4)-connected topological net built up from plenary Dawson-type polyoxoanions and CuII-4,4'-bpy complex cations in polyoxometalate chemistry. - Graphical abstract: Two Dawson-based phosphotungstates (H2en)0.5H[Cu(en)2(H2O)]2{[Cu(en)2](?1-P2W17CuO61)}.8H2O (1) and [4,4'-H2bpy]2{[Cu(4,4'-bpy)3] [Cu(4,4'-bpy)4(H2O)2]2[Cu(4,4'-bpy)][?-P2W18O62]2}.6H2O (2) have been hydrothermally synthesized and structurally characterized. 1 consists of a 1-D linear chain structure constructed from monocopper-substituted Dawson polyoxoanions, while 2 represents the first 2-D sheet-like structure with a (4,4)-connected topological net built up from saturated Dawson-type polyoxoanions and CuII-4,4'-bpy complex cations in polyoxometalate chemistry.

18

Structural and population-based evaluations of TBC1D1 p.Arg125Trp.  

Science.gov (United States)

Obesity is now a leading cause of preventable death in the industrialised world. Understanding its genetic influences can enhance insight into molecular pathogenesis and potential therapeutic targets. A non-synonymous polymorphism (rs35859249, p.Arg125Trp) in the N-terminal TBC1D1 phosphotyrosine-binding (PTB) domain has shown a replicated association with familial obesity in women. We investigated these findings in the Avon Longitudinal Study of Parents and Children (ALSPAC), a large European birth cohort of mothers and offspring, and by generating a predicted model of the structure of this domain. Structural prediction involved the use of three separate algorithms; Robetta, HHpred/MODELLER and I-TASSER. We used the transmission disequilibrium test (TDT) to investigate familial association in the ALSPAC study cohort (N?=?2,292 mother-offspring pairs). Linear regression models were used to examine the association of genotype with mean measurements of adiposity (Body Mass Index (BMI), waist circumference and Dual-energy X-ray absorptiometry (DXA) assessed fat mass), and logistic regression was used to examine the association with odds of obesity. Modelling showed that the R125W mutation occurs in a location of the TBC1D1 PTB domain that is predicted to have a function in a putative protein:protein interaction. We did not detect an association between R125W and BMI (mean per allele difference 0.27 kg/m(2) (95% Confidence Interval: 0.00, 0.53) P?=?0.05) or obesity (odds ratio 1.01 (95% Confidence Interval: 0.77, 1.31, P?=?0.96) in offspring after adjusting for multiple comparisons. Furthermore, there was no evidence to suggest that there was familial association between R125W and obesity (?(2)?=?0.06, P?=?0.80). Our analysis suggests that R125W in TBC1D1 plays a role in the binding of an effector protein, but we find no evidence that the R125W variant is related to mean BMI or odds of obesity in a general population sample. PMID:23667688

Richardson, Tom G; Thomas, Elaine C; Sessions, Richard B; Lawlor, Debbie A; Tavaré, Jeremy M; Day, Ian N M

2013-01-01

19

Identification of pathogenic dematiaceous fungi and related taxa based on large subunit ribosomal DNA D1/D2 domain sequence analysis.  

Science.gov (United States)

The nucleotide sequences of the D1/D2 domains of large subunit (26S) ribosomal DNA for 76 strains of 46 species of pathogenic dematiaceous fungi and related taxa were determined. Intra-species sequence diversity of medically important dematiaceous fungi including Phialophora verrucosa, Fonsecaea pedrosoi, Fonsecaea compacta, Cladophialophora carrionii, Cladophialophora bantiana, Exophiala dermatitidis, Exophiala jeanselmei, Exophiala spinifera, Exophiala moniliae, and Hortaea werneckii were extremely small; as few as 0 changes were detected in C. bantiana, Fonsecaea and Exophiala species, 1 bp in C. carrionii and H. werneckii, and 2 bp in P. verrucosa. Inter-species nucleotide diversity between most species was higher. These data suggested that the D1/D2 domain is sufficiently variable for identification of pathogenic dematiaceous fungi and relevant species. The phylogenetic trees constructed from the sequence data revealed that most human pathogenic species formed a single cluster and that Cladosporium and Phialophora species were distributed polyphyletically into several clusters. PMID:14734185

Abliz, Paride; Fukushima, Kazutaka; Takizawa, Kayoko; Nishimura, Kazuko

2004-01-15

20

Narrow band filter using 1D periodic structure with defects for DWDM systems  

Science.gov (United States)

A 1D binary periodic structure with defect has been analysed using Transfer Matrix Method. For a particular nine layered structure of SiO2 and InP, a number of full stop bands (in other words, zero passbands or forbidden bands) at different regions of the spectrum under investigation are observed. Introducing a central spatial defect in the system by adjusting the layer width, it is possible to achieve an extremely narrow passband centred on 1554.9 nm in the 7th forbidden band. Moreover by varying the defect width, the number of passbands can be increased. These passbands have flat and 100% stopband and hence can be better candidate to drop single or multiple frequencies in WDM systems. It is further observed that with increase in the number of layers and/or defect width, the number of mini pass bands outside the original forbidden band also increases. Also by FDTD simulation it is seen that the field is localised within the defect for the passband frequency.

Ghosh, R.; Ghosh, K. K.; Chakraborty, R.

2013-02-01

 
 
 
 
21

Permittivity and Permeability for Floquet-Bloch Space Harmonics in Infinite 1D Magneto-Dielectric Periodic Structures  

DEFF Research Database (Denmark)

For an infinite 1D periodic structure with unit cells consisting of two planar slabs of magnetodielectric materials, the electric field – as well as magnetic field, electric flux density, magnetic flux density, polarization, and magnetization – can be expressed as infinite series of Floquet-Bloch space harmonics. We discuss how space harmonic permittivity and permeability can be expressed in seemingly different though equivalent forms, and we investigate these parameters of the zeroeth order space harmonic for a particular 1D periodic structure that is based on a previously reported 3D periodic structure with unit cells containing a magneto-dielectric sphere.

Breinbjerg, Olav; Yaghjian, Arthur D.

2014-01-01

22

1-D structured flexible supercapacitor electrodes with prominent electronic/ionic transport capabilities.  

Science.gov (United States)

A highly efficient 1-D flexible supercapacitor with a stainless steel mesh (SSM) substrate is demonstrated. Indium tin oxide (ITO) nanowires are prepared on the surface of the stainless steel fiber (SSF), and MnO2 shell layers are coated onto the ITO/SSM electrode by means of electrodeposition. The ITO NWs, which grow radially on the SSF, are single-crystalline and conductive enough for use as a current collector for MnO2-based supercapacitors. A flake-shaped, nanoporous, and uniform MnO2 shell layer with a thickness of ~130 nm and an average crystallite size of ~2 nm is obtained by electrodeposition at a constant voltage. The effect of the electrode geometry on the supercapacitor properties was investigated using electrochemical impedance spectroscopy, cyclic voltammetry, and a galvanostatic charge/discharge study. The electrodes with ITO NWs exhibit higher specific capacitance levels and good rate capability owing to the superior electronic/ionic transport capabilities resulting from the open pore structure. Moreover, the use of a porous mesh substrate (SSM) increases the specific capacitance to 667 F g(-1) at 5 mV s(-1). In addition, the electrode with ITO NWs and the SSM shows very stable cycle performance (no decrease in the specific capacitance after 5000 cycles). PMID:24397749

Kim, Ju Seong; Shin, Seong Sik; Han, Hyun Soo; Oh, Lee Seul; Kim, Dong Hoe; Kim, Jae-Hun; Hong, Kug Sun; Kim, Jin Young

2014-01-01

23

Study of the band-gap structure of a 1D-photonic crystal by using different numerical approaches  

International Nuclear Information System (INIS)

Comparative studies between the transfer matrices method (TMM) and plane wave method (PWM) approaches have been performed on 1D photonics crystal under different conditions to show the differences between these two kinds of calculations. TMM is suitable for the design of 1D photonic crystal device with high precision and is in good agreement with experimental results, but is not suitable for the 2D and 3D photonic structures which are limited by the complicated boundary conditions at micro interfaces. The result based on the PWM approach to deal approximately with the photonic structure in approximation has not yet been strictly verified by experiment, not even for 1D photonic crystal structures. More efforts will be required to explore its validation under all physical conditions to enhance its application.

24

[The phylogenetic analysis of 15 Geotrichum strains based on 26S rRNA gene D1/D2 region sequencing].  

Science.gov (United States)

The 26S rRNA gene D1/D2 domain sequences of 15 strains originally identified as Galactomyces geotrichum from the Chinese Industry Culture Collection (CICC) were determined. The results indicated that these strains differed from the type strain of Galactomyces geotrichum and other species of the genus remarkably. Two groups were recognized from the 15 strains which possibly represent 2 novel species of Galactomyces. Further molecular study is needed to confirm their taxonomic status. PMID:17552250

Ma, Kai; Liu, Guang-quan; Li, Jin-xia; Yao, Su; Cheng, Chi

2007-04-01

25

Sequence-structure relations of pseudoknot RNA  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Background The analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-structures with at most two mutually crossing bonds (3-noncrossing). These structures are folded by a novel, ab initio prediction algorithm, cross, capable of searching all 3-noncrossing RNA structures. The algorithm outputs the minimum free ...

Ym, Li Linda; Wd, Huang Fenix; Reidys Christian M

2009-01-01

26

Phase structure of (2+1)d strongly coupled lattice gauge theories  

CERN Document Server

We study the chiral phase transition in (2+1)d strongly coupled U(N) lattice gauge theories with staggered fermions. We show with high precision simulations performed directly in the chiral limit that these models undergo a Berezinski-Kosterlitz-Thouless (BKT) transition. We also show that this universality class is unaffected even in the large N limit.

Strouthos, C G

2003-01-01

27

Inhibition of Human Steroid 5-Reductase (AKR1D1) by Finasteride and Structure of the Enzyme-Inhibitor Complex  

Energy Technology Data Exchange (ETDEWEB)

The {Delta}{sup 4}-3-ketosteroid functionality is present in nearly all steroid hormones apart from estrogens. The first step in functionalization of the A-ring is mediated in humans by steroid 5{alpha}- or 5{beta}-reductase. Finasteride is a mechanism-based inactivator of 5{alpha}-reductase type 2 with subnanomolar affinity and is widely used as a therapeutic for the treatment of benign prostatic hyperplasia. It is also used for androgen deprivation in hormone-dependent prostate carcinoma, and it has been examined as a chemopreventive agent in prostate cancer. The effect of finasteride on steroid 5{beta}-reductase (AKR1D1) has not been previously reported. We show that finasteride competitively inhibits AKR1D1 with low micromolar affinity but does not act as a mechanism-based inactivator. The structure of the AKR1D1 {center_dot} NADP{sup +} {center_dot} finasteride complex determined at 1.7 {angstrom} resolution shows that it is not possible for NADPH to reduce the {Delta}{sup 1-2}-ene of finasteride because the cofactor and steroid are not proximal to each other. The C3-ketone of finasteride accepts hydrogen bonds from the catalytic residues Tyr-58 and Glu-120 in the active site of AKR1D1, providing an explanation for the competitive inhibition observed. This is the first reported structure of finasteride bound to an enzyme involved in steroid hormone metabolism.

Drury, J.; Di Costanzo, L; Penning, T; Christianson, D

2009-01-01

28

Structural and Population-Based Evaluations of TBC1D1 p.Arg125Trp  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Obesity is now a leading cause of preventable death in the industrialised world. Understanding its genetic influences can enhance insight into molecular pathogenesis and potential therapeutic targets. A non-synonymous polymorphism (rs35859249, p.Arg125Trp) in the N-terminal TBC1D1 phosphotyrosine-binding (PTB) domain has shown a replicated association with familial obesity in women. We investigated these findings in the Avon Longitudinal Study of Parents and Children (ALSPAC), a large Europea...

Richardson, Tom G.; Thomas, Elaine C.; Sessions, Richard B.; Lawlor, Debbie A.; Tavare?, Jeremy M.; Day, Ian N. M.

2013-01-01

29

A revised 1-D electrical conductivity reference structure beneath North Pacific obtained by semi-global induction study  

International Nuclear Information System (INIS)

Complete text of publication follows. One dimensional (1-D) electrical conductivity structure in the mid-mantle beneath the northern Pacific is revised in order to discuss the mean state of the mantle and to obtain a credible starting model for 3-D inversions. Semi-global geomagnetic depth sounding (GDS) responses obtained at 13 stations and submarine cable magnetotelluric (MT) responses for 8 cables in the period range 1.7 to 113 days were used to obtain the revised structure. We employed an iterative scheme combining surface layer correction to remove the effect of ocean-land heterogeneity in the responses and 1-D inversion to obtain the revised structure. The validity of the scheme is examined by making synthetic tests: We confirmed that the structure obtained using this scheme not only represents the model which explains the corrected response the best but also reflects the actual mean conductivity structure in the mid-mantle depths. The obtained 1-D conductivity in the transition zone by supposing jumps at 400 and 650 km depths (2-jump model) is higher than that of dry Wadsleyite and Ringwoodite measured experimentally by Yoshino et al. (2008). If the high conductivity is entirely due to the effect of water in the transition zone, the region contains 0.5 wt% of water. However, if an additional discontinuity of electrical conductivity is allowed at 500 km depth in the 1-D inversion, the obtained model has lower conductivity than the 2-jump model in the upper 100 km of the transition zone. In this case, the conductivity in the layer is rather close to that of dry Wadsleyite.

30

Syntheses, structures, and properties of two novel cadmium coordination polymers with 1D and 2D structures  

Science.gov (United States)

Two novel complexes [Cd 2(MIP) 2(BDC) 2]n ( 1) [MIP = 2-(3-methoxyphenyl)-1H-imidazo[4,5-f][1,10]phenanthroline, BDC = terephthalic acid] and [Cd(IPM)(NDC)]n ( 2) [IPM = 4-(1H-imidazo[4,5-f][1,10]phenanthrolin-2-yl)-2-methoxyphenol, NDC = naphthalene-1,4-dicarboxylic acid] have been synthesized by hydrothermal reaction and characterized by elemental analysis, IR, single-crystal X-ray diffraction and thermogravimetric analysis (TGA). Complex 1 exhibits 1D zigzag chain structure and complex 2 shows 2D layer topology. The intermolecular C sbnd H⋯O interactions extend the complex 1 into 2D networks, and the existing H-bonds further stabilized the complexes 1-2, which can be proved by TGA experiment. Furthermore, the solid-state fluorescence spectrum of the complex 2 was studied, as well as the ligand IPM. The complex 2 exhibits intense broad emission at 540 nm at room temperature, which is red-shifted by 45 nm relative to that of free ligand IPM.

Yan, Li; Li, Chuanbi; Zhu, Dongsheng; Xu, Lin

2011-09-01

31

Exome Sequencing in Fetuses with Structural Malformations  

Directory of Open Access Journals (Sweden)

Full Text Available Prenatal diagnostic testing is a rapidly advancing field. An accurate diagnosis of structural anomalies and additional abnormalities in fetuses with structural anomalies is important to allow “triage” and designation of prognosis. This will allow parents to make an informed decision relating to the pregnancy. This review outlines the current tests used in prenatal diagnosis, focusing particularly on “new technologies” such as exome sequencing. We demonstrate the utility of exome sequencing above that of conventional karyotyping and Chromosomal Microarray (CMA alone by outlining a recent proof of concept study investigating 30 parent-fetus trios where the fetus is known to have a structural anomaly. This may allow the identification of pathological gene anomalies and consequently improved prognostic profiling, as well as excluding anomalies and distinguishing between de novo and inherited mutations, in order to estimate the recurrence risk in future pregnancies. The potential ethical dilemmas surrounding exome sequencing are also considered, and the future of prenatal genetic diagnosis is discussed.

Fiona L. Mackie

2014-07-01

32

Temperature tuning of band-structure of 1D periodic elastic composites  

Science.gov (United States)

In this paper we show that the bandstructure of a periodic elastic composite, in addition to being dependent upon the micro-constituents and their microarchitecture, may also be controlled by changing the temperature. The essential idea is to fabricate a periodic composite with constituent materials which have temperature dependent elastic properties. As temperature is changed, such a composite is expected to exhibit a bandstructure which changes with the temperature dependent properties of its micro-constituents. For our purpose, we use polyurea and steel to make a 1-D periodic composite. Ultrasonic measurements are done on the sample from 0.5 kHz to 1.5 MHz under changing temperature and the change in the second passband is studied. It is observed that the change in the bandstructure is significant when the temperature is changed from -50°C to 50°C. Experimental results are compared with the theoretical calculations and it is shown that good agreement exists for the observed bandstructure.

Sadeghi, H.; Srivastava, A.; Griswold, R.; Nemat-Nasser, S.

2012-04-01

33

Properties of Floquet-Bloch space harmonics in 1D periodic magneto-dielectric structures  

DEFF Research Database (Denmark)

Recent years have witnessed a significant research interest in Floquet-Bloch analysis for determining the homogenized permittivity and permeability of metamaterials consisting of periodic structures. This work investigates fundamental properties of the Floquet-Bloch space harmonics in a 1-dimensional magneto-dielectric lossless structure supporting a transverse-electric-magnetic Floquet-Bloch wave; in particular, the space harmonic permittivity and permeability, as well as the space harmonic Poynting vector.

Breinbjerg, O.

2012-01-01

34

Structure-based design of novel Chlamydomonas reinhardtii D1-D2 photosynthetic proteins for herbicide monitoring.  

Science.gov (United States)

The D1-D2 heterodimer in the reaction center core of phototrophs binds the redox plastoquinone cofactors, Q(A) and Q(B), the terminal acceptors of the photosynthetic electron transfer chain in the photosystem II (PSII). This complex is the target of the herbicide atrazine, an environmental pollutant competitive inhibitor of Q(B) binding, and consequently it represents an excellent biomediator to develop biosensors for pollutant monitoring in ecosystems. In this context, we have undertaken a study of the Chlamydomonas reinhardtii D1-D2 proteins aimed at designing site directed mutants with increased affinity for atrazine. The three-dimensional structure of the D1 and D2 proteins from C. reinhardtii has been homology modeled using the crystal structure of the highly homologous Thermosynechococcus elongatus proteins as templates. Mutants of D1 and D2 were then generated in silico and the atrazine binding affinity of the mutant proteins has been calculated to predict mutations able to increase PSII affinity for atrazine. The computational approach has been validated through comparison with available experimental data and production and characterization of one of the predicted mutants. The latter analyses indicated an increase of one order of magnitude of the mutant sensitivity and affinity for atrazine as compared to the control strain. Finally, D1-D2 heterodimer mutants were designed and selected which, according to our model, increase atrazine binding affinity by up to 20 kcal/mol, representing useful starting points for the development of high affinity biosensors for atrazine. PMID:19693932

Rea, Giuseppina; Polticelli, Fabio; Antonacci, Amina; Scognamiglio, Viviana; Katiyar, Prashant; Kulkarni, Sudhir A; Johanningmeier, Udo; Giardi, Maria Teresa

2009-10-01

35

Structure/transport relationships in silver-based oxide glasses: 1-D and 2-D NMR information.  

Science.gov (United States)

AgI-doped silver oxide glasses are of interest both for their possible applications in electrochemical devices, and as a model system to study the transport/structure relationships in ionic glasses. Here we summarize the information given by 1-D and 2-D solid-state NMR measurements on both the cations dynamics and short (and medium) range structure of several glassy systems. Emphasis is given to understand how AgI enters into the glass matrix. A new and careful analysis of our previously reported 109Ag 1-D data shows that the glass matrix plays a relevant role in determining the efficiency of carriers formation, as well as their mobility. Finally, as an example of a modern 2-D NMR application to these materials, we report the first 11B and 17O Multiple Quantum MAS study on a glass of the system AgI:Ag2O:2B2O2, which confirms the nearly complete absence of non-bridging oxygens (NBOs) in the silver diborate composition. PMID:15589732

Mustarelli, Piercarlo; Linati, Laura; Tartara, Valentina; Tomasi, Corrado; Magistris, Aldo

2005-01-01

36

X-ray Spontaneous Emission Control By 1D-PBG Structure  

Science.gov (United States)

The control of the decay rate of an excited atom through the photonic mode density (PMD) was pointed out at radiofrequency by Purcell in 1946. Nowadays the development of sophisticated photonic band structures makes it possible to monitor the PMD at shorter radiation wavelengths and then to manipulate the spontaneous emission of atoms in the hard region of the electromagnetic spectrum especially in the visible domain. In this communication we study the possibility of monitoring the x-ray emission by means of one-dimensional photonic band structures such as periodic multilayer systems. Enhancement or inhibition of soft x-ray emissions seems now to be feasible by means of the state-of-the art in x-ray optics.

André, Jean-Michel; Jonnard, Philippe

2010-04-01

37

Band structure and Bloch states in birefringent 1D magnetophotonic crystals: An analytical approach  

CERN Document Server

An analytical formulation for the band structure and Bloch modes in elliptically birefringent magnetophotonic crystals is presented. The model incorporates both the effects of gyrotropy and linear birefringence generally present in magneto-optic thin film devices. Full analytical expressions are obtained for the dispersion relation and Bloch modes in a layered stack photonic crystal and their properties are analyzed. It is shown that other models recently discussed in the literature are contained as special limiting cases of the formulation presented herein.

Lévy, M; Levy, Miguel; Jalali, Amir A

2007-01-01

38

3D mechanical measurements with an atomic force microscope on 1D structures.  

DEFF Research Database (Denmark)

We have developed a simple method to characterize the mechanical properties of three dimensional nanostructures, such as nanorods standing up from a substrate. With an atomic force microscope the cantilever probe is used to deflect a horizontally aligned nanorod at different positions along the nanorod, using the apex of the cantilever itself rather than the tip normally used for probing surfaces. This enables accurate determination of nanostructures' spring constant. From these measurements, Young's modulus is found on many individual nanorods with different geometrical and material structures in a short time. Based on this method Young's modulus of carbon nanofibers and epitaxial grown III-V nanowires has been determined.

KallesØe, Christian; Larsen, Martin Benjamin Barbour Spanget

2012-01-01

39

Global structure of integer partitions sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Integer partitions are deeply related to many phenomena in statistical physics. A question naturally arises which is of interest to physics both on "purely" theoretical and on practical, computational grounds. Is it possible to apprehend the global pattern underlying integer partition sequences and to express the global pattern compactly, in the form of a "matrix" giving all of the partitions of N into exactly M parts? This paper demonstrates that the global structure of int...

Chase, N. M.

2004-01-01

40

Protein function from sequence and structure data.  

Science.gov (United States)

With the large amount of genomics and proteomics data that we are confronted with, computational support for the elucidation of protein function becomes more and more pressing. Many different kinds of biological data harbour signals of protein function, but these signals are often concealed. Computational methods that use protein sequence and structure data can be used for discovering these signals. They provide information that can substantially speed up experimental function elucidation. In this review we concentrate on such methods. PMID:15130830

Domingues, Francisco S; Lengauer, Thomas

2003-01-01

 
 
 
 
41

Syntheses, crystal structures and spectral properties of 1D tetracyanonickelate(II) complexes with 1-ethylimidazole  

Science.gov (United States)

Three new cyano-bridged tetracyanonickelate(II) complexes with 1-ethylimidazole (etim) ligand, [Ni(etim)4Ni(?-CN)2(CN)2]n (1), [Zn(etim)4Ni(?-CN)2(CN)2]n (2) and {[Cd(etim)4Ni(?-CN)2(CN)2]2·2H2O}n (3) have been synthesized and characterized by spectroscopic (IR and Raman) and X-ray diffraction techniques. According to the crystallographic data, it was understood that the complexes with the chain 2,2-TT structures belong to P-1 space group of triclinic crystal system. In the complexes, it was observed that Ni(II), Zn(II) and Cd(II) ions have distorted octahedral geometries. In the [Ni(?-CN)2(CN)2]2- anion, the Ni(II) ion is coordinated by the four carbon atoms of the four cyano ligands, and exhibits square-planar coordination geometry. The crystallographic analyses reveal that the crystal structures of complexes 1-3 are one dimensional linear chain polymers and these chains are held together by the CH⋯?, CH⋯Ni and hydrogen bonding interactions, forming three-dimensional networks.

Çetinkaya, Fulya; Kürkçüo?lu, Güne? Süheyla; Ye?ilel, Okan Zafer; Hökelek, Tuncer; Süzen, Yasemin

2013-09-01

42

Mixed 1D-2D inorganic polymeric zinc ferrocenylphosphonate: crystal structure and electrochemical study.  

Science.gov (United States)

Needs for ferrocene immobilization on robust host structures are considerable since derivative materials may find applications in medical areas, optical devices, or catalysis. Synthesis of phosphonate functionalized ferrocene allowed its subsequent inorganic polymerization with a zinc salt. The crystallographic structure of the compound obtained, Zn(HO(3)PFc)(2).2H(2)O, shows a unique two-dimensional ferrocene arrangement anchored on a one-dimensional Zn-O-P-O-Zn backbone. The ferrocene packing in the title compound is very similar to the packing found in molecular ferrocene. The electroactivity of Zn(HO(3)PFc)(2).2H(2)O is thoroughly studied. It shows a reversible surface oxidation of ferrocene. Mössbauer spectroscopy for the oxidized compound shows an isomer shift of IS(2b) = 0.432 mm x s(-1) and a quadrupolar splitting of QS(2b) = 0.205 mm x s(-1), which is consistent with a stable S = 1/2 ferrocenium state. The magnetic susceptibility study, Mössbauer spectroscopy, and galvanostatic titration show that only the ferrocene moieties present at the surface of the crystallites are reversibly oxidized. This observation is reinforced by a complex impedance study showing mainly resistive behavior and conductivity measurements indicating weak, thermally assisted, conductivity. The general properties of this compound demonstrate that phosphonato functionalization may be a useful approach for all fields concerned by immobilization of ferrocene. PMID:15382944

Oms, Olivier; Le Bideau, Jean; Leroux, Fabrice; van der Lee, Arie; Leclercq, Dominique; Vioux, André

2004-09-29

43

Characterization of the measurement error structure in 1D 1H NMR data for metabolomics studies.  

Science.gov (United States)

NMR-based metabolomics is characterized by high throughput measurements of the signal intensities of complex mixtures of metabolites in biological samples by assaying, typically, bio-fluids or tissue homogenates. The ultimate goal is to obtain relevant biological information regarding the dissimilarity in patho-physiological conditions that the samples experience. For a long time now, this information has been obtained through the analysis of measured NMR signals via multivariate statistics. NMR data are quite complex and the use of such multivariate statistical methods as principal components analysis (PCA) for their analysis assumes that the data are multivariate normal with errors that are identical, independent and normally distributed (i.e. iid normal). There is a consensus that these assumptions are not always true for these data and, thus, several methods have been devised to transform the data or weight them prior to analysis by PCA. The structure of NMR measurement noise, or the extent to which violations of error homoscedasticity affect PCA results have neither been characterized nor investigated. A comprehensive characterization of measurement uncertainties in NMR based metabolomics was achieved in this work using an experiment designed to capture contributions of several sources of error to the total variance in the measurements. The noise structure was found to be heteroscedastic and highly correlated with spectral characteristics that are similar to the mean of the spectra and their standard deviation. A model was subsequently developed that potentially allows errors in NMR measurements to be accurately estimated without the need for extensive replication. PMID:19264164

Karakach, Tobias K; Wentzell, Peter D; Walter, John A

2009-03-23

44

Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques  

Science.gov (United States)

In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques ( 1H, 13C, APT, DEPT, NOE/NOESY, 1H- 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.

Topcu, Gulacti; Ulubelen, Ayhan

2007-05-01

45

Modified Jeener Solid-Echo Pulse Sequences for the Measurement of the Proton Dipolar Spin-Lattice Relaxation-Time ( T1D) of Tissue Solid-like Macromolecular Components  

Science.gov (United States)

Modified Jeener solid-echo pulse sequences are proposed for the measurement of the proton dipolar spin-lattice relaxation time, T1D, of motionally restricted (solid-like) components in the presence of mobile molecular species, such as encountered in biological tissue. A phase-cycled composite-pulse sequence was used for detection of the dipolar signal and cancellation of the Zeeman signal. A homospoil gradient pulse was added to the Jeener echo pulse sequence to enhance dephasing of the transverse magnetization components of mobile species, thereby aiding in elimination of the Zeeman signal during dipolar signal acquisition. A modified Jeener echo sequence incorporating water suppression is also proposed as a means to further depress the Zeeman signal arising from mobile components. The modified Jeener echo sequences were successfully used for the measurement of proton T1D values of solid 2,6-dimethylphenol and Sephadex gels of differing degrees of cross linking and hydration.

Yang, H.; Schleich, T.

46

Sequence–structure relationships in yeast mRNAs  

Digital Repository Infrastructure Vision for European Research (DRIVER)

It is generally accepted that functionally important RNA structure is more conserved than sequence due to compensatory mutations that may alter the sequence without disrupting the structure. For small RNA molecules sequence–structure relationships are relatively well understood. However, structural bioinformatics of mRNAs is still in its infancy due to a virtual absence of experimental data. This report presents the first quantitative assessment of sequence–structure divergence in the cod...

Chursov, Andrey; Walter, Mathias C.; Schmidt, Thorsten; Mironov, Andrei; Shneider, Alexander; Frishman, Dmitrij

2012-01-01

47

Structure Prediction of Partial-Length Protein Sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Protein structure information is essential to understand protein function. Computational methods to accurately predict protein structure from the sequence have primarily been evaluated on protein sequences representing full-length native proteins. Here, we demonstrate that top-performing structure prediction methods can accurately predict the partial structures of proteins encoded by sequences that contain approximately 50% or more of the full-length protein sequence. We hypothesize that structure prediction may be useful for predicting functions of proteins whose corresponding genes are mapped expressed sequence tags (ESTs that encode partial-length amino acid sequences. Additionally, we identify a confidence score representing the quality of a predicted structure as a useful means of predicting the likelihood that an arbitrary polypeptide sequence represents a portion of a foldable protein sequence (“foldability”. This work has ramifications for the prediction of protein structure with limited or noisy sequence information, as well as genome annotation.

Ram Samudrala

2013-07-01

48

Structural variation from heterometallic cluster-based 1D chain to heterometallic tetranuclear cluster: Syntheses, structures and magnetic properties  

Science.gov (United States)

Using the solvothermal method, we present the comparative preparation of {[Co3Na(dmaep)3(ehbd)(N3)3]·DMF}n (1) and [Co2Na2(hmbd)4(N3)2(DMF)2] (2), where Hehbd is 3-ethoxy-2-hydroxy-benzaldehyde, Hhmbd is 3-methoxy-2-hydroxy-benzaldehyde, and Hdmaep is 2-dimethylaminomethyl-6-ethoxy-phenol, which was synthesized by an in-situ reaction. Complexes 1 and 2 were characterized by elemental analysis, IR spectroscopy, and X-ray single-crystal diffraction. Complex 1 is a novel heterometallic cluster-based 1-D chain and 2 is a heterometallic tetranuclear cluster. The {Co3IINa} and {Co2IINa2} cores display dominant ferromagnetic interaction from the nature of the binding modes through ?1,1,1-N3- (end-on, EO).

Zhang, Shu-Hua; Zhao, Ru-Xia; Li, He-Ping; Ge, Cheng-Min; Li, Gui; Huang, Qiu-Ping; Zou, Hua-Hong

2014-08-01

49

Radial 1-D seismic structures in the deep mantle in mantle convection simulations with self-consistently calculated mineralogy  

Science.gov (United States)

Numerical thermo-chemical mantle convection simulations in a spherical annulus geometry with self-consistently calculated mineralogy and mineral physics are used to predict detailed deep mantle seismic structures, particularly local radial profiles of shear wave velocity (Vs) and bulk sound velocity (Vb). The predicted structures are compared to seismological observations and used to guide the interpretation of seismic observations and to test the model. The mantle composition is described as a mixture of MORB (Mid-Oceanic-Ridge-Basalt) and harzburgitic end-members in the Na2O-CaO-FeO-MgO-Al2O3-SiO2system. To assess the influence of chemical variability, four different sets of end-member compositions are evaluated. Results confirm that the post-perovskite (pPv) phase causes anti-correlated S wave and bulk sound velocities in the deep mantle, due to pPv being fast in Vs but slow in bulk sound velocity. Local 1-D seismic profiles display great lateral variability, and often have multiple discontinuities in the deep mantle due to MORB layers in folded slabs, with a positive Vs anomaly and negative bulk sound anomaly, or the perovskite-pPv phase transition. The pPv transition is not visible inside piles of segregated MORB because of the high temperature and small velocity contrast of pPv in MORB. Piles of segregated MORB are seismically slow in both Vs and bulk sound despite being expected to be fast in Vs, because they are hotter than the surrounding material. Anelasticity has a significant influence on profiles of Vs only in the lower thermal boundary layer, which corresponds to below 2600 to 2800 km depth depending on region, where temperatures are higher than the extrapolated adiabat. These results indicate the importance of using a joint geodynamical-mineralogical approach to predict and aid in the interpretation of deep mantle seismic structure, because interpretations based on seismology and mineral physics alone may be misleading and do not capture the strong lateral variability in 1-D structure obtained here: for example, multiple reflections arising from folded slabs and the precise balance between thermal and compositional influences on seismic structure.

Nakagawa, Takashi; Tackley, Paul J.; Deschamps, FréDéRic; Connolly, James A. D.

2012-11-01

50

HOTCFGM-1D: A Coupled Higher-Order Theory for Cylindrical Structural Components with Through-Thickness Functionally Graded Microstructures  

Science.gov (United States)

The objective of this three-year project was to develop and deliver to NASA Lewis one-dimensional and two-dimensional higher-order theories, and related computer codes, for the analysis, optimization and design of cylindrical functionally graded materials/structural components for use in advanced aircraft engines (e.g., combustor linings, rotor disks, heat shields, blisk blades). To satisfy this objective, a quasi one-dimensional version of the higher-order theory, HOTCFGM-1D, and four computer codes based on this theory, for the analysis, design and optimization of cylindrical structural components functionally graded in the radial direction were developed. The theory is applicable to thin multi-phased composite shell/cylinders subjected to macroscopically axisymmetric thermomechanical and inertial loading applied uniformly along the axial direction such that the overall deformation is characterized by a constant average axial strain. The reinforcement phases are uniformly distributed in the axial and circumferential directions, and arbitrarily distributed in the radial direction, thereby allowing functional grading of the internal reinforcement in this direction.

Pindera, Marek-Jerzy; Aboudi, Jacob

1998-01-01

51

Integrating sequence and structural biology with DAS  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The Distributed Annotation System (DAS is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence. Results Here we present several extensions to the current DAS 1.5 protocol. These provide new commands to share alignments, three dimensional molecular structure data, add the possibility for registration and discovery of DAS servers, and provide a convention how to provide different types of data plots. We present examples of web sites and applications that use the new extensions. We operate a public registry of DAS sources, which now includes entries for more than 250 distinct sources. Conclusion Our DAS extensions are essential for the management of the growing number of services and exchange of diverse biological data sets. In addition the extensions allow new types of applications to be developed and scientific questions to be addressed. The registry of DAS sources is available at http://www.dasregistry.org

Finn Robert D

2007-09-01

52

Hydration structure of -NH{2/+} and -COO- of L-proline zwitterion from data of 1D-RISM integral equation method  

Science.gov (United States)

The hydration structure of hydrophilic groups of L-proline zwitterion is studied by means of the 1D-RISM integral equation method. The structural parameters of hydration and features of hydrogen bonding between water and -NH{2/+} and -COO- groups are discussed.

Fedotova, M. V.; Dmitrieva, O. A.

2014-05-01

53

Finding common sequence and structure motifs in a set of RNA sequences.  

Science.gov (United States)

We present a computational scheme to search for the most common motif, composed of a combination of sequence and structure constraints, among a collection of RNA sequences. The method uses a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pairwise comparisons. The overall method has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. Example solutions, and comparisons with other approaches, are provided. The solutions include finding consensus structures identical to published ones. PMID:9322025

Gorodkin, J; Heyer, L J; Stormo, G D

1997-01-01

54

Finding Common Sequence and Structure Motifs in a set of RNA sequences  

DEFF Research Database (Denmark)

We present a computational scheme to search for the most common motif, composed of a combination of sequence and structure constraints, among a collection of RNA sequences. The method uses a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments for pairwise comparisons. The overall method has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. Example solutions, and comparisons with other approaches, are provided. The solutions include finding consensus structure identical to published ones.

Gorodkin, Jan

1997-01-01

55

Unconditional structures of weakly null sequences  

CERN Document Server

The following dichotomy is established for a normalized weakly null sequence in a Banach space: Either every subsequence admits a convex block subsequence equivalent to the unit vector basis of c, the Banach space of null sequences under the supremum norm, or there exists a subsequence which is boundedly convexly complete. This result generalizes J. Elton's dichotomy on weakly null sequences.

Argyros, S A

1999-01-01

56

Histone and histone fold sequences and structures: a database.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A database of aligned histone protein sequences has been constructed based on the results of homology searches of the major public sequence databases. In addition, sequences of proteins identified as containing the histone fold motif and structures of all known histone and histone fold proteins have been included in the current release. Database resources include information on conflicts between similar sequence entries in different source databases, multiple sequence alignments, and links to...

Baxevanis, A. D.; Landsman, D.

1997-01-01

57

X-Ray crystal structure of [HSm{V(IV)O(TPPS)}]n and encapsulation of nitrogen molecules in 1-D channels.  

Science.gov (United States)

The crystal structure of an N(2)-encapusulated MOF, which is stable under open-air conditions at ambient temperature, was determined by single-crystal X-ray diffraction at 123 K. The crystal MOF of [HSm{V(IV)O(TPPS)}](n) designed to have 1-D channels periodically constricted by porphyrins planes adsorbed N(2) at 77 K. The adsorbed N(2) molecules remained in the 1-D channels even after warming to ambient temperature. The single-crystal structure of [HSm{V(IV)O(TPPS)}](n)?N(2) determined by X-ray diffraction indicated that N(2) molecules trapped in the constricted parts block other N(2) molecules in 1-D channels from escaping from the MOF. Such a unique encapsulation mode provides a promising approach toward designing novel MOFs with high gas storage capacity at ambient temperature. PMID:22012574

Chen, Wen-Tong; Yamada, Yusuke; Liu, Guang-Ning; Kubota, Akira; Ichikawa, Takayuki; Kojima, Yoshitsugu; Guo, Guo-Cong; Fukuzumi, Shunichi

2011-12-28

58

Relationships between Th1 or Th2 iNKT Cell Activity and Structures of CD1d-Antigen Complexes: Meta-analysis of CD1d-Glycolipids Dynamics Simulations.  

Science.gov (United States)

A number of potentially bioactive molecules can be found in nature. In particular, marine organisms are a valuable source of bioactive compounds. The activity of an ?-galactosylceramide was first discovered in 1993 via screening of a Japanese marine sponge (Agelas mauritanius). Very rapidly, a synthetic glycololipid analogue of this natural molecule was discovered, called KRN7000. Associated with the CD1d protein, this ?-galactosylceramide 1 (KRN7000) interacts with the T-cell antigen receptor to form a ternary complex that yields T helper (Th) 1 and Th2 responses with opposing effects. In our work, we carried out molecular dynamics simulations (11.5 µs in total) involving eight different ligands (conducted in triplicate) in an effort to find out correlation at the molecular level, if any, between chemical modulation of 1 and the orientation of the known biological response, Th1 or Th2. Comparative investigations of human versus mouse and Th1 versus Th2 data have been carried out. A large set of analysis tools was employed including free energy landscapes. One major result is the identification of a specific conformational state of the sugar polar head, which could be correlated, in the present study, to the biological Th2 biased response. These theoretical tools provide a structural basis for predicting the very different dynamical behaviors of ?-glycosphingolipids in CD1d and might aid in the future design of new analogues of 1. PMID:25376021

Laurent, Xavier; Renault, Nicolas; Farce, Amaury; Chavatte, Philippe; Hénon, Eric

2014-11-01

59

Self-assembly of three new coordination complexes: Formation of 2-D square grid, 1-D chain and tape structures  

Science.gov (United States)

Three distinct coordination complexes, viz., [Co(imi) 2(tmb) 2] ( 1) [where imi = imidazole], {[Ni(tmb) 2(H 2O) 3]·2H 2O} n ( 2) and [Cu 2(?-tmb) 4(CH 3OH) 2] ( 3), have been synthesized hydrothermally by the reactions of metal acetates, 2,4,6-trimethylbenzoic acid (Htmb) and with or without appropriate amine. The Ni analogue of 1 and the Co analogue of 2 have also been synthesized. X-ray single-crystal diffraction suggests that complex 1 represents discrete mononuclear species and complex 2 represents a 1D chain coordination polymer in which the Ni(II) ions are connected by the bridging water molecules. Complex 3 represents a neutral dinuclear complex. In 1, the central metal ions are associated by the carboxylate moiety and imidazole ligands, whereas the central metal atom is coordinated to the carboxylate moiety and the respective solvent molecules in 2 and 3. In 3, the four 2,4,6-trimethylbenzoate moieties act as a bridge connecting two copper (II) ions and the O atoms of methanol coordinate in an anti arrangement to form a square pyramidal geometry, with the methanol molecule at the apical position. In all the three structures the central metal atom sits on a crystallographic inversion centre. In all the cases, the coordination entities are further organized via hydrogen bonding interactions to generate multifarious supramolecular networks. Complexes 1, 2 and 3 have also been characterized by spectroscopic (UV/Vis and IR) and thermal analysis (TGA). In addition, the complexes were found to exhibit antimicrobial activity.The magnetic susceptibility measurements, measured from 8 to 300 K, revealed antiferromagnetic interactions between the Co(II) ions in compound 1 and the Ni(II) ions in 1a, respectively.

Indrani, Murugan; Ramasubramanian, Ramasamy; Fronczek, Frank R.; Vasanthacharya, N. Y.; Kumaresan, Sudalaiandi

2009-08-01

60

Crystal Structure and Function of 5-Formaminoimidazole-4-carboxamide-1-?-d-ribofuranosyl 5?-Monophosphate Synthetase from Methanocaldococcus jannaschii†,‡  

Science.gov (United States)

Purine biosynthesis requires ten enzymatic steps in higher organisms while prokaryotes require an additional enzyme for step six. In most organisms steps nine and ten are catalyzed by the purH gene product, a bifunctional enzyme with both 5-formaminoimidazole-4-carboxamide-5?-monophosphate ribonucleotide (FAICAR) synthase and inosine monophosphate (IMP) cyclohydrolase activity. Recently it was discovered that Archaea utilize different enzymes to catalyze steps nine and ten. An ATP dependent FAICAR synthetase is encoded by the purP gene and IMP cyclohydrolase is encoded by the purO gene. We have determined the X-ray crystal structures of FAICAR synthetase from Methanocaldococcus jannaschii complexed with various ligands, including the tertiary substrate complex and product complex. The enzyme belongs to the ATP grasp superfamily and is predicted to use a formylphosphate intermediate formed by an ATP-dependent phosphorylation. In addition, we have determined the structures of a PurP ortholog from Pyrococcus furiosus, which is functionally unclassified, in three crystal forms. With approximately 50% sequence identity, P. furiosus PurP is structurally homologous to M. jannaschii PurP. A phylogenetic analysis was performed to explore the possible role of this functionally unclassified PurP. PMID:18069798

Zhang, Yang; White, Robert H.; Ealick, Steven E.

2008-01-01

 
 
 
 
61

Computational methods in sequence and structure prediction  

Science.gov (United States)

This dissertation is organized into two parts. In the first part, we will discuss three computational methods for cis-regulatory element recognition in three different gene regulatory networks as the following: (a) Using a comprehensive "Phylogenetic Footprinting Comparison" method, we will investigate the promoter sequence structures of three enzymes (PAL, CHS and DFR) that catalyze sequential steps in the pathway from phenylalanine to anthocyanins in plants. Our result shows there exists a putative cis-regulatory element "AC(C/G)TAC(C)" in the upstream of these enzyme genes. We propose this cis-regulatory element to be responsible for the genetic regulation of these three enzymes and this element, might also be the binding site for MYB class transcription factor PAP1. (b) We will investigate the role of the Arabidopsis gene glutamate receptor 1.1 (AtGLR1.1) in C and N metabolism by utilizing the microarray data we obtained from AtGLR1.1 deficient lines (antiAtGLR1.1). We focus our investigation on the putatively co-regulated transcript profile of 876 genes we have collected in antiAtGLR1.1 lines. By (a) scanning the occurrence of several groups of known abscisic acid (ABA) related cisregulatory elements in the upstream regions of 876 Arabidopsis genes; and (b) exhaustive scanning of all possible 6-10 bps motif occurrence in the upstream regions of the same set of genes, we are able to make a quantative estimation on the enrichment level of each of the cis-regulatory element candidates. We finally conclude that one specific cis-regulatory element group, called "ABRE" elements, are statistically highly enriched within the 876-gene group as compared to their occurrence within the genome. (c) We will introduce a new general purpose algorithm, called "fuzzy REDUCE1", which we have developed recently for automated cis-regulatory element identification. In the second part, we will discuss our newly devised protein design framework. With this framework we have developed a software package which is capable of designing novel protein structures at the atomic resolution. This software package allows us to perform protein structure design with a flexible backbone. The backbone flexibility includes loop region relaxation as well as a secondary structure collective mode relaxation scheme. (Abstract shortened by UMI.)

Lang, Caiyi

62

Finding the most significant common sequence and structure motifs in a set of RNA sequences.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We present a computational scheme to locally align a collection of RNA sequences using sequence and structure constraints. In addition, the method searches for the resulting alignments with the most significant common motifs, among all possible collections. The first part utilizes a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pairwise comparisons. The algorithm fi...

Gorodkin, J.; Heyer, L. J.; Stormo, G. D.

1997-01-01

63

SAAS: Short Amino Acid Sequence - A Promising Protein Secondary Structure Prediction Method of Single Sequence  

Directory of Open Access Journals (Sweden)

Full Text Available In statistical methods of predicting protein secondary structure, many researchers focus on single amino acid frequencies in ?-helices, ?-sheets, and so on, or the impact near amino acids on an amino acid forming a secondary structure. But the paper considers a short sequence of amino acids (3, 4, 5 or 6 amino acids as integer, and statistics short sequence's probability forming secondary structure. Also, many researchers select low homologous sequences as statistical database. But this paper select whole PDB database. In this paper we propose a strategy to predict protein secondary structure using simple statistical method. Numerical computation shows that, short amino acids sequence as integer to statistics, which can easy see trend of short sequence forming secondary structure, and it will work well to select large statistical database (whole PDB database without considering homologous, and Q3 accuracy is ca. 74% using this paper proposed simple statistical method, but accuracy of others statistical methods is less than 70%.

Zhou Yuan Wu

2013-07-01

64

Filovirus Glycoprotein Sequence, Structure and Virulence  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Leading Ebola subtypes exhibit a wide mortality range, here explained at the molecular level by using fractal hydropathic scaling of amino acid sequences based on protein self-organized criticality. Specific hydrophobic features in the hydrophilic mucin-like domain suffice to account for the wide mortality range. Significance statement: Ebola virus is spreading rapidly in Africa. The connection between protein amino acid sequence and mortality is identified here.

Phillips, J. C.

2014-01-01

65

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

Daniels Noah M

2012-10-01

66

Improving protein secondary structure prediction with aligned homologous sequences.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Most recent protein secondary structure prediction methods use sequence alignments to improve the prediction quality. We investigate the relationship between the location of secondary structural elements, gaps, and variable residue positions in multiple sequence alignments. We further investigate how these relationships compare with those found in structurally aligned protein families. We show how such associations may be used to improve the quality of prediction of the secondary structure el...

Di Francesco, V.; Garnier, J.; Munson, P. J.

1996-01-01

67

Structure-based design of novel Chlamydomonas reinhardtii D1-D2 photosynthetic proteins for herbicide monitoring  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The D1-D2 heterodimer in the reaction center core of phototrophs binds the redox plastoquinone cofactors, QA and QB, the terminal acceptors of the photosynthetic electron transfer chain in the photosystem II (PSII). This complex is the target of the herbicide atrazine, an environmental pollutant competitive inhibitor of QB binding, and consequently it represents an excellent biomediator to develop biosensors for pollutant monitoring in ecosystems. In this context, we have undertaken a study o...

Rea, Giuseppina; Polticelli, Fabio; Antonacci, Amina; Scognamiglio, Viviana; Katiyar, Prashant; Kulkarni, Sudhir A.; Johanningmeier, Udo; Giardi, Maria Teresa

2009-01-01

68

Finding the most significant common sequence and structure motifs in a set of RNA sequences.  

Science.gov (United States)

We present a computational scheme to locally align a collection of RNA sequences using sequence and structure constraints. In addition, the method searches for the resulting alignments with the most significant common motifs, among all possible collections. The first part utilizes a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pairwise comparisons. The algorithm finds the multiple alignments using a greedy approach and has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. The choice of scoring system and the method of progressively constructing the final solution are important considerations that are discussed. Example solutions, and comparisons with other approaches, are provided. The solutions include finding consensus structures identical to published ones. PMID:9278497

Gorodkin, J; Heyer, L J; Stormo, G D

1997-09-15

69

Finding the most significant common sequence and structure motifs in a set of RNA sequences  

DEFF Research Database (Denmark)

We present a computational scheme to locally align a collection of RNA sequences using sequence and structure constraints, In addition, the method searches for the resulting alignments with the most significant common motifs, among all possible collections, The first part utilizes a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pairwise comparisons, The algorithm finds the multiple alignments using a greedy approach and has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. The choice of scoring system and the method of progressively constructing the final solution are important considerations that are discussed, Example solutions, and comparisons with other approaches, are provided, The solutions include finding consensus structures identical to published ones.

Gorodkin, Jan

1997-01-01

70

EURDYN-1D: a computer code for the one-dimensional non-linear dynamic analysis of structural systems. Description and users' manual (release 1)  

International Nuclear Information System (INIS)

The goal of the present report is to provide for a comprehensive users' manual describing the capabilities of the computer code EURDYN-1D. It includes information and examples about the type of problems which can be solved with the code and explanation on how to prepare input data and, how to interpret output results. The field of applications of EURDYN-1D is the one dimensional dynamic analysis of general structural systems and the code is particularly suited for fast transient events involving propagation of longitudinal mechanical waves (subsonic) in structures. Both geometrical and physical non-linearities can be taken into account. Typical examples are impact problems, fast dynamic loading due the explosions or sudden release for initial loads due to failures, etc. To these classes belong many problems encountered in the reactor safety field as well as in more common and general technological applications

71

Geometric structure of N = 1, D = 10 and N = 4, D = 4 super Yang-Mills theory  

International Nuclear Information System (INIS)

In this paper we present the group manifold formulation of N = 1, D = 10 and N = 4, D = 4 super Yang-Mills theory. Our result is an off-shell, first-order action in superspace without central charges. Analysis of the Bianchi identities based on a general group theoretical technique described in a previous publication shows that no constraint can be imposed on the curvatures without implying propagation equations. This suggests that our first-order action is probably the only off-shell one: no second-order, off-shell formulation seems to exist. (orig.)

72

Designing polymorphic ISSR primers in order to study gene sequences x and y types glutenin subunits in 1D locus controlling favourable baking quality in elite mutant lines of bread wheat  

International Nuclear Information System (INIS)

Baking quality is one of important traits in qualitative improvement of bread wheat. Gluten prolamins determine wheat flour quality for different technological process such as bread making. Between gluten proteins, High Molecular Glutenin (HMW) group and specially, d allele in 1D locus with x-type and y-type subunits are very valuable in baking quality. In this study, amino acid sequences of x-type subunits (2.1, 2.2, 2.2*, 5) and y-type subunits (10, 12) related to 1D locus were searched, found and compared together using Genedoc software. After amino acid sequences alignment of y-type subunits and x-type subunits, it was characterized that deletion, insertion (duplication) and point mutations in these subunits involved in biological function of proteins. most important insertion and deletion mutations were 185 amino acids sequence insertion of 2.2* subunit and 102 amino acids sequence insertion of x2.2 subunit in position 486 of amino acid sequence and six amino acid sequence deletion IGQGQQ in position 203 of y10 subunit. From important point mutations can be pointed to conversion of serine to cysteine in position 118 of x 5 subunit and substitution of glutamine to histidine in position 626 of x5 subunit. Finally, polymorph ISSR primers in repetitive domains were designed on similarities and differences in subunits of x and y-types. These primers show good banding polymorphisms in elite mutant lines, standard commercial cultivars and F2 populations from crosses. (author)

73

Specific alignment of structured RNA: stochastic grammars and sequence annealing  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Motivation: Whole-genome screens suggest that eukaryotic genomes are dense with non-coding RNAs (ncRNAs). We introduce a novel approach to RNA multiple alignment which couples a generative probabilistic model of sequence and structure with an efficient sequence annealing approach for exploring the space of multiple alignments. This leads to a new software program, Stemloc-AMA, that is both accurate and specific in the alignment of multiple related RNA sequences.

Bradley, Robert K.; Pachter, Lior; Holmes, Ian

2008-01-01

74

A case of Beauveria bassiana keratitis confirmed by internal transcribed spacer and LSU rDNA D1-D2 sequencing  

Science.gov (United States)

We describe a case of fungal keratitis due to Beauveria bassiana in a farmer with Fuchs' dystrophy, treated with amphotericin B. Surgery with penetrating keratoplasty was necessary to resolve the lesions. Susceptibility testing and molecular sequencing permitted the identification and treatment of this rare aetiological agent of invasive fungal disease. PMID:25356350

Ligozzi, M; Maccacaro, L; Passilongo, M; Pedrotti, E; Marchini, G; Koncan, R; Cornaglia, G; Centonze, A R; Lo Cascio, G

2014-01-01

75

Novel ligands specific for mitochondrial benzodiazepine receptors: 6-arylpyrrolo[2,1-d][1,5]benzothiazepine derivatives. Synthesis, structure-activity relationships, and molecular modeling studies.  

Science.gov (United States)

A novel class of ligands specific for MBR receptors has been identified: 6-arylpyrrolo[2,1-d][1,5]benzothiazepine derivatives. The majority of newly synthesized esters 37-64 as well as some intermediate ketones showed micro- or nanomolar affinity for [3H]PK 11195 binding inhibition. A SAR study on 42 compounds and a molecular modeling approach led to a preliminary structural selectivity profile: the 6,7-double bond, the carbamoyloxy, alcanoyloxy, and mesyloxy side chains at the 7-position, and the prospective chloro substitution at the 4-position seemed to be the most important structural features improving affinity. Therefore, 7-[(dimethylcarbamoyl)oxy]- and 7-acetoxy-4-chloro-6-phenylpyrrolo[2,1-d][1,5]benzothiazepine (43 and 57) were synthesized. With 7-[(dimethylcarbamoyl)oxy]-6-(p-methoxyphenyl)pyrrolo[2,1- d][1,5]benzothiazepine (65), these were the most promising compounds with IC50s of respectively 9, 8, and 9 nM, under conditions where PK 11195 had an IC50 of 2 nM. PMID:8182701

Fiorini, I; Nacci, V; Ciani, S M; Garofalo, A; Campiani, G; Savini, L; Novellino, E; Greco, G; Bernasconi, P; Mennini, T

1994-05-13

76

Coalescence phenomena in 1D silver nanostructures  

International Nuclear Information System (INIS)

Different coalescence processes on 1D silver nanostructures synthesized by a PVP assisted reaction in ethylene glycol at 160 deg. C were studied experimentally and theoretically. Analysis by TEM and HRTEM shows different defects found on the body of these materials, suggesting that they were induced by previous coalescence processes in the synthesis stage. TEM observations showed that irradiation with the electron beam eliminates the boundaries formed near the edges of the structures, suggesting that this process can be carried out by the application of other means of energy (i.e. thermal). These results were also confirmed by theoretical calculations by Monte Carlo simulations using a Sutton-Chen potential. A theoretical study by molecular dynamics simulation of the different coalescence processes on 1D silver nanostructures is presented, showing a surface energy driven sequence followed to form the final coalesced structure. Calculations were made at 1000-1300 K, which is near the melting temperature of silver (1234 K). Based on these results, it is proposed that 1D nanostructures can grow through a secondary mechanism based on coalescence, without losing their dimensionality.

77

Coalescence phenomena in 1D silver nanostructures.  

Science.gov (United States)

Different coalescence processes on 1D silver nanostructures synthesized by a PVP assisted reaction in ethylene glycol at 160?°C were studied experimentally and theoretically. Analysis by TEM and HRTEM shows different defects found on the body of these materials, suggesting that they were induced by previous coalescence processes in the synthesis stage. TEM observations showed that irradiation with the electron beam eliminates the boundaries formed near the edges of the structures, suggesting that this process can be carried out by the application of other means of energy (i.e. thermal). These results were also confirmed by theoretical calculations by Monte Carlo simulations using a Sutton-Chen potential. A theoretical study by molecular dynamics simulation of the different coalescence processes on 1D silver nanostructures is presented, showing a surface energy driven sequence followed to form the final coalesced structure. Calculations were made at 1000-1300 K, which is near the melting temperature of silver (1234 K). Based on these results, it is proposed that 1D nanostructures can grow through a secondary mechanism based on coalescence, without losing their dimensionality. PMID:21828529

Gutiérrez-Wing, C; Pérez-Alvarez, M; Mondragón-Galicia, G; Arenas-Alatorre, J; Gutiérrez-Wing, M T; Henk, M C; Negulescu, I I; Rusch, K A

2009-07-22

78

Tensor structure function b1d(x,Q2) of the deuteron at NLO and NNLO at small-x  

International Nuclear Information System (INIS)

The precision of the contemporary experimental data demands that the parton distribution functions (PDF's) should be corrected at least up to next-to-leading order (NLO) and preferably up to next-to-next-to-leading order (NNLO). A general form of tensor structure function b1d(x,Q2) of the deuteron at NLO and NNLO is obtained by using the solution of Dokshitzer, Gribov, Lipatov, Altarelli, Parisi (DGLAP) equation for singlet structure function at small-x. Results are compared with HERA Experiment data. (orig.)

79

Expanding the 2,2'-bipyrimidine bridged 1D homonuclear coordination polymers family: [M(II)(bpym)Cl2] (M = Fe, Co) magnetic and structural characterization.  

Science.gov (United States)

One pot reaction of hydrated chloride salts of Fe(II) and Co(II) with stoichiometric amounts of 2,2'-bipyrimidine (bpym) in a methanol-acetonitrile mixture afforded the corresponding 1D homonuclear coordination polymers, [?-(bpym)MCl2]n. Crystal structures of both complexes are isomorphous in the highly symmetric orthorhombic space group Fddd. The 1D coordination polymers are composed of almost orthogonal alternating bipyrimidine bridges linking the {MCl2} units. The magnetic behaviour of the Fe(II) compound can be well understood as a uniform S = 2 chain with an antiferromagnetic exchange interaction between metal ion sites. In the case of the Co(II) ion, also an antiferromagnetic interaction is operative along the uniform chain, while at low temperatures a long range-ordering is observed due to spin canting originating from the anisotropic behaviour of the Co(II) lowest energy Kramers doublets. PMID:23676951

Alborés, Pablo; Rentschler, Eva

2013-07-14

80

Syntheses, crystal structures and luminescent properties of two new 1D d 1 coordination polymers constructed from 2,2'-bibenzimidazole and 1,4-benzenedicarboxylate  

International Nuclear Information System (INIS)

Two novel interesting d 1 metal coordination polymers, [Zn(H2bibzim)(BDC)] n (1) and [Cd(H2bibzim)(BDC)] n (2) [H2bibzim=2,2'-bibenzimidazole, BDC=1,4-benzenedicarboxylate] have been synthesized under solvothermal conditions and structurally characterized. Both 1 and 2 are constructed from infinite neutral zigzag-like one-dimensional (1D) chains. The ?-? interactions and interchain hydrogen-bonding interactions further extend the 1D arrangement to generate a 3D supramolecular architecture for 1 and 2. Both complexes have high thermal stability and display strong blue fluorescent emissions in the solid state upon photo-excitation at 365 nm at room temperature. They are the first two examples that 2,2'-bibenzimidazole has been introduced into the d 1 coordination polymeric framework

 
 
 
 
81

Occurrence of protein structure elements in conserved sequence regions  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Conserved protein sequence regions are extremely useful for identifying and studying functionally and structurally important regions. By means of an integrated analysis of large-scale protein structure and sequence data, structural features of conserved protein sequence regions were identified. Results Helices and turns were found to be underrepresented in conserved regions, while strands were found to be overrepresented. Similar numbers of loops were found in conserved and random regions. Conclusion These results can be understood in light of the structural constraints on different secondary structure elements, and their role in protein structural stabilization and topology. Strands can tolerate fewer sequence changes and nonetheless keep their specific shape and function. They thus tend to be more conserved than helices, which can keep their shape and function with more changes. Loop behavior can be explained by the presence of both constrained and freely changing loops in proteins. Our detailed statistical analysis of diverse proteins links protein evolution to the biophysics of protein thermodynamic stability and folding. The basic structural features of conserved sequence regions are also important determinants of protein structure motifs and their function.

Pietrokovski Shmuel

2007-01-01

82

Intraspecies diversity of the industrial yeast strains Saccharomyces cerevisiae and Saccharomyces pastorianus based on analysis of the sequences of the internal transcribed spacer (ITS) regions and the D1/D2 region of 26S rDNA.  

Science.gov (United States)

We divided industrial yeast strains of Saccharomyces cerevisiae into three groups based on the sequences of their internal transcribed spacer (ITS) regions. One group contained sake yeasts, shochu yeasts, and one bakery yeast, another group contained wine yeasts, and the third group contained beer and whisky yeasts, including seven bakery yeasts. The three groups were distinguished by polymorphisms at two positions, designated positions B and C, corresponding to nucleotide numbers 279 and 301 respectively in the S288C strain. The yeasts in the Japanese group had one thymine at position B and one thymine at position C. The wine yeasts had one thymine at position B and one cytosine at position C. And the beer and whisky yeasts had two thymines at position B and one cytosine at position C. Strains of S. pastorianus were divided into three groups based on the sequences of their 26S rDNA D1/D2 and ITS regions. PMID:17617725

Kawahata, Miho; Fujii, Tsutomu; Iefuji, Haruyuki

2007-07-01

83

Real-time defect detection in transparent multilayer polymer films using structured illumination and 1D filtering  

Science.gov (United States)

Today, typical polymer films consist of several functional layers, like printable surface or barrier layers. They are produced in coextrusion processes, in which the different materials are extruded through a single die and formed to a blown- or cast film with haul-off speeds up to 500 m/min. In the production of transparent multilayer films certain defects, called "interfacial instabilities", can occur. They emerge from shear stress and turbulences in the material flow during the process and result in a reduction of the mechanical properties and the optical quality of the product. Interfacial instabilities cannot be detected by conventional film inspection systems available on the market because the optical distortions they produce do not change the brightness of a pixel. In this paper, an approach for solving this problem is presented. The film is illuminated with a patterned line-light source in a backlight setting and a CCD line scan camera is used for recording the image lines. The defects can be detected using a 1D filter tuned to the spatial-frequency of the pattern. The distortion caused by the defects leads to a local extremum in the feature image generated by the filter, which can be easily detected by threshold segmentation. The system has been tested in an industrial setting and proved to be fast enough for inline-inspection. Further applications could be in the fast deflectometric inspection of high-gloss surfaces.

Michaeli, Walter; Berdel, Klaus; Osterbrink, Oliver

2009-06-01

84

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%  

DEFF Research Database (Denmark)

Motivation: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding todya as these often are conserved in structure rather than in sequence. Even though the number of available methods is growing, it is still of interest to pairwise detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Results: Here we present such an approach for pairwise local alignment which is based on FILDALIGN and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy as well as for substitution matrices similar to RIBOSUM. The new FOLDALIGN implementation is tested on a dataset where the ncRNAs and eleRNAs have sequence similarity <40% and where the ncRNAs and eleRNAs are energetically indistinguishable from the surrounding genomic sequence context. The method is tested in two ways: (1) its ability to find the common structure between the genes only and (2) its ability to locate ncRNAs and eleRNAs in a genomic context. In case (1), it makes sense to compare with methods like Dynalign, and the performances are very similar, but FOLDALIGN is substantially faster. The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. Availability: The program is available online at http://foldalign.kvl.dk Contact: gorodkin@bioinf.kvl.dk

Havgaard, Jakob Hull; LyngsØ, Rune B.

2005-01-01

85

Crystal Structure of Human Liver delta {4}-3-Ketosteroid 5 beta-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis  

Energy Technology Data Exchange (ETDEWEB)

AKR1D1 (steroid 5{beta}-reductase) reduces all 4-3-ketosteroids to form 5{beta}-dihydrosteroids, a first step in the clearance of steroid hormones and an essential step in the synthesis of all bile acids. The reduction of the carbon-carbon double bond in an a,{beta}-unsaturated ketone by 5{beta}-reductase is a unique reaction in steroid enzymology because hydride transfer from NADPH to the {beta}-face of a 4-3-ketosteroid yields a cis-A/B-ring configuration with an {approx}90 bend in steroid structure. Here, we report the first x-ray crystal structure of a mammalian steroid hormone carbon-carbon double bond reductase, human 4-3-ketosteroid 5{beta}-reductase (AKR1D1), and its complexes with intact substrates. We have determined the structures of AKR1D1 complexes with NADP+ at 1.79- and 1.35- Angstroms resolution (HEPES bound in the active site), NADP+ and cortisone at 1.90- Angstroms resolution, NADP+ and progesterone at 2.03- Angstroms resolution, and NADP+ and testosterone at 1.62- Angstroms resolution. Complexes with cortisone and progesterone reveal productive substrate binding orientations based on the proximity of each steroid carbon-carbon double bond to the re-face of the nicotinamide ring of NADP+. This orientation would permit 4-pro-(R)-hydride transfer from NADPH. Each steroid carbonyl accepts hydrogen bonds from catalytic residues Tyr58 and Glu120. The Y58F and E120A mutants are devoid of activity, supporting a role for this dyad in the catalytic mechanism. Intriguingly, testosterone binds nonproductively, thereby rationalizing the substrate inhibition observed with this particular steroid. The locations of disease-linked mutations thought to be responsible for bile acid deficiency are also revealed.

Di Costanzo,L.; Drury, J.; Penning, T.; Christianson, D.

2008-01-01

86

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

MOTIVATION: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding today as these often are conserved in structure rather than in sequence. Even though the number of available methods is growing, it is still of interest to pairwise detect two genes with low sequence similarity, where the genes are part of a larger genomic region. RESULTS: Here we present such an approach for pairwise local alignment which is based on foldalign and ...

Havgaard, Jh; Lyngsø, Rb; Stormo, Gd; Gorodkin, J.

2005-01-01

87

Application of 1D- and 2D-NMR techniques for the structural studies of glycoprotein-derived carbohydrates  

International Nuclear Information System (INIS)

The first part of this thesis (Chapters 1 to 4) describe the determination of the primary structure for a large number of oligosaccharide-alditols obtained from bronchial sputum of cystic fibrosis patients suffering from chronic bronchitis. The second part (Chapters 5 to 8) is devoted to the application of two-dimensional NMR methods for the structural analysis of oligosaccharides. (H.W.). 163 refs.; 50 figs.; 25 tabs

88

A tale of two ferredoxins: sequence similarity and structural differences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Sequence similarity between proteins is usually considered a reliable indicator of homology. Pyruvate-ferredoxin oxidoreductase and quinol-fumarate reductase contain ferredoxin domains that bind [Fe-S] clusters and are involved in electron transport. Profile-based methods for sequence comparison, such as PSI-BLAST and HMMer, suggest statistically significant similarity between these domains. Results The sequence similarity between these ferredoxin domains resides in the area of the [Fe-S] cluster-binding sites. Although overall folds of these ferredoxins bear no obvious similarity, the regions of sequence similarity display a remarkable local structural similarity. These short regions with pronounced sequence motifs are incorporated in completely different structural environments. In pyruvate-ferredoxin oxidoreductase (bacterial ferredoxin, the hydrophobic core of the domain is completed by two ?-hairpins, whereas in quinol-fumarate reductase (?-helical ferredoxin, the cluster-binding motifs are part of a larger all-?-helical globin-like fold core. Conclusion Functionally meaningful sequence similarity may sometimes be reflected only in local structural similarity, but not in global fold similarity. If detected and used naively, such similarities may lead to incorrect fold predictions.

Sadreyev Ruslan I

2006-04-01

89

RNA secondary structure prediction from multi-aligned sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functi...

Hamada, Michiaki

2013-01-01

90

Music and language perception: expectations, structural integration, and cognitive sequencing.  

Science.gov (United States)

Music can be described as sequences of events that are structured in pitch and time. Studying music processing provides insight into how complex event sequences are learned, perceived, and represented by the brain. Given the temporal nature of sound, expectations, structural integration, and cognitive sequencing are central in music perception (i.e., which sounds are most likely to come next and at what moment should they occur?). This paper focuses on similarities in music and language cognition research, showing that music cognition research provides insight into the understanding of not only music processing but also language processing and the processing of other structured stimuli. The hypothesis of shared resources between music and language processing and of domain-general dynamic attention has motivated the development of research to test music as a means to stimulate sensory, cognitive, and motor processes. PMID:22760955

Tillmann, Barbara

2012-10-01

91

Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences, we predict seven classes from sequences that share twilight-zone identity with the training sequences. Results The proposed MODular Approach to Structural class prediction (MODAS method is unique as it allows for selection of any subset of the classes. MODAS is also the first to utilize a novel, custom-built feature-based sequence representation that combines evolutionary profiles and predicted secondary structure. The features quantify information relevant to the definition of the classes including conservation of residues and arrangement and number of helix/strand segments. Our comprehensive design considers 8 feature selection methods and 4 classifiers to develop Support Vector Machine-based classifiers that are tailored for each of the seven classes. Tests on 5 twilight-zone and 1 high-similarity benchmark datasets and comparison with over two dozens of modern competing predictors show that MODAS provides the best overall accuracy that ranges between 80% and 96.7% (83.5% for the twilight-zone datasets, depending on the dataset. This translates into 19% and 8% error rate reduction when compared against the best performing competing method on two largest datasets. The proposed predictor provides accurate predictions at 58% accuracy for membrane proteins class, which is not considered by majority of existing methods, in spite that this class accounts for only 2% of the data. Our predictive model is analyzed to demonstrate how and why the input features are associated with the corresponding classes. Conclusions The improved predictions stem from the novel features that express collocation of the secondary structure segments in the protein sequence and that combine evolutionary and secondary structure information. Our work demonstrates that conservation and arrangement of the secondary structure segments predicted along the protein chain can successfully predict structural classes which are defined based on the spatial arrangement of the secondary structures. A web server is available at http://biomine.ece.ualberta.ca/MODAS/.

Kurgan Lukasz

2009-12-01

92

Dissociable processes for learning the surface structure and abstract structure of sensorimotor sequences.  

Science.gov (United States)

A sensorimotor sequence may contain information structure at several different levels. In this study, we investigated the hypothesis that two dissociable processes are required for the learning of surface structure and abstract structure, respectively, of sensorimotor sequences. Surface structure is the simple serial order of the sequence elements, whereas abstract structure is defined by relationships between repeating sequence elements. Thus, sequences ABCBAC and DEFEDF have different surface structures but share a common abstract structure, 123213, and are therefore isomorphic. Our simulations of sequence learning performance in serial reaction time (SRT) tasks demonstrated that (1) an existing model of the primate fronto-striatal system is capable of learning surface structure but fails to learn abstract structure, which requires an additional capability, (2) surface and abstract structure can be learned independently by these independent processes, and (3) only abstract structure transfers to isomorphic sequences. We tested these predictions in human subjects. For a sequence with predictable surface and abstract structure, subjects in either explicit or implicit conditions learn the surface structure, but only explicit subjects learn and transfer the abstract structure. For sequences with only abstract structure, learning and transfer of this structure occurs only in the explicit group. These results are parallel to those from the simulations and support our dissociable process hypothesis. Based on the synthesis of the current simulation and empirical results with our previous neuropsychological findings, we propose a neuro-physiological basis for these dissociable processes: Surface structure can be learned by processes that operate under implicit conditions and rely on the fronto-striatal system, whereas learning abstract structure requires a more explicit activation of dissociable processes that rely on a distributed network that includes the left anterior cortex. PMID:9831741

Dominey, P F; Lelekov, T; Ventre-Dominey, J; Jeannerod, M

1998-11-01

93

Evolutionarily consistent families in SCOP: sequence, structure and function  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background SCOP is a hierarchical domain classification system for proteins of known structure. The superfamily level has a clear definition: Protein domains belong to the same superfamily if there is structural, functional and sequence evidence for a common evolutionary ancestor. Superfamilies are sub-classified into families, however, there is not such a clear basis for the family level groupings. Do SCOP families group together domains with sequence similarity, do they group domains with similar structure or by common function? It is these questions we answer, but most importantly, whether each family represents a distinct phylogenetic group within a superfamily. Results Several phylogenetic trees were generated for each superfamily: one derived from a multiple sequence alignment, one based on structural distances, and the final two from presence/absence of GO terms or EC numbers assigned to domains. The topologies of the resulting trees and confidence values were compared to the SCOP family classification. Conclusions We show that SCOP family groupings are evolutionarily consistent to a very high degree with respect to classical sequence phylogenetics. The trees built from (automatically generated structural distances correlate well, but are not always consistent with SCOP (hand annotated groupings. Trees derived from functional data are less consistent with the family level than those from structure or sequence, though the majority still agree. Much of GO and EC annotation applies directly to one family or subset of the family; relatively few terms apply at the superfamily level. Maximum sequence diversity within a family is on average 22% but close to zero for superfamilies.

Pethica Ralph B

2012-10-01

94

The influence of a power law distribution of cluster size on the light transmission of disordered 1D photonic structures  

CERN Document Server

A better understanding of the optical properties of random photonic structures is beneficial for many applications, such as random lasing, optical imaging and photovoltaics. Here we investigated the light transmission properties of disordered photonic structures in which the high refractive index layers are aggregated in clusters. We sorted the size of the clusters from a power law distribution tuning the exponent a of the distribution function. The sorted high refractive layer clusters are randomly distributed within the low refractive index layers. We studied the total light transmission, within the photonic band gap of the corresponding periodic crystal, as a function of the exponent in the distribution. We observed that, for a within the interval [0,3.5], the trend can be fitted with a sigmoidal function.

Bellingeri, Michele

2014-01-01

95

Excitation of defect modes from the extended photonic band-gap structures of 1D photonic lattices  

International Nuclear Information System (INIS)

This paper stuides numerically the model equation in a one dimensional defective photonic lattice by modifying the potential function to a periodic function. It is found that defect modes (DMs) can be regarded as Bloch modes which are excited from the extended photonic band-gap structure at Bloch wave-numbers with kx = 0. The DMs for both positive and negative defects are considered in this method. (classical areas of phenomenology)

96

Tails of the dynamical structure factor of 1D spinless fermions beyond the Tomonaga-Luttinger approximation  

International Nuclear Information System (INIS)

We consider one-dimensional interacting spinless fermions with a non-linear spectrum in a clean quantum wire (non-linear bosonization). We compute diagrammatically the one-dimensional dynamical structure factor, S(?, q), beyond the Tomonaga-Luttinger approximation focusing on its tails, i.e. vertical bar ? vertical bar >> vq. We provide a re-derivation, through diagrammatics, of the result of Pustilnik, Mishchenko, Glazman, and Andreev. We also extend their results to finite temperatures and long-range interactions. As applications we determine curvature and interaction corrections to the small- momentum, high-frequency conductivity and the electron-electron scattering rate. (author)

97

Effects of synthesis temperature and precursor composition on the crystal structure, morphology, and electrode activity of 1D nanostructured manganese oxides  

Energy Technology Data Exchange (ETDEWEB)

1D nanostructured manganese oxides are prepared by oxidation reaction of precursor LiMn{sub 2-x}Cr{sub x}O{sub 4} microcrystals under hydrothermal condition. The crystal structure and morphology of the obtained manganese oxides are strongly dependent on the reaction condition and the chemical composition of the precursors. The {alpha}-MnO{sub 2} nanowires are prepared by reaction at 120 C, and their aspect ratios decrease with the Cr content in the precursor. Treating precursors with persulfate ions at 160-180 C yields the {beta}-MnO{sub 2} nanorods for the precursors LiMn{sub 2-x}Cr{sub x}O{sub 4} with lower Cr content and the {alpha}-MnO{sub 2} nanowires for the precursors with higher Cr content. The structure dependence of the products on the Cr content in the precursors is related to the high octahedral site stabilization energy of Cr{sup 3+} ions and/or to the increase of Mn valence state upon Cr substitution. The increase of Cr content in the precursors degrades the electrode performance for the manganates prepared at 160 C but improves electrode activity for those prepared at 180 C. This observation can be explained by the structural variation and chromium substitution of the hydrothermally treated manganates. We conclude that the use of spinel LiMn{sub 2-x}Cr{sub x}O{sub 4} as precursors provides an effective way to synthesize 1D nanostructured manganate with tailored crystal structure and morphology. (author)

Kim, In Young; Lee, Sun Hee; Ha, Hyung-Wook; Kim, Tae Woo; Hwang, Seong-Ju [Center for Intelligent Nano-Bio Materials (CINBM), Department of Chemistry and Nano Sciences, Ewha Womans University, Seoul 120-750 (Korea); Han, Yoon Soo; Kang, Jin Kyu; Lee, Dong Ha [Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu (Korea)

2010-09-15

98

1D 13C-NMR Data as Molecular Descriptors in Spectra — Structure Relationship Analysis of Oligosaccharides  

Directory of Open Access Journals (Sweden)

Full Text Available Spectra-structure relationships were investigated for estimating the anomeric configuration, residues and type of linkages of linear and branched trisaccharides using 13C-NMR chemical shifts. For this study, 119 pyranosyl trisaccharides were used that are trimers of the ? or ? anomers of D-glucose, D-galactose, D-mannose, L-fucose or L-rhamnose residues bonded through a or b glycosidic linkages of types 1?2, 1?3, 1?4, or 1?6, as well as methoxylated and/or N-acetylated amino trisaccharides. Machine learning experiments were performed for: (1 classification of the anomeric configuration of the first unit, second unit and reducing end; (2 classification of the type of first and second linkages; (3 classification of the three residues: reducing end, middle and first residue; and (4 classification of the chain type. Our previously model for predicting the structure of disaccharides was incorporated in this new model with an improvement of the predictive power. The best results were achieved using Random Forests with 204 di- and trisaccharides for the training set—it could correctly classify 83%, 90%, 88%, 85%, 85%, 75%, 79%, 68% and 94% of the test set (69 compounds for the nine tasks, respectively, on the basis of unassigned chemical shifts.

Florbela Pereira

2012-03-01

99

Statistical mechanics of secondary structures formed by random RNA sequences  

CERN Document Server

The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical studies. First, a two-replica calculation is performed. By mapping the two-replica problem to the denaturation of a single homogeneous RNA in 6-dimensional embedding space, we show that sequence disorder is perturbatively irrelevant, i.e., an RNA molecule with weak sequence disorder is in a molten phase where many secondary structures with comparable total energy coexist. A numerical study of various models at high temperature reproduces behaviors characteristic of the molten phase. On the other hand, a scaling argument based on the extremal statistics of rare regions can be constructed to show that the low temperature phase is unstable to sequence disorder. We performed a detailed numerical study of the low temperature phase using the droplet theory as a guide, and characte...

Bundschuh, R

2001-01-01

100

Massively Parallel Interrogation of Aptamer Sequence, Structure and Function  

Energy Technology Data Exchange (ETDEWEB)

Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. Methodology/Principal Findings. High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and interchip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

Fischer, N O; Tok, J B; Tarasow, T M

2008-02-08

 
 
 
 
101

Synthesis, Structure, and Properties of ?,?-Linked Oligothiazoles with Controlled Sequence.  

Science.gov (United States)

?,?-Linked oligothiazoles with head-to-tail connectivity are presented as a new family of helical scaffolds. Combinations of palladium-catalyzed cross-coupling reactions at the 5- and 4-positions of 2-phenylthiazole led to the synthesis of oligo(2-phenylthiazoles) with ortho linkages with a variety of defined sequences. The secondary structures of the ?,?-linked oligo(2-phenylthiazoles) showed a clear dependence on their sequences. X-ray crystallography of the trimer, tetramer, and hexamer with head-to-tail connection revealed the formation of a helical structure, which was stabilized by a combination of intramolecular forces, including interheteroatom (S???N), CH-?, and ?-? interactions. The introduction of a chiral end-group successfully led to the induction of chirality into the helical conformations. Programmable sequences for controlled geometries and photofunctions have been demonstrated through the manifold connection pathways in ?,?-linked oligothiazoles. PMID:25201229

Nakashima, Takuya; Imamura, Kazuhiko; Yamamoto, Kyohei; Kimura, Yuka; Katao, Shohei; Hashimoto, Yuichiro; Kawai, Tsuyoshi

2014-10-13

102

Syntheses, crystal structures, and characterization of three 1D, 2D and 3D complexes based on mixed multidentate N- and O-donor ligands  

Science.gov (United States)

Three new 1D to 3D complexes, namely, {[Ni(btec)(Himb)2(H2O)2]·6H2O}n (1), {[Cd(btec)0.5(imb)(H2O)]·1.5H2O}n (2), and {[Zn(btec)0.5(imb)]·H2O}n (3) (H4btec=1,2,4,5-benzenetetracarboxylic acid, imb=2-(1H-imidazol-1-methyl)-1H-benzimidazole) have been synthesized by adjusting the central metal ions. Single-crystal X-ray diffraction analyses reveal that complex 1 possesses a 1D chain structure which is further extended into the 3D supramolecular architecture via hydrogen bonds. Complex 2 features a 2D network with Schla¨fli symbol (53·62·7)(52·64). Complex 3 presents a 3D framework with a point symbol of (4·64·8)(42·62·82). Moreover, their IR spectra, PXRD patterns, thermogravimetric curves, and luminescent emissions were studied at room temperature.

Yang, Huai-Xia; Liang, Zhen; Hao, Bao-Lian; Meng, Xiang-Ru

2014-10-01

103

Moments of the spin structure functions g1p and g1d for 0.0522  

International Nuclear Information System (INIS)

The spin structure functions g1 for the proton and the deuteron have been measured over a wide kinematic range in x and Q2 using 1.6 and 5.7 GeV longitudinally polarized electrons incident upon polarized NH3 and ND3 targets at Jefferson Lab. Scattered electrons were detected in the CEBAF Large Acceptance Spectrometer, for 0.0522 and W1 for the proton and deuteron are presented - both have a negative slope at low Q2, as predicted by the extended Gerasimov-Drell-Hearn sum rule. The first extraction of the generalized forward spin polarizability of the proton ?0p is also reported. This quantity shows strong Q2 dependence at low Q2. Our analysis of the Q2 evolution of the first moment of g1 shows agreement in leading order with Heavy Baryon Chiral Perturbation Theory. However, a significant discrepancy is observed between the ?0p data and Chiral Perturbation calculations for ?0p, even at the lowest Q2

104

Crystal Structure of Human Liver [delta][superscript 4]-3-Ketosteroid 5[beta]-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis  

Energy Technology Data Exchange (ETDEWEB)

AKR1D1 (steroid 5{beta}-reductase) reduces all {Delta}{sup 4}-3-ketosteroids to form 5{beta}-dihydrosteroids, a first step in the clearance of steroid hormones and an essential step in the synthesis of all bile acids. The reduction of the carbon-carbon double bond in an {alpha}{beta}-unsaturated ketone by 5{beta}-reductase is a unique reaction in steroid enzymology because hydride transfer from NADPH to the {beta}-face of a {Delta}{sup 4}-3-ketosteroid yields a cis-A/B-ring configuration with an {approx}90{sup o} bend in steroid structure. Here, we report the first x-ray crystal structure of a mammalian steroid hormone carbon-carbon double bond reductase, human {Delta}{sup 4}-3-ketosteroid 5{beta}-reductase (AKR1D1), and its complexes with intact substrates. We have determined the structures of AKR1D1 complexes with NADP{sup +} at 1.79- and 1.35-{angstrom} resolution (HEPES bound in the active site), NADP{sup +} and cortisone at 1.90-{angstrom} resolution, NADP{sup +} and progesterone at 2.03-{angstrom} resolution, and NADP{sup +} and testosterone at 1.62-{angstrom} resolution. Complexes with cortisone and progesterone reveal productive substrate binding orientations based on the proximity of each steroid carbon-carbon double bond to the re-face of the nicotinamide ring of NADP{sup +}. This orientation would permit 4-pro-(R)-hydride transfer from NADPH. Each steroid carbonyl accepts hydrogen bonds from catalytic residues Tyr{sup 58} and Glu{sup 120}. The Y58F and E120A mutants are devoid of activity, supporting a role for this dyad in the catalytic mechanism. Intriguingly, testosterone binds nonproductively, thereby rationalizing the substrate inhibition observed with this particular steroid. The locations of disease-linked mutations thought to be responsible for bile acid deficiency are also revealed.

Di Costanzo, Luigi; Drury, Jason E.; Penning, Trevor M.; Christianson, David W. (UPENN); (UPENN-MED)

2008-07-15

105

Quantifying sequence and structural features of protein-RNA interactions.  

Science.gov (United States)

Increasing awareness of the importance of protein-RNA interactions has motivated many approaches to predict residue-level RNA binding sites in proteins based on sequence or structural characteristics. Sequence-based predictors are usually high in sensitivity but low in specificity; conversely structure-based predictors tend to have high specificity, but lower sensitivity. Here we quantified the contribution of both sequence- and structure-based features as indicators of RNA-binding propensity using a machine-learning approach. In order to capture structural information for proteins without a known structure, we used homology modeling to extract the relevant structural features. Several novel and modified features enhanced the accuracy of residue-level RNA-binding propensity beyond what has been reported previously, including by meta-prediction servers. These features include: hidden Markov model-based evolutionary conservation, surface deformations based on the Laplacian norm formalism, and relative solvent accessibility partitioned into backbone and side chain contributions. We constructed a web server called aaRNA that implements the proposed method and demonstrate its use in identifying putative RNA binding sites. PMID:25063293

Li, Songling; Yamashita, Kazuo; Amada, Karlou Mar; Standley, Daron M

2014-11-01

106

3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper presents 3DCoffee@igs, a web-based tool dedicated to the computation of high-quality multiple sequence alignments (MSAs). 3D-Coffee makes it possible to mix protein sequences and structures in order to increase the accuracy of the alignments. Structures can be either provided as PDB identifiers or directly uploaded into the server. Given a set of sequences and structures, pairs of structures are aligned with SAP while sequence–structure pairs are aligned with Fugue. The resulting...

Poirot, Olivier; Suhre, Karsten; Abergel, Chantal; O Toole, Eamonn; Notredame, Cedric

2004-01-01

107

The structurally constrained protein evolution model accounts for sequence patterns of the L?H superfamily  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Background Structure conservation constrains evolutionary sequence divergence, resulting in observable sequence patterns. Most current models of protein evolution do not take structure into account explicitly, being unsuitable for investigating the effects of structure conservation on sequence divergence. To this end, we recently developed the Structurally Constrained Protein Evolution (SCPE) model. The model starts with the coding sequence of a protein with known th...

Echave Julián; Parisi Gustavo

2004-01-01

108

Structure Elucidation Of Flavonoid Compound from the Leaves of Coleus Atropurpureus Benth using 1d- And 2d-NMR Techniques  

International Nuclear Information System (INIS)

Isolation of flavonoid compound from ethylacetate extract of the leaves of Coleus atropurpureus Benth using column chromatography have been carried out. Structure elucidation of the isolated compounds was done by one-and two-dimensional NMR (1H, 13C, DEPT, COSY, HMQC and HMBC). Analysis of 1D-NMR spectra (1H-NMR showed signals at ? 6-8 ppm for the aromatic region of the flavonoid aglycone and 13C-NMR showed signals for three carbon atoms of the flavonoid ring C at ? 182.8 ppm (C-4), 103.9 ppm (C-3), 166.4 ppm (C-2) and DEPT showed the presence of CH and CH2 group). Analysis of 2D- NMR spectra (COSY showed correlation of proton at ? 7.86 and 6.92 ppm and HMBC showed correlation between proton at ? 6.61 with 166.4 ppm and 6.92 with 123.3 ppm). (author)

109

Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags  

Energy Technology Data Exchange (ETDEWEB)

Computational methods for gene identification in genomic sequences typically have two phases: coding region prediction and gene parsing. While there are many effective methods for predicting coding regions (exons), parsing the predicted exons into proper gene structures, to a large extent, remains an unsolved problem. This paper presents an algorithm for inferring gene structures from predicted exon candidates, based on Expressed Sequence Tags (ESTs) and biological intuition/rules. The algorithm first finds all the related ESTs in the EST database (dbEST) for each predicted exon, and infers the boundaries of one or a series of genes based on the available EST information and biological rules. Then it constructs gene models within each pair of gene boundaries, that are most consistent with the EST information. By exploiting EST information and biological rules, the algorithm can (1) model complicated multiple gene structures, including embedded genes, (2) identify falsely-predicted exons and locate missed exons, and (3) make more accurate exon boundary predictions. The algorithm has been implemented and tested on long genomic sequences with a number of genes. Test results show that very accurate (predicted) gene models can be expected when related ESTs exist for the predicted exons.

Xu, Y.; Mural, R.; Uberbacher, E.

1997-02-01

110

Biophysical and structural considerations for protein sequence evolution  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model.

Grahnen Johan A

2011-12-01

111

High-Throughput Sequencing Based Methods of RNA Structure Investigation  

DEFF Research Database (Denmark)

In this thesis we describe the development of four related methods for RNA structure probing that utilize massive parallel sequencing. Using them, we were able to gather structural data for multiple, long molecules simultaneously. First, we have established an easy to follow experimental and computational protocol for detecting the reverse transcription termination sites (RTTS-Seq). This protocol was subsequently applied to hydroxyl radical footprinting of three dimensional RNA structures to give a probing signal that correlates well with the RNA backbone solvent accessibility. Moreover, we applied RTTS-Seq to detect antisense oligonucleotide binding sites within a transcriptome. In this case, we applied an enrichment strategy to greatly reduce the background. Finally, we have modified the RTTS-Seq to study the secondary structure of 3’ untranslated regions. In the course of this thesis we describe several computational methods. One that alleviates PCR bias by estimating number of unique molecules existing before the amplification, and two methods for data normalization: one applicable when the paired end sequencing is performed, and the other that works with the single read sequencing with known priming sites.

Kielpinski, Lukasz Jan

2014-01-01

112

Two novel 1-D helical chains Zn(II)/Cd(II) polymers based on tetrazolate-1-acetic acid: Crystal structures, solid state fluorescence and thermal behaviors  

Science.gov (United States)

Two new d10 metal complexes with tetrazolate-1-acetic acid, [Zn(1-tza)(Cl)(H2O)] (1) and [Cd(1-tza)(phen)(NO3)] (2) (1-Htza = tetrazole-1-acetic acid, phen = 1,10-phenanthroline), have been prepared, and their structures have been characterized by single-crystal X-ray diffraction. The flexibilities of 1-tza ligands result in 1-D helical chained structures of the two obtained complexes, in which the 1-tza ligands adopt different coordination mode: 1 with ?2-kO1: kN4 and 2 with ?2-kO1, O2: kN3. Compounds 1 exhibits a nonracemic enantiopure topology while compound 2 reveals to be mesomeric structures. The crystal packing in 1 and 2 is controlled mainly by hydrogen bonds and face-to-face ?-? stacking interactions, respectively. Photoluminescence studies show that 1 and 2 exhibit strong luminescence. Moreover, compound 1 exhibits a second-order nonlinear optical coefficient equal to that of potassium dihydrogen phosphate (KDP). The thermal stability of the two complexes has also been investigated.

Lu, Ying-Bing; Jin, Shuang; Jian, Fang-Mei; Xie, Yong-Rong; Luo, Guo-Tian

2014-03-01

113

Structural and thermodynamic properties of molecular complexes of aluminum and gallium trihalides with bifunctional donor pyrazine: decisive role of Lewis acidity in 1D polymer formation.  

Science.gov (United States)

Solid state structures of group 13 metal halide complexes with pyrazine (pyz) of 2:1 and 1:1 composition have been established by X-ray structural analysis. Complexes of 2:1 composition adopt molecular structures MX3·pyz·MX3 with tetrahedral geometry of group 13 metals. Complexes of AlBr3 and GaCl3 of 1:1 composition are 1D polymers (MX3·pyz)? with trigonal bipyramidal geometry of the group 13 metal, while the weaker Lewis acid GaI3 forms the monomeric molecular complex GaI3·pyz, which is isostructural to its pyridine analog GaI3·py. Tensimetry studies of vaporization and thermal dissociation of AlBr3·pyz and AlBr3·pyz·AlBr3 complexes have been carried out using the static method with a glass membrane null-manometer. Thermodynamic characteristics of vaporization and equilibrium gas phase dissociation of the AlBr3·pyz complex have been determined. Comprehensive theoretical studies of (MX3)n·(pyz)m complexes (M = Al, Ga; X = Cl, Br, I; n = 1, 2; m = 1-3) have been carried out at the B3LYP/TZVP level of theory. Donor-acceptor bond energies were obtained taking into account reorganization energies of the fragments. Computational data indicate that the formation of (MX3·pyz)? polymers with coordination number 5 is only slightly more energetically favorable than the formation of molecular complexes of type MX3·pyz for X = Cl, Br. It is expected that on melting (MX3·pyz)? polymers dissociate into individual MX3·pyz molecules. This dovetails with low melting enthalpies of the (MX3·pyz)? complexes. Polymer stability decreases in the order AlCl3 > AlBr3 > GaCl3 > AlI3 > GaBr3 > GaI3. For MI3·pyz complexes computations predict that the monomeric structure motif is more energetically favorable compared to the catena polymer. These theoretical predictions agree well with the experimentally observed monomeric complex GaI3·pyz in the solid state. Thus, the Lewis acidity of the group 13 halides may play a decisive role in the formation of 1D polymeric networks. PMID:23824052

Sevastianova, Tatiana N; Bodensteiner, Michael; Lisovenko, Anna S; Davydova, Elena I; Scheer, Manfred; Susliakova, Tatiana V; Krasnova, Irina S; Timoshkin, Alexey Y

2013-08-28

114

Estimation of network structures only from spike sequences  

Science.gov (United States)

A neuron, the fundamental element of neural systems, interacts with other neurons, often producing very complicated behavior. To analyze, model, or predict such complicated behavior, it is important to understand how neurons are connected as well as how they behave. In this paper, we propose two measures, the spike time metric coefficient and the partial spike time metric coefficient, to estimate the network structure, that is, the topological connectivity between neurons. The proposed measures are based on the spike time metric and partialization analysis. To check the validity, we applied the proposed measures to asynchronous spike sequences that are produced by a mathematical neural network model. It was found that the proposed measure has high performance for estimating the network structures even though the structures have a complex topology such as a small-world structure or a scale-free structure.

Kuroda, Kaori; Ashizawa, Tohru; Ikeguchi, Tohru

2011-10-01

115

The structure of verbal sequences analyzed with unsupervised learning techniques  

CERN Document Server

Data mining allows the exploration of sequences of phenomena, whereas one usually tends to focus on isolated phenomena or on the relation between two phenomena. It offers invaluable tools for theoretical analyses and exploration of the structure of sentences, texts, dialogues, and speech. We report here the results of an attempt at using it for inspecting sequences of verbs from French accounts of road accidents. This analysis comes from an original approach of unsupervised training allowing the discovery of the structure of sequential data. The entries of the analyzer were only made of the verbs appearing in the sentences. It provided a classification of the links between two successive verbs into four distinct clusters, allowing thus text segmentation. We give here an interpretation of these clusters by applying a statistical analysis to independent semantic annotations.

Recanati, Catherine; Bennani, Younès

2007-01-01

116

Structural conservation of a short, functional, peptide-sequence motif  

Science.gov (United States)

1. ABSTRACT Full length, eukaryotic proteins generally consist of several autonomously folding and functioning domains. Many of these domains are known to function by binding and/or modifying other partner proteins based on the recognition of a short, linear amino sequence contained within the target protein. This article reviews the many bioinformatic tools and resources which discover, define and catalogue the various, known protein domains as well as assist users by identifying domain signatures within proteins of interest. We also review the smaller subset of bioinformatic tools which catalogue and help identify the short linear motifs used for domain targeting. It has been suggested that these short, functional, peptide-sequence motifs are normally found in unstructured regions of the target. The role of protein structure in the activity of one representative of these short, functional motifs is explored through an examination of known structures deposited in the Protein Data Bank. PMID:19273121

Fox-Erlich, Susan; Schiller, Martin R.; Gryk, Michael R.

2008-01-01

117

Chromatin structure characteristics of pre-miRNA genomic sequences  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background MicroRNAs (miRNAs are non-coding RNAs with important roles in regulating gene expression. Recent studies indicate that transcription and cleavage of miRNA are coupled, and that chromatin structure may influence miRNA transcription. However, little is known about the relationship between the chromatin structure and cleavage of pre-miRNA from pri-miRNA. Results By analysis of genome-wide nucleosome positioning data sets from human and Caenorhabditis elegans (C. elegans, we found an enrichment of positioned nucleosome on pre-miRNA genomic sequences, which is highly correlated with GC content within pre-miRNA. In addition, obvious enrichments of three histone modifications (H2BK5me1, H3K36me3 and H4K20me1 as well as RNA Polymerase II (RNAPII were observed on pre-miRNA genomic sequences corresponding to the active-promoter miRNAs and expressed miRNAs. Conclusion Our results revealed the chromatin structure characteristics of pre-miRNA genomic sequences, and implied potential mechanisms that can recognize these characteristics, thus improving pre-miRNA cleavage.

Teng Mingxiang

2011-06-01

118

Early-Stage Folding in Proteins (In Silico Sequence-to-Structure Relation  

Directory of Open Access Journals (Sweden)

Full Text Available A sequence-to-structure library has been created based on the complete PDB database. The tetrapeptide was selected as a unit representing a well-defined structural motif. Seven structural forms were introduced for structure classification. The early-stage folding conformations were used as the objects for structure analysis and classification. The degree of determinability was estimated for the sequence-to-structure and structure-to-sequence relations. Probability calculus and informational entropy were applied for quantitative estimation of the mutual relation between them. The structural motifs representing different forms of loops and bends were found to favor particular sequences in structure-to-sequence analysis.

Brylinski Micha?

2005-01-01

119

Data Structures: Sequence Problems, Range Queries, and Fault Tolerance  

DEFF Research Database (Denmark)

The focus of this dissertation is on algorithms, in particular data structures that give provably ecient solutions for sequence analysis problems, range queries, and fault tolerant computing. The work presented in this dissertation is divided into three parts. In Part I we consider algorithms for a range of sequence analysis problems that have risen from applications in pattern matching, bioinformatics, and data mining. On a high level, each problem is dened by a function and some constraints and the job at hand is to locate subsequences that score high with this function and are not invalidated by the constraints. Many variants and similar problems have been proposed leading to several dierent approaches and algorithms. We consider problems where the function is the sum of the elements in the sequence and the constraints only bound the length of the subsequences considered. We give optimal algorithms for several variants of the problem based on a simple idea and classic algorithms and data structures. In Part II we consider range query data structures. This a category of problems where the task is to preprocess an input sequence using as little time and space as possible such that one can eciently compute a certain function on the elements in a given query subsequence. There are many types of functions that has been considered in connection with input from dierent sources. The input could be ip-data sorted by ip-address, real estate prices sorted by zip code, advertising cost sorted by time etc. We consider data structures for two classic statistics functions, namely median and mode. Finally, Part III investigates fault tolerant algorithms and data structures. This deals with the trend of avoiding elaborate error checking and correction circuitry that would impose non-negligible costs in terms of hardware performance and money in the design of todays high speed memory technologies. Hardware, power failures, and environmental conditions such as cosmic rays and alpha particles can all alter the memory in unpredictable ways. In applications where large memory capacities are needed at low cost, it makes sense to assume that the algorithms themselves are in charge for dealing with memory faults. We investigate searching, sorting and counting algorithms and data structures that provably returns sensible information in spite of memory corruptions.

JØrgensen, Allan GrØnlund

2010-01-01

120

The sequence, structure and evolutionary features of HOTAIR in mammals  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background An increasing number of long noncoding RNAs (lncRNAs have been identified recently. Different from all the others that function in cis to regulate local gene expression, the newly identified HOTAIR is located between HoxC11 and HoxC12 in the human genome and regulates HoxD expression in multiple tissues. Like the well-characterised lncRNA Xist, HOTAIR binds to polycomb proteins to methylate histones at multiple HoxD loci, but unlike Xist, many details of its structure and function, as well as the trans regulation, remain unclear. Moreover, HOTAIR is involved in the aberrant regulation of gene expression in cancer. Results To identify conserved domains in HOTAIR and study the phylogenetic distribution of this lncRNA, we searched the genomes of 10 mammalian and 3 non-mammalian vertebrates for matches to its 6 exons and the two conserved domains within the 1800 bp exon6 using Infernal. There was just one high-scoring hit for each mammal, but many low-scoring hits were found in both mammals and non-mammalian vertebrates. These hits and their flanking genes in four placental mammals and platypus were examined to determine whether HOTAIR contained elements shared by other lncRNAs. Several of the hits were within unknown transcripts or ncRNAs, many were within introns of, or antisense to, protein-coding genes, and conservation of the flanking genes was observed only between human and chimpanzee. Phylogenetic analysis revealed discrete evolutionary dynamics for orthologous sequences of HOTAIR exons. Exon1 at the 5' end and a domain in exon6 near the 3' end, which contain domains that bind to multiple proteins, have evolved faster in primates than in other mammals. Structures were predicted for exon1, two domains of exon6 and the full HOTAIR sequence. The sequence and structure of two fragments, in exon1 and the domain B of exon6 respectively, were identified to robustly occur in predicted structures of exon1, domain B of exon6 and the full HOTAIR in mammals. Conclusions HOTAIR exists in mammals, has poorly conserved sequences and considerably conserved structures, and has evolved faster than nearby HoxC genes. Exons of HOTAIR show distinct evolutionary features, and a 239 bp domain in the 1804 bp exon6 is especially conserved. These features, together with the absence of some exons and sequences in mouse, rat and kangaroo, suggest ab initio generation of HOTAIR in marsupials. Structure prediction identifies two fragments in the 5' end exon1 and the 3' end domain B of exon6, with sequence and structure invariably occurring in various predicted structures of exon1, the domain B of exon6 and the full HOTAIR.

Zhu Hao

2011-04-01

 
 
 
 
121

Rift Structure and Distribution of Magmatic Activity of the Southern Chinese Continental Margin Offshore Southern Taiwan from Reflection Imaging, Travel-time Tomography and 1D Thermal Modeling  

Science.gov (United States)

We present new multi-channel seismic reflection images and a wide-angle OBS velocity model from offshore southern Taiwan that delineates the rift architecture and spatial distribution of magmatic bodies across the southern Chinese continental margin in the eastern South China Sea. The timing and distribution of magmatic activity is an important component of rift systems that may control the development of rift structures and sediment deposition. The main structural features in these data include ~3-4 km of passive margin strata deposited on moderately extended continental crust along the continental shelf, and a broad zone of hyper-extended and intruded continental crust across the continental slope and deeper basin. Crust rapidly thins from over 20 km along the continental shelf to less than 4 km at the base of the continental slope in a zone characterized by a shoaling Moho, normal-faulted crust and potentially upper mantle, and up to ~6 km of sedimentary strata. Outboard of this zone, we image tilted fault blocks and crust ~12 km thick. The seismic velocity structure here is consistent with the velocity structure of thinned continental crust observed in previous studies throughout the southwest and central South China Sea, but is incompatible with the distinct layer2/layer3 velocity structure of ocean crust. We observe a zone of large volcanic bodies local to the zone of minimal crustal thickness. The thinned continental crust contains a high-velocity lower crustal layer ~3-5 km thick with seismic velocities of ~6.9 - 7.5 km/s. Such a layer may indicate gabbroic underplating, presumably emplaced by decompression melting during or shortly after rifting. Despite the lower crustal layer and zone of volcanic bodies, there is little evidence for significant extrusive syn-rift magmatism, such as seaward-dipping reflectors. Numerous sills occur throughout the post-rift sedimentary section and post-rift strata are frequently deformed over volcanic bodies, indicating post-rift magmatic activity. We compare our new observations of rift structure and magmatic material with estimates of melt production calculated from a 1D thermal model of pure shear rifting to provide further insights into the interplay between structure and magmatism during rifting.

Lester, R.; McIntosh, K. D.; Lavier, L. L.; Van Avendonk, H. J.

2012-12-01

122

Structural Correlates of Skilled Performance on a Motor Sequence Task  

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Full Text Available The brain regions functionally engaged in motor sequence performance are well established, but the structural characteristics of these regions and the fibre pathways involved have been less well studied. In addition, relatively few studies have combined multiple magnetic resonance imaging (MRI and behavioural performance measures in the same sample. Therefore, the current study used diffusion tensor imaging, probabilistic tractography, and voxel-based morphometry to determine the structural correlates of skilled motor performance. Further, we compared these findings with fMRI results in the same sample. We correlated final performance and rate of improvement measures on a temporal motor sequence task with skeletonised fractional anisotropy (FA and whole brain grey matter (GM volume. Final synchronisation performance was negatively correlated with FA in white matter underlying bilateral sensorimotor cortex – an effect that was mediated by a positive correlation with radial diffusivity. Multi-fibre tractography indicated that this region contained crossing fibres from the corticospinal tract and superior longitudinal fasciculus (SLF. The identified SLF pathway linked parietal and auditory cortical regions that have been shown to be functionally engaged in this task. Thus, we hypothesise that enhanced synchronisation performance on this task may be related to greater fibre integrity of the SLF. Rate of improvement on synchronisation was positively correlated with GM volume in cerebellar lobules HVI and V – regions that showed training-related decreases in activity in the same sample. Taken together, our results link individual differences in brain structure and function to motor sequence performance on the same task. Further, our study illustrates the utility of using multiple MR measures and analysis techniques to specify the interpretation of structural findings.

ChristopherJSteele

2012-10-01

123

Structural Approaches to Sequence Evolution Molecules, Networks, Populations  

CERN Document Server

Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.

Bastolla, Ugo; Roman, H. Eduardo; Vendruscolo, Michele

2007-01-01

124

3-D structure of the Rio Grande Rift from 1-D constrained joint inversion of receiver functions and surface wave dispersion  

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The Southern terminus of the Rio Grande Rift region has been poorly defined in the geologic record, with few seismic studies that provide information on the deeper Rift structure. In consequence, important questions related to tectonic and lithospheric activity of the Rio Grande Rift remain unresolved. To address some of these geological questions, we collect and analyze seismic data from 147 EarthScope Transportable Array (USArray) and other seismic stations in the region, to develop a 3-D crust and upper mantle velocity model. We apply a constrained optimization approach for joint inversion of surface wave and receiver functions using seismic S wave velocities as a model parameter. In particular, we compute receiver functions stacks based on ray parameter, and invert them jointly with collected surface wave group velocity dispersion observations. The inversions estimate 1-D seismic S-wave velocity profiles to 300 km depth, which are then interpolated to a 3-D velocity model using a Bayesian kriging scheme. Our 3-D models show a thin lower velocity crust anomaly along the southeastern Rio Grande Rift, a persistent low velocity anomaly underneath the Colorado Plateau and Basin and Range province, and another one at depth beneath the Jemez lineament, and the southern RGR.

Sosa, Anibal; Thompson, Lennox; Velasco, Aaron A.; Romero, Rodrigo; Herrmann, Robert B.

2014-09-01

125

Beta 1D integrin displaces the beta 1A isoform in striated muscles: localization at junctional structures and signaling potential in nonmuscle cells.  

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The cytoplasmic domains of integrins provide attachment of these extracellular matrix receptors to the cytoskeleton and play a critical role in integrin-mediated signal transduction. In this report we describe the identification, expression, localization, and initial functional characterization of a novel form of beta 1 integrin, termed beta 1D. This isoform contains a unique alternatively spliced cytoplasmic domain of 50 amino acids, with the last 24 amino acids encoded by an additional exon. Of these 24 amino acids, 11 are conserved when compared to the beta 1A isoform, but 13 are unique (Zhidkova, N. I., A. M. Belkin, and R. Mayne. 1995. Biochem. Biophys. Res. Commun. 214:279-285; van der Flier, A., I. Kuikman, C. Baudoin, R, van der Neuf, and A. Sonnenberg. 1995. FEBS Lett. 369:340-344). Using an anti-peptide antibody against the beta 1D integrin subunit, we demonstrated that the beta 1D isoform is synthesized only in skeletal and cardiac muscles, while very low amounts of beta 1A were detected by immunoblot in striated muscles. Whereas beta 1A could not be detected in adult skeletal muscle fibers and cardiomyocytes by immunofluorescence, beta 1D was localized to the sarcolemma of both cell types. In skeletal muscle, beta 1D was concentrated in costameres, myotendinous, and neuromuscular junctions. In cardiac muscle this beta 1 isoform was found in costamers and intercalated discs. beta 1D was associated with alpha 7A and alpha 7B in adult skeletal muscle. In cardiomyocytes of adult heart, alpha 7B was the major partner for the beta 1D isoform. beta 1D could not be detected in proliferating C2C12 myoblasts, but it appeared immediately after myoblast fusion and its amount continued to rise during myotube growth and maturation. In contrast, expression of the beta 1A isoform was downregulated during myodifferentiation in culture and it was completely displaced by beta 1D in mature differentiated myotubes. We also analyzed some functional properties of the beta 1D integrin subunit. Expression of human beta 1D in CHO cells led to its localization at focal adhesions. Clustering of this integrin isoform on the cell surface stimulated tyrosine phosphorylation of pp125FAK (focal adhesion kinase) and caused transient activation of mitogen-activated protein (MAP) kinases. These data indicate that beta 1D and beta 1A integrin isoforms are functionally similar with regard to integrin-mediated signaling. PMID:8567725

Belkin, A M; Zhidkova, N I; Balzac, F; Altruda, F; Tomatis, D; Maier, A; Tarone, G; Koteliansky, V E; Burridge, K

1996-01-01

126

Main: 1D6R [RPSD  

Full Text Available 1D6R ?? Soybean Glycine max (L.) Merrill Bowman-Birk Type Proteinase Inhibitor Precursor Glyci ... ith Bovine Trypsin At 2.3 A Resolution. Structural Basis ... Of Janus-Faced Serine Protease Inhibitor Specifici ...

127

Modulation of DNA radiolysis by sequence, structure and ligands  

International Nuclear Information System (INIS)

DNA structure, topology and interactions with ligands are continuously changing during the cell cycle, through phenomena such as replication or transcription. Until recently, it was considered that ionizing radiations break DNA strands with the same probability at all nucleotide sites. Using restriction fragments and synthetic oligonucleotides, we have shown that DNA is heterogeneously radiosensitive. The breakage probability at a given nucleotide site depends on nucleotide type and sequence, presence of ligands (metal ions, proteins, polyamines) and structural parameters (strandedness, handedness, minor groove depth, topological stress). We have observed that in 'naked'(without ligands) dna, the bent 5'-AATT regions that present a narrow minor groove are less sensitive than 'random DNA'. In a (GC)n sequence, all G sites are more radiosensitive, and all C sites are more radioresistant in a negatively super-coiling-induced left-handed Z-DNA than in the right-handed B-DNA. Some G's located in particular regions of single stranded DNA are more radiosensitive than in double stranded DNA. We have also shown that several natural ligands, such as Cu2+, polyamines or DNA-binding proteins modify DNA radiosensitivity directly of via the structural modifications that they induce in DNA. (authors)

128

Structural Laplacian Eigenmaps for modeling sets of multivariate sequences.  

Science.gov (United States)

A novel embedding-based dimensionality reduction approach, called structural Laplacian Eigenmaps, is proposed to learn models representing any concept that can be defined by a set of multivariate sequences. This approach relies on the expression of the intrinsic structure of the multivariate sequences in the form of structural constraints, which are imposed on dimensionality reduction process to generate a compact and data-driven manifold in a low dimensional space. This manifold is a mathematical representation of the intrinsic nature of the concept of interest regardless of the stylistic variability found in its instances. In addition, this approach is extended to model jointly several related concepts within a unified representation creating a continuous space between concept manifolds. Since a generated manifold encodes the unique characteristic of the concept of interest, it can be employed for classification of unknown instances of concepts. Exhaustive experimental evaluation on different datasets confirms the superiority of the proposed methodology to other state-of-the-art dimensionality reduction methods. Finally, the practical value of this novel dimensionality reduction method is demonstrated in three challenging computer vision applications, i.e., view-dependent and view-independent action recognition as well as human-human interaction classification. PMID:24144690

Lewandowski, Michal; Makris, Dimitrios; Velastin, Sergio A; Nebel, Jean-Christophe

2014-06-01

129

Rational experiment design for sequencing-based RNA structure mapping.  

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Structure mapping is a classic experimental approach for determining nucleic acid structure that has gained renewed interest in recent years following advances in chemistry, genomics, and informatics. The approach encompasses numerous techniques that use different means to introduce nucleotide-level modifications in a structure-dependent manner. Modifications are assayed via cDNA fragment analysis, using electrophoresis or next-generation sequencing (NGS). The recent advent of NGS has dramatically increased the throughput, multiplexing capacity, and scope of RNA structure mapping assays, thereby opening new possibilities for genome-scale, de novo, and in vivo studies. From an informatics standpoint, NGS is more informative than prior technologies by virtue of delivering direct molecular measurements in the form of digital sequence counts. Motivated by these new capabilities, we introduce a novel model-based in silico approach for quantitative design of large-scale multiplexed NGS structure mapping assays, which takes advantage of the direct and digital nature of NGS readouts. We use it to characterize the relationship between controllable experimental parameters and the precision of mapping measurements. Our results highlight the complexity of these dependencies and shed light on relevant tradeoffs and pitfalls, which can be difficult to discern by intuition alone. We demonstrate our approach by quantitatively assessing the robustness of SHAPE-Seq measurements, obtained by multiplexing SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemistry in conjunction with NGS. We then utilize it to elucidate design considerations in advanced genome-wide approaches for probing the transcriptome, which recently obtained in vivo information using dimethyl sulfate (DMS) chemistry. PMID:25332375

Aviran, Sharon; Pachter, Lior

2014-12-01

130

Synthesis and Structure of 1D Na6 Cluster Chain with Short Na-Na Distance: Organic like Aromaticity in Inorganic Metal Cluster  

CERN Document Server

A unique 1D chain of sodium cluster containing (Na6) rings stabilized by a molybdenum containing metalloligand has been synthesized and characterized. DFT calculations show striking resemblance in their aromatic behaviour with the corresponding hydrocarbon analogues

Khatua, S; Chattaraj, P K; Roy, D R; Bhattacharjee*, Manish; Chattaraj*, Pratim K.; Khatua, Snehadrinarayan; Roy, Debesh R.

2006-01-01

131

Knowledge of sequence structure prevents auditory distraction: an ERP study.  

Science.gov (United States)

Infrequent, salient stimuli often capture attention despite their task-irrelevancy, and disrupt on-going goal-directed behavior. A number of studies show that presenting cues signaling forthcoming deviants reduces distraction, which may be a "by-product" of cue-processing interference or the result of direct preparatory processes for the forthcoming distracter. In the present study, instead of "bursts" of cue information, information on the temporal structure of the stimulus sequence was provided. Young adults performed a spatial discrimination task where complex tones moving left or right were presented. In the predictable condition, every 7th tone was a pitch-deviant, while in the random condition the position of deviants was random with a probability of 1/7. Whereas the early event-related potential correlates of deviance-processing (N1 and MMN) were unaffected by predictability, P3a amplitude was significantly reduced in the predictable condition, indicating that prevention of distraction was based on the knowledge about the temporal structure of the stimulus sequence. PMID:24657900

Volosin, Márta; Horváth, János

2014-06-01

132

Polyproline II structure in a sequence of seven alanine residues  

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A sequence of seven alanine residuestoo short to form an -helix and whose side chains do not interact with each otheris a particularly simple model for testing the common description of denatured proteins as structureless random coils. The 3JHN coupling constants of individual alanine residues have been measured from 2 to 56°C by using isotopically labeled samples. The results display a thermal transition between different backbone conformations, which is confirmed by CD spectra. The NMR results suggest that polyproline II is the dominant conformation at 2°C and the content of strand is increased by approximately 10% at 55°C relative to that at 2°C. The polyproline II conformation is consistent with recent studies of short alanine peptides, including structure prediction by ab initio quantum mechanics and solution structures for both a blocked alanine dipeptide and an alanine tripeptide. CD and other optical spectroscopies have found structure in longer "random coil" peptides and have implicated polyproline II, which is a major backbone conformation in residues within loop regions of protein structures. Our result suggests that the backbone conformational entropy in alanine peptides is considerably smaller than estimated by the random coil model. New thermodynamic data confirm this suggestion: the entropy loss on alanine helix formation is only 2.2 entropy units per residue.

Shi, Zhengshuang; Olson, C. Anders; Rose, George D.; Baldwin, Robert L.; Kallenbach, Neville R.

2002-07-01

133

Upper crustal structure of the western Corinth Gulf, Greece, and re-location of the 2010 earthquake sequence  

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The western part of the Corinth Gulf attracts attention due to its high seismic activity. A moderate size Mw5.3 earthquake occurred close to the town of Efpalio on January 18, 2010, followed by a sequence of smaller earthquakes. We used a part of the Efpalio earthquake sequence to derive a local model of the upper crustal structure to a depth of 10 km. In particular, we used arrival times from 51 well-documented events recorded on January 19 and 20 by at least 5 stations at epicentral distances less than about 25 km, including temporary stations. Due to a limited data amount and deployment of seismic stations, we restricted ourselves to a 1-D velocity model, composed of homogeneous layers with constant ratio of the P- and S-wave velocities in all layers. This vp/vs ratio was sought by the Wadati method and its average value of 1.83 was obtained. The arrival time residua were minimized by simultaneous variations of the structural and hypocentral parameters. A variant of the method of conjugate gradients was used for this purpose. In comparison with several previous models, the new structural model is characterized by higher velocities. The hypocentres of the selected earthquakes lay at depths between about 5 and 9 km. Using the new structural model, the other earthquakes of the 2010 Efpalio sequence will be located, and the results will be compared with previous interpretations.

Novotny, O.; Sokos, E.; Plicka, V.; Jansky, J.

2012-04-01

134

Structural basis of sequence-specific collagen recognition by SPARC  

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Protein interactions with the collagen triple helix play a critical role in collagen fibril formation, cell adhesion, and signaling. However, structural insight into sequence-specific collagen recognition is limited to an integrin-peptide complex. A GVMGFO motif in fibrillar collagens (O denotes 4-hydroxyproline) binds 3 unrelated proteins: von Willebrand factor (VWF), discoidin domain receptor 2 (DDR2), and the extracellular matrix protein SPARC/osteonectin/BM-40. We report the crystal structure at 3.2 ? resolution of human SPARC bound to a triple-helical 33-residue peptide harboring the promiscuous GVMGFO motif. SPARC recognizes the GVMGFO motifs of the middle and trailing collagen chains, burying a total of 720 ?2 of solvent-accessible collagen surface. SPARC binding does not distort the canonical triple helix of the collagen peptide. In contrast, a critical loop in SPARC is substantially remodelled upon collagen binding, creating a deep pocket that accommodates the phenylalanine residue of the trailing collagen chain (“Phe pocket”). This highly restrictive specificity pocket is shared with the collagen-binding integrin I-domains but differs strikingly from the shallow collagen-binding grooves of the platelet receptor glycoprotein VI and microbial adhesins. We speculate that binding of the GVMGFO motif to VWF and DDR2 also results in structural changes and the formation of a Phe pocket. PMID:19011090

Hohenester, Erhard; Sasaki, Takako; Giudici, Camilla; Farndale, Richard W.; Bachinger, Hans Peter

2008-01-01

135

Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics  

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Full Text Available Abstract Background The detection of conserved residue clusters on a protein structure is one of the effective strategies for the prediction of functional protein regions. Various methods, such as Evolutionary Trace, have been developed based on this strategy. In such approaches, the conserved residues are identified through comparisons of homologous amino acid sequences. Therefore, the selection of homologous sequences is a critical step. It is empirically known that a certain degree of sequence divergence in the set of homologous sequences is required for the identification of conserved residues. However, the development of a method to select homologous sequences appropriate for the identification of conserved residues has not been sufficiently addressed. An objective and general method to select appropriate homologous sequences is desired for the efficient prediction of functional regions. Results We have developed a novel index to select the sequences appropriate for the identification of conserved residues, and implemented the index within our method to predict the functional regions of a protein. The implementation of the index improved the performance of the functional region prediction. The index represents the degree of conserved residue clustering on the tertiary structure of the protein. For this purpose, the structure and sequence information were integrated within the index by the application of spatial statistics. Spatial statistics is a field of statistics in which not only the attributes but also the geometrical coordinates of the data are considered simultaneously. Higher degrees of clustering generate larger index scores. We adopted the set of homologous sequences with the highest index score, under the assumption that the best prediction accuracy is obtained when the degree of clustering is the maximum. The set of sequences selected by the index led to higher functional region prediction performance than the sets of sequences selected by other sequence-based methods. Conclusions Appropriate homologous sequences are selected automatically and objectively by the index. Such sequence selection improved the performance of functional region prediction. As far as we know, this is the first approach in which spatial statistics have been applied to protein analyses. Such integration of structure and sequence information would be useful for other bioinformatics problems.

Nemoto Wataru

2012-05-01

136

SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences  

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Full Text Available Abstract Background Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. Results SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. Conclusion The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are capable of separating the structural classes in spite of their low dimensionality. We also demonstrate that the SCPRED's predictions can be successfully used as a post-processing filter to improve performance of modern fold classification methods.

Chen Ke

2008-05-01

137

Crystal structure of V?1 T cell receptor in complex with CD1d-sulfatide shows MHC-like recognition of a self-lipid by human ?? T cells.  

Science.gov (United States)

The nature of the antigens recognized by ?? T cells and their potential recognition of major histocompatibility complex (MHC)-like molecules has remained unclear. Members of the CD1 family of lipid-presenting molecules are suggested ligands for V?1 TCR-expressing ?? T cells, the major ?? lymphocyte population in epithelial tissues. We crystallized a V?1 TCR in complex with CD1d and the self-lipid sulfatide, revealing the unusual recognition of CD1d by germline V?1 residues spanning all complementarity-determining region (CDR) loops, as well as sulfatide recognition separately encoded by nongermline CDR3? residues. Binding and functional analysis showed that CD1d presenting self-lipids, including sulfatide, was widely recognized by gut V?1+ ?? T cells. These findings provide structural demonstration of MHC-like recognition of a self-lipid by ?? T cells and reveal the prevalence of lipid recognition by innate-like T cell populations. PMID:24239091

Luoma, Adrienne M; Castro, Caitlin D; Mayassi, Toufic; Bembinster, Leslie A; Bai, Li; Picard, Damien; Anderson, Brian; Scharf, Louise; Kung, Jennifer E; Sibener, Leah V; Savage, Paul B; Jabri, Bana; Bendelac, Albert; Adams, Erin J

2013-12-12

138

SE: an algorithm for deriving sequence alignment from a pair of superimposed structures  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Background Generating sequence alignments from superimposed structures is an important part of many structure comparison programs. The accuracy of the alignment affects structure recognition, classification and possibly function prediction. Many programs use a dynamic programming algorithm to generate the sequence alignment from superimposed structures. However, this procedure requires using a gap penalty and, depending on the value of the penalty used, can introduce...

Kim Changhoon; Vincent James J; Lee Byungkook

2009-01-01

139

Structural properties of replication origins in yeast DNA sequences  

International Nuclear Information System (INIS)

Sequence-dependent DNA flexibility is an important structural property originating from the DNA 3D structure. In this paper, we investigate the DNA flexibility of the budding yeast (S. Cerevisiae) replication origins on a genome-wide scale using flexibility parameters from two different models, the trinucleotide and the tetranucleotide models. Based on analyzing average flexibility profiles of 270 replication origins, we find that yeast replication origins are significantly rigid compared with their surrounding genomic regions. To further understand the highly distinctive property of replication origins, we compare the flexibility patterns between yeast replication origins and promoters, and find that they both contain significantly rigid DNAs. Our results suggest that DNA flexibility is an important factor that helps proteins recognize and bind the target sites in order to initiate DNA replication. Inspired by the role of the rigid region in promoters, we speculate that the rigid replication origins may facilitate binding of proteins, including the origin recognition complex (ORC), Cdc6, Cdt1 and the MCM2-7 complex

140

Enhancing the optical nonlinearity by 1D thin-film photonic crystals with Kerr defect cavities  

Science.gov (United States)

In this paper, we study the linear and nonlinear responses of 1-D photonic bandgap (PBG) structures. We show that, the nonlinear interaction can be greatly enhanced by the use of Kerr defect modes in a 1D dielectric photonic crystal structure, such as low-intensity bistability and multistability, and by optimizing the design of the layer sequence. 1-D PBG structure can also be promising candidate as low-intensity nonlinear phase shifter. Nonlinear z-scan measurements of a 3-cavity thin-film PBG sample show that the nonlinearity is enhanced over the native material by a factor over 30, while maintaining a bandwidth greater than 1T Hz, which is great for all-optical switching.

Chen, Yan; Liu, Yongdong; Blair, Steve

2005-04-01

 
 
 
 
141

Primary structure of a genomic zein sequence of maize.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The nucleotide sequence of a genomic clone (termed Z4 ) of the zein multigene family was compared to the nucleotide sequence of related cDNA clones of zein mRNAs. A tandem duplication of a 96-bp sequence is found in the genomic clone that is not present in the related cDNA clones. When the duplication is disregarded, the nucleotide sequence homology between Z4 and its related cDNAs was approximately 97%. The nucleotide sequence is also compared to other isolated cDNAs. No introns in the codin...

Hu, N. T.; Peifer, M. A.; Heidecker, G.; Messing, J.; Rubenstein, I.

1982-01-01

142

Structure of Intercalated Cs in Zeolite ITQ-4: An Array of Metal Ions and Correlated Electrons Confined in a Pseudo-1D Nanoporous Host  

Science.gov (United States)

The presence of Cs+ ions in the pseudo-1D nanopores of zeolite ITQ-4, Si32O64, is confirmed by x-ray diffraction and atomic pair distribution function analysis. Inside the nanopores the Cs+ ions are found to assemble in zigzag chains and thus form an extended, positively charged sublattice providing charge balance for a low-density electron gas also confined to the nanopores.

Petkov, V.; Billinge, S. J.; Vogt, T.; Ichimura, A. S.; Dye, J. L.

2002-07-01

143

Structural characterization of genomes by large scale sequence-structure threading  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Using sequence-structure threading we have conducted structural characterization of complete proteomes of 37 archaeal, bacterial and eukaryotic organisms (including worm, fly, mouse and human totaling 167,888 genes. Results The reported data represent first rather general evaluation of performance of full sequence-structure threading on multiple genomes providing opportunity to evaluate its general applicability for large scale studies. According to the estimated results the sequence-structure threading has assigned protein folds to more then 60% of eukaryotic, 68% of archaeal and 70% of bacterial proteomes. The repertoires of protein classes, architectures, topologies and homologous superfamilies (according to the CATH 2.4 classification have been established for distant organisms and superkingdoms. It has been found that the average abundance of CATH classes decreases from "alpha and beta" to "mainly beta", followed by "mainly alpha" and "few secondary structures". 3-Layer (aba Sandwich has been characterized as the most abundant protein architecture and Rossman fold as the most common topology. Conclusion The analysis of genomic occurrences of CATH 2.4 protein homologous superfamilies and topologies has revealed the power-law character of their distributions. The corresponding double logarithmic "frequency – genomic occurrence" dependences characteristic of scale-free systems have been established for individual organisms and for three superkingdoms. Supplementary materials to this works are available at 1.

Cherkasov Artem

2004-04-01

144

Molecular structure from a single NMR sequence (fast-PANACEA)  

Science.gov (United States)

The PANACEA experiment combines three standard NMR pulse sequences (INADEQUATE, HSQC and HMBC) into a single entity, and is designed for spectrometers with two or more receivers operating in parallel. For small molecules it offers a direct route to molecular structure. Often the INADEQUATE feature is the rate-determining step, being limited by the low natural abundance of directly coupled 13C sbnd 13C pairs. This new version, fast-PANACEA, speeds up this measurement by two alternative schemes. In the first, the individual 13C sites are excited by selective radiofrequency pulses acting on double-quantum coherence, and encoded according to the rows of a Hadamard matrix. The columns of this matrix are used to decode the experimental data into separate F 2 spectra. This reduction in the number of required scans secures a faster result than the conventional stepwise exploration of the evolution dimension where the Nyquist condition and the resolution requirements must both be satisfied. The second scheme makes use of multiple aliasing in the evolution dimension. Significant speed improvements are achieved by either technique, illustrated by measurements made on samples of menthol and cholesterol. A new stabilization scheme (i-lock) is introduced. This is a software program that corrects the final NMR frequencies based on the observed frequency of a strong X-spin signal. It replaces the conventional deuterium lock, permitting measurements on neat liquids such as peanut oil and silicone oil, and offering advantages where deuterated solvents are undesirable.

Kup?e, ?riks; Freeman, Ray

2010-09-01

145

Adipose pyruvate carboxylase: amino acid sequence and domain structure deduced from cDNA sequencing.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The complete amino acid sequence of 3T3-L1 adipocyte pyruvate carboxylase (PC) [pyruvate:carbon-dioxide ligase (ADP-forming), EC 6.4.1.1] has been deduced from sequencing overlapping cDNA clones obtained from an adipocyte cDNA library constructed in the lambda Zap vector. The encoding mRNA for PC promoter contains 4067 nt, including a 3534-nt coding sequence and noncoding regions of 100 and 433 nt at the 5' and 3' ends, respectively. The biotinylated lysine of the encoded PC promoter (1178 am...

Zhang, J.; Xia, W. L.; Brew, K.; Ahmad, F.

1993-01-01

146

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure—frequent compensating base changes—is increasingly likely to cause sequence-based alignment methods to misalign, or even refuse to align, homologous ncRNAs, consequently obscuring that structural signal. We have used CMfinder, a structure-oriented local alignment tool, to search the ENCODE r...

Torarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.; Bramsen, Jesper B.; Hansen, Claus; Kjems, Jørgen; Tommerup, Niels; Ruzzo, Walter L.; Gorodkin, Jan

2008-01-01

147

Exploring the sequence-structure protein landscape in the glycosyltransferase family  

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To understand the molecular basis of glycosyltransferases’ (GTFs) catalytic mechanism, extensive structural information is required. Here, fold recognition methods were employed to assign 3D protein shapes (folds) to the currently known GTF sequences, available in public databases such as GenBank and Swissprot. First, GTF sequences were retrieved and classified into clusters, based on sequence similarity only. Intracluster sequence similarity was chosen sufficiently high to ensure that the ...

Zhang, Ziding; Kochhar, Sunil; Grigorov, Martin

2003-01-01

148

Protein sequence complexity revisited. Relationship with fractal 3D structure, topological and kinetic parameters  

Science.gov (United States)

The study of protein sequence complexity is not a new area and several methodological approaches are available in order to describe or represent the protein sequence information. The present study explored the relationship between sequence complexity and structural fractal dimension, secondary structure information, number of domains and also kinetic parameters considering several methodologies. Our results indicate that some sequence complexity indexes are sensitive enough to differentiate native from random sequences, even when the differences are small. We also found that proteins with increased complexity present a higher number of domains, increased length and mean solvent accessibility. Moreover, proteins with lower complexity revealed an increased folding and unfolding constant rate. Interestingly, we found a significant correlation between protein sequence complexity and structural fractal dimension and a significant effect of the secondary structure classes.

Tejera, E.; Nieto-Villar, J.; Rebelo, I.

2014-09-01

149

X-ray structure of 1D-coordination polymer of copperII bearing 1,4-pyrazine-2,3-dicarboxylic acid and 2-aminopyrimidine  

Directory of Open Access Journals (Sweden)

Full Text Available The new 1D-coordination polymer of CuII ion, {(2- apymH2[Cu(pyzdc2] .6H2O}n, (2-apym = 2-aminopyrimidine, pyzdcH2 = 1,4- pyrazine-2,3-dicarboxylic acid, was synthesized based on proton transfer mechanism and characterized by elemental analysis, infrared spectroscopy, and single crystal X-ray diffraction. The coordination polymer consists of infinite anionic chains of [Cu(pyzdc2]2- anion bridged crossing double chain running along a-axis and discrete (2-apymH+ fragment. The CuII ion is located on inversion centre in the basal plane of an elongated octahedron and two oxygen atoms from adjacent (pyzdc2-ligands occupy axial position. The interaction between oxygen atoms of water molecules along with the dicarboxylic acid play an important role in the overall supramolecular assembly.

Mirzaei Masoud

2012-01-01

150

Numerical 1D PIC-simulations of ion acceleration during laser-plasma interaction: Optimization of a two-component multilayered target structure  

International Nuclear Information System (INIS)

Ion beam acceleration is simulated using a one-dimensional 1D2P PIC code. The dependences of the maximum energy and width of the energy spectrum of the generated ion beams on the duration and intensity of laser radiation, as well as on the target parameters (thickness and number of layers, types and densities of atoms), are investigated. The optimal target configuration at which the energy of the accelerated ions is maximum (5-160 MeV for intensities of 5 x 1018-5 x 1020 W/cm2) is found. The optimal target configuration is shown to depend on the intensity and be independent of the laser pulse duration.

151

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure  

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Human and mouse genome sequences contain roughly 100,000 regions that are unalignable in primary sequence and neighbor corresponding alignable regions between both organisms. These pairs are generally assumed to be nonconserved, although the level of structural conservation between these has never been investigated. Owing to the limitations in computational methods, comparative genomics has been lacking the ability to compare such nonconserved sequence regions for conserved structural RNA ele...

Torarinsson, Elfar; Sawera, Milena; Havgaard, Jakob H.; Fredholm, Merete; Gorodkin, Jan

2006-01-01

152

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.  

Science.gov (United States)

With the rapid increase in the size of the genome sequence database, computational analysis of RNA will become increasingly important in revealing structure-function relationships and potential drug targets. RNA secondary structure prediction for a single sequence is 73 % accurate on average for a large database of known secondary structures. This level of accuracy provides a good starting point for determining a secondary structure either by comparative sequence analysis or by the interpretation of experimental studies. Dynalign is a new computer algorithm that improves the accuracy of structure prediction by combining free energy minimization and comparative sequence analysis to find a low free energy structure common to two sequences without requiring any sequence identity. It uses a dynamic programming construct suggested by Sankoff. Dynalign, however, restricts the maximum distance, M, allowed between aligned nucleotides in the two sequences. This makes the calculation tractable because the complexity is simplified to O(M(3)N(3)), where N is the length of the shorter sequence. The accuracy of Dynalign was tested with sets of 13 tRNAs, seven 5 S rRNAs, and two R2 3' UTR sequences. On average, Dynalign predicted 86.1 % of known base-pairs in the tRNAs, as compared to 59.7 % for free energy minimization alone. For the 5 S rRNAs, the average accuracy improves from 47.8 % to 86.4 %. The secondary structure of the R2 3' UTR from Drosophila takahashii is poorly predicted by standard free energy minimization. With Dynalign, however, the structure predicted in tandem with the sequence from Drosophila melanogaster nearly matches the structure determined by comparative sequence analysis. PMID:11902836

Mathews, David H; Turner, Douglas H

2002-03-22

153

Crystallographic structure of an active, sequence-engineered ribonuclease.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

X-ray diffraction methods were used to test a synthetic-modeling approach to the sequence engineering of bovine pancreatic ribonuclease. A model of RNase S-peptide (residues 1-20), having a simplified amino acid sequence but retaining elements deduced to be essential for conformation and function, was previously synthesized and found to form a catalytically active and stable complex with native S-protein (residues 21-24). We have now obtained a 3-A-resolution electron density map of this semi...

Taylor, H. C.; Komoriya, A.; Chaiken, I. M.

1985-01-01

154

Designing to see and share structure in number sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This paper reports on a design experiment in the domain of number sequences conducted in the course of the WebLabs project. We iteratively designed and tested a set of activities and tools in which 10-14 year old students used the ToonTalk programming environment to construct models of sequences and series, and then shared their models and their observations about them utilising a webbased collaboration system. We report on the evolution of a design pattern (programming method) called ‘Stre...

Mor, Yishay; Noss, Richard; Hoyles, Celia; Kahn, Ken; Simpson, Gordon

2006-01-01

155

The chemical structure of DNA sequence signals for RNA transcription  

Science.gov (United States)

The proposed recognition sites for RNA transcription for E. coli NRA polymerase, bacteriophage T7 RNA polymerase, and eukaryotic RNA polymerase Pol II are evaluated in the light of the requirements for efficient recognition. It is shown that although there is good experimental evidence that specific nucleic acid sequence patterns are involved in transcriptional regulation in bacteria and bacterial viruses, among the sequences now available, only in the case of the promoters recognized by bacteriophage T7 polymerase does it seem likely that the pattern is sufficient. It is concluded that the eukaryotic pattern that is investigated is not restrictive enough to serve as a recognition site.

George, D. G.; Dayhoff, M. O.

1982-01-01

156

Improving protein structure similarity searches using domain boundaries based on conserved sequence information  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The identification of protein domains plays an important role in protein structure comparison. Domain query size and composition are critical to structure similarity search algorithms such as the Vector Alignment Search Tool (VAST, the method employed for computing related protein structures in NCBI Entrez system. Currently, domains identified on the basis of structural compactness are used for VAST computations. In this study, we have investigated how alternative definitions of domains derived from conserved sequence alignments in the Conserved Domain Database (CDD would affect the domain comparisons and structure similarity search performance of VAST. Results Alternative domains, which have significantly different secondary structure composition from those based on structurally compact units, were identified based on the alignment footprints of curated protein sequence domain families. Our analysis indicates that domain boundaries disagree on roughly 8% of protein chains in the medium redundancy subset of the Molecular Modeling Database (MMDB. These conflicting sequence based domain boundaries perform slightly better than structure domains in structure similarity searches, and there are interesting cases when structure similarity search performance is markedly improved. Conclusion Structure similarity searches using domain boundaries based on conserved sequence information can provide an additional method for investigators to identify interesting similarities between proteins with known structures. Because of the improvement in performance of structure similarity searches using sequence domain boundaries, we are in the process of implementing their inclusion into the VAST search and MMDB resources in the NCBI Entrez system.

Madej Tom

2009-05-01

157

Structure of the Prime Distribution within the Sequence of Natural Numbers  

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In the course of studies of the measure of chaos for the distribution of the prime numbers among the positive integers N arched structures have been found. It is given a brief description of the fine structure of the positive integers sequence, including the distribution of the prime numbers. A new non-Eratostenian sieve was built to demonstrate the multi-periodicity in the structure of the positive integers sequence. This sieve presents an infinite triangular matrix, which ...

Vityazev, Andrei V.; Pechernikova, Galina V.

2006-01-01

158

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA. Results Here we introduce an all-against-all sequence- and three-dimensional (3D structure-based comparison of a representative set of RNA structures, which have allowed us to quantitatively confirm that: (i there is a measurable relationship between sequence and structure conservation that weakens for alignments resulting in below 60% sequence identity, (ii evolution tends to conserve more RNA structure than sequence, and (iii there is a twilight zone for RNA homology detection. Discussion The computational analysis here presented quantitatively describes the relationship between sequence and structure for RNA molecules and defines a twilight zone region for detecting RNA homology. Our work could represent the theoretical basis and limitations for future developments in comparative RNA 3D structure prediction.

Capriotti Emidio

2010-06-01

159

Structator: fast index-based search for RNA sequence-structure patterns  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running time that is only linear in the size of sequence databases. Furthermore, established index data structures for fast sequence matching, like suffix trees or arrays, cannot benefit from the complementarity constraints introduced by the secondary structure of RNAs. Results We present a novel method and readily applicable software for time efficient matching of RNA sequence-structure patterns in sequence databases. Our approach is based on affix arrays, a recently introduced index data structure, preprocessed from the target database. Affix arrays support bidirectional pattern search, which is required for efficiently handling the structural constraints of the pattern. Structural patterns like stem-loops can be matched inside out, such that the loop region is matched first and then the pairing bases on the boundaries are matched consecutively. This allows to exploit base pairing information for search space reduction and leads to an expected running time that is sublinear in the size of the sequence database. The incorporation of a new chaining approach in the search of RNA sequence-structure patterns enables the description of molecules folding into complex secondary structures with multiple ordered patterns. The chaining approach removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our method runs up to two orders of magnitude faster than previous methods. Conclusions The presented method's sublinear expected running time makes it well suited for RNA sequence-structure pattern matching in large sequence databases. RNA molecules containing several stem-loop substructures can be described by multiple sequence-structure patterns and their matches are efficiently handled by a novel chaining method. Beyond our algorithmic contributions, we provide with Structator a complete and robust open-source software solution for index-based search of RNA sequence-structure patterns. The Structator software is available at http://www.zbh.uni-hamburg.de/Structator.

Will Sebastian

2011-05-01

160

RNA global alignment in the joint sequence-structure space using elastic shape analysis.  

Science.gov (United States)

The functions of RNAs, like proteins, are determined by their structures, which, in turn, are determined by their sequences. Comparison/alignment of RNA molecules provides an effective means to predict their functions and understand their evolutionary relationships. For RNA sequence alignment, most methods developed for protein and DNA sequence alignment can be directly applied. RNA 3-dimensional structure alignment, on the other hand, tends to be more difficult than protein structure alignment due to the lack of regular secondary structures as observed in proteins. Most of the existing RNA 3D structure alignment methods use only the backbone geometry and ignore the sequence information. Using both the sequence and backbone geometry information in RNA alignment may not only produce more accurate classification, but also deepen our understanding of the sequence-structure-function relationship of RNA molecules. In this study, we developed a new RNA alignment method based on elastic shape analysis (ESA). ESA treats RNA structures as three dimensional curves with sequence information encoded on additional dimensions so that the alignment can be performed in the joint sequence-structure space. The similarity between two RNA molecules is quantified by a formal distance, geodesic distance. Based on ESA, a rigorous mathematical framework can be built for RNA structure comparison. Means and covariances of full structures can be defined and computed, and probability distributions on spaces of such structures can be constructed for a group of RNAs. Our method was further applied to predict functions of RNA molecules and showed superior performance compared with previous methods when tested on benchmark datasets. The programs are available at http://stat.fsu.edu/ ?jinfeng/ESA.html. PMID:23585278

Laborde, Jose; Robinson, Daniel; Srivastava, Anuj; Klassen, Eric; Zhang, Jinfeng

2013-06-01

 
 
 
 
161

Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima  

DEFF Research Database (Denmark)

The recently published complete DNA sequence of the bacterium Thermotoga maritima provides evidence, based on protein sequence conservation, for lateral gene transfer between Archaea and Bacteria. We introduce a new method of periodicity analysis of DNA sequences, based on structural parameters, which brings independent evidence for the lateral gene transfer in the genome of T.maritima, The structural analysis relates the Archaea-like DNA sequences to the genome of Pyrococcus horikoshii. Analysis of 24 complete genomic DNA sequences shows different periodicity patterns for organisms of different origin, The typical genomic periodicity for Bacteria is 11 bp whilst it is 10 bp for Archaea, Eukaryotes have more complex spectra but the dominant period in the yeast Saccharomyces cerevisiae is 10.2 bp. These periodicities are most likely reflective of differences in chromatin structure.

Worning, Peder; Jensen, Lars Juhl

2000-01-01

162

Unraveling the sequence and structure of the protein osteocalcin from a 42 ka fossil horse  

Science.gov (United States)

We report the first complete amino acid sequence and evidence of secondary structure for osteocalcin from a temperate fossil. The osteocalcin derives from a 42 ka equid bone excavated from Juniper Cave, Wyoming. Results were determined by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-MS) and Edman sequencing with independent confirmation of the sequence in two laboratories. The ancient sequence was compared to that of three modern taxa: horse ( Equus caballus), zebra ( Equus grevyi), and donkey ( Equus asinus). Although there was no difference in sequence among modern taxa, MALDI-MS and Edman sequencing show that residues 48 and 49 of our modern horse are Thr, Ala rather than Pro, Val as previously reported (Carstanjen B., Wattiez, R., Armory, H., Lepage, O.M., Remy, B., 2002. Isolation and characterization of equine osteocalcin. Ann. Med. Vet.146(1), 31-38). MALDI-MS and Edman sequencing data indicate that the osteocalcin sequence of the 42 ka fossil is similar to that of modern horse. Previously inaccessible structural attributes for ancient osteocalcin were observed. Glu 39 rather than Gln 39 is consistent with deamidation, a process known to occur during fossilization and aging. Two post-translational modifications were documented: Hyp 9 and a disulfide bridge. The latter suggests at least partial retention of secondary structure. As has been done for ancient DNA research, we recommend standards for preparation and criteria for authenticating results of ancient protein sequencing.

Ostrom, Peggy H.; Gandhi, Hasand; Strahler, John R.; Walker, Angela K.; Andrews, Philip C.; Leykam, Joseph; Stafford, Thomas W.; Kelly, Robert L.; Walker, Danny N.; Buckley, Mike; Humpula, James

2006-04-01

163

Content, Structure, and Sequence of the Detailing Discipline at Kendall College of Art and Design.  

Science.gov (United States)

A study identified the appropriate general content, structure, and sequence for a detailing discipline that promoted student achievement to professional levels. Its focus was the detailing discipline, a sequence of studio courses within the furniture design program at Kendall College of Art and Design, Grand Rapids, Michigan. (Detailing, an…

Mulder, Bruce E.

164

Synthesis and structure elucidation of a series of pyranochromene chalcones and flavanones using 1D and 2D NMR spectroscopy and X-ray crystallography.  

Science.gov (United States)

A series of novel pyranochromene chalcones and corresponding flavanones were synthesized. This is the first report on the confirmation of the absolute configuration of chromene-based flavanones using X-ray crystallography. These compounds were characterized by 2D NMR spectroscopy, and their assignments are reported herein. The 3D structure of the chalcone 3b and flavanone 4g was determined by X-ray crystallography, and the structure of the flavanone was confirmed to be in the S configuration at C-2. PMID:24623606

Pawar, Sunayna S; Koorbanally, Neil A

2014-06-01

165

Structure and sequence variation of mink interleukin-6 gene  

International Nuclear Information System (INIS)

Aleutian disease (AD) is the number one disease threat to the survival and future of the mink industry in Nova Scotia and the world. Several ranchers have gone out of business in recent years in Nova Scotia as a direct result of AD. Currently, the control measure for AD consists of testing and slaughtering of infected mink. This practice has not been effective in controlling the disease. Finding a means of controlling AD is the number one priority for the mink industry in Nova Scotia. An effective control measure will have a long-term positive effect on the rural economy by improving production potential of mink and reducing production cost. It has been shown that antiviral antibodies produced by activated immune system cells sometimes combine with interleukin-6 (IL-6) to form immune complexes that cause AD in mink. There is evidence of a significant relationship between nucleotide variations in IL-6 gene and the onset of certain diseases in humans, which bears similar symptoms to AD. Furthermore, pathological symptoms of AD resemble those of other conditions, such as systemic lupus erythematosus (SLE) and Castleman Diseases in humans, where overproduction of IL-6 coincides with the severity of the disease. These findings suggest that IL-6 could be a candidate gene and warrant investigation vis-a-vis differences among mink genotypes in resistance or tolerance to ADV infection. The sequence of the IL-6 gene in mink was done and identification of polymorphisms was used identification of polymorphisms was used to evaluate the potential role of this gene in the immune system response to infections. The 4678 bp promoter region, five exons and four introns of the interleukin-6 (IL-6) gene were bi-directionally sequenced in four unrelated mink from each of the wild, black, brown, pastel and sapphire mink (Genbank accession number (EF620932). The 344 bp promoter region of the gene contained several transcription binding sites. One exonic and seven intronic single nucleotide polymorphisms (SNP) were detected by sequencing of the 20 mink and genotyping of an additional 82 animals from the five colour types. Only two intronic SNP were segregating at high frequencies, indicating that the level of polymorphisms in the mink IL-6 gene was low. A bi-allelic tetranucleotide repeat was detected in the promoter region, with the frequency of 0.0, 0.17, 0.25, 0.25 and 0.40 in the wild, black, pastel, brown and sapphire mink, respectively, suggesting that this locus may influence immune response to infection. A polymorphic (CA)16 with 10 alleles was also detected in intron 2. (author)

166

Structure of fault zones in cohesive volcanic sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Normal fault systems are basic features in commercially important geological structures like e.g. sedimentary basins. While the interpretation of seismic data sets reveals the structure of the strata and its offset by larger faults, the properties of the fault planes itself remain undetermined. The information on e.g. permeability of laterally confined fault systems is derived from outcrops or theoretical models. The scope of the faulting research focuses on softer unconsolidated materials as...

Holland, Marc

2004-01-01

167

RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The recent interest sparked due to the discovery of a variety of functions for non-coding RNA molecules has highlighted the need for suitable tools for the analysis and the comparison of RNA sequences. Many trans-acting non-coding RNA genes and cis-acting RNA regulatory elements present motifs, conserved both in structure and sequence, that can be hardly detected by primary sequence analysis alone. We present an algorithm that takes as input a set of unaligned RNA sequences expected to share ...

Pavesi, Giulio; Mauri, Giancarlo; Stefani, Marco; Pesole, Graziano

2004-01-01

168

3-D simulation of nanopore structure for DNA sequencing.  

Science.gov (United States)

In this paper, we propose a method for simulating nanopore structure by using conventional 3-D simulation tool to mimic the I-V behavior of the nanopore structure. In the simulation, we use lightly doped silicon for ionic solution where some parameters like electron affinity and dielectric constant are fitted to consider the ionic solution. By using this method, we can simulate the I-V behavior of nanopore structure depending on the location and the size of the sphere shaped silicon oxide which is considered to be an indicator of a DNA base. In addition, we simulate an Ionic Field Effect Transistor (IFET) which has basically the nanopore structure, and show that the simulated curves follow sufficiently the I-V behavior of the measurement data. Therefore, we think it is reasonable to apply parameter modeling mentioned above to simulate nanopore structure. The key idea is to modify electron affinity of silicon which is used to mimic the KCl solution to avoid band bending and depletion inside the nanopore. We could efficiently utilize conventional 3-D simulation tool to simulate the I-V behavior of nanopore structures. PMID:22966538

Park, Jun-Mo; Pak, Y Eugene; Chun, Honggu; Lee, Jong-Ho

2012-07-01

169

Sequence- and structure-based prediction of eukaryotic proteinphosphorylation sites  

DEFF Research Database (Denmark)

Protein phosphorylation at serine, threonine or tyrosine residues affects a multitude of cellular signaling processes. Howis specificity in substrate recognition and phosphorylation by protein kinases achieved? Here, we present an artificialneural network method that predicts phosphorylation sites in independent sequences with a sensitivity in the range from69 % to 96 %. As an example, we predict novel phosphorylation sites in the p300/CBP protein that may regulateinteraction with transcription factors and histone acetyltransferase activity. In addition, serine and threonine residues inp300/CBP that can be modified by O-linked glycosylation with N-acetylglucosamine are identified. Glycosylation mayprevent phosphorylation at these sites, a mechanism named yin-yang regulation. The prediction server is available on theInternet at http://www.cbs.dtu.dk/services/NetPhos/or via e-mail to NetPhos@cbs. dtu.dk. Copyright 1999 AcademicPress.

Brunak, SØren

1999-01-01

170

Implicit structured sequence learning: an fMRI study of the structural mere-exposure effect.  

Science.gov (United States)

In this event-related fMRI study we investigated the effect of 5 days of implicit acquisition on preference classification by means of an artificial grammar learning (AGL) paradigm based on the structural mere-exposure effect and preference classification using a simple right-linear unification grammar. This allowed us to investigate implicit AGL in a proper learning design by including baseline measurements prior to grammar exposure. After 5 days of implicit acquisition, the fMRI results showed activations in a network of brain regions including the inferior frontal (centered on BA 44/45) and the medial prefrontal regions (centered on BA 8/32). Importantly, and central to this study, the inclusion of a naive preference fMRI baseline measurement allowed us to conclude that these fMRI findings were the intrinsic outcomes of the learning process itself and not a reflection of a preexisting functionality recruited during classification, independent of acquisition. Support for the implicit nature of the knowledge utilized during preference classification on day 5 come from the fact that the basal ganglia, associated with implicit procedural learning, were activated during classification, while the medial temporal lobe system, associated with explicit declarative memory, was consistently deactivated. Thus, preference classification in combination with structural mere-exposure can be used to investigate structural sequence processing (syntax) in unsupervised AGL paradigms with proper learning designs. PMID:24550865

Folia, Vasiliki; Petersson, Karl Magnus

2014-01-01

171

Implicit Structured Sequence Learning: An FMRI Study of the Structural Mere-Exposure Effect  

Directory of Open Access Journals (Sweden)

Full Text Available In this event-related FMRI study we investigated the effect of five days of implicit acquisition on preference classification by means of an artificial grammar learning (AGL paradigm based on the structural mere-exposure effect and preference classification using a simple right-linear unification grammar. This allowed us to investigate implicit AGL in a proper learning design by including baseline measurements prior to grammar exposure. After 5 days of implicit acquisition, the FMRI results showed activations in a network of brain regions including the inferior frontal (centered on BA 44/45 and the medial prefrontal regions (centered on BA 8/32. Importantly, and central to this study, the inclusion of a naive preference FMRI baseline measurement allowed us to conclude that these FMRI findings were the intrinsic outcomes of the learning process itself and not a reflection of a preexisting functionality recruited during classification, independent of acquisition. Support for the implicit nature of the knowledge utilized during preference classification on day 5 come from the fact that the basal ganglia, associated with implicit procedural learning, were activated during classification, while the medial temporal lobe system, associated with explicit declarative memory, was consistently deactivated. Thus, preference classification in combination with structural mere-exposure can be used to investigate structural sequence processing (syntax in unsupervised AGL paradigms with proper learning designs.

Karl MagnusPetersson

2014-02-01

172

Appearance of a ZERO-n and a ZERO-?eff Gap in Different Frequency Ranges in a Single 1d Photonic Band Gap Structure  

Science.gov (United States)

We present a scheme to realize both the zero-n and the zero-?eff gap in a one-dimensional photonic band gap structure containing metamaterials. The frequency dispersion of the effective electric permittivity and magnetic permeability of the metamaterials in the adjacent layers in one period are represented by the Drude model and the resonant model. The chosen structure is composed of alternate double-negative and double-positive layers which exhibit a zero-n gap in a certain frequency range whereas in a higher frequency range it behaves as alternate permittivity negative and permeability negative layers to exhibit a zero-?eff gap. Some properties and benefits of having the zero-n and the zero-?eff gap in the same physical system are discussed.

Ali, Munazza Zulfiqar; Abdullah, Tariq

173

$Z^+(4430)$ as a $D_1'{D}^* $ ($D_1{D}^* $) molecular state  

CERN Document Server

We reexamine whether $Z^+(4430)$ could be a $D_1'-{D}^*$ or $D_1-{D}^*$ molecular state after considering both the pion and $\\sigma$ meson exchange potentials and introducing the form factor to take into account the structure effect of the interaction vertex. Our numerical analysis with Matlab package MATSLISE indicates the contribution from the sigma meson exchange is small for the $D_1'-{D}^*$ system and significant for the $D_1-{D}^*$ system. The S-wave $D_1-\\bar{D}^*$ molecular state with only $J^{P}=0^-$ and $D_1'-{D}^*$ molecular states with $J^P=0^-,1^-,2^-$ may exist with reasonable parameters. One should investigate whether the broad width of $D_1'$ disfavors the possible formation of molecular states in the future. The bottom analog $Z_B$ of $Z^+(4430)$ has a larger binding energy, which may be searched at Tevatron and LHC. Experimental measurement of the quantum number of $Z^+(4430)$ may help uncover its underlying structure.

Liu, Xiang; Deng, Wei-Zhen; Zhu, Shi-Lin

2008-01-01

174

In silico structural study of random amino acid sequence proteins not present in nature.  

Science.gov (United States)

The three-dimensional structures of a set of 'never born proteins' (NBP, random amino acid sequence proteins with no significant homology with known proteins) were predicted using two methods: Rosetta and the one based on the 'fuzzy-oil-drop' (FOD) model. More than 3000 different random amino acid sequences have been generated, filtered against the non redundant protein sequence data base, to remove sequences with significant homology with known proteins, and subjected to three-dimensional structure prediction. Comparison between Rosetta and FOD predictions allowed to select the ten top (highest structural similarity) and the ten bottom (the lowest structural similarity) structures from the ranking list organized according to the RMS-D value. The selected structures were taken for detailed analysis to define the scale of structural accordance and discrepancy between the two methods. The structural similarity measurements revealed discrepancies between structures generated on the basis of the two methods. Their potential biological function appeared to be quite different as well. The ten bottom structures appeared to be 'unfoldable' for the FOD model. Some aspects of the general characteristics of the NBPs are also discussed. The calculations were performed on the EUChinaGRID grid platform to test the performance of this infrastructure for massive protein structure predictions. PMID:20020465

Prymula, Katarzyna; Piwowar, Monika; Kochanczyk, Marek; Flis, Lukasz; Malawski, Maciej; Szepieniec, Tomasz; Evangelista, Giovanni; Minervini, Giuseppe; Polticelli, Fabio; Wi?niowski, Zdzis?aw; Sa?apa, Kinga; Matczy?ska, Ewa; Roterman, Irena

2009-12-01

175

ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins.  

Science.gov (United States)

The fortran program ESPript was created in 1993, to display on a PostScript figure multiple sequence alignments adorned with secondary structure elements. A web server was made available in 1999 and ESPript has been linked to three major web tools: ProDom which identifies protein domains, PredictProtein which predicts secondary structure elements and NPS@ which runs sequence alignment programs. A web server named ENDscript was created in 2002 to facilitate the generation of ESPript figures containing a large amount of information. ENDscript uses programs such as BLAST, Clustal and PHYLODENDRON to work on protein sequences and such as DSSP, CNS and MOLSCRIPT to work on protein coordinates. It enables the creation, from a single Protein Data Bank identifier, of a multiple sequence alignment figure adorned with secondary structure elements of each sequence of known 3D structure. Similar 3D structures are superimposed in turn with the program PROFIT and a final figure is drawn with BOBSCRIPT, which shows sequence and structure conservation along the Calpha trace of the query. ESPript and ENDscript are available at http://genopole.toulouse.inra.fr/ESPript. PMID:12824317

Gouet, Patrice; Robert, Xavier; Courcelle, Emmanuel

2003-07-01

176

Primary structure similarity analysis of proteins sequences by a new graphical representation.  

Science.gov (United States)

A new graphical description of the primary structure of protein sequences is introduced. First, a three-dimensional space discrete point set of a protein sequence is created based on the three main physicochemical properties of the amino acids. Secondly, a continuous cubic B-spline curve interpolating the amino acid points is constructed to represent the shape of the protein sequence. Then the geometric properties (curvature and torsion) of the continuous curve are extracted for the purpose of analyzing the similarity between protein sequences. Finally, an improved Canberra distance comparison is introduced for the similarity analysis of protein sequences with different lengths. Experimental results show that our method is effective for the similarity comparison of protein sequences. PMID:25242152

Xu, S C; Li, Z; Zhang, S P; Hu, J L

2014-10-01

177

Quantification of transition dipole strengths using 1D and 2D spectroscopy for the identification of molecular structures via exciton delocalization: Application to ?-helices  

Science.gov (United States)

Vibrational and electronic transition dipole strengths are often good probes of molecular structures, especially in excitonically coupled systems of chromophores. One cannot determine transition dipole strengths using linear spectroscopy unless the concentration is known, which in many cases it is not. In this paper, we report a simple method for measuring transition dipole moments from linear absorption and 2D IR spectra that does not require knowledge of concentrations. Our method is tested on several model compounds and applied to the amide I? band of a polypeptide in its random coil and ?-helical conformation as modulated by the solution temperature. It is often difficult to confidently assign polypeptide and protein secondary structures to random coil or ?-helix by linear spectroscopy alone, because they absorb in the same frequency range. We find that the transition dipole strength of the random coil state is 0.12 ± 0.013 D2, which is similar to a single peptide unit, indicating that the vibrational mode of random coil is localized on a single peptide unit. In an ?-helix, the lower bound of transition dipole strength is 0.26 ± 0.03 D2. When taking into account the angle of the amide I? transition dipole vector with respect to the helix axis, our measurements indicate that the amide I? vibrational mode is delocalized across a minimum of 3.5 residues in an ?-helix. Thus, one can confidently assign secondary structure based on exciton delocalization through its effect on the transition dipole strength. Our method will be especially useful for kinetically evolving systems, systems with overlapping molecular conformations, and other situations in which concentrations are difficult to determine. PMID:23163364

Grechko, Maksim; Zanni, Martin T.

2012-01-01

178

STRUCTURE AND EVOLUTION OF PRE-MAIN-SEQUENCE CIRCUMSTELLAR DISKS  

International Nuclear Information System (INIS)

We present new subarcsecond (?0.''7) Combined Array for Research in Millimeter-wave Astronomy (CARMA) observations of the 1.3 mm continuum emission from circumstellar disks around 11 low- and intermediate-mass pre-main-sequence stars. High-resolution observations for three additional sources were obtained from the literature. In all cases the disk emission is spatially resolved. We adopt a self-consistent accretion disk model based on the similarity solution for the disk surface density and constrain the dust radial density distribution on spatial scales of about 40 AU. Disk surface densities appear to be correlated with the stellar ages where the characteristic disk radius increases from ?20 AU to ?100 AU over about 5 Myr. This disk expansion is accompanied by a decrease in the mass accretion rate, suggesting that our sample disks form an evolutionary sequence. Interpreting our results in terms of the temporal evolution of a viscous ?-disk, we estimate (1) that at the beginning of the disk evolution about 60% of the circumstellar material was located inside radii of 25-40 AU, (2) that disks formed with masses from 0.05 to 0.4 M sun, and (3) that the viscous timescale at the disk initial radius is about 0.1-0.3 Myr. Viscous disk models tightly link the surface density ?(R) with the radial profile of the disk viscosity ?(R) ? R ?. We find values of ? ranging from -0.8 to 0.8, suggesting that the viscosity dependence on the orbital raddependence on the orbital radius can be very different in the observed disks. Adopting the ? parameterization for the viscosity, we argue that ? must decrease with the orbital radius and that it may vary between 0.5 and 10-4. From the inferred disk initial radii we derive specific angular momenta, j, for parent cores of (0.8 - 4) x 10-4 km s-1 pc. Comparison with the values of j in dense cores suggests that about 10% of core angular momentum and 30% of the core mass are conserved in the formation of the star/disk system. We demonstrate that the similarity solution for the surface density for ? < 0 can explain the properties of some 'transitional disks' without requiring discontinuities in the disk surface density. In the case of LkCa 15, a smooth distribution of material from few stellar radii to about 240 AU can produce both the observed spectral energy distribution and the spatially resolved continuum emission at millimeter wavelengths. Finally we show that among the observed sample, TW Hya is the only object that has a disk radius comparable with the early solar nebula.

179

Four basic symmetry types in the universal 7-cluster structure of 143 complete bacterial genomic sequences  

CERN Document Server

Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively short genomic fragments (200-400bp). We found a universal 7-cluster structure in bacterial genomic sequences and explained its properties. We show that codon usage of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy. Based on the analysis of 143 completely sequenced bacterial genomes available in Genbank in August 2004, we show that there are four "pure" types of the 7-cluster structure observed. All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site: http://www.ihes.fr/~zinovyev/7clusters The finding can be readily introduced into any software for gene prediction, sequence alignment or bacterial genomes classification.

Gorban, A N; Zinovyev, A Yu

2011-01-01

180

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences  

Science.gov (United States)

More than a simple carrier of the genetic information, messenger RNA (mRNA) coding regions can also harbor functional elements that evolved to control different post-transcriptional processes, such as mRNA splicing, localization and translation. Functional elements in RNA molecules are often encoded by secondary structure elements. In this aticle, we introduce Structural Profile Assignment of RNA Coding Sequences (SPARCS), an efficient method to analyze the (secondary) structure profile of protein-coding regions in mRNAs. First, we develop a novel algorithm that enables us to sample uniformly the sequence landscape preserving the dinucleotide frequency and the encoded amino acid sequence of the input mRNA. Then, we use this algorithm to generate a set of artificial sequences that is used to estimate the Z-score of classical structural metrics such as the sum of base pairing probabilities and the base pairing entropy. Finally, we use these metrics to predict structured and unstructured regions in the input mRNA sequence. We applied our methods to study the structural profile of the ASH1 genes and recovered key structural elements. A web server implementing this discovery pipeline is available at http://csb.cs.mcgill.ca/sparcs together with the source code of the sampling algorithm. PMID:23748952

Zhang, Yang; Ponty, Yann; Blanchette, Mathieu; Lecuyer, Eric; Waldispuhl, Jerome

2013-01-01

 
 
 
 
181

Structure and Active Stie Residues of Pg1D, an N-Acetyltransferase from the Bacillosamine Synthetic Pathway Required for N-Glycan Synthesis in Campylobacter jejuni  

Energy Technology Data Exchange (ETDEWEB)

Campylobacter jejuni is highly unusual among bacteria in forming N-linked glycoproteins. The heptasaccharide produced by its pgl system is attached to protein Asn through its terminal 2, 4-diacetamido-2, 4,6-trideoxy-d-Glc (QuiNAc4NAc or N, N'-diacetylbacillosamine) moiety. The crucial, last part of this sugar's synthesis is the acetylation of UDP-2-acetamido-4-amino-2, 4,6-trideoxy-d-Glc by the enzyme PglD, with acetyl-CoA as a cosubstrate. We have determined the crystal structures of PglD in CoA-bound and unbound forms, refined to 1.8 and 1.75 Angstroms resolution, respectively. PglD is a trimer of subunits each comprised of two domains, an N-terminal {alpha}/{beta}-domain and a C-terminal left-handed {beta}-helix. Few structural differences accompany CoA binding, except in the C-terminal region following the {beta}-helix (residues 189-195), which adopts an extended structure in the unbound form and folds to extend the {beta}-helix upon binding CoA. Computational molecular docking suggests a different mode of nucleotide-sugar binding with respect to the acetyl-CoA donor, with the molecules arranged in an 'L-shape', compared with the 'in-line' orientation in related enzymes. Modeling indicates that the oxyanion intermediate would be stabilized by the NH group of Gly143', with His125' the most likely residue to function as a general base, removing H+ from the amino group prior to nucleophilic attack at the carbonyl carbon of acetyl-CoA. Site-specific mutations of active site residues confirmed the importance of His125', Glu124', and Asn118. We conclude that Asn118 exerts its function by stabilizing the intricate hydrogen bonding network within the active site and that Glu124' may function to increase the pKa of the putative general base, His125'.

Rangarajan,E.; Ruane, K.; Sulea, T.; Watson, D.; Proteau, A.; Leclerc, S.; Cygler, M.; Matte, A.; Young, N.

2008-01-01

182

Investigation of the protein osteocalcin of Camelops hesternus: Sequence, structure and phylogenetic implications  

Science.gov (United States)

Ancient DNA sequences offer an extraordinary opportunity to unravel the evolutionary history of ancient organisms. Protein sequences offer another reservoir of genetic information that has recently become tractable through the application of mass spectrometric techniques. The extent to which ancient protein sequences resolve phylogenetic relationships, however, has not been explored. We determined the osteocalcin amino acid sequence from the bone of an extinct Camelid (21 ka, Camelops hesternus) excavated from Isleta Cave, New Mexico and three bones of extant camelids: bactrian camel ( Camelus bactrianus); dromedary camel ( Camelus dromedarius) and guanaco ( Llama guanacoe) for a diagenetic and phylogenetic assessment. There was no difference in sequence among the four taxa. Structural attributes observed in both modern and ancient osteocalcin include a post-translation modification, Hyp 9, deamidation of Gln 35 and Gln 39, and oxidation of Met 36. Carbamylation of the N-terminus in ancient osteocalcin may result in blockage and explain previous difficulties in sequencing ancient proteins via Edman degradation. A phylogenetic analysis using osteocalcin sequences of 25 vertebrate taxa was conducted to explore osteocalcin protein evolution and the utility of osteocalcin sequences for delineating phylogenetic relationships. The maximum likelihood tree closely reflected generally recognized taxonomic relationships. For example, maximum likelihood analysis recovered rodents, birds and, within hominins, the Homo-Pan-Gorilla trichotomy. Within Artiodactyla, character state analysis showed that a substitution of Pro 4 for His 4 defines the Capra-Ovis clade within Artiodactyla. Homoplasy in our analysis indicated that osteocalcin evolution is not a perfect indicator of species evolution. Limited sequence availability prevented assigning functional significance to sequence changes. Our preliminary analysis of osteocalcin evolution represents an initial step towards a complete character analysis aimed at determining the evolutionary history of this functionally significant protein. We emphasize that ancient protein sequencing and phylogenetic analyses using amino acid sequences must pay close attention to post-translational modifications, amino acid substitutions due to diagenetic alteration and the impacts of isobaric amino acids on mass shifts and sequence alignments.

Humpula, James F.; Ostrom, Peggy H.; Gandhi, Hasand; Strahler, John R.; Walker, Angela K.; Stafford, Thomas W.; Smith, James J.; Voorhies, Michael R.; George Corner, R.; Andrews, Phillip C.

2007-12-01

183

The polarizability and dynamic structure factor of the 1D Bose gas near the Tonks-Girardeau limit at finite temperatures  

CERN Document Server

Correlation functions related to the dynamic density response of the one-dimensional Bose gas in the model of Lieb and Liniger are calculated. An exact Bose-Fermi mapping is used to work in a fermionic representation with a pseudopotential Hamiltonian. The Hartree-Fock and generalized random phase approximations are derived and the dynamic polarizability is calculated. The results are valid to first order in $1/\\gamma$ where $\\gamma$ is Lieb-Liniger coupling parameter. Approximations for the dynamic and static structure factor at finite temperature are presented. Due to the exact Bose-Fermi duality, the results apply for spinless fermions with weak p-wave interactions as well as for strongly interacting bosons.

Cherny, A Yu; Cherny, Alexander Yu.; Brand, Joachim

2006-01-01

184

Three new 2-D metal-organic frameworks containing 1-D metal chains bridged by N-benzesulfonyl-glutamic acid: Syntheses, crystal structures and properties  

International Nuclear Information System (INIS)

To explore the possibility of obtaining the metal-organic frameworks (MOFs) bearing the bsgluH2 ligand, two new Cd(II) and one Cu(II) coordination polymers, [Cd(bsglu)(bipy)] n (1), [Cd(bsglu).(H2O)] n (2) and {[Cu2(bsglu)2(bipy)2].4H2O} n (3) (bsglu=N-benzesulfonyl-glutamic acid bianion, bipy=2,2'-bipyridine) were synthesized and characterized by IR, elemental analysis and X-ray diffraction analysis. Compounds 1 and 3 exhibit one-dimensional coordination chains, which are further connected to form two-dimensional supramolecular networks through ?-? aromatic stacking interactions in a novel zipper-like way. Compound 2 presents a two-dimensional layer structure. To the best of our knowledge, 2 is the first two-dimensional complex formed from transition metal and bsgluH2 ligand. Interestingly, the bsglu anion exhibits remarkable versatile coordination modes in these complexes. Fluorescent analyses show that 1 exhibits photoluminescence in the solid state. Magnetic measurements for 3 revealed that the Cu(II) chain exhibit a weak antiferromagnetic behavior with a J value of -0.606 cm-1. - Graphical abstract: Three new complexes, [Cd(bsglu)(bipy)] n (1), [Cd(bsglu).(H2O)] n (2) and {[Cu2(bsglu)2(bipy)2].4H2O} n (3), constructed from Cd(II) or Cu(II) salt with N-benzesulfonyl-glutamic acid were synthesized and characterized. Compounds 1 and 3 exhibit one-dimensional chains which are further connected to form two-dimensional supramolecular networks through ?-? aromatic stacking interactions in a novel zipper-like way. Compound 2 presents a two-dimensional layer structure. Luminescence of 1 and magnetic properties of 3 are also investigated

185

Resolution-optimized NMR measurement of {sup 1}D{sub CH}, {sup 1}D{sub CC} and {sup 2}D{sub CH} residual dipolar couplings in nucleic acid bases  

Energy Technology Data Exchange (ETDEWEB)

New methods are described for accurate measurement of multiple residual dipolar couplings in nucleic acid bases. The methods use TROSY-type pulse sequences for optimizing resolution and sensitivity, and rely on the E.COSY principle to measure the relatively small two-bond {sup 2}D{sub CH} couplings at high precision. Measurements are demonstrated for a 24-nt stem-loop RNA sequence, uniformly enriched in {sup 13}C, and aligned in Pf1. The recently described pseudo-3D method is used to provide homonuclear {sup 1}H-{sup 1}H decoupling, which minimizes cross-correlation effects and optimizes resolution. Up to seven {sup 1}H-{sup 13}C and {sup 13}C-{sup 13}C couplings are measured for pyrimidines (U and C), including {sup 1}D{sub C5H5}, {sup 1}D{sub C6H6}, {sup 2}D{sub C5H6}, {sup 2}D{sub C6H5}, {sup 1}D{sub C5C4}, {sup 1}D{sub C5C6}, and {sup 2}D{sub C4H5}. For adenine, four base couplings ({sup 1}D{sub C2H2}, {sup 1}D{sub C8H8}, {sup 1}D{sub C4C5}, and {sup 1}D{sub C5C6}) are readily measured whereas for guanine only three couplings are accessible at high relative accuracy ({sup 1}D{sub C8H8}, {sup 1}D{sub C4C5}, and {sup 1}D{sub C5C6}). Only three dipolar couplings are linearly independent in planar structures such as nucleic acid bases, permitting cross validation of the data and evaluation of their accuracies. For the vast majority of dipolar couplings, the error is found to be less than {+-}3% of their possible range, indicating that the measurement accuracy is not limiting when using these couplings as restraints in structure calculations. Reported isotropic values of the one- and two-bond J couplings cluster very tightly for each type of nucleotide.

Boisbouvier, Jerome; Bryce, David L.; O' Neil-Cabello, Erin [Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (United States); Nikonowicz, Edward P. [Rice University, Department of Biochemistry and Cell Biology (United States); Bax, Ad [Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (United States)], E-mail: bax@nih.gov

2004-11-15

186

Moments of the Spin Structure Functions g_1^p and g_1^d for 0.05 < Q^2 < 3.0 GeV^2  

CERN Document Server

The spin structure functions g_1 for the proton and the deuteron have been measured over a wide kinematic range in x and Q2 using 1.6 and 5.7 GeV longitudinally polarized electrons incident upon polarized NH_3 and ND_3 targets at Jefferson Lab. Scattered electrons were detected in the CEBAF Large Acceptance Spectrometer, for 0.05 < Q^2 < 5 GeV^2 and W < 3 GeV. The first moments of g_1 for the proton and deuteron are presented -- both have a negative slope at low Q2, as predicted by the extended Gerasimov-Drell-Hearn sum rule. The first result for the generalized forward spin polarizability of the proton gamma_0^p is also reported, and shows evidence of scaling above Q^2 = 1.5 GeV^2. Although the first moments of g_1 are consistent with Chiral Perturbation Theory (ChPT) calculations up to approximately Q^2 = 0.06 GeV^2, a significant discrepancy is observed between the \\gamma_0^p data and ChPT for gamma_0^p,even at the lowest Q2.

Prok, Y; Burkert, V D; Deur, A; Dharmawardane, K V; Dodge, G E; Griffioen, K A; Kuhn, S E; Minehart, R; Adams, G; Amaryan, M J; Anghinolfi, M; Asryan, G; Audit, G; Avakian, H; Bagdasaryan, H; Baillie, N; Ball, J P; Baltzell, N A; Barrow, S; Battaglieri, M; Beard, K; Bedlinskiy, I; Bektasoglu, M; Bellis, M; Benmouna, N; Berman, B L; Biselli, A S; Blaszczyk, L; Boiarinov, S; Bonner, B E; Bouchigny, S; Bradford, R; Branford, D; Briscoe, W J; Brooks, W K; Bültmann, S; Butuceanu, C; Calarco, J R; Careccia, S L; Carman, D S; Casey, L; Cazes, A; Chen, S; Cheng, L; Cole, P L; Collins, P; Coltharp, P; Cords, D; Corvisiero, P; Crabb, D; Credé, V; Cummings, J P; Dale, D; Dashyan, N; De Masi, R; De Vita, R; De Sanctis, E; Degtyarenko, P V; Denizli, H; Dennis, L; Dhuga, K S; Dickson, R; Djalali, C; Doughty, D; Dugger, M; Dytman, S; Dzyubak, O P; Egiyan, H; Egiyan, K S; El Fassi, L; Elouadrhiri, L; Eugenio, P; Fatemi, R; Fedotov, G; Feldman, G; Fersh, R G; Feuerbach, R J; Forest, T A; Fradi, A; Funsten, H; Garçon, M; Gavalian, G; Gevorgyan, N; Gilfoyle, G P; Giovanetti, K L; Girod, F X; Goetz, J T; Golovatch, E; Gothe, R W; Guidal, M; Guillo, M; Guler, N; Guo, L; Gyurjyan, V; Hadjidakis, C; Hafidi, K; Hakobyan, H; Hanretty, C; Hardie, J; Hassall, N; Heddle, D; Hersman, F W; Hicks, K; Hleiqawi, I; Holtrop, M; Huertas, M; Hyde-Wright, C E; Ilieva, Y; Ireland, D G; Ishkhanov, B S; Isupov, E L; Ito, M M; Jenkins, D; Jo, H S; Johnstone, J R; Joo, K; Jüngst, H G; Kalantarians, N; Keith, C D; Kellie, J D; Khandaker, M; Kim, K Y; Kim, K; Kim, W; Klein, A; Klein, F J; Klusman, M; Kossov, M; Krahn, Z; Kramer, L H; Kubarovski, V; Kühn, J; Kuleshov, S V; Kuznetsov, V; Lachniet, J; Laget, J M; Langheinrich, J; Lawrence, D; Ji Li; Lima, A C S; Livingston, K; Lu, H Y; Lukashin, K; MacCormick, M; Marchand, C; Markov, N; Mattione, P; McAleer, S; McKinnon, B; McNabb, J W C; Mecking, B A; Mestayer, M D; Meyer, C A; Mibe, T; Mikhailov, K; Mirazita, M; Miskimen, R; Mokeev, V; Morand, L; Moreno, B; Moriya, K; Morrow, S A; Moteabbed, M; Müller, J; Munevar, E; Mutchler, G S; Nadel-Turonski, P; Nasseripour, R; Niccolai, S; Niculescu, G; Niculescu, I; Niczyporuk, B B; Niroula, M R; Niyazov, R A; Nozar, M; O'Rielly, G V; Osipenko, M; Ostrovidov, A I; Park, K; Pasyuk, E; Paterson, C; Anefalos Pereira, S; Philips, S A; Pierce, J; Pivnyuk, N; Pocanic, D; Pogorelko, O; Popa, I; Pozdniakov, S; Preedom, B M; Price, J W; Procureur, S; Protopopescu, D; Qin, L M; Raue, B A; Riccardi, G; Ricco, G; Ripani, M; Ritchie, B G; Rosner, G; Rossi, P; Rowntree, D; Rubin, P D; Sabati, F; Salamanca, J; Salgado, C; Santoro, e J P; Sapunenko, V; Schumacher, R A; Seely, M L; Serov, V S; Sharabyan, Yu G; Sharov, D; Shaw, J; Shvedunov, N V; Skabelin, A V; Smith, E S; Smith, L C; Sober, D I; Sokhan, D; Stavinsky, A; Stepanyan, S S; Stepanyan, S; Stokes, B E; Stoler, P; Strakovsky, I I; Strauch, S; Suleiman, R; Taiuti, M; Tedeschi, D J; Tkabladze, A; Tkachenko, S; Todor, L; Ungaro, M; Vineyard, M F; Vlassov, A V; Watts, D P; Weinstein, L B; Weygand, D P; Williams, M; Wolin, E; Wood, M H; Yegneswaran, A; Yun, J; Zana, L; Zhang, J; Zhao, B; Zhao, Z W

2008-01-01

187

Intricate heterogeneous structures of the top 300 km of the Earth's inner core inferred from global array data: I. Regional 1D attenuation and velocity profiles  

Science.gov (United States)

We apply a waveform inversion method based on simulated annealing to complex core phase data observed by globally deployed seismic arrays, and present regional variation of depth profiles of attenuation and velocity for the top half of the inner core. Whereas measured attenuation parameters exhibit consistent trends for data sampling the eastern hemisphere of the inner core, for the western hemisphere, there is a remarkable difference between data sampling the inner core beneath Africa (W1) and beneath north America (W2). Obtained attenuation profiles suggest that intricate heterogeneities appear to be confined in the top 300 km. The profile for the eastern hemisphere has a high attenuation zone in the top 150 km that gradually diminishes with depth. Conversely, for the western hemisphere, the profile for W1 shows constant low attenuation and that for W2 represents a gradual increase from the inner core boundary to a peak at around 200 km depth. Velocity profiles, obtained from differential traveltimes between PKP(DF) and PKP(CD, BC) phases, for the eastern and western hemispheres are respectively about 0.8% faster and 0.6% slower than the reference model at the top of the inner core, and the difference nearly disappears at about 200 km depth. Our result suggests the presence of intricate quasi-hemispherical structures in the top ˜200-300 km of the inner core.

Iritani, R.; Takeuchi, N.; Kawakatsu, H.

2014-05-01

188

Energies, fine structure, hyperfine structure and Auger widths of the core-excited states for the Li isoelectronic sequence  

Energy Technology Data Exchange (ETDEWEB)

The relativistic energies, fine structures, hyperfine structures, Auger rates and widths of the core-excited states for the Li isoelectronic sequence (Z = 10-20) are studied using the saddle-point variational method and the saddle-point complex-rotation method. The oscillator strengths, radiative rates, wavelengths and lifetimes are also reported. Properties such as fine-structure splitting, radiative and Auger rate regularly change along the Li isoelectronic sequence are discussed. The results are compared with other theoretical and experimental data in the literature.

Zhu Jingjing; Gou Bingcong; Wang Yuedong [Department of Physics, Beijing Institute of Technology, Beijing 100081 (China)], E-mail: crystal66180@163.com, E-mail: goubing@sina.com

2008-03-28

189

1D helix, 2D brick-wall and herringbone, and 3D interpenetration d10 metal-organic framework structures assembled from pyridine-2,6-dicarboxylic acid N-oxide.  

Science.gov (United States)

Five novel interesting d(10) metal coordination polymers, [Zn(PDCO)(H2O)2]n (PDCO = pyridine-2,6-dicarboxylic acid N-oxide) (1), [Zn2(PDCO)2(4,4'-bpy)2(H2O)2.3H2O]n (bpy = bipyridine) (2), [Zn(PDCO)(bix)]n (bix = 1,4-bis(imidazol-1-ylmethyl)benzene) (3), [Zn(PDCO)(bbi).0.5H2O]n (bbi = 1,1'-(1,4-butanediyl)bis(imidazole)) (4), and [Cd(PDCO)(bix)(1.5).1.5H2O]n (5), have been synthesized under hydrothermal conditions and structurally characterized. Polymer 1 possesses a one-dimensional (1D) helical chainlike structure with 4(1) helices running along the c-axis with a pitch of 10.090 Angstroms. Polymer 2 has an infinite chiral two-dimensional (2D) brick-wall-like layer structure in the ac plane built from achiral components, while both 3 and 4 exhibit an infinite 2D herringbone architecture, respectively extended in the ac and ab plane. Polymer 5 features a most remarkable and unique three-dimensional (3D) porous framework with 2-fold interpenetration related by symmetry, which contains channels in the b and c directions, both distributed in a rectangular grid fashion. Compounds 1-5, with systematic variation in dimensionality from 1D to 2D to 3D, are the first examples of d(10) metal coordination polymers into which pyridinedicarboxylic acid N-oxide has been introduced. In addition, polymers 1, 4, and 5 display strong blue fluorescent emissions in the solid state. Polymer 3 exhibits a strong SHG response, estimated to be approximately 0.9 times that of urea. PMID:16180879

Wen, Li-Li; Dang, Dong-Bin; Duan, Chun-Ying; Li, Yi-Zhi; Tian, Zheng-Fang; Meng, Qing-Jin

2005-10-01

190

[Information about the protein secondary structure improves quality of an alignment of protein sequences].  

Science.gov (United States)

All popular algorithms of pair-wise alignment of protein primary structures (e.g. Smith-Waterman (SW), FASTA, BLAST, et al.) utilize only amino acid sequences. The SW-algorithm is the most accurate among them, i.e. it produces alignments that are most similar to the alignments obtained by superposition of protein 3D-structures. But even the SW-algorithm is unable to restore the 3D-based alignment if similarity of amino acid sequences (%id) is below 30%. We have proposed a novel alignment method that explicitly takes into account the secondary structure of the compared proteins. We have shown that it creates significantly more accurate alignments compared to SW-algorithm. In particular, for sequences with %id < 30% the average accuracy of the new method is 58% compared to 35% for SW-algorithm (the accuracy of an algorithmic sequence alignment is the part of restored position of a "golden standard" alignment obtained by superposition of corresponding 3D-structures). The accuracy of the proposed method is approximately identical both for experimental, and for theoretically predicted secondary structures. Thus the method can be applied for alignment of protein sequences even if protein 3D-structure is unknown. The program is available at ftp://194.149.64.196/STRUSWER/. PMID:16813172

Litvinov, I I; Lobanov, M Iu; Mironov, A A; Finkel'sht?n, M A

2006-01-01

191

Sequence Analysis of the Protein Structure Homology Modeling of Growth Hormone Gene from Salmo trutta caspius  

Directory of Open Access Journals (Sweden)

Full Text Available In view of the growth hormone protein investigated and characterized from Salmo trutta caspius. Growth hormone gene in the Salmo trutta caspius have six exons in the full length that is translated into a Molecular Weight (kDa: ssDNA: 64.98 and dsDNA: 129.6. There are also 210 amino acid residue. The assembled full length of DNA contains open reading frame of growth hormone gene that contains 15 sequences in the full length. The average GC content is 47% and AT content is 53%. This protein multiple alignment has shown that this peptide is 100% identical to the corresponding homologous protein in the growth hormone protein which including Salmo salar (Accession number: AAA49558.1 and Rainbow trout (Salmo trutta (Accession number: AAA49555.1" sequences. The sequence of protein had deposited in Gene Bank, Accession number: AEK70940. Also we were analyzed second and third structure between sequences reported in Gene Bank Network system. The results are shown, there are homology between second structure in three sequences including: Salmo trutta caspius, Salmo salar and Rainbow trout. Regarding third structure, Salmo trutta caspius and Salmo salar are same type, but Rainbow trout has different homology with Salmo trutta caspius and Salmo salar. However, the sequences were observed three parallel " helix and in second structure there were almost same percent ? sheet.

Abolhasan Rezaei

2012-03-01

192

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction  

Science.gov (United States)

Protein sequence alignment is essential for template-based protein structure prediction and function annotation. We collect 20 sequence alignment algorithms, 10 published and 10 newly developed, which cover all representative sequence- and profile-based alignment approaches. These algorithms are benchmarked on 538 non-redundant proteins for protein fold-recognition on a uniform template library. Results demonstrate dominant advantage of profile-profile based methods, which generate models with average TM-score 26.5% higher than sequence-profile methods and 49.8% higher than sequence-sequence alignment methods. There is no obvious difference in results between methods with profiles generated from PSI-BLAST PSSM matrix and hidden Markov models. Accuracy of profile-profile alignments can be further improved by 9.6% or 21.4% when predicted or native structure features are incorporated. Nevertheless, TM-scores from profile-profile methods including experimental structural features are still 37.1% lower than that from TM-align, demonstrating that the fold-recognition problem cannot be solved solely by improving accuracy of structure feature predictions. PMID:24018415

Yan, Renxiang; Xu, Dong; Yang, Jianyi; Walker, Sara; Zhang, Yang

2013-01-01

193

Active motif finder - a bio-tool based on mutational structures in DNA sequences.  

Science.gov (United States)

Active Motif Finder (AMF) is a novel algorithmic tool, designed based on mutations in DNA sequences. Tools available at present for finding motifs are based on matching a given motif in the query sequence. AMF describes a new algorithm that identifies the occurrences of patterns which possess all kinds of mutations like insertion, deletion and mismatch. The algorithm is mainly based on the Alignment Score Matrix (ASM) computation by comparing input motif with full length sequence. Much of the effort in bioinformatics is directed to identify these motifs in the sequences of newly discovered genes. The proposed bio-tool serves as an open resource for analysis and useful for studying polymorphisms in DNA sequences. AMF can be searched via a user-friendly interface. This tool is intended to serve the scientific community working in the areas of chemical and structural biology, and is freely available to all users, at http://www.sastra.edu/scbt/amf/. PMID:23554723

Udayakumar, Mani; Shanmuga-Priya, Palaniyandi; Hemavathi, Kamalakannan; Seenivasagam, Rengasamy

2011-11-01

194

From 1D chain to 3D network: a new family of inorganic-organic hybrid semiconductors MO3(L)(x) (M = Mo, W; L = organic linker) built on perovskite-like structure modules.  

Science.gov (United States)

MO3 (M = Mo, W) or VI-VI binary compounds are important semiconducting oxides that show great promise for a variety of applications. In an effort to tune and enhance their properties in a systematic manner we have applied a designing strategy to deliberately introduce organic linker molecules in these perovskite-like crystal lattices. This approach has led to a wealth of new hybrid structures built on one-dimensional (1D) and two-dimensional (2D) VI-VI modules. The hybrid semiconductors exhibit a number of greatly improved properties and new functionality, including broad band gap tunability, negative thermal expansion, largely reduced thermal conductivity, and significantly enhanced dielectric constant compared to their MO3 parent phases. PMID:24152119

Zhang, Xiao; Hejazi, Mehdi; Thiagarajan, Suraj J; Woerner, William R; Banerjee, Debasis; Emge, Thomas J; Xu, Wenqian; Teat, Simon J; Gong, Qihan; Safari, Ahmad; Yang, Ronggui; Parise, John B; Li, Jing

2013-11-20

195

SuGra on G2 Structure Backgrounds that Asymptote to AdS4 and Holographic Duals of Confining 2+1d Gauge Theories with N=1 SUSY  

CERN Document Server

In this work the solution generated by performing a U-duality on a deformation of the Maldacena-Nastase solution is studied. This is a solution of type-IIA with a metric that is asymptotically AdS4 and supports a G2 structure. It is believed to be dual to a 2+1d, N=1 gauge theory similar to the baryonic branch of Klebanov-Strassler with an additional intermediate scale. An improved radial coordinate is used allowing the derivation of UV series solutions to the BPS equation that persist to all orders. A study of the properties of the dual field theory is performed which includes an operator analysis, Wilson loops and a proposal for gauge couplings. The gauge theory dual appears to be a confining Chern-Simons quiver with gauge couplings that become constant at high energies.

Macpherson, Niall T

2013-01-01

196

SuGra on G 2 structure backgrounds that asymptote to AdS4 and holographic duals of confining 2 + 1 d gauge theories with mathcal{N}=1 SUSY  

Science.gov (United States)

In this work the solution generated by performing a U-duality on a deformation of the Maldacena-Nastase solution is studied. This is a solution of type-IIA with a metric that is asymptotically AdS4 and supports a G 2 structure. It is believed to be dual to a 2+1 d, {N}=1 gaugetheorysimilartothebaryonicbranchofKlebanov-Strasslerwithanadditional intermediate scale. An improved radial coordinate is used allowing the derivation of UV series solutions to the BPS equation that persist to all orders. A study of the properties of the dual field theory is performed which includes an operator analysis, Wilson loops and a proposal for gauge couplings. The gauge theory dual appears to be a confining Chern-Simons quiver with gauge couplings that become constant at high energies.

Macpherson, Niall T.

2013-04-01

197

Combinatorial variation of structure in considerations of compound lumping in one- and two-dimensional property representations of condensable atmospheric organic compounds. 1. Lumping by 1-D volatility with nC fixed  

Science.gov (United States)

Many current models that aim to predict urban and regional levels of organic particulate matter (OPM) use either the 2 product (2p) framework for secondary organic aerosol (SOA) formation, or a static 1-D volatility basis set (1-D-VBS). These approaches assume that: 1) the compounds involved in OPM condensation/evaporation can be lumped simply by volatility with no specificity regarding carbon number nC, MW, or polar functionality; 2) water uptake does not occur; and 3) the compounds are non-ionizing. This work considers the consequences for uniphasic PM caused by the first two assumptions due to effects of the condensed-phase mean molecular weight MWbar and activity coefficients (?i), including when RH (relative humidity) > 0. Setting nC = 10 for all bins, multiple chemical structures were developed for each bin of a 1-D-VBS for un-aged SOA in the ?-pinene/ozone system. For each bin, a group-contribution vapor pressure (pLo) prediction method was used to find multiple structures such that the groups-based log pLo for nC = 10 and variable numbers of aldehyde, ketone, hydroxyl, and carboxylic acid groups agrees, within ±0.5, with the bin volatility. The number of possible combinations with one structure taken from each bin was 17,640. The Raster-Roulette Organic Aerosol (RROA) model was used to calculate the equilibrium mass concentrations (?g m-3) of OPM (Mo) and co-condensed water (Mw) at 25 °C for each combination for ranges of RH and ?HC (change in parent hydrocarbon concentration). UNIFAC was used to determine the needed values of ?i. Frequency distributions from RROA for Mo, Mw, and the O:C ratio were developed. For Mo levels typical of the ambient atmosphere, then for the 1-D-VBS and all bins constrained at nC = 10, significant RH-induced enhancement of OPM condensation was observed in the distributions. The spread of the distributions was found to increase rapidly as the level of OPM decreased. The within-bin spread of ±0.5 log units in the groups-based estimates of log pL,iowas found to cause significant spread in the distributions at lower Mo values. At the chosen nC (=10), the groups-based log pL,iovalues show a spread of ±2 log units in a plot of log pL,iovs. O:C. When seeking to advance to 2-D-grid predictive modeling of atmospheric OPM, use of an O:C vs. nC grid will therefore require reliable information (or at least empirical calibration) as to the distributions of the likely structures at each gridpoint.

Pankow, James F.; Niakan, Negar; Asher, William E.

2013-12-01

198

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure  

DEFF Research Database (Denmark)

Human and mouse genome sequences contain roughly 100,000 regions that are unalignable in primary sequence and neighbor corresponding alignable regions between both organisms. These pairs are generally assumed to be nonconserved, although the level of structural conservation between these has never been investigated. Owing to the limitations in computational methods, comparative genomics has been lacking the ability to compare such nonconserved sequence regions for conserved structural RNA elements. We have investigated the presence of structural RNA elements by conducting a local structural alignment, using FOLDALIGN, on a subset of these 100,000 corresponding regions and estimate that 1800 contain common RNA structures. Comparing our results with the recent mapping of transcribed fragments (transfrags) in human, we find that high-scoring candidates are twice as likely to be found in regions overlapped by transfrags than regions that are not overlapped by transfrags. To verify the coexpression between predicted candidates in human and mouse, we conducted expression studies by RT-PCR and Northern blotting on mouse candidates, which overlap with transfrags on human chromosome 20. RT-PCR results confirmed expression of 32 out of 36 candidates, whereas Northern blots confirmed four out of 12 candidates. Furthermore, many RT-PCR results indicate differential expression in different tissues. Hence, our findings suggest that there are corresponding regions between human and mouse, which contain expressed non-coding RNA sequences not alignable in primary sequence.

Torarinsson, Elfar; Sawera, Milena

2006-01-01

199

On the structure of generalized Appell sequences of paravector valued homogeneous monogenic polynomials  

Science.gov (United States)

The fact that generalized Appell sequences of monogenic polynomials in the setting of hypercomplex function theory also satisfy a corresponding binomial type theorem allows to obtain their explicit structure. Recently it has been obtained a complete characterization in the case of paravector valued homogeneous polynomials of three real variables. The aim of this contribution is the study of paravector valued homogeneous polynomials of four real variables, where new types of generalized Appell sequences could be detected.

Cruz, C.; Falcão, M. I.; Malonek, H. R.

2012-09-01

200

Sequence Polymorphism in the ?-Tubulin Gene Reveals Heterogeneous and Variable Population Structures in Cryptosporidium parvum  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Restriction fragment length polymorphism (RFLP) analysis of isolates of Cryptosporidium parvum has revealed two subgroups, termed H and C. The limited resolution of the RFLP method precludes an in-depth study of the genetic structure of C. parvum populations. Published C. parvum restriction polymorphisms lie within protein-coding regions known to be more homogeneous than noncoding sequences. To better assess the degrees of heterogeneity between and within C. parvum isolates, sequence polymorp...

Widmer, Giovanni; Tchack, Laurie; Chappell, Cynthia L.; Tzipori, Saul

1998-01-01

 
 
 
 
201

Species specific amino acid sequence – Protein local structure relationships: An analysis in the light of a structural alphabet  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Protein structure analysis and prediction methods are based on non-redundant data extracted from the available protein structures, regardless of the species from which the protein originates. Hence, these datasets represent the global knowledge on protein folds, which constitutes a generic distribution of amino acid sequence – protein structure (AAS-PS) relationships. In this study, we try to elucidate whether the AAS-PS relationship could possess specificities depending...

Brevern, Alexandre; Joseph, Agnel Praveen

2011-01-01

202

A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. Description We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. Conclusion We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation.

Kondrashov Fyodor A

2007-11-01

203

Comparative analysis of MR sequences to detect structural brain lesions in tuberous sclerosis  

Energy Technology Data Exchange (ETDEWEB)

Tuberous sclerosis (TS) is a neurocutaneous genetically inherited disease with variable penetrance characterized by dysplasias and hamartomas affecting multiple organs. MR is the imaging method of choice to demonstrate structural brain lesions in TS. To compare MR sequences and determine which is most useful for the demonstration of each type of brain lesion in TS patients. We reviewed MR scans of 18 TS patients for the presence of cortical tubers, white matter lesions (radial bands), subependymal nodules, and subependymal giant cell astrocytoma (SGCA) on the following sequences: (1) T1-weighted spin-echo (T1 SE) images before and after gadolinium (Gd) injection; (2) nonenhanced T1 SE sequence with an additional magnetization transfer contrast medium pulse on resonance (T1 SE/MTC); and (3) fluid-attenuated inversion recovery (FLAIR) sequence. Cortical tubers were found in significantly (P<0.05) larger numbers and more conspicuously in FLAIR and T1 SE/MTC sequences. The T1 SE/MTC sequence was far superior to other methods in detecting white matter lesions (P<0.01). There was no significant difference between the T1 SE/MTC and T1 SE (before and after Gd injection) sequences in the detection of subependymal nodules; FLAIR sequence showed less sensitivity than the others in identifying the nodules. T1 SE sequences after Gd injection demonstrated better the limits of the SGCA. We demonstrated the importance of appropriate MRI sequences for diagnosis of the most frequent brain lesions in TS. Our study reinforces the fact that each sequence has a particular application according to the type of TS lesion. Gd injection might be useful in detecting SGCA; however, the parameters of size and location are also important for a presumptive diagnosis of these tumors. (orig.)

Pinto Gama, Hugo Pereira; Campos Meirelles, Rogerio Goncalves de; Mendonca do Rego, Jose Iram [Santa Casa de Misericordia de Sao Paulo, Section of Radiology, Sao Paulo (Brazil); Rocha, Antonio Jose da; Silva, Carlos Jorge da [Santa Casa de Misericordia de Sao Paulo, Section of Radiology, Centro de Medicina Diagnostica Fleury, Sao Paulo (Brazil); Braga, Flavio Tulio [Federal University of Sao Paulo, Escola Paulista de Medicina, Section of Radiology, Centro de Medicina Diagnostica Fleury, Santa Casa de Misericordia de Sao Paulo, Department of Diagnostic Imaging, Sao Paulo (Brazil); Martins Maia, Antonio Carlos [Federal University of Sao Paulo, Escola Paulista de Medicina, Section of Radiology, Centro de Medicina Diagnostica Fleury, Department of Neurology, Sao Paulo (Brazil); Lederman, Henrique Manoel [Federal University of Sao Paulo, Escola Paulista de Medicina, Division of Diagnostic Imaging in Pediatrics, Department of Diagnostic Imaging, Sao Paulo (Brazil)

2006-02-01

204

Comparative analysis of MR sequences to detect structural brain lesions in tuberous sclerosis  

International Nuclear Information System (INIS)

Tuberous sclerosis (TS) is a neurocutaneous genetically inherited disease with variable penetrance characterized by dysplasias and hamartomas affecting multiple organs. MR is the imaging method of choice to demonstrate structural brain lesions in TS. To compare MR sequences and determine which is most useful for the demonstration of each type of brain lesion in TS patients. We reviewed MR scans of 18 TS patients for the presence of cortical tubers, white matter lesions (radial bands), subependymal nodules, and subependymal giant cell astrocytoma (SGCA) on the following sequences: (1) T1-weighted spin-echo (T1 SE) images before and after gadolinium (Gd) injection; (2) nonenhanced T1 SE sequence with an additional magnetization transfer contrast medium pulse on resonance (T1 SE/MTC); and (3) fluid-attenuated inversion recovery (FLAIR) sequence. Cortical tubers were found in significantly (P<0.05) larger numbers and more conspicuously in FLAIR and T1 SE/MTC sequences. The T1 SE/MTC sequence was far superior to other methods in detecting white matter lesions (P<0.01). There was no significant difference between the T1 SE/MTC and T1 SE (before and after Gd injection) sequences in the detection of subependymal nodules; FLAIR sequence showed less sensitivity than the others in identifying the nodules. T1 SE sequences after Gd injection demonstrated better the limits of the SGCA. We demonstrated the importance of appropriate MRI sequences for diagnosis of the most frequent brnces for diagnosis of the most frequent brain lesions in TS. Our study reinforces the fact that each sequence has a particular application according to the type of TS lesion. Gd injection might be useful in detecting SGCA; however, the parameters of size and location are also important for a presumptive diagnosis of these tumors. (orig.)

205

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Previous efforts to determine structures of non-coding RNA (ncRNA) probed only one RNA at a time with enzymes and chemicals, using gel electrophoresis to identify reactive positions. To accelerate RNA structure inference, we have developed FragSeq, a high-throughput RNA structure probing method that uses high-throughput RNA sequencing on fragments generated by nuclease P1, which specifically cleaves single stranded nucleic acids. In experiments probing the entire mouse nuclear transcriptome, ...

Underwood, Jason G.; Uzilov, Andrew V.; Katzman, Sol; Onodera, Courtney S.; Mainzer, Jacob E.; Mathews, David H.; Lowe, Todd M.; Salama, Sofie R.; Haussler, David

2010-01-01

206

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of secondary structure and RNA–RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene. We present web servers to analyze multiple RNA sequences for common RNA structure and for RNA interaction sites. The web servers are based on the recent PET (Probabilistic Evolutionary and T...

Seemann, Stefan E.; Menzel, Peter; Backofen, Rolf; Gorodkin, Jan

2011-01-01

207

Comparative genomics beyond sequence-based alignments : RNA structures in the ENCODE regions  

DEFF Research Database (Denmark)

Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment methods to misalign, or even refuse to align, homologous ncRNAs, consequently obscuring that structural signal. We have used CMfinder, a structure-oriented local alignment tool, to search the ENCODE regions of vertebrate multiple alignments. In agreement with other studies, we find a large number of potential RNA structures in the ENCODE regions. We report 6587 candidate regions with an estimated false-positive rate of 50%. More intriguingly, many of these candidates may be better represented by alignments taking the RNA secondary structure into account than those based on primary sequence alone, often quite dramatically. For example, approximately one-quarter of our predicted motifs show revisions in >50% of their aligned positions. Furthermore, our results are strongly complementary to those discovered by sequence-alignment-based approaches--84% of our candidates are not covered by Washietl et al., increasing the number of ncRNA candidates in the ENCODE region by 32%. In a group of 11 ncRNA candidates that were tested by RT-PCR, 10 were confirmed to be present as RNA transcripts in human tissue, and most show evidence of significant differential expression across tissues. Our results broadly suggest caution in any analysis relying on multiple sequence alignments in less well-conserved regions, clearly support growing appreciation for the biological significance of ncRNAs, and strongly support the argument for considering RNA structure directly in any searches for these elements.

Torarinsson, Elfar; Yao, Zizhen

2008-01-01

208

SeqHound: biological sequence and structure database as a platform for bioinformatics research  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. Results SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. Conclusions The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit.

Dumontier Michel

2002-10-01

209

1D oxide nanostructures from chemical solutions.  

Science.gov (United States)

Nanotechnology has motivated a tremendous effort in the synthesis approaches to grow free standing or hierarchical nanomaterials such as nanowires and nanorods. Bottom-up approaches based on chemistry are an important approach to produce nanomaterials, and here the concepts of growing oxide 1D nanostructures from chemical solutions are reviewed. The thermodynamic and kinetic aspects of the nucleation and growth of oxide compounds in solutions are presented with emphasis on hydrothermal and molten salt synthesis. The importance of solubility of precursors, the precursor chemistry, role of organic additives as well as the chemical complexity and dimensionality and symmetry of the crystal structure of the compound grown are highlighted. PMID:24129769

Einarsrud, Mari-Ann; Grande, Tor

2014-04-01

210

Computational Design of the Sequence and Structure of a Protein-Binding Peptide  

Energy Technology Data Exchange (ETDEWEB)

The de novo design of protein-binding peptides is challenging because it requires the identification of both a sequence and a backbone conformation favorable for binding. We used a computational strategy that iterates between structure and sequence optimization to redesign the C-terminal portion of the RGS14 GoLoco motif peptide so that it adopts a new conformation when bound to G{alpha}{sub i1}. An X-ray crystal structure of the redesigned complex closely matches the computational model, with a backbone root-mean-square deviation of 1.1 {angstrom}.

Sammond, Deanne W.; Bosch, Dustin E.; Butterfoss, Glenn L.; Purbeck, Carrie; Machius, Mischa; Siderovski, David P.; Kuhlman, Brian (UNC)

2012-08-10

211

Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device  

DEFF Research Database (Denmark)

We show how a bird’s-eye view of genomic structure can be obtained at ?1-kb resolution from long (?2 Mb) DNA molecules extracted from whole chromosomes in a nanofluidic laboratoryon-a-chip. We use an improved single-molecule denaturation mapping approach to detect repetitive elements and known as well as unique structural variation. Following its mapping, a molecule of interest was rescued fromthe chip;amplified and localized to a chromosome by FISH; and interrogated down to 1-bp resolution with a commercial sequencer, thereby reconciling haplotype-phased chromosome substructure with sequence.

Marie, Rodolphe; Pedersen, Jonas Nyvold

2013-01-01

212

Origination of the Split Structure of Spliceosomal Genes from Random Genetic Sequences  

Science.gov (United States)

The mechanism by which protein-coding portions of eukaryotic genes came to be separated by long non-coding stretches of DNA, and the purpose for this perplexing arrangement, have remained unresolved fundamental biological problems for three decades. We report here a plausible solution to this problem based on analysis of open reading frame (ORF) length constraints in the genomes of nine diverse species. If primordial nucleic acid sequences were random in sequence, functional proteins that are innately long would not be encoded due to the frequent occurrence of stop codons. The best possible way that a long protein-coding sequence could have been derived was by evolving a split-structure from the random DNA (or RNA) sequence. Results of the systematic analyses of nine complete genome sequences presented here suggests that perhaps the major underlying structural features of split-genes have evolved due to the indigenous occurrence of split protein-coding genes in primordial random nucleotide sequence. The results also suggest that intron-rich genes containing short exons may have been the original form of genes intrinsically occurring in random DNA, and that intron-poor genes containing long exons were perhaps derived from the original intron-rich genes. PMID:18941625

Singh, Chandan Kumar; Senapathy, Periannan

2008-01-01

213

Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily.  

Science.gov (United States)

The cupin superfamily is extremely diverse and includes catalytically inactive seed storage proteins, sugar-binding metal-independent epimerases, and metal-dependent enzymes possessing dioxygenase, decarboxylase, and other activities. Although numerous proteins of this superfamily have been structurally characterized, the functions of many of them have not been experimentally determined. We report the first use of protein similarity networks (PSNs) to visualize trends of sequence and structure in order to make functional inferences in this remarkably diverse superfamily. PSNs provide a way to visualize relatedness of structure and sequence among a given set of proteins. Structure- and sequence-based clustering of cupin members reflects functional clustering. Networks based only on cupin domains and networks based on the whole proteins provide complementary information. Domain-clustering supports phylogenetic conclusions that the N- and C-terminal domains of bicupin proteins evolved independently. Interestingly, although many functionally similar enzymatic cupin members bind the same active site metal ion, the structure and sequence clustering does not correlate with the identity of the bound metal. It is anticipated that the application of PSNs to this superfamily will inform experimental work and influence the functional annotation of databases. PMID:24040257

Uberto, Richard; Moomaw, Ellen W

2013-01-01

214

Structural infection and anomalous phase sequences in complex oxides prepared from nanodispersed components  

International Nuclear Information System (INIS)

The complex oxides prepared by solid-phase synthesis from nanoscopic components are studied using X-ray diffraction. It is demonstrated that the use of nanoscopic components in the solid-phase synthesis of lutetium borate LuBO3 and europium molybdate Eu2(MoO4)3 leads to anomalous sequences of phase transformations in these compounds: the vaterite ? calcite ? vaterite sequence for LuBO3 and the ? ? ? ? ? sequence for Eu2(MoO4)3 are observed instead of the previously known sequences, namely, the calcite ? vaterite sequence for LuBO3 and the ? ? ? sequence for Eu2(MoO4)3. The revealed anomalous sequences do not depend on the procedure used for preparing reactants and are determined by the nanoscopic sizes of the initial components. It is found that microscopic additions of a number of simple oxides can suppress the kinetics of solid-phase synthesis of particular complex oxides and initiate the formation of new phases in the synthesis of other complex oxides (the so-called structural infection effect)

215

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.  

Science.gov (United States)

We describe genome mapping on nanochannel arrays. In this approach, specific sequence motifs in single DNA molecules are fluorescently labeled, and the DNA molecules are uniformly stretched in thousands of silicon channels on a nanofluidic device. Fluorescence imaging allows the construction of maps of the physical distances between occurrences of the sequence motifs. We demonstrate the analysis, individually and as mixtures, of 95 bacterial artificial chromosome (BAC) clones that cover the 4.7-Mb human major histocompatibility complex region. We obtain accurate, haplotype-resolved, sequence motif maps hundreds of kilobases in length, resulting in a median coverage of 114× for the BACs. The final sequence motif map assembly contains three contigs. With an average distance of 9 kb between labels, we detect 22 haplotype differences. We also use the sequence motif maps to provide scaffolds for de novo assembly of sequencing data. Nanochannel genome mapping should facilitate de novo assembly of sequencing reads from complex regions in diploid organisms, haplotype and structural variation analysis and comparative genomics. PMID:22797562

Lam, Ernest T; Hastie, Alex; Lin, Chin; Ehrlich, Dean; Das, Somes K; Austin, Michael D; Deshpande, Paru; Cao, Han; Nagarajan, Niranjan; Xiao, Ming; Kwok, Pui-Yan

2012-08-01

216

Structural characterization of HDPE/LLDPE blend-based nano composites obtained by different blending sequence  

International Nuclear Information System (INIS)

The blending sequence affects the morphology formation of the nanocomposites. In this work, the blending sequences were explored to determine its influence in the rheological behavior of HDPE/LLDPE/OMMT nanocomposites. The nanocomposites were obtained by melt-intercalation using a mixture of LLDPE-g-MA and HDPE-g-MA as compatibilizer system in a torque rheometer at 180 deg C and five blending sequences were studied. The materials structures were characterized by wide angle X-ray diffraction (WAXD) and by rheological properties. The nanoclay's addition increased the shear viscosity at low shear rates, changing the behavior of HDPE/LLDPE matrix to a Bingham model behavior with an apparent yield stress. Intense interactions were obtained for the blending sequence where LLDPE and/or LLDPE-g-MA were first reinforced with organoclay since the intercalation process occurs preferentially in the amorphous phase. (author)

217

Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes  

DEFF Research Database (Denmark)

The hydrolases and transferases that constitute the alpha-amylase family are multidomain proteins, but each has a catalytic domain in the form of a (beta/alpha)(8)-barrel, with the active site being at the C-terminal end of the barrel beta-strands. Although the enzymes are believed to share the same catalytic acids and a common mechanism of action, they have been assigned to three separate families - 13, 70 and 77 - in the classification scheme for glycoside hydrolases and transferases that is based on amino acid sequence similarities. Each enzyme has one glutamic acid and two aspartic acid residues necessary for activity, while most enzymes of the family also contain two histidine residues critical for transition state stabilisation. These five residues occur in four short sequences conserved throughout the family, and within such sequences some key amino acid residues are related to enzyme specificity. A table is given showing motifs distinctive for each specificity as extracted from 316 sequences, which should aid in identifying the enzyme from primary structure information. Where appropriate, existing problems with identification of some enzymes of the family are pointed out. For enzymes of known three-dimensional structure, action is discussed in terms of molecular architecture. The sequence-specificity and structure-specificity relationships described may provide useful pointers for rational protein engineering.

MacGregor, E. A.; Janecek, S.

2001-01-01

218

Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background RNA-binding proteins (RBPs play diverse roles in eukaryotic RNA processing. Despite their pervasive functions in coding and noncoding RNA biogenesis and regulation, elucidating the sequence specificities that define protein-RNA interactions remains a major challenge. Recently, CLIP-seq (Cross-linking immunoprecipitation followed by high-throughput sequencing has been successfully implemented to study the transcriptome-wide binding patterns of SRSF1, PTBP1, NOVA and fox2 proteins. These studies either adopted traditional methods like Multiple EM for Motif Elicitation (MEME to discover the sequence consensus of RBP's binding sites or used Z-score statistics to search for the overrepresented nucleotides of a certain size. We argue that most of these methods are not well-suited for RNA motif identification, as they are unable to incorporate the RNA structural context of protein-RNA interactions, which may affect to binding specificity. Here, we describe a novel model-based approach--RNAMotifModeler to identify the consensus of protein-RNA binding regions by integrating sequence features and RNA secondary structures. Results As an example, we implemented RNAMotifModeler on SRSF1 (SF2/ASF CLIP-seq data. The sequence-structural consensus we identified is a purine-rich octamer 'AGAAGAAG' in a highly single-stranded RNA context. The unpaired probabilities, the probabilities of not forming pairs, are significantly higher than negative controls and the flanking sequence surrounding the binding site, indicating that SRSF1 proteins tend to bind on single-stranded RNA. Further statistical evaluations revealed that the second and fifth bases of SRSF1octamer motif have much stronger sequence specificities, but weaker single-strandedness, while the third, fourth, sixth and seventh bases are far more likely to be single-stranded, but have more degenerate sequence specificities. Therefore, we hypothesize that nucleotide specificity and secondary structure play complementary roles during binding site recognition by SRSF1. Conclusion In this study, we presented a computational model to predict the sequence consensus and optimal RNA secondary structure for protein-RNA binding regions. The successful implementation on SRSF1 CLIP-seq data demonstrates great potential to improve our understanding on the binding specificity of RNA binding proteins.

Wang Xin

2011-12-01

219

Reading the three-dimensional structure of a protein from its amino acid sequence  

CERN Document Server

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of a protein whose sequence is known. This situation is not particularly satisfactory, in keeping with the fact that while linear sequencing of the amino acids specifying a protein is relatively simple to carry out, the determination of the folded-native-conformation can only be done by an elaborate X-ray diffraction analysis performed on crystals of the protein or, if the protein is very small, by nuclear magnetic resonance techniques. Using insight obtained from lattice model simulations of the folding of small proteins (fewer than 100 residues), in particular of the fact that this phenomenon is essentially controlled by conserved contacts among strongly interacting amino acids, which also stabilize local elementary structures formed early in the folding process and leading...

Broglia, R A

2000-01-01

220

Sequence of the human 40-kDa keratin reveals an unusual structure with very high sequence identity to the corresponding bovine keratin  

International Nuclear Information System (INIS)

The complete amino acid and DNA sequences of the human 40-kDa keratin are reported. The DNA sequence encodes a protein of 44,098 Da, which is unique in that it lacks the terminal non-?-helical tail segment found in all other keratins. When the human 40-kDa keratin amino acid sequence is compared to the corresponding bovine keratin, the overall identity is 89%. The coil-forming regions are 89% identical and the head regions are 88% identical. This similarity is also evident in the DNA sequence of the coding region, the 5' upstream sequences, and the 3' noncoding sequences. The high degree of cross-species identity between bovine and human 40-kDa keratins suggests that there is strong evolutionary pressure to conserve the structure of this keratin. This in turn suggests an important and universal role for this intermediate filament subunit in all species

 
 
 
 
221

Folding pathways of proteins with increasing degree of sequence identities but different structure and function.  

Science.gov (United States)

Much experimental work has been devoted in comparing the folding behavior of proteins sharing the same fold but different sequence. The recent design of proteins displaying very high sequence identities but different 3D structure allows the unique opportunity to address the protein-folding problem from a complementary perspective. Here we explored by ?-value analysis the pathways of folding of three different heteromorphic pairs, displaying increasingly high-sequence identity (namely, 30%, 77%, and 88%), but different structures called G(A) (a 3-? helix fold) and G(B) (an ?/? fold). The analysis, based on 132 site-directed mutants, is fully consistent with the idea that protein topology is committed very early along the pathway of folding. Furthermore, data reveals that when folding approaches a perfect two-state scenario, as in the case of the G(A) domains, the structural features of the transition state appear very robust to changes in sequence composition. On the other hand, when folding is more complex and multistate, as for the G(B)s, there are alternative nuclei or accessible pathways that can be alternatively stabilized by altering the primary structure. The implications of our results in the light of previous work on the folding of different members belonging to the same protein family are discussed. PMID:22652570

Giri, Rajanish; Morrone, Angela; Travaglini-Allocatelli, Carlo; Jemth, Per; Brunori, Maurizio; Gianni, Stefano

2012-10-30

222

Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information  

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Full Text Available Abstract Background Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to known structures is available. Structural properties are also routinely used in protein analysis even when homology is available, largely because homology modelling is lower throughput than, say, secondary structure prediction. Nonetheless, predictors of secondary structure and solvent accessibility are virtually always ab initio. Results Here we develop high-throughput machine learning systems for the prediction of protein secondary structure and solvent accessibility that exploit homology to proteins of known structure, where available, in the form of simple structural frequency profiles extracted from sets of PDB templates. We compare these systems to their state-of-the-art ab initio counterparts, and with a number of baselines in which secondary structures and solvent accessibilities are extracted directly from the templates. We show that structural information from templates greatly improves secondary structure and solvent accessibility prediction quality, and that, on average, the systems significantly enrich the information contained in the templates. For sequence similarity exceeding 30%, secondary structure prediction quality is approximately 90%, close to its theoretical maximum, and 2-class solvent accessibility roughly 85%. Gains are robust with respect to template selection noise, and significant for marginal sequence similarity and for short alignments, supporting the claim that these improved predictions may prove beneficial beyond the case in which clear homology is available. Conclusion The predictive system are publicly available at the address http://distill.ucd.ie.

Vullo Alessandro

2007-06-01

223

A sequence-based survey of the complex structural organization of tumor genomes  

Energy Technology Data Exchange (ETDEWEB)

The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using End Sequencing Profiling (ESP), which relies on paired-end sequencing of cloned tumor genomes. In this study, brain, breast, ovary and prostate tumors along with three breast cancer cell lines were surveyed with ESP yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent. Sequencing and fluorescence in situ hybridization (FISH) confirmed translocations and complex tumor genome structures that include coamplification and packaging of disparate genomic loci with associated molecular heterogeneity. Comparison of the tumor genomes suggests recurrent rearrangements. Some are likely to be novel structural polymorphisms, whereas others may be bona fide somatic rearrangements. A recurrent fusion transcript in breast tumors and a constitutional fusion transcript resulting from a segmental duplication were identified. Analysis of end sequences for single nucleotide polymorphisms (SNPs) revealed candidate somatic mutations and an elevated rate of novel SNPs in an ovarian tumor. These results suggest that the genomes of many epithelial tumors may be far more dynamic and complex than previously appreciated and that genomic fusions including fusion transcripts and proteins may be common, possibly yielding tumor-specific biomarkers and therapeutic targets.

Collins, Colin; Raphael, Benjamin J.; Volik, Stanislav; Yu, Peng; Wu, Chunxiao; Huang, Guiqing; Linardopoulou, Elena V.; Trask, Barbara J.; Waldman, Frederic; Costello, Joseph; Pienta, Kenneth J.; Mills, Gordon B.; Bajsarowicz, Krystyna; Kobayashi, Yasuko; Sridharan, Shivaranjani; Paris, Pamela; Tao, Quanzhou; Aerni, Sarah J.; Brown, Raymond P.; Bashir, Ali; Gray, Joe W.; Cheng, Jan-Fang; de Jong, Pieter; Nefedov, Mikhail; Ried, Thomas; Padilla-Nash, Hesed M.; Collins, Colin C.

2008-04-03

224

The nucleotide sequence and genome structure of mung bean yellow mosaic geminivirus.  

Science.gov (United States)

Complete nucleotide sequences of the infectious cloned DNA components (DNA 1 and DNA 2) of mung bean yellow mosaic virus (MYMV) were determined. MYMV DNA 1 and DNA 2 consists of 2,723 and 2,675 nucleotides respectively. DNA 1 and DNA 2 have little sequence similarity except for a region of approximately 200 bases which is almost identical in the two molecules. Analysis of open reading frames revealed nine potential coding regions for proteins of mol. wt. > 10,000, six in DNA 1 and three in DNA 2. The nucleotide sequence of MYMV DNA was compared with that of bean golden mosaic virus (BGMV), tomato golden mosaic virus (TGMV) and African cassava mosaic virus (ACMV). The 200-base region common to the two DNAs of each virus had little sequence similarity, except for a highly conserved 33-36 base sequence potentially capable of forming a stable hairpin structure. The potential coding regions in the MYMV DNAs had counterparts in the BGMV, TGMV and ACMV, suggesting an overall similarity in genome organization, except for absence of 1L3 in MYMV DNA 1. The most highly conserved ORFs, MYMV 1R1, BGMV 1R1, TGMV 1R1 and ACMV 1R1, are the putative genes for the coat proteins of MYMV, BGMV, TGMV and ACMV, respectively. MYMV 1L1 has also a high degree of sequence similarity with BGMV 1L1, TGMV 1L1 and ACMV 1L1. PMID:8231962

Morinaga, T; Ikegami, M; Miura, K

1993-01-01

225

Can Clustal-style progressive pairwise alignment of multiple sequences be used in RNA secondary structure prediction?  

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Full Text Available Abstract Background In ribonucleic acid (RNA molecules whose function depends on their final, folded three-dimensional shape (such as those in ribosomes or spliceosome complexes, the secondary structure, defined by the set of internal basepair interactions, is more consistently conserved than the primary structure, defined by the sequence of nucleotides. Results The research presented here investigates the possibility of applying a progressive, pairwise approach to the alignment of multiple RNA sequences by simultaneously predicting an energy-optimized consensus secondary structure. We take an existing algorithm for finding the secondary structure common to two RNA sequences, Dynalign, and alter it to align profiles of multiple sequences. We then explore the relative successes of different approaches to designing the tree that will guide progressive alignments of sequence profiles to create a multiple alignment and prediction of conserved structure. Conclusion We have found that applying a progressive, pairwise approach to the alignment of multiple ribonucleic acid sequences produces highly reliable predictions of conserved basepairs, and we have shown how these predictions can be used as constraints to improve the results of a single-sequence structure prediction algorithm. However, we have also discovered that the amount of detail included in a consensus structure prediction is highly dependent on the order in which sequences are added to the alignment (the guide tree, and that if a consensus structure does not have sufficient detail, it is less likely to provide useful constraints for the single-sequence method.

Turcotte Marcel

2007-06-01

226

Bioinformatical approaches to RNA structure prediction & Sequencing of an ancient human genome  

DEFF Research Database (Denmark)

Stinus Lindgreen has been working in two different fields during his Ph.D. The first part has been focused on computational approaches to predict the structure of non-coding RNA molecules at the base pairing level. This has resulted in the analysis of various measures of the base pairing potential in families of related RNA sequences. Also, the program MASTR was developed to perform simultaneous alignment of multiple RNA sequences and prediction of a common secondary structure. The webserver WAR was developed to make it easy for non-computer savy researchers to use the many RNA structure prediction tools that exist. The second part has been focused on the mapping and genotyping of ancient genomic DNA. The development of next generation sequencing technologies combined with the use of ancient DNA material present the researchers with some special challenges in the analyses. This work resulted in the publication of the first genome of an ancient human individual, where close to the theoretical maximum of the genome sequence was recovered with high confidence. Part of the project was the development of the program SNPest for genotyping and SNP calling that models various sources of error and predicts genotypes with the highest posterior probability.

Lindgreen, Stinus

2010-01-01

227

Large scale identification and categorization of protein sequences using structured logistic regression  

DEFF Research Database (Denmark)

Structured Logistic Regression (SLR) is a newly developed machine learning tool first proposed in the context of text categorization. Current availability of extensive protein sequence databases calls for an automated method to reliably classify sequences and SLR seems well-suited for this task. The classification of P-type ATPases, a large family of ATP-driven membrane pumps transporting essential cations, was selected as a test-case that would generate important biological information as well as provide a proof-of-concept for the application of SLR to a large scale bioinformatics problem.

Pedersen, BjØrn Panella; Ifrim, Georgiana

2014-01-01

228

Studies on structure-based sequence alignment and phylogenies of beta-lactamases.  

Science.gov (United States)

The ?-lactamases enzymes cleave the amide bond in ?-lactam ring, rendering ?-lactam antibiotics harmless to bacteria. In this communication we have studied structure-function relationship and phylogenies of class A, B and D beta-lactamases using structure-based sequence alignment and phylip programs respectively. The data of structure-based sequence alignment suggests that in different isolates of TEM-1, mutations did not occur at or near sequence motifs. Since deletions are reported to be lethal to structure and function of enzyme. Therefore, in these variants antibiotic hydrolysis profile and specificity will be affected. The alignment data of class A enzyme SHV-1, CTX-M-15, class D enzyme, OXA-10, and class B enzyme VIM-2 and SIM-1 show sequence motifs along with other part of polypeptide are essentially conserved. These results imply that conformations of betalactamases are close to native state and possess normal hydrolytic activities towards beta-lactam antibiotics. However, class B enzyme such as IMP-1 and NDM-1 are less conserved than other class A and D studied here because mutation and deletions occurred at critically important region such as active site. Therefore, the structure of these beta-lactamases will be altered and antibiotic hydrolysis profile will be affected. Phylogenetic studies suggest that class A and D beta-lactamases including TOHO-1 and OXA-10 respectively evolved by horizontal gene transfer (HGT) whereas other member of class A such as TEM-1 evolved by gene duplication mechanism. Taken together, these studies justify structure-function relationship of beta-lactamases and phylogenetic studies suggest these enzymes evolved by different mechanisms. PMID:24966539

Salahuddin, Parveen; Khan, Asad U

2014-01-01

229

Identification of microRNA precursors with new sequence-structure features  

Digital Repository Infrastructure Vision for European Research (DRIVER)

MicroRNAs are an important subclass of non-coding RNAs (ncRNA), and serve as main players into RNA interference (RNAi). Mature microRNA derived from stem-loop structure called precursor. Identification of precursor microRNA (pre-miRNA) is essential step to target microRNA in whole genome. The present work proposed 25 novel local features for identifying stem- loop structure of pre-miRNAs, which captures characteristics on both the sequence and structure. Firstly, we pulled the stem of hairpin...

Ying-Jie Zhao; Qing-Shan Ni; Zheng-Zhi Wang

2009-01-01

230

Structural Sequences of Group IV Transition Metals Under Ultra-High Pressure.  

Science.gov (United States)

Crystal structures of many elemental metals tend to have certain structural sequences when viewed as functions of atomic number. Transition metals are known to have hcp - bcc - hcp - fcc structural sequence when viewed as a function of atomic number. This thesis work gives the first experimental evidence of a pressure-induced structural sequence in transition metals and, fro ma crystal structure point of view, the first experimental evidence of a pressure -induced phase transformation from a group IV transition metal to a group V transition metal. High pressure energy dispersive X-ray diffraction (EDXD) studies were carried out on group IV transition metals hafnium (Hf) to 252 GPa, zirconium (ZR) to 36 GPa, and titinium (Ti) to 209 GPa at room temperature by using synchrotron X-ray source. all the three group IV transition metals have a hcp structure at room pressure and have an omega phase in an intermediate pressure range. At ultra high pressure a new structural phase transformation between the omega phase and a bcc phase (isostructural with group V transition metals) was observed in Hf and Zr. Equilibrium transformation pressures for the hcp to omega, the omega to bcc phase transformations at room temperature are 38 +/- 8 GPa, 71 +/- 1 GPa for Hf and 2.2 GPa, 35 +/- 5 GPa for Zr, respectively. In Ti, only the hcp to omega phase transition was observed above 8 GPa and the omega phase was stable to at least 87 GPa. The Equations of state of these group IV transition metals were obtained, which indicates that these omega -bcc phase transformations are first-order phase transitions accompanying with a volume change of 1.5% decrease for Zr and 2.1% decrease for Hf. High pressure/high temperature energy dispersive x-ray diffraction studies were also carried out on Zr metal to 36 GPa to investigate the thermal (entropy) contribution to the structural sequences in transition metals. A negative slope of 39 +/- 5 ^ {o}K/GPa along the omega-bcc phase boundary was observed in this experiment, which gives the first experimental evidence indicating thermal (entropy) contribution to the structural sequences in transition metals and shows that the omega phase of Zr metal has lower entropy than in its pressure-induced bcc phase (isostructural with a group V transition metal).

Xia, Hui

1991-05-01

231

A 1-D dusty plasma photonic crystal  

Energy Technology Data Exchange (ETDEWEB)

It is demonstrated numerically that a 1-D plasma crystal made of micron size cylindrical dust particles can, in principle, work as a photonic crystal for terahertz waves. The dust rods are parallel to each other and arranged in a linear string forming a periodic structure of dielectric-plasma regions. The dispersion equation is found by solving the waves equation with the boundary conditions at the dust-plasma interface and taking into account the dielectric permittivity of the dust material and plasma. The wavelength of the electromagnetic waves is in the range of a few hundred microns, close to the interparticle separation distance. The band gaps of the 1-D plasma crystal are numerically found for different types of dust materials, separation distances between the dust rods and rod diameters. The distance between levitated dust rods forming a string in rf plasma is shown experimentally to vary over a relatively wide range, from 650 ?m to about 1350 ?m, depending on the rf power fed into the discharge.

Mitu, M. L.; Tico?, C. M. [National Institute for Laser, Plasma and Radiation Physics, 077125 Bucharest (Romania); Toader, D.; Banu, N.; Scurtu, A. [National Institute for Laser, Plasma and Radiation Physics, 077125 Bucharest (Romania); Department of Physics, University of Bucharest, 077125 Bucharest (Romania)

2013-09-21

232

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments  

Science.gov (United States)

This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee. PMID:24972831

Di Tommaso, Paolo; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

2014-01-01

233

A structural study for the optimisation of functional motifs encoded in protein sequences  

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Full Text Available Abstract Background A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that – at least in some cases – the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more, functional and/or structural key residues are not represented in the pattern. Multiple sequence alignments are commonly used to build functional sequence patterns. If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure. Results Here we present a new procedure aimed at improving the sensitivity and/ or specificity of poorly-performing patterns. The procedure can be summarised as follows: 1. residues structurally conserved in different proteins, that are true positives for a pattern, are identified by means of a computational technique and by visual inspection. 2. the sequence positions of the structurally conserved residues falling outside the pattern are used to build extended sequence patterns. 3. the extended patterns are optimised on the SWISS-PROT database for their sensitivity and specificity. The method was applied to eight PROSITE patterns. Whenever structurally conserved residues are found in the surface region close to the pattern (seven out of eight cases, the addition of information inferred from structural analysis is shown to improve pattern selectivity and in some cases selectivity and sensitivity as well. In some of the cases considered the procedure allowed the identification of functionally interesting residues, whose biological role is also discussed. Conclusion Our method can be applied to any type of functional motif or pattern (not only PROSITE ones which is not able to select all and only the true positive hits and for which at least two true positive structures are available. The computational technique for the identification of structurally conserved residues is already available on request and will be soon accessible on our web server. The procedure is intended for the use of pattern database curators and of scientists interested in a specific protein family for which no specific or selective patterns are yet available.

Helmer-Citterich Manuela

2004-04-01

234

Stabilization of the fibrous structure of an ?-helix-forming peptide by sequence reversal  

International Nuclear Information System (INIS)

The ?3-peptide, which comprises three repeats of the sequence Leu-Glu-Thr-Leu-Ala-Lys-Ala and forms an amphipathic ?-helix, is unique among various ?-helix-forming peptides in that it assembles into fibrous structures that can be observed by transmission electron microscopy. As part of our investigation of the structure-stability relationships of the ?3-peptide, we synthesized the r3-peptide, whose amino acid sequence is the reverse of that of the ?3-peptide, and we investigated the effects of sequence reversal on ?-helix stability and the formation of fibrous structures. Unexpectedly, the r3-peptide formed a more-stable ?-helix and longer fibers than did the ?3-peptide. The stability of the r3-peptide helix decreased when the ionic strength of the buffer was increased and when the pH of the buffer was adjusted to 2 or 12. These results suggest that the r3-peptide underwent a 'magnet-like' oligomerization and that an increase in the charge-distribution inequality may be the driving force for the formation of fibrous structures

235

Sequence co-evolution gives 3D contacts and structures of protein complexes.  

Science.gov (United States)

Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein-protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein-protein interaction networks and used for interaction predictions at residue resolution. PMID:25255213

Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

2014-01-01

236

Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships.  

Science.gov (United States)

Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 ?- and ?-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as "core" for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf) yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification provides the bases for new analyses of the three-dimensional structure and for mutagenesis studies. PMID:24019874

Howard, James B; Kechris, Katerina J; Rees, Douglas C; Glazer, Alexander N

2013-01-01

237

Amino acid sequences and structures of chicken and turkey beta 2-microglobulin.  

DEFF Research Database (Denmark)

The complete amino acid sequences of chicken and turkey beta 2-microglobulins have been determined by analyses of tryptic, V8-proteolytic and cyanogen bromide fragments, and by N-terminal sequencing. Mass spectrometric analysis of chicken beta 2-microglobulin supports the sequence-derived Mr of 11,048. The higher apparent Mr obtained for the avian beta 2-microglobulins as compared to human beta 2-microglobulin by SDS-PAGE is not understood. Chicken and turkey beta 2-microglobulin consist of 98 residues and deviate at seven positions: 60, 66, 74-76, 78 and 82. The chicken and turkey sequences are identical to human beta 2-microglobulin at 46 and 47 positions, respectively, and to bovine beta 2-microglobulin at 47 positions, i.e. there is about 47% identity between avian and mammalian beta 2-microglobulins. The known X-ray crystallographic structures of bovine beta 2-microglobulin and human HLA-A2 complex suggest that the seven chicken to turkey differences are exposed to solvent in the avian MHC class I complex. The key residues of beta 2-microglobulin involved in alpha chain contacts within the MHC class I molecule are highly conserved between chicken and man. This explains that heterologous human beta 2-microglobulin can substitute the chicken beta 2-microglobulin in exchange studies with B-F (chicken MHC class I molecule), and suggests that the MHC class I structure is conserved over long evolutionary distances. Udgivelsesdato: null-null

SkjØdt, K

1991-01-01

238

An anatomically structured sensory-motor sequence learning system displays some general linguistic capacities.  

Science.gov (United States)

The capacity in primates to master temporal-sequential constraints from the external world might provide a basis for accommodating similar constraints in language. While the neural specialization required for language clearly distinguishes man from the other primates, it is less clear to what extent this specialization constitutes a drastic neurophysiological divergence versus a variation on an existing sequencing capability. In an effort to address this issue, an anatomically structured neural network model, previously developed to reproduce complex sensory-motor sequences and the corresponding single-unit recordings from primate prefrontal cortex, is studied in a simple linguistic context. The model is presented sentences from a small language and demonstrates a simple capacity to "understand" and generalize at different levels. Interactions between variations on (a) the model architecture and (b) the target language structure agree with data from crosslinguistic aphasia studies. These results support the hypothesis that a brain architecture for nonlinguistic cognitive functions (in this case sensory-motor sequencing) can provide a basis for a general sequence processing component of linguistic function. PMID:9262851

Dominey, P F

1997-08-01

239

ERP analysis of cognitive sequencing: a left anterior negativity related to structural transformation processing.  

Science.gov (United States)

A major objective of cognitive neuroscience is to identify those neurocomputational processes that may be shared by multiple cognitive functions vs those that are highly specific. This problem of identifying general vs specialized functions is of particular interest in the domain of language processing. Within this domain, event related brain potential (ERP) studies have demonstrated a left anterior negativity (LAN) in a range 300-700 ms, associated with syntactic processing, often linked to grammatical function words. These words have little or no semantic content, but rather play a role in encoding syntactic structure required for parsing. In the current study we test the hypothesis that the LAN reflects the operation of a more general sequence processing capability in which special symbols encode structural information that, when combined with past elements in the sequence, allows the prediction of successor elements. We recorded ERPs during a non-linguistic sequencing task that required subjects (n = 10) to process special symbols possessing the functional property defined above. When compared to ERPs in a control condition, function symbol processing elicits a left anterior negative shift between temporal and spatial characteristics quite similar to the LAN described during function word processing in language, supporting our hypothesis. These results are discussed in the context of related studies of syntactic and cognitive sequence processing. PMID:11043546

Hoen, M; Dominey, P F

2000-09-28

240

Describing sequencing results of structural chromosome rearrangements with a suggested next-generation cytogenetic nomenclature.  

Science.gov (United States)

With recent rapid advances in genomic technologies, precise delineation of structural chromosome rearrangements at the nucleotide level is becoming increasingly feasible. In this era of "next-generation cytogenetics" (i.e., an integration of traditional cytogenetic techniques and next-generation sequencing), a consensus nomenclature is essential for accurate communication and data sharing. Currently, nomenclature for describing the sequencing data of these aberrations is lacking. Herein, we present a system called Next-Gen Cytogenetic Nomenclature, which is concordant with the International System for Human Cytogenetic Nomenclature (2013). This system starts with the alignment of rearrangement sequences by BLAT or BLAST (alignment tools) and arrives at a concise and detailed description of chromosomal changes. To facilitate usage and implementation of this nomenclature, we are developing a program designated BLA(S)T Output Sequence Tool of Nomenclature (BOSToN), a demonstrative version of which is accessible online. A standardized characterization of structural chromosomal rearrangements is essential both for research analyses and for application in the clinical setting. PMID:24746958

Ordulu, Zehra; Wong, Kristen E; Currall, Benjamin B; Ivanov, Andrew R; Pereira, Shahrin; Althari, Sara; Gusella, James F; Talkowski, Michael E; Morton, Cynthia C

2014-05-01

 
 
 
 
241

IMPROVEMENTS OF RIVER MODELING 1D DATA PREPARATION  

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Full Text Available Improvements of river modeling 1D data preparation. The importance of hydrographical networks data and the need for detailed studies do generate an increase of projects in this specialized area and a diversification of river mathematical modeling software. River mathematical modeling can be done in two ways, namely; the "2D mode" and the “1D mode”. The “2D mode” is where a digital terrain model of a full hydrographical basin must be produced and "1D mode" is where only cross sections, long sections and structures elevations needs to be presented in a graphical environment and in a specific formats for the mathematical modeling software. This paper will show the principle of a custom built GIS, specially created to help the preparation of 1D river modeling data. The benefits are; elimination of human errors, automated processing, increasing productivity, flexible output and cost reduction.

ION-MARIAN MOISOIU

2012-11-01

242

MultiSeq: unifying sequence and structure data for evolutionary analysis  

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Full Text Available Abstract Background Since the publication of the first draft of the human genome in 2000, bioinformatic data have been accumulating at an overwhelming pace. Currently, more than 3 million sequences and 35 thousand structures of proteins and nucleic acids are available in public databases. Finding correlations in and between these data to answer critical research questions is extremely challenging. This problem needs to be approached from several directions: information science to organize and search the data; information visualization to assist in recognizing correlations; mathematics to formulate statistical inferences; and biology to analyze chemical and physical properties in terms of sequence and structure changes. Results Here we present MultiSeq, a unified bioinformatics analysis environment that allows one to organize, display, align and analyze both sequence and structure data for proteins and nucleic acids. While special emphasis is placed on analyzing the data within the framework of evolutionary biology, the environment is also flexible enough to accommodate other usage patterns. The evolutionary approach is supported by the use of predefined metadata, adherence to standard ontological mappings, and the ability for the user to adjust these classifications using an electronic notebook. MultiSeq contains a new algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of a homologous group of distantly related proteins. The method, based on the multidimensional QR factorization of multiple sequence and structure alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. Conclusion MultiSeq is a major extension of the Multiple Alignment tool that is provided as part of VMD, a structural visualization program for analyzing molecular dynamics simulations. Both are freely distributed by the NIH Resource for Macromolecular Modeling and Bioinformatics and MultiSeq is included with VMD starting with version 1.8.5. The MultiSeq website has details on how to download and use the software: http://www.scs.uiuc.edu/~schulten/multiseq/

Wright Dan

2006-08-01

243

De novo prediction of structured RNAs from genomic sequences  

DEFF Research Database (Denmark)

Growing recognition of the numerous, diverse and important roles played by non-coding RNA in all organisms motivates better elucidation of these cellular components. Comparative genomics is a powerful tool for this task and is arguably preferable to any high-throughput experimental technology currently available, because evolutionary conservation highlights functionally important regions. Conserved secondary structure, rather than primary sequence, is the hallmark of many functionally important RNAs, because compensatory substitutions in base-paired regions preserve structure. Unfortunately, such substitutions also obscure sequence identity and confound alignment algorithms, which complicates analysis greatly. This paper surveys recent computational advances in this difficult arena, which have enabled genome-scale prediction of cross-species conserved RNA elements. These predictions suggest that a wealth of these elements indeed exist

Gorodkin, Jan; Hofacker, Ivo L.

2010-01-01

244

Comparative mapping of sequence-based and structure-based protein domains  

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Full Text Available Abstract Background Protein domains have long been an ill-defined concept in biology. They are generally described as autonomous folding units with evolutionary and functional independence. Both structure-based and sequence-based domain definitions have been widely used. But whether these types of models alone can capture all essential features of domains is still an open question. Methods Here we provide insight on domain definitions through comparative mapping of two domain classification databases, one sequence-based (Pfam and the other structure-based (SCOP. A mapping score is defined to indicate the significance of the mapping, and the properties of the mapping matrices are studied. Results The mapping results show a general agreement between the two databases, as well as many interesting areas of disagreement. In the cases of disagreement, the functional and evolutionary characteristics of the domains are examined to determine which domain definition is biologically more informative.

Chandonia John-Marc

2005-03-01

245

Sequence- and structure-dependent DNA base dynamics: Synthesis, structure, and dynamics of site and sequence specifically spin-labeled DNA  

International Nuclear Information System (INIS)

A nitroxide spin-labeled analogue of thymidine (1a), in which the methyl group is replaced by an acetylene-tethered nitroxide, was evaluated as a probe for structural and dynamics studies of sequence specifically spin-labeled DNA. Residue 1a was incorporated into synthetic deoxyoligonucleotides by using automated phosphite triester methods. 1H NMR, CD, and thermal denaturation studies indicate that 1a (T) does not significantly alter the structure of 5'-d(CGCGAATT*CGCG) from that of the native dodecamer. EPR studies on monomer, single-stranded, and duplexed DNA show that 1a readily distinguishes environments of different rigidity. Comparison of the general line-shape features of the observed EPR spectra of several small duplexes (12-mer, 24-mer) with simulated EPR spectra assuming isotropic motion suggests that probe 1a monitors global tumbling of small duplexes. Increasing the length of the DNA oligomers results in significant deviation from isotropic motion, with line-shape features similar to those of calculated spectra of objects with isotropic rotational correlation times of 20-100 ns. EPR spectra of a spin-labeled GT mismatch and a T bulge in long DNAs are distinct from those of spin-labeled Watson-Crick paired DNAs, further demonstrating the value of EPR as a tool in the evaluation of local dynamic and structural features in macromolecules

246

Fluorescence energy transfer as a probe for nucleic acid structures and sequences.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The primary or secondary structure of single-stranded nucleic acids has been investigated with fluorescent oligonucleotides, i.e., oligonucleotides covalently linked to a fluorescent dye. Five different chromophores were used: 2-methoxy-6-chloro-9-amino-acridine, coumarin 500, fluorescein, rhodamine and ethidium. The chemical synthesis of derivatized oligonucleotides is described. Hybridization of two fluorescent oligonucleotides to adjacent nucleic acid sequences led to fluorescence excitati...

Mergny, J. L.; Boutorine, A. S.; Garestier, T.; Belloc, F.; Rouge?e, M.; Bulychev, N. V.; Koshkin, A. A.; Bourson, J.; Lebedev, A. V.; Valeur, B.

1994-01-01

247

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Motivation: Predicting RNA–RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods for the prediction of interactions are all based on single sequences. Since comparative methods have already been useful in RNA structure determination, we assume that conserved RNA–RNA interactions also imply conserved function. Of these, we further assume that a non-negligible amount of the existing RNA–RNA interactions have also acquired compensating bas...

Seemann, Stefan E.; Richter, Andreas S.; Gesell, Tanja; Backofen, Rolf; Gorodkin, Jan

2011-01-01

248

Retinoblastoma susceptibility genes contain 5' sequences with a high propensity to form guanine-tetrad structures.  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Retinoblastoma susceptibility genes contain significant runs of oligoguanine at their 5' ends. Oligonucleotides having these sequences underwent complex formation in the presence of sodium ions, in which there was association of four strands. Formation of this structure was completely prevented if guanine was replaced by 7-deazaguanine, indicating the importance of guanine N7 in the formation of the complex. Complex formation lead to protection of guanine N7 against methylation by dimethyl su...

Murchie, A. I.; Lilley, D. M.

1992-01-01

249

Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq  

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The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution and population structure. Here, we apply a multiplexed, reduced genome sequencing strategy (known as RAD-seq) to genotype a large collection of S. cerevisiae ...

Cromie, Gareth A.; Hyma, Katie E.; Ludlow, Catherine L.; Garmendia-torres, Cecilia; Gilbert, Teresa L.; May, Patrick; Huang, Angela A.; Dudley, Aime?e M.; Fay, Justin C.

2013-01-01

250

Improving protein structure prediction using multiple sequence-based contact predictions  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Although residue-residue contact maps dictate the topology of proteins, sequence-based ab initio contact predictions have been found little use in actual structure prediction due to the low accuracy. We developed a composite set of nine SVM-based contact predictors which are used in I-TASSER simulation in combination with sparse template contact restraints. When testing the strategy on 273 non-homologous targets, remarkable improvements of I-TASSER models were observed for both easy and hard ...

Wu, Sitao; Szilagyi, Andras; Zhang, Yang

2011-01-01

251

PETcofold : predicting conserved interactions and structures of two multiple alignments of RNA sequences  

DEFF Research Database (Denmark)

MOTIVATION: Predicting RNA-RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods for the prediction of interactions are all based on single sequences. Since comparative methods have already been useful in RNA structure determination, we assume that conserved RNA-RNA interactions also imply conserved function. Of these, we further assume that a non-negligible amount of the existing RNA-RNA interactions have also acquired compensating base changes throughout evolution. We implement a method, PETcofold, that can take covariance information in intra-molecular and inter-molecular base pairs into account to predict interactions and secondary structures of two multiple alignments of RNA sequences. RESULTS: PETcofold's ability to predict RNA-RNA interactions was evaluated on a carefully curated dataset of 32 bacterial small RNAs and their targets, which was manually extracted from the literature. For evaluation of both RNA-RNA interaction and structure prediction, we were able to extract only a few high-quality examples: one vertebrate small nucleolar RNA and four bacterial small RNAs. For these we show that the prediction can be improved by our comparative approach. Furthermore, PETcofold was evaluated on controlled data with phylogenetically simulated sequences enriched for covariance patterns at the interaction sites. We observed increased performance with increased amounts of covariance. AVAILABILITY: The program PETcofold is available as source code and can be downloaded from http://rth.dk/resources/petcofold. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Seemann, Ernst Stefan; Richter, Andreas S.

2011-01-01

252

Revised Mimivirus major capsid protein sequence reveals intron-containing gene structure and extra domain  

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Full Text Available Abstract Background Acanthamoebae polyphaga Mimivirus (APM is the largest known dsDNA virus. The viral particle has a nearly icosahedral structure with an internal capsid shell surrounded with a dense layer of fibrils. A Capsid protein sequence, D13L, was deduced from the APM L425 coding gene and was shown to be the most abundant protein found within the viral particle. However this protein remained poorly characterised until now. A revised protein sequence deposited in a database suggested an additional N-terminal stretch of 142 amino acids missing from the original deduced sequence. This result led us to investigate the L425 gene structure and the biochemical properties of the complete APM major Capsid protein. Results This study describes the full length 3430 bp Capsid coding gene and characterises the 593 amino acids long corresponding Capsid protein 1. The recombinant full length protein allowed the production of a specific monoclonal antibody able to detect the Capsid protein 1 within the viral particle. This protein appeared to be post-translationnally modified by glycosylation and phosphorylation. We proposed a secondary structure prediction of APM Capsid protein 1 compared to the Capsid protein structure of Paramecium Bursaria Chlorella Virus 1, another member of the Nucleo-Cytoplasmic Large DNA virus family. Conclusion The characterisation of the full length L425 Capsid coding gene of Acanthamoebae polyphaga Mimivirus provides new insights into the structure of the main Capsid protein. The production of a full length recombinant protein will be useful for further structural studies.

Suzan-Monti Marie

2009-05-01

253

Fast computational methods for predicting protein structure from primary amino acid sequence  

Science.gov (United States)

The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.

Agarwal, Pratul Kumar (Knoxville, TN)

2011-07-19

254

Hypotheses that correlate the sequence, structure, and mechanical properties of spider silk proteins.  

Science.gov (United States)

Several types of silks and silk protein coding genes have been characterized from orb-web weaving spiders. When the protein sequences of major ampullate, minor ampullate, and flagelliform silks from Nephila clavipes are compared, they can be summarized as sets of shared amino acid motifs. Four of these motifs and their likely secondary structures are described. Each structural element, termed a module, is then associated with its impact on the mechanical properties of a silk fiber. In particular, correlations are drawn between an alanine-rich 'crystalline module' and tensile strength and between a proline-containing 'elasticity module' and extensibility. PMID:10342774

Hayashi, C Y; Shipley, N H; Lewis, R V

1999-01-01

255

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis  

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Full Text Available Abstract Background Chaos Game Representation (CGR is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2-L distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations. Results The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm. Conclusions The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance and analytical (lack of unifying mathematical framework. CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems.

Vinga Susana

2012-05-01

256

Quantitative 1D saturation profiles on chalk by NMR.  

DEFF Research Database (Denmark)

Quantitative one-dimensional saturation profiles showing the distribution of water and oil in chalk core samples are calculated from NMR measurements utilizing a 1D CSI spectroscopy pulse sequence. Saturation profiles may be acquired under conditions of fluid flow through the sample. Results reveal that strong saturation gradients exist in chalk core samples after core floods, due to capillary effects. The method is useful in analysis of corefloods, e.g., for determination of capillary pressure functions

Olsen, Dan; Topp, Simon

1996-01-01

257

Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments.  

Science.gov (United States)

Primers were designed to amplify a 592-bp region within a conserved structural gene (g20) found in some cyanophages. The goal was to use this gene as a proxy to infer genetic richness in natural cyanophage communities and to determine if sequences were more similar in similar environments. Gene products were amplified from samples from the Gulf of Mexico, the Arctic, Southern, and Northeast and Southeast Pacific Oceans, an Arctic cyanobacterial mat, a catfish production pond, lakes in Canada and Germany, and a depth of ca. 3,246 m in the Chuckchi Sea. Amplicons were separated by denaturing gradient gel electrophoresis, and selected bands were sequenced. Phylogenetic analysis revealed four previously unknown groups of g20 clusters, two of which were entirely found in freshwater. Also, sequences with >99% identities were recovered from environments that differed greatly in temperature and salinity. For example, nearly identical sequences were recovered from the Gulf of Mexico, the Southern Pacific Ocean, an Arctic freshwater cyanobacterial mat, and Lake Constance, Germany. These results imply that closely related hosts and the viruses infecting them are distributed widely across environments or that horizontal gene exchange occurs among phage communities from very different environments. Moreover, the amplification of g20 products from deep in the cyanobacterium-sparse Chuckchi Sea suggests that this primer set targets bacteriophages other than those infecting cyanobacteria. PMID:15640224

Short, Cindy M; Suttle, Curtis A

2005-01-01

258

Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq  

Science.gov (United States)

The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution and population structure. Here, we apply a multiplexed, reduced genome sequencing strategy (restriction site?associated sequencing or RAD-seq) to genotype a large collection of S. cerevisiae strains isolated from a wide range of geographical locations and environmental niches. The method permits the sequencing of the same 1% of all genomes, producing a multiple sequence alignment of 116,880 bases across 262 strains. We find diversity among these strains is principally organized by geography, with European, North American, Asian, and African/S. E. Asian populations defining the major axes of genetic variation. At a finer scale, small groups of strains from cacao, olives, and sake are defined by unique variants not present in other strains. One population, containing strains from a variety of fermentations, exhibits high levels of heterozygosity and a mixture of alleles from European and Asian populations, indicating an admixed origin for this group. We propose a model of geographic differentiation followed by human-associated admixture, primarily between European and Asian populations and more recently between European and North American populations. The large collection of genotyped yeast strains characterized here will provide a useful resource for the broad community of yeast researchers. PMID:24122055

Cromie, Gareth A.; Hyma, Katie E.; Ludlow, Catherine L.; Garmendia-Torres, Cecilia; Gilbert, Teresa L.; May, Patrick; Huang, Angela A.; Dudley, Aimee M.; Fay, Justin C.

2013-01-01

259

Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs  

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Full Text Available As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson-Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunvioidae adopt multibranched conformations occasionally stabilized by kissing loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunvioidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures ?either global or local ? determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.

RicardoFlores

2012-06-01

260

Evolutionary conservation of sequence and secondary structures inCRISPR repeats  

Energy Technology Data Exchange (ETDEWEB)

Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.

Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

2006-09-01

 
 
 
 
261

Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers  

Science.gov (United States)

Motivation: Systematic Evolution of Ligands by EXponential Enrichment (SELEX) represents a state-of-the-art technology to isolate single-stranded (ribo)nucleic acid fragments, named aptamers, which bind to a molecule (or molecules) of interest via specific structural regions induced by their sequence-dependent fold. This powerful method has applications in designing protein inhibitors, molecular detection systems, therapeutic drugs and antibody replacement among others. However, full understanding and consequently optimal utilization of the process has lagged behind its wide application due to the lack of dedicated computational approaches. At the same time, the combination of SELEX with novel sequencing technologies is beginning to provide the data that will allow the examination of a variety of properties of the selection process. Results: To close this gap we developed, Aptamotif, a computational method for the identification of sequence–structure motifs in SELEX-derived aptamers. To increase the chances of identifying functional motifs, Aptamotif uses an ensemble-based approach. We validated the method using two published aptamer datasets containing experimentally determined motifs of increasing complexity. We were able to recreate the author's findings to a high degree, thus proving the capability of our approach to identify binding motifs in SELEX data. Additionally, using our new experimental dataset, we illustrate the application of Aptamotif to elucidate several properties of the selection process. Contact: przytyck@ncbi.nlm.nih.gov, Zuben.Sauna@fda.hhs.gov PMID:22689764

Hoinka, Jan; Zotenko, Elena; Friedman, Adam; Sauna, Zuben E.; Przytycka, Teresa M.

2012-01-01

262

[Freshwater sponge silicateins: comparison of sequences and exon-intron structure of genes].  

Science.gov (United States)

Siliceous sponge spicules contain silicateins--proteins taking part in biogenic silica precipitation and determination of the spicule morphological features. The exon-intron structure of four silicatein-alpha isoforms: -alpha1,-alpha2, -alpha3 and -alpha4 from endemic baikalian sponge Lubomirskia baicalensis was studied. For eight sponge species, including both cosmopolitan (Spongilla lacustris, Ephydatia muelleri, E. fluviatilis) and Baikal endemic (L. baicalensis, L. incrustans, Baikalospongia intermedia, B. fungiformis, Sw. papyracea) species, seventeen gene fragment sequences of different silicatein isoforms were determined. It was shown that cosmopolitan and endemic Baikalian sponges differ from each other by gene structure (have different length ofintrons). Among Baikalian sponges silicatein-alpha1 has the most variable intron length, and silicatein-alpha4 is the most conservative. Phylogenetic analysis of amino-acid silicatein sequences allow identify different silicatein isoforms, which authentically differ form four clusters on phylogenetic tree. Phylogenetic analysis of exon-intron sequences gives the possibility to separate different sponge species in the clusters. PMID:21954593

Kaliuzhnaia, O V; Kras'ko, A G; Grebeniuk, V A; Itskovich, V B; Semiturkina, N A; Solovarov, I S; Mueller, W E G; Belikov, S I

2011-01-01

263

Structural basis of Ets1 cooperative binding to palindromic sequences on stromelysin-1 promoter DNA  

Energy Technology Data Exchange (ETDEWEB)

Ets1 is a member of the Ets family of transcription factors. Ets1 is autoinhibited and its activation requires heterodimerization with a partner protein or DNA-mediated homodimerization for cooperative DNA binding. In the latter case, Ets1 molecules bind to palindromic sequences in which two Ets-binding sites (EBS) are separated by four base pairs, for example in the promoters of stromelysin-1 and p53. Interestingly, counteraction of autoinhibition requires the autoinhibitory region encoded by exon VII of the gene. The structural basis for the requirement of autoinhibitory sequences for Ets1 binding to palindromic EBS still remains unresolved. Here we report the crystal structure of two Ets1 molecules bound to an EBS palindrome of the stromelysin-1 promoter DNA, providing a plausible explanation for the requirement of exon VII-encoded sequences for Ets1 cooperative DNA binding. The proposed mechanism was verified both in vitro by surface plasmon resonance and in vivo by transcription-based assays.

Babayeva, Nigar D.; Wilder, Phillip J.; Shiina, Masaaki; Mino, Koshiki; Desler, Michelle; Ogata, Kazuhiro; Rizzino, Angie; Tahirov, Tahir H. (Nebraska-Med); (Yokohama)

2010-09-03

264

Comparative Analysis of Structure and Sequences of Oryza sativa Superoxide Dismutase  

Directory of Open Access Journals (Sweden)

Full Text Available One of the major classes of antioxidant enzymes, which protect the cellular and subcellular components against harmful reactive oxygen species (ROS, is superoxide dismutase (SOD. SODs play pivotal role in scavenging highly reactive free oxygen radicals and protecting cells from toxic effects. In Oryza sativa three types of SODs are available based on their metal content viz. Cu-Zn SOD, Mn SOD and Fe SOD. In the present study attempts were made to critically assess the structure and phylogenetic relationship among Oryza sativa SODs. The sequence similarity search using local BLAST shows that Mn SODs and Fe SODs have greater degree of similarity compared with that of Cu-Zn SODs. The multiple alignment reveals that seven amino acids were found to be totally conserved. The secondary structure shows that Mn SODs and Fe SODs have similar helixes, sheets, turns and coils compared with that of Cu-Zn SODs. The comparative analysis also displayed greater resemblance in primary, secondary and tertiary structures of Fe SODs and Mn SODs. Comparison between the structure and sequence analysis reveals that Mn SOD and Fe SOD are found to be closely related whereas Cu-Zn SOD evolves independently.

Aiyar Balasubramanian

2012-09-01

265

Identification of microRNA precursors with new sequence-structure features  

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Full Text Available MicroRNAs are an important subclass of non-coding RNAs (ncRNA, and serve as main players into RNA interference (RNAi. Mature microRNA derived from stem-loop structure called precursor. Identification of precursor microRNA (pre-miRNA is essential step to target microRNA in whole genome. The present work proposed 25 novel local features for identifying stem- loop structure of pre-miRNAs, which captures characteristics on both the sequence and structure. Firstly, we pulled the stem of hairpins and aligned the bases in bulges and internal loops used ‘?’, and then counted 24 base-pairs (‘AA’, ‘AU’, …, ‘?G’, except ‘??’ in pulled stem (formalized by length of pulled stem as features vector of Support Vector Machine (SVM. Performances of three classifiers with our features and different kernels trained on human data were all superior to Triplet-SVM-classifier’s in po- sitive and negative testing data sets. Moreover, we achieved higher prediction accuracy through combining 7 global sequence-structure. The result indicates validity of novel local features.

Ying-Jie Zhao

2009-12-01

266

Role of sequence and membrane composition in structure of transmembrane domain of Amyloid Precursor Protein  

Science.gov (United States)

Aggregation of proteins of known sequence is linked to a variety of neurodegenerative disorders. The amyloid ? (A?) protein associated with Alzheimer's Disease (AD) is derived from cleavage of the 99 amino acid C-terminal fragment of Amyloid Precursor Protein (APP-C99) by ?-secretase. Certain familial mutations of APP-C99 have been shown to lead to altered production of A? protein and the early onset of AD. We describe simulation studies exploring the structure of APP-C99 in micelle and membrane environments. Our studies explore how changes in sequence and membrane composition influence (1) the structure of monomeric APP-C99 and (2) APP-C99 homodimer structure and stability. Comparison of simulation results with recent NMR studies of APP-C99 monomers and dimers in micelle and bicelle environments provide insight into how critical aspects of APP-C99 structure and dimerization correlate with secretase processing, an essential component of the A? protein aggregation pathway and AD.

Straub, John

2013-03-01

267

A two-layer $\\alpha\\omega$ dynamo model, and its implications for 1-D dynamos  

CERN Document Server

I will discuss an attempt at representing an interface dynamo in a simplified, essentially 1D framework. The operation of the dynamo is broken up into two 1D layers, one containing the $\\alpha$ effect and the other containing the $\\omega$ effect, and these two layers are allowed to communicate with each other by the simplest possible representation of diffusion, an analogue of Newton's law of cooling. Dynamical back-reaction of the magnetic field on them with diagrams I computed for a comparable purely 1D model. The bifurcation structure shows remarkable similarity, but a couple of subtle changes imply dramatically different physical behaviour for the model. In particular, the solar-like dynamo mode found in the 1-layer model is not stable in the 2-layer version; instead there is an (apparent) homoclinic bifurcation and a sequence of periodic, quasiperiodic, and chaotic modes. I argue that the fragility of these models makes them effectively useless as predictors or interpreters of more complex dynamos.

Roald, C B

1999-01-01

268

Genome sequences and structures of two biologically distinct strains of Grapevine leafroll-associated virus 2 and sequence analysis.  

Science.gov (United States)

Grapevine leafroll-associated virus 2 (GLRaV-2), a member of the genus Closterovirus within Closteroviridae, is implicated in several important diseases of grapevines including "leafroll", "graft-incompatibility", and "quick decline" worldwide. Several GLRaV-2 isolates have been detected from different grapevine genotypes. However, the genomes of these isolates were not sequenced or only partially sequenced. Consequently, the relationship of these viral isolates at the molecular level has not been determined. Here, we group the various GLRaV-2 isolates into four strains based on their coat protein gene sequences. We show that isolates "PN" (originated from Vitis vinifera cv. "Pinot noir"), "Sem" (from V. vinifera cv. "Semillon") and "94/970" (from V. vinifera cv. "Muscat of Alexandria") belong to the same strain, "93/955" (from hybrid "LN-33") and "H4" (from V. rupestris "St. George") each represents a distinct strain, while Grapevine rootstock stem lesion-associated virus. PMID:15965606

Meng, Baozhong; Li, Caihong; Goszczynski, Dariusz E; Gonsalves, Dennis

2005-08-01

269

Sequence composition and environment effects on residue fluctuations in protein structures  

Science.gov (United States)

Structure fluctuations in proteins affect a broad range of cell phenomena, including stability of proteins and their fragments, allosteric transitions, and energy transfer. This study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations in protein-protein complexes. A one-node-per-residue elastic network model accounting for the nonhomogeneous protein mass distribution and the interatomic interactions through the renormalized inter-residue potential is developed. Two factors, a protein mass distribution and a residue environment, were found to determine the scale of residue fluctuations. Surface residues undergo larger fluctuations than core residues in agreement with experimental observations. Ranking residues over the normalized scale of fluctuations yields a distinct classification of amino acids into three groups: (i) highly fluctuating-Gly, Ala, Ser, Pro, and Asp, (ii) moderately fluctuating-Thr, Asn, Gln, Lys, Glu, Arg, Val, and Cys, and (iii) weakly fluctuating-Ile, Leu, Met, Phe, Tyr, Trp, and His. The structural instability in proteins possibly relates to the high content of the highly fluctuating residues and a deficiency of the weakly fluctuating residues in irregular secondary structure elements (loops), chameleon sequences, and disordered proteins. Strong correlation between residue fluctuations and the sequence composition of protein loops supports this hypothesis. Comparing fluctuations of binding site residues (interface residues) with other surface residues shows that, on average, the interface is more rigid than the rest of the protein surface and Gly, Ala, Ser, Cys, Leu, and Trp have a propensity to form more stable docking patches on the interface. The findings have broad implications for understanding mechanisms of protein association and stability of protein structures.

Ruvinsky, Anatoly M.; Vakser, Ilya A.

2010-10-01

270

Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for functional prediction. Knowledge of catalytic sites provides a valuable insight into protein function. Although many computational methods have been developed to predict catalytic residues and active sites, their accuracy remains low, with a significant number of false positives. In this paper, we present a novel method for the prediction of catalytic sites, using a carefully selected, supervised machine learning algorithm coupled with an optimal discriminative set of protein sequence conservation and structural properties. Results To determine the best machine learning algorithm, 26 classifiers in the WEKA software package were compared using a benchmarking dataset of 79 enzymes with 254 catalytic residues in a 10-fold cross-validation analysis. Each residue of the dataset was represented by a set of 24 residue properties previously shown to be of functional relevance, as well as a label {+1/-1} to indicate catalytic/non-catalytic residue. The best-performing algorithm was the Sequential Minimal Optimization (SMO algorithm, which is a Support Vector Machine (SVM. The Wrapper Subset Selection algorithm further selected seven of the 24 attributes as an optimal subset of residue properties, with sequence conservation, catalytic propensities of amino acids, and relative position on protein surface being the most important features. Conclusion The SMO algorithm with 7 selected attributes correctly predicted 228 of the 254 catalytic residues, with an overall predictive accuracy of more than 86%. Missing only 10.2% of the catalytic residues, the method captures the fundamental features of catalytic residues and can be used as a "catalytic residue filter" to facilitate experimental identification of catalytic residues for proteins with known structure but unknown function.

Wu Cathy H

2006-06-01

271

Unusual structure of ribosomal DNA in the copepod Tigriopus californicus: intergenic spacer sequences lack internal subrepeats.  

Science.gov (United States)

Eukaryotic nuclear ribosomal DNA (rDNA) is typically arranged as a series of tandem repeats coding for 18S, 5.8S, and 28S ribosomal RNAs. Transcription of rDNA repeats is initiated in the intergenic spacer (IGS) region upstream of the 18S gene. The IGS region itself typically consists of a set of subrepeats that function as transcriptional enhancers. Two important evolutionary forces have been proposed to act on the IGS region: first, selection may favor changes in the number of subrepeats that adaptively adjust rates of rDNA transcription, and second, coevolution of IGS sequence with RNA polymerase I transcription factors may lead to species specificity of the rDNA transcription machinery. To investigate the potential role of these forces on population differentiation and hybrid breakdown in the intertidal copepod Tigriopus californicus, we have characterized the rDNA of five T. californicus populations from the Pacific Coast of North America and one sample of T. brevicornicus from Scotland. Major findings are as follows: (1) the structural genes for 18S and 28S are highly conserved across T. californicus populations, in contrast to other nuclear and mitochondrial DNA (mtDNA) genes previously studied in these populations. (2) There is extensive differentiation among populations in the IGS region; in the extreme, no homology is observed across the IGS sequences (>2 kb) from the two Tigriopus species. (3) None of the Tigriopus IGS sequences have the subrepeat structure common to other eukaryotic IGS regions. (4) Segregation of rDNA in laboratory crosses indicates that rDNA is located on at least two separate chromosomes in T. californicus. These data suggest that although IGS length polymorphism does not appear to play the adaptive role hypothesized in some other eukaryotic systems, sequence divergence in the rDNA promoter region within the IGS could lead to population specificity of transcription in hybrids. PMID:15656977

Burton, R S; Metz, E C; Flowers, J M; Willett, C S

2005-01-01

272

Mod-seq: high-throughput sequencing for chemical probing of RNA structure.  

Science.gov (United States)

The functions of RNA molecules are intimately linked to their ability to fold into complex secondary and tertiary structures. Thus, understanding how these molecules fold is essential to determining how they function. Current methods for investigating RNA structure often use small molecules, enzymes, or ions that cleave or modify the RNA in a solvent-accessible manner. While these methods have been invaluable to understanding RNA structure, they can be fairly labor intensive and often focus on short regions of single RNAs. Here we present a new method (Mod-seq) and data analysis pipeline (Mod-seeker) for assaying the structure of RNAs by high-throughput sequencing. This technique can be utilized both in vivo and in vitro, with any small molecule that modifies RNA and consequently impedes reverse transcriptase. As proof-of-principle, we used dimethyl sulfate (DMS) to probe the in vivo structure of total cellular RNAs in Saccharomyces cerevisiae. Mod-seq analysis simultaneously revealed secondary structural information for all four ribosomal RNAs and 32 additional noncoding RNAs. We further show that Mod-seq can be used to detect structural changes in 5.8S and 25S rRNAs in the absence of ribosomal protein L26, correctly identifying its binding site on the ribosome. While this method is applicable to RNAs of any length, its high-throughput nature makes Mod-seq ideal for studying long RNAs and complex RNA mixtures. PMID:24664469

Talkish, Jason; May, Gemma; Lin, Yizhu; Woolford, John L; McManus, C Joel

2014-05-01

273

Automated Aufbau of antibody structures from given sequences using Macromoltek's SmrtMolAntibody.  

Science.gov (United States)

This study was a part of the second antibody modeling assessment. The assessment is a blind study of the performance of multiple software programs used for antibody homology modeling. In the study, research groups were given sequences for 11 antibodies and asked to predict their corresponding structures. The results were measured using root-mean-square deviation (rmsd) between the submitted models and X-ray crystal structures. In 10 of 11 cases, the results using SmrtMolAntibody show good agreement between the submitted models and X-ray crystal structures. In the first stage, the average rmsd was 1.4 Å. Average rmsd values for the framework was 1.2 Å and for the H3 loop was 3.0 Å. In stage two, there was a slight improvement with an rmsd for the H3 loop of 2.9 Å. PMID:24777752

Berrondo, Monica; Kaufmann, Susana; Berrondo, Manuel

2014-08-01

274

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences  

DEFF Research Database (Denmark)

The function of non-coding RNA genes largely depends on their secondary structure and the interaction with other molecules. Thus, an accurate prediction of secondary structure and RNA-RNA interaction is essential for the understanding of biological roles and pathways associated with a specific RNA gene. We present web servers to analyze multiple RNA sequences for common RNA structure and for RNA interaction sites. The web servers are based on the recent PET (Probabilistic Evolutionary and Thermodynamic) models PETfold and PETcofold, but add user friendly features ranging from a graphical layer to interactive usage of the predictors. Additionally, the web servers provide direct access to annotated RNA alignments, such as the Rfam 10.0 database and multiple alignments of 16 vertebrate genomes with human. The web servers are freely available at: http://rth.dk/resources/petfold/

Seemann, Ernst Stefan; Menzel, Karl Peter

2011-01-01

275

Sequence composition and environment effects on residue fluctuations in protein structures  

CERN Document Server

The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations in protein-protein complexes. A one-node-per residue elastic network model accounting for the nonhomogeneous protein mass distribution and the inter-atomic interactions through the renormalized inter-residue potential is developed. Two factors, a protein mass distribution and a residue environment, were found to determine the scale of residue fluctuations. Surface residues undergo larger fluctuations than core residues, showing agreement with experimental observations. Ranking residues over the normalized scale of fluctuations yields a distinct classification of amino acids into three groups. The structural instability in proteins possibly relates to the high con...

Ruvinsky, Anatoly M

2009-01-01

276

Structural growth sequences and electronic properties of gold clusters: Highly symmetric tubelike cages  

International Nuclear Information System (INIS)

The structural growth sequences and electronic properties of Aun (n=14+6m and m=0, 1, 2, 3, 4, 5, 6, and 10) clusters have been investigated using the DMol3 DFT package. The structures of Aun (n=20, 26, 32, 38, 44, 50, and 74) are obtained in turn by directly adding a gold ring of six atoms on the tubelike configuration of Au14 cluster. These tubelike gold clusters are all highly symmetric cages. Their average atomic coordination numbers, nearest-neighbor distances and average tube radius are very near. The average binding energies of Aun clusters increase substantially with size n. Au14, Au26, and Au44 have larger energy gaps and ionization potentials than their neighboring clusters. During the studied clusters, Au74 cluster has the highest average energy, ionization potential and the lowest electron affinity, which are corresponding to its highest structural and chemical stability, respectively.

277

Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background The black tiger shrimp (Penaeus monodon is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the P. monodon genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs from 20,926 non-redundant reads representing 0.45% of the P. monodon genome were obtained for repetitive and protein-coding sequence analyses. Results We found that microsatellite sequences were highly abundant in the P. monodon genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT and poly (AAT, were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, via self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, i.e., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the P. monodon genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP gene and the Innexin 3 gene homologues appear to be present in high abundance in the P. monodon genome. Conclusions The redundancy of various repeat types in the P. monodon genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.

Chen Ming

2011-05-01

278

PAIRpred: partner-specific prediction of interacting residues from sequence and structure.  

Science.gov (United States)

We present a novel partner-specific protein-protein interaction site prediction method called PAIRpred. Unlike most existing machine learning binding site prediction methods, PAIRpred uses information from both proteins in a protein complex to predict pairs of interacting residues from the two proteins. PAIRpred captures sequence and structure information about residue pairs through pairwise kernels that are used for training a support vector machine classifier. As a result, PAIRpred presents a more detailed model of protein binding, and offers state of the art accuracy in predicting binding sites at the protein level as well as inter-protein residue contacts at the complex level. We demonstrate PAIRpred's performance on Docking Benchmark 4.0 and recent CAPRI targets. We present a detailed performance analysis outlining the contribution of different sequence and structure features, together with a comparison to a variety of existing interface prediction techniques. We have also studied the impact of binding-associated conformational change on prediction accuracy and found PAIRpred to be more robust to such structural changes than existing schemes. As an illustration of the potential applications of PAIRpred, we provide a case study in which PAIRpred is used to analyze the nature and specificity of the interface in the interaction of human ISG15 protein with NS1 protein from influenza A virus. Python code for PAIRpred is available at http://combi.cs.colostate.edu/supplements/pairpred/. PMID:24243399

Minhas, Fayyaz ul Amir Afsar; Geiss, Brian J; Ben-Hur, Asa

2014-07-01

279

Structural features of the nucleotide sequences of virus and organelle genomes  

Directory of Open Access Journals (Sweden)

Full Text Available The four nucleotides (bases, A, T (U, G and C in small genomes, virus DNA/RNA, organelle and plastid genomes were also arranged sophisticatedly in the structural features in a single-strand with 1 reverse-complement symmetry of base or base sequences, 2 bias of four bases, 3 multiple fractality of the distribution of each four bases depending on the distance in double logarithmic plot (power spectrum of L (the distance of a base to the next base vs. P (L (the probability of the base-distribution at L, although their genomes were composed of low numbers of the four bases, and the base-symmetry was rather lower than the prokaryotic-and the eukaryotic cells. In the case of the genomic DNA composed of less than 10,000 nt, it was better than to be partitioned at 10 of the L-value, and the structural features for the biologically active genomic DNA were observed as the large genomes. As the results, the base sequences of the genomic DNA including the genomic-RNA might be universal in all genomes. In addition, the relationship between the structural features of the genome and the biological complexity was discussed.

Masaharu Takeda

2011-11-01

280

Structural parameters and reaction sequence in PLZT by X-ray diffraction  

International Nuclear Information System (INIS)

Ferroelectric ceramics ceramics of (Pb1-x Lax) (Zry Ti1-x) O3, with x=0.08 and 0.10 and y=0.65, were investigated by XRD technique, using a rotary anode generator and Rietveld Method. The X-ray patterns, obtained at room temperature and 600 deg C, were analysed with a procedure which allowed us to verify different behaviour for each powder synthesis method used (oxide mixture and chemical precipitation) and to obtain a sequences of the reaction, as well as, the structural parameters of the monophasic compositions. (author)

 
 
 
 
281

Specificity and phenetic relationships of iron- and manganese-containing superoxide dismutases on the basis of structure and sequence comparisons.  

Science.gov (United States)

The iron- and manganese-containing superoxide dismutases (Fe/Mn-SOD) share the same chemical function and spatial structure but can be distinguished according to their modes of oligomerization and their metal ion specificity. They appear as homodimers or homotetramers and usually require a specific metal for activity. On the basis of 261 aligned SOD sequences and 12 superimposed x-ray structures, two phenetic trees were constructed, one sequence-based and the other structure-based. Their comparison reveals the imperfect correlation of sequence and structural changes; hyperthermophilicity requires the largest sequence alterations, whereas dimer/tetramer and manganese/iron specificities are induced by the most sizable structural differences within the monomers. A systematic investigation of sequence and structure characteristics conserved in all aligned SOD sequences or in subsets sharing common oligomeric and/or metal specificities was performed. Several residues were identified as guaranteeing the common function and dimeric conformation, others as determining the tetramer formation, and yet others as potentially responsible for metal specificity. Some form cation-pi interactions between an aromatic ring and a fully or partially positively charged group, suggesting that these interactions play a significant role in the structure and function of SOD enzymes. Dimer/tetramer- and iron/manganese-specific fingerprints were derived from the set of conserved residues; they can be used to propose selected residue substitutions in view of the experimental validation of our in silico derived hypotheses. PMID:14672935

Wintjens, René; Noël, Christophe; May, Alex C W; Gerbod, Delphine; Dufernez, Fabienne; Capron, Monique; Viscogliosi, Eric; Rooman, Marianne

2004-03-01

282

Ribosomal ITS sequences allow resolution of freshwater sponge phylogeny with alignments guided by secondary structure prediction.  

Science.gov (United States)

Freshwater sponges include six extant families which belong to the suborder Spongillina (Porifera). The taxonomy of freshwater sponges is problematic and their phylogeny and evolution are not well understood. Sequences of the ribosomal internal transcribed spacers (ITS1 and ITS2) of 11 species from the family Lubomirskiidae, 13 species from the family Spongillidae, and 1 species from the family Potamolepidae were obtained to study the phylogenetic relationships between endemic and cosmopolitan freshwater sponges and the evolution of sponges in Lake Baikal. The present study is the first one where ITS1 sequences were successfully aligned using verified secondary structure models and, in combination with ITS2, used to infer relationships between the freshwater sponges. Phylogenetic trees inferred using maximum likelihood, neighbor-joining, and parsimony methods and Bayesian inference revealed that the endemic family Lubomirskiidae was monophyletic. Our results do not support the monophyly of Spongillidae because Lubomirskiidae formed a robust clade with E. muelleri, and Trochospongilla latouchiana formed a robust clade with the outgroup Echinospongilla brichardi (Potamolepidae). Within the cosmopolitan family Spongillidae the genera Radiospongilla and Eunapius were found to be monophyletic, while Ephydatia muelleri was basal to the family Lubomirskiidae. The genetic distances between Lubomirskiidae species being much lower than those between Spongillidae species are indicative of their relatively recent radiation from a common ancestor. These results indicated that rDNA spacers sequences can be useful in the study of phylogenetic relationships of and the identification of species of freshwater sponges. PMID:19009316

Itskovich, Valeria; Gontcharov, Andrey; Masuda, Yoshiki; Nohno, Tsutomu; Belikov, Sergey; Efremova, Sofia; Meixner, Martin; Janussen, Dorte

2008-12-01

283

A shared system for learning serial and temporal structure of sensori-motor sequences? Evidence from simulation and human experiments.  

Science.gov (United States)

This research investigates the influences of temporal structure on the representation of serial order. Experiments are performed in a neural network model of sequence learning and in human subjects. In the sequence learning model, a recurrent network of leaky integrator neurons encodes a succession of internal states that become associated, by reinforcement learning, with the correct sequential responses. First, the model is shown to learn a simple temporal discrimination task. The model is then exposed to two novel serial reaction time (SRT) experiments. In the standard SRT task (M.J. Nissen, P. Bullemer, Attentional requirements of learning: evidence from performance measures, Cogn. Psychol. 19 (1987) 1-32 [16]), reaction times for stimuli presented in a repeating sequence are reduced with respect to those for random stimuli, providing a measure of sequence learning. The novelty of the current experiments is that imbedded in the serial order of the sequences, there is a temporal structure of delays. The model is sensitive to both the serial structure and the temporal structure of the sequences. This observation is then confirmed in human subjects. These results demonstrate how a novel recurrent architecture encodes the interaction of temporal and serial structure and provide insight into related aspects of human sensori-motor sequence learning. PMID:9479067

Dominey, P F

1998-01-01

284

Complete sequence of the genome of the human isolate of Andes virus CHI-7913: comparative sequence and protein structure analysis  

Directory of Open Access Journals (Sweden)

Full Text Available We report here the complete genomic sequence of the Chilean human isolate of Andes virus CHI-7913. The S, M, and L genome segment sequences of this isolate are 1,802, 3,641 and 6,466 bases in length, with an overall GC content of 38.7%. These genome segments code for a nucleocapsid protein of 428 amino acids, a glycoprotein precursor protein of 1,138 amino acids and a RNA-dependent RNA polymerase of 2,152 amino acids. In addition, the genome also has other ORFs coding for putative proteins of 34 to 103 amino acids. The encoded proteins have greater than 98% overall similarity with the proteins of Andes virus isolates AH-1 and Chile R123. Among other sequenced Hantavirus, CHI-7913 is more closely related to Sin Nombre virus, with an overall protein similarity of 92%. The characteristics of the encoded proteins of this isolate, such as hydrophobic domains, glycosylation sites, and conserved amino acid motifs shared with other Hantavirus and other members of the Bunyaviridae family, are identified and discussed.

NICOLE D TISCHLER

2003-01-01

285

Complete sequence of the genome of the human isolate of Andes virus CHI-7913: comparative sequence and protein structure analysis  

Scientific Electronic Library Online (English)

Full Text Available SciELO Chile | Language: English Abstract in english We report here the complete genomic sequence of the Chilean human isolate of Andes virus CHI-7913. The S, M, and L genome segment sequences of this isolate are 1,802, 3,641 and 6,466 bases in length, with an overall GC content of 38.7%. These genome segments code for a nucleocapsid protein of 428 am [...] ino acids, a glycoprotein precursor protein of 1,138 amino acids and a RNA-dependent RNA polymerase of 2,152 amino acids. In addition, the genome also has other ORFs coding for putative proteins of 34 to 103 amino acids. The encoded proteins have greater than 98% overall similarity with the proteins of Andes virus isolates AH-1 and Chile R123. Among other sequenced Hantavirus, CHI-7913 is more closely related to Sin Nombre virus, with an overall protein similarity of 92%. The characteristics of the encoded proteins of this isolate, such as hydrophobic domains, glycosylation sites, and conserved amino acid motifs shared with other Hantavirus and other members of the Bunyaviridae family, are identified and discussed.

NICOLE D, TISCHLER; JORGE, FERNÁNDEZ; ILSE, MÜLLER; RODRIGO, MARTÍNEZ; HÉCTOR, GALENO; ELIECER, VILLAGRA; JUDITH, MORA; EUGENIO, RAMÍREZ; MARIO, ROSEMBLATT; PABLO D.T., VALENZUELA.

286

Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations.  

Science.gov (United States)

Deletion of tumor-suppressor genes as well as other genomic rearrangements pervade cancer genomes across numerous types of solid tumor and hematologic malignancies. However, even for a specific rearrangement, the breakpoints may vary between individuals, such as the recurrent CDKN2A deletion. Characterizing the exact breakpoints for structural variants (SVs) is useful for designating patient-specific tumor biomarkers. We propose AmBre (Amplification of Breakpoints), a method to target SV breakpoints occurring in samples composed of heterogeneous tumor and germline DNA. Additionally, AmBre validates SVs called by whole-exome/genome sequencing and hybridization arrays. AmBre involves a PCR-based approach to amplify the DNA segment containing an SV's breakpoint and then confirms breakpoints using sequencing by Pacific Biosciences RS. To amplify breakpoints with PCR, primers tiling specified target regions are carefully selected with a simulated annealing algorithm to minimize off-target amplification and maximize efficiency at capturing all possible breakpoints within the target regions. To confirm correct amplification and obtain breakpoints, PCR amplicons are combined without barcoding and simultaneously long-read sequenced using a single SMRT cell. Our algorithm efficiently separates reads based on breakpoints. Each read group supporting the same breakpoint corresponds with an amplicon and a consensus amplicon sequence is called. AmBre was used to discover CDKN2A deletion breakpoints in cancer cell lines: A549, CEM, Detroit562, MOLT4, MCF7, and T98G. Also, we successfully assayed RUNX1-RUNX1T1 reciprocal translocations by finding both breakpoints in the Kasumi-1 cell line. AmBre successfully targets SVs where DNA harboring the breakpoints are present in 1:1000 mixtures. PMID:24307551

Patel, Anand; Schwab, Richard; Liu, Yu-Tsueng; Bafna, Vineet

2014-02-01

287

High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Protein alignments are an essential tool for many bioinformatics analyses. While sequence alignments are accurate for proteins of high sequence similarity, they become unreliable as they approach the so-called 'twilight zone' where sequence similarity gets indistinguishable from random. For such distant pairs, structure alignment is of much better quality. Nevertheless, sequence alignment is the only choice in the majority of cases where structural data is not available. This situation demands development of methods that extend the applicability of accurate sequence alignment to distantly related proteins. Results We develop a sequence alignment method that combines the prediction of a structural profile based on the protein's sequence with the alignment of that profile using our recently published alignment tool SABERTOOTH. In particular, we predict the contact vector of protein structures using an artificial neural network based on position-specific scoring matrices generated by PSI-BLAST and align these predicted contact vectors. The resulting sequence alignments are assessed using two different tests: First, we assess the alignment quality by measuring the derived structural similarity for cases in which structures are available. In a second test, we quantify the ability of the significance score of the alignments to recognize structural and evolutionary relationships. As a benchmark we use a representative set of the SCOP (structural classification of proteins database, with similarities ranging from closely related proteins at SCOP family level, to very distantly related proteins at SCOP fold level. Comparing these results with some prominent sequence alignment tools, we find that SABERTOOTH produces sequence alignments of better quality than those of Clustal W, T-Coffee, MUSCLE, and PSI-BLAST. HHpred, one of the most sophisticated and computationally expensive tools available, outperforms our alignment algorithm at family and superfamily levels, while the use of SABERTOOTH is advantageous for alignments at fold level. Our alignment scheme will profit from future improvements of structural profiles prediction. Conclusions We present the automatic sequence alignment tool SABERTOOTH that computes pairwise sequence alignments of very high quality. SABERTOOTH is especially advantageous when applied to alignments of remotely related proteins. The source code is available at http://www.fkp.tu-darmstadt.de/sabertooth_project/, free for academic users upon request.

Bastolla Ugo

2010-05-01

288

Structural basis for sequence-specific recognition of DNA by TAL effectors.  

Science.gov (United States)

TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair by using two hypervariable residues [known as repeat variable diresidues (RVDs)] at positions 12 and 13. Here, we report the crystal structures of an 11.5-repeat TAL effector in both DNA-free and DNA-bound states. Each TAL repeat comprises two helices connected by a short RVD-containing loop. The 11.5 repeats form a right-handed, superhelical structure that tracks along the sense strand of DNA duplex, with RVDs contacting the major groove. The 12th residue stabilizes the RVD loop, whereas the 13th residue makes a base-specific contact. Understanding DNA recognition by TAL effectors may facilitate rational design of DNA-binding proteins with biotechnological applications. PMID:22223738

Deng, Dong; Yan, Chuangye; Pan, Xiaojing; Mahfouz, Magdy; Wang, Jiawei; Zhu, Jian-Kang; Shi, Yigong; Yan, Nieng

2012-02-10

289

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing  

Energy Technology Data Exchange (ETDEWEB)

Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.

Wu, Xueling; Zhou, Tongqing; Zhu, Jiang; Zhang, Baoshan; Georgiev, Ivelin; Wang, Charlene; Chen, Xuejun; Longo, Nancy S.; Louder, Mark; McKee, Krisha; O?Dell, Sijy; Perfetto, Stephen; Schmidt, Stephen D.; Shi, Wei; Wu, Lan; Yang, Yongping; Yang, Zhi-Yong; Yang, Zhongjia; Zhang, Zhenhai; Bonsignori, Mattia; Crump, John A.; Kapiga, Saidi H.; Sam, Noel E.; Haynes, Barton F.; Simek, Melissa; Burton, Dennis R.; Koff, Wayne C.; Doria-Rose, Nicole A.; Connors, Mark; Mullikin, James C.; Nabel, Gary J.; Roederer, Mario; Shapiro, Lawrence; Kwong, Peter D.; Mascola, John R. (Tumaini); (NIH); (Duke); (Kilimanjaro Repro.); (IAVI)

2013-03-04

290

Improving protein structure prediction using multiple sequence-based contact predictions.  

Science.gov (United States)

Although residue-residue contact maps dictate the topology of proteins, sequence-based ab initio contact predictions have been found little use in actual structure prediction due to the low accuracy. We developed a composite set of nine SVM-based contact predictors that are used in I-TASSER simulation in combination with sparse template contact restraints. When testing the strategy on 273 nonhomologous targets, remarkable improvements of I-TASSER models were observed for both easy and hard targets, with p value by Student's t test30%, which essentially converts "nonfoldable" targets into "foldable" ones. In CASP9, I-TASSER employed ab initio contact predictions, and generated models for 26 FM targets with a GDT-score 16% and 44% higher than the second and third best servers from other groups, respectively. These findings demonstrate a new avenue to improve the accuracy of protein structure prediction especially for free-modeling targets. PMID:21827953

Wu, Sitao; Szilagyi, Andras; Zhang, Yang

2011-08-10

291

DNA breaks and repair in interstitial telomere sequences: Influence of chromatin structure  

International Nuclear Information System (INIS)

Interstitial Telomeric Sequences (ITS) are over-involved in spontaneous and radiationinduced chromosome aberrations in chinese hamster cells. We have performed a study to investigate the origin of their instability, spontaneously or after low doses irradiation. Our results demonstrate that ITS have a particular chromatin structure: short nucleotide repeat length, less compaction of the 30 nm chromatin fiber, presence of G-quadruplex structures. These features would modulate breaks production and would favour the recruitment of alternative DNA repair mechanisms, which are prone to produce chromosome aberrations. These pathways could be at the origin of chromosome aberrations in ITS whereas NHEJ and HR Double Strand Break repair pathways are rather required for a correct repair in these regions. (author)

292

Intriguing sequence of GaFeO3 structures and electronic states to 70 GPa  

Science.gov (United States)

Structural studies of the ferrimagnetic (TN = 200 K) Mott insulator GaFeO3 (SG Pc21n) to 70 GPa, complemented by 57Fe Mössbauer spectroscopy and resistance (R) measurements at compression, decompression, and recompression, reveal a fascinating sequence of structures. Starting at ˜25 GPa a new structure, an orthorhombic perovskite (Pv) (SG Pbnm), is sluggishly formed followed by a volume V(P) drop of 5.4%. The complete formation of the Pv occurs at 42 GPa. In the 0-33 GPa range TN reaches 300 K and R(P) decreases by one order of magnitude. At 53 GPa an isostructural transition is detected, characterized by a discontinuous drop of V(P) by ˜3%. Mössbauer spectra (MS) reveal a nonmagnetic component coexisting with the magnetic one at ˜60 GPa. Its abundance increases and above 77 GPa no sign of a magnetic hyperfine interaction is detected down to 5 K. Concurrently, one observes a continuous yet precipitous decrease in R(P) taking place in the 53-68 GPa range, leading to an onset of the metallic state at P = 68 GPa. These electronic/magnetic features of the high pressure (HP) Pv are consistent with a Mott transition. With pressure decrease below 50 GPa, the insulating Pv is recovered, and at ˜24 GPa a 1st-order structural transition takes place to a LiNbO3-type structure with SG R3c. This structure remains stable down to ambient pressure and with recompression it is stable up to 50 GPa, afterwards it transforms back to the HP Pv structure. It is noteworthy that this transition occurs at the same pressure, regardless of the preceding structures: Pbnm or R3c. The results are compared with hematite (Fe2O3, SG R3¯c) and other ferric oxides. The mechanisms of the transitions are discussed.

Arielly, R.; Xu, W. M.; Greenberg, E.; Rozenberg, G. Kh.; Pasternak, M. P.; Garbarino, G.; Clark, S.; Jeanloz, R.

2011-09-01

293

Structural organization of glycophorin A and B genes: Glycophorin B gene evolved by homologous recombination at Alu repeat sequences  

International Nuclear Information System (INIS)

Glycophorins A (GPA) and B (GPB) are two major sialoglycoproteins of the human erythrocyte membrane. Here the authors present a comparison of the genomic structures of GPA and GPB developed by analyzing DNA clones isolated from a K562 genomic library. Nucleotide sequences of exon-intron junctions and 5' and 3' flanking sequences revealed that the GPA and GPB genes consist of 7 and 5 exons, respectively, and both genes have >95% identical sequence from the 5' flanking region to the region ? 1 kilobase downstream from the exon encoding the transmembrane regions. In this homologous part of the genes, GPB lacks one exon due to a point mutation at the 5' splicing site of the third intron, which inactivates the 5' cleavage event of splicing and leads to ligation of the second to the fourth exon. Following these very homologous sequences, the genomic sequences for GPA and GPB diverge significantly and no homology can be detected in their 3' end sequences. The analysis of the Alu sequences and their flanking direct repeat sequences suggest that an ancestral genomic structure has been maintained in the GPA gene, whereas the GPB gene has arisen from the acquisition of 3' sequences different from those of the GPA gene by homologous recombination at the Alu repeats during or after gene duplication

294

Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows  

Science.gov (United States)

Background Highly mutable RNA viruses exist in infected hosts as heterogeneous populations of genetically close variants known as quasispecies. Next-generation sequencing (NGS) allows for analysing a large number of viral sequences from infected patients, presenting a novel opportunity for studying the structure of a viral population and understanding virus evolution, drug resistance and immune escape. Accurate reconstruction of genetic composition of intra-host viral populations involves assembling the NGS short reads into whole-genome sequences and estimating frequencies of individual viral variants. Although a few approaches were developed for this task, accurate reconstruction of quasispecies populations remains greatly unresolved. Results Two new methods, AmpMCF and ShotMCF, for reconstruction of the whole-genome intra-host viral variants and estimation of their frequencies were developed, based on Multicommodity Flows (MCFs). AmpMCF was designed for NGS reads obtained from individual PCR amplicons and ShotMCF for NGS shotgun reads. While AmpMCF, based on covering formulation, identifies a minimal set of quasispecies explaining all observed reads, ShotMCS, based on packing formulation, engages the maximal number of reads to generate the most probable set of quasispecies. Both methods were evaluated on simulated data in comparison to Maximum Bandwidth and ViSpA, previously developed state-of-the-art algorithms for estimating quasispecies spectra from the NGS amplicon and shotgun reads, respectively. Both algorithms were accurate in estimation of quasispecies frequencies, especially from large datasets. Conclusions The problem of viral population reconstruction from amplicon or shotgun NGS reads was solved using the MCF formulation. The two methods, ShotMCF and AmpMCF, developed here afford accurate reconstruction of the structure of intra-host viral population from NGS reads. The implementations of the algorithms are available at http://alan.cs.gsu.edu/vira.html (AmpMCF) and http://alan.cs.gsu.edu/NGS/?q=content/shotmcf (ShotMCF). PMID:23902469

2013-01-01

295

RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction  

Science.gov (United States)

The global Csr regulatory system controls bacterial gene expression post-transcriptionally. CsrA of Escherichia coli is an RNA binding protein that plays a central role in repressing several stationary phase processes and activating certain exponential phase functions. CsrA regulates translation initiation of several genes by binding to the mRNA leaders and blocking ribosome binding. CsrB and CsrC are noncoding regulatory RNAs that are capable of sequestering CsrA and antagonizing its activity. Each of the known target transcripts contains multiple CsrA binding sites, although considerable sequence variation exists among these RNA targets, with GGA being the most highly conserved element. High-affinity RNA ligands containing single CsrA binding sites were identified from a combinatorial library using systematic evolution of ligands by exponential enrichment (SELEX). The SELEX-derived consensus was determined as RUACARGGAUGU, with the ACA and GGA motifs being 100% conserved and the GU sequence being present in all but one ligand. The majority (51/55) of the RNAs contained GGA in the loop of a hairpin within the most stable predicted structure, an arrangement similar to several natural CsrA binding sites. Strikingly, the identity of several nucleotides that were predicted to form base pairs in each stem were 100% conserved, suggesting that primary sequence information was embedded within the base-paired region. The affinity of CsrA for several selected ligands was measured using quantitative gel mobility shift assays. A mutational analysis of one selected ligand confirmed that the conserved ACA, GGA, and GU residues were critical for CsrA binding and that RNA secondary structure participates in CsrA–RNA recognition. PMID:16131593

DUBEY, ASHOK K.; BAKER, CAROL S.; ROMEO, TONY; BABITZKE, PAUL

2005-01-01

296

Ebola Virus RNA Editing Depends on the Primary Editing Site Sequence and an Upstream Secondary Structure  

Science.gov (United States)

Ebolavirus (EBOV), the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. In this study, we report for the first time that minigenomes containing the glycoprotein gene editing site can undergo RNA editing, thereby eliminating the requirement for a biosafety level 4 laboratory to study EBOV RNA editing. Using a newly developed dual-reporter minigenome, we have characterized the mechanism of EBOV RNA editing, and have identified cis-acting sequences that are required for editing, located between 9 nt upstream and 9 nt downstream of the editing site. Moreover, we show that a secondary structure in the upstream cis-acting sequence plays an important role in RNA editing. EBOV RNA editing is glycoprotein gene-specific, as a stretch encoding for 7 adenosine residues located in the viral polymerase gene did not serve as an editing site, most likely due to an absence of the necessary cis-acting sequences. Finally, the EBOV protein VP30 was identified as a trans-acting factor for RNA editing, constituting a novel function for this protein. Overall, our results provide novel insights into the RNA editing mechanism of EBOV, further understanding of which might result in novel intervention strategies against this viral pathogen. PMID:24146620

Mehedi, Masfique; Hoenen, Thomas; Robertson, Shelly; Ricklefs, Stacy; Dolan, Michael A.; Taylor, Travis; Falzarano, Darryl; Ebihara, Hideki; Porcella, Stephen F.; Feldmann, Heinz

2013-01-01

297

Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound.  

Science.gov (United States)

The genetic etiology of non-aneuploid fetal structural abnormalities is typically investigated by karyotyping and array-based detection of microscopically detectable rearrangements, and submicroscopic copy-number variants (CNVs), which collectively yield a pathogenic finding in up to 10% of cases. We propose that exome sequencing may substantially increase the identification of underlying etiologies. We performed exome sequencing on a cohort of 30 non-aneuploid fetuses and neonates (along with their parents) with diverse structural abnormalities first identified by prenatal ultrasound. We identified candidate pathogenic variants with a range of inheritance models, and evaluated these in the context of detailed phenotypic information. We identified 35 de novo single-nucleotide variants (SNVs), small indels, deletions or duplications, of which three (accounting for 10% of the cohort) are highly likely to be causative. These are de novo missense variants in FGFR3 and COL2A1, and a de novo 16.8 kb deletion that includes most of OFD1. In five further cases (17%) we identified de novo or inherited recessive or X-linked variants in plausible candidate genes, which require additional validation to determine pathogenicity. Our diagnostic yield of 10% is comparable to, and supplementary to, the diagnostic yield of existing microarray testing for large chromosomal rearrangements and targeted CNV detection. The de novo nature of these events could enable couples to be counseled as to their low recurrence risk. This study outlines the way for a substantial improvement in the diagnostic yield of prenatal genetic abnormalities through the application of next-generation sequencing. PMID:24476948

Carss, Keren J; Hillman, Sarah C; Parthiban, Vijaya; McMullan, Dominic J; Maher, Eamonn R; Kilby, Mark D; Hurles, Matthew E

2014-06-15

298

Population Structure of Clinical Vibrio parahaemolyticus from 17 Coastal Countries, Determined through Multilocus Sequence Analysis  

Science.gov (United States)

Vibrio parahaemolyticus is a leading cause of food-borne gastroenteritis worldwide. Although this bacterium has been the subject of much research, the population structure of clinical strains from worldwide collections remains largely undescribed, and the recorded outbreaks of V. parahaemolyticus gastroenteritis highlight the need for the subtyping of this species. We present a broad phylogenetic analysis of 490 clinical V. parahaemolyticus isolates from 17 coastal countries through multilocus sequence analysis (MLST). The 490 tested isolates fell into 161 sequence types (STs). The eBURST algorithm revealed that the 161 clinically relevant STs belonged to 8 clonal complexes, 11 doublets, and 94 singletons, showing a high level of genetic diversity. CC3 was found to be a global epidemic clone of V. parahaemolyticus, and ST-3 was the only ST with an international distribution. recA was observed to be evolving more rapidly, exhibiting the highest degree of nucleotide diversity (0.028) and the largest number of polymorphic nucleotide sites (177). We also found that the high variability of recA was an important cause of differences between the results of the eBURST and ME tree analyses, suggesting that recA has a much greater influence on the apparent evolutionary classification of V. parahaemolyticus based on the current MLST scheme. In conclusion, it is evident that a high degree of genetic diversity within the V. parahaemolyticus population and multiple sequence types are contributing to the burden of disease around the world. MLST, with a fully extractable database, is a powerful system for analysis of the clonal relationships of strains at a global scale. With the addition of more strains, the pubMLST database will provide more detailed and accurate information, which will be conducive to our future research on the population structure of V. parahaemolyticus. PMID:25225911

Lu, Jun; Wang, Guangzhou; Zhou, Lin; Min, Lingfeng; Han, Chongxu

2014-01-01

299

Structural Analysis of Single-Point Mutations Given an RNA Sequence: A Case Study with RNAMute  

Directory of Open Access Journals (Sweden)

Full Text Available We introduce here for the first time the RNAMute package, a pattern-recognition-based utility to perform mutational analysis and detect vulnerable spots within an RNA sequence that affect structure. Mutations in these spots may lead to a structural change that directly relates to a change in functionality. Previously, the concept was tried on RNA genetic control elements called "riboswitches" and other known RNA switches, without an organized utility that analyzes all single-point mutations and can be further expanded. The RNAMute package allows a comprehensive categorization, given an RNA sequence that has functional relevance, by exploring the patterns of all single-point mutants. For illustration, we apply the RNAMute package on an RNA transcript for which individual point mutations were shown experimentally to inactivate spectinomycin resistance in Escherichia coli. Functional analysis of mutations on this case study was performed experimentally by creating a library of point mutations using PCR and screening to locate those mutations. With the availability of RNAMute, preanalysis can be performed computationally before conducting an experiment.

Churkin Alexander

2006-01-01

300

Partial primary structure of human pregnancy zone protein: extensive sequence homology with human alpha 2-macroglobulin  

DEFF Research Database (Denmark)

Human pregnancy zone protein (PZP) is a major pregnancy-associated protein. Its quaternary structure (two covalently bound 180-kDa subunits, which are further non-covalently assembled into a tetramer of 720 kDa) is similar to that of human alpha 2-macroglobulin (alpha 2M). Here we show, from the results of complete or partial sequence determination of a random selection of 38 tryptic peptides covering 685 residues of the subunit of PZP, that PZP and alpha 2M indeed are extensively homologous. In the stretches of PZP sequenced so far, the degree of identically placed residues in the two proteins is 68%, indicating a close evolutionary relationship between PZP and alpha 2M. Although the function of PZP in pregnancy is largely unknown, its close structural relationship to alpha 2M suggests analogous proteinase binding properties and a potential for being taken up in cells by receptor-mediated endocytosis. In this regard our studies indicate a bait region in PZP significantly different from that present in alpha 2M. PZP could be the human equivalent of the acute-phase alpha-macroglobulins (e.g., rat alpha 2M and rabbit alpha 1M) described earlier

Sottrup-Jensen, Lars; Folkersen, J

1984-01-01

 
 
 
 
301

Developing 1D nanostructure arrays for future nanophotonics  

Directory of Open Access Journals (Sweden)

Full Text Available AbstractThere is intense and growing interest in one-dimensional (1-D nanostructures from the perspective of their synthesis and unique properties, especially with respect to their excellent optical response and an ability to form heterostructures. This review discusses alternative approaches to preparation and organization of such structures, and their potential properties. In particular, molecular-scale printing is highlighted as a method for creating organized pre-cursor structure for locating nanowires, as well as vapor–liquid–solid (VLS templated growth using nano-channel alumina (NCA, and deposition of 1-D structures with glancing angle deposition (GLAD. As regards novel optical properties, we discuss as an example, finite size photonic crystal cavity structures formed from such nanostructure arrays possessing highQand small mode volume, and being ideal for developing future nanolasers.

Cooke DG

2006-01-01

302

Developing 1D nanostructure arrays for future nanophotonics  

Science.gov (United States)

There is intense and growing interest in one-dimensional (1-D) nanostructures from the perspective of their synthesis and unique properties, especially with respect to their excellent optical response and an ability to form heterostructures. This review discusses alternative approaches to preparation and organization of such structures, and their potential properties. In particular, molecular-scale printing is highlighted as a method for creating organized pre-cursor structure for locating nanowires, as well as vapor–liquid–solid (VLS) templated growth using nano-channel alumina (NCA), and deposition of 1-D structures with glancing angle deposition (GLAD). As regards novel optical properties, we discuss as an example, finite size photonic crystal cavity structures formed from such nanostructure arrays possessing highQand small mode volume, and being ideal for developing future nanolasers.

Polanyi, John C; Yang, JodySY; Wu, Zhanghua; Philipose, Usha; Xu, Tao; Yang, Susan; Kavanagh, KL; Liu, JQ; Yang, L; Wang, Y; Robbie, Kevin; Yang, J; Kaminska, K; Cooke, DG; Hegmann, FA; Budz, AJ; Haugen, HK

2006-01-01

303

In Silico sequence analysis and molecular modeling of the three-dimensional structure of DAHP synthase from Pseudomonas fragi.  

Science.gov (United States)

The shikimate pathway is involved in production of aromatic amino acids in microorganisms and plants. The enzymes of this biosynthetic pathway are a potential target for the design of antimicrobial compounds and herbicides. 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHPS) catalyzes the first step of the pathway. The gene encoding DAHPS was cloned and sequenced from Pseudomonas fragi, the bacterium responsible for spoilage of milk, dairy products and meat. Amino acid sequence deduced from the nucleotide sequence revealed that P. fragi DAHPS (Pf-DAHPS) consists of 448 amino acids with calculated molecular weight of ?50 kDa and isoelectric point of 5.81. Primary sequence analysis of Pf-DAHPS shows that it has more than 84% identity with DAHPS of other Pseudomonas species, 46% identity with Mycobacterium tuberculosis DAHPS (Mt-DAHPS), the type II DAHPS and less than 11% sequence identity with the type I DAHPS. The three-dimensional structure of Pf-DAHPS was predicted by homology modeling based on the crystal structure of Mt-DAHPS. Pf-DAHPS model contains a (?/?)(8) TIM barrel structure. Sequence alignment, phylogenetic analysis and 3D structure model classifies Pf-DAHPS as a type II DAHPS. Sequence analysis revealed the presence of DAHPS signature motif DxxHxN in Pf-DAHPS. Highly conserved sequence motif RxxxxxxKPRT(S/T) and xGxR present in type II DAHPS were also identified in Pf-DAHPS sequence. High sequence homology of DAHPS within Pseudomonas species points to the option of designing a broad spectrum drug for the genus. Pf-DAHPS 3D model provides molecular insights that may be beneficial in rationale inhibitor design for developing effective food preservative against P. fragi. PMID:20517625

Tapas, Satya; Kumar Patel, Girijesh; Dhindwal, Sonali; Tomar, Shailly

2011-04-01

304

Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background DNA repair is the general term for the collection of critical mechanisms which repair many forms of DNA damage such as methylation or ionizing radiation. DNA repair has mainly been studied in experimental and clinical situations, and relatively few information-based approaches to new extracting DNA repair knowledge exist. As a first step, automatic detection of DNA repair proteins in genomes via informatics techniques is desirable; however, there are many forms of DNA repair and it is not a straightforward process to identify and classify repair proteins with a single optimal method. We perform a study of the ability of homology and machine learning-based methods to identify and classify DNA repair proteins, as well as scan vertebrate genomes for the presence of novel repair proteins. Combinations of primary sequence polypeptide frequency, secondary structure, and homology information are used as feature information for input to a Support Vector Machine (SVM. Results We identify that SVM techniques are capable of identifying portions of DNA repair protein datasets without admitting false positives; at low levels of false positive tolerance, homology can also identify and classify proteins with good performance. Secondary structure information provides improved performance compared to using primary structure alone. Furthermore, we observe that machine learning methods incorporating homology information perform best when data is filtered by some clustering technique. Analysis by applying these methodologies to the scanning of multiple vertebrate genomes confirms a positive correlation between the size of a genome and the number of DNA repair protein transcripts it is likely to contain, and simultaneously suggests that all organisms have a non-zero minimum number of repair genes. In addition, the scan result clusters several organisms' repair abilities in an evolutionarily consistent fashion. Analysis also identifies several functionally unconfirmed proteins that are highly likely to be involved in the repair process. A new web service, INTREPED, has been made available for the immediate search and annotation of DNA repair proteins in newly sequenced genomes. Conclusion Despite complexity due to a multitude of repair pathways, combinations of sequence, structure, and homology with Support Vector Machines offer good methods in addition to existing homology searches for DNA repair protein identification and functional annotation. Most importantly, this study has uncovered relationships between the size of a genome and a genome's available repair repetoire, and offers a number of new predictions as well as a prediction service, both which reduce the search time and cost for novel repair genes and proteins.

Akutsu Tatsuya

2009-01-01

305

Influence of loading sequence and stress ratio on Fatigue damage accumulation of a structural component  

Scientific Electronic Library Online (English)

Full Text Available SciELO Portugal | Language: English Abstract in portuguese Este artigo apresenta resultados experimentais relativos à acumulação de dano de fadiga de um componente estrutural de aço P355NL1. O componente estrutural é uma placa rectangular com duplo entalhe. Foram aplicadas sequências de dois e múltiplos blocos de carga de amplitude constante, para várias co [...] mbinações de razões de tensão remotas, nomeadamente R=0, R=0.15 e R=0.3. Também foram analisados os efeitos da aplicação de blocos de amplitude variável, aplicados de acordo com um espectro de carga predefinido. Este estudo foi complementado com resultados de ensaios realizados em amplitude constante, os quais serviram para os cálculos de acumulação de dano. Em geral, o carregamento por blocos demonstra que o dano provocado por fadiga apresenta uma evolução não linear com o número de ciclos de carga, sendo esta evolução de dano função da sequência de carga, do nível de tensão e da razão de tensões. Geralmente, a aplicação de carregamentos de amplitude variável indicia um importante efeito da razão de tensões na acumulação de dano por fadiga. Particularmente, é observado um efeito claro da sequência de carga nos carregamentos compostos por dois blocos de carga, com razão de tensões nula. Para as outras razões de tensões (altas), os efeitos da sequência de carga são praticamente desprezáveis; contudo a evolução de dano continua a ser não linear. Abstract in english This paper presents experimental results about the fatigue damage accumulation behaviour of a structural component made of P355NL1 steel. The structural component is a rectangular double notched plate. Two and multiple alternated constant amplitude block sequences were applied for various combinatio [...] ns of remote stress ranges. Three stress ratios were investigated, namely R=0, R=0.15 and R=0.3. Variable amplitude blocks were also investigated according predefined stress spectra. Constant amplitude data was also generated which is applied for damage calculation purposes. In general, the block loading demonstrates that fatigue damage evolves nonlinearly with the number of loading cycles, function of the load sequence, stress level and stress ratios. Generally, the application of variable amplitude loading suggests an important stress ratio effect on fatigue damage accumulation. In particular, a clear load sequence effect is verified for the two block loading, with null stress ratio. For the other (higher) stress ratios, the load sequence effects are almost negligible; however the damage evolution still is non-linear.

Hélder F. S. G., Pereira; Abílio M.P. de, Jesus; Alfredo S., Ribeiro; António A., Fernandes.

306

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha).  

Science.gov (United States)

Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure. PMID:24665338

Larson, Wesley A; Seeb, Lisa W; Everett, Meredith V; Waples, Ryan K; Templin, William D; Seeb, James E

2014-03-01

307

Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure.  

Science.gov (United States)

One of the main hurdles for the development of an effective and broadly protective vaccine against nonencapsulated isolates of Haemophilus influenzae (NTHi) lies in the genetic diversity of the species, which renders extremely difficult the identification of cross-protective candidate antigens. To assess whether a population structure of NTHi could be defined, we performed genome sequencing of a collection of diverse clinical isolates representative of both carriage and disease and of the diversity of the natural population. Analysis of the distribution of polymorphic sites in the core genome and of the composition of the accessory genome defined distinct evolutionary clades and supported a predominantly clonal evolution of NTHi, with the majority of genetic information transmitted vertically within lineages. A correlation between the population structure and the presence of selected surface-associated proteins and lipooligosaccharide structure, known to contribute to virulence, was found. This high-resolution, genome-based population structure of NTHi provides the foundation to obtain a better understanding, of NTHi adaptation to the host as well as its commensal and virulence behavior, that could facilitate intervention strategies against disease caused by this important human pathogen. PMID:24706866

De Chiara, Matteo; Hood, Derek; Muzzi, Alessandro; Pickard, Derek J; Perkins, Tim; Pizza, Mariagrazia; Dougan, Gordon; Rappuoli, Rino; Moxon, E Richard; Soriani, Marco; Donati, Claudio

2014-04-01

308

Chaos in 1D radiative edge plasmas  

International Nuclear Information System (INIS)

Bifurcation and chaos in radiative edge plasmas are investigated on the basis of a periodically driven reaction-diffusion equation which results from the time dependent 1d heat conduction equation including a given periodically time-modulated impurity density. The temporal problem shows the transition to chaos through the Feigenbaum route. In 1d and time dependent plasmas Hopf bifurcation and intermittency phenomena exist. The application to a carbon seeded plasma shows the existence of different oscillation regimes. (orig.)

309

Social exploration of 1D games  

DEFF Research Database (Denmark)

In this paper the apparently meaningless concept of a 1 dimensional computer game is explored, via netnography. A small number of games was designed and implemented, in close contact with online communities of players and developers, providing evidence that 1 dimension is enough to produce interesting gameplay, to allow for level design and even to leave room for artistic considerations on 1D rendering. General techniques to re-design classic 2D games into 1D are also emerging from this exploration.

Valente, Andrea; Marchetti, Emanuela

2013-01-01

310

Analysis of sequence dependent variations in secondary and tertiary structure of tRNA molecules.  

Science.gov (United States)

The double helical regions of the five tRNA(Phe) and two tRNA(Asp) crystal structures have been analyzed using the local basepair step parameters. The sequence dependent effects in the mini double helices of tRNA are very similar to those observed in the crystal structures of oligonucleotides in the A-form, the purine-pyrimidine and purine-purine steps have small roll angles when compared to the fiber models of A-DNA as well as A-RNA, while the pyrimidine-purine doublet steps have large roll angles. The orientation of the basepairs in the D-stem is unusual and invariant i.e. they are different from the other three stems but are very similar in all the five tRNA(Phe) crystal structures, presumably due to tertiary interaction of the Watson-Crick basepairs with other bases, with all bases being highly conserved. The origin of the differences between the tertiary structures of tRNA(Phe) and tRNA(Asp) from yeast has also been investigated. It is found that even though the angle between the acceptor arm and the D-stem is very similar in the two structures, the angle subtended by the acceptor arm and the anticodon arm is smaller in the tRNA(Phe) structure (by more than 10 degrees). This is due to differences in the orientation of the two mini helices constituting the anticodon arm, which are inclined to each other by approximately 25 degrees in tRNA(Phe) and 16 degrees in tRNA(Asp). In addition, the acceptor arm, the D-stem and the anticodon stem are nearly coplanar in tRNA(Phe), while in tRNA(Asp) the anticodon stem projects out of the plane defined by the acceptor arm and the anticodon stem. These two features together lead to a larger separation between the acceptor and anticodon ends in tRNA(Asp) and indicate that the junction between the D-stem and the anticodon stem is quite variable, with features characteristic of a ball-and-socket type joint and determined for each tRNA molecule by the base sequence at the junction. PMID:7946073

Bhattacharyya, D; Bansal, M

1994-06-01

311

Polaron in a quasi 1D cylindrical quantum wire  

Directory of Open Access Journals (Sweden)

Full Text Available Polaron states in a quasi 1D cylindrical quantum wire with a parabolic confinement potential are investigated applying the Feynman variational principle. The effect of the wire radius on the polaron ground state energy level, the mass and the Fröhlich electron-phonon-coupling constant are obtained for the case of a quasi 1D cylindrical quantum wire. The effect of anisotropy of the structure on the polaron ground state energy level and the mass are also investigated. It is observed that as the wire radius tends to zero, the polaron mass and energy diverge logarithmically. The polaron mass and energy differ from the canonical strong-coupling behavior by the Fröhlich electron-phonon coupling constant and the radius of the quasi 1D cylindrical quantum wire that are expressed through a logarithmic function. Moreover, it is observed that the polaron energy and mass for strong coupling for the case of the quasi 1D cylindrical quantum wire are greater than those for bulk crystals. It is also observed that the anisotropy of the structure considerably affects both the polaron ground state energy level and the mass. It is found that as the radius of the cylindrical wire reduces, the regimes of the weak and intermediate coupling polaron shorten while the region of the strong coupling polaron broadens and extends into those of the weak and intermediate ones. Analytic expressions for the polaron ground state energy level and mass are derived for the case of strong coupling polarons.

I.Nsangou

2005-01-01

312

A rostro-caudal gradient of structured sequence processing in the left inferior frontal gyrus.  

Science.gov (United States)

In this paper, we present two novel perspectives on the function of the left inferior frontal gyrus (LIFG). First, a structured sequence processing perspective facilitates the search for functional segregation within the LIFG and provides a way to express common aspects across cognitive domains including language, music and action. Converging evidence from functional magnetic resonance imaging and transcranial magnetic stimulation studies suggests that the LIFG is engaged in sequential processing in artificial grammar learning, independently of particular stimulus features of the elements (whether letters, syllables or shapes are used to build up sequences). The LIFG has been repeatedly linked to processing of artificial grammars across all different grammars tested, whether they include non-adjacent dependencies or mere adjacent dependencies. Second, we apply the sequence processing perspective to understand how the functional segregation of semantics, syntax and phonology in the LIFG can be integrated in the general organization of the lateral prefrontal cortex (PFC). Recently, it was proposed that the functional organization of the lateral PFC follows a rostro-caudal gradient, such that more abstract processing in cognitive control is subserved by more rostral regions of the lateral PFC. We explore the literature from the viewpoint that functional segregation within the LIFG can be embedded in a general rostro-caudal abstraction gradient in the lateral PFC. If the lateral PFC follows a rostro-caudal abstraction gradient, then this predicts that the LIFG follows the same principles, but this prediction has not yet been tested or explored in the LIFG literature. Integration might provide further insights into the functional architecture of the LIFG and the lateral PFC. PMID:22688637

Uddén, Julia; Bahlmann, Jörg

2012-07-19

313

Blood flow quantification using 1D CFD parameter identification  

Science.gov (United States)

Patient-specific measurements of cerebral blood flow provide valuable diagnostic information concerning cerebrovascular diseases rather than visually driven qualitative evaluation. In this paper, we present a quantitative method to estimate blood flow parameters with high temporal resolution from digital subtraction angiography (DSA) image sequences. Using a 3D DSA dataset and a 2D+t DSA sequence, the proposed algorithm employs a 1D Computational Fluid Dynamics (CFD) model for estimation of time-dependent flow values along a cerebral vessel, combined with an additional Advection Diffusion Equation (ADE) for contrast agent propagation. The CFD system, followed by the ADE, is solved with a finite volume approximation, which ensures the conservation of mass. Instead of defining a new imaging protocol to obtain relevant data, our cost function optimizes the bolus arrival time (BAT) of the contrast agent in 2D+t DSA sequences. The visual determination of BAT is common clinical practice and can be easily derived from and be compared to values, generated by a 1D-CFD simulation. Using this strategy, we ensure that our proposed method fits best to clinical practice and does not require any changes to the medical work flow. Synthetic experiments show that the recovered flow estimates match the ground truth values with less than 12% error in the mean flow rates.

Brosig, Richard; Kowarschik, Markus; Maday, Peter; Katouzian, Amin; Demirci, Stefanie; Navab, Nassir

2014-03-01

314

Computer analysis of phytochrome sequences and reevaluation of the phytochrome secondary structure by Fourier transform infrared spectroscopy.  

Science.gov (United States)

A repertoire of various methods of computer sequence analysis was applied to phytochromes in order to gain new insights into their structure and function. A statistical analysis of 23 complete phytochrome sequences revealed regions of non-random amino acid composition, which are supposed to be of particular structural or functional importance. All phytochromes other than phyD and phyE from Arabidopsis have at least one such region at the N-terminus between residues 2 and 35. A sequence similarity search of current databases indicated striking homologies between all phytochromes and a hypothetical 84.2-kDa protein from the cyanobacterium Synechocystis. Furthermore, scanning the phytochrome sequences for the occurrence of patterns defined in the PROSITE database detected the signature of the WD repeats of the beta-transducin family within the functionally important 623-779 region (sequence numbering of phyA from Avena) in a number of phytochromes. A multiple sequence alignment performed with 23 complete phytochrome sequences is made available via the IMB Jena World-Wide Web server (http://www.imb-jena.de/PHYTO.html). It can be used as a working tool for future theoretical and experimental studies. Based on the multiple alignment striking sequence differences between phytochromes A and B were detected directly at the N-terminal end, where all phytochromes B have an additional stretch of 15-42 amino acids. There is also a variety of positions with totally conserved but different amino acids in phytochromes A and B. Most of these changes are found in the sequence segment 150-200. It is, therefore, suggested that this region might be of importance in determining the photosensory specificity of the two phytochromes. The secondary structure prediction based on the multiple alignment resulted in a small but significant beta-sheet content. This finding is confirmed by a reevaluation of the secondary structure using FTIR spectroscopy. PMID:9252112

Sühnel, J; Hermann, G; Dornberger, U; Fritzsche, H

1997-07-18

315

Syntheses, structures and electrochemical properties of a class of 1-D double chain polyoxotungstate hybrids [H(2)dap][Cu(dap)(2)](0.5)[Cu(dap)(2)(H2O)][Ln(H(2)O)3(?-GeW(11)O(39))]·3H(2)O.  

Science.gov (United States)

A series of novel organic-inorganic hybrid 1-D double chain germanotungstates [H2dap][Cu(dap)2]0.5[Cu(dap)2(H2O)][Ln(H2O)3(?-GeW11O39)]·3H2O [Ln = La(III) (1), Pr(III) (2), Nd(III) (3), Sm(III) (4), Eu(III) (5), Tb(III) (6), Er(III) (7)] (dap = 1,2-diaminopropane) have been hydrothermally prepared and structurally characterized by elemental analyses, powder X-ray diffraction (PXRD), IR spectra, thermogravimetric (TG) analyses, X-ray photoelectron spectroscopy (XPS) and single-crystal X-ray diffraction. The most prominent structural feature of 1-7 is that the [Ln(H2O)3(?-GeW11O39)](5-) moieties are firstly connected with each other via the W-O-Ln-O-W bridges creating a 1-D {[Cu(dap)2(H2O)][Ln(H2O)3(?-GeW11O39)]}n(3n-) polymeric chain and then two adjacent antiparallel 1-D polymeric chains are linked together through [Cu(dap)2](2+) linkages giving rise to the rare organic-inorganic hybrid 1-D Cu(II)-Ln(III) heterometallic double-chain architectures. To the best of our knowledge, 1-7 represent the first 1-D double-chain Cu(II)-Ln(III) heterometallic germanotungstates. The variable-temperature magnetic susceptibilities of 2, 4 and 7 have been investigated. Furthermore, the solid-state electrochemical and electro-catalytic properties of 3 and 4 have been measured in 0.5 mol L(-1) Na2SO4 + H2SO4 aqueous solution by entrapping them in a carbon paste electrode. 3 and 4 display apparent electro-catalytic activities for nitrite, bromate and hydrogen peroxide reduction. PMID:24554042

Zhao, Jun-Wei; Li, Yan-Zhou; Ji, Fan; Yuan, Jing; Chen, Li-Juan; Yang, Guo-Yu

2014-04-21

316

1D design style implications for mask making and CEBL  

Science.gov (United States)

At advanced nodes, CMOS logic is being designed in a highly regular design style because of the resolution limitations of optical lithography equipment. Logic and memory layouts using 1D Gridded Design Rules (GDR) have been demonstrated to nodes beyond 12nm.[1-4] Smaller nodes will require the same regular layout style but with multiple patterning for critical layers. One of the significant advantages of 1D GDR is the ease of splitting layouts into lines and cuts. A lines and cuts approach has been used to achieve good pattern fidelity and process margin to below 12nm.[4] Line scaling with excellent line-edge roughness (LER) has been demonstrated with self-aligned spacer processing.[5] This change in design style has important implications for mask making: • The complexity of the masks will be greatly reduced from what would be required for 2D designs with very complex OPC or inverse lithography corrections. • The number of masks will initially increase, as for conventional multiple patterning. But in the case of 1D design, there are future options for mask count reduction. • The line masks will remain simple, with little or no OPC, at pitches (1x) above 80nm. This provides an excellent opportunity for continual improvement of line CD and LER. The line pattern will be processed through a self-aligned pitch division sequence to divide pitch by 2 or by 4. • The cut masks can be done with "simple OPC" as demonstrated to beyond 12nm.[6] Multiple simple cut masks may be required at advanced nodes. "Coloring" has been demonstrated to below 12nm for two colors and to 8nm for three colors. • Cut/hole masks will eventually be replaced by e-beam direct write using complementary e-beam lithography (CEBL).[7-11] This transition is gated by the availability of multiple column e-beam systems with throughput adequate for high- volume manufacturing. A brief description of 1D and 2D design styles will be presented, followed by examples of 1D layouts. Mask complexity for 1D layouts patterned directly will be compared to mask complexity for lines and cuts at nodes larger than 20nm. No such comparison is possible below 20nm since single-patterning does not work below ~80nm pitch using optical exposure tools. Also discussed will be recently published wafer results for line patterns with pitch division by-2 and by-4 at sub-12nm nodes, plus examples of post-etch results for 1D patterns done with cut masks and compared to cuts exposed by a single-column e-beam direct write system.

Smayling, Michael C.

2013-09-01

317

Cluster Segmentation of Thermal Image Sequences Using kd-Tree Structure  

Science.gov (United States)

This paper presents optimization methods for the K-means segmentation algorithm for a sequence of thermal images. Images of the sample response in the frequency domain to the thermal stimulation with a known spectrum were subjected to cluster segmentation, grouping pixels with similar frequency characteristics. Compared were all pixel characteristics in the function of the frame number and grouped using the minimal sum of deviations of the pixels from their segment mean for all the frames of the processed image sequence. A new initialization method for the K-means algorithm, using density information, was used. A K-means algorithm with a kd-tree structure C# implementation was tested for speed and accuracy. This algorithm divides the set of pixels to the subspaces in the hierarchy of a binary tree. This allows skipping the calculation of distances of pixels to some centroids and pruning a set of centroid clusters through the hierarchy tree. Results of the segmentation were compared with the K-means and FCM algorithm MATLAB implementations.

?wita, R.; Suszy?ski, Z.

2014-08-01

318

A rare (3,4,5)-connected metal-organic framework featuring an unprecedented 1D + 2D ? 3D self-interpenetrated array and an O-atom lined pore surface: structure and controlled drug release.  

Science.gov (United States)

A rare (3,4,5)-connected self-interpenetrated metal-organic framework with an O-atom lined pore surface has been constructed from Zn(ii) and H4L (H4L = 5,5'-(1,3,6,8-tetraoxobenzo[lmn][3,8]phenanthroline-2,7(1H,3H,6H,8H)diyl)-diisophthalic acid), which features an unprecedented 1D + 2D ? 3D self-interpenetrated array and shows good controlled drug release properties. PMID:25371973

Zhong, Di-Chang; Liao, Lie-Qiang; Deng, Ji-Hua; Chen, Qing; Lian, Ping; Luo, Xu-Zhong

2014-12-25

319

CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles  

DEFF Research Database (Denmark)

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6 A when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is

Nielsen, Morten; Lundegaard, Claus

2010-01-01

320

Structural growth sequences and electronic properties of gold clusters: Highly symmetric tubelike cages  

Energy Technology Data Exchange (ETDEWEB)

The structural growth sequences and electronic properties of Au{sub n} (n=14+6m and m=0, 1, 2, 3, 4, 5, 6, and 10) clusters have been investigated using the DMol{sup 3} DFT package. The structures of Au{sub n} (n=20, 26, 32, 38, 44, 50, and 74) are obtained in turn by directly adding a gold ring of six atoms on the tubelike configuration of Au{sub 14} cluster. These tubelike gold clusters are all highly symmetric cages. Their average atomic coordination numbers, nearest-neighbor distances and average tube radius are very near. The average binding energies of Au{sub n} clusters increase substantially with size n. Au{sub 14}, Au{sub 26}, and Au{sub 44} have larger energy gaps and ionization potentials than their neighboring clusters. During the studied clusters, Au{sub 74} cluster has the highest average energy, ionization potential and the lowest electron affinity, which are corresponding to its highest structural and chemical stability, respectively.

Zhao Lixia, E-mail: zlx@ecust.edu.c [Department of Physics, East China University of Science and Technology, Shanghai 200237 (China); Lei Yongmin; Zhang Meng; Feng Xiaojuan; Luo Youhua [Department of Physics, East China University of Science and Technology, Shanghai 200237 (China)

2009-06-01

 
 
 
 
321

Copper-Peptide complex structure and reactivity when found in conserved his-xaa-his sequences.  

Science.gov (United States)

Oxygen-activating copper proteins may possess His-Xaa-His chelating sequences at their active sites and additionally exhibit imidiazole group ?N vs ?N tautomeric preferences. As shown here, such variations strongly affect copper ion's coordination geometry, redox behavior, and oxidative reactivity. Copper(I) complexes bound to either ?-HGH or ?-HGH tripeptides were synthesized and characterized. Structural investigations using X-ray absorption spectroscopy, density functional theory calculations, and solution conductivity measurements reveal that ?-HGH forms the Cu(I) dimer complex [{Cu(I)(?-HGH)}2](2+) (1) while ?-HGH binds Cu(I) to give the monomeric complex [Cu(I)(?-HGH)](+) (2). Only 2 exhibits any reactivity, forming a strong CO adduct, [Cu(I)(?-HGH)(CO)](+), with properties closely matching those of the copper monooxygenase PHM. Also, 2 is reactive toward O2 or H2O2, giving a new type of O2-adduct or Cu(II)-OOH complex, respectively. PMID:25171435

Park, Ga Young; Lee, Jung Yoon; Himes, Richard A; Thomas, Gnana S; Blackburn, Ninian J; Karlin, Kenneth D

2014-09-10

322

Term structure of 4d-electron configurations and calculated spectrum in Sn-isonuclear sequence  

International Nuclear Information System (INIS)

Theoretical calculations of term structure are carried out for the ground configurations 4dw, of atomic ions in the Sn isonuclear sequence. Atomic computations are performed to give a detailed account of the transitions in Sn+6 to Sn+13 ions. The spectrum is calculated for the most important excited configurations 4p5 4dn+1, 4dn-1 4f1, and 4dn-1 5p1 with respect to the ground configuration 4dn, with n=8-1, respectively. The importance of 4p-4d, 4d-4f, and 4d-5p transitions is stressed, as well as the need for the configuration-interaction CI treatment of the ?n=0 transitions. In the region of importance for extreme ultraviolet (EUV) lithography around 13.4nm, the strongest lines were expected to be 4dn-4p5 4dn+1 and 4dn-4dn-1 4f1

323

Automatic extraction of runway structures in infrared remote sensing image sequences  

Science.gov (United States)

Today's flight safety, especially during aircraft landing approach to an airport, is often affected by adverse weather conditions. One of the promising technologies to increase the pilot's situation awareness is the Enhanced and Synthetic Vision System (ESVS): the combination of sensor vision and synthetic vision systems. In this paper we present one aspect of the sensor vision system, an algorithm that is using only a sequence of infrared images to detect possible runway structures and obstacles on it during the aircraft landing approach. No additional information from database, INS or GPS is used at this processing stage. The algorithm generates several runway and obstacle hypotheses and the final decision in ESVS is taken in the further processing stage: fusion of radar and IR data hypotheses and synthetic vision data. The functionality of the algorithm was tested extensively during several flight campaigns with landing approaches to different German and European airports in 2003 and 2004.

Stephan, Christian; Palubinskas, Gintautas; Müller, Rupert

2005-10-01

324

Genetic structuring of European anchovy (Engraulis encrasicolus) populations through mitochondrial DNA sequences.  

Science.gov (United States)

Mitochondrial DNA sequence variation in 655 bpfragments of the cytochrome oxidase c subunit I gene, known as the DNA barcode, of European anchovy (Engraulis encrasicolus) was evaluated by analyzing 1529 individuals representing 16 populations from the Black Sea, through the Marmara Sea and the Aegean Sea to the Mediterranean Sea. A total of 19 (2.9%) variable sites were found among individuals, and these defined 10 genetically diverged populations with an overall mean distance of 1.2%. The highest nucleotide divergence was found between samples of eastern Mediterranean and northern Aegean (2.2%). Evolutionary history analysis among 16 populations clustered the Mediterranean Sea clades in one main branch and the other clades in another branch. Diverging pattern of the European anchovy populations correlated with geographic dispersion supports the genetic structuring through the Black Sea-Marmara Sea-Aegean Sea-Mediterranean Sea quad. PMID:22397375

Keskin, Emre; Atar, Hasan Huseyin

2012-04-01

325

Crystal Structure of Human Thymine DNA Glycosylase Bound to DNA Elucidates Sequence-Specific Mismatch Recognition  

Energy Technology Data Exchange (ETDEWEB)

Cytosine methylation at CpG dinucleotides produces m{sup 5}CpG, an epigenetic modification that is important for transcriptional regulation and genomic stability in vertebrate cells. However, m{sup 5}C deamination yields mutagenic G{center_dot}T mispairs, which are implicated in genetic disease, cancer, and aging. Human thymine DNA glycosylase (hTDG) removes T from G{center_dot}T mispairs, producing an abasic (or AP) site, and follow-on base excision repair proteins restore the G{center_dot}C pair. hTDG is inactive against normal A{center_dot}T pairs, and is most effective for G{center_dot}T mispairs and other damage located in a CpG context. The molecular basis of these important catalytic properties has remained unknown. Here, we report a crystal structure of hTDG (catalytic domain, hTDG{sup cat}) in complex with abasic DNA, at 2.8 {angstrom} resolution. Surprisingly, the enzyme crystallized in a 2:1 complex with DNA, one subunit bound at the abasic site, as anticipated, and the other at an undamaged (nonspecific) site. Isothermal titration calorimetry and electrophoretic mobility-shift experiments indicate that hTDG and hTDG{sup cat} can bind abasic DNA with 1:1 or 2:1 stoichiometry. Kinetics experiments show that the 1:1 complex is sufficient for full catalytic (base excision) activity, suggesting that the 2:1 complex, if adopted in vivo, might be important for some other activity of hTDG, perhaps binding interactions with other proteins. Our structure reveals interactions that promote the stringent specificity for guanine versus adenine as the pairing partner of the target base and interactions that likely confer CpG sequence specificity. We find striking differences between hTDG and its prokaryotic ortholog (MUG), despite the relatively high (32%) sequence identity.

Maiti, A.; Morgan, M.T.; Pozharski, E.; Drohat, A.C.

2009-05-19

326

Creation and structure determination of an artificial protein with three complete sequence repeats.  

Science.gov (United States)

Symfoil-4P is a de novo protein exhibiting the threefold symmetrical ?-trefoil fold designed based on the human acidic fibroblast growth factor. First three asparagine-glycine sequences of Symfoil-4P are replaced with glutamine-glycine (Symfoil-QG) or serine-glycine (Symfoil-SG) sequences protecting from deamidation, and His-Symfoil-II was prepared by introducing a protease digestion site into Symfoil-QG so that Symfoil-II has three complete repeats after removal of the N-terminal histidine tag. The Symfoil-QG and SG and His-Symfoil-II proteins were expressed in Eschericha coli as soluble protein, and purified by nickel affinity chromatography. Symfoil-II was further purified by anion-exchange chromatography after removing the HisTag by proteolysis. Both Symfoil-QG and Symfoil-II were crystallized in 0.1 M Tris-HCl buffer (pH 7.0) containing 1.8 M ammonium sulfate as precipitant at 293 K; several crystal forms were observed for Symfoil-QG and II. The maximum diffraction of Symfoil-QG and II crystals were 1.5 and 1.1 Å resolution, respectively. The Symfoil-II without histidine tag diffracted better than Symfoil-QG with N-terminal histidine tag. Although the crystal packing of Symfoil-II is slightly different from Symfoil-QG and other crystals of Symfoil derivatives having the N-terminal histidine tag, the refined crystal structure of Symfoil-II showed pseudo-threefold symmetry as expected from other Symfoils. Since the removal of the unstructured N-terminal histidine tag did not affect the threefold structure of Symfoil, the improvement of diffraction quality of Symfoil-II may be caused by molecular characteristics of Symfoil-II such as molecular stability. PMID:24121347

Adachi, Motoyasu; Shimizu, Rumi; Kuroki, Ryota; Blaber, Michael

2013-11-01

327

On the Structure of Abstract Hubbard Trees and the Space of Abstract Kneading Sequences of Degree Two  

CERN Document Server

One of the fundamental properties of the Mandelbrot set is that the set of postcritically finite parameters is structured like a tree. We extend this result to the set of quadratic kneading sequences and show that this space contains no irrational decorations. Along the way, we prove a combinatorial analogue to the correspondence principle of dynamic and parameter rays. Our key tool is to work simultaneously with the two equivalent combinatorial concepts of Hubbard trees and kneading sequences.

Kaffl, A

2007-01-01

328

Molecular characterization of the maize Rp1-D rust resistance haplotype and its mutants.  

Science.gov (United States)

The Rp1-D gene for resistance to maize common rust (Puccinia sorghi) is a member of a complex locus (haplotype) composed of Rp1-D and approximately eight other gene homologs. The identity of Rp1-D was demonstrated by using two independent gene-tagging approaches with the transposons Mutator and Dissociation. PIC20, a disease resistance (R) gene analog probe previously mapped to the rp1 locus, detected insertion of Dissociation in an Rp1-D mutation and excision in three revertants. Independent libraries probed with the PIC20 or Mutator probes resulted in isolation of the same gene sequence. Rp1-D belongs to the nucleotide binding site, leucine-rich repeat class of R genes. However, unlike the rust resistance genes M and L6 from flax, the maize Rp1-D gene does not encode an N-terminal domain with similarity to the signal transduction domains of the Drosophila Toll protein and mammalian interleukin-1 receptor. Although the abundance of transcripts of genes from the rp1 complex changed with leaf age, there was no evidence of any change due to inoculation with avirulent or virulent rust biotypes. A set of 27 Rp1-D mutants displayed at least nine different deletions of Rp1-D gene family members that were consistent with unequal crossing-over events. One mutation (Rp1-D*-24) resulted in deletion of all but one gene family member. Other unique deletions were observed in the disease lesion mimic Rp1-D*-21 and the partially susceptible mutant Rp1-D*-5. Different rp1 specificities have distinct DNA fingerprints (haplotypes). Analysis of recombinants between rp1 specificities indicated that recombination had occurred within the rp1 gene complex. Similar analyses indicated that the rust R genes at the rp5 locus, 2 centimorgans distal to rp1, are not closely related to Rp1-D. PMID:10402435

Collins, N; Drake, J; Ayliffe, M; Sun, Q; Ellis, J; Hulbert, S; Pryor, T

1999-07-01

329

Upstream Design and 1D-CAE  

Science.gov (United States)

Recently, engineering design environment of Japan is changing variously. Manufacturing companies are being challenged to design and bring out products that meet the diverse demands of customers and are competitive against those produced by rising countries(1). In order to keep and strengthen the competitiveness of Japanese companies, it is necessary to create new added values as well as conventional ones. It is well known that design at the early stages has a great influence on the final design solution. Therefore, design support tools for the upstream design is necessary for creating new added values. We have established a research society for 1D-CAE (1 Dimensional Computer Aided Engineering)(2), which is a general term for idea, methodology and tools applicable for the upstream design support, and discuss the concept and definition of 1D-CAE. This paper reports our discussion about 1D-CAE.

Sawada, Hiroyuki

330

Structural influence of C8-phenoxy-guanine in the NarI recognition DNA sequence.  

Science.gov (United States)

Phenoxyl radicals can covalently attach to the C8 site of 2'-deoxyguanosine (dG) to generate oxygen-linked biaryl ether C8-dG adducts. To assess the structural impact of an O-linked C8-dG adduct in duplex DNA, C8-phenoxy-G ((PhO)G) and C8-4-fluorophenoxy-G ((4FPhO)G) were incorporated into the G(3) position of the 12-mer NarI recognition sequence (5'-CTCGGCXCCATC, where X = G, (PhO)G, or (4FPhO)G) using solid-phase DNA synthesis with O-linked C8-dG phosphoramidites. The modified strands were hybridized to six different complementary strands that include regular base pairing to C [NarI'(C)], mismatches with G, A, T [NarI'(N)], and an abasic site [NarI'(THF)], and a 10-mer sequence to model a -2 deletion duplex [NarI'(-2)]. All duplex structures were characterized using UV-vis thermal melting temperature analysis, and in each instance, the O-linked C8-phenoxy-G adducts were found to destabilize the duplex relative to the unmodified controls. The most stable duplex structures match the O-linked C8-dG adduct against C and a G mismatch, which are comparable in terms of stability. These duplexes were further characterized using circular dichroism, dynamic (19)F nuclear magnetic resonance experiments, and molecular dynamics simulations. On the basis of these findings, (PhO)dG adopts the B conformation opposite C, with the phenoxy moiety residing in the solvent-exposed major groove. However, opposite the G mismatch, (PhO)dG adopts a "W-type" wedge conformation with the phenoxy group residing in the minor groove. These studies predict that the O-linked C8-dG lesion (PhO)G will have a weak mutagenic effect, as determined for the corresponding single-ringed nitrogen-linked C8-dG adduct derived from aniline. PMID:23984847

Kuska, Michael S; Witham, Aaron A; Sproviero, Michael; Manderville, Richard A; Majdi Yazdi, Mohadeseh; Sharma, Purshotam; Wetmore, Stacey D

2013-09-16

331

Structural Basis and Sequence Rules for Substrate Recognition by Tankyrase Explain the Basis for Cherubism Disease  

Energy Technology Data Exchange (ETDEWEB)

The poly(ADP-ribose)polymerases Tankyrase 1/2 (TNKS/TNKS2) catalyze the covalent linkage of ADP-ribose polymer chains onto target proteins, regulating their ubiquitylation, stability, and function. Dysregulation of substrate recognition by Tankyrases underlies the human disease cherubism. Tankyrases recruit specific motifs (often called RxxPDG hexapeptides) in their substrates via an N-terminal region of ankyrin repeats. These ankyrin repeats form five domains termed ankyrin repeat clusters (ARCs), each predicted to bind substrate. Here we report crystal structures of a representative ARC of TNKS2 bound to targeting peptides from six substrates. Using a solution-based peptide library screen, we derive a rule-based consensus for Tankyrase substrates common to four functionally conserved ARCs. This 8-residue consensus allows us to rationalize all known Tankyrase substrates and explains the basis for cherubism-causing mutations in the Tankyrase substrate 3BP2. Structural and sequence information allows us to also predict and validate other Tankyrase targets, including Disc1, Striatin, Fat4, RAD54, BCR, and MERIT40.

Guettler, Sebastian; LaRose, Jose; Petsalaki, Evangelia; Gish, Gerald; Scotter, Andy; Pawson, Tony; Rottapel, Robert; Sicheri, Frank (Mount Sinai Hospital); (OCI)

2012-02-07

332

Granular biomass structure and population dynamics in Sequencing Batch Biofilter Granular Reactor (SBBGR).  

Science.gov (United States)

The aim of this paper is to study the microbial and structural changes occurring during the transition from flocculent (used as inoculum) to biofilm and granular sludge in a Sequencing Batch Biofilter Granular Reactor (SBBGR). SBBGR is a new and promising technology characterised by low sludge production (5-6 times lower than in conventional treatment plants), high biomass concentration (up to 35 g TSS/L(bed)), high COD conversion capacity, high effluent quality and operation flexibility. Molecular in situ detection methods and microscopy staining procedures were employed in combination with the traditional measurements (i.e., oxygen uptake rate, COD removal efficiency) to evaluate the microbial activity and composition of the granular biomass. The granules structure was investigated by electron scanning microscopy, phase contrast analysis of granule sections and specific extracellular polymeric substances (EPS) stainings. Evident changes in biomass composition was observed during the shift from activated to granular sludge while a stable presence of active bacterial populations (mainly Proteobacteria) was found within mature granules. PMID:19962885

De Sanctis, M; Di Iaconi, C; Lopez, A; Rossetti, S

2010-04-01

333

Structural basis and sequence rules for substrate recognition by Tankyrase explain the basis for cherubism disease.  

Science.gov (United States)

The poly(ADP-ribose)polymerases Tankyrase 1/2 (TNKS/TNKS2) catalyze the covalent linkage of ADP-ribose polymer chains onto target proteins, regulating their ubiquitylation, stability, and function. Dysregulation of substrate recognition by Tankyrases underlies the human disease cherubism. Tankyrases recruit specific motifs (often called RxxPDG "hexapeptides") in their substrates via an N-terminal region of ankyrin repeats. These ankyrin repeats form five domains termed ankyrin repeat clusters (ARCs), each predicted to bind substrate. Here we report crystal structures of a representative ARC of TNKS2 bound to targeting peptides from six substrates. Using a solution-based peptide library screen, we derive a rule-based consensus for Tankyrase substrates common to four functionally conserved ARCs. This 8-residue consensus allows us to rationalize all known Tankyrase substrates and explains the basis for cherubism-causing mutations in the Tankyrase substrate 3BP2. Structural and sequence information allows us to also predict and validate other Tankyrase targets, including Disc1, Striatin, Fat4, RAD54, BCR, and MERIT40. PMID:22153077

Guettler, Sebastian; LaRose, Jose; Petsalaki, Evangelia; Gish, Gerald; Scotter, Andy; Pawson, Tony; Rottapel, Robert; Sicheri, Frank

2011-12-01

334

Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric has gained prominence. It is based on the deep theory of Kolmogorov Complexity and universality is its most novel striking feature. Since it can only be approximated via data compression, USM is a methodology rather than a formula quantifying the similarity of two strings. Three approximations of USM are available, namely UCD (Universal Compression Dissimilarity, NCD (Normalized Compression Dissimilarity and CD (Compression Dissimilarity. Their applicability and robustness is tested on various data sets yielding a first massive quantitative estimate that the USM methodology and its approximations are of value. Despite the rich theory developed around USM, its experimental assessment has limitations: only a few data compressors have been tested in conjunction with USM and mostly at a qualitative level, no comparison among UCD, NCD and CD is available and no comparison of USM with existing methods, both based on alignments and not, seems to be available. Results We experimentally test the USM methodology by using 25 compressors, all three of its known approximations and six data sets of relevance to Molecular Biology. This offers the first systematic and quantitative experimental assessment of this methodology, that naturally complements the many theoretical and the preliminary experimental results available. Moreover, we compare the USM methodology both with methods based on alignments and not. We may group our experiments into two sets. The first one, performed via ROC (Receiver Operating Curve analysis, aims at assessing the intrinsic ability of the methodology to discriminate and classify biological sequences and structures. A second set of experiments aims at assessing how well two commonly available classification algorithms, UPGMA (Unweighted Pair Group Method with Arithmetic Mean and NJ (Neighbor Joining, can use the methodology to perform their task, their performance being evaluated against gold standards and with the use of well known statistical indexes, i.e., the F-measure and the partition distance. Based on the experiments, several conclusions can be drawn and, from them, novel valuable guidelines for the use of USM on biological data. The main ones are reported next. Conclusion UCD and NCD are indistinguishable, i.e., they yield nearly the same values of the statistical indexes we have used, accross experiments and data sets, while CD is almost always worse than both. UPGMA seems to yield better classification results with respect to NJ, i.e., better values of the statistical indexes (10% difference or above, on a substantial fraction of experiments, compressors and USM approximation choices. The compression program PPMd, based on PPM (Prediction by Partial Matching, for generic data and Gencompress for DNA, are the best performers among the compression algorithms we have used, although the difference in performance, as measured by statistical indexes, between them and the other algorithms depends critically on the data set and may not be as large as expected. PPMd used with UCD or NCD and UPGMA, on sequence data is very close, although worse, in performance with the alignment methods (less than 2% difference on the F-measure. Yet, it scales well with data set size and it can work on data other than sequences. In summary, our quantitative analysis naturally complements the rich theory behind USM and supports the conclusion that the methodology is worth using because of its robustness, flexibility, scalability, and competitiveness with existing techniques. In particular, the methodology applies to all biological

Manzini Giovanni

2007-07-01

335

Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Protein-Carbohydrate interactions are crucial in many biological processes with implications to drug targeting and gene expression. Nature of protein-carbohydrate interactions may be studied at individual residue level by analyzing local sequence and structure environments in binding regions in comparison to non-binding regions, which provide an inherent control for such analyses. With an ultimate aim of predicting binding sites from sequence and structure, overall statistics of binding regions needs to be compiled. Sequence-based predictions of binding sites have been successfully applied to DNA-binding proteins in our earlier works. We aim to apply similar analysis to carbohydrate binding proteins. However, due to a relatively much smaller region of proteins taking part in such interactions, the methodology and results are significantly different. A comparison of protein-carbohydrate complexes has also been made with other protein-ligand complexes. Results We have compiled statistics of amino acid compositions in binding versus non-binding regions- general as well as in each different secondary structure conformation. Binding propensities of each of the 20 residue types and their structure features such as solvent accessibility, packing density and secondary structure have been calculated to assess their predisposition to carbohydrate interactions. Finally, evolutionary profiles of amino acid sequences have been used to predict binding sites using a neural network. Another set of neural networks was trained using information from single sequences and the prediction performance from the evolutionary profiles and single sequences were compared. Best of the neural network based prediction could achieve an 87% sensitivity of prediction at 23% specificity for all carbohydrate-binding sites, using evolutionary information. Single sequences gave 68% sensitivity and 55% specificity for the same data set. Sensitivity and specificity for a limited galactose binding data set were obtained as 63% and 79% respectively for evolutionary information and 62% and 68% sensitivity and specificity for single sequences. Propensity and other sequence and structural features of carbohydrate binding sites have also been compared with our similar extensive studies on DNA-binding proteins and also with protein-ligand complexes. Conclusion Carbohydrates typically show a preference to bind aromatic residues and most prominently tryptophan. Higher exposed surface area of binding sites indicates a role of hydrophobic interactions. Neural networks give a moderate success of prediction, which is expected to improve when structures of more protein-carbohydrate complexes become available in future.

Ahmad Shandar

2007-01-01

336

Novel sequence variations in LAMA2 and SGCG genes modulating cis-acting regulatory elements and RNA secondary structure  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english In this study, we detected new sequence variations in LAMA2 and SGCG genes in 5 ethnic populations, and analysed their effect on enhancer composition and mRNA structure. PCR amplification and DNA sequencing were performed and followed by bioinformatics analyses using ESEfinder as well as MFOLD softw [...] are. We found 3 novel sequence variations in the LAMA2 (c.3174+22_23insAT and c.6085 +12delA) and SGCG (c.*102A/C) genes. These variations were present in 210 tested healthy controls from Tunisian, Moroccan, Algerian, Lebanese and French populations suggesting that they represent novel polymorphisms within LAMA2 and SGCG genes sequences. ESEfinder showed that the c.*102A/C substitution created a new exon splicing enhancer in the 3'UTR of SGCG genes, whereas the c.6085 +12delA deletion was situated in the base pairing region between LAMA2 mRNA and the U1snRNA spliceosomal components. The RNA structure analyses showed that both variations modulated RNA secondary structure. Our results are suggestive of correlations between mRNA folding and the recruitment of spliceosomal components mediating splicing, including SR proteins. The contribution of common sequence variations to mRNA structural and functional diversity will contribute to a better study of gene expression.

Olfa, Siala; Ikhlass Hadj, Salem; Abdelaziz, Tlili; Imen, Ammar; Hanen, Belguith; Faiza, Fakhfakh.

337

Using Chou's pseudo amino acid composition to predict protein quaternary structure: a sequence-segmented PseAAC approach.  

Science.gov (United States)

In the protein universe, many proteins are composed of two or more polypeptide chains, generally referred to as subunits, which associate through noncovalent interactions and, occasionally, disulfide bonds to form protein quaternary structures. It has long been known that the functions of proteins are closely related to their quaternary structures; some examples include enzymes, hemoglobin, DNA polymerase, and ion channels. However, it is extremely labor-expensive and even impossible to quickly determine the structures of hundreds of thousands of protein sequences solely from experiments. Since the number of protein sequences entering databanks is increasing rapidly, it is highly desirable to develop computational methods for classifying the quaternary structures of proteins from their primary sequences. Since the concept of Chou's pseudo amino acid composition (PseAAC) was introduced, a variety of approaches, such as residue conservation scores, von Neumann entropy, multiscale energy, autocorrelation function, moment descriptors, and cellular automata, have been utilized to formulate the PseAAC for predicting different attributes of proteins. Here, in a different approach, a sequence-segmented PseAAC is introduced to represent protein samples. Meanwhile, multiclass SVM classifier modules were adopted to classify protein quaternary structures. As a demonstration, the dataset constructed by Chou and Cai [(2003) Proteins 53:282-289] was adopted as a benchmark dataset. The overall jackknife success rates thus obtained were 88.2-89.1%, indicating that the new approach is quite promising for predicting protein quaternary structure. PMID:18427713

Zhang, Shao-Wu; Chen, Wei; Yang, Feng; Pan, Quan

2008-10-01

338

The investigation of the secondary structures of various peptide sequences of ?-casein by the multicanonical simulation method  

Science.gov (United States)

The structural properties of Arginine-Glutamic acid-Leucine-Glutamic acid-Glutamic acid-Leucine-Asparagine-Valine-Proline-Glycine (RELEELNVPG, in one letter code), Glutamic acid-Glutamic acid-Glutamine-Glutamine-Glutamine-Threonine-Glutamic acid (EEQQQTE) and Glutamic acid-Aspartic acid-Glutamic acid-Leucine-Glutamine-Aspartic acid-Lysine-Isoleucine (EDELQDKI) peptide sequences of ?-casein were studied by three-dimensional molecular modeling. In this work, the three-dimensional conformations of each peptide from their primary sequences were obtained by multicanonical simulations. With using major advantage of this simulation technique, Ramachandran plots were prepared and analysed to predict the relative occurrence probabilities of ?-turn, ?-turn and helical structures. Structural predictions of these sequences of ?-casein molecule indicate the presence of high level of helical structures and ?III-turns. The occurrence probabilities of inverse and classical ?-turns were low. The probability of helical structure of each sequence significantly decreased when the temperature increased. Our results show these peptides have highly helical structure and better agreement with the results of spectroscopic techniques and other prediction methods.

Ya?ar, F.; Çelik, S.; Köksel, H.

2006-05-01

339

Determinación de la estructura de bases de Schiff derivadas de 2-aminofenol, nitro y flúor sustituidas, utilizando la RMN 1D y 2D / Structure determination of the Schiff bases derivated from 2- aminophenol, nitro and fluorid substituted, using RMN 1D and 2D  

Scientific Electronic Library Online (English)

Full Text Available SciELO Peru | Language: Spanish Abstract in spanish En este trabajo se presenta el resultado de la síntesis de bases de Schiff a partir del 2-amino fenol con 4-nitro y 2-fluorbenzaldehído y se caracterizan los productos, usando el microanálisis, la espectroscopía infrarroja, la espectroscopía de RMN de H¹ y C13 y la RMN en dos dimensiones (COSY y HMB [...] C ), para determinar sus estructuras. Además, se estudia el corrimiento que sufren los carbonos con respecto al tipo de sustituyente del aldehído en la base de Schiff. Abstract in english In this work the result of the synthesis of a base of Schiff is presented, starting from the 2-amino phenol with 4-nitro and 2- fluorbenzaldehyde and the products are characterized, using the microanalysis, the infrared spectroscopy, the spectroscopy of RMN of H¹ and C13 and the RMN in two dimension [...] s (COSY and HMBC), to determine their structures. In addition, the shifts that suffering the carbon atoms respecting to the type of sustituents in the Schiff base are studied.

Sergio, Zamorano; Juan, Camus.

2011-01-01

340

Characterization of Microbial Population Structures in Recreational Waters and Primary Sources of Fecal Pollution with a Next-Generation Sequencing Approach  

Science.gov (United States)

The invention of new approaches to DNA sequencing commonly referred to as next generation sequencing technologies is revolutionizing the study of microbial diversity. In this chapter, we discuss the characterization of microbial population structures in recreational waters and p...

 
 
 
 
341

X-ray sequence and crystal structure of luffaculin 1, a novel type 1 ribosome-inactivating protein  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Protein sequence can be obtained through Edman degradation, mass spectrometry, or cDNA sequencing. High resolution X-ray crystallography can also be used to derive protein sequence information, but faces the difficulty in distinguishing the Asp/Asn, Glu/Gln, and Val/Thr pairs. Luffaculin 1 is a new type 1 ribosome-inactivating protein (RIP isolated from the seeds of Luffa acutangula. Besides rRNA N-glycosidase activity, luffaculin 1 also demonstrates activities including inhibiting tumor cells' proliferation and inducing tumor cells' differentiation. Results The crystal structure of luffaculin 1 was determined at 1.4 Å resolution. Its amino-acid sequence was derived from this high resolution structure using the following criteria: 1 high resolution electron density; 2 comparison of electron density between two molecules that exist in the same crystal; 3 evaluation of the chemical environment of residues to break down the sequence assignment ambiguity in residue pairs Glu/Gln, Asp/Asn, and Val/Thr; 4 comparison with sequences of the homologous proteins. Using the criteria 1 and 2, 66% of the residues can be assigned. By incorporating with criterion 3, 86% of the residues were assigned, suggesting the effectiveness of chemical environment evaluation in breaking down residue ambiguity. In total, 94% of the luffaculin 1 sequence was assigned with high confidence using this improved X-ray sequencing strategy. Two N-acetylglucosamine moieties, linked respectively to the residues Asn77 and Asn84, can be identified in the structure. Residues Tyr70, Tyr110, Glu159 and Arg162 define the active site of luffaculin 1 as an RNA N-glycosidase. Conclusion X-ray sequencing method can be effective to derive sequence information of proteins. The evaluation of the chemical environment of residues is a useful method to break down the assignment ambiguity in Glu/Gln, Asp/Asn, and Val/Thr pairs. The sequence and the crystal structure confirm that luffaculin 1 is a new type 1 RIP.

Meehan Edward J

2007-04-01

342

The HIVToolbox 2 Web System Integrates Sequence, Structure, Function and Mutation Analysis  

Science.gov (United States)

There is enormous interest in studying HIV pathogenesis for improving the treatment of patients with HIV infection. HIV infection has become one of the best-studied systems for understanding how a virus can hijack a cell. To help facilitate discovery, we previously built HIVToolbox, a web system for visual data mining. The original HIVToolbox integrated information for HIV protein sequence, structure, functional sites, and sequence conservation. This web system has been used for almost 40,000 searches. We report improvements to HIVToolbox including new functions and workflows, data updates, and updates for ease of use. HIVToolbox2, is an improvement over HIVToolbox with new functions. HIVToolbox2 has new functionalities focused on HIV pathogenesis including drug-binding sites, drug-resistance mutations, and immune epitopes. The integrated, interactive view enables visual mining to generate hypotheses that are not readily revealed by other approaches. Most HIV proteins form multimers, and there are posttranslational modification and protein-protein interaction sites at many of these multimerization interfaces. Analysis of protease drug binding sites reveals an anatomy of drug resistance with different types of drug-resistance mutations regionally localized on the surface of protease. Some of these drug-resistance mutations have a high prevalence in specific HIV-1 M subtypes. Finally, consolidation of Tat functional sites reveals a hotspot region where there appear to be 30 interactions or posttranslational modifications. A cursory analysis with HIVToolbox2 has helped to identify several global patterns for HIV proteins. An initial analysis with this tool identifies homomultimerization of almost all HIV proteins, functional sites that overlap with multimerization sites, a global drug resistance anatomy for HIV protease, and specific distributions of some DRMs in specific HIV M subtypes. HIVToolbox2 is an open-access web application available at [http://hivtoolbox2.bio-toolkit.com]. PMID:24886930

Sargeant, David P.; Deverasetty, Sandeep; Strong, Christy L.; Alaniz, Izua J.; Bartlett, Alexandria; Brandon, Nicholas R.; Brooks, Steven B.; Brown, Frederick A.; Bufi, Flaviona; Chakarova, Monika; David, Roxanne P.; Dobritch, Karlyn M.; Guerra, Horacio P.; Hedden, Michael W.; Kumra, Rma; Levitt, Kelvy S.; Mathew, Kiran R.; Matti, Ray; Maza, Dorothea Q.; Mistry, Sabyasachy; Novakovic, Nemanja; Pomerantz, Austin; Portillo, Josue; Rafalski, Timothy F.; Rathnayake, Viraj R.; Rezapour, Noura; Songao, Sarah; Tuggle, Sean L.; Yousif, Sandy; Dorsky, David I.; Schiller, Martin R.

2014-01-01

343

Analysis of the population structure of Anaplasma phagocytophilum using multilocus sequence typing.  

Science.gov (United States)

Anaplasma phagocytophilum is a Gram-negative obligate intracellular bacterium that replicates in neutrophils. It is transmitted via tick-bite and causes febrile disease in humans and animals. Human granulocytic anaplasmosis is regarded as an emerging infectious disease in North America, Europe and Asia. However, although increasingly detected, it is still rare in Europe. Clinically apparent A. phagocytophilum infections in animals are mainly found in horses, dogs, cats, sheep and cattle. Evidence from cross-infection experiments that A. phagocytophilum isolates of distinct host origin are not uniformly infectious for heterologous hosts has led to several approaches of molecular strain characterization. Unfortunately, the results of these studies are not always easily comparable, because different gene regions and fragment lengths were investigated. Multilocus sequence typing is a widely accepted method for molecular characterization of bacteria. We here provide for the first time a universal typing method that is easily transferable between different laboratories. We validated our approach on an unprecedented large data set of almost 400 A. phagocytophilum strains from humans and animals mostly from Europe. The typability was 74% (284/383). One major clonal complex containing 177 strains was detected. However, 54% (49/90) of the sequence types were not part of a clonal complex indicating that the population structure of A. phagocytophilum is probably semiclonal. All strains from humans, dogs and horses from Europe belonged to the same clonal complex. As canine and equine granulocytic anaplasmosis occurs frequently in Europe, human granulocytic anaplasmosis is likely to be underdiagnosed in Europe. Further, wild boars and hedgehogs may serve as reservoir hosts of the disease in humans and domestic animals in Europe, because their strains belonged to the same clonal complex. In contrast, as they were only distantly related, roe deer, voles and shrews are unlikely to harbor A. phagocytophilum strains infectious for humans, domestic or farm animals. PMID:24699849

Huhn, Christian; Winter, Christina; Wolfsperger, Timo; Wüppenhorst, Nicole; Strašek Smrdel, Katja; Skuballa, Jasmin; Pfäffle, Miriam; Petney, Trevor; Silaghi, Cornelia; Dyachenko, Viktor; Pantchev, Nikola; Straubinger, Reinhard K; Schaarschmidt-Kiener, Daniel; Ganter, Martin; Aardema, Matthew L; von Loewenich, Friederike D

2014-01-01

344

Plasmonic Excitations of 1D Metal-Dielectric Interfaces in 2D Systems: 1D Surface Plasmon Polaritons  

Science.gov (United States)

Surface plasmon-polariton (SPP) excitations of metal-dielectric interfaces are a fundamental light-matter interaction which has attracted interest as a route to spatial confinement of light far beyond that offered by conventional dielectric optical devices. Conventionally, SPPs have been studied in noble-metal structures, where the SPPs are intrinsically bound to a 2D metal-dielectric interface. Meanwhile, recent advances in the growth of hybrid 2D crystals, which comprise laterally connected domains of distinct atomically thin materials, provide the first realistic platform on which a 2D metal-dielectric system with a truly 1D metal-dielectric interface can be achieved. Here we show for the first time that 1D metal-dielectric interfaces support a fundamental 1D plasmonic mode (1DSPP) which exhibits cutoff behavior that provides dramatically improved light confinement in 2D systems. The 1DSPP constitutes a new basic category of plasmon as the missing 1D member of the plasmon family: 3D bulk plasmon, 2DSPP, 1DSPP, and 0D localized SP.

Mason, Daniel R.; Menabde, Sergey G.; Yu, Sunkyu; Park, Namkyoo

2014-04-01

345

Plasmonic Excitations of 1D Metal-Dielectric Interfaces in 2D Systems: 1D Surface Plasmon Polaritons  

Science.gov (United States)

Surface plasmon-polariton (SPP) excitations of metal-dielectric interfaces are a fundamental light-matter interaction which has attracted interest as a route to spatial confinement of light far beyond that offered by conventional dielectric optical devices. Conventionally, SPPs have been studied in noble-metal structures, where the SPPs are intrinsically bound to a 2D metal-dielectric interface. Meanwhile, recent advances in the growth of hybrid 2D crystals, which comprise laterally connected domains of distinct atomically thin materials, provide the first realistic platform on which a 2D metal-dielectric system with a truly 1D metal-dielectric interface can be achieved. Here we show for the first time that 1D metal-dielectric interfaces support a fundamental 1D plasmonic mode (1DSPP) which exhibits cutoff behavior that provides dramatically improved light confinement in 2D systems. The 1DSPP constitutes a new basic category of plasmon as the missing 1D member of the plasmon family: 3D bulk plasmon, 2DSPP, 1DSPP, and 0D localized SP. PMID:24686894

Mason, Daniel R.; Menabde, Sergey G.; Yu, Sunkyu; Park, Namkyoo

2014-01-01

346

First Observation of Upsilon(1D) States  

CERN Document Server

The CLEO III experiment has recently accumulated a large statistics sample of 4.73 x 10^6 Upsilon(3S) decays. We present the first evidence for the production of the triplet Upsilon(1D) states in the four-photon cascade, Upslion(3S) -> gamma chi_b(2P), chi_b(2P) -> gamma Upsilon(1D), Upsilon(1D) -> gamma chi_b(1P), chi_b(1P) -> gamma Upsilon(1S), followed by the Upsilon(1S) annihilation to e+ e- or mu+ mu-. The signal has a significance of 9.7 standard deviations. The measured product branching ratio for these five decays, (3.3 +- 0.6 +- 0.5) x 10^{-5}, is consistent with the theoretical estimates. We see a 6.8 standard deviation signal for a state with a mass of 10162.2 +- 1.6 MeV/c^2, consistent with the Upsilon(1D_2) assignment. We also present improved measurements of the Upsilon(3S) -> pi0 pi0 Upsilon(1S) branching ratio and the associated di-pion mass distribution.

Csorna, S E; Bonvicini, G; Cinabro, D; Dubrovin, M; McGee, S; Bornheim, A; Lipeles, E; Pappas, S P; Shapiro, A; Sun, W M; Weinstein, A J; Mahapatra, R; Briere, R A; Chen, G P; Ferguson, T; Tatishvili, G T; Vogel, H; Adam, N E; Alexander, J P; Berkelman, K; Boisvert, V; Cassel, David G; Drell, P S; Duboscq, J E; Ecklund, K M; Ehrlich, R; Galik, R S; Gibbons, L; Gittelman, B; Gray, S W; Hartill, D L; Heltsley, B K; Hsu, L; Jones, C D; Kandaswamy, J; Kreinick, D L; Magerkurth, A; Mahlke-Krüger, H; Meyer, T O; Mistry, N B; Nordberg, E; Patterson, J R; Peterson, D; Pivarski, J; Riley, D; Sadoff, A J; Schwarthoff, H; Shepherd, M R; Thayer, J G; Urner, D; Viehhauser, G; Warburton, A; Weinberger, M; Athar, S B; Avery, P; Breva-Newell, L; Potlia, V; Stöck, H; Yelton, J; Brandenburg, G; Kim, D Y J; Wilson, R; Benslama, K; Eisenstein, B I; Ernst, J; Gollin, G D; Hans, R M; Karliner, I; Lowrey, N; Plager, C; Sedlack, C; Selen, M; Thaler, J J; Williams, J; Edwards, K W; Ammar, R; Besson, D; Zhao, X; Anderson, S; Frolov, V V; Kubota, Y; Lee, S J; Li, S Z; Poling, R A; Smith, A; Stepaniak, C J; Urheim, J; Metreveli, Z V; Seth, K K; Tomaradze, A G; Zweber, P; Ahmed, S; Alam, M S; Jian, L; Saleem, M; Wappler, F; Eckhart, E; Gan, K K; Gwon, C; Hart, T; Honscheid, K; Hufnagel, D; Kagan, H; Kass, R; Pedlar, T K; Thayer, J B; Von Törne, E; Wilksen, T; Zoeller, M M; Muramatsu, H; Richichi, S J; Severini, H; Skubic, P L; Dytman, S A; Müller, J A; Nam, S; Savinov, V; Chen, S; Hinson, J W; Lee, J; Miller, D H; Pavlunin, V; Shibata, E I; Shipsey, I P J; Cronin-Hennessy, D; Lyon, A L; Park, C S; Park, W; Thorndike, E H; Coan, T E; Gao, Y S; Liu, F; Maravin, Y; Stroynowski, R; Artuso, M; Boulahouache, C; Bukin, K; Dambasuren, E; Khroustalev, K; Mountain, R; Nandakumar, R; Skwarnicki, T; Stone, S; Wang, J C; Mahmood, A H

2002-01-01

347

Main: 1D8U [RPSD  

Full Text Available 1D8U ?? Rice Oryza sativa L. Non-Symbiotic Hemoglobin 1 Name=Hb1; Synonyms=Glb1a; Oryza Sativa ... s Jr. M.Hargrove, E.A.Brucker, B.Stec, G.Sarath, R.Arredondo -Peter, R.V.Klucas, J.S.Olson, G.N.Phillips Jr. Cry ...

348

1-D equations of radiation hydrodynamics  

International Nuclear Information System (INIS)

The radiation transfer equation is derived in the comoving frame, in curvilinear coordinates, to first order in u/c, no symmetry being assumed. This equation is then specialized to 1-D, and its moments are calculated for the limiting case of Thomson scattering. The equations of radiation hydrodynamics are also given

349

[Divergence of the polytene chromosome banding sequences as a reflection of evolutionary rearrangements of the genome linear structure].  

Science.gov (United States)

Banding sequences of five chromosomal arms (A, C, D, E, and F), accounting for about 70% of the total genome size in 63 Chironomus species, were used as phylogenetic markers to analyze divergence patterns of the linear genome structure during the evolution. The number of chromosomal breakpoints between the pairs of banding sequences compared served as a measure of divergence. It was demonstrated that the greater the divergence between the species compared, the higher the number of chromosomal breakpoints and the smaller the size of the conserved chromosomal regions. A banding sequences comparison in sibling species demonstrated a lower number of chromosomal breakpoints; the breakpoint number was maximum in a comparison of the banding sequences in the subgenera Chironomus and Camptochironomus. The use of the number of chromosomal breakpoints as a divergence measure provided establishment of phylogenetic relationships between 63 Chironomus species and discrimination of sibling species groups and cytocomplexes on a phylogenetic tree. PMID:15810608

Gunderina, L I; Kiknadze, I I; Istomina, A G; Gusev, V D; Miroshnichenko, L A

2005-02-01

350

SFAPS: An R package for structure/function analysis of protein sequences based on informational spectrum method.  

Science.gov (United States)

The R package SFAPS has been developed for structure/function analysis of protein sequences based on information spectrum method. The informational spectrum method employs the electron-ion interaction potential parameter as the numerical representation for the protein sequence, and obtains the characteristic frequency of a particular protein interaction after computing the Discrete Fourier Transform for protein sequences. The informational spectrum method is often used to analyze protein sequences, so we developed this software tool, which is implemented as an add-on package to the freely available and widely used statistical language R. Our package is distributed as open source code for Linux, Unix and Microsoft Windows. It is released under the GNU General Public License. The R package along with its source code and additional material are freely available at http://mlsbl.tongji.edu.cn/DBdownload.asp. PMID:25132640

Deng, Su-Ping; Huang, De-Shuang

2014-10-01

351

Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Maturation inhibitors such as Bevirimat are a new class of antiretroviral drugs that hamper the cleavage of HIV-1 proteins into their functional active forms. They bind to these preproteins and inhibit their cleavage by the HIV-1 protease, resulting in non-functional virus particles. Nevertheless, there exist mutations in this region leading to resistance against Bevirimat. Highly specific and accurate tools to predict resistance to maturation inhibitors can help to identify patients, who might benefit from the usage of these new drugs. Results We tested several methods to improve Bevirimat resistance prediction in HIV-1. It turned out that combining structural and sequence-based information in classifier ensembles led to accurate and reliable predictions. Moreover, we were able to identify the most crucial regions for Bevirimat resistance computationally, which are in line with experimental results from other studies. Conclusions Our analysis demonstrated the use of machine learning techniques to predict HIV-1 resistance against maturation inhibitors such as Bevirimat. New maturation inhibitors are already under development and might enlarge the arsenal of antiretroviral drugs in the future. Thus, accurate prediction tools are very useful to enable a personalized therapy.

Dybowski J Nikolaj

2011-11-01

352

Term structure of 4d-electron configurations and calculated spectrum in Sn-isonuclear sequence  

Energy Technology Data Exchange (ETDEWEB)

Theoretical calculations of term structure are carried out for the ground configurations 4d{sup w}, of atomic ions in the Sn isonuclear sequence. Atomic computations are performed to give a detailed account of the transitions in Sn{sup +6} to Sn{sup +13} ions. The spectrum is calculated for the most important excited configurations 4p{sup 5} 4d{sup n+1}, 4d{sup n-1} 4f{sup 1}, and 4d{sup n-1} 5p{sup 1} with respect to the ground configuration 4d{sup n}, with n=8-1, respectively. The importance of 4p-4d, 4d-4f, and 4d-5p transitions is stressed, as well as the need for the configuration-interaction CI treatment of the {delta}n=0 transitions. In the region of importance for extreme ultraviolet (EUV) lithography around 13.4nm, the strongest lines were expected to be 4d{sup n}-4p{sup 5} 4d{sup n+1} and 4d{sup n}-4d{sup n-1} 4f{sup 1}.

Al-Rabban, Moza M. [Department of Physics, University of Qatar, PO Box 24905, Doha (Qatar)]. E-mail: mmalrabban@hotmail.com

2006-01-15

353

Evolutionary patterns in the sequence and structure of transfer RNA: early origins of archaea and viruses.  

Science.gov (United States)

Transfer RNAs (tRNAs) are ancient molecules that are central to translation. Since they probably carry evolutionary signatures that were left behind when the living world diversified, we reconstructed phylogenies directly from the sequence and structure of tRNA using well-established phylogenetic methods. The trees placed tRNAs with long variable arms charging Sec, Tyr, Ser, and Leu consistently at the base of the rooted phylogenies, but failed to reveal groupings that would indicate clear evolutionary links to organismal origin or molecular functions. In order to uncover evolutionary patterns in the trees, we forced tRNAs into monophyletic groups using constraint analyses to generate timelines of organismal diversification and test competing evolutionary hypotheses. Remarkably, organismal timelines showed Archaea was the most ancestral superkingdom, followed by viruses, then superkingdoms Eukarya and Bacteria, in that order, supporting conclusions from recent phylogenomic studies of protein architecture. Strikingly, constraint analyses showed that the origin of viruses was not only ancient, but was linked to Archaea. Our findings have important implications. They support the notion that the archaeal lineage was very ancient, resulted in the first organismal divide, and predated diversification of tRNA function and specificity. Results are also consistent with the concept that viruses contributed to the development of the DNA replication machinery during the early diversification of the living world. PMID:18369418

Sun, Feng-Jie; Caetano-Anollés, Gustavo

2008-03-01

354

A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology.  

Science.gov (United States)

Conventional drug design embraces the "one gene, one drug, one disease" philosophy. Polypharmacology, which focuses on multi-target drugs, has emerged as a new paradigm in drug discovery. The rational design of drugs that act via polypharmacological mechanisms can produce compounds that exhibit increased therapeutic potency and against which resistance is less likely to develop. Additionally, identifying multiple protein targets is also critical for side-effect prediction. One third of potential therapeutic compounds fail in clinical trials or are later removed from the market due to unacceptable side effects often caused by off-target binding. In the current work, we introduce a multidimensional strategy for the identification of secondary targets of known small-molecule inhibitors in the absence of global structural and sequence homology with the primary target protein. To demonstrate the utility of the strategy, we identify several targets of 4,5-dihydroxy-3-(1-naphthyldiazenyl)-2,7-naphthalenedisulfonic acid, a known micromolar inhibitor of Trypanosoma brucei RNA editing ligase 1. As it is capable of identifying potential secondary targets, the strategy described here may play a useful role in future efforts to reduce drug side effects and/or to increase polypharmacology. PMID:20098496

Durrant, Jacob D; Amaro, Rommie E; Xie, Lei; Urbaniak, Michael D; Ferguson, Michael A J; Haapalainen, Antti; Chen, Zhijun; Di Guilmi, Anne Marie; Wunder, Frank; Bourne, Philip E; McCammon, J Andrew

2010-01-01

355

Sequence and 3D structure based analysis of TNT degrading proteins in Arabidopsis thaliana.  

Science.gov (United States)

TNT, accidentally released at several manufacturing sites, contaminates ground water and soil. It has a toxic effect to algae and invertebrate, and chronic exposure to TNT also causes harmful effects to human. On the other hand, many plants including Arabidopsis thaliana have the ability to metabolize TNT either completely or at least to a reduced less toxic form. In A. thaliana, the enzyme UDP glucosyltransferase (UDPGT) can further conjugate the reduced forms 2-HADNT and 4-HADNT (2-hydroxylamino-4, 6- dinitrotoluene and 4-hydroxylamino-2, 6- dinitrotoluene) of TNT. Based on the experimental analysis, existing literature and phylogenetic analysis, it is evident that among 107 UDPGT proteins only six are involved in the TNT degrading process. A total of 13 UDPGT proteins including five of these TNT degrading proteins fall within the same group of phylogeny. Thus, these 13 UDPGT proteins have been classified into two groups, TNT-degrading and TNT-non-degrading proteins. To understand the differences in TNT-degrading capacities; using homology modeling we first predicted two structures, taking one representative sequence from both the groups. Next, we performed molecular docking of the modeled structure and TNT reduced form 2-hydroxylamino-4, 6- dinitrotoluene (2-HADNT). We observed that while the Trp residue located within the active site region of the TNT- degrading protein showed ?-Cation interaction; such type of interaction was absent in TNT-non-degrading protein, as the respective Trp residue lay outside of the pocket in this case. We observed the conservation of this ?-Cation interaction during MD simulation of TNT-degrading protein. Thus, the position and the orientation of the active site residue Trp could explain the presence and absence of TNT-degrading capacity of the UDPGT proteins. PMID:24590695

Bhattacherjee, Amrita; Mandal, Rahul Shubhra; Das, Santasabuj; Kundu, Sudip

2014-03-01

356

A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Covariance models (CMs are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N3 in memory. This is only practical for small RNAs. Results I describe a divide and conquer variant of the alignment algorithm that is analogous to memory-efficient Myers/Miller dynamic programming algorithms for linear sequence alignment. The new algorithm has an O(N2 log N memory complexity, at the expense of a small constant factor in time. Conclusions Optimal ribosomal RNA structural alignments that previously required up to 150 GB of memory now require less than 270 MB.

Eddy Sean R

2002-07-01

357

Active motif finder - a bio-tool based on mutational structures in DNA sequences  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Active Motif Finder (AMF) is a novel algorithmic tool, designed based on mutations in DNA sequences. Tools available at present for finding motifs are based on matching a given motif in the query sequence. AMF describes a new algorithm that identifies the occurrences of patterns which possess all kinds of mutations like insertion, deletion and mismatch. The algorithm is mainly based on the Alignment Score Matrix (ASM) computation by comparing input motif with full length sequence. Much of the...

Udayakumar, Mani; Shanmuga-priya, Palaniyandi; Hemavathi, Kamalakannan; Seenivasagam, Rengasamy

2011-01-01

358

Iron-based 1D nanostructures by electrospinning process  

Energy Technology Data Exchange (ETDEWEB)

Iron-based 1D nanostructures have been successfully prepared using an electrospinning technique and varying the pyrolysis atmospheres. Hematite (Fe{sub 2}O{sub 3}) nanotubes and polycrystalline Fe{sub 3}C nanofibers were obtained by simple air or mixed gas (H{sub 2}, Ar) annealing treatments. Using the air annealing treatment, a high control of the morphology as well as of the wall thickness of the nanotubes was demonstrated with a direct influence of the starting polymer concentration. When mixed gases (H{sub 2} and Ar) were used for the annealing treatments, for the first time polycrystalline Fe{sub 3}C nanofibers composed of carbon graphitic planes were obtained, ensuring Fe{sub 3}C nanoparticle stability and nanofiber cohesion. The morphology and structural properties of all these iron-based 1D nanostructures were fully characterized by SEM, TEM, XRD and Raman spectroscopy.

Eid, Cynthia; Asmar, Roy; Khoury, Antonio [Laboratoire de Physique Appliquee (LPA) associe a l' ecole doctorale des Sciences et Technologies, Departement de Physique, Universite Libanaise, Faculte des Sciences II, 90656 Jdeidet El Metn (Lebanon); Brioude, Arnaud; Salles, Vincent; Monteil, Yves; Miele, Philippe [Laboratoire des Multimateriaux et Interfaces (UMR CNRS 5615), Universite Lyon1, Universite de Lyon, 43 Bd du 11 Novembre 1918, Villeurbanne Cedex (France); Plenet, Jean-Claude [Laboratoire de Physique de la Matiere condensee et Nanostructures, CNRS UMR 5586, Universite Lyon1, Universite de Lyon, 43 Bd du 11 Novembre 1918, Villeurbanne Cedex (France); Khoury, Randa, E-mail: arnaud.brioude@univ-lyon1.fr [Laboratoire de Chimie, Faculte d' Agronomie, Universite Libanaise, Fanar, Faculte des Sciences II, 90656 Jdeidet El Metn (Lebanon)

2010-03-26

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Sandia reactor kinetics codes: SAK and PK1D  

International Nuclear Information System (INIS)

The Sandia Kinetics code (SAK) is a one-dimensional coupled thermal-neutronics transient analysis code for use in simulation of reactor transients. The time-dependent cross section routines allow arbitrary time-dependent changes in material properties. The one-dimensional heat transfer routines are for cylindrical geometry and allow arbitrary mesh structure, temperature-dependent thermal properties, radiation treatment, and coolant flow and heat-transfer properties at the surface of a fuel element. The Point Kinetics 1 Dimensional Heat Transfer Code (PK1D) solves the point kinetics equations and has essentially the same heat-transfer treatment as SAK. PK1D can address extended reactor transients with minimal computer execution time

360

Noise correlations in 1D Bose mixtures in optical lattices  

Science.gov (United States)

We study the noise correlations of one-dimensional(1D) Bose mixtures, as a probe of their quantum phases. In [1], we discuss the rich structure of many-body phases, such as paired and counterflow superfluidity in such 1D mixtures. We now ask the question what is the signature of these phases in the correlations of the atomic cloud afte