Sample records for 1d structural sequences

  1. Novel 1-D Sandwich Photonic Bandgap Structure

    Institute of Scientific and Technical Information of China (English)

    庞云波; 高葆新


    A sandwich photonic bandgap (PBG) structure is a novel PBG structure whose periodic lattice is buried in the middle of a substrate. Neither drilling nor suspending the substrate is required, and the integrity of the ground plane is maintained. This paper presents several modification techniques for sandwich PBG structure fabrication. The forbidden gap can be improved by adopting the chirping technique, applying the tapering technique, enlarging the periodic elements, adjusting the location of the periodic lattice in the substrate, and using different dielectric media H-shape elements. A finite difference time domain method is applied to analyze the structures. Deep and wide stopbands can be obtained using the modified sandwich structures. Experimental measurement results agree well with the theoretical analysis.

  2. Molecular cloning, sequence analysis and pharmacological properties of the porcine 5-HT(1D) receptor.

    NARCIS (Netherlands)

    P.L. Bhalla (Pankaj); H.S. Sharma (Hari); T. Wurch (Thierry); P.J. Pauwels (Petrus); P.R. Saxena (Pramod Ranjan)


    textabstractA cDNA encoding the full-length 5-HT(1D) receptor derived from porcine cerebral cortex was amplified, cloned and sequenced, using guinea-pig 5-HT(1D) receptor coding sequence oligonucleotide primers in reverse transcription-polymerase chain reaction (RT - PC

  3. Data of evolutionary structure change: 1D5IL-2GJJA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1D5IL-2GJJA 1D5I 2GJJ L A -DIKMTQSPSSMYASLGERVTITCKASQDIN------SY... 219 ALA CA 310 SER CA 336 2GJJ A 2GJJA PEVVKTGASVK 5.283660888671875 1 2GJJ... A 2GJJA RLEIK----RGEVQsequence

  4. Comments on the Bifurcation Structure of 1D Maps

    DEFF Research Database (Denmark)

    Belykh, V.N.; Mosekilde, Erik


    -within-a-box structure of the total bifurcation set. This presents a picture in which the homoclinic orbit bifurcations act as a skeleton for the bifurcational set. At the same time, experimental results on continued subharmonic generation for piezoelectrically amplified sound waves, predating the Feigenbaum theory...

  5. 1D Grating structures designed by the time domain topology optimization

    DEFF Research Database (Denmark)

    Yang, Lirong; Lavrinenko, Andrei; Sigmund, Ole;


    We report on the time domain application of topology optimization to 1D photonic devices. The method is confirmed to converge to the global minimum when optimizing a Bragg grating structure.......We report on the time domain application of topology optimization to 1D photonic devices. The method is confirmed to converge to the global minimum when optimizing a Bragg grating structure....

  6. Tunable Design of Structural Colors Produced by Pseudo-1D Photonic Crystals of Graphene Oxide. (United States)

    Tong, Liping; Qi, Wei; Wang, Mengfan; Huang, Renliang; Su, Rongxin; He, Zhimin


    It is broadly observed that graphene oxide (GO) films appear transparent with a thickness of about several nanometers, whereas they appear dark brown or almost black with thickness of more than 1 μm. The basic color mechanism of GO film on a sub-micrometer scale, however, is not well understood. This study reports on GO pseudo-1D photonic crystals (p1D-PhCs) exhibiting tunable structural colors in the visible wavelength range owing to its 1D Bragg nanostructures. Striking structural colors of GO p1D-PhCs could be tuned by simply changing either the volume or concentration of the aqueous GO dispersion during vacuum filtration. Moreover, the quantitative relationship between thickness and reflection wavelength of GO p1D-PhCs has been revealed, thereby providing a theoretical basis to rationally design structural colors of GO p1D-PhCs. The spectral response of GO p1D-PhCs to humidity is also obtained clearly showing the wavelength shift of GO p1D-PhCs at differently relative humidity values and thus encouraging the integration of structural color printing and the humidity-responsive property of GO p1D-PhCs to develop a visible and fast-responsive anti-counterfeiting label. The results pave the way for a variety of potential applications of GO in optics, structural color printing, sensing, and anti-counterfeiting.

  7. Analysis of the rotational structure in the high-resolution infrared spectra of trans-hexatriene-1,1-d2 and -cis-1-d1 (United States)

    Craig, Norman C.; Fuson, Hannah A.; Tian, Hengfeng; Blake, Thomas A.


    Mixtures of trans-hexatriene-1,1-d2, -cis-1-d1, and -trans-1-d1 have been synthesized. Anharmonic frequencies and harmonic intensities were predicted with the B3LYP/cc-pVTZ model for the out-of-plane (a″) modes of the three isotopologues. Assignments are proposed for most of the a″ vibrational modes above 500 cm-1. Ground state (GS) rotational constants have been determined for the 1,1-d2 and cis-1-d1 species from the analysis of rotational structure of C-type bands in the high-resolution (0.0015 cm-1) infrared spectra in a mixture of the three isotopologues. The GS constants for the 1,1-d2 species are A0 = 0.8018850(6), B0 = 0.0418540(6), and C0 = 0.0397997(4) cm-1. The GS constants for the cis-1-d1 species are A0 = 0.809388(1), B0 = 0.043532(2), and C0 = 0.041320(1) cm-1. Small inertial defects confirm planarity for both species. These ground state rotational constants are intended for use in determining a semiexperimental equilibrium structure and evaluating the influence of chain length on π-electron delocalization in polyenes.

  8. Transformation of 1-D Chiral-chained Titanium Phosphate to 2-D Layer Structure Through a 1-D Zigzag Chain

    Institute of Scientific and Technical Information of China (English)

    CHEN Chao; YANG Yu-lin; LI Wei-sheng; LIU Yun-ling; YI Zhuo; GUO Yang-hong; PANG Wen-qin


    The transformation of titanium phosphate from 1-D chiral- chain(JTP-A) to 2-D layer(TP-J1) has been carefully investigated. Through a hydrolysis-condensation self-assembly pathway, the crystals of TP-J1 can be obtained from the JTP-A phase under hydrothermal conditions. An intermediate material with zigzag chain during the transformation was observed by XRD characterization. A hypothesis of the transformation mechanism is also described in this article. It is noteworthy that ethylenediamine plays an important role in the transformation.

  9. The structure of nanocomposite 1D cationic conductor crystal@SWNT. (United States)

    Kiselev, N A; Kumskov, A S; Zakalyukin, R M; Vasiliev, A L; Chernisheva, M V; Eliseev, A A; Krestinin, A V; Freitag, B; Hutchison, J L


    Nanocomposites consisting of one-dimensional (1D) crystals of the cationic conductors CuI, CuBr and AgBr inside single-walled carbon nanotubes, mainly (n, 0), were obtained using the capillary technique. 1D crystal structure models were proposed based on the high resolution transmission electron microscopy performed on a FEI Titan 80-300 at 80 kV with aberration correction. According to the models and image simulations there are two modifications of 1D crystal: hexagonal close-packed bromine (iodine) anion sublattice (growth direction ) and 1D crystal cubic structure (growth direction ) compressed transversely to the nanotube (D(m) ∼1.33 nm) axis. Tentatively this kind of 1D crystal can be considered as monoclinic. One modification of the anion sublattice reversibly transforms into the other inside the nanotube, probably initiated by electron beam heating. As demonstrated by micrographs, copper or silver cations can occupy octahedral positions or are statistically distributed across two tetrahedral positions. A 1DAgBr@SWNT (18, 0; 19, 0) pseudoperiodic 'lattice distortion' is revealed resulting from convolution of the nanotube wall function image with 1D cubic crystal function image.

  10. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving. (United States)

    Pauli, Guido F; Niemitz, Matthias; Bisson, Jonathan; Lodewyk, Michael W; Soldi, Cristian; Shaw, Jared T; Tantillo, Dean J; Saya, Jordy M; Vos, Klaas; Kleinnijenhuis, Roel A; Hiemstra, Henk; Chen, Shao-Nong; McAlpine, James B; Lankin, David C; Friesen, J Brent


    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of "structural correctness" depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D (1)H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D (1)H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by (1)H iterative full spin analysis (HiFSA). Fully characterized 1D (1)H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication.

  11. Analysis of Rotational Structure in the High-Resolution Infrared Spectra of the TRANS-HEXATRIENE-1,1-D2 and -CIS-1-D1 Species (United States)

    Craig, Norman C.; Fuson, Hannah A.; Tian, Hengfeng; Blake, Thomas A.


    Hexatriene-1,1-D2 with some admixture of the cis-1-D1 and trans-1-D1 species was synthesized by reaction of 2,4-pentadienal and (methyl-D3)-triphenylphosphonium iodide (Wittig reagent). The trans isomer was isolated by preparative gas chromatography, and the high-resolution (0.0015 Cm-1) infrared spectrum was recorded on a Bruker IFS 125HR instrument. The rotational structure in two C-type bands for the 1,1-D2 species was analyzed. For this species the bands at 902.043 and 721.864 Cm-1 yielded composite ground state rotational constants of A0 = 0.801882(1), B0 = 0.041850(2), and C0 = 0.039804(1) Cm-1. For the cis-1-D1 species the C-type band at 803.018 Cm-1 gave A0 = 0.809384(2), B0 = 0.043530(3), and C0 = 0.041321(2) Cm-1. By iodine-catalyzed isomerization, we have obtained some of the much less favored cis isomer and hope to obtain microwave spectra for its three deuterium-substituted species. The rotational constants reported here contribute to data needed for determining a semi-experimental structure for trans-hexatriene, which should show that the structural consequences of pi-electron delocalization increase with the chain length of polyenes.

  12. An evaluation of LSU rDNA D1-D2 sequences for their use in species identification

    Directory of Open Access Journals (Sweden)

    Tautz Diethard


    Full Text Available Abstract Background Identification of species via DNA sequences is the basis for DNA taxonomy and DNA barcoding. Currently there is a strong focus on using a mitochondrial marker for this purpose, in particular a fragment from the cytochrome oxidase I gene (COI. While there is ample evidence that this marker is indeed suitable across a broad taxonomic range to delineate species, it has also become clear that a complementation by a nuclear marker system could be advantageous. Ribosomal RNA genes could be suitable for this purpose, because of their global occurrence and the possibility to design universal primers. However, it has so far been assumed that these genes are too highly conserved to allow resolution at, or even beyond the species level. On the other hand, it is known that ribosomal gene regions harbour also highly divergent parts. We explore here the information content of two adjacent divergence regions of the large subunit ribosomal gene, the D1-D2 region. Results Universal primers were designed to amplify the D1-D2 region from all metazoa. We show that amplification products in the size between 800–1300 bp can be obtained across a broad range of animal taxa, provided some optimizations of the PCR procedure are implemented. Although the ribosomal genes occur in multiple copies in the genomes, we find generally very little intra-individual polymorphism (Cottus and genus Aphyosemion show that the D1-D2 LSU sequence can resolve even very closely related species with the same fidelity as COI sequences. In one case we can even show that a mitochondrial transfer must have occurred, since the nuclear sequence confirms the taxonomic assignment, while the mitochondrial sequence would have led to the wrong classification. We have further explored whether hybrids between species can be detected with the nuclear sequence and we show for a test case of natural hybrids among cyprinid fish species (Alburnus alburnus and Rutilus rutilus that this

  13. Optical reflectance and omnidirectional bandgaps in Fibonacci quasicrystals type 1-D multilayer structures containing exponentially graded material (United States)

    Singh, Bipin K.; Thapa, Khem B.; Pandey, Praveen C.


    A theoretical study of optical reflectance and reflection bands of 1-D photonic quasi-crystals (Fibonacci type arrangement) composed of exponentially graded material is presented. The proposed structures consist of two different layers, one of them is of constant refractive index (L) and the other one is of exponentially graded refractive index (S) dielectric materials. Four different generations (2nd, 3rd, 4th and 5th) of the Fibonacci sequence for 10 periods in one dimension (1-D) are considered and compared in view of their optical reflectance and bandgaps for both TE and TM polarisations. Also, we proposed some heterostructures made by the combination of different Fibonacci generations and their periods to obtain suitable omnidirectional reflection band. We used the transfer matrix method (TMM) to obtain the reflectance, bandgaps and omnidirectional reflectional bandgaps (ODR) of such structures in near infrared spectrum (800-2200 nm) at different angles of incidence. We show that ODR exists in these types of structures. The number of ODRs and total bandgap depend on the Fibonacci generations. Extraordinary ODR bandgaps are obtained in the case of heterostructures formed by the combination of different generations of the Fibonacci sequence. The ODR for these structures is similar to the ODR of photonic crystals containing left-handed materials. This work would be useful to study the Fibonacci type photonic crystals having graded index materials and also it will open new window to design several photonic crystal devices like sensors, reflectors, etc. in the infrared region.

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

    CERN Document Server

    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


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

  15. Low band gap frequencies and multiplexing properties in 1D and 2D mass spring structures (United States)

    Aly, Arafa H.; Mehaney, Ahmed


    This study reports on the propagation of elastic waves in 1D and 2D mass spring structures. An analytical and computation model is presented for the 1D and 2D mass spring systems with different examples. An enhancement in the band gap values was obtained by modeling the structures to obtain low frequency band gaps at small dimensions. Additionally, the evolution of the band gap as a function of mass value is discussed. Special attention is devoted to the local resonance property in frequency ranges within the gaps in the band structure for the corresponding infinite periodic lattice in the 1D and 2D mass spring system. A linear defect formed of a row of specific masses produces an elastic waveguide that transmits at the narrow pass band frequency. The frequency of the waveguides can be selected by adjusting the mass and stiffness coefficients of the materials constituting the waveguide. Moreover, we pay more attention to analyze the wave multiplexer and DE-multiplexer in the 2D mass spring system. We show that two of these tunable waveguides with alternating materials can be employed to filter and separate specific frequencies from a broad band input signal. The presented simulation data is validated through comparison with the published research, and can be extended in the development of resonators and MEMS verification.

  16. Computational Study and Analysis of Structural Imperfections in 1D and 2D Photonic Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Maskaly, Karlene Rosera [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)


    increasing RMS roughness. Again, the homogenization approximation is able to predict these results. The problem of surface scratches on 1D photonic crystals is also addressed. Although the reflectivity decreases are lower in this study, up to a 15% change in reflectivity is observed in certain scratched photonic crystal structures. However, this reflectivity change can be significantly decreased by adding a low index protective coating to the surface of the photonic crystal. Again, application of homogenization theory to these structures confirms its predictive power for this type of imperfection as well. Additionally, the problem of a circular pores in 2D photonic crystals is investigated, showing that almost a 50% change in reflectivity can occur for some structures. Furthermore, this study reveals trends that are consistent with the 1D simulations: parameter changes that increase the absolute reflectivity of the photonic crystal will also increase its tolerance to structural imperfections. Finally, experimental reflectance spectra from roughened 1D photonic crystals are compared to the results predicted computationally in this thesis. Both the computed and experimental spectra correlate favorably, validating the findings presented herein.

  17. Data of evolutionary structure change: 1D6QA-2G4QA [Confc[Archive

    Lifescience Database Archive (English)


  18. A Stochastic Wavelet Finite Element Method for 1D and 2D Structures Analysis

    Directory of Open Access Journals (Sweden)

    Xingwu Zhang


    Full Text Available A stochastic finite element method based on B-spline wavelet on the interval (BSWI-SFEM is presented for static analysis of 1D and 2D structures in this paper. Instead of conventional polynomial interpolation, the scaling functions of BSWI are employed to construct the displacement field. By means of virtual work principle and BSWI, the wavelet finite elements of beam, plate, and plane rigid frame are obtained. Combining the Monte Carlo method and the constructed BSWI elements together, the BSWI-SFEM is formulated. The constructed BSWI-SFEM can deal with the problems of structural response uncertainty caused by the variability of the material properties, static load amplitudes, and so on. Taking the widely used Timoshenko beam, the Mindlin plate, and the plane rigid frame as examples, numerical results have demonstrated that the proposed method can give a higher accuracy and a better constringency than the conventional stochastic finite element methods.

  19. Data of evolutionary structure change: 1D3AB-1LLDA [Confc[Archive

    Lifescience Database Archive (English)


  20. Data of evolutionary structure change: 1D0GD-2RJLA [Confc[Archive

    Lifescience Database Archive (English)


  1. Effect of copper doping on the crystal structure and morphology of 1D nanostructured manganese oxides. (United States)

    Lee, Sun Hee; Park, Dae Hoon; Hwang, Seong-Ju; Choy, Jin-Ho


    We have tried to control the aspect ratio and physicochemical properties of 1D nanostructured manganese oxides through copper doping. Copper-doped manganese oxide nanostructures have been synthesized by one-pot hydrothermal treatment for the mixed solution of permanganate anions and copper cations. According to powder X-ray diffraction and electron microscopic analyses, all the present materials commonly crystallize with alpha-MnO2-type structure but their aspect ratio decreases significantly with increasing the content of copper. Such a variation of crystallite dimension is attributable to the limitation of crystal growth by the incorporation of copper ions. X-ray absorption spectroscopic studies at Mn K- and Cu K-edges clearly demonstrate that the average oxidation state of manganese ions is increased by the substitution of divalent copper ions. Electrochemical measurements reveal the improvement of the electrode performance of nanostructured manganate upon copper doping, which can be interpreted as a result of the decrease of aspect ratio and the increase of Mn valence state. From the present experimental findings, it becomes certain that the present Cu doping method can provide an effective way of controlling the crystal dimension and electrochemical property of 1D nanostructured manganese oxide.

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

    Directory of Open Access Journals (Sweden)

    Tom G Richardson

    Full Text Available 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 (χ(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.

  3. Data of evolutionary structure change: 1B99C-2AZ1D [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available GSDS--VESAN >E --HHHHH> ATOM 316...>D 2AZ1D HGSDHEDEGANE >E HHH...pdbID>1B99 C 1B99C EELLT-EVKPN ...> - > ATOM 3319 CA GLU C 141 17.330 5.755...DChain>2AZ1D DELVDWDRDAS re>GG EEGGHcture

  4. Data of evolutionary structure change: 1D7EA-1OTAA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1D7EA-1OTAA 1D7E 1OTA A A>VAL CA 559 PHE CA 524 1OTA A 1OTAA KKALSGDSYWVF E EE...9981689453 7.820000171661377 tion> 0.8790000081062...1399 0.36500000953674316 -0.3330000042915344 -0.25200000405311584 -0.9089999794960022

  5. Data of evolutionary structure change: 1D5NC-1UNFX [Confc[Archive

    Lifescience Database Archive (English)


  6. Data of evolutionary structure change: 1D5ND-1UNFX [Confc[Archive

    Lifescience Database Archive (English)


  7. Optical bullets in (2+1)D photonic structures and their interaction with localized defects (United States)

    Dohnal, Tomas


    This dissertation studies light propagation in Kerr-nonlinear two dimensional waveguides with a Bragg resonant, periodic structure in the propagation direction. The model describing evolution of the electric field envelopes is the system of 2D Nonlinear Coupled Mode Equations (2D CME). The periodic structure induces a range of frequencies (frequency gap) in which linear waves do not propagate. It is shown that, similarly to the ID case of a fiber grating, the 2D nonlinear system supports localized solitary wave solutions, referred to as 2D gap solitons, which have frequencies inside the linear gap and can travel at, any speed smaller than or equal to the speed of light in the corresponding homogeneous medium. Such solutions are constructed numerically via Newton's iteration. Convergence is obtained only near the upper edge of the gap. Gap solitons with a nonzero velocity are constructed by numerically following a bifurcation curve parameterized by the velocity v. It is shown that gap solitons are saddle points of the corresponding Hamiltonian functional and that no (constrained) local minima of the Hamiltonian exist. The linear stability problem is formulated and reasons for the failure of the standard Hamiltonian PDE approach for determining linear stability are discussed. In the second part of the dissertation interaction of 2D gap solitons with localized defects is studied and trapping of slow enough 2D gap solitons is demonstrated. This study builds on [JOSA B 19, 1635 (2002)], where such trapping of 1D gap solitons is considered. Analogously to this 1D problem trapping in the 2D model is explained as a resonant energy transfer into one or more defect modes existent for the particular defect. For special localized defects exact linear modes are found explicitly via the separation of variables. Numerical computation of linear defect modes is used for more general defects. Corresponding nonlinear modes are then constructed via Newton's iteration by following a

  8. MAGNETIC CORE SHELL STRUCTURES: from 0D to 1D assembling. (United States)

    Ficai, Denisa; Ficai, Anton; Dinu, Elena; Oprea, Ovidiu; Sonmez, Maria; Keler, Memduh Kagan; Sahin, Yesim Muge; Ekren, Nazmi; Inan, Ahmet Talat; Daglilar, Sibel; Gunduz, Oguzhan


    Material research and development studies are focused on different techniques of bringing out nanomaterials with desired characteristics and properties. From the point of view of materials development, nowadays scientists are strongly focused on obtaining materials with predefined characteristics and properties. The morphology control seems to be a determinant factor and increasing attention is devoted to this aspect. At this moment it is possible to engineer the material's features by using different methods and materials combination for both medical and industrial applications. In the applications of chemistry and synthesis, biology, mechanics, optics solar cells and microelectronics tailoring the adjustable parameters of stoichiometry, chemical structure, shape and segregation are evaluated and opens new fields. Because of the magnetic features of nanoparticles and durable particle size, less than 100 nm, this study is aiming to describe their uses in practical applications. That's why the whole hydrodynamic magnetic core shell topic will be reviewed on this paper. Additionally, the properties acting in general sight in solid-state physics are utilized for material selection and for defining issue connecting the core, shell structure and their producing properties. Here, in the study of core/shell nanoparticle various physical and chemical synthesis routes and the effect of electrospun method are briefly discussed. Starting from a real void of the scientific literature, the existent data related to the 1D magnetic electrospun materials are reviewed. The perspectives in the medical, environmental or energetic sector is great and bring some real advantages related to the 0D core@shell structures because both mechanical and biological properties are dependent on the morphology of the materials.

  9. Identification of Trichosporon spp. Strains by Sequencing D1/D2 Region and Sub-typing by Sequencing Ribosomal Intergenic Spacer Region of Ribosomal DNA

    Institute of Scientific and Technical Information of China (English)

    Jingsi ZENG; Cristina Maria de Souza Motta; Kazutaka Fukushima; Kayoko Takizawa; Oliane Maria Correia Magalhes; Rejane Pereira Neves; Kazuko Nishimura


    To re-identify and further group 25 isolates of Trichosporon spp. identified morphologically previously, sequences of D1/D2 region of large subunit (LSU) of ribosomal DNA (rDNA) of 25 tested strains for identification and those of ribosomal intergenic space 1 (IGS1) region of 11 strains for sub-grouping were detected. The identifications of tested strains were changed except 6 strains. According to the alignment of the IGS1 region, 6 T. asahii isolates tested fell into 4 groups and 5 T. faecale isolates into 3 groups. Polymorphism of 2 T.japonicum isolates was found in 10 positions. With the alignments obtained in this research compared with the relative GenBank entries, it was found that T. asahii, T.faecale and T.japonicum species were divided into 7, 3 and 2 subtypes respectively. Morphological and biophysical methods are not sufficient for Trichosporon spp. identification. Sequencing becomes neces-sary for Trichosporon diagnosis. There is obvious diversity within a species.

  10. Synthesis and Crystal Structure of the First Hybrid Manganese Phosphate with 1-D Framework of Dinuclear Structure

    Institute of Scientific and Technical Information of China (English)


    A novel hybrid manganese phosphate, [(bipy)Mn(H2PO4)2] (bipy = 2,2'-bipyridine) 1, was synthesized, and its structure is characteristic of 1-D framework involving a dinuclear structure made up of edge-sharing Mn(II) octahedra. 1 crystallizes in the monoclinic system, space group C2/c with a = 12.230(2), b = 17.800(4), c = 13.530(3)(A), β = 105.00(3)o, V = 2845.0(10)(A)3, Z = 8. Dc = 1.892 g/cm3, F(000) = 1640, Mr = 405.10, μ(MoKα) = 1.198 mm-1, R = 0.0306 and wR = 0.0657 for 2093 observed reflections (I > 2σ(I)).

  11. Data of evolutionary structure change: 1D5IH-3FZUH [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available ntryIDChain> CKATG--YTFSS >EEEE -- GGG> 3FZU H 3FZUH CAASGFRFTFNN ...>EEEE GGGure> ATOM 1790 CA CYS H 22 34.95...SW >EEEE ---- > ATOM 2413 CA ALA...pdbChain> 1D5IH ARGHSYYFYDGDYW >EE

  12. Data of evolutionary structure change: 1BU1D-1OOTA [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1BU1D-1OOTA 1BU1 1OOT D A -IIVVALYDYEAIHHEDLSFQKGDQMVVLEESGE---WW...14> 1OOT A 1OOTA...tryChain> -21.645000457763672 -6.38100004196167 51.89799880981445 ...76022339 -0.7429999709129333 -0.09000000357627869 tion> 1.78559505939483641OOT A 1OOTA WTGRV--NGREG

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

    CERN Document Server

    Strouthos, C G


    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.

  14. Crystal Structures of Human TBC1D1 and TBC1D4 (AS160) RabGTPase-activating Protein (RabGAP) Domains Reveal Critical Elements for GLUT4 Translocation

    Energy Technology Data Exchange (ETDEWEB)

    S Park; W Jin; S Shoelson


    We have solved the x-ray crystal structures of the RabGAP domains of human TBC1D1 and human TBC1D4 (AS160), at 2.2 and 3.5 {angstrom} resolution, respectively. Like the yeast Gyp1p RabGAP domain, whose structure was solved previously in complex with mouse Rab33B, the human TBC1D1 and TBC1D4 domains both have 16 {alpha}-helices and no {beta}-sheet elements. We expected the yeast Gyp1p RabGAP/mouse Rab33B structure to predict the corresponding interfaces between cognate mammalian RabGAPs and Rabs, but found that residues were poorly conserved. We further tested the relevance of this model by Ala-scanning mutagenesis, but only one of five substitutions within the inferred binding site of the TBC1D1 RabGAP significantly perturbed catalytic efficiency. In addition, substitution of TBC1D1 residues with corresponding residues from Gyp1p did not enhance catalytic efficiency. We hypothesized that biologically relevant RabGAP/Rab partners utilize additional contacts not described in the yeast Gyp1p/mouse Rab33B structure, which we predicted using our two new human TBC1D1 and TBC1D4 structures. Ala substitution of TBC1D1 Met{sup 930}, corresponding to a residue outside of the Gyp1p/Rab33B contact, substantially reduced catalytic activity. GLUT4 translocation assays confirmed the biological relevance of our findings. Substitutions with lowest RabGAP activity, including catalytically dead RK and Met{sup 930} and Leu{sup 1019} predicted to perturb Rab binding, confirmed that biological activity requires contacts between cognate RabGAPs and Rabs beyond those in the yeast Gyp1p RabGAP/mouse Rab33B structure.

  15. Simulation of unsteady state performance of a secondary air system by the 1D-3D-Structure coupled method (United States)

    Wu, Hong; Li, Peng; Li, Yulong


    This paper describes the calculation method for unsteady state conditions in the secondary air systems in gas turbines. The 1D-3D-Structure coupled method was applied. A 1D code was used to model the standard components that have typical geometric characteristics. Their flow and heat transfer were described by empirical correlations based on experimental data or CFD calculations. A 3D code was used to model the non-standard components that cannot be described by typical geometric languages, while a finite element analysis was carried out to compute the structural deformation and heat conduction at certain important positions. These codes were coupled through their interfaces. Thus, the changes in heat transfer and structure and their interactions caused by exterior disturbances can be reflected. The results of the coupling method in an unsteady state showed an apparent deviation from the existing data, while the results in the steady state were highly consistent with the existing data. The difference in the results in the unsteady state was caused primarily by structural deformation that cannot be predicted by the 1D method. Thus, in order to obtain the unsteady state performance of a secondary air system more accurately and efficiently, the 1D-3D-Structure coupled method should be used.

  16. Molecular identification of veterinary yeast isolates by use of sequence-based analysis of the D1/D2 region of the large ribosomal subunit. (United States)

    Garner, Cherilyn D; Starr, Jennifer K; McDonough, Patrick L; Altier, Craig


    Conventional methods of yeast identification are often time-consuming and difficult; however, recent studies of sequence-based identification methods have shown promise. Additionally, little is known about the diversity of yeasts identified from various animal species in veterinary diagnostic laboratories. Therefore, in this study, we examined three methods of identification by using 109 yeast samples isolated during a 1-year period from veterinary clinical samples. Comparison of the three methods-traditional substrate assimilation, fatty acid profile analysis, and sequence-based analysis of the region spanning the D1 and D2 regions (D1/D2) of the large ribosomal subunit-showed that sequence analysis provided the highest percent identification among the three. Sequence analysis identified 87% of isolates to the species level, whereas substrate assimilation and fatty acid profile analysis identified only 54% and 47%, respectively. Less-stringent criteria for identification increased the percentage of isolates identified to 98% for sequence analysis, 62% for substrate assimilation, and 55% for fatty acid profile analysis. We also found that sequence analysis of the internal transcribed spacer 2 (ITS2) region provided further identification for 36% of yeast not identified to the species level by D1/D2 sequence analysis. Additionally, we identified a large variety of yeast from animal sources, with at least 30 different species among the isolates tested, and with the majority not belonging to the common Candida spp., such as C. albicans, C. glabrata, C. tropicalis, and the C. parapsilosis group. Thus, we determined that sequence analysis of the D1/D2 region was the best method for identification of the variety of yeasts found in a veterinary population.

  17. From 1D to 3D: A new route to fabricate tridimensional structures via photo-generation of silver networks

    NARCIS (Netherlands)

    Wang, Zhanhua; Shen, Huaizhong; Wu, Yuxin; Fang, Liping; Ye, Shunsheng; Wang, Zhaoyi; Liu, Wendong; Cheng, Zhongkai; Zhang, Junhu; Yang, Bai


    A rapid and cost effective method has been developed to fabricate 3 dimensional (3D) ordered structures by photo-generating silver networks inside a 1D layered heterogeneous laminate composed of poly(vinyl alcohol) (PVA) and poly(methyl methacrylate) (PMMA). By designing the photo-mask meticulously,

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

    DEFF Research Database (Denmark)

    Breinbjerg, Olav; Yaghjian, Arthur D.


    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...

  19. From 1D chain to 3D network: A theoretical study on TiO{sub 2} low dimensional structures

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Ling-ju; He, Tao, E-mail: [CAS Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190 (China); Zeng, Zhi [Chinese Academy of Sciences, Institute of Solid State Physics, Hefei 230031 (China)


    We have performed a systematic study on a series of low dimensional TiO{sub 2} nanostructures under density functional theory methods. The geometries, stabilities, growth mechanism, and electronic structures of 1D chain, 2D ring, 2D ring array, and 3D network of TiO{sub 2} nanostructures are analyzed. Based on the Ti{sub 2}O{sub 4} building unit, a series of 1D TiO{sub 2} nano chains and rings can be built. Furthermore, 2D ring array and 3D network nanostructures can be constructed from 1D chains and rings. Among non-periodic TiO{sub 2} chain and ring structures, one series of ring structures is found to be more stable. The geometry model of the 2D ring arrays and 3D network structures in this work has provided a theoretical understanding on the structure information in experiments. Based on these semiconductive low dimensional structures, moreover, it can help to understand and design new hierarchical TiO{sub 2} nanostructure in the future.

  20. 鹅AKR1D1基因编码区克隆、序列分析及在卵泡中的表达特性研究%Molecular Cloning,Bioinformatics of the Goose AKR1D1 Gene cDNA Coding Domain Sequence,and Its Differential Expression Profiles in Ovarian Follicles of Different Stages

    Institute of Scientific and Technical Information of China (English)

    张文捷; 李欣欣; 刘贺贺; 王继文


    [Objective]The study was to clone the A K R 1D1 gene's cDNA coding domain sequence of geese and predict its structure,function and expression profiles.[Methods]Using Tianfu meat-type geese as materials,we cloned the goose's A KR1D1 coding domain sequence (CDS) by RTPCR,and predicted its protein structure and functions through several bioinformational tools and analyzed its expression in ovarian follicles of different stages of goose by real-time quantitative PCR.[Results]The results showed that the goose's AKR1D1 CDS consisted of 981 nucleotides that encoded 326 amino acids residues, and the amino acid homology of goose A KR1D1 shared 95.71% identity with chicken. The analysis of amino acid sequence revealed that the goose AKR1D1 encoded water-soluble protein and its relative molecular weight was 37 263.7 Da. Subcellular location of A KR1D1 was primarily in the cytoplasm and chondriosome,and it did not belong to the secreted protein. It is predicted that the AKR1D1 protein contained 18 phosphorylation sites,3 glycosylation sites. The secondary structure of AKR1D1 was mainly composed of random coil,while the tertiary structure of domain area showed a formic form helix structure. The results of real-time quantitative PCR revealed that goose AKR1D1 expressed most in theca layer and granulosa layer with 2~4 mm,at the lowest in theca layer of F5 and granulosa layer of F1.[Conclusion]A KR1D1 may play an important role in the recruitment,selection,screening,atresia and ovulation of the follicle by regulating the dynamic balance of steroid hormones.%【目的】克隆鹅AKR1D1基因编码区序列,预测其蛋白结构、功能,并研究其在鹅各等级卵泡中的表达特性。【方法】以天府肉鹅母系为材料,采用RT-PCR技术克隆鹅AKR1D1基因编码区序列,利用多种生物信息学分析软件预测其结构与功能,并应用荧光定量PCR技术检测其在各等级卵泡中的表达特性。【结果】结果表明:鹅AKR1D1

  1. Protein folds and families: sequence and structure alignments. (United States)

    Holm, L; Sander, C


    Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). As a result, the HSSP database not only provides aligned sequence families, but also implies secondary and tertiary structures covering 36% of all sequences in Swiss-Prot. The structure classification by Dali and the sequence families in HSSP can be browsed jointly from a web interface providing a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences. In particular, this results in a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The organization of protein structures and families provides a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The databases are available from

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

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

  3. Sequence-structure relations of biopolymers

    CERN Document Server

    Barrett, Christopher; Reidys, Christian M


    Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as structural semantics of sequence data that allows for a different interpretation than conventional sequence alignment. Structural semantics could enable us to identify more general embedded "patterns" in DNA and RNA sequences. Results: We compute the partition function of sequences with respect to a fixed structure and connect this computation to the mutual information of a sequence-structure pair for RNA secondary structures. We present a Boltzmann sampler and obtain the a priori probability of specific sequence patterns. We present a detailed analysis for the three PDB-structures, 2JXV (hairpin), 2N3R (3-branch multi-loop) and 1EHZ (tRNA). We localize specific sequence patterns, contrast the energy spectrum of the Boltzmann sampled sequences versus those sequences that refold ...

  4. Optical properties in 1D photonic crystal structure using Si/C60 multilayers

    Institute of Scientific and Technical Information of China (English)

    Chen Jing; Tang Jiyu; Han Peide; Chen Junfang


    The feasibility of using Si/C60 mulfilayer films as one-dimensional(1D)photonie band gap crystals was investigated by theoretical calculations using a transfer matrix method(TMM).The response has been studied both within and out of the periodic plane of Si/C60 multilayers.It is found that Si/C60 multilayer films show incomplete photonic band gap(PBG)behavior in the visible frequency range.The fabricated Si/C60 multilayers with two pairs of 70 am C60 and 30 nm Si layers exhibit a PBG at central wavelength of about 600 nm.and the highest reflectivity call reach 99%.As a consequence,this photonic crystal may be important for fabricating a photonic crystal with an incomplete band gap in the visible frequency range.

  5. Optical properties in 1D photonic crystal structure using Si/C{sub 60} multilayers

    Energy Technology Data Exchange (ETDEWEB)

    Chen Jing; Tang Jiyu; Chen Junfang [College of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006 (China); Han Peide, E-mail:, E-mail: [College of Materials Science and Engineering, Taiyuan University of Technology, Taiyuan 030024 (China)


    The feasibility of using Si/C{sub 60} multilayer films as one-dimensional (1D) photonic band gap crystals was investigated by theoretical calculations using a transfer matrix method (TMM). The response has been studied both within and out of the periodic plane of Si/C{sub 60} multilayers. It is found that Si/C{sub 60} multilayer films show incomplete photonic band gap (PBG) behavior in the visible frequency range. The fabricated Si/C{sub 60} multilayers with two pairs of 70 nm C{sub 60} and 30 nm Si layers exhibit a PBG at central wavelength of about 600 nm, and the highest reflectivity can reach 99%. As a consequence, this photonic crystal may be important for fabricating a photonic crystal with an incomplete band gap in the visible frequency range.

  6. Assembling carbon fiber–graphene–carbon fiber hetero-structures into 1D–2D–1D junction fillers and patterned structures for improved microwave absorption (United States)

    Li, Huimin; Liu, Lin; Li, Hai-Bing; Song, Wei-Li; Bian, Xing-Ming; Zhao, Quan-Liang; Chen, Mingji; Yuan, Xujin; Chen, Haosen; Fang, Daining


    Since carbon-based structures of various dimensions, including one-dimensional (1D) carbon nanotubes, two-dimensional (2D) graphene and three-dimensional (3D) carbon foams, have attracted significant attention as microwave absorption fillers, we present an exceptional hetero-junction filler with a 1D–2D–1D feature, achieved by manipulating 2D graphene into 1D carbon fibers in the fiber-extruding process under the electric field. The as-fabricated 1D–2D–1D structural fillers exhibited much-improved dielectric properties and promoted microwave absorption performance in their composites, which is linked to the establishment of enhanced polarization capability, the generation of increased electric loss pathway and the creation of more favorable electromagnetic energy consumption conditions. The results suggest that employing 2D graphene in the 1D–2D–1D nanostructures played the critical role in tuning the electromagnetic response ability, because of its intrinsic electric advantages and dimensional features. To broaden the effective absorption bandwidth, periodic pattern-absorbing structures were designed, which showed combined absorption advantages for various thicknesses. Our strategy for fabricating 1D–2D–1D structural fillers illuminates a universal approach for manipulating dimensions and structures in the nanotechnology.

  7. Structure Preserving Spatial Discretization of a 1-D Piezoelectric Timoshenko Beam

    NARCIS (Netherlands)

    Voss, T.; Scherpen, J. M. A.


    In this paper we show how to spatially discretize a distributed model of a piezoelectric beam representing the dynamics of an inflatable space reflector in port-Hamiltonian (pH) form. This model can then be used to design a controller for the shape of the inflatable structure. Inflatable structures

  8. Nucleic acid sequences encoding D1 and D1/D2 domains of human coxsackievirus and adenovirus receptor (CAR) (United States)

    Freimuth, Paul I.


    The invention provides recombinant human CAR (coxsackievirus and adenovirus receptor) polypeptides which bind adenovirus. Specifically, polypeptides corresponding to adenovirus binding domain D1 and the entire extracellular domain of human CAR protein comprising D1 and D2 are provided. In another aspect, the invention provides nucleic acid sequences encoding these domains and expression vectors for producing the domains and bacterial cells containing such vectors. The invention also includes an isolated fusion protein comprised of the D1 polypeptide fused to a polypeptide which facilitates folding of D1 when expressed in bacteria. The functional D1 domain finds application in a therapeutic method for treating a patient infected with a CAR D1-binding virus, and also in a method for identifying an antiviral compound which interferes with viral attachment. The invention also provides a method for specifically targeting a cell for infection by a virus which binds to D1.

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

    CERN Document Server

    Lévy, M; Levy, Miguel; Jalali, Amir A


    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.

  10. Reversible supra-channel effects: 3D kagome structure and catalysis via a molecular array of 1D coordination polymers. (United States)

    Lee, Haeri; Noh, Tae Hwan; Jung, Ok-Sang


    Self-assembly of CuX2 (X(-) = ClO4(-) and BF4(-)) with 2,3-bis(nicotinoyloxy)naphthalene yields a 1D loop-chain skeleton. The loop-chains form an ensemble constituting a unique 3D kagome-type structure with both hexagonal and trigonal supra-channels. The unprecedented supra-channel effects on the catalytic oxidation of 3,5-di-tert-butylcatechol to 3,5-di-tert-butylbenzoquinone were investigated.

  11. Recent COMPASS results on the polarized structure function $g_{1}^{d}$ of the deuteron

    CERN Document Server

    Quintans, Catarina


    The study of the spin dependent structure functions of the deuteron is part of a broad physics program addressed by the COMPASS collaboration at CERN. The longitudinal spin asymmetry $A^{d}_{1}$ is evaluated from data on inelastic scattering of longitudinally polarised muons off a large $^{6}$LiD polarised target. Recent results on $g^{d}_{1}$ both for low and high Q$^{2}$ are presented. The obtained values for the first moment $\\Gamma^{d}_{1}$ and the flavor-singlet axial current $a_{0}$ are also shown.

  12. 3D mechanical measurements with an atomic force microscope on 1D structures

    DEFF Research Database (Denmark)

    Kallesøe, Christian; Larsen, Martin Benjamin Barbour Spanget; Bøggild, Peter;


    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....

  13. Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques (United States)

    Topcu, Gulacti; Ulubelen, Ayhan


    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.

  14. 1D cyanide complexes with 2-pyridinemethanol: Synthesis, crystal structures and spectroscopic properties (United States)

    Sayın, Elvan; Kürkçüoğlu, Güneş Süheyla; Yeşilel, Okan Zafer; Hökelek, Tuncer


    Two new one-dimensional coordination polymers, [Cu(hmpH)2Pd(μ-CN)2(CN)2]n (1) and [Cu(hmpH)2Pt(μ-CN)2(CN)2]n (2), (hmpH = 2-pyridinemethanol), have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal and elemental analyses techniques. Single crystal X-ray diffraction analysis indicates that complexes 1 and 2 are isomorphous and isostructural, and crystallize in the triclinic system and P-1 space group. The Pd(II) or Pt(II) ions are four coordinated with four cyanide-carbon atoms in a square planar geometry. Cu(II) ion displays a distorted octahedral coordination by two N-atoms and two O-atoms of hmpH ligands, two bridging cyanide groups. In one dimensional structure of the complexes, [M(CN)4]2- (M = Pd(II) or Pt(II)) anions and [Cu(hmpH)2]2+ cations are linked via bridging cyanide ligands. In the complexes, the presence of intramolecular C-H⋯M (M = Pd(II) or Pt(II)) interactions with distance values of 3.00-2.95 Å are established, respectively.

  15. Controlled Self-Assembly of Cyclophane Amphiphiles: From 1D Nanofibers to Ultrathin 2D Topological Structures

    Energy Technology Data Exchange (ETDEWEB)

    Cai, Zhengxu; Li, Lianwei; Lo, Wai-Yip; Zhao, Donglin; Wu, Qinghe; Zhang, Na; Su, Yu-An; Chen, Wei; Yu, Luping


    A novel series of amphiphilic TC-PEG molecules were designed and synthesized based on the orthogonal cyclophane unit. These molecules were able to self-assemble from 1D nanofibers and nanobelts to 2D ultrathin nanosheets (3 nm thick) in a controlled way by tuning the length of PEG side chains. The special structure of the cyclophane moiety allowed control in construction of nanostructures through programmed noncovalent interactions (hydrophobic hydrophilic interaction and pi-pi interaction). The self-assembled nanostructures were characterized by combining real space imaging (TEM, SEM, and AFM) and reciprocal space scattering (GIWAXS) techniques. This unique supramolecular system may provide a new strategy for the design of materials with tunable nanomorphology and functionality.

  16. Optimization of quasi-normal eigenvalues for 1-D wave equations in inhomogeneous media; description of optimal structures

    CERN Document Server

    Karabash, Illya M


    The paper is devoted to optimization of quasi-normal eigenvalues of a spectral problem associated with a 1-D wave equation in an inhomogeneous medium. The wave equation is equipped with a radiation boundary condition, and so the set of quasi-normal eigenvalues lies in $\\C_+$. The problem is to design for a given $\\alpha \\in \\R$ the structure of the inhomogeneous medium such that it generates a quasi-normal eigenvalue on the line $\\alpha + \\i \\R$ with a minimal possible imaginary part. We consider the problem for three admissible families of structures. Two of these families have a natural mechanical interpretation as classes of Krein strings with total mass and static moment constraints. For these two classes we find optimal quasi-normal eigenvalues explicitly. The third class of admissible structures is connected with the problem of optimal design for photonic crystals. For this class, the paper gives a wider statement of the optimization problem, proves existence of optimal structures, and study their prope...

  17. Structural variation from heterometallic cluster-based 1D chain to heterometallic tetranuclear cluster: Syntheses, structures and magnetic properties (United States)

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


    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 μ1,1,1-N3- (end-on, EO).

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shu-Hua, E-mail: [College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004 (China); Zhao, Ru-Xia; Li, He-Ping; Ge, Cheng-Min; Li, Gui; Huang, Qiu-Ping [College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004 (China); Zou, Hua-Hong, E-mail: [School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004 (China)


    Using the solvothermal method, we present the comparative preparation of ([Co{sub 3}Na(dmaep){sub 3}(ehbd)(N{sub 3}){sub 3}]·DMF){sub n} (1) and [Co{sub 2}Na{sub 2}(hmbd){sub 4}(N{sub 3}){sub 2}(DMF){sub 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 (Co{sub 3}{sup II}Na) and (Co{sub 2}{sup II}Na{sub 2}) cores display dominant ferromagnetic interaction from the nature of the binding modes through μ{sub 1,1,1}-N{sub 3}{sup –} (end-on, EO). - Graphical abstract: Two novel cobalt complexes have been prepared. Compound 1 consists of tetranuclear (Co{sub 3}{sup II}Na) units, which further formed a 1-D chain. Compound 2 is heterometallic tetranuclear cluster. Two complexes display dominant ferromagnetic interaction. - Highlights: • Two new heterometallic complexes have been synthesized by solvothermal method. • The stereospecific blockade of the ligands in the synthesis system seems to be the most important synthetic parameter. • The magnetism studies show that 1 and 2 exhibit ferromagnetic interactions. • Complex 1 shows slowing down of magnetization and not blocking of magnetization.

  19. Fibonacci Sequence and Supramolecular Structure of DNA. (United States)

    Shabalkin, I P; Grigor'eva, E Yu; Gudkova, M V; Shabalkin, P I


    We proposed a new model of supramolecular DNA structure. Similar to the previously developed by us model of primary DNA structure [11-15], 3D structure of DNA molecule is assembled in accordance to a mathematic rule known as Fibonacci sequence. Unlike primary DNA structure, supramolecular 3D structure is assembled from complex moieties including a regular tetrahedron and a regular octahedron consisting of monomers, elements of the primary DNA structure. The moieties of the supramolecular DNA structure forming fragments of regular spatial lattice are bound via linker (joint) sequences of the DNA chain. The lattice perceives and transmits information signals over a considerable distance without acoustic aberrations. Linker sequences expand conformational space between lattice segments allowing their sliding relative to each other under the action of external forces. In this case, sliding is provided by stretching of the stacked linker sequences.

  20. Contrasting 1D tunnel-structured and 2D layered polymorphs of V2O5: relating crystal structure and bonding to band gaps and electronic structure. (United States)

    Tolhurst, Thomas M; Leedahl, Brett; Andrews, Justin L; Marley, Peter M; Banerjee, Sarbajit; Moewes, Alexander


    New V2O5 polymorphs have risen to prominence as a result of their open framework structures, cation intercalation properties, tunable electronic structures, and wide range of applications. The application of these materials and the design of new, useful polymorphs requires understanding their defining structure-property relationships. We present a characterization of the band gap and electronic structure of nanowires of the novel ζ-phase and the orthorhombic α-phase of V2O5 using X-ray spectroscopy and density functional theory calculations. The band gap is found to decrease from 1.90 ± 0.20 eV in the α-phase to 1.50 ± 0.20 eV in the ζ-phase, accompanied by the loss of the α-phase's characteristic split-off dxy band in the ζ-phase. States of dxy origin continue to dominate the conduction band edge in the new polymorph but the inequivalence of the vanadium atoms and the increased local symmetry of [VO6] octahedra results in these states overlapping with the rest of the V 3d conduction band. ζ-V2O5 exhibits anisotropic conductivity along the b direction, defining a 1D tunnel, in contrast to α-V2O5 where the anisotropic conductivity is along the ab layers. We explain the structural origins of the differences in electronic properties that exist between the α- and ζ-phase.

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

    Pindera, Marek-Jerzy; Aboudi, Jacob


    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.

  2. Synthesis and Crystal Structure of a Novel 1D Magnesium (Ⅱ) Coordination Polymer Constructed by L-Cysteic Acid

    Institute of Scientific and Technical Information of China (English)

    LI Hai-Ye; LIAO Bei-Ling; JIANG Yi-Min; ZHANG Shu-Hua; LI Jun-Xia


    A novel coordination polymer [Mg(L)(H2O)2]·H2O] (LH2=L-cysteic acid) has been synthesized and characterized by elemental analysis, IR and single-crystal X-ray diffraction.The crystal crystallizes in orthorhombic system, space group P212121, with a=5.962(3), b=11.224(6), c=13.664(7)(A), V=914.3(8) (A)3, Z=4, Mr=245.50, Dc=1.783 g/cm3,μ=0.445 mm-1,flack parameter=0.32(16), F(000)=512, the final R=0.0458 and wR=0.1172 for 1578 observed reflections with I > 2σ(Ⅰ). The Mg(Ⅱ) atom shows an octahedral geometry defined by two carboxyl O atoms from two different L-cysteic acid ligands, one carboxyl O atom and one amino N atom from the adjacent ligand, and two aqua ligands. The Mg(Ⅱ) atoms are bridged by L-cysteic acid ligands, leading to a 1D infinite zigzag chain. In the structure there are extensive hydrogen bonds,through which the complex completes its 3D framework structure.

  3. Synthesis and Crystal Structure of a Novel 1D Mercury(II) Iodide Coordination Polymer Containing 40-Membered Macrocycle%Synthesis and Crystal Structure of a Novel 1D Mercury(II) Iodide Coordination Polymer Containing 40-Membered Macrocycle

    Institute of Scientific and Technical Information of China (English)

    GAN Xiao-Ping; KONG Ling; WU Peng; LV Chen; TU Yu-Long; CHEN Yi-Xin; ZHOU Hong-Ping; WU Jie-Ying; TIAN Yu-Peng


    A mercury coordination polymer [Hg3(TizT)216]n (Mr = 1921.72, TizT = 2,4,6- tri(imidazole- 1-yl)- 1,3,5-triazine) containing a 40-membered macrocycle which was constructed by four TizT ligands and four mercury(II) iodide molecules had been synthesized by the reaction of HgI2 with TizT. The complex was characterized by elemental analysis, FT-IR, ^1H NMR spectra and X-ray crystallography. The crystal of the complex belongs to the monoclinic system and C2/c space group with a = 35.840(5), b = 8.169(5), c = 14.980(5) A, β = 104.466(5)°, Z= 4, V= 4247(3) A^3, De = 3.006 g·cm^-3, μ= 15.223 mm^-1, F(000) = 3384, Rint = 0.0504, wR = 0.0833 and constructs a chair-like conformation of cyclohexane one by one, which forms a 1-D polymer through the fashion of fused ring aromatic hydrocarbon. The hydrogen bonds and π-π interactions shape the 2-D network structure. The two compounds excited weak fluorescence.

  4. Measurement of the Deuteron Spin Structure Function $g_{1}^{d(x)}$ for $1(GeV/c)^{2} < Q^{2} < 40 (GeV/c)^{2}$

    CERN Document Server

    Anthony, P L; Averett, T; Band, H R; Berisso, M C; Borel, H; Bosted, P E; Bultmann, S L; Buénerd, M; Chupp, T E; Churchwell, S; Court, G R; Crabb, D; Day, D; Decowski, P; De Pietro, P; Erbacher, R; Erickson, R; Feltham, A; Fonvieille, H; Frlez, E; Gearhart, R A; Ghazikhanian, V; Gómez, J; Griffioen, K A; Harris, C; Houlden, M A; Hughes, E W; Hyde-Wright, C E; Igo, G; Incerti, S; Jensen, J; Johnson, J R; King, P M; Kolomensky, Yu G; Kuhn, S E; Lindgren, R; Lombard-Nelsen, R M; Marroncle, J; McCarthy, J; McKee, P; Meyer, Werner T; Mitchell, G; Mitchell, J; Olson, M; Penttila, S; Peterson, G; Petratos, G G; Pitthan, R; Pocanic, D; Prepost, R; Prescott, C; Qin, L M; Raue, B A; Reyna, D; Rochester, L S; Rock, S E; Rondon-Aramayo, O A; Sabatie, F; Sick, I; Smith, T; Sorrell, L; Staley, F; Lorant, S St; Stuart, L M; Szalata, Z M; Terrien, Y; Tobias, A; Todor, L; Toole, T; Trentalange, S; Walz, D; Welsh, R C; Wesselmann, F R; Wright, T R; Young, C C; Zeier, M; Zhu, H; Zihlmann, B


    New measurements are reported on the deuteron spin structure function g_1^d. These results were obtained from deep inelastic scattering of 48.3 GeV electrons on polarized deuterons in the kinematic range 0.01 < x < 0.9 and 1 < Q^2 < 40 (GeV/c)^2. These are the first high dose electron scattering data obtained using lithium deuteride (6Li2H) as the target material. Extrapolations of the data were performed to obtain moments of g_1^d, including Gamma_1^d, and the net quark polarization Delta Sigma.

  5. Hydrothermal Synthesis, Crystal Structure and Thermal Properties of a Novel Samarium Complex with 1D Nano-chain Structure

    Institute of Scientific and Technical Information of China (English)

    LI Ya-Juan; LIANG Qing; SONG Hui-hua; JIA Mi-ying; SHI Shi-Kao; ZHANG Jian-jun


    @@ 1 Introduction The design and construction of metal-organic polymers has been a field of rapid growth in materials chemistry because of their intriguing topologies and potential applications as functional materials[1-6]. In this regard, every effort has been devoted to the deli-berate design and control of self-assembly infinite coordination networks via selecting the chemistry structures of ligands. Multidentate carboxylate ligands are widely adopted for construction of coordination frameworks due to their rich coordination modes[7-13].

  6. On constitutive functions for hindered settling velocity in 1-D settler models: Selection of appropriate model structure. (United States)

    Torfs, Elena; Balemans, Sophie; Locatelli, Florent; Diehl, Stefan; Bürger, Raimund; Laurent, Julien; François, Pierre; Nopens, Ingmar


    Advanced 1-D models for Secondary Settling Tanks (SSTs) explicitly account for several phenomena that influence the settling process (such as hindered settling and compression settling). For each of these phenomena a valid mathematical expression needs to be selected and its parameters calibrated to obtain a model that can be used for operation and control. This is, however, a challenging task as these phenomena may occur simultaneously. Therefore, the presented work evaluates several available expressions for hindered settling based on long-term batch settling data. Specific attention is paid to the behaviour of these hindered settling functions in the compression region in order to evaluate how the modelling of sludge compression is influenced by the choice of a certain hindered settling function. The analysis shows that the exponential hindered settling forms, which are most commonly used in traditional SST models, not only account for hindered settling but partly lump other phenomena (compression) as well. This makes them unsuitable for advanced 1-D models that explicitly include each phenomenon in a modular way. A power-law function is shown to be more appropriate to describe the hindered settling velocity in advanced 1-D SST models.

  7. Synthesis,crystal structure and fluorescence property of 1-D europium complex with 2,3-difluorobenzoate

    Institute of Scientific and Technical Information of China (English)

    宋金浩; 吴小说; 李夏


    A new chain europium complex [Eu(2,3-DFBA)3·(H2O)2]n(2,3-DFBA=2,3-difluorobenzoate) was synthesized by solvent method.X-ray single-crystal diffraction analysis revealed that Eu3+ ions were linked through 2,3-DFBA groups via alternate bidentate-bridging and tridentate chelating-bridging coordination modes to form a one-dimensional(1-D) polymeric chain.Each Eu3+ ion is eight-coordinated by six O atoms of five 2,3-DFBA ligands and two water molecules.The abundant hydrogen bonds between chains resulted in a two...

  8. Chiral cyanide-bridged 1D FeⅢ-MnⅢ heterobimetallic chains: Synthesis,structures and magnetic properties%Chiral cyanide-bridged 1D FeⅢ-MnⅢ heterobimetallic chains:Synthesis,structures and magnetic properties

    Institute of Scientific and Technical Information of China (English)

    YAO MinXia; ZHENG Qi; GAO Feng; LI YiZhi; ZUO JingLin


    Two couples of enantiomerically pure chiral cyano-bridged heterobimetallic one-dimensional(1D)chain complexes:[Mn((R,R)-Salphen)Fe(Tp)(CN)3]n(1)and[Mn((S,S)-Salphen)Te(Tp)(CN)3]n(2)(Salphen =N,N1-I,2-diphenyl ethylenebis(salicylideneiminato)dianion,Tp =tris(pyrazolyl)hydroborate),[Mn((R,R)-Salphen)Fe(Tp*)(CN)3·2H2O]n(3)and[Mn((S,S)-Salphen)Fe(Tp*)(CN)3.2H2O]n(4)(Tp* =hydridotris(3,5-dimethylpyrazol- l-yl)borate),have been successfully synthesized by the reactions of MnⅢ schiff-base complexes with the tricyanometalate building block,[(LTp)Fe(CN)3]-(LTp =Tp or Tp*).All complexes are made up of neutral cyano-bridged zigzag double chains with(-Fe-C≡ N-Mn-N≡C-)n as the repeating unit.Circular dichroism(CD)spectra confirm the enantiomeric nature of the optically active complexes.Magnetic studies demonstrate that ferromagnetic interactions are operative in these complexes.The ferromagnetic couplings become weak in the chains with the bending of the Mn-N ≡C angles.

  9. Crystal structure, characterization and magnetic properties of a 1D copper(II) polymer incorporating a Schiff base with carboxylate side arm

    Indian Academy of Sciences (India)



    A new 1D polymeric copper(II) complex [{Cu(L)$(CF_{3}COO)}2]_{n}$ has been synthesized using apotentially tetradentate Schiff base ligand, HL, ((E)-2-((pyridin-2-yl)methyleneamino)-5-chlorobenzoic acid)and characterized by different spectroscopic methods. Single crystal X-ray structural characterization revealsthat the side arm carboxylate group of the coordinated Schiff base exhibits a $μ_{1,3}$ -bridging mode and connectsthe neighbouring copper(II) ions leading to a zigzag 1D chain structure where the copper(II) ions displaydistorted square pyramidal geometries. Variable temperature magnetic susceptibility measurement reveals aweak antiferromagnetic exchange (J = −0.47±0.01 $cm_{−1}) prevails between copper(II) ions in the chainmediated by the bridging carboxylate group, is also supported by the room temperature EPR spectral study.Electrochemical property of the complex is also reported.

  10. Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR


    Shoshan, Michal S.; Tshuva, Edit Y.; Shalev, Deborah E.


    Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox reactions. The Cu (I) complex of the peptide model of a Cu (I) binding metallochaperone protein, which includes the sequence MTCSGCSRPG (underlined is conserved), was determined in solution under inert conditions by NMR spectroscopy.

  11. A symmetry-related sequence-structure relation of proteins

    Institute of Scientific and Technical Information of China (English)

    XU Ruizhen; LI Mingfen; CHEN Hanlin; HUANG Yanzhao; XIAO Yi


    Proteins have regular tertiary structures but irregular amino acid sequences. This made it very difficult to decode the structural information in the protein sequences. Here we demonstrate that many small αprotein domains have hidden sequence symmetries characteristic of their pseudo-symmetric tertiary structures. We also present a modified method of recurrent plot to reveal this kind of the hidden sequence symmetry. The results may enable us to understand part of the relations between protein sequences and their tertiary structures.

  12. Direct Printing of 1-D and 2-D Electronically Conductive Structures by Molten Lead-Free Solder

    Directory of Open Access Journals (Sweden)

    Chien-Hsun Wang


    Full Text Available This study aims to determine the effects of appropriate experimental parameters on the thermophysical properties of molten micro droplets, Sn-3Ag-0.5Cu solder balls with an average droplet diameter of 50 μm were prepared. The inkjet printing parameters of the molten micro droplets, such as the dot spacing, stage velocity and sample temperature, were optimized in the 1D and 2D printing of metallic microstructures. The impact and mergence of molten micro droplets were observed with a high-speed digital camera. The line width of each sample was then calculated using a formula over a temperature range of 30 to 70 °C. The results showed that a metallic line with a width of 55 μm can be successfully printed with dot spacing (50 μm and the stage velocity (50 mm∙s−1 at the substrate temperature of 30 °C. The experimental results revealed that the height (from 0.63 to 0.58 and solidification contact angle (from 72° to 56° of the metallic micro droplets decreased as the temperature of the sample increased from 30 to 70 °C. High-speed digital camera (HSDC observations showed that the quality of the 3D micro patterns improved significantly when the droplets were deposited at 70 °C.

  13. 1D zigzag chain and 0D monomer Cd(II)/Zn(II) compounds based on flexible phenylenediacetic ligand: Synthesis, crystal structures and fluorescent properties (United States)

    Yang, Fang; Ren, Yixia; Li, Dongsheng; Fu, Feng; Qi, Guangcai; Wang, Yaoyu


    Three novel Cd(II)/Zn(II) compounds, [Cd 2(poda) 2(phen) 3(H 2O)] n· nEtOH·3 nH 2O (1), [Zn(poda) 2(bpy)(H 2O)] n(2) and [Zn(Hpoda) 2(bpy)] (3) (H 2poda = 1,2-phenylenediacetic acid, phen = 1,10-phenanthroline, bpy = 2,2'-bipyridyl), have been synthesized and characterized by IR, TG, fluorescent spectrum and single-crystal X-ray diffraction techniques. In 1, poda 2- anions link the adjacent Cd(II) centers to generate a 1D zigzag chain. Furthermore, an unprecedented four-footed "8-shaped" mixed water-ethanol (H 2O) 6(C 2H 5OH) 2 cluster connects four double chains based on 1D zigzag chain into 3D supramolecular architecture. By bis(chelate-monodentate) fashion of poda 2- ligand, compound 2 exhibits 1D zigzag chains, which forming a dense zipper-like 2D structure via strong π-π stacking interactions. Differed from 1 and 2, compound 3 has a mononuclear motif, and displays a 3D 6-connected α-Po net hydrogen-bonded topology. The structure-related solid-state fluorescence spectra of compounds 1 and 2 have been determined.

  14. A case of Beauveria bassiana keratitis confirmed by internal transcribed spacer and LSU rDNA D1-D2 sequencing. (United States)

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


    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.

  15. On maximal eigenfrequency separation in two-material structures: the 1D and 2D scalar cases

    DEFF Research Database (Denmark)

    Jensen, Jakob Søndergaard; Pedersen, Niels Leergaard


    We present a method to maximize the separation of two adjacent eigenfrequencies in structures with two material components. The method is based on finite element analysis and topology optimization in which an iterative algorithm is used to find the optimal distribution of the materials. Results a...

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

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Huai-Xia, E-mail: [Pharmacy College, Henan University of Traditional Chinese Medicine, Zhengzhou 450008 (China); Liang, Zhen; Hao, Bao-Lian [Pharmacy College, Henan University of Traditional Chinese Medicine, Zhengzhou 450008 (China); Meng, Xiang-Ru, E-mail: [The College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001 (China)


    Three new 1D to 3D complexes, namely, ([Ni(btec)(Himb){sub 2}(H{sub 2}O){sub 2}]·6H{sub 2}O){sub n} (1), ([Cd(btec){sub 0.5}(imb)(H{sub 2}O)]·1.5H{sub 2}O){sub n} (2), and ([Zn(btec){sub 0.5}(imb)]·H{sub 2}O){sub n} (3) (H{sub 4}btec=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 (5{sup 3}·6{sup 2}·7)(5{sup 2}·6{sup 4}). Complex 3 presents a 3D framework with a point symbol of (4·6{sup 4}·8)(4{sup 2}·6{sup 2}·8{sup 2}). Moreover, their IR spectra, PXRD patterns, thermogravimetric curves, and luminescent emissions were studied at room temperature. - Graphical abstract: Three new 1D to 3D complexes with different structural and topological motifs have been obtained by modifying the central metal ions. Additionally, their IR, TG analyses and fluorescent properties are also investigated. - Highlights: • Three complexes based on mixed multidentate N- and O-donor ligands. • The complexes are characterized by IR, luminescence and TGA techniques. • Benzenetetracarboxylates display different coordination modes in complexes 1–3. • Changing the metal ions can result in complexes with completely different structures.

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

    CERN Document Server

    Bellingeri, Michele


    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.

  18. Tailoring the spin waves band structure of 1D magnonic crystals consisting of L-shaped iron/permalloy nanowires (United States)

    Gubbiotti, G.; Silvani, R.; Tacchi, S.; Madami, M.; Carlotti, G.; Yang, Z.; Adeyeye, A. O.; Kostylev, M.


    We have investigated both experimentally and numerically the magnonic band structure of arrays of closely spaced Fe/permalloy nanowires (NWs) with an L-shape cross-section using the Brillouin light scattering technique and GPU-based micromagnetic simulations. NWs consist of a 340 nm wide and 10 nm thick permalloy layer covered by a 170 nm wide Fe overlayer. The thickness of the latter was varied in the range from 0 to 10 nm in order to analyze its influence on the magnonic band structure. We found that both the frequency and the spatial profile of the most intense and dispersive mode, can be efficiently tuned by the presence of the thin Fe NW overlayer. In particular, by increasing the Fe thickness, one observes a substantial frequency increase, while the spatial profile of the mode narrows and moves to the permalloy NW portion not covered by Fe. In addition, the presence of the Fe overlayer causes a significant increase of the number of detected modes and a change of their intensity in the Brillouin spectra as a function of the Bloch wave number. These results show that it is possible to engineer the band structure of magnonic crystals consisting of bi-layered, L-shaped, NWs by a careful control of the overlayer thickness.

  19. Molecular Identification of Veterinary Yeast Isolates by Use of Sequence-Based Analysis of the D1/D2 Region of the Large Ribosomal Subunit▿


    Garner, Cherilyn D.; Starr, Jennifer K.; McDonough, Patrick L.; Altier, Craig


    Conventional methods of yeast identification are often time-consuming and difficult; however, recent studies of sequence-based identification methods have shown promise. Additionally, little is known about the diversity of yeasts identified from various animal species in veterinary diagnostic laboratories. Therefore, in this study, we examined three methods of identification by using 109 yeast samples isolated during a 1-year period from veterinary clinical samples. Comparison of the three me...

  20. The supramolecular interaction mediated chiral 1D cyanide-bridged metamagnet: synthesis, crystal structures and magnetic properties. (United States)

    Zhang, Daopeng; Bian, Yongzhong; Qin, Jie; Wang, Ping; Chen, Xia


    Two cyanide-bridged enantiopure one-dimensional single chain complexes, [Mn((R,R)-Salcy)Fe(pcq)(CN)3]2n·1.5nDMF (1) and [Mn((S,S)-Salcy)Fe(pcq)(CN)3]2n·1.5nDMF (2), have been synthesized and structurally characterized. Systematically magnetic investigations show the antiferromagnetic coupling between the cyanide-bridged Mn(III)-Fe(III) centers and the interesting metamagnetic behavior at about 5.0 K resulted from the intermolecular π-π interaction.

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

    Directory of Open Access Journals (Sweden)

    Florbela Pereira


    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 α or β 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.

  2. Synthesis and Crystal Structure of a 1-D Coordination Polymer {[Cu(NIT4py)2(ip)]·6H2O}n

    Institute of Scientific and Technical Information of China (English)

    WANG Shu-Ping; GAO Dong-Zhao; LIAO Dai-Zheng; JIANG Zong-Hui; YAN Shi-Ping; LI Li-Cun


    A new complex {[Cu(NIT4py)2(ip)]·6H2O}n (NIT4py=2-(4'-pyridinyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide and ip = isophthalate dianion) has been synthesized and structurally characterized by X-ray diffraction. It crystallizes in orthorhombic, space group Cmcm with a = 25.161(3), b =10.045(1), c = 15.450(2)(A), C32H48N6O14Cu, Mr = 804.30, V = 3904.8(8)(A)3, Z = 4, Dc = 1.368 g/cm3,μ(MoKα) = 0.630 mm-1, F(000) = 1692, the final R = 0.0326 and wR = 0.0787 for 1843 independent reflections with Rint = 0.0372. Each Cu(II) ion is four-coordinated by two carboxylate oxygen atoms and two pyridyl-N atoms from NIT4py radicals to furnish a rhombus geometry. The central Cu(II) ion is located at an inversion center and a crystallographic two-fold axis. Each isophthalate dianion binds two Cu(II) ions in bis-monodentate mode, leading to a 1-D chain, and these 1-D chains are further linked into a 2-D network via hydrogen-bonding interactions.

  3. Tools for integrated sequence-structure analysis with UCSF Chimera

    Directory of Open Access Journals (Sweden)

    Huang Conrad C


    Full Text Available Abstract Background Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit; (c can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals. Results The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided. Conclusion The tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is

  4. Nonlinear Correlations of Protein Sequences and Symmetries of Their Structures

    Institute of Scientific and Technical Information of China (English)

    LI Ming-Feng; HUANG Yan-Zhao; XIAO Yi


    @@ We investigate the nonlinear correlations of protein sequences by using the nonlinear prediction method developed in nonlinear dynamical theory.It is found that a lot of protein sequences show strong nonlinear correlations and have deterministic structures.Further investigations show that the strong nonlinear correlations of these protein sequences are due to the symmetries of their tertiary structures.Furthermore, the correlation lengths of the sequences are related to the degrees of the symmetries.These results support the duplication mechanism of protein evolution and also reveal one aspect how amino acid sequences encode their spatial structures.

  5. Synthesis, structure and magnetic properties of 5-(4-Sulfophenylazo) salicylate-bridged 1D coordination polymers containing linear trinuclear metal clusters (United States)

    Liu, Hong; Song, Li-jun; Ju, Zhan-feng; Li, Wei; Zhang, Jie


    Three new trinuclear metal complexes with an azobenzene-containing ligand [M 3(Sasa) 2(Py) 2(H 2O) 8] (Na 2HSasa = 5-(4-Sulfophenylazo) salicylic acid disodium salt; Py = pyridine; M = Cu, Co, Zn), are synthesized through the interface diffusion and structurally characterized by single crystal X-ray diffraction, XRPD analysis and spectral methods. The metal ions in distorted octahedral coordination environments are connected by Sasa ligands to form 1D coordination polymer chain containing the linear trinuclear units with single syn-anti carboxylate bridges. The extensive hydrogen bonding interactions hold these chains together into 3D supramolecular network. Weak antiferromagnetic interactions between adjacent metal ions with J = -1.85 cm -1 and J = -2.81 cm -1 dominate the magnetic properties of Cu(II) and Co(II) complexes, separately.

  6. Synthesis, Crystal Structure, and Electroconducting Properties of a 1D Mixed-Valence Cu(I–Cu(II Coordination Polymer with a Dicyclohexyl Dithiocarbamate Ligand

    Directory of Open Access Journals (Sweden)

    Kenji Nakatani


    Full Text Available A new mixed-valence Cu(I–Cu(II 1D coordination polymer, [CuI4CuIIBr4(Cy2dtc2]n, with an infinite chain structure is synthesized by the reaction of Cu(Cy2dtc2 (Cy2dtc− = dicyclohexyl dithiocarbamate, C13H22NS2 with CuBr·S(CH32. The as-synthesized polymer consists of mononuclear copper(II units of CuII(Cy2dtc2 and tetranuclear copper(I cluster units, CuI4Br4. In the cluster unit, all the CuI ions have distorted trigonal pyramidal coordination geometries, and the CuI–CuI or CuI–CuII distances between the nearest copper ions are shorter than the sum of van der Waals radii for Cu–Cu.

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

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Heyer, Laurie J.; Stormo, Gary D.


    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...

  8. Synthesis and Crystal Structure of 1D Coordination Polymer of N,N'-Bis(3-pyridylmethyl)-1,4-benzenedicarboxamide and Cobalt(II) Nitrate

    Institute of Scientific and Technical Information of China (English)

    GE,Chun-Hua(葛春华); ZHANG,Xiang-Dong(张向东); TONG,Jian(佟健); ZHANG,Peng(张鹏); GUO,Fang(郭放); LIU,Qi-Tao(刘祁涛)


    A noval cobalt(II)coordination polymer,{[Co(bpmb)(H2O)2(C2H5OH)2]·(NO3)2}∞(1),where bpmb=N,N'-bis(3-pyridylmethyl)-1,4-benzenedicarboxamide,was synthesized by self-assembly of the two topic ligands with cobalt nitrate in ethanol solution,and characterized structurally by X-ray crystallography analysis.The crystal data belong to triclinic,space group Pwith cell parameters a=0.8911(3)nm,b=0.9042(3)nm,c=1.0068(3)nm,α=73.083(5)°,β=81.069(5)°,γ=76.210(5)°,R1=0.0518,wR2=0.0947.The results of structure analysis indicate that each bpmb ligand coordinates two Co(II)atoms and each metal atom is in octahedral coordination geometry with four oxygen atoms of two ethanol and two water molecules,two nitrogen atoms from two different bpmb ligands in trans position forming an infinite 1D chain-like structure.There are hydrogen bonding and π-π stacking interaction among these chains,leading to supramolecular formation with 3D net structure.

  9. Identification of protein superfamily from structure- based sequence motif

    Institute of Scientific and Technical Information of China (English)


    The structure-based sequence motif of the distant proteins in evolution, protein tyrosine phosphatases (PTP) Ⅰ and Ⅱ superfamilies, as an example, has been defined by the structural comparison, structure-based sequence alignment and analyses on substitution patterns of residues in common sequence conserved regions. And the phosphatases Ⅰ and Ⅱ can be correctly identified together by the structure-based PTP sequence motif from SWISS-PROT and TrEBML databases. The results show that the correct rates of identification are over 98%. This is the first time to identify PTP Ⅰ and Ⅱ together by this motif.

  10. Synthesis, characterization, properties and crystal structure of heterometallic 1D coordination polymers{[CuLZn· CuLZn(H2O)]·H2O}n

    Institute of Scientific and Technical Information of China (English)

    TAO Ruojie; LI Fu an; ZANG Shuangquan; CHENG Yanxiang; NIU Jingyang


    Copper-zinc heterometallic 1D chain coordination polymer has been synthesized and characterized by elemental analysis, and IR spectra etc. The crystal structure was determined by single-crystal X-ray diffraction analyses. The title complex is 1 D chain coordination polymer with the chemical formula {[CuLZn·CuLZn(H2O)]·H2O}n, where H4L=N-(2-hydroxybenzamido)-N'-(3-carboxy-Isalicylidene)ethylenediamine. Its structural unit is comprosed of two tetranuclear cycles formed by two dissymmetrical tetranuclear units. These units polymerized each other to form 1D chain coordination polymer.

  11. Resolution-optimized NMR measurement of (1)D(CH), (1)D(CC) and (2)D(CH) residual dipolar couplings in nucleic acid bases. (United States)

    Boisbouvier, Jérôme; Bryce, David L; O'neil-Cabello, Erin; Nikonowicz, Edward P; Bax, Ad


    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 (2)D(CH) couplings at high precision. Measurements are demonstrated for a 24-nt stem-loop RNA sequence, uniformly enriched in (13)C, and aligned in Pf1. The recently described pseudo-3D method is used to provide homonuclear (1)H-(1)H decoupling, which minimizes cross-correlation effects and optimizes resolution. Up to seven (1)H-(13)C and (13)C-(13)C couplings are measured for pyrimidines (U and C), including (1)D(C5H5), (1)D(C6H6), (2)D(C5H6), (2)D(C6H5), (1)D(C5C4), (1)D(C5C6), and (2)D(C4H5). For adenine, four base couplings ((1)D(C2H2), (1)D(C8H8), (1)D(C4C5), and (1)D(C5C6)) are readily measured whereas for guanine only three couplings are accessible at high relative accuracy ((1)D(C8H8), (1)D(C4C5), and (1)D(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.

  12. Combining oximes with azides to create a novel 1-D [NaCo(III)(2)] system: synthesis, structure and solid-state NMR. (United States)

    Pathmalingam, Thushan; Habib, Fatemah; Widdifield, Cory M; Loiseau, Francis; Burchell, Tara J; Gorelsky, Serge I; Beauchemin, André M; Bryce, David L; Murugesu, Muralee


    The synthesis and structure of a novel complex with the formula [NaCo(III)(2)(dmo)(2)(mu-N(3))(3)(N(3))(2)](infinity), , are reported. Complex was synthesized from the reaction of 1-(dimethylamino)propan-2-one oxime (Hdmo), CoCl(2).6H(2)O, and NaN(3) in MeOH. It crystallizes in the monoclinic space group C2/c. The molecular structure consists of one Na(I) and two Co(III) ions bridged by two oxime ligands, two end-to-end azide and three end-on azide anions. The units are linked, forming a 1-D chain. This complex was characterized by UV-Vis spectroscopy where the data confirm the presence of low-spin Co(III) ions. Solid-state (23)Na NMR experiments indicate the presence of one magnetically unique site in the repeating unit, that sample purity in the bulk powdered form is high, and that it possesses microcrystalline order. Solid-state (59)Co NMR experiments at ultra-high field (B(0) = 21.1 T) are in agreement with the structure obtained through X-ray crystallography where the Co(III) ions are coordinated to five nitrogen atoms as well as an oxygen atom.

  13. Mononuclear, dinuclear and 1-D polymeric complexes of Cd(II) of a pyridyl pyrazole ligand: Syntheses, crystal structures and photoluminescence studies (United States)

    Das, Kinsuk; Konar, Saugata; Jana, Atanu; Barik, Anil Kumar; Roy, Sangita; Kar, Susanta Kumar


    The syntheses, crystal structures and photoluminescence properties of four new Cd(II) complexes are reported using strongly coordinating ligand 3,5-dimethyl-1-(2'-pyridyl) pyrazole (L) in presence of anionic ancillary bridging ligands as nitrite, chloride and dicyanamide. Among the complexes two (1 and 2) are monomeric, 3 is μ2 - chloro bridged dimer and the last one (4) is a mixed alternate chloro - end to end (EE) dicyanamide bridged 1D polymer. All the four complexes have been X-ray crystallographically characterized. The ligand L behaves as a potent bidentate neutral N, N donor. Geometrical diversity of Cd(II) complexes is due to no loss or gain of crystal field stability with the variation of geometry. Consequently the stability of a structure depends on steric requirements. The ligand L shows considerable fluorescence and all four complexes in methanol exhibit interesting photoluminescence properties with different emission intensities. The band maxima and fluorescence efficiency (in methanol) are found to be dependent on the coordination chromophore and structural rigidity induced by the incorporated Cd(II) ion. Among the synthesized complexes 1 exhibits the highest fluorescence intensity in methanol.

  14. Lipophilic bismuth phosphates: a molecular tetradecanuclear cage and a 1D-coordination polymer. Synthesis, structure and conversion to BiPO4. (United States)

    Chandrasekhar, Vadapalli; Metre, Ramesh K; Suriya Narayanan, Ramakirushnan


    The reaction of the phosphate monoester {(ArO)PO(OH)2} (Ar = 2,6-i-Pr2C6H3) with BiPh3 in a 1 : 1 ratio in refluxing toluene afforded a tetradecabismuth-oxo-phosphate cage [{(ArO)PO3}10{(ArO)PO2OH}2(Bi14O10)·2(CH3OH)]·3C6H12·3CH3OH·2H2O (Ar = 2,6-i-Pr2C6H3) (1). On the other hand the reaction of the phosphate diester {((t)BuO)2PO(OH)} with BiPh3 in a 1 : 1 ratio at room temperature in ethanol afforded the 1D-coordination polymer [Bi(C6H5)2((t)BuO)2PO2]n (2). The molecular structure of 1 reveals that the cage is comprised of a central planar Bi6 rim and two Bi4 poles. The entire aggregate is held together by multiple coordination of O(2-), [(ArO)P(O)(OH)](-), [(ArO)PO3](2-) and methanol ligands. 2 is a 1D-coordination polymer where adjacent bismuth is bridged by isobidentate [((t)BuO)2PO2](-) ligands. In solution, however, 2 decomposes into the monomeric repeat unit [Ph2Bi{((t)BuO)2PO2}] which is indicated by ESI-MS studies. Thermolysis of 1 and 2 at 700 °C affords a pure phase of BiPO4.

  15. PSSARD: protein sequence-structure analysis relational database. (United States)

    Guruprasad, Kunchur; Srikanth, K; Babu, A V N


    We have implemented a relational database comprising a representative dataset of amino acid sequences and their associated secondary structure. The representative amino acid sequences were selected according to the PDB_SELECT program by choosing proteins corresponding to protein crystal structure data deposited in the protein data bank that share less than 25% overall pair-wise sequence identity. The secondary structure was extracted from the protein data bank website. The information content in the database includes the protein description, PDB code, crystal structure resolution, total number of amino acid residues in the protein chain, amino acid sequence, secondary structure conformation and its summary. The database is freely accessible from the website mentioned below and is useful to query on any of the above fields. The database is particularly useful to quickly retrieve amino acid sequences that are compatible to any super-secondary structure conformation from several proteins simultaneously.

  16. Dynamics in Sequence Space for RNA Secondary Structure Design. (United States)

    Matthies, Marco C; Bienert, Stefan; Torda, Andrew E


    We have implemented a method for the design of RNA sequences that should fold to arbitrary secondary structures. A popular energy model allows one to take the derivative with respect to composition, which can then be interpreted as a force and used for Newtonian dynamics in sequence space. Combined with a negative design term, one can rapidly sample sequences which are compatible with a desired secondary structure via simulated annealing. Results for 360 structures were compared with those from another nucleic acid design program using measures such as the probability of the target structure and an ensemble-weighted distance to the target structure.

  17. One-Dimensional (1-D) Nanoscale Heterostructures

    Institute of Scientific and Technical Information of China (English)

    Guozhen SHEN; Di CHEN; Yoshio BANDO; Dmitri GOLBERG


    One-dimensional (1-D) nanostructures have been attracted much attention as a result of their exceptional properties, which are different from bulk materials. Among 1-D nanostructures, 1-D heterostructures with modulated compositions and interfaces have recently become of particular interest with respect to potential applications in nanoscale building blocks of future optoelectronic devices and systems. Many kinds of methods have been developed for the synthesis of 1-D nanoscale heterostructures. This article reviews the most recent development, with an emphasize on our own recent efforts, on 1-D nanoscale heterostructures, especially those synthesized from the vapor deposition methods, in which all the reactive precursors are mixed together in the reaction chamber. Three types of 1-D nanoscale heterostructures, defined from their morphologies characteristics, are discussed in detail, which include 1-D co-axial core-shell heterostructures, 1-D segmented heterostructures and hierarchical heterostructures. This article begins with a brief survey of various methods that have been developed for synthesizing 1-D nanoscale heterostructures and then mainly focuses on the synthesis, structures and properties of the above three types of nanoscale heterostructures. Finally, this review concludes with personal views towards the topic of 1-D nanoscale heterostructures.

  18. Spatial structure and dispersion of drift mirror waves coupled with Alfvén waves in a 1-D inhomogeneous plasma

    Directory of Open Access Journals (Sweden)

    D. Yu. Klimushkin


    Full Text Available The paper employs the frame of a 1-D inhomogeneous model of space plasma,to examine the spatial structure and growth rate of drift mirror modes, often suggested for interpreting some oscillation types in space plasma. Owing to its coupling with the Alfvén mode, the drift mirror mode attains dispersion across magnetic shells (dependence of the frequency on the wave-vector's radial component, kr. The spatial structure of a mode confined across magnetic shells is studied. The scale of spatial localization of the wave is shown to be determined by the plasma inhomogeneity scale and by the azimuthal component of the wave vector. The wave propagates across magnetic shells, its amplitude modulated along the radial coordinate by the Gauss function. Coupling with the Alfvén mode strongly influences the growth rate of the drift mirror instability. The mirror mode can only exist in a narrow range of parameters. In the general case, the mode represents an Alfvén wave modified by plasma inhomogeneity.

  19. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

    Directory of Open Access Journals (Sweden)

    Daniels Noah M


    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.

  20. Evolutionary optimization of biopolymers and sequence structure maps

    Energy Technology Data Exchange (ETDEWEB)

    Reidys, C.M.; Kopp, S.; Schuster, P. [Institut fuer Molekulare Biotechnologie, Jena (Germany)


    Searching for biopolymers having a predefined function is a core problem of biotechnology, biochemistry and pharmacy. On the level of RNA sequences and their corresponding secondary structures we show that this problem can be analyzed mathematically. The strategy will be to study the properties of the RNA sequence to secondary structure mapping that is essential for the understanding of the search process. We show that to each secondary structure s there exists a neutral network consisting of all sequences folding into s. This network can be modeled as a random graph and has the following generic properties: it is dense and has a giant component within the graph of compatible sequences. The neutral network percolates sequence space and any two neutral nets come close in terms of Hamming distance. We investigate the distribution of the orders of neutral nets and show that above a certain threshold the topology of neutral nets allows to find practically all frequent secondary structures.

  1. Forest-atmosphere BVOC exchange in diverse and structurally complex canopies: 1-D modeling of a mid-successional forest in northern Michigan

    Energy Technology Data Exchange (ETDEWEB)

    Bryan, Alexander M.; Cheng, Susan J.; Ashworth, Kirsti; Guenther, Alex B.; Hardiman, Brady; Bohrer, Gil; Steiner, A. L.


    Foliar emissions of biogenic volatile organic compounds (BVOC)dimportant precursors of tropospheric ozone and secondary organic aerosolsdvary widely by vegetation type. Modeling studies to date typi-cally represent the canopy as a single dominant tree type or a blend of tree types, yet many forests are diverse with trees of varying height. To assess the sensitivity of biogenic emissions to tree height vari-ation, we compare two 1-D canopy model simulations in which BVOC emission potentials are homo-geneous or heterogeneous with canopy depth. The heterogeneous canopy emulates the mid-successional forest at the University of Michigan Biological Station (UMBS). In this case, high-isoprene-emitting fo-liage (e.g., aspen and oak) is constrained to the upper canopy, where higher sunlight availability increases the light-dependent isoprene emission, leading to 34% more isoprene and its oxidation products as compared to the homogeneous simulation. Isoprene declines from aspen mortality are 10% larger when heterogeneity is considered. Overall, our results highlight the importance of adequately representing complexities of forest canopy structure when simulating light-dependent BVOC emissions and chemistry.

  2. Synthesis and Crystal Structure of a 1D Alternate Chain Polymer [Zn2(NBA)2(4,4--bipy)]n

    Institute of Scientific and Technical Information of China (English)

    WANG Ke-Wei; YIN Pei-Xiu; SHEN Yi-Cheng; LI Zhao-Ji; QIN Ye-Yan; YAO Yuan-Gen


    A one-dimensional zinc-containing coordination polymer, [Zn2(NBA)2(4,4--bipy)]n (NBA = 3-nitrobenzoic acid, 4,4--bipy = 4,4--bipyrindine), has been solvothermally synthesized and characterized by single-crystal X-ray diffraction, IR and elemental analysis.The crystal structure is of monoclinic, space group C2/c with a = 24.6478(2), b = 14.0964(3), c = 11.4275(2) -, β =108.7870(10)°, V = 3758.89(11) -3, C38H20N6O16Zn2, Mr = 947.34, Z = 4, Dc = 1.674 g/cm3, μ = 1.363 mm-1, F(000) = 1912, R = 0.0720 and wR = 0.2277 for 2841 observed reflections (I > 2((I)).In this compound, NBA in syn-syn coordination mode bridges zinc centers into dimeric- zinctetracarboxylate [Zn2(COO)4] secondary building units (SBUs) which are linked through μ-4,4--bpy affording 1D alternating chains.These adjacent chains are further stacked through intermolecular π…π interactions to form a 3D framework.

  3. Nucleosome DNA sequence structure of isochores

    Directory of Open Access Journals (Sweden)

    Trifonov Edward N


    Full Text Available Abstract Background Significant differences in G+C content between different isochore types suggest that the nucleosome positioning patterns in DNA of the isochores should be different as well. Results Extraction of the patterns from the isochore DNA sequences by Shannon N-gram extension reveals that while the general motif YRRRRRYYYYYR is characteristic for all isochore types, the dominant positioning patterns of the isochores vary between TAAAAATTTTTA and CGGGGGCCCCCG due to the large differences in G+C composition. This is observed in human, mouse and chicken isochores, demonstrating that the variations of the positioning patterns are largely G+C dependent rather than species-specific. The species-specificity of nucleosome positioning patterns is revealed by dinucleotide periodicity analyses in isochore sequences. While human sequences are showing CG periodicity, chicken isochores display AG (CT periodicity. Mouse isochores show very weak CG periodicity only. Conclusions Nucleosome positioning pattern as revealed by Shannon N-gram extension is strongly dependent on G+C content and different in different isochores. Species-specificity of the pattern is subtle. It is reflected in the choice of preferentially periodical dinucleotides.

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

    DEFF Research Database (Denmark)

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


    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 ve...

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

    CERN Document Server

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


    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

  6. Strain-Gated Field Effect Transistor of a MoS2-ZnO 2D-1D Hybrid Structure. (United States)

    Chen, Libo; Xue, Fei; Li, Xiaohui; Huang, Xin; Wang, Longfei; Kou, Jinzong; Wang, Zhong Lin


    Two-dimensional (2D) molybdenum disulfide (MoS2) is an exciting material due to its unique electrical, optical, and piezoelectric properties. Owing to an intrinsic band gap of 1.2-1.9 eV, monolayer or a-few-layer MoS2 is used for fabricating field effect transistors (FETs) with high electron mobility and on/off ratio. However, the traditional FETs are controlled by an externally supplied gate voltage, which may not be sensitive enough to directly interface with a mechanical stimulus for applications in electronic skin. Here we report a type of top-pressure/force-gated field effect transistors (PGFETs) based on a hybrid structure of a 2D MoS2 flake and 1D ZnO nanowire (NW) array. Once an external pressure is applied, the piezoelectric polarization charges created at the tips of ZnO NWs grown on MoS2 act as a gate voltage to tune/control the source-drain transport property in MoS2. At a 6.25 MPa applied stimulus on a packaged device, the source-drain current can be tuned for ∼25%, equivalent to the results of applying an extra -5 V back gate voltage. Another type of PGFET with a dielectric layer (Al2O3) sandwiched between MoS2 and ZnO also shows consistent results. A theoretical model is proposed to interpret the received data. This study sets the foundation for applying the 2D material-based FETs in the field of artificial intelligence.

  7. Construction of copper-based coordination polymers with 1D chain, 2D plane and wavy networks: Syntheses, structures, thermal behaviors and photoluminescence properties

    Indian Academy of Sciences (India)

    Jianghua Li; Chi Zhang


    Three Cu-based coordination polymers (CPs), including [CuII ( -1 -NCS)2 (O-1 -DMF)2 (2 -3,3’-bptz)] (1), [CuI (1,3-2-NCS)(2-3,3’-bptz)] (2) and [(CuI (1,3-μ2- NCS))(2-4,4’-bptz)] (3) (DMF = , -dimethyl formamide, 3,3’-bptz = 3,6-bis(3-pyridyl)tetrazine and 4,4’-bptz = 3,6-bis(4-pyridyl)tetrazine) have been successfully constructed by solution diffusion reactions by using Cu(NO3)2 ·3H2O or CuNCS and KNCS with 3,3’-bptz / 4,4’-bptz ligands, respectively. The resulting crystalline materials have been characterized by the single-crystal X-ray diffraction analyses, elemental analyses, FT-IR spectra, thermogravimetric analyses and powder X-ray diffraction (PXRD). Single crystal X-ray analyses revealed that CP 1 is organized in one-dimensional (1D) chain in which the Cu(II) ions are coordinated by 1 -NCS− anions and 1-DMF molecules, and linked by 2-3,3’-bptz bridging ligands. CPs ,2 and 3 are structural isomers. CP 2 exhibits two-dimensional (2D) (4,4)-plane-like network in which Cu(I) ions are linked by 2-NCS − and 2-3,3’-bptz ligands. In CP 3, Cu(I) ions are connected by 2 -NCS − and 2-4,4’-bptz ligands to form 2D saw-tooth wavy network. In addition, the photoluminescence properties of CPs 1-3 were also investigated in the solid state at room temperature.

  8. Algorithm of detecting structural variations in DNA sequences (United States)

    Nałecz-Charkiewicz, Katarzyna; Nowak, Robert


    Whole genome sequencing enables to use the longest common subsequence algorithm to detect genetic structure variations. We propose to search position of short unique fragments, genetic markers, to achieve acceptable time and space complexity. The markers are generated by algorithms searching the genetic sequence or its Fourier transformation. The presented methods are checked on structural variations generated in silico on bacterial genomes giving the comparable or better results than other solutions.

  9. Accuracy of structure-based sequence alignment of automatic methods

    Directory of Open Access Journals (Sweden)

    Lee Byungkook


    Full Text Available Abstract Background Accurate sequence alignments are essential for homology searches and for building three-dimensional structural models of proteins. Since structure is better conserved than sequence, structure alignments have been used to guide sequence alignments and are commonly used as the gold standard for sequence alignment evaluation. Nonetheless, as far as we know, there is no report of a systematic evaluation of pairwise structure alignment programs in terms of the sequence alignment accuracy. Results In this study, we evaluate CE, DaliLite, FAST, LOCK2, MATRAS, SHEBA and VAST in terms of the accuracy of the sequence alignments they produce, using sequence alignments from NCBI's human-curated Conserved Domain Database (CDD as the standard of truth. We find that 4 to 9% of the residues on average are either not aligned or aligned with more than 8 residues of shift error and that an additional 6 to 14% of residues on average are misaligned by 1–8 residues, depending on the program and the data set used. The fraction of correctly aligned residues generally decreases as the sequence similarity decreases or as the RMSD between the Cα positions of the two structures increases. It varies significantly across CDD superfamilies whether shift error is allowed or not. Also, alignments with different shift errors occur between proteins within the same CDD superfamily, leading to inconsistent alignments between superfamily members. In general, residue pairs that are more than 3.0 Å apart in the reference alignment are heavily (>= 25% on average misaligned in the test alignments. In addition, each method shows a different pattern of relative weaknesses for different SCOP classes. CE gives relatively poor results for β-sheet-containing structures (all-β, α/β, and α+β classes, DaliLite for "others" class where all but the major four classes are combined, and LOCK2 and VAST for all-β and "others" classes. Conclusion When the sequence

  10. Sequence structure of Lowary/Widom clones forming strong nucleosomes. (United States)

    Trifonov, Edward N


    Lowary and Widom selected from random sequences those which form exceptionally stable nucleosomes, including clone 601, the current champion of strong nucleosome (SN) sequences. This unique sequence database (LW sequences) carries sequence elements which confer stability on the nucleosomes formed on the sequences, and, thus, may serve as source of information on the structure of "ideal" or close to ideal nucleosome DNA sequence. An important clue is also provided by crystallographic study of Vasudevan and coauthors on clone 601 nucleosomes. It demonstrated that YR·YR dinucleotide stacks (primarily TA·TA) follow one another at distances 10 or 11 bases or multiples thereof, such that they all are located on the interface between DNA and histone octamer. Combining this important information with alignment of the YR-containing 10-mers and 11-mers from LW sequences, the bendability matrices of the stable nucleosome DNA are derived. The matrices suggest that the periodically repeated TA (YR), RR, and YY dinucleotides are the main sequence features of the SNs. This consensus coincides with the one for recently discovered SNs with visibly periodic DNA sequences. Thus, the experimentally observed stable LW nucleosomes and SNs derived computationally appear to represent the same entity - exceptionally stable SNs.

  11. A benchmark of multiple sequence alignment programs upon structural RNAs

    DEFF Research Database (Denmark)

    Gardner, P. P.; Wilm, A.; Washietl, S.


    , we systematically test the performance of existing alignment algorithms on structural RNAs. This work was aimed at achieving the following goals: (i) to determine conditions where it is appropriate to apply common sequence alignment methods to the structural RNA alignment problem. This indicates......To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents are not considered for nucleic acids; instead, rather ad hoc models are generally favoured. Here...... where and when researchers should consider augmenting the alignment process with auxiliary information, such as secondary structure and (ii) to determine which sequence alignment algorithms perform well under the broadest range of conditions. We find that sequence alignment alone, using the current...

  12. A new (2+1)D cluster finding algorithm based on photometric redshifts: large scale structure in the Chandra Deep Field South

    CERN Document Server

    Trevese, D; Fontana, A; Giallongo, E; Trevese, Dario; Castellano, Marco; Fontana, Adriano; Giallongo, Emanuele


    Aims: We study galaxy clustering and explore the dependence of galaxy properties on the the environment up to a redshift z~1, on the basis of a deep multi-band survey in the Chandra Deep Field South. Methods: We have developed a new method which combines galaxy angular positions and photometric redshifts to estimate the local galaxy number-density. This allows both the detection of overdensities in the galaxy distribution and the study of the properties of the galaxy population as a function of the environmental density. Results: We detect two moderate overdensities at z~0.7 and z~1 previously identified spectroscopically. We find that the fraction of red galaxies within each structure increases with volume density, extending to z~1 previous results. We measure ``red sequence'' slopes consistent with the values found in X-ray selected clusters, supporting the notion that the mass-metallicity relation hold constant up to z~1. Conclusions: Our method based on photometric redshifts allows to extend structure det...

  13. Informational structure of genetic sequences and nature of gene splicing (United States)

    Trifonov, E. N.


    Only about 1/20 of DNA of higher organisms codes for proteins, by means of classical triplet code. The rest of DNA sequences is largely silent, with unclear functions, if any. The triplet code is not the only code (message) carried by the sequences. There are three levels of molecular communication, where the same sequence ``talks'' to various bimolecules, while having, respectively, three different appearances: DNA, RNA and protein. Since the molecular structures and, hence, sequence specific preferences of these are substantially different, the original DNA sequence has to carry simultaneously three types of sequence patterns (codes, messages), thus, being a composite structure in which one had the same letter (nucleotide) is frequently involved in several overlapping codes of different nature. This multiplicity and overlapping of the codes is a unique feature of the Gnomic, language of genetic sequences. The coexisting codes have to be degenerate in various degrees to allow an optimal and concerted performance of all the encoded functions. There is an obvious conflict between the best possible performance of a given function and necessity to compromise the quality of a given sequence pattern in favor of other patterns. It appears that the major role of various changes in the sequences on their ``ontogenetic'' way from DNA to RNA to protein, like RNA editing and splicing, or protein post-translational modifications is to resolve such conflicts. New data are presented strongly indicating that the gene splicing is such a device to resolve the conflict between the code of DNA folding in chromatin and the triplet code for protein synthesis.

  14. Protein 3D structure computed from evolutionary sequence variation.

    Directory of Open Access Journals (Sweden)

    Debora S Marks

    Full Text Available The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7-4.8 Å C(α-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of

  15. Code domains in tandem repetitive DNA sequence structures. (United States)

    Vogt, P


    Traditionally, many people doing research in molecular biology attribute coding properties to a given DNA sequence if this sequence contains an open reading frame for translation into a sequence of amino acids. This protein coding capability of DNA was detected about 30 years ago. The underlying genetic code is highly conserved and present in every biological species studied so far. Today, it is obvious that DNA has a much larger coding potential for other important tasks. Apart from coding for specific RNA molecules such as rRNA, snRNA and tRNA molecules, specific structural and sequence patterns of the DNA chain itself express distinct codes for the regulation and expression of its genetic activity. A chromatin code has been defined for phasing of the histone-octamer protein complex in the nucleosome. A translation frame code has been shown to exist that determines correct triplet counting at the ribosome during protein synthesis. A loop code seems to organize the single stranded interaction of the nascent RNA chain with proteins during the splicing process, and a splicing code phases successive 5' and 3' splicing sites. Most of these DNA codes are not exclusively based on the primary DNA sequence itself, but also seem to include specific features of the corresponding higher order structures. Based on the view that these various DNA codes are genetically instructive for specific molecular interactions or processes, important in the nucleus during interphase and during cell division, the coding capability of tandem repetitive DNA sequences has recently been reconsidered.

  16. Choosing the best pulse sequences, acquisition parameters, postacquisition processing strategies, and probes for natural product structure elucidation by NMR spectroscopy. (United States)

    Reynolds, William F; Enríquez, Raúl G


    The relative merits of different pairs of two-dimensional NMR pulse sequences (COSY-90 vs COSY-45, NOESY vs T-ROESY, HSQC vs HMQC, HMBC vs CIGAR, etc.) are compared and recommendations are made for the preferred choice of sequences for natural product structure elucidation. Similar comparisons are made between different selective 1D sequences and the corresponding 2D sequences. Many users of 2D NMR use longer than necessary relaxation delays and neglect to use forward linear prediction processing. It is shown that using shorter relaxation delays in combination with forward linear prediction allows one to get better resolved spectra in less time. The relative merits of different probes and likely future probe developments are also discussed.

  17. Massively Parallel Interrogation of Aptamer Sequence, Structure and Function

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

  18. Massively parallel interrogation of aptamer sequence, structure and function.

    Directory of Open Access Journals (Sweden)

    Nicholas O Fischer

    Full Text Available BACKGROUND: 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 inter-chip 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. CONCLUSION AND SIGNIFICANCE: 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.

  19. Hinge Atlas: relating protein sequence to sites of structural flexibility


    Yang Julie; Lu Long J; Flores Samuel C; Carriero Nicholas; Gerstein Mark B


    Abstract Background Relating features of protein sequences to structural hinges is important for identifying domain boundaries, understanding structure-function relationships, and designing flexibility into proteins. Efforts in this field have been hampered by the lack of a proper dataset for studying characteristics of hinges. Results Using the Molecular Motions Database we have created a Hinge Atlas of manually annotated hinges and a statistical formalism for calculating the enrichment of v...

  20. Model identification for DNA sequence-structure relationships. (United States)

    Hawley, Stephen Dwyer; Chiu, Anita; Chizeck, Howard Jay


    We investigate the use of algebraic state-space models for the sequence dependent properties of DNA. By considering the DNA sequence as an input signal, rather than using an all atom physical model, computational efficiency is achieved. A challenge in deriving this type of model is obtaining its structure and estimating its parameters. Here we present two candidate model structures for the sequence dependent structural property Slide and a method of encoding the models so that a recursive least squares algorithm can be applied for parameter estimation. These models are based on the assumption that the value of Slide at a base-step is determined by the surrounding tetranucleotide sequence. The first model takes the four bases individually as inputs and has a median root mean square deviation of 0.90 A. The second model takes the four bases pairwise and has a median root mean square deviation of 0.88 A. These values indicate that the accuracy of these models is within the useful range for structure prediction. Performance is comparable to published predictions of a more physically derived model, at significantly less computational cost.

  1. Aerogels of 1D Coordination Polymers: From a Non-Porous Metal-Organic Crystal Structure to a Highly Porous Material

    Directory of Open Access Journals (Sweden)

    Adrián Angulo-Ibáñez


    Full Text Available The processing of an originally non-porous 1D coordination polymer as monolithic gel, xerogel and aerogel is reported as an alternative method to obtain novel metal-organic porous materials, conceptually different to conventional crystalline porous coordination polymer (PCPs or metal-organic frameworks (MOFs. Although the work herein reported is focused upon a particular kind of coordination polymer ([M(μ-ox(4-apy2]n, M: Co(II, Ni(II, the results are of interest in the field of porous materials and of MOFs, as the employed synthetic approach implies that any coordination polymer could be processable as a mesoporous material. The polymerization conditions were fixed to obtain stiff gels at the synthesis stage. Gels were dried at ambient pressure and at supercritical conditions to render well shaped monolithic xerogels and aerogels, respectively. The monolithic shape of the synthesis product is another remarkable result, as it does not require a post-processing or the use of additives or binders. The aerogels of the 1D coordination polymers are featured by exhibiting high pore volumes and diameters ranging in the mesoporous/macroporous regions which endow to these materials the ability to deal with large-sized molecules. The aerogel monoliths present markedly low densities (0.082–0.311 g·cm−3, an aspect of interest for applications that persecute light materials.

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

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Lyngsø, Rune B.; Stormo, Gary D.


    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....... 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...

  3. Statistical mechanics of secondary structures formed by random RNA sequences. (United States)

    Bundschuh, R; Hwa, T


    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 molecule in six-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 external 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 characterized the statistics of large-scale, low-energy excitations of the secondary structures from the ground state structure. We find the excitation energy to grow very slowly (i.e., logarithmically) with the length scale of the excitation, suggesting the existence of a marginal glass phase. The transition between the low-temperature glass phase and the high-temperature molten phase is also characterized numerically. It is revealed by a change in the coefficient of the logarithmic excitation energy, from being disorder dominated to being entropy dominated.

  4. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.


    The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

  5. Comparative sequence-structure analysis of Aves insulin. (United States)

    Islam, Md Mirazul; Aktaruzzaman, M; Mohamed, Zahurin


    Normal blood glucose level depends on the availability of insulin and its ability to bind insulin receptor (IR) that regulates the downstream signaling pathway. Insulin sequence and blood glucose level usually vary among animals due to species specificity. The study of genetic variation of insulin, blood glucose level and diabetics symptoms development in Aves is interesting because of its optimal high blood glucose level than mammals. Therefore, it is of interest to study its evolutionary relationship with other mammals using sequence data. Hence, we compiled 32 Aves insulin from GenBank to compare its sequence-structure features with phylogeny for evolutionary inference. The analysis shows long conserved motifs (about 14 residues) for functional inference. These sequences show high leucine content (20%) with high instability index (>40). Amino acid position 11, 14, 16 and 20 are variable that may have contribution to binding to IR. We identified functionally critical variable residues in the dataset for possible genetic implication. Structural models of these sequences were developed for surface analysis towards functional representation. These data find application in the understanding of insulin function across species.

  6. Novel 1D Copper(ll) Helical Chain Formed by Weak Coordination-driven Self-assembly: Synthesis, Structure, and Magnetic Property

    Institute of Scientific and Technical Information of China (English)

    黄婉云; 陈自卢; 邹华红; 刘冬成; 梁福沛


    A novel 1D copper(II) helical chain is constructed through the connection of tetranuclear copper(ll) units [Cu4(L)(Py)4] (H8L=N,N'-(BINOL-3,3'-dicarboxyl)-disalicylhydrazide, where BINOL is 1,l'-binaphthalenyl-2,2'- diol, py=pyridine) by weak coordination-driven self-assembly, and characterized by IR, single crystal X-ray dif- fraction, thermogravimetric analysis, and X-ray power diffraction analysis. Interestingly, the helical chains are packed in an alternating left-(M) and right-handed (P) chirality, the orientation of the helices was determined by the axial chirality of the ligand. The complex shows antiferromagnetic interactions between the copper centers.

  7. Biophysical and structural considerations for protein sequence evolution

    Directory of Open Access Journals (Sweden)

    Grahnen Johan A


    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.

  8. The structure of verbal sequences analyzed with unsupervised learning techniques

    CERN Document Server

    Recanati, Catherine; Bennani, Younès


    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.

  9. Effect of the band structure in a rigorous two-body model with long-range interactions in 1D optical lattices (United States)

    Kristensen, Tom; Simoni, Andrea; Launay, Jean-Michel


    We compute scattering and bound state properties for two ultracold molecules in a pure 1D optical lattice. We introduce reference functions with complex quasi-momentum that naturally account for the effect of excited energy bands. Our exact results for a short-range interaction are first compared with the simplest version of the standard Bose-Hubbard (BH) model. Such comparison allows us to highlight the effect of the excited bands, of the non-on-site interaction and of tunneling with distant neighbor, that are not taken into account in the BH model. The effective interaction can depend strongly on the particle quasi-momenta and can present a resonant behavior even in a deep lattice. As a second step, we study scattering of two polar particles in the optical lattice. Peculiar Wigner threshold laws stem from the interplay of the long range dipolar interaction and the presence of the energy bands. We finally assess the validity of an extended Bose-Hubbard model for dipolar gases based on our exact two-body calculations. This work was supported by the Agence Nationale de la Recherche (Contract No. ANR-12-BS04-0020-01).

  10. Incorporating secondary structural features into sequence information for predicting protein structural class. (United States)

    Liao, Bo; Peng, Ting; Chen, Haowen; Lin, Yaping


    Knowledge of structural classes is applied in numerous important predictive tasks that address structural and functional features of proteins, although the prediction accuracy of the protein structural classes is not high. In this study, 45 different features were rationally designed to model the differences between protein structural classes, among which, 30 of them reflect the combined protein sequence information. In terms of correlation function, the protein sequence can be converted to a digital signal sequence, from which we can generate 20 discrete Fourier spectrum numbers. According to the segments of amino with different characteristics occurring in protein sequences, the frequencies of the 10 kinds of segments of amino acid (motifs) in protein are calculated. Other features include the secondary structural information :10 features were proposed to model the strong adjacent correlations in the secondary structural elements and capture the long-range spatial interactions between secondary structures, other 5 features were designed to differentiate α/β from α+β classes , which is a major problem of the existing algorithm. The methods were proposed based on a large set of low-identity sequences for which secondary structure is predicted from their sequence (based on PSI-PRED). By means of this method, the overall prediction accuracy of four benchmark datasets were all improved. Especially for the dataset FC699, 25PDB and D1189 which are 1.26%, 1% and 0.85% higher than the best previous method respectively.

  11. Sequence analysis and structural implications of rotavirus capsid proteins. (United States)

    Parbhoo, N; Dewar, J B; Gildenhuys, S

    Rotavirus is the major cause of severe virus-associated gastroenteritis worldwide in children aged 5 and younger. Many children lose their lives annually due to this infection and the impact is particularly pronounced in developing countries. The mature rotavirus is a non-enveloped triple-layered nucleocapsid containing 11 double stranded RNA segments. Here a global view on the sequence and structure of the three main capsid proteins, VP2, VP6 and VP7 is shown by generating a consensus sequence for each of these rotavirus proteins, for each species obtained from published data of representative rotavirus genotypes from across the world and across species. Degree of conservation between species was represented on homology models for each of the proteins. VP7 shows the highest level of variation with 14-45 amino acids showing conservation of less than 60%. These changes are localised to the outer surface alluding to a possible mechanism in evading the immune system. The middle layer, VP6 shows lower variability with only 14-32 sites having lower than 70% conservation. The inner structural layer made up of VP2 showed the lowest variability with only 1-16 sites having less than 70% conservation across species. The results correlate with each protein's multiple structural roles in the infection cycle. Thus, although the nucleotide sequences vary due to the error-prone nature of replication and lack of proof reading, the corresponding amino acid sequence of VP2, 6 and 7 remain relatively conserved. Benefits of this knowledge about the conservation include the ability to target proteins at sites that cannot undergo mutational changes without influencing viral fitness; as well as possibility to study systems that are highly evolved for structure and function in order to determine how to generate and manipulate such systems for use in various biotechnological applications.

  12. Improving protein structural class prediction using novel combined sequence information and predicted secondary structural features. (United States)

    Dai, Qi; Wu, Li; Li, Lihua


    Protein structural class prediction solely from protein sequences is a challenging problem in bioinformatics. Numerous efficient methods have been proposed for protein structural class prediction, but challenges remain. Using novel combined sequence information coupled with predicted secondary structural features (PSSF), we proposed a novel scheme to improve prediction of protein structural classes. Given an amino acid sequence, we first transformed it into a reduced amino acid sequence and calculated its word frequencies and word position features to combine novel sequence information. Then we added the PSSF to the combine sequence information to predict protein structural classes. The proposed method was tested on four benchmark datasets in low homology and achieved the overall prediction accuracies of 83.1%, 87.0%, 94.5%, and 85.2%, respectively. The comparison with existing methods demonstrates that the overall improvements range from 2.3% to 27.5%, which indicates that the proposed method is more efficient, especially for low-homology amino acid sequences.

  13. Data structures of genome and protein sequences indexing

    Directory of Open Access Journals (Sweden)

    Adeleh asadi


    Full Text Available Data structure is a tool for storage and retrieval of information which is named logic and mathematic way of specific data organization. various sequences of genes and proteins in various creatures increases the amount of data in genome databases, and finding appropriate data structure and indexing are subject for many studies. String data structures are general data structure for genome indexing, and this article would review the many used three types of string data structure, suffix tree, suffix array, and Directed Acyclic Word Graphs. This paper is a review of the literature related to three types of data, including genome databases indexing field, tree, postfix, postfix and graphs spiral array directly introduces the word. Findings of this research show that suffix tree and Directed Acyclic Word Graph (DAWG structures need much space however suffix array need less space. Against the Directed Acyclic Word Graph, suffix array can be stored on Memory Stick. Suffix tree and Directed Acyclic Word Graph are a dynamic structures but as suffix array is a Sorted out structure, it could hardly be changed.

  14. Glass-based 1-D dielectric microcavities (United States)

    Chiasera, Alessandro; Scotognella, Francesco; Valligatla, Sreeramulu; Varas, Stefano; Jasieniak, Jacek; Criante, Luigino; Lukowiak, Anna; Ristic, Davor; Gonçalves, Rogeria Rocha; Taccheo, Stefano; Ivanda, Mile; Righini, Giancarlo C.; Ramponi, Roberta; Martucci, Alessandro; Ferrari, Maurizio


    We have developed a reliable RF sputtering techniques allowing to fabricate glass-based one dimensional microcavities, with high quality factor. This property is strongly related to the modification of the density of states due to the confinement of the gain medium in a photonic band gap structure. In this short review we present some of the more recent results obtained by our team exploiting these 1D microcavities. In particular we present: (1) Er3+ luminescence enhancement of the 4I13/2 → 4I15/2 transition; (2) broad band filters based on disordered 1-D photonic structures; (3) threshold defect-mode lasing action in a hybrid structure.

  15. A Precise Packing Sequence for Self-Assembled Convex Structures (United States)

    Chen, Ting; Zhang, Zhenli; Glotzer, Sharon


    We present molecular simulations of the self-assembly of cone-shaped particles with patchy, attractive interactions[1,2]. Upon cooling from random initial conditions, we find that the cones self assemble into clusters and that clusters comprised of particular numbers of cones have a unique and precisely packed structure that is robust over a range of cone angles. These precise clusters form precise packing sequence that for small sizes is identical to that observed in evaporation-driven assembly of colloidal spheres. This sequence is reproduced and extended in simulations of two simple models of spheres self-assembling from random initial conditions subject to convexity constraints, and contains six of the most common virus capsid structures obtained in vivo including large chiral clusters, and a cluster that may correspond to several non- icosahedral, spherical virus capsid structures obtained in vivo. For prolate spheroidal convexity conditions, we demonstrate the formation of several prolate virus structures from self-assembling hard spheres[3]. [1] Chen T, Zhang ZL, Glotzer SC, PNAS, in press ( 0608592) [2] Chen T, Zhang ZL, Glotzer SC, [3] Chen T, Glotzer SC

  16. Structure and sequence analysis of influenza A virus nucleoprotein

    Institute of Scientific and Technical Information of China (English)

    NG; Andy; Ka-Leung; SHAW; Pang-Chui


    Influenza A virus nucleoprotein (NP) forms homo-oligomers and multiple copies of NP wrap around genomic RNA, along with a trimeric polymerase making up ribonucleoprotein (RNP) complex. Sequence comparison of more than 2500 influenza A NP showed that this protein contains 30.1 % of polymorphic residues. NP is composed of a head and a body domain and a tail loop/ linker region. The head domain is more conserved than the body domain, as revealed from the structure-based sequence alignment. NP oligomerization is mediated by the insertion of the non-polymorphic and structurally conserved tail loop of one NP molecule to a groove of another NP. The different form of NP oligomers is due to the flexibility of the polymorphic linkers that join the tail loop to the rest of the protein. The RNA binding property of NP is known to involve the protruding element and the flexible basic loop between the head and body domains, both having high degree of primary sequence conservation. To bind RNA, NP may first capture the RNA by the flexible basic loop and then the RNA is clamped by the protruding element.

  17. Structure and sequence analysis of influenza A virus nucleoprotein

    Institute of Scientific and Technical Information of China (English)

    NG Andy Ka-Leung; WANG Jia-Huai; SHAW Pang-Chui


    Influenza A virus nucleoprotein (NP) forms homo-oligomenrs and multiple copies of NP wrap around genomic RNA, along with a trimeric polymerase making up ribonucleoprotein (RNP) complex. Se-quence comparison of more than 2500 influenza A NP showed that this protein contains 30.1% of po-lymorphic residues. NP is composed of a head and a body domain and a tail loop/linker region. The head domain is more conserved than the body domain, as revealed from the structure-based sequence alignment. NP oligomerization is mediated by the insertion of the non-polymorphic and structurally conserved tail loop of one NP molecule to a groove of another NP. The different form of NP oligomers is due to the flexibility of the polymorphic linkers that join the tail loop to the rest of the protein. The RNA binding property of NP is known to involve the protruding element and the flexible basic loop between the head and body domains, both having high degree of primary sequence conservation. To bind RNA, NP may first capture the RNA by the flexible basic loop and then the RNA is clamped by the protruding element.

  18. Effects of GWAS-associated genetic variants on lncRNAs within IBD and T1D candidate loci

    DEFF Research Database (Denmark)

    Mirza, Aashiq H; Kaur, Simranjeet; Brorsson, Caroline A;


    Long non-coding RNAs are a new class of non-coding RNAs that are at the crosshairs in many human diseases such as cancers, cardiovascular disorders, inflammatory and autoimmune disease like Inflammatory Bowel Disease (IBD) and Type 1 Diabetes (T1D). Nearly 90% of the phenotype-associated single......, we systemically identified all annotated IBD and T1D loci-associated lncRNAs, and mapped nominally significant GWAS/ImmunoChip SNPs for IBD and T1D within these lncRNAs. Additionally, we identified tissue-specific cis-eQTLs, and strong linkage disequilibrium (LD) signals associated with these SNPs....... We explored sequence and structure based attributes of these lncRNAs, and also predicted the structural effects of mapped SNPs within them. We also identified lncRNAs in IBD and T1D that are under recent positive selection. Our analysis identified putative lncRNA secondary structure-disruptive SNPs...

  19. Structural insight into the sequence dependence of nucleosome positioning. (United States)

    Wu, Bin; Mohideen, Kareem; Vasudevan, Dileep; Davey, Curt A


    Nucleosome positioning displays sequence dependency and contributes to genomic regulation in a site-specific manner. We solved the structures of nucleosome core particle composed of strong positioning TTTAA elements flanking the nucleosome center. The positioning strength of the super flexible TA dinucleotide is consistent with its observed central location within minor groove inward regions, where it can contribute maximally to energetically challenging minor groove bending, kinking and compression. The marked preference for TTTAA and positioning power of the site 1.5 double helix turns from the nucleosome center relates to a unique histone protein motif at this location, which enforces a sustained, extremely narrow minor groove via a hydrophobic "sugar clamp." Our analysis sheds light on the basis of nucleosome positioning and indicates that the histone octamer has evolved not to fully minimize sequence discrimination in DNA binding.

  20. Fast and low-cost structured light pattern sequence projection. (United States)

    Wissmann, Patrick; Forster, Frank; Schmitt, Robert


    We present a high-speed and low-cost approach for structured light pattern sequence projection. Using a fast rotating binary spatial light modulator, our method is potentially capable of projection frequencies in the kHz domain, while enabling pattern rasterization as low as 2 μm pixel size and inherently linear grayscale reproduction quantized at 12 bits/pixel or better. Due to the circular arrangement of the projected fringe patterns, we extend the widely used ray-plane triangulation method to ray-cone triangulation and provide a detailed description of the optical calibration procedure. Using the proposed projection concept in conjunction with the recently published coded phase shift (CPS) pattern sequence, we demonstrate high accuracy 3-D measurement at 200 Hz projection frequency and 20 Hz 3-D reconstruction rate.

  1. Structural Approaches to Sequence Evolution Molecules, Networks, Populations

    CERN Document Server

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


    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.

  2. Fabrication and investigation of 1D and 2D structures in LiNbO 3 thin films by pulsed laser ablation (United States)

    Meriche, F.; Boudrioua, A.; Kremer, R.; Dogheche, E.; Neiss-Clauss, E.; Mouras, R.; Fischer, A.; Beghoul, M.-R.; Fogarassy, E.; Boutaoui, N.


    Lithium niobate thin films were deposited on sapphire substrate by radio-frequency magnetron sputtering technique. One and two dimensional structures have been made using a KrF excimer laser at 248 nm and 6 ns pulse width, under various conditions of ablation, in order to assess the applicability of laser direct-writing of photonic waveguides. The optical and waveguiding properties of LiNbO 3 thin films were studied by prism-coupling technique, while micro-Raman spectroscopy was used for structural and composition characterization, as well as laser processing mechanism investigation. The surface morphology of the processed structures was obtained by a Nomarski optical microscope, an atomic force microscope and a White Light Interferometer Microscope.

  3. Synthesis, Crystal Structure and Thermal Stability of 1D Linear Silver(I Coordination Polymers with 1,1,2,2-Tetra(pyrazol-1-ylethane

    Directory of Open Access Journals (Sweden)

    Evgeny Semitut


    Full Text Available Two new linear silver(I nitrate coordination polymers with bitopic ligand 1,1,2,2-tetra(pyrazol-1-ylethane were synthesized. Synthesized compounds were characterized by IR spectroscopy, elemental analysis, powder X-ray diffraction and thermal analysis. Silver coordination polymers demonstrated a yellow emission near 500 nm upon excitation at 360 nm. Crystal structures of coordination polymers were determined and structural peculiarities are discussed. In both of the structures, silver ions are connected via bridging ligand molecules to form polymeric chains with a five-atomic environment. The coordination environment of the central atom corresponds to a distorted trigonal bipyramid with two N atoms of different ligands in apical positions. The Ag–N bond distances vary in a wide range of 2.31–2.62 Å, giving strongly distorted metallacycles. Thermolysis of coordination polymers in reductive atmosphere (H2/He leads to the formation of silver nanoparticles with a narrow size distribution.

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

    Pawar, Sunayna S; Koorbanally, Neil A


    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.

  5. Hinge Atlas: relating protein sequence to sites of structural flexibility

    Directory of Open Access Journals (Sweden)

    Yang Julie


    Full Text Available Abstract Background Relating features of protein sequences to structural hinges is important for identifying domain boundaries, understanding structure-function relationships, and designing flexibility into proteins. Efforts in this field have been hampered by the lack of a proper dataset for studying characteristics of hinges. Results Using the Molecular Motions Database we have created a Hinge Atlas of manually annotated hinges and a statistical formalism for calculating the enrichment of various types of residues in these hinges. Conclusion We found various correlations between hinges and sequence features. Some of these are expected; for instance, we found that hinges tend to occur on the surface and in coils and turns and to be enriched with small and hydrophilic residues. Others are less obvious and intuitive. In particular, we found that hinges tend to coincide with active sites, but unlike the latter they are not at all conserved in evolution. We evaluate the potential for hinge prediction based on sequence. Motions play an important role in catalysis and protein-ligand interactions. Hinge bending motions comprise the largest class of known motions. Therefore it is important to relate the hinge location to sequence features such as residue type, physicochemical class, secondary structure, solvent exposure, evolutionary conservation, and proximity to active sites. To do this, we first generated the Hinge Atlas, a set of protein motions with the hinge locations manually annotated, and then studied the coincidence of these features with the hinge location. We found that all of the features have bearing on the hinge location. Most interestingly, we found that hinges tend to occur at or near active sites and yet unlike the latter are not conserved. Less surprisingly, we found that hinge residues tend to be small, not hydrophobic or aliphatic, and occur in turns and random coils on the surface. A functional sequence based hinge predictor was

  6. Topological characterization of crystalline ice structures from coordination sequences

    CERN Document Server

    Herrero, Carlos P


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

  7. Avocado sunblotch viroid: primary sequence and proposed secondary structure. (United States)

    Symons, R H


    The sequence of the 247 nucleotide residues of the single strand circular RNA of avocado sunblotch viroid (ASBV) was determined using partial enzymic cleavage methods on overlapping viroid fragments obtained by partial ribonuclease digestion followed by 32p-labelling in vitro at their 5'-ends. ASBV is much smaller than potato spindle tuber viroid (PSTV; 359 residues) and chrysanthemum stunt viroid (CSV; 356 residues). A secondary structure model for ASBV is proposed and contains 67% of its residues base paired. In contrast to the extensive (69%) sequence homology of CSV with PSTV, only 18% of the ASBV sequence is homologous to PSTV and CSV. There are eight potential polypeptide translation products with chain lengths from 4 to 63 amino acid residues coded for by the plus (infectious) strand and four potential translation products (2 to 60 residues) coded for by the minus strand. An improved method is described for the synthesis of gamma-32p-ATP of high specific activity. PMID:7322921

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

    DEFF Research Database (Denmark)

    Jørgensen, Allan Grønlund

    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...... 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...

  9. Synthesis of cadmium complexes of 4'-chloro-terpyridine: From discrete dimer to 1D chain polymer, crystal structure and antibacterial activity

    Indian Academy of Sciences (India)

    Lotfali Saghatforoush; Laura Valencia Matarranz; Firoozeh Chalabian; Shahriare Ghammamy; Fatemeh Katouzian


    Two new Cd(II) complexes with the ligand 4'-chloro-2,2':6',2"-terpyridine (Cltpy), [Cd(Cltpy)(N3)(CH3COO)], 1, and [Cd(Cltpy)(NCS)(CH3COO)], 2, have been synthesized and characterized by CHN elemental analyses, 1HNMR-, 13C NMR-, IR spectroscopy and structurally analysed by X-ray singlecrystal diffraction. The single crystal X-ray analyses show that the coordination number in these complexes is seven with three terpyridine (Cltpy) N-donor atoms, two acetate oxygens and two anionic bridged ligands. The crystal structure of 2 comprises a one-dimensional polymeric network bridged by NCS− anions. The antibacterial activities of Cltpy and its Cd(II) complexes are tested against different bacteria. Both complexes have shown good activity against all the tested bacteria. Against Klebsiella pneumonia and Staphylococcus aureus, antibacterial activity of complexes is higher than Cltpy ligand. The higher activity of complexes may be explained on the basis of chelation theory.

  10. 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)

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


    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'.

  11. Syntheses and Crystal Structures of Two Novel 1-D Metal Complexes with Dicyanamide:[Zn(pheen)(dca)2]n and [Cu(quin)2(dca)2]n

    Institute of Scientific and Technical Information of China (English)

    吴阿清; 郑发鲲; 蔡丽珍; 郭国聪; 黄锦顺


    The two complexes [Zn(phen)(dca)2]n 1 (phen = 1,10-phenanthroline, dca = di-cyanamide) and [Cu(quin)2(dca)2]n 2 (quin = quinoline) were synthesized by self-assembly reactions of Zn(CH3COO)2·4H2O with Nadca and phen ligands, and CuCl2(2H2O with Nadca and quin ligands, respectively. Their crystal structures were determined by single-crystal X-ray diffraction analyses. Crystallographic data for complex 1: (C16H8N8Zn)n, Mr = 377.67, monoclinic, space group P21/c, a = 10.1322(5), b = 11.0218(6), c = 14.1351(6) (A), β = 101.077(2)°, V = 1549.1(1) (A)3, Z = 4 , Dc = 1.619 g/cm3, μ(MoKα) = 1.602 mm-1, F(000) = 760, R = 0.0698 and wR = 0.1558; and for complex 2: (C22H14N8Cu)n, Mr = 453.95, orthorhombic, space group Cmc21, a = 16.679(4), b = 9.153(2), c = 12.937(3) (A), V = 1975.0(7) (A)3, Z = 4, Dc = 1.527 g/cm3, μ(MoKα) = 1.134 mm-1, F(000) = 924, R = 0.0486 and wR = 0.0981. The structures of complexes 1 and 2 consist of infinite zigzag chains, and their metal atoms have slightly distorted square pyramidal coordination environments with two N atoms of phen or quin ligands and three nitrile N atoms of dca ligands. The secondary long Zn-N bonds and π-π stacking interactions make the chains into a three-dimensional network in complex 1.

  12. Two new 1D chains of Ni2Na2 heterometallic double half-cubane building units: Synthesis, structures and variable temperature magnetic study

    Indian Academy of Sciences (India)

    Kartik Chandra Mondal; Bappaditya Gole; You Song; Stuart R Batten; David R Turner; Partha Sarathi Mukherjee


    An equimolar mixture of Ni(NO3)2·6H2O and pyridine-2-aldehyde with two equivalents of NaN3 in methanol in the presence of NaOMe resulted in the formation of light green precipitate which upon crystallization from dimethylformamide (DMF) yielded light green single crystals [{Ni2Na2(pic)4(N3)2(H2O)2(MeOH)}· MeOH·3H2O] (1) and [{Ni2Na2(pic)4(N3)2(H2O)4}$\\cdot$2DMF$\\cdot$H2O] (2) (pic = pyridine-2-carboxylate) at room temperature and high temperature (100°C), respectively. Variable temperature magnetic studies revealed the existence of overall ferromagnetic behaviour with ≈ +10 cm-1 and ≈ −2 to −7 cm-1 for 1 and 2, respectively. Negative values as well as variation of upon slight distortion of structure by varying reaction temperature were observed. The X-band Electron Paramagnetic Resonance (EPR) spectra of both 2 and 3 were recorded below 50 K. The structural distortion was also implicated from the EPR spectra. Density Functional Theory (DFT) calculations on both complexes were performed in two different ways to corroborate the magnetic results. Considering only Ni$^{\\text{II}}_{2}$ dimeric unit, results were = +20.65 cm-1 and = −3.16 cm-1 for 1, and =+24.56 cm-1 and =−4.67 cm-1 for 2. However, considering Ni$^{\\text{II}}_{2}$Na$^{I}_{2}$ cubane as magnetic core the results were =+16.35 cm-1 (1), +19.54 cm-1 (2); =−3.05 cm-1 (1), −4.25 cm-1 (2).

  13. 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

    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


    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.

  14. Moments of the Spin Structure Functions g1p and g1d for 0.05 < Q2 < 3.0 GeV2

    Energy Technology Data Exchange (ETDEWEB)

    Prok, Yelena; Bosted, Peter; Burkert, Volker; Deur, Alexandre; Dharmawardane, Kahanawita; Dodge, Gail; Griffioen, Keith; Kuhn, Sebastian; Minehart, Ralph; Adams, Gary; Amaryan, Moscov; Amaryan, Moskov; Anghinolfi, Marco; Asryan, G.; Audit, Gerard; Avagyan, Harutyun; Baghdasaryan, Hovhannes; Baillie, Nathan; Ball, J.P.; Ball, Jacques; Baltzell, Nathan; Barrow, Steve; Battaglieri, Marco; Beard, Kevin; Bedlinskiy, Ivan; Bektasoglu, Mehmet; Bellis, Matthew; Benmouna, Nawal; Berman, Barry; Biselli, Angela; Blaszczyk, Lukasz; Boyarinov, Sergey; Bonner, Billy; Bouchigny, Sylvain; Bradford, Robert; Branford, Derek; Briscoe, William; Brooks, William; Bultmann, S.; Bueltmann, Stephen; Butuceanu, Cornel; Calarco, John; Careccia, Sharon; Carman, Daniel; Casey, Liam; Cazes, Antoine; Chen, Shifeng; Cheng, Lu; Cole, Philip; Collins, Patrick; Coltharp, Philip; Cords, Dieter; Corvisiero, Pietro; Crabb, Donald; Crede, Volker; Cummings, John; Dale, Daniel; Dashyan, Natalya; De Masi, Rita; De Vita, Raffaella; De Sanctis, Enzo; Degtiarenko, Pavel; Denizli, Haluk; Dennis, Lawrence; Dhuga, Kalvir; Dickson, Richard; Djalali, Chaden; Doughty, David; Dugger, Michael; Dytman, Steven; Dzyubak, Oleksandr; Egiyan, Hovanes; Egiyan, Kim; Elfassi, Lamiaa; Elouadrhiri, Latifa; Eugenio, Paul; Fatemi, Renee; Fedotov, Gleb; Feldman, Gerald; Fersch, Robert; Feuerbach, Robert; Forest, Tony; Fradi, Ahmed; Funsten, Herbert; Garcon, Michel; Gavalian, Gagik; Gevorgyan, Nerses; Gilfoyle, Gerard; Giovanetti, Kevin; Girod, Francois-Xavier; Goetz, John; Golovach, Evgeny; Gothe, Ralf; Guidal, Michel; Guillo, Matthieu; Guler, Nevzat; Guo, Lei; Gyurjyan, Vardan; Hadjidakis, Cynthia; Hafidi, Kawtar; Hakobyan, Hayk; Hanretty, Charles; Hardie, John; Hassall, Neil; Heddle, David; Hersman, F.; Hicks, Kenneth; Hleiqawi, Ishaq; Holtrop, Maurik; Huertas, Marco; Hyde, Charles; Ilieva, Yordanka; Ireland, David; Ishkhanov, Boris; Isupov, Evgeny; Ito, Mark; Jenkins, David; Jo, Hyon-Suk; Johnstone, John; Joo, Kyungseon; Juengst, Henry; Kalantarians, Narbe; Keith, Christopher; Kellie, James; Khandaker, Mahbubul; Kim, Kui; Kim, Kyungmo; Kim, Wooyoung; Klein, Andreas; Klein, Franz; Klusman, Mike; Kossov, Mikhail; Krahn, Zebulun; Kramer, Laird; Kubarovsky, Valery; Kuhn, Joachim; Kuleshov, Sergey; Kuznetsov, Viacheslav; Lachniet, Jeff; Laget, Jean; Langheinrich, Jorn; Lawrence, Dave; Lima, Ana; Livingston, Kenneth; Lu, Haiyun; Lukashin, K.; MacCormick, Marion; Marchand, Claude; Markov, Nikolai; Mattione, Paul; McAleer, Simeon; McKinnon, Bryan; McNabb, John; Mecking, Bernhard; Mestayer, Mac; Meyer, Curtis; Mibe, Tsutomu; Mikhaylov, Konstantin; Mirazita, Marco; Miskimen, Rory; Mokeev, Viktor; Morand, Ludyvine; Moreno, Brahim; Moriya, Kei; Morrow, Steven; Moteabbed, Maryam; Mueller, James; Munevar Espitia, Edwin; Mutchler, Gordon; Nadel-Turonski, Pawel; Nasseripour, Rakhsha; Niccolai, Silvia; Niculescu, Gabriel; Niculescu, Maria-Ioana; Niczyporuk, Bogdan; Niroula, Megh; Niyazov, Rustam; Nozar, Mina; O' Rielly, Grant; Osipenko, Mikhail; Ostrovidov, Alexander; Park, Kijun; Pasyuk, Evgueni; Paterson, Craig; Anefalos Pereira, S.; Philips, Sasha; Pierce, J.; Pivnyuk, Nikolay; Pocanic, Dinko; Pogorelko, Oleg; Popa, Iulian; Pozdnyakov, Sergey; Preedom, Barry; Price, John; Procureur, Sebastien; Protopopescu, Dan; Qin, Liming; Raue, Brian; Riccardi, Gregory; Ricco, Giovanni; Ripani, Marco; Ritchie, Barry; Rosner, Guenther; Rossi, Patrizia; Rowntree, David; Rubin, Philip; Sabatie, Franck; Salamanca, Julian; Salgado, Carlos; Santoro, Joseph; Sapunenko, Vladimir; Schumacher, Reinhard; Seely, Mikell; Serov, Vladimir; Sharabian, Youri; Sharov, Dmitri; Shaw, Jeffrey; Shvedunov, Nikolay; Skabelin, Alexander; Smith, Elton; Smith, Lee; Sober, Daniel; Sokhan, Daria; Stavinskiy, Aleksey; Stepanyan, Samuel; Stepanyan, Stepan; Stokes, Burnham; Stoler, Paul; Strakovski, Igor; Strauch, Steffen; Suleiman, Riad; Taiuti, Mauro; Tedeschi, David; Tkabladze, Avtandil; Tkachenko, Svyatoslav; Todor, Luminita; Ungaro, Maurizio; V


    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.

  15. Ammonia detection of 1-D ZnO/polypyrrole nanocomposite: Effect of CSA doping and their structural, chemical, thermal and gas sensing behavior (United States)

    Jain, Shilpa; Karmakar, Narayan; Shah, Akshara; Kothari, D. C.; Mishra, Satyendra; Shimpi, Navinchandra G.


    Nanocomposites of polypyrrole (PPy) with varying concentration of ZnO nanorods (ZnO NRs) were synthesized using in-situ oxidative polymerization technique. The prepared nanocomposites (PPy, PPy-ZnO and CSA doped PPy-ZnO) were studied for various oxidizing and reducing gases at room temperature and found to be more selective towards ammonia gas. Various concentrations of ZnO NRs in Ppy matrix were studied and 15% was found to be optimum in terms of sensor response (66% towards 120 ppm NH3). Further, with 15% doping of camphor sulphonic acid (CSA) in PPy-ZnO nanocomposite for 15% ZnO NRs in Ppy matrix, sensor response increased from 66 to 79% towards 120 ppm of NH3. Structural, Optical and thermal behavior of nanocomposites were studied using powder X-ray diffraction (XRD), Fourier Transform Infra-Red (FTIR) spectroscopy, X-ray Photoelectron Spectroscopy (XPS), UV-vis (UV-vis) absorption spectroscopy, room temperature Photoluminescence (PL) Spectroscopy, Thermo-gravimetric analysis (TGA) and Field Emission Scanning Electron Microscopy (FESEM). ZnO has been completely embedded inside the polymeric chains as observed from in SEM. Meanwhile, FT-IR spectra indicate better conjugation and interaction in nanocomposites. With CSA doping interaction grows stronger due to extended delocalization over π electrons leading to higher sensor response and with response time and recovery time of 24 s and 34 s respectively. CSA doped PPy-ZnO (15%) nanocomposites observed to be a potential candidate for ammonia detection at lower ppm level.

  16. Structure and sequence of the saimiriine herpesvirus 1 genome. (United States)

    Tyler, Shaun; Severini, Alberto; Black, Darla; Walker, Matthew; Eberle, R


    We report here the complete genome sequence of the squirrel monkey α-herpesvirus saimiriine herpesvirus 1 (HVS1). Unlike the simplexviruses of other primate species, only the unique short region of the HVS1 genome is bounded by inverted repeats. While all Old World simian simplexviruses characterized to date lack the herpes simplex virus RL1 (γ34.5) gene, HVS1 has an RL1 gene. HVS1 lacks several genes that are present in other primate simplexviruses (US8.5, US10-12, UL43/43.5 and UL49A). Although the overall genome structure appears more like that of varicelloviruses, the encoded HVS1 proteins are most closely related to homologous proteins of the primate simplexviruses. Phylogenetic analyses confirm that HVS1 is a simplexvirus. Limited comparison of two HVS1 strains revealed a very low degree of sequence variation more typical of varicelloviruses. HVS1 is thus unique among the primate α-herpesviruses in that its genome has properties of both simplexviruses and varicelloviruses.

  17. Diffusion and particle mobility in 1D system

    NARCIS (Netherlands)

    Borman, V. D.; Johansson, B.; Skorodumova, N. V.; Tronin, I. V.; Tronin, V. N.; Troyan, V. I.


    The transport properties of one-dimensional (1D) systems have been studied theoretically. Contradictory experimental results on molecular transport in quasi-1D systems, such as zeolite structures, when both diffusion transport acceleration and the existence of the diffusion mode with lower particle

  18. Nucleotide sequence of the structural gene for tryptophanase of Escherichia coli K-12.


    Deeley, M C; Yanofsky, C


    The tryptophanase structural gene, tnaA, of Escherichia coli K-12 was cloned and sequenced. The size, amino acid composition, and sequence of the protein predicted from the nucleotide sequence agree with protein structure data previously acquired by others for the tryptophanase of E. coli B. Physiological data indicated that the region controlling expression of tnaA was present in the cloned segment. Sequence data suggested that a second structural gene of unknown function was located distal ...

  19. 1D polymeric copper(I) complex [Cu2(μ-(2,6-Cl-ba)2en)(μ-I)2]n with exceptionally short Cusbnd Cu distance: Synthesis, characterization, thermal study and crystal structure (United States)

    Khalaji, Aliakbar Dehno; Peyghoun, Seyyed Javad; Akbari, Alireza; Feizi, Nourollah; Dusek, Michal; Eigner, Vaclav


    A new 1D polymeric three coordinated copper(I) complex, [Cu2(μ-(2,6-Cl-ba)2en)(μ-I)2]n, with the bidentate Schiff base ligand N,N‧-bis(2,6-dichlorobenzylidene)ethane-1,2-diamine containing a flexible spacer (dbnd NCH2sbnd CH2sbnd Ndbnd) was synthesized and characterized by elemental analyses, UV-Vis, FT-IR and 1H NMR spectroscopy and thermal analaysis. Its molecular structure was determined by single-crystal X-ray diffraction and shows the (2,6-Cl-ba)2en acts as a bis-monodentate bridging ligand forming the dinuclear [Cu2(μ-(2,6-Cl-ba)2en)] groups. Such dinuclear groups are bridged by two iodine anions [(μ-I)2] to form a 1D polymeric copper(I) complex. The copper(I) ions are coordinated in a distorted trigonal planar geometry by two I atoms and one nitrogen atom of Schiff base ligand (2,6-Cl-ba)2en.

  20. A novel predictor for protein structural class based on integrated information of the secondary structure sequence. (United States)

    Zhang, Lichao; Zhao, Xiqiang; Kong, Liang; Liu, Shuxia


    The structural class has become one of the most important features for characterizing the overall folding type of a protein and played important roles in many aspects of protein research. At present, it is still a challenging problem to accurately predict protein structural class for low-similarity sequences. In this study, an 18-dimensional integrated feature vector is proposed by fusing the information about content and position of the predicted secondary structure elements. The consistently high accuracies of jackknife and 10-fold cross-validation tests on different low-similarity benchmark datasets show that the proposed method is reliable and stable. Comparison of our results with other methods demonstrates that our method is an effective computational tool for protein structural class prediction, especially for low-similarity sequences.

  1. Identification of similar regions of protein structures using integrated sequence and structure analysis tools

    Directory of Open Access Journals (Sweden)

    Heiland Randy


    Full Text Available Abstract Background Understanding protein function from its structure is a challenging problem. Sequence based approaches for finding homology have broad use for annotation of both structure and function. 3D structural information of protein domains and their interactions provide a complementary view to structure function relationships to sequence information. We have developed a web site and an API of web services that enables users to submit protein structures and identify statistically significant neighbors and the underlying structural environments that make that match using a suite of sequence and structure analysis tools. To do this, we have integrated S-BLEST, PSI-BLAST and HMMer based superfamily predictions to give a unique integrated view to prediction of SCOP superfamilies, EC number, and GO term, as well as identification of the protein structural environments that are associated with that prediction. Additionally, we have extended UCSF Chimera and PyMOL to support our web services, so that users can characterize their own proteins of interest. Results Users are able to submit their own queries or use a structure already in the PDB. Currently the databases that a user can query include the popular structural datasets ASTRAL 40 v1.69, ASTRAL 95 v1.69, CLUSTER50, CLUSTER70 and CLUSTER90 and PDBSELECT25. The results can be downloaded directly from the site and include function prediction, analysis of the most conserved environments and automated annotation of query proteins. These results reflect both the hits found with PSI-BLAST, HMMer and with S-BLEST. We have evaluated how well annotation transfer can be performed on SCOP ID's, Gene Ontology (GO ID's and EC Numbers. The method is very efficient and totally automated, generally taking around fifteen minutes for a 400 residue protein. Conclusion With structural genomics initiatives determining structures with little, if any, functional characterization

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

    Directory of Open Access Journals (Sweden)

    Chen Ke


    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

  3. An Improved Protein Structural Prediction Method by Incorporating Both Sequence and Structure Information. (United States)

    Wei, Leyi; Liao, Minghong; Gao, Xing; Zou, Quan


    Protein structural classes information is beneficial for secondary and tertiary structure prediction, protein folds prediction, and protein function analysis. Thus, predicting protein structural classes is of vital importance. In recent years, several computational methods have been developed for low-sequence-similarity (25% - 40%) protein structural classes prediction. However, the reported prediction accuracies are actually not satisfactory. Aiming to further improve the prediction accuracies, we propose three different feature extraction methods and construct a comprehensive feature set that captures both sequence and structure information. By applying a random forest (RF) classifier to the feature set, we further develop a novel method for structural classes prediction. We test the proposed method on three benchmark datasets (25PDB, 640, and 1189) with low sequence similarity, and obtain the overall prediction accuracies of 93.5%, 92.6%, and 93.4%, respectively. Compared with six competing methods, the accuracies we achieved are 3.4%, 6.2%, and 8.7% higher than that achieved by the best-performing methods, showing the superiority of our method. Moreover, due to the limitation of the size of the three benchmark datasets, we further test the proposed method on three updated large-scale datasets with different sequence similarity (40%, 30%, and 25%). The proposed method achieves above 90% accuracies for all the three datasets, consistency with the accuracies on the above three benchmark datasets. Experimental results suggest our method as an effective and promising tool for structural classes prediction. Currently, a webserver that implements the proposed method is available on

  4. An Analysis of the Syllabic Structure of English Mute in the Light of Sonority Sequencing Principle

    Institute of Scientific and Technical Information of China (English)



    Syllable is the hierarchic natural feature of a language,and there are rules of the phonological sequences of the syllabic structure.Based on the Sonority Sequencing Principle (SSP),this paper will try to discuss and analyze phonological sequences of the syllabic structure of English mutes.

  5. An Analysis of the Syllabic Structure of English Mute in the Light of Sonority Sequencing Principle

    Institute of Scientific and Technical Information of China (English)



    Syllable is the hierarchic natural feature of a language,and there are rules of the phonological sequences of the syllabic structure.Based on the Sonority Sequencing Principle(SSP),this paper will try to discuss and analyze phonological sequences of the syllabic structure of English mutes.

  6. 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. (United States)

    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


    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.

  7. Synthesis, structure, and magnetic properties of three 1D chain complexes based on high-spin metal-cyanide clusters: [Mn(III)6M(III)] (M = Cr, Fe, Co). (United States)

    Zhou, Hong-Bo; Wang, Jun; Wang, Hui-Sheng; Xu, Yong-Lu; Song, Xiao-Jiao; Song, You; You, Xiao-Zeng


    On the basis of high-spin metal-cyanide clusters of Mn(III)(6)M(III) (M = Cr, Fe, Co), three one-dimensional (1D) chain complexes, [Mn(salen)](6)[Cr(CN)(6)](2)·6CH(3)OH·H(2)O (1), [Mn(5-CH(3))salen)](6)[Fe(CN)(6)](2)·2CH(3)CN·10H(2)O (2), and [Mn(5-CH(3))salen)](6)[Co(CN)(6)](2)·2CH(3)CN·10H(2)O (3) [salen = N,N'-ethylenebis(salicylideneiminato) dianion], have been synthesized and characterized structurally as well as magnetically. Complexes 2 and 3 are isomorphic but slightly different from complex 1. All three complexes contain a 1D chain structure which is comprised of alternating high-spin metal-cyanide clusters of [Mn(6)M](3+) and a bridging group [M(CN)(6)](3-) in the trans mode. Furthermore, the three complexes all exhibit extended 3D supramolecular networks originating from short intermolecular contacts. Magnetic investigation indicates that the coupling mechanisms are intrachain antiferromagnetic interactions for 1 and ferromagnetic interactions for 2, respectively. Complex 3 is a magnetic dilute system due to the diamagnetic nature of Co(III). Further magnetic investigations show that complexes 1 and 2 are dominated by the 3D antiferromagnetic ordering with T(N) = 7.2 K for 1 and 9.5 K for 2. It is worth noting that the weak frequency-dependent phenomenon of AC susceptibilities was observed in the low-temperature region in both 1 and 2, suggesting the presence of slow magnetic relaxations.

  8. Assembly of 1D, 2D and 3D lanthanum(iii) coordination polymers with perchlorinated benzenedicarboxylates: positional isomeric effect, structural transformation and ring-opening polymerisation of glycolide. (United States)

    Chen, Sheng-Chun; Dai, An-Qi; Huang, Kun-Lin; Zhang, Zhi-Hui; Cui, Ai-Jun; He, Ming-Yang; Chen, Qun


    Utilizing a series of positional isomers of tetrachlorinated benzenedicarboxylic acid ligands, seven La(iii)-based coordination polymers were solvothermally synthesized and structurally characterized. Their structural dimensionalities varying from 1D double chains, to the 2D 3,4,5-connected network, to 3D 6-connected pcu topological nets are only governed by the positions of carboxyl groups on the tetrachlorinated benzene ring. A comprehensive analysis and comparison reveals that the size of the carbonyl solvent molecules (DMF, DEF, DMA, and NMP) can affect the coordination geometries around the La(iii) ions, the coordination modes of carboxylate groups, the packing arrangements, and the void volumes of the overall crystal lattices. One as-synthesized framework further shows an unprecedented structural transformation from a 3D 6-connected network to a 3D 4,5-connected net through the dissolution and reformation pathway in water, suggesting that these easily hydrolyzed lanthanide complexes may serve as precursors to produce new high-dimensional frameworks. The bulk solvent-free melt polymerisation of glycolide utilizing these La(iii) complexes as initiators has been reported herein for the first time. All complexes were found to promote the polymerization of glycolide over a temperature range of 200 to 220 °C, producing poly(glycolic acid) (PGA) with a molecular weight up to 93,280. Under the same experimental conditions, the different catalytic activities for these complexes may result from their structural discrepancy.

  9. A DNA Structure-Based Bionic Wavelet Transform and Its Application to DNA Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Fei Chen


    Full Text Available DNA sequence analysis is of great significance for increasing our understanding of genomic functions. An important task facing us is the exploration of hidden structural information stored in the DNA sequence. This paper introduces a DNA structure-based adaptive wavelet transform (WT – the bionic wavelet transform (BWT – for DNA sequence analysis. The symbolic DNA sequence can be separated into four channels of indicator sequences. An adaptive symbol-to-number mapping, determined from the structural feature of the DNA sequence, was introduced into WT. It can adjust the weight value of each channel to maximise the useful energy distribution of the whole BWT output. The performance of the proposed BWT was examined by analysing synthetic and real DNA sequences. Results show that BWT performs better than traditional WT in presenting greater energy distribution. This new BWT method should be useful for the detection of the latent structural features in future DNA sequence analysis.

  10. The Gain Properties of 1-D Active Photonic Crystal

    Institute of Scientific and Technical Information of China (English)


    The terminology 'ID frequency'(w ID) is proposed after analyzing the 1D active photonic crystal based on the transfer matrix method. The relationship between wID and the structure parameters of the photonic crystal is investigated.

  11. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. (United States)

    Pei, Jimin; Grishin, Nick V


    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at

  12. Training set reduction methods for protein secondary structure prediction in single-sequence condition



    Orphan proteins are characterized by the lack of significant sequence similarity to database proteins. To infer the functional properties of the orphans, more elaborate techniques that utilize structural information are required. In this regard, the protein structure prediction gains considerable importance. Secondary structure prediction algorithms designed for orphan proteins (also known as single-sequence algorithms) cannot utilize multiple alignments or alignment prof...

  13. High-Throughput Sequencing Based Methods of RNA Structure Investigation

    DEFF Research Database (Denmark)

    Kielpinski, Lukasz Jan

    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...

  14. Synthesis and Structural Characterization of a Cyano-bridged 1-D Lanthanum(Ⅲ)-iron(Ⅲ)Complex [La(DMSO)5(H2O)](μ-CN)2[Fe(CN)4]·H2O

    Institute of Scientific and Technical Information of China (English)


    A new lanthanumⅢ-ironⅢ complex [La(DMSO)5(H2O)](μ-CN)2[Fe(CN)4]·H2O 1 (DMSO=dimethylsulfoxide) has been prepared by a facile approach, ball-milling method, and characterized by X-ray diffraction. The crystal belongs to monoclinic, space group P21/n with a=9.7125(3), b=21.5336(7), c=14.3804(5) (A), β=93.242(3)°, C16H34FeLaN6O7S5, Mr=777.55, V=3002.8(2)(A)3, Z=4, Dc=1.720 g/cm3, S=1.053, μ(MoKα)=2.278 mm-1, F(000)=1564, R=0.0490 and wR=0.1270. The crystal structure analysis of 1 reveals a slightly distorted squareantiprism eightfold-coordinated La(Ⅲ) ion and a 1-D zigzag chain structure extending through the Fe-CN-La-NC-Fe linkages. The [La(DMSO)5(H2O)](μ-CN)2[Fe(CN)4] species are held together via hydrogen bonds to form a three-dimensional framework.

  15. The synthesis and structure of a chiral 1D aluminophosphate chain compound: d-Co(en) 3[AlP 2O 8]·6.5H 2O (United States)

    Chen, Peng; Li, Jiyang; Yu, Jihong; Wang, Yu; Pan, Qinhe; Xu, Ruren


    A new chiral one-dimensional (1D) aluminophosphate chain compound [ d-Co(en) 3][AlP 2O 8]·6.5H 2O (designated AlPO-CJ22) has been hydrothermally synthesized by using the optically pure d-Co(en) 3I 3 complex as the template. Single-crystal structural analysis reveals that its structure is built up from alternating connection of AlO 4 and PO 2(=O 2) tetrahedra to form corner-shared Al 2P 2 four-membered ring (4-MR) chains. The d-Co(en) 33+ complex cations extended along the 2 1 screw axis interact with the inorganic chains through hydrogen-bonds of N⋯O atoms in a helical fashion. Optical rotation measurement shows that AlPO-CJ22 is chiral as with d-Co(en) 33+ complex cations. Crystal data: orthorhombic, I2 12 12 1, a=8.5573(8) Å, b=22.613(2) Å, c=22.605(2) Å, Z=8, R1=0.067, wR2=0.1291, and Flack parameter: -0.02(3). CCDC number: 254179.

  16. Quantitative 1D saturation profiles on chalk by NMR

    DEFF Research Database (Denmark)

    Olsen, Dan; Topp, Simon; Stensgaard, Anders;


    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...

  17. Large cryptic internal sequence repeats in protein structures from Homo sapiens

    Indian Academy of Sciences (India)

    R Sarani; N A Udayaprakash; R Subashini; P Mridula; T Yamane; K Sekar


    Amino acid sequences are known to constantly mutate and diverge unless there is a limiting condition that makes such a change deleterious. However, closer examination of the sequence and structure reveals that a few large, cryptic repeats are nevertheless sequentially conserved. This leads to the question of why only certain repeats are conserved at the sequence level. It would be interesting to find out if these sequences maintain their conservation at the three-dimensional structure level. They can play an active role in protein and nucleotide stability, thus not only ensuring proper functioning but also potentiating malfunction and disease. Therefore, insights into any aspect of the repeats – be it structure, function or evolution – would prove to be of some importance. This study aims to address the relationship between protein sequence and its three-dimensional structure, by examining if large cryptic sequence repeats have the same structure.

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

    DEFF Research Database (Denmark)

    Worning, Peder; Jensen, Lars Juhl; Nelson, K. E.;


    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...

  19. Cyano-bridged coordination polymer hydrogel-derived Sn-Fe binary oxide nanohybrids with structural diversity: from 3D, 2D, to 2D/1D and enhanced lithium-storage performance (United States)

    Zhang, Weiyu; Zhu, Xiaoshu; Chen, Xuguang; Zhou, Yiming; Tang, Yawen; Ding, Liangxin; Wu, Ping


    Metal oxide nanohybrids with uniform dimensions and controlled architectures possess unique compositional and structural superiorities, and thus harbor promising potential for a series of applications in energy, catalysis, and sensing systems. Herein, we propose a facile, general, and scalable cyano-bridged coordination polymer hydrogel-derived thermal-oxidation route for the construction of main-group metal and transition-metal heterometallic oxide nanohybrids with controlled constituents and architectures. The formation of Sn-Fe binary oxide nanohybrids has been demonstrated as an example by using cyano-bridged Sn(iv)-Fe(ii) bimetallic coordination polymer hydrogels (i.e., SnCl4-K4Fe(CN)6 cyanogels, Sn-Fe cyanogels) as precursors. The physicochemical properties of Sn-Fe cyanogels with different Sn/Fe ratios have been systematically examined, and it is found that perfect Sn-Fe cyanogels without unbridged Sn(iv) or Fe(ii) can be formed with Sn/Fe ratios from 2 : 1 to 1 : 2. More importantly, the simple adjustment of Sn/Fe ratios in the Sn-Fe cyanogel precursors can realize flexible dimensional control of the Sn-Fe binary oxide nanohybrids, and 2D/1D SnO2-Fe2O3 hierarchitectures, 2D SnO2-Fe2O3 nanosheets, and 3D SnO2-Fe2O3 networks have been synthesized using the Sn-Fe 1 : 2, Sn-Fe 1 : 1, and Sn-Fe 2 : 1 cyanogels as precursors, respectively. To demonstrate their compositional/structural superiorities and potential applications, the lithium-storage utilization of the Sn-Fe binary oxide nanohybrids has been selected as an objective application, and the nanohybrids exhibit Sn/Fe ratio-dependent lithium-storage performance. As a representative example, the 2D/1D SnO2-Fe2O3 hierarchitectures manifest markedly enhanced Li-storage performance in terms of reversible capacities and cycling stability in comparison with their constituent units, i.e., bare SnO2 nanosheets and Fe2O3 nanorods. The proposed cyanogel-derived thermal-oxidation strategy could open up new

  20. FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information

    Indian Academy of Sciences (India)

    Tungadri Bose; Anirban Dutta; Mohammed Mh; Hemang Gandhi; Sharmila S Mande


    Given the importance of RNA secondary structures in defining their biological role, it would be convenient for researchers seeking RNA data if both sequence and structural information pertaining to RNA molecules are made available together. Current nucleotide data repositories archive only RNA sequence data. Furthermore, storage formats which can frugally represent RNA sequence as well as structure data in a single file, are currently unavailable. This article proposes a novel storage format, `FASTR’, for concomitant representation of RNA sequence and structure. The storage efficiency of the proposed FASTR format has been evaluated using RNA data from various microorganisms. Results indicate that the size of FASTR formatted files (containing both RNA sequence as well as structure information) are equivalent to that of FASTA-format files, which contain only RNA sequence information. RNA secondary structure is typically represented using a combination of a string of nucleotide characters along with the corresponding dot-bracket notation indicating structural attributes. `FASTR’ – the novel storage format proposed in the present study enables a frugal representation of both RNA sequence and structural information in the form of a single string. In spite of having a relatively smaller storage footprint, the resultant `fastr’ string(s) retain all sequence as well as secondary structural information that could be stored using a dot-bracket notation. An implementation of the `FASTR’ methodology is available for download at

  1. 4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

    Directory of Open Access Journals (Sweden)

    Schultz Jörg


    Full Text Available Abstract Background In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions. Hand-crafted and hand-improved alignments are necessary and meanwhile good common practice. For RNA sequences often the primary sequence as well as a secondary structure consensus is well known, e.g., the cloverleaf structure of the t-RNA. Recently, some alignment editors are proposed that are able to include and model both kinds of information. However, with the advent of a large amount of reliable RNA sequences together with their solved secondary structures (available from e.g. the ITS2 Database, we are faced with the problem to handle sequences and their associated secondary structures synchronously. Results 4SALE fills this gap. The application allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis. Conclusion 4SALE, which provides an user-friendly and intuitive interface, is a comprehensive toolbox for RNA analysis based on sequence and secondary structure information. The program connects sequence and structure databases like the ITS2 Database to phylogeny programs as for example the CBCAnalyzer. 4SALE is written in JAVA and therefore platform independent. The software is freely available and distributed from the website at

  2. Sequence, structure, and cooperativity in folding of elementary protein structural motifs. (United States)

    Lai, Jason K; Kubelka, Ginka S; Kubelka, Jan


    Residue-level unfolding of two helix-turn-helix proteins--one naturally occurring and one de novo designed--is reconstructed from multiple sets of site-specific (13)C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa-Jernigan statistical potentials), local structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako-Saitô-Muñoz-Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model proteins and their fragments and (13)C-amide I' bands for multiple isotopologues of each protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two motifs is different, reflecting the order of local stability. We introduce free energy profiles for "experimental" reaction coordinates--namely, the degree of local folding as sensed by site-specific (13)C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture.

  3. TBC1D24 genotype–phenotype correlation (United States)

    Balestrini, Simona; Milh, Mathieu; Castiglioni, Claudia; Lüthy, Kevin; Finelli, Mattea J.; Verstreken, Patrik; Cardon, Aaron; Stražišar, Barbara Gnidovec; Holder, J. Lloyd; Lesca, Gaetan; Mancardi, Maria M.; Poulat, Anne L.; Repetto, Gabriela M.; Banka, Siddharth; Bilo, Leonilda; Birkeland, Laura E.; Bosch, Friedrich; Brockmann, Knut; Cross, J. Helen; Doummar, Diane; Félix, Temis M.; Giuliano, Fabienne; Hori, Mutsuki; Hüning, Irina; Kayserili, Hulia; Kini, Usha; Lees, Melissa M.; Meenakshi, Girish; Mewasingh, Leena; Pagnamenta, Alistair T.; Peluso, Silvio; Mey, Antje; Rice, Gregory M.; Rosenfeld, Jill A.; Taylor, Jenny C.; Troester, Matthew M.; Stanley, Christine M.; Ville, Dorothee; Walkiewicz, Magdalena; Falace, Antonio; Fassio, Anna; Lemke, Johannes R.; Biskup, Saskia; Tardif, Jessica; Ajeawung, Norbert F.; Tolun, Aslihan; Corbett, Mark; Gecz, Jozef; Afawi, Zaid; Howell, Katherine B.; Oliver, Karen L.; Berkovic, Samuel F.; Scheffer, Ingrid E.; de Falco, Fabrizio A.; Oliver, Peter L.; Striano, Pasquale; Zara, Federico


    Objective: To evaluate the phenotypic spectrum associated with mutations in TBC1D24. Methods: We acquired new clinical, EEG, and neuroimaging data of 11 previously unreported and 37 published patients. TBC1D24 mutations, identified through various sequencing methods, can be found online ( Results: Forty-eight patients were included (28 men, 20 women, average age 21 years) from 30 independent families. Eighteen patients (38%) had myoclonic epilepsies. The other patients carried diagnoses of focal (25%), multifocal (2%), generalized (4%), and unclassified epilepsy (6%), and early-onset epileptic encephalopathy (25%). Most patients had drug-resistant epilepsy. We detail EEG, neuroimaging, developmental, and cognitive features, treatment responsiveness, and physical examination. In silico evaluation revealed 7 different highly conserved motifs, with the most common pathogenic mutation located in the first. Neuronal outgrowth assays showed that some TBC1D24 mutations, associated with the most severe TBC1D24-associated disorders, are not necessarily the most disruptive to this gene function. Conclusions: TBC1D24-related epilepsy syndromes show marked phenotypic pleiotropy, with multisystem involvement and severity spectrum ranging from isolated deafness (not studied here), benign myoclonic epilepsy restricted to childhood with complete seizure control and normal intellect, to early-onset epileptic encephalopathy with severe developmental delay and early death. There is no distinct correlation with mutation type or location yet, but patterns are emerging. Given the phenotypic breadth observed, TBC1D24 mutation screening is indicated in a wide variety of epilepsies. A TBC1D24 consortium was formed to develop further research on this gene and its associated phenotypes. PMID:27281533

  4. 1D molecular ladder of the ionic complex of terbium-4-sebacoylbis(1-phenyl-3-methyl-5-pyrazolonate) and sodium dibenzo-18-crown-6: synthesis, crystal structure, and photophysical properties. (United States)

    Remya, P N; Biju, S; Reddy, M L P; Cowley, Alan H; Findlater, Michael


    On the basis of the novel heterocyclic beta-diketone, 4-sebacoylbis(1-phenyl-3-methyl-5-pyrazolone (H 2SbBP), three new lanthanide complexes Tb 2(SbBP) 3(H 2O) 2 ( 1), Gd 2(SbBP) 3(H 2O) 2 ( 2), and [Tb(SbBP) 2] [Na(DB18C6)H 2O] ( 3) have been synthesized and characterized by various spectroscopic techniques. The single-crystal X-ray diffraction analysis of 3 reveals that the complex crystallizes in the monoclinic space group C2/ c with a = 25.300(6) A, b = 19.204(7) A, c = 15.391(3) A, beta = 93.17(3) degrees , and V = 7466(4) A (3). The crystal structure of 3 is heterodinuclear and features a Tb (3+) center surrounded by two tetradentate bispyrazolone ligands in a somewhat distorted square-antiprismatic geometry. The Na (+) coordination environment is distorted hexagonal pyramidal and involves six oxygen atoms furnished by DB18C6 and one oxygen atom from a water molecule. The X-ray diffraction study of 3 also revealed an interesting 1D molecular ladder structure based on C-H/pi, intra- and intermolecular hydrogen-bonding interactions. The photophysical properties of 1 and 3 in solid state have been investigated, and the quantum yields and (5)D 4 lifetimes were found to be 4.82 +/- 0.01% and 18.13 +/- 0.82% and 1.11 +/- 0.01 and 2.82 +/- 0.02 ms, respectively.

  5. Relaxation of a 1-D gravitational system

    CERN Document Server

    Valageas, P


    We study the relaxation towards thermodynamical equilibrium of a 1-D gravitational system. This OSC model shows a series of critical energies $E_{cn}$ where new equilibria appear and we focus on the homogeneous ($n=0$), one-peak ($n=\\pm 1$) and two-peak ($n=2$) states. Using numerical simulations we investigate the relaxation to the stable equilibrium $n=\\pm 1$ of this $N-$body system starting from initial conditions defined by equilibria $n=0$ and $n=2$. We find that in a fashion similar to other long-range systems the relaxation involves a fast violent relaxation phase followed by a slow collisional phase as the system goes through a series of quasi-stationary states. Moreover, in cases where this slow second stage leads to a dynamically unstable configuration (two peaks with a high mass ratio) it is followed by a new sequence ``violent relaxation/slow collisional relaxation''. We obtain an analytical estimate of the relaxation time $t_{2\\to \\pm 1}$ through the mean escape time of a particle from its potent...

  6. Structure Prediction and Analysis of Neuraminidase Sequence Variants (United States)

    Thayer, Kelly M.


    Analyzing protein structure has become an integral aspect of understanding systems of biochemical import. The laboratory experiment endeavors to introduce protein folding to ascertain structures of proteins for which the structure is unavailable, as well as to critically evaluate the quality of the prediction obtained. The model system used is the…

  7. Structure and Evolution of Pre-Main Sequence Stars

    CERN Document Server

    Schulz, Norbert S; Bautz, Mark W; Canizares, Claude C; Davis, John; Dewey, Dan; Huenemoerder, David P; Heilmann, Ralf; Houck, John; Marshall, Herman L; Nowak, Mike; Schattenburg, Mark; Audard, Marc; Drake, Jeremy; Gagne, Marc; Kastner, Joel; Kallman, Tim; Lautenegger, Maurice; Lee, Julia; Miller, Jon; Montmerle, Thierry; Mukai, Koji; Osten, Rachel; Parerels, Frits; Pollock, Andy; Preibisch, Thomas; Raymond, John; Reale, Fabio; Smith, Randall; Testa, Paola; Weintraub, David


    Low-mass pre-main sequence (PMS) stars are strong and variable X-ray emitters, as has been well established by EINSTEIN and ROSAT observatories. It was originally believed that this emission was of thermal nature and primarily originated from coronal activity (magnetically confined loops, in analogy with Solar activity) on contracting young stars. Broadband spectral analysis showed that the emission was not isothermal and that elemental abundances were non-Solar. The resolving power of the Chandra and XMM X-ray gratings spectrometers have provided the first, tantalizing details concerning the physical conditions such as temperatures, densities, and abundances that characterize the X-ray emitting regions of young star. These existing high resolution spectrometers, however, simply do not have the effective area to measure diagnostic lines for a large number of PMS stars over required to answer global questions such as: how does magnetic activity in PMS stars differ from that of main sequence stars, how do they ...

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


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


    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 withi...

  9. Predicting RNA secondary structures from sequence and probing data. (United States)

    Lorenz, Ronny; Wolfinger, Michael T; Tanzer, Andrea; Hofacker, Ivo L


    RNA secondary structures have proven essential for understanding the regulatory functions performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success is in part due to the availability of efficient computational methods for predicting RNA secondary structures. Recent advances focus on dealing with the inherent uncertainty of prediction by considering the ensemble of possible structures rather than the single most stable one. Moreover, the advent of high-throughput structural probing has spurred the development of computational methods that incorporate such experimental data as auxiliary information.

  10. Using structure to explore the sequence alignment space of remote homologs.

    Directory of Open Access Journals (Sweden)

    Andrew Kuziemko


    Full Text Available Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

  11. The Study of Correlation Structures of DNA Sequences A Critical Review

    CERN Document Server

    Li, W


    The study of correlation structure in the primary sequences of DNA is reviewed. The issues reviewed include: symmetries among 16 base-base correlation functions, accurate estimation of correlation measures, the relationship between $1/f$ and Lorentzian spectra, heterogeneity in DNA sequences, different modeling strategies of the correlation structure of DNA sequences, the difference of correlation structure between coding and non-coding regions (besides the period-3 pattern), and source of broad distribution of domain sizes. Although some of the results remain controversial, a body of work on this topic constitutes a good starting point for future studies.

  12. RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments. (United States)

    Schnattinger, Thomas; Schöning, Uwe; Marchfelder, Anita; Kestler, Hans A


    Incorporating secondary structure information into the alignment process improves the quality of RNA sequence alignments. Instead of using fixed weighting parameters, sequence and structure components can be treated as different objectives and optimized simultaneously. The result is not a single, but a Pareto-set of equally optimal solutions, which all represent different possible weighting parameters. We now provide the interactive graphical software tool RNA-Pareto, which allows a direct inspection of all feasible results to the pairwise RNA sequence-structure alignment problem and greatly facilitates the exploration of the optimal solution set.

  13. Allelic diversity and population structure of Bacillus sphaericus as revealed by multilocus sequence typing. (United States)

    Ge, Yong; Hu, Xiaomin; Zheng, Dasheng; Wu, Yiming; Yuan, Zhiming


    The genetic diversity of 35 Bacillus sphaericus strains was analyzed by a newly developed multilocus sequence typing (MLST) scheme, toxin gene pool survey, and mosquito bioassay. The results demonstrated that strains assigned to the same sequence type (ST) had the same occurrence of toxin genes. Further sequence analysis revealed that toxic strains presented a nearly clonal population structure, whereas nontoxic strains had a high level of heterogeneity and were significantly distinct from toxic strains.

  14. Shark myelin basic protein: amino acid sequence, secondary structure, and self-association. (United States)

    Milne, T J; Atkins, A R; Warren, J A; Auton, W P; Smith, R


    Myelin basic protein (MBP) from the Whaler shark (Carcharhinus obscurus) has been purified from acid extracts of a chloroform/methanol pellet from whole brains. The amino acid sequence of the majority of the protein has been determined and compared with the sequences of other MBPs. The shark protein has only 44% homology with the bovine protein, but, in common with other MBPs, it has basic residues distributed throughout the sequence and no extensive segments that are predicted to have an ordered secondary structure in solution. Shark MBP lacks the triproline sequence previously postulated to form a hairpin bend in the molecule. The region containing the putative consensus sequence for encephalitogenicity in the guinea pig contains several substitutions, thus accounting for the lack of activity of the shark protein. Studies of the secondary structure and self-association have shown that shark MBP possesses solution properties similar to those of the bovine protein, despite the extensive differences in primary structure.

  15. Sequence Memory Constraints Give Rise to Language-Like Structure through Iterated Learning (United States)

    Cornish, Hannah; Dale, Rick; Kirby, Simon; Christiansen, Morten H.


    Human language is composed of sequences of reusable elements. The origins of the sequential structure of language is a hotly debated topic in evolutionary linguistics. In this paper, we show that sets of sequences with language-like statistical properties can emerge from a process of cultural evolution under pressure from chunk-based memory constraints. We employ a novel experimental task that is non-linguistic and non-communicative in nature, in which participants are trained on and later asked to recall a set of sequences one-by-one. Recalled sequences from one participant become training data for the next participant. In this way, we simulate cultural evolution in the laboratory. Our results show a cumulative increase in structure, and by comparing this structure to data from existing linguistic corpora, we demonstrate a close parallel between the sets of sequences that emerge in our experiment and those seen in natural language. PMID:28118370

  16. Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure. (United States)

    Herman, Joseph L; Challis, Christopher J; Novák, Ádám; Hein, Jotun; Schmidler, Scott C


    For sequences that are highly divergent, there is often insufficient information to infer accurate alignments, and phylogenetic uncertainty may be high. One way to address this issue is to make use of protein structural information, since structures generally diverge more slowly than sequences. In this work, we extend a recently developed stochastic model of pairwise structural evolution to multiple structures on a tree, analytically integrating over ancestral structures to permit efficient likelihood computations under the resulting joint sequence-structure model. We observe that the inclusion of structural information significantly reduces alignment and topology uncertainty, and reduces the number of topology and alignment errors in cases where the true trees and alignments are known. In some cases, the inclusion of structure results in changes to the consensus topology, indicating that structure may contain additional information beyond that which can be obtained from sequences. We use the model to investigate the order of divergence of cytoglobins, myoglobins, and hemoglobins and observe a stabilization of phylogenetic inference: although a sequence-based inference assigns significant posterior probability to several different topologies, the structural model strongly favors one of these over the others and is more robust to the choice of data set.

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

    Directory of Open Access Journals (Sweden)

    Vasiliki eFolia


    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.

  18. Large Scale Identification and Categorization of Protein Sequences Using Structured Logistic Regression

    DEFF Research Database (Denmark)

    Pedersen, Bjørn Panella; Ifrim, Georgiana; Liboriussen, Poul


    Abstract Background 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...

  19. seeMotif: exploring and visualizing sequence motifs in 3D structures. (United States)

    Chang, Darby Tien-Hao; Chien, Ting-Ying; Chen, Chien-Yu


    Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation. As increasing numbers of motifs are detected experimentally or predicted computationally, characterizing the functional roles of motifs and identifying the potential synergetic relationships between them are important next steps. A good way to investigate novel motifs is to utilize the abundant 3D structures that have also been accumulated at an astounding rate in recent years. This article reports the development of the web service seeMotif, which provides users with an interactive interface for visualizing sequence motifs on protein structures from the Protein Data Bank (PDB). Researchers can quickly see the locations and conformation of multiple motifs among a number of related structures simultaneously. Considering the fact that PDB sequences are usually shorter than those in sequence databases and/or may have missing residues, seeMotif has two complementary approaches for selecting structures and mapping motifs to protein chains in structures. As more and more structures belonging to previously uncharacterized protein families become available, combining sequence and structure information gives good opportunities to facilitate understanding of protein functions in large-scale genome projects. Available at:, or

  20. Sequence Planning for On-Orbit Assembly of Large Space Truss Structures in a Multirobot Environment

    Institute of Scientific and Technical Information of China (English)

    GUO Jifeng; WANG Ping; CUI Naigang


    An approach to sequence planning for on-orbit assembly of large space truss structures in a multirobot environment is presented. A hierarchical representation of large space truss structures at the structural volume element level and strut level is adopted. The representation of connectivity matrix and directed graph is respectively presented at the strut level and SVE level. The multirobot environment that consists of autonomous space robots and struts is supposed. Then the multirobot serial assembly strategy, assembly states, assembly tasks and assembly sequences are described. The assembly sequence planning algorithms at the strut level and SVE level are respectively discussed. The results of the simulations show that this approach is feasible and efficient. Two extensions of this approach include more accurate assessment of the efficiency representation and improvements in planning algorithm. In the future, the assembly sequence planning of more large space truss structures and complex multirobot environments and assembly tasks will be considered.

  1. Can Computationally Designed Protein Sequences Improve Secondary Structure Prediction? (United States)


    ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) U.S. Army...1997) using a significantly larger database of known structures than previously reported in the literature. Methods In this work, the Astral SCOP 1.75

  2. An Algorithm for Finding Conserved Secondary Structure Motifs in Unaligned RNA Sequences

    Institute of Scientific and Technical Information of China (English)

    Giulio Pavesi; Giancarlo Mauri; Graziano Pesole


    Several experiments and observations have revealed the fact that small local distinct structural features in RNA molecules are correlated with their biological function, for example, in post-transcriptional regulation of gene expression. Thus, finding similar structural features in a set of RNA sequences known to play the same biological function could provide substantial information concerning which parts of the sequences are responsible for the function itself. Unfortunately, finding common structural elements in RNA molecules is a very challenging task, even if limited to secondary structure. The main difficulty lies in the fact that in nearly all the cases the structure of the molecules is unknown, has to be somehow predicted, and that sequences with little or no similarity can fold into similar structures. Although they differ in some details, the approaches proposed so far are usually based on the preliminary alignment of the sequences and attempt to predict common structures (either local or global, or for some selected regions) for the aligned sequences. These methods give good results when sequence and structure similarity are very high, but function less well when similarity is limited to small and local elements, like single stem-loop motifs. Instead of aligning the sequences, the algorithm we present directly searches for regions of the sequences that can fold into similar structures, where the degree of similarity can be defined by the user. Any information concerning sequence similarity in the motifs can be used either as a search constraint, or a posteriori, by post-processing the output. The search for the regions sharing structural similarity is implemented with the affix tree, a novel text-indexing structure that significantly accelerates the search for patterns having a symmetric layout, such as those forming stem-loop structures. Tests based on experimentally known structures have shown that the algorithm is able to identify functional motifs in

  3. Genome3D: exploiting structure to help users understand their sequences


    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W. A.; Chothia, Cyrus; Cozzetto, Domenico; Dana, José M.; Filippis, Ioannis; Gough, Julian; Jones, David T.; Kelley, Lawrence A; Kleywegt, Gerard J.; Minneci, Federico; Mistry, Jaina


    Genome3D ( is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the resource. We have annotated representatives from Pfam families to improve coverage of diverse sequences and added a fast sequence search to the website to allow users to find Genome3D-annotated sequences similar to their own. We have improved and exte...

  4. Using deep RNA sequencing for the structural annotation of the Laccaria bicolor mycorrhizal transcriptome.

    Directory of Open Access Journals (Sweden)

    Peter E Larsen

    Full Text Available BACKGROUND: Accurate structural annotation is important for prediction of function and required for in vitro approaches to characterize or validate the gene expression products. Despite significant efforts in the field, determination of the gene structure from genomic data alone is a challenging and inaccurate process. The ease of acquisition of transcriptomic sequence provides a direct route to identify expressed sequences and determine the correct gene structure. METHODOLOGY: We developed methods to utilize RNA-seq data to correct errors in the structural annotation and extend the boundaries of current gene models using assembly approaches. The methods were validated with a transcriptomic data set derived from the fungus Laccaria bicolor, which develops a mycorrhizal symbiotic association with the roots of many tree species. Our analysis focused on the subset of 1501 gene models that are differentially expressed in the free living vs. mycorrhizal transcriptome and are expected to be important elements related to carbon metabolism, membrane permeability and transport, and intracellular signaling. Of the set of 1501 gene models, 1439 (96% successfully generated modified gene models in which all error flags were successfully resolved and the sequences aligned to the genomic sequence. The remaining 4% (62 gene models either had deviations from transcriptomic data that could not be spanned or generated sequence that did not align to genomic sequence. The outcome of this process is a set of high confidence gene models that can be reliably used for experimental characterization of protein function. CONCLUSIONS: 69% of expressed mycorrhizal JGI "best" gene models deviated from the transcript sequence derived by this method. The transcriptomic sequence enabled correction of a majority of the structural inconsistencies and resulted in a set of validated models for 96% of the mycorrhizal genes. The method described here can be applied to improve gene

  5. Using deep RNA sequencing for the structural annotation of the laccaria bicolor mycorrhizal transcriptome.

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, P. E.; Trivedi, G.; Sreedasyam, A.; Lu, V.; Podila, G. K.; Collart, F. R.; Biosciences Division; Univ. of Alabama


    Accurate structural annotation is important for prediction of function and required for in vitro approaches to characterize or validate the gene expression products. Despite significant efforts in the field, determination of the gene structure from genomic data alone is a challenging and inaccurate process. The ease of acquisition of transcriptomic sequence provides a direct route to identify expressed sequences and determine the correct gene structure. We developed methods to utilize RNA-seq data to correct errors in the structural annotation and extend the boundaries of current gene models using assembly approaches. The methods were validated with a transcriptomic data set derived from the fungus Laccaria bicolor, which develops a mycorrhizal symbiotic association with the roots of many tree species. Our analysis focused on the subset of 1501 gene models that are differentially expressed in the free living vs. mycorrhizal transcriptome and are expected to be important elements related to carbon metabolism, membrane permeability and transport, and intracellular signaling. Of the set of 1501 gene models, 1439 (96%) successfully generated modified gene models in which all error flags were successfully resolved and the sequences aligned to the genomic sequence. The remaining 4% (62 gene models) either had deviations from transcriptomic data that could not be spanned or generated sequence that did not align to genomic sequence. The outcome of this process is a set of high confidence gene models that can be reliably used for experimental characterization of protein function. 69% of expressed mycorrhizal JGI 'best' gene models deviated from the transcript sequence derived by this method. The transcriptomic sequence enabled correction of a majority of the structural inconsistencies and resulted in a set of validated models for 96% of the mycorrhizal genes. The method described here can be applied to improve gene structural annotation in other species, provided

  6. TBC1D24 genotype-phenotype correlation: Epilepsies and other neurologic features


    Balestrini, S; Milh, M.; Castiglioni, C.; Lüthy, K.; Finelli, M. J.; Verstreken, P.; Cardon, A; Stražišar, B. G.; Holder, J. L.; Lesca, G; Mancardi, M. M.; Poulat, A. L.; Repetto, G. M.; Banka, S.; Bilo, L.


    Objective: To evaluate the phenotypic spectrum associated with mutations in TBC1D24. Methods: We acquired new clinical, EEG, and neuroimaging data of 11 previously unreported and 37 published patients. TBC1D24 mutations, identified through various sequencing methods, can be found online ( Results: Forty-eight patients were included (28 men, 20 women, average age 21 years) from 30 independent families. Eighteen patients (38%) had myoclonic epilepsies. The other patients...

  7. Band Structure of 1-D Photonic Crystal for Oblique Incident Electromagnetic Wave Packet%一维光子晶体斜入射波包的带隙结构

    Institute of Scientific and Technical Information of China (English)

    高洁; 房丽敏; 李华刚; 麦志杰


    Dispersion relation of 1-D photonic crystal is deduced by the method of transfer matrix, with coordinate transformation of arbitrary Fourier exponent of electromagnetic wave packet which is obliquely incident. By analyzing the dispersion relation, it is easy to find the difference between the first band gap under obliquely incident wave packet and that of plane wave, respectively. Meanwhile, the former gap is located in the latter one, for the former one is narrower than the latter one in width. Characteristic of band gap is obtained under obliquely incident wave packet, by comparing the first band gap structure with that of plane wave considering edge position and width of the gap. The condition of approximately substituting plane wave for wave packet to calculate band gap is analyzed, according to related factors such as different incident angle of central wave vector and angle spectrum of wave packet. The results demonstrate that the first band gap structure is closely related to incident angle of central wave vector and angle spectrum of wave packet. With smaller incident angle, the first band gap structure caused by wave packet would become closer to that of plane wave; and with smaller angle spectrum of wave packet, the width and position of the first band gap is closer to those of plane wave.%对波包的任意傅里叶分量进行坐标变换后,利用转移矩阵法推导出波包斜入射情形下一维光子晶体的色散关系表达式,利用色散关系曲线分析得出波包斜入射的第一带隙结构,与以往平面波的第一带隙结构不同,波包的带隙宽度小于平面波的带隙宽度,并且在位置上前者带隙包含在后者内部.比较了一维光子晶体分别在波包入射与平面波入射情形下带隙位置和宽度,分析了波包中心入射角的变化以及波包的角分布范围的变化对带隙结构的影响,得到了一维光子晶体对波包斜入射的带隙结构的基本特征,确定了计算波包带

  8. MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships.

    KAUST Repository

    Kosinski, Jan


    SUMMARY: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure. MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at Website implemented in HTML and JavaScript with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

  9. Simulation of Organic Solar Cells Using AMPS-1D Program

    Directory of Open Access Journals (Sweden)

    Samah G. Babiker


    Full Text Available The analysis of microelectronic and photonic structure in one dimension program [AMPS-1D] program has been successfully used to study inorganic solar cells. In this work the program has been used to optimize the performance of the organic solar cells. The cells considered consist of poly(2-methoxy-5-(3,7- dimethyloctyloxy-1,4-phenylenevinylene [MDMO-PPV

  10. Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce. (United States)

    Yehdego, Daniel T; Zhang, Boyu; Kodimala, Vikram K R; Johnson, Kyle L; Taufer, Michela; Leung, Ming-Ying


    Secondary structures of ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Experimental observations and computing limitations suggest that we can approach the secondary structure prediction problem for long RNA sequences by segmenting them into shorter chunks, predicting the secondary structures of each chunk individually using existing prediction programs, and then assembling the results to give the structure of the original sequence. The selection of cutting points is a crucial component of the segmenting step. Noting that stem-loops and pseudoknots always contain an inversion, i.e., a stretch of nucleotides followed closely by its inverse complementary sequence, we developed two cutting methods for segmenting long RNA sequences based on inversion excursions: the centered and optimized method. Each step of searching for inversions, chunking, and predictions can be performed in parallel. In this paper we use a MapReduce framework, i.e., Hadoop, to extensively explore meaningful inversion stem lengths and gap sizes for the segmentation and identify correlations between chunking methods and prediction accuracy. We show that for a set of long RNA sequences in the RFAM database, whose secondary structures are known to contain pseudoknots, our approach predicts secondary structures more accurately than methods that do not segment the sequence, when the latter predictions are possible computationally. We also show that, as sequences exceed certain lengths, some programs cannot computationally predict pseudoknots while our chunking methods can. Overall, our predicted structures still retain the accuracy level of the original prediction programs when compared with known experimental secondary structure.

  11. Diffusion and particle mobility in 1D system

    Energy Technology Data Exchange (ETDEWEB)

    Borman, V.D. [Moscow Engineering Physics Institute (State University), Kashirskoe shosse, 31, 115409 Moscow (Russian Federation); Johansson, B. [Condensed Matter Theory Group, Department of Physics, Box 530, Uppsala University, S-75121 Uppsala (Sweden); Applied Materials Physics, Department of Materials and Engineering, Royal Institute of Technology (KTH), S-10044 Stockholm (Sweden); Skorodumova, N.V. [Condensed Matter Theory Group, Department of Physics, Box 530, Uppsala University, S-75121 Uppsala (Sweden); Tronin, I.V. [Moscow Engineering Physics Institute (State University), Kashirskoe shosse, 31, 115409 Moscow (Russian Federation)]. E-mail:; Tronin, V.N. [Moscow Engineering Physics Institute (State University), Kashirskoe shosse, 31, 115409 Moscow (Russian Federation); Troyan, V.I. [Moscow Engineering Physics Institute (State University), Kashirskoe shosse, 31, 115409 Moscow (Russian Federation)


    The transport properties of one-dimensional (1D) systems have been studied theoretically. Contradictory experimental results on molecular transport in quasi-1D systems, such as zeolite structures, when both diffusion transport acceleration and the existence of the diffusion mode with lower particle mobility (single-file diffusion ({approx}t{sup 1/2})) have been reported, are consolidated in a consistent model. Transition from the single-file diffusion mode to an Einstein-like diffusion {approx}t with diffusion coefficient increasing with the density has been predicted to occur at large observation times.

  12. Investigation of the protein osteocalcin of Camelops hesternus: Sequence, structure and phylogenetic implications (United States)

    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.


    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

  13. Identification of 5' capped structure and 3' terminal sequence of hepatitis E virus isolated from Morocco

    Institute of Scientific and Technical Information of China (English)

    Guo-Bing Chen; Ji-Hong Meng


    AIM: To examine 5' and 3' terminal sequences of hepatitis E virus (HEV) isolated from Morocco, to confirm 5' methylated cap structure of the genome, and to investigate whether the 3' UTR can be used to distinguish HEV genotypes instead of HEV complete genome sequence.METHODS: RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) was employed to obtain the 5' and 3' terminal sequences of HEV Morocco strain. The 3' UTR sequence of the Morocco strain was compared with that of the other 29 HEV strains using the DNAStar software.RESULTS: The 5' PCR product was obtained only from the RLM-RACE based on the capped RNA template. The 5' UTR of the Morocco strain had 26 nucleotides, and the 3' UTR had 65 nucleotides upstream to the polyA. The 5' UTR between HEV strains had only point mutations of nucleotides.The phylogenetic tree based on the sequences of 3' UTR was not the same as that based on the complete sequences.CONCLUSION: The genome of HEV Morocco strain was methylated cap structure. The 3' terminal sequence can not be used for distinguishing HEV genotype for all HEV strains in place of the whole HEV genome sequence.

  14. 1D nanocrystals with precisely controlled dimensions, compositions, and architectures (United States)

    Pang, Xinchang; He, Yanjie; Jung, Jaehan; Lin, Zhiqun


    The ability to synthesize a diverse spectrum of one-dimensional (1D) nanocrystals presents an enticing prospect for exploring nanoscale size- and shape-dependent properties. Here we report a general strategy to craft a variety of plain nanorods, core-shell nanorods, and nanotubes with precisely controlled dimensions and compositions by capitalizing on functional bottlebrush-like block copolymers with well-defined structures and narrow molecular weight distributions as nanoreactors. These cylindrical unimolecular nanoreactors enable a high degree of control over the size, shape, architecture, surface chemistry, and properties of 1D nanocrystals. We demonstrate the synthesis of metallic, ferroelectric, upconversion, semiconducting, and thermoelectric 1D nanocrystals, among others, as well as combinations thereof.

  15. Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure. (United States)

    van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira


    The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.

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

    CERN Document Server

    Roald, C B


    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.

  17. Developing 1D nanostructure arrays for future nanophotonics

    Directory of Open Access Journals (Sweden)

    Cooke DG


    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.

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

    Directory of Open Access Journals (Sweden)

    Abolhasan Rezaei


    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 β sheet.

  19. Key Issues in Modeling of Complex 3D Structures from Video Sequences

    Directory of Open Access Journals (Sweden)

    Shengyong Chen


    Full Text Available Construction of three-dimensional structures from video sequences has wide applications for intelligent video analysis. This paper summarizes the key issues of the theory and surveys the recent advances in the state of the art. Reconstruction of a scene object from video sequences often takes the basic principle of structure from motion with an uncalibrated camera. This paper lists the typical strategies and summarizes the typical solutions or algorithms for modeling of complex three-dimensional structures. Open difficult problems are also suggested for further study.

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

    DEFF Research Database (Denmark)

    Torarinsson, Elfar; Sawera, Milena; Havgaard, Jakob Hull;


    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...... 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...

  1. Evolutionary evidence for alternative structure in RNA sequence co-variation.

    Directory of Open Access Journals (Sweden)

    Justin Ritz

    Full Text Available Sequence conservation and co-variation of base pairs are hallmarks of structured RNAs. For certain RNAs (e.g. riboswitches, a single sequence must adopt at least two alternative secondary structures to effectively regulate the message. If alternative secondary structures are important to the function of an RNA, we expect to observe evolutionary co-variation supporting multiple conformations. We set out to characterize the evolutionary co-variation supporting alternative conformations in riboswitches to determine the extent to which alternative secondary structures are conserved. We found strong co-variation support for the terminator, P1, and anti-terminator stems in the purine riboswitch by extending alignments to include terminator sequences. When we performed Boltzmann suboptimal sampling on purine riboswitch sequences with terminators we found that these sequences appear to have evolved to favor specific alternative conformations. We extended our analysis of co-variation to classic alignments of group I/II introns, tRNA, and other classes of riboswitches. In a majority of these RNAs, we found evolutionary evidence for alternative conformations that are compatible with the Boltzmann suboptimal ensemble. Our analyses suggest that alternative conformations are selected for and thus likely play functional roles in even the most structured of RNAs.

  2. Protein secondary structure prediction for a single-sequence using hidden semi-Markov models



    Abstract Background The accuracy of protein secondary structure prediction has been improving steadily towards the 88% estimated theoretical limit. There are two types of prediction algorithms: Single-sequence prediction algorithms imply that information about other (homologous) proteins is not available, while algorithms of the second type imply that information about homologous proteins is available, and use it intensively. The single-sequence algorithms could make an important contribution...

  3. A Java applet for multiple linked visualization of protein structure and sequence. (United States)

    Oldfield, Thomas J


    The amount of biological data available from experimental techniques is huge, and rapidly expanding. The ability to make sense of this vast amount of data requires that we make correlations between distinct biological disciplines using visualization techniques to highlight the critical information. This article describes the visualization techniques of dynamic data brushing, view context maintenance, fisheye sequence view, and a magic lens that have been developed to display protein structure and sequence information.

  4. Synthesis, characterization and crystal structure determination of Mn (II) ion based 1D polymer constructed from 2, 2‧ bipyridyl and azide group, its thermal stability, magnetic properties and Hirshfeld surface analysis (United States)

    Mudsainiyan, R. K.; Jassal, Amanpreet Kaur; Chawla, S. K.


    The 1-D polymeric complex (I) is having formula [Mn(2,2‧-BP).(N3)2]n, which has been crystallized in distilled water and characterized by elemental analyses, FT-IR spectrum, powder X-ray diffraction analyses and single-crystal diffraction analysis. This polymer possesses 1D helical chains or coils where Mn-azide-Mn forms the base of the coil which is alternatively garlanded by rigid bi-pyridine rings, where coordinates are in anti-fashion. The Mn (II) ions in the repeating units are linked by two end-on azide groups which extend through the two end-to-end azide ligands to the next unit forming a 1-D polymeric chain. The present study suggests that the use of this rigid and neutral building block leads to give better arrangement of the polymeric motif with [010] chains in 2-c uninodal net. During investigation of strong or weak intermolecular interactions, X-ray diffraction analysis and Hirshfeld surface analysis give rise to comparable results but in Hirshfeld surface analysis, two-third times more results of close contacts are obtained. The fingerprint plots demonstrate that these weak non-bonding interactions are important for stabilizing the crystal packing. Magnetic properties of the complex (I) were analyzed on the basis of an alternating ferro- and antiferromagnetic Heisenberg chain of Mn (II) ions. The J-exchange parameters found are J1=64.3 K (45.3 cm-1), and J2=-75.7 K (-53.3 cm-1). Magnetic properties are discussed in comparison with those of other similar molecular magnets of [Mn(L-L)(N3)2]n type.

  5. Automatic phylogenetic classification of bacterial beta-lactamase sequences including structural and antibiotic substrate preference information. (United States)

    Ma, Jianmin; Eisenhaber, Frank; Maurer-Stroh, Sebastian


    Beta lactams comprise the largest and still most effective group of antibiotics, but bacteria can gain resistance through different beta lactamases that can degrade these antibiotics. We developed a user friendly tree building web server that allows users to assign beta lactamase sequences to their respective molecular classes and subclasses. Further clinically relevant information includes if the gene is typically chromosomal or transferable through plasmids as well as listing the antibiotics which the most closely related reference sequences are known to target and cause resistance against. This web server can automatically build three phylogenetic trees: the first tree with closely related sequences from a Tachyon search against the NCBI nr database, the second tree with curated reference beta lactamase sequences, and the third tree built specifically from substrate binding pocket residues of the curated reference beta lactamase sequences. We show that the latter is better suited to recover antibiotic substrate assignments through nearest neighbor annotation transfer. The users can also choose to build a structural model for the query sequence and view the binding pocket residues of their query relative to other beta lactamases in the sequence alignment as well as in the 3D structure relative to bound antibiotics. This web server is freely available at


    Institute of Scientific and Technical Information of China (English)

    YUAN Dongwu; ZHU Shannong; YANG Xiaozhen


    Triad sequence distributions in a series of P(AM/AA) with different AA% were calculated from copolymerization reactivity ratio r1 and r2 based on first order Markov statistic model, and the calculated data compared with observed ones from 13C-NMR spectra showed good agreement with each other, The sequence distribution in P(AM/AA) obtained under our experimental conditions fits in with first order Markov statistic model. A significant sequence structure difference was observed between P(AM/AA) and alkaline hydrolyzed polyacrylamide, ABA triad (acrylate unit center), AAA and AAB triads (acrylamide unit center) dominated in hydrolyzed ones.

  7. Heat Capacity of 1D Molecular Chains (United States)

    Bagatskii, M. I.; Barabashko, M. S.; Sumarokov, V. V.; Jeżowski, A.; Stachowiak, P.


    The heat capacity of 1D chains of nitrogen and methane molecules (adsorbed in the outer grooves of bundles of closed-cap single-walled carbon nanotubes) has been studied in the temperature ranges 2-40 and 2-60 K, respectively. The temperature dependence of the heat capacity of 1D chains of nitrogen molecules below 3 K is close to a linear. It was found that the rotational heat capacity of methane molecules is a significant part of the total heat capacity of the chains throughout the whole investigated temperature range, whereas in the case of nitrogen, the librations are significant only above 15 K. The dependence of the heat capacity for methane below 10 K indicates the presence of a Schottky anomaly caused by the tunneling between the lowest energy levels of the CH4 molecule rotational spectra. Characteristic features observed in the temperature dependence of the heat capacity of 1D methane crystals are also discussed.

  8. Synthesis, characterization and crystal structure determination of Mn (II) ion based 1D polymer constructed from 2, 2′ bipyridyl and azide group, its thermal stability, magnetic properties and Hirshfeld surface analysis

    Energy Technology Data Exchange (ETDEWEB)

    Mudsainiyan, R.K., E-mail:; Jassal, Amanpreet Kaur; Chawla, S.K., E-mail:


    The 1-D polymeric complex (I) is having formula [Mn(2,2′-BP).(N{sub 3}){sub 2}]{sub n}, which has been crystallized in distilled water and characterized by elemental analyses, FT-IR spectrum, powder X-ray diffraction analyses and single-crystal diffraction analysis. This polymer possesses 1D helical chains or coils where Mn–azide–Mn forms the base of the coil which is alternatively garlanded by rigid bi-pyridine rings, where coordinates are in anti-fashion. The Mn (II) ions in the repeating units are linked by two end-on azide groups which extend through the two end-to-end azide ligands to the next unit forming a 1-D polymeric chain. The present study suggests that the use of this rigid and neutral building block leads to give better arrangement of the polymeric motif with [010] chains in 2-c uninodal net. During investigation of strong or weak intermolecular interactions, X-ray diffraction analysis and Hirshfeld surface analysis give rise to comparable results but in Hirshfeld surface analysis, two-third times more results of close contacts are obtained. The fingerprint plots demonstrate that these weak non-bonding interactions are important for stabilizing the crystal packing. Magnetic properties of the complex (I) were analyzed on the basis of an alternating ferro- and antiferromagnetic Heisenberg chain of Mn (II) ions. The J-exchange parameters found are J{sub 1}=64.3 K (45.3 cm{sup −1}), and J{sub 2}=−75.7 K (−53.3 cm{sup −1}). Magnetic properties are discussed in comparison with those of other similar molecular magnets of [Mn(L–L)(N{sub 3}){sub 2}]{sub n} type. - - Highlights: • Synthesized 1-D polymeric complex of Mn (II) ions with 2, 2′ bipyridyl and azide group. • X-ray data of complex (I) is in a good agreement with TGA and other spectroscopic techniques. • DFT calculations were done and compared with the parameter of experimental and theoretical data. • Intermolecular interactions calculated by Hirshfeld surface analysis

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

    Energy Technology Data Exchange (ETDEWEB)

    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)


    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.)

  10. Social exploration of 1D games

    DEFF Research Database (Denmark)

    Valente, Andrea; Marchetti, Emanuela


    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 intere...... 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....

  11. CATH: an expanded resource to predict protein function through structure and sequence (United States)

    Dawson, Natalie L.; Lewis, Tony E.; Das, Sayoni; Lees, Jonathan G.; Lee, David; Ashford, Paul; Orengo, Christine A.; Sillitoe, Ian


    The latest version of the CATH-Gene3D protein structure classification database has recently been released (version 4.1, The resource comprises over 300 000 domain structures and over 53 million protein domains classified into 2737 homologous superfamilies, doubling the number of predicted protein domains in the previous version. The daily-updated CATH-B, which contains our very latest domain assignment data, provides putative classifications for over 100 000 additional protein domains. This article describes developments to the CATH-Gene3D resource over the last two years since the publication in 2015, including: significant increases to our structural and sequence coverage; expansion of the functional families in CATH; building a support vector machine (SVM) to automatically assign domains to superfamilies; improved search facilities to return alignments of query sequences against multiple sequence alignments; the redesign of the web pages and download site. PMID:27899584

  12. Development of steady-state electrical-heating fluorescence-sensing (SEF) technique for thermal characterization of one dimensional (1D) structures by employing graphene quantum dots (GQDs) as temperature sensors (United States)

    Wan, Xiang; Li, Changzheng; Yue, Yanan; Xie, Danmei; Xue, Meixin; Hu, Niansu


    A fluorescence signal has been demonstrated as an effective implement for micro/nanoscale temperature measurement which can be realized by either direct fluorescence excitation from materials or by employing nanoparticles as sensors. In this work, a steady-state electrical-heating fluorescence-sensing (SEF) technique is developed for the thermal characterization of one-dimensional (1D) materials. In this method, the sample is suspended between two electrodes and applied with steady-state Joule heating. The temperature response of the sample is monitored by collecting a simultaneous fluorescence signal from the sample itself or nanoparticles uniformly attached on it. According to the 1D heat conduction model, a linear temperature dependence of heating powers is obtained, thus the thermal conductivity of the sample can be readily determined. In this work, a standard platinum wire is selected to measure its thermal conductivity to validate this technique. Graphene quantum dots (GQDs) are employed as the fluorescence agent for temperature sensing. Parallel measurement by using the transient electro-thermal (TET) technique demonstrates that a small dose of GQDs has negligible influence on the intrinsic thermal property of platinum wire. This SEF technique can be applied in two ways: for samples with a fluorescence excitation capability, this method can be implemented directly; for others with weak or no fluorescence excitation, a very small portion of nanoparticles with excellent fluorescence excitation can be used for temperature probing and thermophysical property measurement.

  13. Intermediate divergence levels maximize the strength of structure-sequence correlations in enzymes and viral proteins. (United States)

    Jackson, Eleisha L; Shahmoradi, Amir; Spielman, Stephanie J; Jack, Benjamin R; Wilke, Claus O


    Structural properties such as solvent accessibility and contact number predict site-specific sequence variability in many proteins. However, the strength and significance of these structure-sequence relationships vary widely among different proteins, with absolute correlation strengths ranging from 0 to 0.8. In particular, two recent works have made contradictory observations. Yeh et al. (Mol. Biol. Evol. 31:135-139, 2014) found that both relative solvent accessibility (RSA) and weighted contact number (WCN) are good predictors of sitewise evolutionary rate in enzymes, with WCN clearly out-performing RSA. Shahmoradi et al. (J. Mol. Evol. 79:130-142, 2014) considered these same predictors (as well as others) in viral proteins and found much weaker correlations and no clear advantage of WCN over RSA. Because these two studies had substantial methodological differences, however, a direct comparison of their results is not possible. Here, we reanalyze the datasets of the two studies with one uniform analysis pipeline, and we find that many apparent discrepancies between the two analyses can be attributed to the extent of sequence divergence in individual alignments. Specifically, the alignments of the enzyme dataset are much more diverged than those of the virus dataset, and proteins with higher divergence exhibit, on average, stronger structure-sequence correlations. However, the highest structure-sequence correlations are observed at intermediate divergence levels, where both highly conserved and highly variable sites are present in the same alignment.

  14. Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

    Directory of Open Access Journals (Sweden)

    Jiang Du


    Full Text Available The goal of human genome re-sequencing is obtaining an accurate assembly of an individual's genome. Recently, there has been great excitement in the development of many technologies for this (e.g. medium and short read sequencing from companies such as 454 and SOLiD, and high-density oligo-arrays from Affymetrix and NimbelGen, with even more expected to appear. The costs and sensitivities of these technologies differ considerably from each other. As an important goal of personal genomics is to reduce the cost of re-sequencing to an affordable point, it is worthwhile to consider optimally integrating technologies. Here, we build a simulation toolbox that will help us optimally combine different technologies for genome re-sequencing, especially in reconstructing large structural variants (SVs. SV reconstruction is considered the most challenging step in human genome re-sequencing. (It is sometimes even harder than de novo assembly of small genomes because of the duplications and repetitive sequences in the human genome. To this end, we formulate canonical problems that are representative of issues in reconstruction and are of small enough scale to be computationally tractable and simulatable. Using semi-realistic simulations, we show how we can combine different technologies to optimally solve the assembly at low cost. With mapability maps, our simulations efficiently handle the inhomogeneous repeat-containing structure of the human genome and the computational complexity of practical assembly algorithms. They quantitatively show how combining different read lengths is more cost-effective than using one length, how an optimal mixed sequencing strategy for reconstructing large novel SVs usually also gives accurate detection of SNPs/indels, how paired-end reads can improve reconstruction efficiency, and how adding in arrays is more efficient than just sequencing for disentangling some complex SVs. Our strategy should facilitate the sequencing of

  15. Sequence determination and modeling of structural motifs for the smallest monomeric aminoacyl-tRNA synthetase.


    Hou, Y M; Shiba, K; Mottes, C; Schimmel, P.


    Polypeptide chains of 19 previously studied Escherichia coli aminoacyl-tRNA synthetases are as large as 951 amino acids and, depending on the enzyme, have quaternary structures of alpha, alpha 2, alpha 2 beta 2, and alpha 4. These enzymes have been organized into two classes which are defined by sequence motifs that are associated with specific three-dimensional structures. We isolated, cloned, and sequenced the previously uncharacterized gene for E. coli cysteine-tRNA synthetase (EC

  16. Multi-scaling hierarchical structure analysis on the sequence of E. coli complete genome

    Institute of Scientific and Technical Information of China (English)


    We have applied the newly developed hierarchical structure theory for complex systems to analyze the multi-scaling structures of the nucleotide density distribution along a linear DNA sequence from the complete Escherichia coli genome. The hierarchical symmetry in the nucleotide density distribution was demonstrated. In particular, we have shown that the G, C density distribution that represents a strong H-bonding between the two DNA chains is more coherent with smaller similarity parameter compared to that of A, T density distribution, indicating a better organized multi-scaling fluctuation field for G, C density distribution along the genome sequence. The biological significance of these findings is under investigation.

  17. Circular dichroism spectroscopic studies on structures formed by telomeric DNA sequences in vitro

    Institute of Scientific and Technical Information of China (English)


    Telomere plays an important role in cellular processes, such as cell aging, death and carcinogenisis. Having special sequences, it can form quadruplex structure in vitro. Circular dichroism (CD) spectroscopic studies show that TTAGGG, (TTAGGG)2 and (TTAGGG)4 can all form quadruplex in vitro and exist mainly as parallel quadruplex without metal ions. Both K+ and Na+ can stabilize the tetrameric structure and facilitate the forming of anti-parallel conformation. Furthermore, the conformations of quadruplex can also be affected by sequence length, the nature and concentration of metal ions.

  18. First Observation of Upsilon(1D) States

    CERN Document Server

    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


    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.

  19. The structure contours of the Calico sequence boundary in the Kaiparowits Plateau, southern Utah (csbstrc*g) (United States)

    U.S. Geological Survey, Department of the Interior — This is a polygon coverage of the structure contours of the Calico sequence boundary in the Kaiparowits Plateau, southern Utah. Sequence boundary elevations are...

  20. Typhoidal Salmonellae: Use of Multi-Locus Sequence Typing to Determine Population Structure. (United States)

    Sharma, Priyanka; Dahiya, Sushila; Balaji, Veeraraghavan; Kanga, Anil; Panda, Preetilata; Das, Rashna; Dhanraju, Anbumani; Mendiratta, Deepak Kumar; Sood, Seema; Das, Bimal Kumar; Kapil, Arti


    Enteric fever is an invasive infection predominantly caused by Salmonella enterica serovars Typhi and Paratyphi A. The pathogens have evolved from other nontyphoidal salmonellaeto become invasive and host restricted. Emergence of antimicrobial resistance in typhoidal salmonellae in some countries is a major therapeutic concern as the travelers returning from endemic countries carry resistant strains to non endemic areas. In order to understand the epidemiology and to design disease control strategies molecular typing of the pathogen is very important. We performed Multilocus Sequence Typing (MLST) of 251 S. Typhi and 18 S. Paratyphi strains isolated from enteric fever patients from seven centers across India during 2010-2013to determine the population structure and prevalence of MLST sequence types in India. MLST analysis revealed the presence of five sequence types (STs) of typhoidal salmonellae in India namely ST1, ST2 and ST3 for S. Typhi and ST85 and ST129 for S. Paratyphi A.S. Typhi strains showed monophyletic lineage and clustered in to 3 Sequence Types-ST1, ST2 and ST3 and S. Paratyphi A isolates segregated in two sequence types ST85 and ST129 respectively. No association was found between antimicrobial susceptibility and sequence types. This study found ST1 as the most prevalent sequence type of S. Typhi in India followed by ST2, which is in concordance with previous studies and MLST database. In addition a rare sequence type ST3 has been found which is reported for the first time from the Indian subcontinent. Amongst S. Paratyphi A, the most common sequence type is ST129 as also reported from other parts of world. This distribution and prevalence suggest the common spread of the sequence types across the globe and these findings can help in understanding the disease distribution.

  1. Structure and chromosomal localization of DNA sequences related to ribosomal subrepeats in Vicia faba. (United States)

    Maggini, F; Cremonini, R; Zolfino, C; Tucci, G F; D'Ovidio, R; Delre, V; DePace, C; Scarascia Mugnozza, G T; Cionini, P G


    Subrepeating sequences of 325 bp found in the ribosomal intergenic spacer (IGS) of Vicia faba and responsible for variations in the length of the polycistronic units for rRNA were isolated and used as probes for in situ hybridization. Hybridization occurs at many regions of the metaphase chromosomes besides those bearing rRNA genes, namely chromosome ends and all the heterochromatic regions revealed by enhanced fluorescence after quinacrine staining. The DNA homologous to the 325 bp repeats that does not reside in the IGS was isolated, cloned and sequenced. It is composed of tandemly arranged 336 bp elements, each comprising two highly related 168 bp sequences. This structure is very similar to that of the IGS repeats and ca. 75% nucleotide sequence identity can be observed between these and the 168 bp doublets. The most obvious difference lies in the deletion, in the former, of a 14 bp segment from one of the two related sequences. It is hypothesized that the IGS repeats are derived from the 336 bp elements and have been transposed to ribosomal cistrons from other genome fractions. The possible relations between these sequences and others with similar structural features found in other species are discussed.

  2. Using maximum entropy model to predict protein secondary structure with single sequence. (United States)

    Ding, Yong-Sheng; Zhang, Tong-Liang; Gu, Quan; Zhao, Pei-Ying; Chou, Kuo-Chen


    Prediction of protein secondary structure is somewhat reminiscent of the efforts by many previous investigators but yet still worthy of revisiting it owing to its importance in protein science. Several studies indicate that the knowledge of protein structural classes can provide useful information towards the determination of protein secondary structure. Particularly, the performance of prediction algorithms developed recently have been improved rapidly by incorporating homologous multiple sequences alignment information. Unfortunately, this kind of information is not available for a significant amount of proteins. In view of this, it is necessary to develop the method based on the query protein sequence alone, the so-called single-sequence method. Here, we propose a novel single-sequence approach which is featured by that various kinds of contextual information are taken into account, and that a maximum entropy model classifier is used as the prediction engine. As a demonstration, cross-validation tests have been performed by the new method on datasets containing proteins from different structural classes, and the results thus obtained are quite promising, indicating that the new method may become an useful tool in protein science or at least play a complementary role to the existing protein secondary structure prediction methods.

  3. Sequence and structural analyses of nuclear export signals in the NESdb database. (United States)

    Xu, Darui; Farmer, Alicia; Collett, Garen; Grishin, Nick V; Chook, Yuh Min


    We compiled >200 nuclear export signal (NES)-containing CRM1 cargoes in a database named NESdb. We analyzed the sequences and three-dimensional structures of natural, experimentally identified NESs and of false-positive NESs that were generated from the database in order to identify properties that might distinguish the two groups of sequences. Analyses of amino acid frequencies, sequence logos, and agreement with existing NES consensus sequences revealed strong preferences for the Φ1-X(3)-Φ2-X(2)-Φ3-X-Φ4 pattern and for negatively charged amino acids in the nonhydrophobic positions of experimentally identified NESs but not of false positives. Strong preferences against certain hydrophobic amino acids in the hydrophobic positions were also revealed. These findings led to a new and more precise NES consensus. More important, three-dimensional structures are now available for 68 NESs within 56 different cargo proteins. Analyses of these structures showed that experimentally identified NESs are more likely than the false positives to adopt α-helical conformations that transition to loops at their C-termini and more likely to be surface accessible within their protein domains or be present in disordered or unobserved parts of the structures. Such distinguishing features for real NESs might be useful in future NES prediction efforts. Finally, we also tested CRM1-binding of 40 NESs that were found in the 56 structures. We found that 16 of the NES peptides did not bind CRM1, hence illustrating how NESs are easily misidentified.

  4. Prediction of Spontaneous Protein Deamidation from Sequence-Derived Secondary Structure and Intrinsic Disorder.

    Directory of Open Access Journals (Sweden)

    J Ramiro Lorenzo

    Full Text Available Asparagine residues in proteins undergo spontaneous deamidation, a post-translational modification that may act as a molecular clock for the regulation of protein function and turnover. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding. We present NGOME, an algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. Compared to previous algorithms, NGOME does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Four case studies of specific proteins show how NGOME may help the user identify deamidation-prone asparagine residues, often related to protein gain of function, protein degradation or protein misfolding in pathological processes. A fifth case study applies NGOME at a proteomic scale and unveils a correlation between asparagine deamidation and protein degradation in yeast. NGOME is freely available as a webserver at the National EMBnet node Argentina, URL: in the subpage "Protein and nucleic acid structure and sequence analysis".

  5. Calibration of a 1D/1D urban flood model using 1D/2D model results in the absence of field data. (United States)

    Leandro, J; Djordjević, S; Chen, A S; Savić, D A; Stanić, M


    Recently increased flood events have been prompting researchers to improve existing coupled flood-models such as one-dimensional (1D)/1D and 1D/two-dimensional (2D) models. While 1D/1D models simulate sewer and surface networks using a one-dimensional approach, 1D/2D models represent the surface network by a two-dimensional surface grid. However their application raises two issues to urban flood modellers: (1) stormwater systems planning/emergency or risk analysis demands for fast models, and the 1D/2D computational time is prohibitive, (2) and the recognized lack of field data (e.g. Hunter et al. (2008)) causes difficulties for the calibration/validation of 1D/1D models. In this paper we propose to overcome these issues by calibrating a 1D/1D model with the results of a 1D/2D model. The flood-inundation results show that: (1) 1D/2D results can be used to calibrate faster 1D/1D models, (2) the 1D/1D model is able to map the 1D/2D flood maximum extent well, and the flooding limits satisfactorily in each time-step, (3) the 1D/1D model major differences are the instantaneous flow propagation and overestimation of the flood-depths within surface-ponds, (4) the agreement in the volume surcharged by both models is a necessary condition for the 1D surface-network validation and (5) the agreement of the manholes discharge shapes measures the fitness of the calibrated 1D surface-network.

  6. [Characterization of 5S rRNA gene sequence and secondary structure in gymnosperms]. (United States)

    Liu, Zhan-Lin; Zhang, Da-Ming; Wang, Xiao-Ru


    In higher plants the primary and the secondary structures of 5S ribosomal RNA gene are considered highly conservative. Little is known about the 5S rRNA gene structure, organization and variation in gyimnosperms. In this study we analyzed sequence and structure variation of 5S rRNA gene in Pinus through cloning and sequencing multiple copies of 5S rDNA repeats from individual trees of five pines, P. bungeana, P. tabulaeformis, P. yunnanensis, P. massoniana and P. densata. Pinus bungeana is from the subgenus Strobus while the other four are from the subgenus Pinus (diploxylon pines). Our results revealed variations in both primary and secondary structure among copies of 5S rDNA within individual genomes and between species. 5S rRNA gene in Pinus is 120 bp long in most of the 122 clones we sequenced except for one or two deletions in three clones. Among these clones 50 unique sequences were identified and they were shared by different pine species. Our sequences were compared to 13 sequences each representing a different gymnosperm species, and to six sequences representing both angiosperm monocots and dicots. Average sequence similarity was 97.1% among Pinus species and 94.3% between Pinus and other gymnosperms. Between gymnosperms and angiosperms the sequence similarity decreased to 88.1%. Similar to other molecular data, significant sequence divergence was found between the two Pinus subgenera. The 5S gene tree (neighbor-joining tree) grouped the four diploxylon pines together and separated them distinctly from P. bungeana. Comparison of sequence divergence within individuals and between species suggested that concerted evolution has been very weak especially after the divergence of the four diploxylon pines. The phylogenetic information contained in the 5S rRNA gene is limited due to its shorter length and the difficulties in identifying orthologous and paralogous copies of rDNA multigene family further complicate its phylogenetic application. Pinus densata is a

  7. Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes. (United States)

    MacGregor, E A; Janecek, S; Svensson, B


    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.

  8. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server. (United States)

    Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles


    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at

  9. Development of 1D Liner Compression Code for IDL (United States)

    Shimazu, Akihisa; Slough, John; Pancotti, Anthony


    A 1D liner compression code is developed to model liner implosion dynamics in the Inductively Driven Liner Experiment (IDL) where FRC plasmoid is compressed via inductively-driven metal liners. The driver circuit, magnetic field, joule heating, and liner dynamics calculations are performed at each time step in sequence to couple these effects in the code. To obtain more realistic magnetic field results for a given drive coil geometry, 2D and 3D effects are incorporated into the 1D field calculation through use of correction factor table lookup approach. Commercial low-frequency electromagnetic fields solver, ANSYS Maxwell 3D, is used to solve the magnetic field profile for static liner condition at various liner radius in order to derive correction factors for the 1D field calculation in the code. The liner dynamics results from the code is verified to be in good agreement with the results from commercial explicit dynamics solver, ANSYS Explicit Dynamics, and previous liner experiment. The developed code is used to optimize the capacitor bank and driver coil design for better energy transfer and coupling. FRC gain calculations are also performed using the liner compression data from the code for the conceptual design of the reactor sized system for fusion energy gains.


    Institute of Scientific and Technical Information of China (English)

    LIN Qinghuang; WANG Huifen; LIU Deshan; ZHOU Qixiang


    Several novel aromatic liquid crystalline copolyesters with regular sequence structure were prepared by melt Schotten-Baumann polycondensation via complex monomer. Polarizing microscope with hot stage,thermal analysis and X-ray diffraction were used to investigate the structure and properties of the copolyesters . The effects of structural units, such as flexible spacer, noncolinear meta-linked phenylene unit, crankshaft unit, kink with flexible bridging unit and various substituted benzene rings on melting temperature of aromatic copolyesters were studied and discussed on the basis of crystalline structure of the polymers.

  11. Sequence, Stability, Structure of G-Quadruplexes and Their Drug Interactions (United States)

    Chen, Yuwei; Yang, Danzhou


    Although DNA is most widely known to store and pass along genetic information, the discovery of G-quadruplex structures has illuminated a new role of DNA in biology. DNA G-quadruplexes are four-stranded globular nucleic acid secondary structures formed in specific G-rich sequences with biological significance, such as human telomeres and oncogene promoters. This review focuses on the unimolecular DNA G-quadruplexes, which can readily form in solution under physiological conditions and are considered to be most biologically relevant. Available structural data show a great conformational diversity of unimolecular G-quadruplexes, amenable to small molecule drug targeting. The relationship of sequence, structure, and stability of unimolecular DNA G-quadruplexes, as well as the recent progress on interactions with small molecule compounds and insights into rational design of G-quadruplex-interactive molecules, will be discussed. PMID:22956454

  12. Gleaning structural and functional information from correlations in protein multiple sequence alignments. (United States)

    Neuwald, Andrew F


    The availability of vast amounts of protein sequence data facilitates detection of subtle statistical correlations due to imposed structural and functional constraints. Recent breakthroughs using Direct Coupling Analysis (DCA) and related approaches have tapped into correlations believed to be due to compensatory mutations. This has yielded some remarkable results, including substantially improved prediction of protein intra- and inter-domain 3D contacts, of membrane and globular protein structures, of substrate binding sites, and of protein conformational heterogeneity. A complementary approach is Bayesian Partitioning with Pattern Selection (BPPS), which partitions related proteins into hierarchically-arranged subgroups based on correlated residue patterns. These correlated patterns are presumably due to structural and functional constraints associated with evolutionary divergence rather than to compensatory mutations. Hence joint application of DCA- and BPPS-based approaches should help sort out the structural and functional constraints contributing to sequence correlations.

  13. Welding sequence effects on residual stress distribution in offshore wind monopile structures

    Directory of Open Access Journals (Sweden)

    Ali Mehmanparast


    Full Text Available Residual stresses are often inevitably introduced into the material during the fabrication processes, such as welding, and are known to have significant effects on the subsequent fatigue crack growth behavior of welded structures. In this paper, the importance of welding sequence on residual stress distribution in engineering components has been reviewed. In addition, the findings available in the literature have been used to provide an accurate interpretation of the fatigue crack growth data on specimens extracted from the welded plates employed in offshore wind monopile structures. The results have been discussed in terms of the role of welding sequence in damage inspection and structural integrity assessment of offshore renewable energy structures.

  14. Sequence and secondary structure of the mitochondrial 16S ribosomal RNA gene of Ixodes scapularis. (United States)

    Krakowetz, Chantel N; Chilton, Neil B


    The complete DNA sequences and secondary structure of the mitochondrial (mt) 16S ribosomal (r) RNA gene were determined for six Ixodes scapularis adults. There were 44 variable nucleotide positions in the 1252 bp sequence alignment. Most (95%) nucleotide alterations did not affect the integrity of the secondary structure of the gene because they either occurred at unpaired positions or represented compensatory changes that maintained the base pairing in helices. A large proportion (75%) of the intraspecific variation in DNA sequence occurred within Domains I, II and VI of the 16S gene. Therefore, several regions within this gene may be highly informative for studies of the population genetics and phylogeography of I. scapularis, a major vector of pathogens of humans and domestic animals in North America.

  15. The Structure of a Bernoulli Process Variation of the Fibonacci Sequence

    CERN Document Server

    Benson, Brian A


    We consider the structure of a variation of the Fibonacci sequence which is determined by a Bernoulli process. The associated structure of all Bernoulli variations of the Fibonacci sequence can be represented by a directed binary tree, which we denote X, with vertex labels representing the specific state of the recurrence variation. Since X is a binary tree, we can consider the term of a sequence variation given by a finite traversal of X represented by a binary code t. We then prove that the traversal of X that is the reflection of the digits of t gives exactly the integer term corresponding to t. We consider how to further this result with the statement of an additional conjecture. Finally, we give connections to Fibonacci expansions, the Stern-Brocot tree, and we apply our methods to the Three Hat Problem as seen in ``Puzzle Corner'' of the ``Technology Review'' magazine.

  16. Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC. (United States)

    Robeyns, Koen; Herdewijn, Piet; Van Meervelt, Luc


    CeNA oligonucleotides consist of a phosphorylated backbone where the deoxyribose sugars are replaced by cyclohexene moieties. The X-ray structure determination and analysis of a fully modified octamer sequence GTGTACAC, which is the first crystal structure of a carbocyclic-based nucleic acid, is presented. This particular sequence was built with left-handed building blocks and crystallizes as a left-handed double helix. The helix can be characterized as belonging to the (mirrored) A-type family. Crystallographic data were processed up to 1.53 A, and the octamer sequence crystallizes in the space group R32. The sugar puckering is found to adopt the 3H2 half-chair conformation which mimics the C3'-endo conformation of the ribose sugar. The double helices stack on top of each other to form continuous helices, and static disorder is observed due to this end-to-end stacking.


    Institute of Scientific and Technical Information of China (English)

    CHEN Xiaonong; HU Liping; YAN Baozhen; JIAO Shuke


    The quantitative description of the sequence structure of emulsion-processed SBR and solution-processed SBR (by lithium catalyst)was carried out based on their spectral data of 13C-NMR.The calculating formulae which could be used to obtain diad concentration from the peak intensities of carbon spectra, average block length, average number of block, and the microstructure composition of the molecular chain were derived. The quantitative result showed that on the molecular chain styrene unit had the tendency to attach to trans-1,4 butadiene unit. The calculated result of the microstructure was in good agreement with that obtained through IR measurement.

  18. Didactical Structures as an Outcome of Research on Teaching-Learning Sequences? Special Issue (United States)

    Lijnse, Piet; Klaassen, Kees


    This paper describes 'didactical structures' as a possible outcome of research on teaching-learning sequences. Starting from an explicit didactical perspective, in this case a so-called problem-posing approach, the research emphasis lies on the didactical quality with which this particular perspective can be put into classroom practice in the…

  19. Community structure of arbuscular mycorrhizal fungi in undisturbed vegetation revealed by analyses of LSU rdna sequences

    DEFF Research Database (Denmark)

    Rosendahl, Søren; Holtgrewe-Stukenbrock, Eva


    Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with plant roots and are found in most ecosystems. In this study the community structure of AMF in a clade of the genus Glomus was examined in undisturbed costal grassland using LSU rDNA sequences amplified from roots of Hieracium pi...

  20. Homogenization of 1D and 2D magnetoelastic lattices

    Directory of Open Access Journals (Sweden)

    Schaeffer Marshall


    Full Text Available This paper investigates the equivalent in-plane mechanical properties of one dimensional (1D and two dimensional (2D, periodic magneto-elastic lattices. A lumped parameter model describes the lattices using magnetic dipole moments in combination with axial and torsional springs. The homogenization procedure is applied to systems linearized about stable configurations, which are identified by minimizing potential energy. Simple algebraic expressions are derived for the properties of 1D structures. Results for 1D lattices show that a variety of stiffness changes are possible through reconfiguration, and that magnetization can either stiffen or soften a structure. Results for 2D hexagonal and re-entrant lattices show that both reconfigurations and magnetization have drastic effects on the mechanical properties of lattice structures. Lattices can be stiffened or softened and the Poisson’s ratio can be tuned. Furthermore for certain hexagonal lattices the sign of Poisson’s ratio can change by varying the lattice magnetization. In some cases presented, analytical and numerically estimated equivalent properties are validated through numerical simulations that also illustrate the unique characteristics of the investigated configurations.

  1. Phosphorylation-Dependent PIH1D1 Interactions Define Substrate Specificity of the R2TP Cochaperone Complex

    Directory of Open Access Journals (Sweden)

    Zuzana Hořejší


    Full Text Available The R2TP cochaperone complex plays a critical role in the assembly of multisubunit machines, including small nucleolar ribonucleoproteins (snoRNPs, RNA polymerase II, and the mTORC1 and SMG1 kinase complexes, but the molecular basis of substrate recognition remains unclear. Here, we describe a phosphopeptide binding domain (PIH-N in the PIH1D1 subunit of the R2TP complex that preferentially binds to highly acidic phosphorylated proteins. A cocrystal structure of a PIH-N domain/TEL2 phosphopeptide complex reveals a highly specific phosphopeptide recognition mechanism in which Lys57 and 64 in PIH1D1, along with a conserved DpSDD phosphopeptide motif within TEL2, are essential and sufficient for binding. Proteomic analysis of PIH1D1 interactors identified R2TP complex substrates that are recruited by the PIH-N domain in a sequence-specific and phosphorylation-dependent manner suggestive of a common mechanism of substrate recognition. We propose that protein complexes assembled by the R2TP complex are defined by phosphorylation of a specific motif and recognition by the PIH1D1 subunit.

  2. WebScipio: An online tool for the determination of gene structures using protein sequences

    Directory of Open Access Journals (Sweden)

    Waack Stephan


    Full Text Available Abstract Background Obtaining the gene structure for a given protein encoding gene is an important step in many analyses. A software suited for this task should be readily accessible, accurate, easy to handle and should provide the user with a coherent representation of the most probable gene structure. It should be rigorous enough to optimise features on the level of single bases and at the same time flexible enough to allow for cross-species searches. Results WebScipio, a web interface to the Scipio software, allows a user to obtain the corresponding coding sequence structure of a here given a query protein sequence that belongs to an already assembled eukaryotic genome. The resulting gene structure is presented in various human readable formats like a schematic representation, and a detailed alignment of the query and the target sequence highlighting any discrepancies. WebScipio can also be used to identify and characterise the gene structures of homologs in related organisms. In addition, it offers a web service for integration with other programs. Conclusion WebScipio is a tool that allows users to get a high-quality gene structure prediction from a protein query. It offers more than 250 eukaryotic genomes that can be searched and produces predictions that are close to what can be achieved by manual annotation, for in-species and cross-species searches alike. WebScipio is freely accessible at

  3. YORP torques with 1D thermal model

    CERN Document Server

    Breiter, Slawomir; Czekaj, Maria


    A numerical model of the Yarkovsky-O'Keefe-Radzievskii-Paddack (YORP) effect for objects defined in terms of a triangular mesh is described. The algorithm requires that each surface triangle can be handled independently, which implies the use of a 1D thermal model. Insolation of each triangle is determined by an optimized ray-triangle intersection search. Surface temperature is modeled with a spectral approach; imposing a quasi-periodic solution we replace heat conduction equation by the Helmholtz equation. Nonlinear boundary conditions are handled by an iterative, FFT based solver. The results resolve the question of the YORP effect in rotation rate independence on conductivity within the nonlinear 1D thermal model regardless of the accuracy issues and homogeneity assumptions. A seasonal YORP effect in attitude is revealed for objects moving on elliptic orbits when a nonlinear thermal model is used.

  4. Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure. (United States)

    Marsh, Joseph A; Teichmann, Sarah A


    Protein structure is dynamic: the intrinsic flexibility of polypeptides facilitates a range of conformational fluctuations, and individual protein chains can assemble into complexes. Proteins are also dynamic in evolution: significant variations in secondary, tertiary and quaternary structure can be observed among divergent members of a protein family. Recent work has highlighted intriguing similarities between these structural and evolutionary dynamics occurring at various levels. Here we review evidence showing how evolutionary changes in protein sequence and structure are often closely related to local protein flexibility and disorder, large-scale motions and quaternary structure assembly. We suggest that these correspondences can be largely explained by neutral evolution, while deviations between structural and evolutionary dynamics can provide valuable functional insights. Finally, we address future prospects for the field and practical applications that arise from a deeper understanding of the intimate relationship between protein structure, dynamics, function and evolution.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.


    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.

  6. Galaxy Structure as a Driver of the Star Formation Sequence Slope and Scatter (United States)

    Whitaker, Katherine E.; 3D-HST Collaboration


    It is well established that (1) star-forming galaxies follow a relation between their star formation rate (SFR) and stellar mass (M*), the "star formation sequence," and (2) the SFRs of galaxies correlate with their structure, where star-forming galaxies are less concentrated than quiescent galaxies at fixed mass. In this talk, we consider whether the scatter and slope of the star formation sequence is correlated with systematic variations in the Sérsic indices, n, of galaxies across the SFR-M* plane. Using a mass-complete sample of 23,848 galaxies at 0.5 3D-HST photometric catalogs, we find that the scatter of the star formation sequence is related in part to galaxy structure; the scatter due to variations in n at fixed mass for star-forming galaxies ranges from 0.14 ± 0.02 dex at z ˜ 2 to 0.30 ± 0.04 dex at z unity for disk-like galaxies, galaxies with n > 2 (implying more dominant bulges) have significantly lower SFR/M* than the main ridgeline of the star formation sequence. These results suggest that bulges in massive z ˜ 2 galaxies are actively building up, where the stars in the central concentration are relatively young. At z < 1, the presence of older bulges within star-forming galaxies lowers global SFR/M*, decreasing the slope and contributing significantly to the scatter of the star formation sequence.

  7. SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

    Directory of Open Access Journals (Sweden)

    Steven N Hart

    Full Text Available BACKGROUND: Structural variation (SV represents a significant, yet poorly understood contribution to an individual's genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints. RESULTS: We developed and validated SoftSearch using real and synthetic datasets. SoftSearch's key features are 1 not requiring secondary (or exhaustive primary alignment, 2 portability into established sequencing workflows, and 3 is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.. SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call. CONCLUSIONS: We show that SoftSearch can identify more true SVs by combining multiple sequence features. SoftSearch was able to call clinically relevant SVs in the BRCA2 gene not reported by other tools while offering significantly improved overall performance.

  8. The nucleotide sequence and genome structure of mung bean yellow mosaic geminivirus. (United States)

    Morinaga, T; Ikegami, M; Miura, K


    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.

  9. Structure-based identification of new high-affinity nucleosome binding sequences. (United States)

    Battistini, Federica; Hunter, Christopher A; Moore, Irene K; Widom, Jonathan


    The substrate for the proteins that express genetic information in the cell is not naked DNA but an assembly of nucleosomes, where the DNA is wrapped around histone proteins. The organization of these nucleosomes on genomic DNA is influenced by the DNA sequence. Here, we present a structure-based computational approach that translates sequence information into the energy required to bend DNA into a nucleosome-bound conformation. The calculations establish the relationship between DNA sequence and histone octamer binding affinity. In silico selection using this model identified several new DNA sequences, which were experimentally found to have histone octamer affinities comparable to the highest-affinity sequences known. The results provide insights into the molecular mechanism through which DNA sequence information encodes its organization. A quantitative appreciation of the thermodynamics of nucleosome positioning and rearrangement will be one of the key factors in understanding the regulation of transcription and in the design of new promoter architectures for the purposes of tuning gene expression dynamics.

  10. Role of sequence and structural polymorphism on the mechanical properties of amyloid fibrils.

    Directory of Open Access Journals (Sweden)

    Gwonchan Yoon

    Full Text Available Amyloid fibrils playing a critical role in disease expression, have recently been found to exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is comparable to that of other mechanical proteins such as microtubule, actin filament, and spider silk. These remarkable mechanical properties of amyloid fibrils are correlated with their functional role in disease expression. This suggests the importance in understanding how these excellent mechanical properties are originated through self-assembly process that may depend on the amino acid sequence. However, the sequence-structure-property relationship of amyloid fibrils has not been fully understood yet. In this work, we characterize the mechanical properties of human islet amyloid polypeptide (hIAPP fibrils with respect to their molecular structures as well as their amino acid sequence by using all-atom explicit water molecular dynamics (MD simulation. The simulation result suggests that the remarkable bending rigidity of amyloid fibrils can be achieved through a specific self-aggregation pattern such as antiparallel stacking of β strands (peptide chain. Moreover, we have shown that a single point mutation of hIAPP chain constituting a hIAPP fibril significantly affects the thermodynamic stability of hIAPP fibril formed by parallel stacking of peptide chain, and that a single point mutation results in a significant change in the bending rigidity of hIAPP fibrils formed by antiparallel stacking of β strands. This clearly elucidates the role of amino acid sequence on not only the equilibrium conformations of amyloid fibrils but also their mechanical properties. Our study sheds light on sequence-structure-property relationships of amyloid fibrils, which suggests that the mechanical properties of amyloid fibrils are encoded in their sequence-dependent molecular architecture.

  11. Synthesis, Crystal Structural Characterization and Electrochemical Properties of a 1D Tape-like Polymer of Cobalt Adamantanedicarboxylate: [Co_2(adc)_2(py)_4(H_2O)]_n

    Institute of Scientific and Technical Information of China (English)

    LI Hong-Mei; XIONG Hong-Bo; LUO Geng-Geng; DAI Jing-Cao


    The new complex, [Co2(adc)2(py)4(H2O)}n 1 (adc = 1,3-adamantanedicarboxylate, py = pyridine), has been hydrothermally synthesized as polymeric solid, and characterized by X-ray diffraction, elemental analysis, IR spectra and thermogravimetric analysis. Complex 1 crystallizes in monoclinic, space group C2/c with a = 18.932(4), b = 19.779(4), c = 12.352(3) , β = 112.03(3)o, V = 4288(2) 3, Z = 4, GOF = 0.998, R = 0.0518 and wR = 0.1074. X-ray single-crystal analysis reveals that 1 presents a 3D simple parallel rod-like supramolecular array constructed by 1D tape-like polymeric motif through aromatic π-π stacking interaction. Electrochemical investigation shows that 1 exhibits appreciable electrocatalytic activity for the reduction reaction of nitrite.

  12. The molecular basis for recognition of CD1d/α-galactosylceramide by a human non-Vα24 T cell receptor.

    Directory of Open Access Journals (Sweden)

    Jacinto López-Sagaseta

    Full Text Available CD1d-mediated presentation of glycolipid antigens to T cells is capable of initiating powerful immune responses that can have a beneficial impact on many diseases. Molecular analyses have recently detailed the lipid antigen recognition strategies utilized by the invariant Vα24-Jα18 TCR rearrangements of iNKT cells, which comprise a subset of the human CD1d-restricted T cell population. In contrast, little is known about how lipid antigens are recognized by functionally distinct CD1d-restricted T cells bearing different TCRα chain rearrangements. Here we present crystallographic and biophysical analyses of α-galactosylceramide (α-GalCer recognition by a human CD1d-restricted TCR that utilizes a Vα3.1-Jα18 rearrangement and displays a more restricted specificity for α-linked glycolipids than that of iNKT TCRs. Despite having sequence divergence in the CDR1α and CDR2α loops, this TCR employs a convergent recognition strategy to engage CD1d/αGalCer, with a binding affinity (∼2 µM almost identical to that of an iNKT TCR used in this study. The CDR3α loop, similar in sequence to iNKT-TCRs, engages CD1d/αGalCer in a similar position as that seen with iNKT-TCRs, however fewer actual contacts are made. Instead, the CDR1α loop contributes important contacts to CD1d/αGalCer, with an emphasis on the 4'OH of the galactose headgroup. This is consistent with the inability of Vα24- T cells to respond to α-glucosylceramide, which differs from αGalCer in the position of the 4'OH. These data illustrate how fine specificity for a lipid containing α-linked galactose is achieved by a TCR structurally distinct from that of iNKT cells.

  13. Training set reduction methods for protein secondary structure prediction in single-sequence condition. (United States)

    Aydin, Zafer; Altunbasak, Yucel; Pakatci, Isa Kemal; Erdogan, Hakan


    Orphan proteins are characterized by the lack of significant sequence similarity to database proteins. To infer the functional properties of the orphans, more elaborate techniques that utilize structural information are required. In this regard, the protein structure prediction gains considerable importance. Secondary structure prediction algorithms designed for orphan proteins (also known as single-sequence algorithms) cannot utilize multiple alignments or alignment profiles, which are derived from similar proteins. This is a limiting factor for the prediction accuracy. One way to improve the performance of a single-sequence algorithm is to perform re-training. In this approach, first, the models used by the algorithm are trained by a representative set of proteins and a secondary structure prediction is computed. Then, using a distance measure, the original training set is refined by removing proteins that are dissimilar to the given protein. This step is followed by the re-estimation of the model parameters and the prediction of the secondary structure. In this paper, we compare training set reduction methods that are used to re-train the hidden semi-Markov models employed by the IPSSP algorithm [1]. We found that the composition based reduction method has the highest performance compared to the alignment based and the Chou-Fasman based reduction methods. In addition, threshold-based reduction performed better than the reduction technique that selects the first 80% of the dataset proteins.

  14. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

    Directory of Open Access Journals (Sweden)

    John A Capra


    Full Text Available Identifying a protein's functional sites is an important step towards characterizing its molecular function. Numerous structure- and sequence-based methods have been developed for this problem. Here we introduce ConCavity, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. In large-scale testing on a diverse set of single- and multi-chain protein structures, we show that ConCavity substantially outperforms existing methods for identifying both 3D ligand binding pockets and individual ligand binding residues. As part of our testing, we perform one of the first direct comparisons of conservation-based and structure-based methods. We find that the two approaches provide largely complementary information, which can be combined to improve upon either approach alone. We also demonstrate that ConCavity has state-of-the-art performance in predicting catalytic sites and drug binding pockets. Overall, the algorithms and analysis presented here significantly improve our ability to identify ligand binding sites and further advance our understanding of the relationship between evolutionary sequence conservation and structural and functional attributes of proteins. Data, source code, and prediction visualizations are available on the ConCavity web site (

  15. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. (United States)

    Capra, John A; Laskowski, Roman A; Thornton, Janet M; Singh, Mona; Funkhouser, Thomas A


    Identifying a protein's functional sites is an important step towards characterizing its molecular function. Numerous structure- and sequence-based methods have been developed for this problem. Here we introduce ConCavity, a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. In large-scale testing on a diverse set of single- and multi-chain protein structures, we show that ConCavity substantially outperforms existing methods for identifying both 3D ligand binding pockets and individual ligand binding residues. As part of our testing, we perform one of the first direct comparisons of conservation-based and structure-based methods. We find that the two approaches provide largely complementary information, which can be combined to improve upon either approach alone. We also demonstrate that ConCavity has state-of-the-art performance in predicting catalytic sites and drug binding pockets. Overall, the algorithms and analysis presented here significantly improve our ability to identify ligand binding sites and further advance our understanding of the relationship between evolutionary sequence conservation and structural and functional attributes of proteins. Data, source code, and prediction visualizations are available on the ConCavity web site (

  16. Bayesian segmental models with multiple sequence alignment profiles for protein secondary structure and contact map prediction. (United States)

    Chu, Wei; Ghahramani, Zoubin; Podtelezhnikov, Alexei; Wild, David L


    In this paper, we develop a segmental semi-Markov model (SSMM) for protein secondary structure prediction which incorporates multiple sequence alignment profiles with the purpose of improving the predictive performance. The segmental model is a generalization of the hidden Markov model where a hidden state generates segments of various length and secondary structure type. A novel parameterized model is proposed for the likelihood function that explicitly represents multiple sequence alignment profiles to capture the segmental conformation. Numerical results on benchmark data sets show that incorporating the profiles results in substantial improvements and the generalization performance is promising. By incorporating the information from long range interactions in beta-sheets, this model is also capable of carrying out inference on contact maps. This is an important advantage of probabilistic generative models over the traditional discriminative approach to protein secondary structure prediction. The Web server of our algorithm and supplementary materials are available at

  17. Inferring the Clonal Structure of Viral Populations from Time Series Sequencing.

    Directory of Open Access Journals (Sweden)

    Donatien F Chedom


    Full Text Available RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We would like to identify the underlying evolutionary structures. We utilize two sources of information to attempt this; within segment linkage information, and mutation prevalence. We demonstrate that clone haplotypes, their prevalence, and maximum parsimony reticulate evolutionary structures can be identified, although the solutions may not be unique, even for complete sets of information. This is applied to a chain of influenza infection, where we infer evolutionary structures, including reassortment, and demonstrate some of the difficulties of interpretation that arise from deep sequencing due to artifacts such as template switching during PCR amplification.

  18. Selective Sequence for the Peptide-Triggered Phase Transition of Lyotropic Liquid-Crystalline Structures. (United States)

    Liu, Qingtao; Dong, Yao-Da; Boyd, Ben J


    A novel concept of using mixed lipids to construct selective peptide-sequence-sensing lyotropic liquid-crystalline (LLC) dispersion systems was investigated. The LLC systems were constructed using a mixture of phytantriol, a lipid that forms lyotropic liquid-crystalline phases, and a novel synthesized peptide-lipid (peplipid) for sensing a target peptide with the RARAR sequence. The internal structure of the dispersed LLC particles was converted from the lamellar structure (liposomes) to the inverse bicontinuous cubic phase (cubosomes) in the presence of the target peptide. The addition of common human proteins did not induce any structural change, indicating a high selectivity of interaction with the target peptide. The concept has potential for the design of targeted controlled release drug delivery agents.

  19. Secondary structure, a missing component of sequence-based minimotif definitions.

    Directory of Open Access Journals (Sweden)

    David P Sargeant

    Full Text Available Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis of occurrences of minimotifs in structured and disordered regions of proteins, and review of the literature support a new model for minimotif definitions that includes sequence, structure, and function.

  20. Inferring Aftershock Sequence Properties and Tectonic Structure Using Empirical Signal Detectors (United States)

    Junek, William N.; Kværna, Tormod; Pirli, Myrto; Schweitzer, Johannes; Harris, David B.; Dodge, Douglas A.; Woods, Mark T.


    Seismotectonic studies of the 2008 Storfjorden aftershock sequence were limited to data acquired by the permanent, but sparse, regional seismic network in the Svalbard archipelago. Storfjorden's remote location and harsh polar environment inhibited deployment of temporary seismometers that would have improved observations of sequence events. The lack of good station coverage prevented the detection and computation of hypocenter locations of many low magnitude events (mb < 2.5) in the NORSAR analyst-reviewed bulletin. As a result, the fine structure of the sequence's space-time distribution was not captured. In this study, an autonomous event detection and clustering framework is employed to build a more complete catalog of Storfjorden events using data from the Spitsbergen (SPITS) array. The new catalog allows the spatiotemporal distribution of seismicity within the fjord to be studied in greater detail. Information regarding the location of active event clusters provides a means of inferring the tectonic structure within the fault zone. The distribution of active clusters and moment tensor solutions for the Storfjorden sequence suggests there are at least two different structures within the fjord: a NE-SW trending linear feature with oblique-normal to strike-slip faulting and E-W trending normal faults.

  1. Evol and ProDy for bridging protein sequence evolution and structural dynamics (United States)

    Mao, Wenzhi; Liu, Ying; Chennubhotla, Chakra; Lezon, Timothy R.; Bahar, Ivet


    Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics. Availability and implementation: ProDy and Evol are open-source and freely available under MIT License from Contact: PMID:24849577

  2. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

    KAUST Repository

    Cui, Xuefeng


    Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. Method: We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence–structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. Results: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM–HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods.

  3. Stem-loop structures of the repetitive DNA sequences located at human centromeres

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, G.; Garcia, A.E.; Ratliff, R.; Moyzis, R.K. [Los Alamos National Lab., NM (United States); Catasti, P.; Hong, Lin; Yau, P. [California Univ., Davis, CA (United States). Dept. of Biological Chemistry; Bradbury, E.M. [Los Alamos National Lab., NM (United States)]|[California Univ., Davis, CA (United States). Dept. of Biological Chemistry


    The presence of the highly conserved repetitive DNA sequences in the human centromeres argues for a special role of these sequences in their biological functions - most likely achieved by the formation of unusual structures. This prompted us to carry out quantitative one- and two-dimensional nuclear magnetic resonance (lD/2D NMR) spectroscopy to determine the structural properties of the human centromeric repeats, d(AATGG){sub n.d}(CCATT){sub n}. The studies on centromeric DNAs reveal that the complementary sequence, d(AATGG){sub n.d}(CCATT){sub n}, adopts the usual Watson-Crick B-DNA duplex and the pyrimidine-rich d(CCATT){sub n} strand is essentially a random coil. However, the purine-rich d(AATGG){sub n} strand is shown to adopt unusual stem-loop structures for repeat lengths, n=2,3,4, and 6. In addition to normal Watson-Crick A{center_dot}T pairs, the stem-loop structures are stabilized by mismatch A{center_dot}G and G{center_dot}G pairs in the stem and G-G-A stacking in the loop. Stem-loop structures of d(AATGG)n are independently verified by gel electrophoresis and nuclease digestion studies. Thermal melting studies show that the DNA repeats, d(AATGG){sub n}, are as stable as the corresponding Watson-Crick duplex d(AATGG){sub n.d}(CCATT){sub n}. Therefore, the sequence d(AATGG){sub n} can, indeed, nucleate a stem-loop structure at little free-energy cost and if, during mitosis, they are located on the chromosome surface they can provide specific recognition sites for kinetochore function.

  4. How the Sequence of a Gene Specifies Structural Symmetry in Proteins.

    Directory of Open Access Journals (Sweden)

    Xiaojuan Shen

    Full Text Available Internal symmetry is commonly observed in the majority of fundamental protein folds. Meanwhile, sufficient evidence suggests that nascent polypeptide chains of proteins have the potential to start the co-translational folding process and this process allows mRNA to contain additional information on protein structure. In this paper, we study the relationship between gene sequences and protein structures from the viewpoint of symmetry to explore how gene sequences code for structural symmetry in proteins. We found that, for a set of two-fold symmetric proteins from left-handed beta-helix fold, intragenic symmetry always exists in their corresponding gene sequences. Meanwhile, codon usage bias and local mRNA structure might be involved in modulating translation speed for the formation of structural symmetry: a major decrease of local codon usage bias in the middle of the codon sequence can be identified as a common feature; and major or consecutive decreases in local mRNA folding energy near the boundaries of the symmetric substructures can also be observed. The results suggest that gene duplication and fusion may be an evolutionarily conserved process for this protein fold. In addition, the usage of rare codons and the formation of higher order of secondary structure near the boundaries of symmetric substructures might have coevolved as conserved mechanisms to slow down translation elongation and to facilitate effective folding of symmetric substructures. These findings provide valuable insights into our understanding of the mechanisms of translation and its evolution, as well as the design of proteins via symmetric modules.

  5. Auslander-Reiten sequences and $t$-structures on the homotopy category of an abelian category

    CERN Document Server

    Backelin, Erik


    Let $\\Cab$ be an abelian category and let $\\KC$ be the bounded homotopy category of cochain complexes in $\\Cab$. We consider a $t$-structure on $\\KC$ that maps to the standard $t$-structure on the derived category $\\DC$ under the localization functor. Let $\\A$ be the heart of the $t$-structure. In the case when $\\Cab$ has finite length we show that objects of $\\Cab$ correspond to projective objects of $\\A$ and that simple objects of $\\A$ (if they exist) are given by Auslander's and Reiten's almost split sequences in $\\Cab$.

  6. The stability of 1-D soliton in transverse direction (United States)

    Verma, Deepa; Bera, Ratan Kumar; Das, Amita; Kaw, Predhiman


    The complete characterization of the exact 1-D solitary wave solutions (both stationary and propagating) for light plasma coupled system have been studied extensively in the parameter space of light frequency and the group speed [Poornakala et al., Phys. Plasmas 9(5), 1820 (2002)]. It has been shown in 1-D that solutions with single light wave peak and paired structures are stable and hence long lived. However, solutions having multiple peaks of light wave are unstable due to Raman scattering instability [Saxena et al., Phys. Plasmas 14, 072307 (2007)]. Here, we have shown with the help of 2-D fluid simulation that single peak and paired solutions too get destabilized by the transverse filamentation instability. The numerical growth rates obtained from simulations is seen to compare well with the analytical values. It is also shown that multiple peaks solitons first undergo the regular 1-D forward Raman scattering instability. Subsequently, they undergo a distinct second phase of destabilization through transverse filamentation instability. This is evident from the structure as well as the plot of the perturbed energy which shows a second phase of growth after saturating initially. The growth rate of the filamentation instability being comparatively slower than the forward Raman instability this phase comes quite late and is clearly distinguishable.

  7. Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures. (United States)

    Koehler, Jacob; Rawlings, Chris; Verrier, Paul; Mitchell, Rowan; Skusa, Andre; Ruegg, Alexander; Philippi, Stephan


    The structure of a closely integrated data warehouse is described that is designed to link different types and varying numbers of biological networks, sequence analysis methods and experimental results such as those coming from microarrays. The data schema is inspired by a combination of graph based methods and generalised data structures and makes use of ontologies and meta-data. The core idea is to consider and store biological networks as graphs, and to use generalised data structures (GDS) for the storage of further relevant information. This is possible because many biological networks can be stored as graphs: protein interactions, signal transduction networks, metabolic pathways, gene regulatory networks etc. Nodes in biological graphs represent entities such as promoters, proteins, genes and transcripts whereas the edges of such graphs specify how the nodes are related. The semantics of the nodes and edges are defined using ontologies of node and relation types. Besides generic attributes that most biological entities possess (name, attribute description), further information is stored using generalised data structures. By directly linking to underlying sequences (exons, introns, promoters, amino acid sequences) in a systematic way, close interoperability to sequence analysis methods can be achieved. This approach allows us to store, query and update a wide variety of biological information in a way that is semantically compact without requiring changes at the database schema level when new kinds of biological information is added. We describe how this datawarehouse is being implemented by extending the text-mining framework ONDEX to link, support and complement different bioinformatics applications and research activities such as microarray analysis, sequence analysis and modelling/simulation of biological systems. The system is developed under the GPL license and can be downloaded from

  8. Synthesis and Crystal Structure of a Novel 1D Chain-like Organic Inorganic Hybrid Rare Earth Derivative of Polyoxometalate: H0.5[Sm(H2O)6]0.25[Sm(H2O)5]0.25{[Sm(H2O)7][Sm(H2O)2- (DMSO)] [SiW11O39]}·4.5H2O

    Institute of Scientific and Technical Information of China (English)

    Jun Wei ZHAO; Jing Ping WANG; Jing Yang NIU


    A 1D chain-like organic-inorganic hybrid rare earth derivative of polyoxometalate (DMSO) and characterized by elemental analysis, IR spectra and single crystal X-ray diffraction.The neighboring polyanionic units {[Sm(H2O)7][Sm(H2O)2(DMSO)][SiW11O39]}2- are bridged together to a 1D chain structure by means of [Sm(H2O)2(DMSO)]3+ ion.

  9. Phase diagram of a bulk 1d lattice Coulomb gas (United States)

    Démery, V.; Monsarrat, R.; Dean, D. S.; Podgornik, R.


    The exact solution, via transfer matrix, of the simple one-dimensional lattice Coulomb gas (1d LCG) model can reproduce peculiar features of ionic liquid capacitors, such as overscreening, layering, and camel- and bell-shaped capacitance curves. Using the same transfer matrix method, we now compute the bulk properties of the 1d LCG in the constant voltage ensemble. We unveil a phase diagram with rich structure exhibiting low-density disordered and high-density ordered phases, separated by a first-order phase transition at low temperature; the solid state at full packing can be ordered or not, depending on the temperature. This phase diagram, which is strikingly similar to its three-dimensional counterpart, also sheds light on the behaviour of the confined system.

  10. Iron-based 1D nanostructures by electrospinning process. (United States)

    Eid, Cynthia; Brioude, Arnaud; Salles, Vincent; Plenet, Jean-Claude; Asmar, Roy; Monteil, Yves; Khoury, Randa; Khoury, Antonio; Miele, Philippe


    Iron-based 1D nanostructures have been successfully prepared using an electrospinning technique and varying the pyrolysis atmospheres. Hematite (Fe(2)O(3)) nanotubes and polycrystalline Fe(3)C nanofibers were obtained by simple air or mixed gas (H(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(2) and Ar) were used for the annealing treatments, for the first time polycrystalline Fe(3)C nanofibers composed of carbon graphitic planes were obtained, ensuring Fe(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.

  11. Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake.

    Directory of Open Access Journals (Sweden)

    Qingping Xu

    Full Text Available Imelysin-like proteins define a superfamily of bacterial proteins that are likely involved in iron uptake. Members of this superfamily were previously thought to be peptidases and were included in the MEROPS family M75. We determined the first crystal structures of two remotely related, imelysin-like proteins. The Psychrobacter arcticus structure was determined at 2.15 Å resolution and contains the canonical imelysin fold, while higher resolution structures from the gut bacteria Bacteroides ovatus, in two crystal forms (at 1.25 Å and 1.44 Å resolution, have a circularly permuted topology. Both structures are highly similar to each other despite low sequence similarity and circular permutation. The all-helical structure can be divided into two similar four-helix bundle domains. The overall structure and the GxHxxE motif region differ from known HxxE metallopeptidases, suggesting that imelysin-like proteins are not peptidases. A putative functional site is located at the domain interface. We have now organized the known homologous proteins into a superfamily, which can be separated into four families. These families share a similar functional site, but each has family-specific structural and sequence features. These results indicate that imelysin-like proteins have evolved from a common ancestor, and likely have a conserved function.

  12. 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.

  13. Genome sequence, comparative analysis and haplotype structure of the domestic dog. (United States)

    Lindblad-Toh, Kerstin; Wade, Claire M; Mikkelsen, Tarjei S; Karlsson, Elinor K; Jaffe, David B; Kamal, Michael; Clamp, Michele; Chang, Jean L; Kulbokas, Edward J; Zody, Michael C; Mauceli, Evan; Xie, Xiaohui; Breen, Matthew; Wayne, Robert K; Ostrander, Elaine A; Ponting, Chris P; Galibert, Francis; Smith, Douglas R; DeJong, Pieter J; Kirkness, Ewen; Alvarez, Pablo; Biagi, Tara; Brockman, William; Butler, Jonathan; Chin, Chee-Wye; Cook, April; Cuff, James; Daly, Mark J; DeCaprio, David; Gnerre, Sante; Grabherr, Manfred; Kellis, Manolis; Kleber, Michael; Bardeleben, Carolyne; Goodstadt, Leo; Heger, Andreas; Hitte, Christophe; Kim, Lisa; Koepfli, Klaus-Peter; Parker, Heidi G; Pollinger, John P; Searle, Stephen M J; Sutter, Nathan B; Thomas, Rachael; Webber, Caleb; Baldwin, Jennifer; Abebe, Adal; Abouelleil, Amr; Aftuck, Lynne; Ait-Zahra, Mostafa; Aldredge, Tyler; Allen, Nicole; An, Peter; Anderson, Scott; Antoine, Claudel; Arachchi, Harindra; Aslam, Ali; Ayotte, Laura; Bachantsang, Pasang; Barry, Andrew; Bayul, Tashi; Benamara, Mostafa; Berlin, Aaron; Bessette, Daniel; Blitshteyn, Berta; Bloom, Toby; Blye, Jason; Boguslavskiy, Leonid; Bonnet, Claude; Boukhgalter, Boris; Brown, Adam; Cahill, Patrick; Calixte, Nadia; Camarata, Jody; Cheshatsang, Yama; Chu, Jeffrey; Citroen, Mieke; Collymore, Alville; Cooke, Patrick; Dawoe, Tenzin; Daza, Riza; Decktor, Karin; DeGray, Stuart; Dhargay, Norbu; Dooley, Kimberly; Dooley, Kathleen; Dorje, Passang; Dorjee, Kunsang; Dorris, Lester; Duffey, Noah; Dupes, Alan; Egbiremolen, Osebhajajeme; Elong, Richard; Falk, Jill; Farina, Abderrahim; Faro, Susan; Ferguson, Diallo; Ferreira, Patricia; Fisher, Sheila; FitzGerald, Mike; Foley, Karen; Foley, Chelsea; Franke, Alicia; Friedrich, Dennis; Gage, Diane; Garber, Manuel; Gearin, Gary; Giannoukos, Georgia; Goode, Tina; Goyette, Audra; Graham, Joseph; Grandbois, Edward; Gyaltsen, Kunsang; Hafez, Nabil; Hagopian, Daniel; Hagos, Birhane; Hall, Jennifer; Healy, Claire; Hegarty, Ryan; Honan, Tracey; Horn, Andrea; Houde, Nathan; Hughes, Leanne; Hunnicutt, Leigh; Husby, M; Jester, Benjamin; Jones, Charlien; Kamat, Asha; Kanga, Ben; Kells, Cristyn; Khazanovich, Dmitry; Kieu, Alix Chinh; Kisner, Peter; Kumar, Mayank; Lance, Krista; Landers, Thomas; Lara, Marcia; Lee, William; Leger, Jean-Pierre; Lennon, Niall; Leuper, Lisa; LeVine, Sarah; Liu, Jinlei; Liu, Xiaohong; Lokyitsang, Yeshi; Lokyitsang, Tashi; Lui, Annie; Macdonald, Jan; Major, John; Marabella, Richard; Maru, Kebede; Matthews, Charles; McDonough, Susan; Mehta, Teena; Meldrim, James; Melnikov, Alexandre; Meneus, Louis; Mihalev, Atanas; Mihova, Tanya; Miller, Karen; Mittelman, Rachel; Mlenga, Valentine; Mulrain, Leonidas; Munson, Glen; Navidi, Adam; Naylor, Jerome; Nguyen, Tuyen; Nguyen, Nga; Nguyen, Cindy; Nguyen, Thu; Nicol, Robert; Norbu, Nyima; Norbu, Choe; Novod, Nathaniel; Nyima, Tenchoe; Olandt, Peter; O'Neill, Barry; O'Neill, Keith; Osman, Sahal; Oyono, Lucien; Patti, Christopher; Perrin, Danielle; Phunkhang, Pema; Pierre, Fritz; Priest, Margaret; Rachupka, Anthony; Raghuraman, Sujaa; Rameau, Rayale; Ray, Verneda; Raymond, Christina; Rege, Filip; Rise, Cecil; Rogers, Julie; Rogov, Peter; Sahalie, Julie; Settipalli, Sampath; Sharpe, Theodore; Shea, Terrance; Sheehan, Mechele; Sherpa, Ngawang; Shi, Jianying; Shih, Diana; Sloan, Jessie; Smith, Cherylyn; Sparrow, Todd; Stalker, John; Stange-Thomann, Nicole; Stavropoulos, Sharon; Stone, Catherine; Stone, Sabrina; Sykes, Sean; Tchuinga, Pierre; Tenzing, Pema; Tesfaye, Senait; Thoulutsang, Dawa; Thoulutsang, Yama; Topham, Kerri; Topping, Ira; Tsamla, Tsamla; Vassiliev, Helen; Venkataraman, Vijay; Vo, Andy; Wangchuk, Tsering; Wangdi, Tsering; Weiand, Michael; Wilkinson, Jane; Wilson, Adam; Yadav, Shailendra; Yang, Shuli; Yang, Xiaoping; Young, Geneva; Yu, Qing; Zainoun, Joanne; Zembek, Lisa; Zimmer, Andrew; Lander, Eric S


    Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

  14. Optical properties of structures composed of periodic, quasi-periodic, and aperiodic sequences of particulate monolayers (United States)

    Loiko, V. A.; Miskevich, A. A.


    The spectra of the coherent transmission and reflection coefficients of multilayers consisting of the periodic, Fibonacci (quasi-periodic), and Thue-Morse (aperiodic) sequences of plane-parallel monolayers of monodisperse spherical alumina and silica particles are investigated using the quasi-crystalline approximation (QCA) and the transfer matrix method (TMM). The additional opportunities for the transmission and reflection spectra manipulation in comparison with the periodic sequence of monolayers are demonstrated. Photonic band gaps in the spectra of the particulate structures are shifted to the short-wavelength range in comparison with those for systems of homogeneous layers. The shift is larger for the Thue-Morse sequence. The widths of the photonic band gaps for particulate systems are narrower than the ones for multilayers consisting of homogeneous layers of an equivalent volume of matter. The results can be used to create optical, optoelectronics, and photonics devices—for example, multispectral filters, light emitting diodes, solar cells, displays.

  15. Multi-scale coding of genomic information: From DNA sequence to genome structure and function

    Energy Technology Data Exchange (ETDEWEB)

    Arneodo, Alain, E-mail: alain.arneodo@ens-lyon.f [Universite de Lyon, F-69000 Lyon (France); Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS, Ecole Normale Superieure de Lyon, F-69007 Lyon (France); Vaillant, Cedric, E-mail: cedric.vaillant@ens-lyon.f [Universite de Lyon, F-69000 Lyon (France); Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS, Ecole Normale Superieure de Lyon, F-69007 Lyon (France); Audit, Benjamin, E-mail: benjamin.audit@ens-lyon.f [Universite de Lyon, F-69000 Lyon (France); Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS, Ecole Normale Superieure de Lyon, F-69007 Lyon (France); Argoul, Francoise, E-mail: francoise.argoul@ens-lyon.f [Universite de Lyon, F-69000 Lyon (France); Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS, Ecole Normale Superieure de Lyon, F-69007 Lyon (France); D' Aubenton-Carafa, Yves, E-mail: daubenton@cgm.cnrs-gif.f [Centre de Genetique Moleculaire, CNRS, Allee de la Terrasse, 91198 Gif-sur-Yvette (France); Thermes, Claude, E-mail: claude.thermes@cgm.cnrs-gif.f [Centre de Genetique Moleculaire, CNRS, Allee de la Terrasse, 91198 Gif-sur-Yvette (France)


    Understanding how chromatin is spatially and dynamically organized in the nucleus of eukaryotic cells and how this affects genome functions is one of the main challenges of cell biology. Since the different orders of packaging in the hierarchical organization of DNA condition the accessibility of DNA sequence elements to trans-acting factors that control the transcription and replication processes, there is actually a wealth of structural and dynamical information to learn in the primary DNA sequence. In this review, we show that when using concepts, methodologies, numerical and experimental techniques coming from statistical mechanics and nonlinear physics combined with wavelet-based multi-scale signal processing, we are able to decipher the multi-scale sequence encoding of chromatin condensation-decondensation mechanisms that play a fundamental role in regulating many molecular processes involved in nuclear functions.

  16. 3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale (United States)

    Mazzocco, Giovanni; Lazniewski, Michal; Migdał, Piotr; Szczepińska, Teresa; Radomski, Jan P.; Plewczynski, Dariusz


    The influenza virus type A (IVA) is an important pathogen which is able to cause annual epidemics and even pandemics. This fact is the consequence of the antigenic shifts and drifts capabilities of IVA, caused by the high mutation rate and the reassortment capabilities of the virus. The hemagglutinin (HA) protein constitutes the main IVA antigen and has a crucial role in the infection mechanism, being responsible for the recognition of host-specific sialic acid derivatives. Despite the relative abundance of HA sequence and serological studies, comparative structure-based analysis of HA are less investigated. The 3DFlu database contains well annotated HA representatives: 1192 models and 263 crystallographic structures. The relations between these proteins are defined using different metrics and are visualized as a network in the provided web interface. Moreover structural and sequence comparison of the proteins can be explored. Metadata information (e.g. protein identifier, IVA strain, year and location of infection) can enhance the exploration of the presented data. With our database researchers gain a useful tool for the exploration of high quality HA models, viewing and comparing changes in the HA viral subtypes at several information levels (sequence, structure, ESP). The complete and integrated view of those relations might be useful to determine the efficiency of transmission, pathogenicity and for the investigation of evolutionary tendencies of the influenza virus. Database URL: PMID:27694207

  17. Identification of selectivity determinants in CYP monooxygenases by modelling and systematic analysis of sequence and structure. (United States)

    Seifert, Alexander; Pleiss, Jurgen


    Cytochrome P450 monooxygenases (CYPs) form a large, ubiquitous enzyme family and are of great interest in red and white biotechnology. To investigate the effect of protein structure on selectivity, the binding of substrate molecules near to the active site was modelled by molecular dynamics simulations. From a comprehensive and systematic comparison of more than 6300 CYP sequences and 31 structures using the Cytochrome P450 Engineering Database (CYPED), residues were identified which are predicted to point close to the heme centre and thus restrict accessibility for substrates. As a result, sequence-structure-function relationships are described that can be used to predict selectivity-determining positions from CYP sequences and structures. Based on this analysis, a minimal library consisting of bacterial CYP102A1 (P450(BM3)) and 24 variants was constructed. All variants were functionally expressed in E. coli, and the library was screened with four terpene substrates. Only 3 variants showed no activity towards all 4 terpenes, while 11 variants demonstrated either a strong shift or improved regio- or stereoselectivity during oxidation of at least one substrate as compared to CYP102A1 wild type. The minimal library also contains variants that show interesting side products which are not generated by the wild type enzyme. By two additional rounds of molecular modelling, diversification, and screening, the selectivity of one of these variants for a new product was optimised with a minimal screening effort. We propose this as a generic approach for other CYP substrates.


    Energy Technology Data Exchange (ETDEWEB)



    We present a new hybrid Monte Carlo method for 1-D equilibrium diffusion problems in which the radiation field coexists with matter in local thermodynamic equilibrium. This method, the Equilibrium Discrete Diffusion Monte Carlo (EqDDMC) method, combines Monte Carlo particles with spatially discrete diffusion solutions. We verify the EqDDMC method with computational results from three slab problems. The EqDDMC method represents an incremental step toward applying this hybrid methodology to non-equilibrium diffusion, where it could be simultaneously coupled to Monte Carlo transport.

  19. Molecular characterization of zebrafish Oatp1d1 (Slco1d1), a novel organic anion-transporting polypeptide. (United States)

    Popovic, Marta; Zaja, Roko; Fent, Karl; Smital, Tvrtko


    The organic anion-transporting polypeptide (OATP/Oatp) superfamily includes a group of polyspecific transporters that mediate transport of large amphipathic, mostly anionic molecules across cell membranes of eukaryotes. OATPs/Oatps are involved in the disposition and elimination of numerous physiological and foreign compounds. However, in non-mammalian species, the functional properties of Oatps remain unknown. We aimed to elucidate the role of Oatp1d1 in zebrafish to gain insights into the functional and structural evolution of the OATP1/Oatp1 superfamily. We show that diversification of the OATP1/Oatp1 family occurs after the emergence of jawed fish and that the OATP1A/Oatp1a and OATP1B/Oatp1b subfamilies appeared at the root of tetrapods. The Oatp1d subfamily emerged in teleosts and is absent in tetrapods. The zebrafish Oatp1d1 is similar to mammalian OATP1A/Oatp1a and OATP1B/Oatp1b members, with the main physiological role in transport and balance of steroid hormones. Oatp1d1 activity is dependent upon pH gradient, which could indicate bicarbonate exchange as a mode of transport. Our analysis of evolutionary conservation and structural properties revealed that (i) His-79 in intracellular loop 3 is conserved within OATP1/Oatp1 family and is crucial for the transport activity; (ii) N-glycosylation impacts membrane targeting and is conserved within the OATP1/Oatp1 family with Asn-122, Asn-133, Asn-499, and Asn-512 residues involved; (iii) the evolutionarily conserved cholesterol recognition interaction amino acid consensus motif is important for membrane localization; and (iv) Oatp1d1 is present in dimeric and possibly oligomeric form in the cell membrane. In conclusion, we describe the first detailed characterization of a new Oatp transporter in zebrafish, offering important insights into the functional evolution of the OATP1/Oatp1 family and the physiological role of Oatp1d1.

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

    Directory of Open Access Journals (Sweden)

    James B Howard

    Full Text Available 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 α- and β-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

  1. Timing of developmental sequences in different brain structures: physiological and pathological implications. (United States)

    Dehorter, N; Vinay, L; Hammond, C; Ben-Ari, Y


    The developing brain is not a small adult brain. Voltage- and transmitter-gated currents, like network-driven patterns, follow a developmental sequence. Studies initially performed in cortical structures and subsequently in subcortical structures have unravelled a developmental sequence of events in which intrinsic voltage-gated calcium currents are followed by nonsynaptic calcium plateaux and synapse-driven giant depolarising potentials, orchestrated by depolarizing actions of GABA and long-lasting NMDA receptor-mediated currents. The function of these early patterns is to enable heterogeneous neurons to fire and wire together rather than to code specific modalities. However, at some stage, behaviourally relevant activities must replace these immature patterns, implying the presence of programmed stop signals. Here, we show that the developing striatum follows a developmental sequence in which immature patterns are silenced precisely when the pup starts locomotion. This is mediated by a loss of the long-lasting NMDA-NR2C/D receptor-mediated current and the expression of a voltage-gated K(+) current. At the same time, the descending inputs to the spinal cord become fully functional, accompanying a GABA/glycine polarity shift and ending the expression of developmental patterns. Therefore, although the timetable of development differs in different brain structures, the g sequence is quite similar, relying first on nonsynaptic events and then on synaptic oscillations that entrain large neuronal populations. In keeping with the 'neuroarcheology' theory, genetic mutations or environmental insults that perturb these developmental sequences constitute early signatures of developmental disorders. Birth dating developmental disorders thus provides important indicators of the event that triggers the pathological cascade leading ultimately to disease.

  2. Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships. (United States)

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


    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 α- and β-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

  3. ERP analysis of cognitive sequencing: a left anterior negativity related to structural transformation processing. (United States)

    Hoen, M; Dominey, P F


    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.

  4. An anatomically structured sensory-motor sequence learning system displays some general linguistic capacities. (United States)

    Dominey, P F


    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.

  5. Comparison of sequence-based and structure-based phylogenetic trees of homologous proteins: Inferences on protein evolution

    Indian Academy of Sciences (India)

    S Balaji; N Srinivasan


    Several studies based on the known three-dimensional (3-D) structures of proteins show that two homologous proteins with insignificant sequence similarity could adopt a common fold and may perform same or similar biochemical functions. Hence, it is appropriate to use similarities in 3-D structure of proteins rather than the amino acid sequence similarities in modelling evolution of distantly related proteins. Here we present an assessment of using 3-D structures in modelling evolution of homologous proteins. Using a dataset of 108 protein domain families of known structures with at least 10 members per family we present a comparison of extent of structural and sequence dissimilarities among pairs of proteins which are inputs into the construction of phylogenetic trees. We find that correlation between the structure-based dissimilarity measures and the sequence-based dissimilarity measures is usually good if the sequence similarity among the homologues is about 30% or more. For protein families with low sequence similarity among the members, the correlation coefficient between the sequence-based and the structure-based dissimilarities are poor. In these cases the structure-based dendrogram clusters proteins with most similar biochemical functional properties better than the sequence-similarity based dendrogram. In multi-domain protein families and disulphide-rich protein families the correlation coefficient for the match of sequence-based and structure-based dissimilarity (SDM) measures can be poor though the sequence identity could be higher than 30%. Hence it is suggested that protein evolution is best modelled using 3-D structures if the sequence similarities (SSM) of the homologues are very low.

  6. E1DS: catalytic site prediction based on 1D signatures of concurrent conservation



    Large-scale automatic annotation of protein sequences remains challenging in postgenomics era. E1DS is designed for annotating enzyme sequences based on a repository of 1D signatures. The employed sequence signatures are derived using a novel pattern mining approach that discovers long motifs consisted of several sequential blocks (conserved segments). Each of the sequential blocks is considerably conserved among the protein members of an EC group. Moreover, a signature includes at least thre...

  7. Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes. (United States)

    Kulkarni, Manasi; Nirwan, Neha; van Aelst, Kara; Szczelkun, Mark D; Saikrishnan, Kayarat


    Engineering restriction enzymes with new sequence specificity has been an unaccomplished challenge, presumably because of the complexity of target recognition. Here we report detailed analyses of target recognition by Type ISP restriction-modification enzymes. We determined the structure of the Type ISP enzyme LlaGI bound to its target and compared it with the previously reported structure of a close homologue that binds to a distinct target, LlaBIII. The comparison revealed that, although the two enzymes use almost a similar set of structural elements for target recognition, the residues that read the bases vary. Change in specificity resulted not only from appropriate substitution of amino acids that contacted the bases but also from new contacts made by positionally distinct residues directly or through a water bridge. Sequence analyses of 552 Type ISP enzymes showed that the structural elements involved in target recognition of LlaGI and LlaBIII were structurally well-conserved but sequentially less-conserved. In addition, the residue positions within these structural elements were under strong evolutionary constraint, highlighting the functional importance of these regions. The comparative study helped decipher a partial consensus code for target recognition by Type ISP enzymes.

  8. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. (United States)

    Hoang, Charmaine; Chen, Junjun; Vizthum, Caroline A; Kandel, Jason M; Hamilton, Christopher S; Mueller, Eugene G; Ferré-D'Amaré, Adrian R


    RluA is a dual-specificity enzyme responsible for pseudouridylating 23S rRNA and several tRNAs. The 2.05 A resolution structure of RluA bound to a substrate RNA comprising the anticodon stem loop of tRNA(Phe) reveals that enzyme binding induces a dramatic reorganization of the RNA. Instead of adopting its canonical U turn conformation, the anticodon loop folds into a new structure with a reverse-Hoogsteen base pair and three flipped-out nucleotides. Sequence conservation, the cocrystal structure, and the results of structure-guided mutagenesis suggest that RluA recognizes its substrates indirectly by probing RNA loops for their ability to adopt the reorganized fold. The planar, cationic side chain of an arginine intercalates between the reverse-Hoogsteen base pair and the bottom pair of the anticodon stem, flipping the nucleotide to be modified into the active site of RluA. Sequence and structural comparisons suggest that pseudouridine synthases of the RluA, RsuA, and TruA families employ an equivalent arginine for base flipping.

  9. Prediction of protein structural features from sequence data based on Shannon entropy and Kolmogorov complexity. (United States)

    Bywater, Robert Paul


    While the genome for a given organism stores the information necessary for the organism to function and flourish it is the proteins that are encoded by the genome that perhaps more than anything else characterize the phenotype for that organism. It is therefore not surprising that one of the many approaches to understanding and predicting protein folding and properties has come from genomics and more specifically from multiple sequence alignments. In this work I explore ways in which data derived from sequence alignment data can be used to investigate in a predictive way three different aspects of protein structure: secondary structures, inter-residue contacts and the dynamics of switching between different states of the protein. In particular the use of Kolmogorov complexity has identified a novel pathway towards achieving these goals.

  10. Evol and ProDy for bridging protein sequence evolution and structural dynamics


    Bakan, Ahmet; Dutta, Anindita; Mao, Wenzhi; Liu, Ying; Chennubhotla, Chakra; Lezon, Timothy R.; Bahar, Ivet


    Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolu...

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

    Directory of Open Access Journals (Sweden)

    Suzan-Monti Marie


    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.

  12. Fifty Years Later: The Sequence, Structure and Function of Lacewing Cross-beta Silk

    Energy Technology Data Exchange (ETDEWEB)

    Weisman, Sarah; Okada, Shoko; Mudie, Stephen T.; Huson, Mickey G.; Trueman, Holly E.; Sriskantha, Alagacone; Haritos, Victoria S.; Sutherland, Tara D.; (CSIRO/MSE); (CSIRO)


    Classic studies of protein structure in the 1950s and 1960s demonstrated that green lacewing egg stalk silk possesses a rare native cross-beta sheet conformation. We have identified and sequenced the silk genes expressed by adult females of a green lacewing species. The two encoded silk proteins are 109 and 67 kDa in size and rich in serine, glycine and alanine. Over 70% of each protein sequence consists of highly repetitive regions with 16-residue periodicity. The repetitive sequences can be fitted to an elegant cross-beta sheet structural model with protein chains folded into regular 8-residue long beta strands. This model is supported by wide-angle X-ray scattering data and tensile testing from both our work and the original papers. We suggest that the silk proteins assemble into stacked beta sheet crystallites bound together by a network of cystine cross-links. This hierarchical structure gives the lacewing silk high lateral stiffness nearly threefold that of silkworm silk, enabling the egg stalks to effectively suspend eggs and protect them from predators.

  13. Interpolation on a fixed interval discrete-valued sequence with random structure

    Directory of Open Access Journals (Sweden)

    D. H. Ilyasova


    Full Text Available Discrete-valued sequences with random structure are widely used to describe electronic systems that operate under a priori uncertainty. An optimal interpolation algorithm on a fixed interval discrete-valued sequence with random structure have been obtained considering the Markov property of an extended process, which includes the value of a discrete-type sequence and its structure. This algorithm is recursive, and describes the evolution of the joint interpolation probability of the extended process in reverse time. Analysis of the optimal interpolation algorithm on a fixed interval was implemented by the example of decoding of a convolutional code by means of statistical computer modeling. For this example interpolation algorithm reduces the bit error probability to 3-4 times compared with the algorithm of filtering due to the fact that it takes into account all the received observations. The increase of statistical dependence between input symbols leads to a decrease in bit error rate in filtration and interpolation algorithms.

  14. SVM-PB-Pred: SVM based protein block prediction method using sequence profiles and secondary structures. (United States)

    Suresh, V; Parthasarathy, S


    We developed a support vector machine based web server called SVM-PB-Pred, to predict the Protein Block for any given amino acid sequence. The input features of SVM-PB-Pred include i) sequence profiles (PSSM) and ii) actual secondary structures (SS) from DSSP method or predicted secondary structures from NPS@ and GOR4 methods. There were three combined input features PSSM+SS(DSSP), PSSM+SS(NPS@) and PSSM+SS(GOR4) used to test and train the SVM models. Similarly, four datasets RS90, DB433, LI1264 and SP1577 were used to develop the SVM models. These four SVM models developed were tested using three different benchmarking tests namely; (i) self consistency, (ii) seven fold cross validation test and (iii) independent case test. The maximum possible prediction accuracy of ~70% was observed in self consistency test for the SVM models of both LI1264 and SP1577 datasets, where PSSM+SS(DSSP) input features was used to test. The prediction accuracies were reduced to ~53% for PSSM+SS(NPS@) and ~43% for PSSM+SS(GOR4) in independent case test, for the SVM models of above two same datasets. Using our method, it is possible to predict the protein block letters for any query protein sequence with ~53% accuracy, when the SP1577 dataset and predicted secondary structure from NPS@ server were used. The SVM-PB-Pred server can be freely accessed through

  15. Population genetic structure and historical demography of Oratosquilla oratoria revealed by mitochondrial DNA sequences. (United States)

    Zhang, D; Ding, Ge; Ge, B; Zhang, H; Tang, B


    Genetic diversity, population genetic structure and molecular phylogeographic pattern of mantis shrimp Oratosquilla oratoria in Bohai Sea and South China Sea were analyzed by mitochondrial DNA sequences. Nucleotide and haplotype diversities were 0.00409-0.00669 and 0.894-0.953 respectively. Neighbor-Joining phylogenetic tree clustered two distinct lineages. Both phylogenetic tree and median-joining network showed the consistent genetic structure corresponding to geographical distribution. Mismatch distributions, negative neutral test and "star-like" network supported a sudden population expansion event. And the time was estimated about 44000 and 50000 years ago.

  16. Hypotheses that correlate the sequence, structure, and mechanical properties of spider silk proteins. (United States)

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


    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.

  17. The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective. (United States)

    Rivas, Elena


    Any method for RNA secondary structure prediction is determined by four ingredients. The architecture is the choice of features implemented by the model (such as stacked basepairs, loop length distributions, etc.). The architecture determines the number of parameters in the model. The scoring scheme is the nature of those parameters (whether thermodynamic, probabilistic, or weights). The parameterization stands for the specific values assigned to the parameters. These three ingredients are referred to as "the model." The fourth ingredient is the folding algorithms used to predict plausible secondary structures given the model and the sequence of a structural RNA. Here, I make several unifying observations drawn from looking at more than 40 years of methods for RNA secondary structure prediction in the light of this classification. As a final observation, there seems to be a performance ceiling that affects all methods with complex architectures, a ceiling that impacts all scoring schemes with remarkable similarity. This suggests that modeling RNA secondary structure by using intrinsic sequence-based plausible "foldability" will require the incorporation of other forms of information in order to constrain the folding space and to improve prediction accuracy. This could give an advantage to probabilistic scoring systems since a probabilistic framework is a natural platform to incorporate different sources of information into one single inference problem.

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

    Directory of Open Access Journals (Sweden)

    Vinga Susana


    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.

  19. Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species. (United States)

    West, Claire; James, Stephen A; Davey, Robert P; Dicks, Jo; Roberts, Ian N


    The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the internal transcribed spacer region, frequently used in plant phylogenetics, is now recognized as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analyzed data sets from the Saccharomyces Genome Resequencing Project, characterizing rDNA sequence variation within multiple strains of the baker's yeast Saccharomyces cerevisiae and its nearest wild relative Saccharomyces paradoxus in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterization of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intraspecies phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridization events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of

  20. Mapping of the serotonin 5-HT{sub 1D{alpha}} autoreceptor gene (HTR1D) on chromosome 1 using a silent polymorphism in the coding region

    Energy Technology Data Exchange (ETDEWEB)

    Ozaki, N.; Lappalainen, J.; Linnoila, M. [National Institute on Alcohol Abuse and Alcoholism, Rockville, MD (United States)] [and others


    Serotonin (5-HT){sub ID} receptors are 5-HT release-regulating autoreceptors in the human brain. Abnormalities in brain 5-HT function have been hypothesized in the pathophysiology of various psychiatric disorders, including obsessive-compulsive disorder, autism, mood disorders, eating disorders, impulsive violent behavior, and alcoholism. Thus, mutations occurring in 5-HT autoreceptors may cause or increase the vulnerability to any of these conditions. 5-HT{sub 1D{alpha}} and 5-HT{sub 1D{Beta}} subtypes have been previously localized to chromosomes 1p36.3-p34.3 and 6q13, respectively, using rodent-human hybrids and in situ localization. In this communication, we report the detection of a 5-HT{sub 1D{alpha}} receptor gene polymorphism by single strand conformation polymorphism (SSCP) analysis of the coding sequence. The polymorphism was used for fine scale linkage mapping of 5-HT{sub 1D{alpha}} on chromosome 1. This polymorphism should also be useful for linkage studies in populations and in families. Our analysis also demonstrates that functionally significant coding sequence variants of the 5-HT{sub 1D{alpha}} are probably not abundant either among alcoholics or in the general population. 14 refs., 1 fig., 1 tab.

  1. 纳米级的一维II-VI族化合物的合成及其电子结构研究%One-dimensional (1D) Ⅱ-Ⅳ Based Nanostructures-synthesis and Electronic Structure Study

    Institute of Scientific and Technical Information of China (English)


    @@ Various single crystalline IIB-VIA one-dimensional nanostructures have been fabricated using thermal evaporation. Although these nanostructures possess large amount of unpassivated surface, it does not lead to dissociation of excitons, which fact indicates the high purity and high quality of the electronic structure of these nanostructures.

  2. Diamond-based 1-D imaging arrays

    Energy Technology Data Exchange (ETDEWEB)

    Lansley, S.P.; Williams, O.A.; Ye, H. [Electronic and Electrical Engineering, University College London, Torrington Place, London WC1E 7JE (United Kingdom); Rizvi, N.; Whitfield, M.D.; Jackman, R.B. [Exitech Limited, Hanborough Park, Long Hanborough, Oxford OX8 8LH (United Kingdom); McKeag, R.D. [Centronic Ltd., Centronic House, King Henry' s Drive, New Addington, Croydon CR9 OBG (United Kingdom)


    Diamond has shown great promise for the fabrication of high sensitivity, low dark current, fast and visible-blind deep UV photodetectors. In addition to careful choice of substrate material, defect passivation treatments applied to the diamond after growth have been found to considerably enhance the detector characteristics achieved. In this paper we report on the first purposefully designed 1-D CVD diamond imaging array for the detection of nanosecond 193 nm excimer laser pulses using this approach. It is shown to perform extremely well, giving less than 2% pixel-to-pixel variation in signal response, and is fast enough to avoid any sign of charge build up during prolonged operation. (Abstract Copyright [2002], Wiley Periodicals, Inc.)

  3. Sequence-structure relationship study in all-α transmembrane proteins using an unsupervised learning approach. (United States)

    Esque, Jérémy; Urbain, Aurélie; Etchebest, Catherine; de Brevern, Alexandre G


    Transmembrane proteins (TMPs) are major drug targets, but the knowledge of their precise topology structure remains highly limited compared with globular proteins. In spite of the difficulties in obtaining their structures, an important effort has been made these last years to increase their number from an experimental and computational point of view. In view of this emerging challenge, the development of computational methods to extract knowledge from these data is crucial for the better understanding of their functions and in improving the quality of structural models. Here, we revisit an efficient unsupervised learning procedure, called Hybrid Protein Model (HPM), which is applied to the analysis of transmembrane proteins belonging to the all-α structural class. HPM method is an original classification procedure that efficiently combines sequence and structure learning. The procedure was initially applied to the analysis of globular proteins. In the present case, HPM classifies a set of overlapping protein fragments, extracted from a non-redundant databank of TMP 3D structure. After fine-tuning of the learning parameters, the optimal classification results in 65 clusters. They represent at best similar relationships between sequence and local structure properties of TMPs. Interestingly, HPM distinguishes among the resulting clusters two helical regions with distinct hydrophobic patterns. This underlines the complexity of the topology of these proteins. The HPM classification enlightens unusual relationship between amino acids in TMP fragments, which can be useful to elaborate new amino acids substitution matrices. Finally, two challenging applications are described: the first one aims at annotating protein functions (channel or not), the second one intends to assess the quality of the structures (X-ray or models) via a new scoring function deduced from the HPM classification.

  4. High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

    Directory of Open Access Journals (Sweden)

    Soichi Inagaki

    Full Text Available Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

  5. Dynamic decoupling in the presence of 1D random walk (United States)

    Chakrabarti, Arnab; Chakraborty, Ipsita; Bhattacharyya, Rangeet


    In the recent past, many dynamic decoupling sequences have been proposed for the suppression of decoherence of spins connected to thermal baths of various natures. Dynamic decoupling schemes for suppressing decoherence due to Gaussian diffusion have also been developed. In this work, we study the relative performances of dynamic decoupling schemes in the presence of a non-stationary Gaussian noise such as a 1D random walk. Frequency domain analysis is not suitable to determine the performances of various dynamic decoupling schemes in suppressing decoherence due to such a process. Thus, in this work, we follow a time domain calculation to arrive at the following conclusions: in the presence of such a noise, we show that (i) the traditional Carr-Purcell-Meiboom-Gill (CPMG) sequence outperforms Uhrig’s dynamic decoupling scheme, (ii) CPMG remains the optimal sequence for suppression of decoherence due to random walk in the presence of an external field gradient. Later, the theoretical predictions are experimentally verified by using nuclear magnetic resonance spectroscopy on spin 1/2 particles diffusing in a liquid medium.

  6. Sequence-structure-function relations of the mosquito leucine-rich repeat immune proteins

    Directory of Open Access Journals (Sweden)

    Povelones Michael


    Full Text Available Abstract Background The discovery and characterisation of factors governing innate immune responses in insects has driven the elucidation of many immune system components in mammals and other organisms. Focusing on the immune system responses of the malaria mosquito, Anopheles gambiae, has uncovered an array of components and mechanisms involved in defence against pathogen infections. Two of these immune factors are LRIM1 and APL1C, which are leucine-rich repeat (LRR containing proteins that activate complement-like defence responses against malaria parasites. In addition to their LRR domains, these leucine-rich repeat immune (LRIM proteins share several structural features including signal peptides, patterns of cysteine residues, and coiled-coil domains. Results The identification and characterisation of genes related to LRIM1 and APL1C revealed putatively novel innate immune factors and furthered the understanding of their likely molecular functions. Genomic scans using the shared features of LRIM1 and APL1C identified more than 20 LRIM-like genes exhibiting all or most of their sequence features in each of three disease-vector mosquitoes with sequenced genomes: An. gambiae, Aedes aegypti, and Culex quinquefasciatus. Comparative sequence analyses revealed that this family of mosquito LRIM-like genes is characterised by a variable number of 6 to 14 LRRs of different lengths. The "Long" LRIM subfamily, with 10 or more LRRs, and the "Short" LRIMs, with 6 or 7 LRRs, also share the signal peptide, cysteine residue patterning, and coiled-coil sequence features of LRIM1 and APL1C. The "TM" LRIMs have a predicted C-terminal transmembrane region, and the "Coil-less" LRIMs exhibit the characteristic LRIM sequence signatures but lack the C-terminal coiled-coil domains. Conclusions The evolutionary plasticity of the LRIM LRR domains may provide templates for diverse recognition properties, while their coiled-coil domains could be involved in the formation

  7. Effects of the antimicrobial tylosin on the microbial community structure of an anaerobic sequencing batch reactor. (United States)

    Shimada, Toshio; Li, Xu; Zilles, Julie L; Morgenroth, Eberhard; Raskin, Lutgarde


    The effects of the antimicrobial tylosin on a methanogenic microbial community were studied in a glucose-fed laboratory-scale anaerobic sequencing batch reactor (ASBR) exposed to stepwise increases of tylosin (0, 1.67, and 167 mg/L). The microbial community structure was determined using quantitative fluorescence in situ hybridization (FISH) and phylogenetic analyses of bacterial 16S ribosomal RNA (rRNA) gene clone libraries of biomass samples. During the periods without tylosin addition and with an influent tylosin concentration of 1.67 mg/L, 16S rRNA gene sequences related to Syntrophobacter were detected and the relative abundance of Methanosaeta species was high. During the highest tylosin dose of 167 mg/L, 16S rRNA gene sequences related to Syntrophobacter species were not detected and the relative abundance of Methanosaeta decreased considerably. Throughout the experimental period, Propionibacteriaceae and high GC Gram-positive bacteria were present, based on 16S rRNA gene sequences and FISH analyses, respectively. The accumulation of propionate and subsequent reactor failure after long-term exposure to tylosin are attributed to the direct inhibition of propionate-oxidizing syntrophic bacteria closely related to Syntrophobacter and the indirect inhibition of Methanosaeta by high propionate concentrations and low pH.

  8. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. (United States)

    Short, Cindy M; Suttle, Curtis A


    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.

  9. Structural analysis of a repetitive protein sequence motif in strepsirrhine primate amelogenin.

    Directory of Open Access Journals (Sweden)

    Rodrigo S Lacruz

    Full Text Available Strepsirrhines are members of a primate suborder that has a distinctive set of features associated with the development of the dentition. Amelogenin (AMEL, the better known of the enamel matrix proteins, forms 90% of the secreted organic matrix during amelogenesis. Although AMEL has been sequenced in numerous mammalian lineages, the only reported strepsirrhine AMEL sequences are those of the ring-tailed lemur and galago, which contain a set of additional proline-rich tandem repeats absent in all other primates species analyzed to date, but present in some non-primate mammals. Here, we first determined that these repeats are present in AMEL from three additional lemur species and thus are likely to be widespread throughout this group. To evaluate the functional relevance of these repeats in strepsirrhines, we engineered a mutated murine amelogenin sequence containing a similar proline-rich sequence to that of Lemur catta. In the monomeric form, the MQP insertions had no influence on the secondary structure or refolding properties, whereas in the assembled form, the insertions increased the hydrodynamic radii. We speculate that increased AMEL nanosphere size may influence enamel formation in strepsirrhine primates.

  10. Main: 1D6R [RPSD[Archive

    Lifescience Database Archive (English)

    Full Text Available 1D6R 大豆 Soybean Glycine max (L.) Merrill Bowman-Birk Type Proteinase Inhibitor Precursor Glycine Ma...x Molecule: Trypsinogen; Chain: A; Fragment: Cationic Precursor; Molecule: Bowman-Birk Prote...inase Inhibitor Precursor; Chain: I Hydrolase (Bowman-Birk Proteinase Inhibitor Precursor) J.Koepke...r Crystal Structure Of Cancer Chemopreventive Bowman-Birk Inhibitor In Ternary Complex With Bovine Trypsin A... 477 2000 Protease Inhibitor, Serine Protease, Bowman-Birk Inhibitor SWS:TRY1_BOV

  11. Breakdown of 1D water wires inside Charged Carbon Nanotubes

    CERN Document Server

    Pant, Shashank


    Using Molecular Dynamics approach we investigated the structure, dynamics of water confined inside pristine and charged 6,6 carbon nanotubes (CNTs). This study reports the breakdown of 1D water wires and the emergence of triangular faced water on incorporating charges in 6,6 CNTs. Incorporation of charges results in high potential barriers to the flipping of water molecules due to the formation of a large number of hydrogen bonds. The PMF analyses show the presence of ~2 kcal/mol barrier for the movement of water inside pristine CNT and almost negligible barrier in charged CNTs.

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

    Directory of Open Access Journals (Sweden)

    Ricardo eFlores


    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.

  13. Tunability and Sensing Properties of Plasmonic/1D Photonic Crystal. (United States)

    Shaban, Mohamed; Ahmed, Ashour M; Abdel-Rahman, Ehab; Hamdy, Hany


    Gold/one-dimensional photonic crystal (Au/1D-PC) is fabricated and applied for sensitive sensing of glucose and different chemical molecules of various refractive indices. The Au layer thickness is optimized to produce surface plasmon resonance (SPR) at the right edge of the photonic band gap (PBG). As the Au deposition time increased to 60 sec, the PBG width is increased from 46 to 86 nm in correlation with the behavior of the SPR. The selectivity of the optimized Au/1D-PC sensor is tested upon the increase of the environmental refractive index of the detected molecules. The resonance wavelength and the PBG edges increased linearly and the transmitted intensity increased nonlinearly as the environment refractive index increased. The SPR splits to two modes during the detection of chloroform molecules based on the localized capacitive coupling of Au particles. Also, this structure shows high sensitivity at different glucose concentrations. The PBG and SPR are shifted to longer wavelengths, and PBG width is decreased linearly with a rate of 16.04 Å/(μg/mm(3)) as the glucose concentration increased. The proposed structure merits; operation at room temperature, compact size, and easy fabrication; suggest that the proposed structure can be efficiently used for the biomedical and chemical application.

  14. Tunability and Sensing Properties of Plasmonic/1D Photonic Crystal (United States)

    Shaban, Mohamed; Ahmed, Ashour M.; Abdel-Rahman, Ehab; Hamdy, Hany


    Gold/one-dimensional photonic crystal (Au/1D-PC) is fabricated and applied for sensitive sensing of glucose and different chemical molecules of various refractive indices. The Au layer thickness is optimized to produce surface plasmon resonance (SPR) at the right edge of the photonic band gap (PBG). As the Au deposition time increased to 60 sec, the PBG width is increased from 46 to 86 nm in correlation with the behavior of the SPR. The selectivity of the optimized Au/1D-PC sensor is tested upon the increase of the environmental refractive index of the detected molecules. The resonance wavelength and the PBG edges increased linearly and the transmitted intensity increased nonlinearly as the environment refractive index increased. The SPR splits to two modes during the detection of chloroform molecules based on the localized capacitive coupling of Au particles. Also, this structure shows high sensitivity at different glucose concentrations. The PBG and SPR are shifted to longer wavelengths, and PBG width is decreased linearly with a rate of 16.04 Å/(μg/mm3) as the glucose concentration increased. The proposed structure merits; operation at room temperature, compact size, and easy fabrication; suggest that the proposed structure can be efficiently used for the biomedical and chemical application. PMID:28176799

  15. Multilocus sequence subtyping and genetic structure of Cryptosporidium muris and Cryptosporidium andersoni. (United States)

    Wang, Rongjun; Jian, Fuchun; Zhang, Longxian; Ning, Changshen; Liu, Aiqin; Zhao, Jinfeng; Feng, Yaoyu; Qi, Meng; Wang, Helei; Lv, Chaochao; Zhao, Guanghui; Xiao, Lihua


    In this study, nine C. muris and 43 C. andersoni isolates from various animals in China were subtyped by a multilocus sequence typing (MLST) tool. DNA sequence analyses showed the presence of 1-2 subtypes of C. muris and 2-6 subtypes of C. andersoni at each of the four loci (MS1, MS2, MS3, and MS16), nine of which represented new subtypes. Altogether, two C. muris and 10 C. andersoni MLST subtypes were detected. Linkage disequilibrium analysis indicated although the overall population structure of the two parasites was clonal, the Chinese C. andersoni in cattle has an epidemic structure. Three and two clusters were produced in the C. muris and C. andersoni populations by Structure 2.3.3 analysis, with Chinese C. muris and C. andersoni substructures differing from other countries. Thus, this study suggested the prevalence of C. andersoni in China is not attributed to the introduction of dairy cattle. More studies involving more genetic loci and systematic sampling are needed to better elucidate the population genetic structure of C. muris and C. andersoni in the world and the genetic basis for the difference in host specificity among the two most common gastric parasites.

  16. Genetic structure of Florida green turtle rookeries as indicated by mitochondrial DNA control region sequences (United States)

    Shamblin, Brian M.; Bagley, Dean A.; Ehrhart, Llewellyn M.; Desjardin, Nicole A.; Martin, R. Erik; Hart, Kristen M.; Naro-Maciel, Eugenia; Rusenko, Kirt; Stiner, John C.; Sobel, Debra; Johnson, Chris; Wilmers, Thomas; Wright, Laura J.; Nairn, Campbell J.


    Green turtle (Chelonia mydas) nesting has increased dramatically in Florida over the past two decades, ranking the Florida nesting aggregation among the largest in the Greater Caribbean region. Individual beaches that comprise several hundred kilometers of Florida’s east coast and Keys support tens to thousands of nests annually. These beaches encompass natural to highly developed habitats, and the degree of demographic partitioning among rookeries was previously unresolved. We characterized the genetic structure of ten Florida rookeries from Cape Canaveral to the Dry Tortugas through analysis of 817 base pair mitochondrial DNA (mtDNA) control region sequences from 485 nesting turtles. Two common haplotypes, CM-A1.1 and CM-A3.1, accounted for 87 % of samples, and the haplotype frequencies were strongly partitioned by latitude along Florida’s Atlantic coast. Most genetic structure occurred between rookeries on either side of an apparent genetic break in the vicinity of the St. Lucie Inlet that separates Hutchinson Island and Jupiter Island, representing the finest scale at which mtDNA structure has been documented in marine turtle rookeries. Florida and Caribbean scale analyses of population structure support recognition of at least two management units: central eastern Florida and southern Florida. More thorough sampling and deeper sequencing are necessary to better characterize connectivity among Florida green turtle rookeries as well as between the Florida nesting aggregation and others in the Greater Caribbean region.

  17. Chromatin structure of repeating CTG/CAG and CGG/CCG sequences in human disease. (United States)

    Wang, Yuh-Hwa


    In eukaryotic cells, chromatin structure organizes genomic DNA in a dynamic fashion, and results in regulation of many DNA metabolic processes. The CTG/CAG and CGG/CCG repeating sequences involved in several neuromuscular degenerative diseases display differential abilities for the binding of histone octamers. The effect of the repeating DNA on nucleosome assembly could be amplified as the number of repeats increases. Also, CpG methylation, and sequence interruptions within the triplet repeats exert an impact on the formation of nucleosomes along these repeating DNAs. The two most common triplet expansion human diseases, myotonic dystrophy 1 and fragile X syndrome, are caused by the expanded CTG/CAG and CGG/CCG repeats, respectively. In addition to the expanded repeats and CpG methylation, histone modifications, chromatin remodeling factors, and noncoding RNA have been shown to coordinate the chromatin structure at both myotonic dystrophy 1 and fragile X loci. Alterations in chromatin structure at these two loci can affect transcription of these disease-causing genes, leading to disease symptoms. These observations have brought a new appreciation that a full understanding of disease gene expression requires a knowledge of the structure of the chromatin domain within which the gene resides.

  18. One common structural feature of "words" in protein sequences and human texts. (United States)

    Zemková, M; Trifonov, E N; Zahradník, D


    Frequently discussed analogy between genetic and human texts is explored by comparison of alternation of polar and non-polar amino-acid residues in proteins and alternation of consonants and vowels in human texts. In human languages, the usage of possible combinations of consonants and vowels is influenced by pronounceability of the combinations. Similarly, oligopeptide composition of proteins is influenced by requirements of protein folding and stability. One special type of structure often present in proteins is amphipathic α-helices in which polar and non-polar amino acids alternate with the period 3.5 residues, not unlike alternation of consonants and vowels. In this study, we evaluated the contribution made by amphipathic alternations to the protein sequence texts (20-24%). Their proportion is lower than respective values for alternating words in human texts (57-89%). The proteomes (full sets of proteins for selected organisms) were transformed into ranked sequences of n-grams (words of length n), including periodical amphipathic structures. Similarly, human texts were transformed into sequences of alternating consonants and vowels. Analysis of the vocabularies shows that in both types of texts (human languages and proteins) the alternating words are dominant or highly preferred, thus, strengthening the analogy between these two types of texts. The contribution of amphipathic words in the upper parts of the ranked lists for 10 analyzed proteomes varies between 58 and 74%. In human texts respective values range between 90 and 100%.

  19. Structural insights and ab initio sequencing within the DING proteins family

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Mikael, E-mail: [Weizmann Institute of Science, Rehovot (Israel); Liebschner, Dorothee [CRM2, Nancy Université (France); Gotthard, Guillaume; Chabriere, Eric [AFMB, Université Aix-Marseille II (France)


    DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.

  20. Evolutionary conservation of sequence and secondary structures inCRISPR repeats

    Energy Technology Data Exchange (ETDEWEB)

    Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip


    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.

  1. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. (United States)

    Di Tommaso, Paolo; Moretti, Sebastien; Xenarios, Ioannis; Orobitg, Miquel; Montanyola, Alberto; Chang, Jia-Ming; Taly, Jean-François; Notredame, Cedric


    This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both and its main mirror

  2. Sequence, structure, and stacking: specifics of tRNA anchoring to the T box riboswitch. (United States)

    Grigg, Jason C; Ke, Ailong


    The term riboswitch usually refers to small molecule sensing regulatory modules in the 5' untranslated regions of a mRNA. They are typically comprised of separate ligand binding and regulatory domains. The T box riboswitch is unique from other identified riboswitches because its effector is an essential macromolecule, tRNA. It senses the aminoacylation state of tRNA to regulate genes involved in a variety of functions relating to amino acid metabolism and tRNA aminoacylation. T box riboswitches performs an intuitively simple process using a complex structured RNA element and, until recently, the underlying mechanisms were poorly understood. Only two sequence-specific contacts had been previously identified: (1) between the specifier sequence (codon) and the tRNA anticodon and (2) between an anti-terminator stem loop and the tRNA acceptor arm CCA tail. tRNA aminoacylation blocks the latter interaction and therefore serves as the switch between termination and anti-termination. Outside of these two contacts, the structure and functions of T box riboswitches have come to light in some recent studies. We recently described the X-ray crystal structure of the highly conserved T box riboswitch distal Stem I region and demonstrated that this region interacts with the tRNA elbow to anchor it to the riboswitch. Independently, Lehmann et al. used sequence homology search to arrive at a similar model for Stem I-tRNA interactions. The model was further supported by two recent structures of the Stem I-tRNA complex, determined independently by our group and by Zhang and Ferré-D'Amaré. This article highlights some of these contributions to synthesize an updated model for tRNA recognition by the T box riboswitch.

  3. Synthesis and Crystal Structure of 1-D Chain Copper(Ⅱ) Complex:[Cu(L)Cl2]n(L = 2,5-Di-2-pyridyl-1,3,4-oxodiazole)

    Institute of Scientific and Technical Information of China (English)

    李建荣; 郭国聪; 卜显和; 黄锦顺


    The title complex, [Cu(L)Cl2]n (L = 2,5-di-2-pyridyl-1,3,4-oxodiazole) 1, has mixture solvent of CH3CN and CH2Cl2 (L is generated from the metal-assisted hydrolysis reaction of bptz) and structurally characterized. It crystallizes in space group C2/c of monoclinic system with cell parameters: a = 9.812(2), b = 12.679(3), c = 1 1.111(2) A, β = 103.92(3)°, V = 1341.6(5)A3, Z = 4, Dc = 1.776 g/cm3, Mr= 358.66, F(000) = 716, μ = 2.024 mm-1 and S = 1.004. The final R = 0.0346 and wR = 0.0938 for 1011 observed reflections with I > 2σ(I). The Cu( Ⅱ ) ion is six-coordinated by four N atoms of two L ligands and two Cl- ions in a distorted octahedral geometry. The ligand L acts as a bis-bidentate ligand to bridge the Cu( Ⅱ ) ions, resulting in an infinite chain structure.

  4. Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. (United States)

    Palmenberg, Ann C; Spiro, David; Kuzmickas, Ryan; Wang, Shiliang; Djikeng, Appolinaire; Rathe, Jennifer A; Fraser-Liggett, Claire M; Liggett, Stephen B


    Infection by human rhinovirus (HRV) is a major cause of upper and lower respiratory tract disease worldwide and displays considerable phenotypic variation. We examined diversity by completing the genome sequences for all known serotypes (n = 99). Superimposition of capsid crystal structure and optimal-energy RNA configurations established alignments and phylogeny. These revealed conserved motifs; clade-specific diversity, including a potential newly identified species (HRV-D); mutations in field isolates; and recombination. In analogy with poliovirus, a hypervariable 5' untranslated region tract may affect virulence. A configuration consistent with nonscanning internal ribosome entry was found in all HRVs and may account for rapid translation. The data density from complete sequences of the reference HRVs provided high resolution for this degree of modeling and serves as a platform for full genome-based epidemiologic studies and antiviral or vaccine development.

  5. Welding sequences optimization of box structure based on genetic algorithm method

    Institute of Scientific and Technical Information of China (English)

    CUI Xiao-fang; MA Jun; MENG Kai; ZHAO Wen-zhong; ZHAO Hai-yan


    In this article, The genetic algorithm method was proposed, that is, to establish the box structure's nonlinear three-dimension optimization numerical model based on thermo-mechanical coupling algorithm, and the objective function of welding distortion has been utilized to determine an optimum welding sequence by optimization simulation. The validity of genetic algorithm method combining with the thermo-mechanical nonlinear finite element model is verified by comparison with the experimental data where available. By choosing the appropriate objective function for the considered case, an optimum welding sequence is determined by a genetic algorithm. All done in this study indicates that the new method presented in this article will have important practical application for designing the welding technical parameters in the future.

  6. On the Davenport constant and on the structure of extremal zero-sum free sequences

    CERN Document Server

    Geroldinger, Alfred; Philipp, Andreas


    Let $G = C_{n_1} \\oplus ... \\oplus C_{n_r}$ with $1 < n_1 \\t ... \\t n_r$ be a finite abelian group, $\\mathsf d^* (G) = n_1 + ... + n_r - r$, and let $\\mathsf d (G)$ denote the maximal length of a zero-sum free sequence over $G$. Then $\\mathsf d (G) \\ge \\mathsf d^* (G)$, and the standing conjecture is that equality holds for $G = C_n^r$. We show that equality does not hold for $C_2 \\oplus C_{2n}^r$, where $n \\ge 3$ is odd and $r \\ge 4$. This gives new information on the structure of extremal zero-sum free sequences over $C_{2n}^r$.

  7. Modeling structure-function relationships in synthetic DNA sequences using attribute grammars.

    Directory of Open Access Journals (Sweden)

    Yizhi Cai


    Full Text Available Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology.

  8. Unusual structure of ribosomal DNA in the copepod Tigriopus californicus: intergenic spacer sequences lack internal subrepeats. (United States)

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


    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.

  9. TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors.

    Directory of Open Access Journals (Sweden)

    Johannes Eichner

    Full Text Available One of the key mechanisms of transcriptional control are the specific connections between transcription factors (TF and cis-regulatory elements in gene promoters. The elucidation of these specific protein-DNA interactions is crucial to gain insights into the complex regulatory mechanisms and networks underlying the adaptation of organisms to dynamically changing environmental conditions. As experimental techniques for determining TF binding sites are expensive and mostly performed for selected TFs only, accurate computational approaches are needed to analyze transcriptional regulation in eukaryotes on a genome-wide level. We implemented a four-step classification workflow which for a given protein sequence (1 discriminates TFs from other proteins, (2 determines the structural superclass of TFs, (3 identifies the DNA-binding domains of TFs and (4 predicts their cis-acting DNA motif. While existing tools were extended and adapted for performing the latter two prediction steps, the first two steps are based on a novel numeric sequence representation which allows for combining existing knowledge from a BLAST scan with robust machine learning-based classification. By evaluation on a set of experimentally confirmed TFs and non-TFs, we demonstrate that our new protein sequence representation facilitates more reliable identification and structural classification of TFs than previously proposed sequence-derived features. The algorithms underlying our proposed methodology are implemented in the two complementary tools TFpredict and SABINE. The online and stand-alone versions of TFpredict and SABINE are freely available to academics at and

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

    Directory of Open Access Journals (Sweden)

    Bjørn P Pedersen

    Full Text Available BACKGROUND: 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. RESULTS: Using SLR, we have built classifiers to identify and automatically categorize P-type ATPases into one of 11 pre-defined classes. The SLR-classifiers are compared to a Hidden Markov Model approach and shown to be highly accurate and scalable. Representing the bulk of currently known sequences, we analysed 9.3 million sequences in the UniProtKB and attempted to classify a large number of P-type ATPases. To examine the distribution of pumps on organisms, we also applied SLR to 1,123 complete genomes from the Entrez genome database. Finally, we analysed the predicted membrane topology of the identified P-type ATPases. CONCLUSIONS: Using the SLR-based classification tool we are able to run a large scale study of P-type ATPases. This study provides proof-of-concept for the application of SLR to a bioinformatics problem and the analysis of P-type ATPases pinpoints new and interesting targets for further biochemical characterization and structural analysis.

  11. Correlation between sequence, structure and function for trisporoid processing proteins in the model zygomycete Mucor mucedo. (United States)

    Ellenberger, Sabrina; Schuster, Stefan; Wöstemeyer, Johannes


    Terpenoids, steroids, carotenoids, phytoenes and other chemically related substance groups fulfill multiple functions in all realms of the organismic world. This analysis focuses on trisporoids that operate as pheromones in the phylogenetically ancient fungal group of mucoralean zygomycetes. Trisporoids serve as pheromones for recognizing complementary mating partners and for inducing the differentiation program towards sexual spore formation. Trisporoids are synthesized by oxidative degradation of β-carotene. Structurally, they are related to retinoids in mammals and abscisic acid in vascular plants. In order to evaluate evolutionary relationships between proteins involved in trisporoid binding and also for checking possibilities to recognize functionally related proteins by sequence and structure comparisons, we compared representative proteins of different origins. Towards this goal, we calculated three-dimensional structures for 4-dihydromethyltrisporate dehydrogenase (TSP1) and 4-dihydrotrisporin dehydrogenase (TSP2), the two proteins involved in trisporic acid synthesis that have unequivocally been correlated with their catalytic function for the model zygomycete Mucor mucedo. TSP1 is an aldo-keto reductase with a TIM-barrel structure, TSP2 belongs to short-chain dehydrogenases, characterized by a Rossmann fold. Evidently, functional conservation, even implying very similar substrates and identical cosubstrates of enzymes in a single organism, turns out to be essentially independent of basic protein structure. The binding sites for NADP and trisporoid ligands in the proteins were determined by docking studies, revealing those regions affecting substrate specificity. Despite the pronounced differences in amino acid sequence and tertiary structure, the surfaces around the active sites are comparable between TSP1 and TSP2. Two binding regions were identified, one sterically open and a second closed one. In contrast to TSP1, all docking models for TSP2 place the

  12. Dickeya species relatedness and clade structure determined by comparison of recA sequences. (United States)

    Parkinson, Neil; Stead, David; Bew, Janice; Heeney, John; Tsror Lahkim, Leah; Elphinstone, John


    Using sequences from the recA locus, we have produced a phylogeny of 188 Dickeya strains from culture collections and identified species relatedness and subspecies clade structure within the genus. Of the six recognized species, Dickeya paradisiaca, D. chrysanthemi and D. zeae were discriminated with long branch lengths. The clade containing the D. paradisiaca type strain included just one additional strain, isolated from banana in Colombia. Strains isolated from Chrysanthemum and Parthenium species made up most of the clade containing the D. chrysanthemi type strain, and the host range of this species was extended to include potato. The D. zeae clade had the largest number of sequevars and branched into two major sister clades that contained all of the Zea mays isolates, and were identified as phylotypes PI and PII. The host range was increased from six to 13 species, including potato. The recA sequence of an Australian sugar-cane strain was sufficiently distinct to rank as a new species-level branch. In contrast to these species, Dickeya dadantii, D. dianthicola and D. dieffenbachiae were distinguished with shorter branch lengths, indicating relatively closer relatedness. The recA sequence for the type strain of D. dadantii clustered separately from other strains of the species. However, sequence comparison of three additional loci revealed that the D. dadantii type strain grouped together with the six other D. dadantii strains that were sequenced. Analysis of all four loci indicated that the D. dadantii strains were most closely related to D. dieffenbachiae. Three further branches (DUC-1, -2 and -3) were associated with these three species, which all diverged from a common origin and can be considered as a species complex. The large clade containing the D. dianthicola type strain comprised 58 strains and had little sequence diversity. One sequevar accounted for the majority of these strains, which were isolated nearly exclusively from eight hosts from Europe

  13. 一维SEMDY和旋转坐标NOE差谱NMR新技术用于天然化合物中寡糖的结构研究%The Structure Determination of Oligosaccharide Chains in Naturally Occurring Compounds by 1D-SEMDY and NOE Difference Spectroscopy in Rotating Frame

    Institute of Scientific and Technical Information of China (English)

    缪振春; 冯锐; 周永新; 魏锋


    Two new saponins containing five sugars have been isolated from the ethanol extract of the root of Dipsocus japonicus and their structures established as(3-O-α-L-rhammopyranosyl(1→3)- α-D-glycopyranosyl(1→3)-α-L-rhammopyranosyl(1→2)-α-L-arabinopyranosyl-hederagenin-28-O-α-D-glycopranoside(1)and3-O-α-D--glycopyranosyl(1→4)] α-L-rhamnopyranosyl(1→3)]- α-D-glycopyranosyl(1→3)- α-L[WTBZ]-rhamnopyranosyl(1→2)- α-L-arabinopyranosyl-oleanoic acid(2).Two new NMR techniques,1D-SEMDY and NOE difference spectroscopy in rotating frame have been successfully used to determine the chemical structure of oligosaccharide chains of the saponins.The results obtained showed that the sites of glycosylation and the sequence of sugars in the saponins can be determined unambiguously and total assignment of severely overlapping pro~ton resonance of sugar residues were achieved,without having recourse to chemical degration or modification.%报告从日本续断根部的乙醇提取物中分得二个新的五糖三萜皂甙,应用一维SEMDY和旋转坐标NOE差谱等NMR新技术互相配合的方法对它们的结构进行了研究,确定为:3-O-α-L-吡喃鼠李糖(1→3)-β-D-吡喃葡萄糖(1→3)-α-L-吡喃鼠李糖(1→2)-α-L-吡喃阿拉伯糖-常春藤甙元-28-O-β-吡喃葡萄糖酯甙(1),和3-O-[β-D-吡喃葡萄糖(1→4)] [α-L-吡喃鼠李糖(1→3)]-β-D-吡喃葡萄糖(1→3)-α-L-吡喃鼠李糖(1→2)-α-L-吡喃阿拉伯糖-齐墩果酸(2)·结果表明,一维SEMDY和旋转坐标NOE差谱技术互相配合的方法测定寡糖链结构十分有效,高度重叠的糖基1H-NMR信号可按一定规律分离,容易鉴别,糖基之间的连接顺序和连接位置可以准确测定,不需要对化合物进行化学降解或衍生化。

  14. Tracing crosslinguistic influences in structural sequences: What does key structure analysis have to offer?

    Directory of Open Access Journals (Sweden)

    Ilmari Ivaska


    Full Text Available Following the detection-based approach, this article detects statistically significant frequency differences between the data of written Finnish by learners from various language backgrounds. It analyses crosslinguistic influences in a data-driven manner, as the analysis focuses on the morphological forms and their combinations (n-grams that prove to be the best predictors of differing first languages. Following the methodology applied – key structure analysis – the article then goes on to analyse the found n-grams in terms of their inner and cotextual variation in order to find out which linguistic phenomenon actually distinguishes the subsets of data. The results show several quantitative differences that may be due to the crosslinguistic influences and they were all detected in a data-driven manner without hypotheses of potential differences. The method can be useful especially in finding and analysing elusive crosslinguistic influences that cannot be interpreted to be transferred directly from the respective first languages.

  15. Determining optimal pattern sequences for three-dimensional structured light sensory systems. (United States)

    Marin, Veronica E; Nejat, Goldie


    Structured light (SL) techniques are used for three-dimensional (3D) measurements of objects in a wide variety of applications. SL-based sensory systems obtain the 3D surface profile of an object from the deformation of light patterns projected onto the object of interest. The number of fringes used in the projected light patterns has a direct effect on the 3D reconstruction errors. This paper presents a novel methodology for determining the optimal sequence of multi-fringe patterns that minimizes reconstruction errors caused by random noise. Experiments conducted with a variety of objects as well as a comparison study demonstrate the effectiveness of the proposed methodology.

  16. Impact of Insertion Sequences and Recombination on the Population Structure of Staphylococcus haemolyticus.

    Directory of Open Access Journals (Sweden)

    Ons Bouchami

    Full Text Available Staphylococcus haemolyticus is one of the most common pathogens associated with medical-device related infections, but its molecular epidemiology is poorly explored. In the current study, we aimed to better understand the genetic mechanisms contributing to S. haemolyticus diversity in the hospital environment and their impact on the population structure and clinical relevant phenotypic traits. The analysis of a representative S. haemolyticus collection by multilocus sequence typing (MLST has identified a single highly prevalent and diverse genetic lineage of nosocomial S. haemolyticus clonal complex (CC 29 accounting for 91% of the collection of isolates disseminated worldwide. The examination of the sequence changes at MLST loci during clonal diversification showed that recombination had a higher impact than mutation in shaping the S. haemolyticus population. Also, we ascertained that another mechanism contributing significantly to clonal diversification and adaptation was mediated by insertion sequence (IS elements. We found that all nosocomial S. haemolyticus, belonging to different STs, were rich in IS1272 copies, as determined by Southern hybridization of macrorestriction patterns. In particular, we observed that the chromosome of a S. haemolyticus strain within CC29 was highly unstable during serial growth in vitro which paralleled with IS1272 transposition events and changes in clinically relevant phenotypic traits namely, mannitol fermentation, susceptibility to beta-lactams, biofilm formation and hemolysis. Our results suggest that recombination and IS transposition might be a strategy of adaptation, evolution and pathogenicity of the major S. haemolyticus prevalent lineage in the hospital environment.

  17. Galaxy Structure as a Driver of the Star Formation Sequence Slope and Scatter

    CERN Document Server

    Whitaker, Katherine E; Bezanson, Rachel; Brammer, Gabriel B; van Dokkum, Pieter G; Kriek, Mariska T; Labbe, Ivo; Leja, Joel; Momcheva, Ivelina G; Nelson, Erica J; Rigby, Jane R; Rix, Hans-Walter; Skelton, Rosalind E; van der Wel, Arjen; Wuyts, Stijn


    It is well established that (1) star-forming galaxies follow a relation between their star formation rate (SFR) and stellar mass (M$_{\\star}$), the "star-formation sequence", and (2) the SFRs of galaxies correlate with their structure, where star-forming galaxies are less concentrated than quiescent galaxies at fixed mass. Here, we consider whether the scatter and slope of the star-formation sequence is correlated with systematic variations in the Sersic indices, $n$, of galaxies across the SFR-M$_{\\star}$ plane. We use a mass-complete sample of 23,848 galaxies at $0.52$ (implying more dominant bulges) have significantly lower SFR/M$_{\\star}$ than the main ridgeline of the star-formation sequence. These results suggest that bulges in massive $z\\sim2$ galaxies are actively building up, where the stars in the central concentration are relatively young. At $z<1$, the presence of older bulges within star-forming galaxies lowers global SFR/M$_{\\star}$, decreasing the slope and contributing significantly to the ...

  18. Gene structure of the human DDX3 and chromosome mapping of its related sequences. (United States)

    Kim, Y S; Lee, S G; Park, S H; Song, K


    The human DDX3 gene (GenBank accession No. U50553) is the human homologue of the mouse Ddx3 gene and is a member of the gene family that contains DEAD motifs. Previously, we mapped the gene to the Xp11.3-11.23. In this report, we describe the structural organization of the human DDX3 gene. It consisted of 17 exons that span approximately 16 kb. An Alu element was present in the intron 13. Its organization was the same as that of the human DBY gene, a closely related sequence present on the Y chromosome. We also identified two processed pseudogenes (DDX3) with a sequence that is highly homologous to those of DDX3 cDNAs, but contain a translation termination codon within its open-reading frame. Pseudogenes are mapped on human chromosomes 4 and X, respectively. In this paper, we discuss the relationships between DDX3 and its related sequences that have been isolated.

  19. Rabbit serum amyloid protein A: expression and primary structure deduced from cDNA sequences. (United States)

    Rygg, M; Marhaug, G; Husby, G; Dowton, S B


    Serum amyloid A protein (SAA), the precursor of amyloid protein A (AA) in deposits of secondary amyloidosis, is an acute phase plasma apolipoprotein produced by hepatocytes. The primary structure of SAA demonstrates high interspecies homology. Several isoforms exist in individual species, probably with different amyloidogenic potential. The nucleotide sequences of two different rabbit serum amyloid A cDNA clones have been analysed, one (corresponding to SAA1) 569 base pairs (bp) long and the other (corresponding to SAA2) 513 bp long. Their deduced amino acid sequences differ at five amino acid positions, four of which are located in the NH2-terminal region of the protein. The deduced amino acid sequence of SAA2 corresponds to rabbit protein AA previously described except for one amino acid in position 22. Eighteen hours after turpentine stimulation, rabbit SAA mRNA is abundant in liver, while lower levels are present in spleen. None of the other extrahepatic organs studied showed any SAA mRNA expression. A third mRNA species (1.9 kb) hybridizing with a single-stranded RNA probe transcribed from the rabbit SAA cDNA, was identified. SAA1 and SAA2 mRNA were found in approximately equal amounts in turpentine-stimulated rabbit liver, but seem to be coordinately decreased after repeated inflammatory stimulation.

  20. Estimating Rheological Parameters of Anhydrite from Folded Evaporite sequences: Implications for Internal Dynamics of Salt Structure (United States)

    Adamuszek, Marta; Dabrowski, Marcin; Schmalholz, Stefan M.; Urai, Janos L.; Raith, Alexander


    Salt structures have been identified as a potential target for hydrocarbon, CO2, or radioactive waste storage. The most suitable locations for magazines are considered in the thick and relatively homogeneous rock salt layers. However, salt structures often consist of the evaporite sequence including rock salt intercalated with other rock types e.g.: anhydrite, gypsum, potassium and magnesium salt, calcite, dolomite, or shale. The presence of such heterogeneities causes a serious disturbance in the structure management. Detailed analysis of the internal architecture and internal dynamics of the salt structure are crucial for evaluating them as suitable repositories and also their long-term stability. The goal of this study is to analyse the influence of the presence of anhydrite layers on the internal dynamics of salt structures. Anhydrite is a common rock in evaporite sequences. Its physical and mechanical properties strongly differ from the properties of rock salt. The density of anhydrite is much higher than the density of salt, thus anhydrite is likely to sink in salt causing the disturbance of the surrounding structures. This suggestion was the starting point to the discussion about the long-term stability of the magazines in salt structures [1]. However, the other important parameter that has to be taken into account is the viscosity of anhydrite. The high viscosity ratio between salt and anhydrite can restrain the layer from sinking. The rheological behaviour of anhydrite has been studied in laboratory experiments [2], but the results only provide information about the short-term behaviour. The long-term behaviour can be best predicted using indirect methods e.g. based on the analysis of natural structures that developed over geological time scale. One of the most promising are fold structures, the shape of which is very sensitive to the rheological parameters of the deforming materials. Folds can develop in mechanically stratified materials during layer

  1. Coherent thermal conductance of 1-D photonic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Tschikin, Maria [Institut für Physik, Carl von Ossietzky Universität, D-26111 Oldenburg (Germany); Ben-Abdallah, Philippe [Laboratoire Charles Fabry, UMR 8501, Institut d' Optique, CNRS, Université Paris-Sud, 2, Avenue Augustin Fresnel, RD128, 91127 Palaiseau Cedex (France); Biehs, Svend-Age, E-mail: [Institut für Physik, Carl von Ossietzky Universität, D-26111 Oldenburg (Germany)


    We present an exact calculation of coherent thermal conductance in 1-D multilayer photonic crystals using the S-matrix method. In particular, we study the thermal conductance in a bilayer structure of Si/vacuum or Al{sub 2}O{sub 3}/vacuum slabs by means of the exact radiative heat flux expression. Based on the results obtained for the Al{sub 2}O{sub 3}/vacuum structure we show by comparison with previous works that the material losses and (localized) surface modes supported by the inner layers play a fundamental role and cannot be omitted in the definition of thermal conductance. Our results could have significant implications in the conception of efficient thermal barriers.

  2. Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations. (United States)

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


    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.

  3. Allelic Diversity and Population Structure in Oenococcus oeni as Determined from Sequence Analysis of Housekeeping Genes (United States)

    de las Rivas, Blanca; Marcobal, Ángela; Muñoz, Rosario


    Oenococcus oeni is the organism of choice for promoting malolactic fermentation in wine. The population biology of O. oeni is poorly understood and remains unclear. For a better understanding of the mode of genetic variation within this species, we investigated by using multilocus sequence typing (MLST) with the gyrB, pgm, ddl, recP, and mleA genes the genetic diversity and genetic relationships among 18 O. oeni strains isolated in various years from wines of the United States, France, Germany, Spain, and Italy. These strains have also been characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S-23S rRNA gene intergenic spacer region (ISR). Ribotyping grouped the strains into two groups; however, the RFLP analysis of the ISRs showed no differences in the strains analyzed. In contrast, MLST in oenococci had a good discriminatory ability, and we have found a higher genetic diversity than indicated by ribotyping analysis. All sequence types were represented by a single strain, and all the strains could be distinguished from each other because they had unique combinations of alleles. Strains assumed to be identical showed the same sequence type. Phylogenetic analyses indicated a panmictic population structure in O. oeni. Sequences were analyzed for evidence of recombination by split decomposition analysis and analysis of clustered polymorphisms. All results indicated that recombination plays a major role in creating the genetic heterogeneity of O. oeni. A low standardized index of association value indicated that the O. oeni genes analyzed are close to linkage equilibrium. This study constitutes the first step in the development of an MLST method for O. oeni and the first example of the application of MLST to a nonpathogenic food production bacteria. PMID:15574919

  4. Prediction of new high pressure structural sequence in thorium carbide: A first principles study

    Energy Technology Data Exchange (ETDEWEB)

    Sahoo, B. D., E-mail:; Joshi, K. D.; Gupta, Satish C. [Applied Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)


    In the present work, we report the detailed electronic band structure calculations on thorium monocarbide. The comparison of enthalpies, derived for various phases using evolutionary structure search method in conjunction with first principles total energy calculations at several hydrostatic compressions, yielded a high pressure structural sequence of NaCl type (B1) → Pnma → Cmcm → CsCl type (B2) at hydrostatic pressures of ∼19 GPa, 36 GPa, and 200 GPa, respectively. However, the two high pressure experimental studies by Gerward et al. [J. Appl. Crystallogr. 19, 308 (1986); J. Less-Common Met. 161, L11 (1990)] one up to 36 GPa and other up to 50 GPa, on substoichiometric thorium carbide samples with carbon deficiency of ∼20%, do not report any structural transition. The discrepancy between theory and experiment could be due to the non-stoichiometry of thorium carbide samples used in the experiment. Further, in order to substantiate the results of our static lattice calculations, we have determined the phonon dispersion relations for these structures from lattice dynamic calculations. The theoretically calculated phonon spectrum reveal that the B1 phase fails dynamically at ∼33.8 GPa whereas the Pnma phase appears as dynamically stable structure around the B1 to Pnma transition pressure. Similarly, the Cmcm structure also displays dynamic stability in the regime of its structural stability. The B2 phase becomes dynamically stable much below the Cmcm to B2 transition pressure. Additionally, we have derived various thermophysical properties such as zero pressure equilibrium volume, bulk modulus, its pressure derivative, Debye temperature, thermal expansion coefficient and Gruneisen parameter at 300 K and compared these with available experimental data. Further, the behavior of zero pressure bulk modulus, heat capacity and Helmholtz free energy has been examined as a function temperature and compared with the experimental data of Danan [J

  5. Prediction of new high pressure structural sequence in thorium carbide: A first principles study (United States)

    Sahoo, B. D.; Joshi, K. D.; Gupta, Satish C.


    In the present work, we report the detailed electronic band structure calculations on thorium monocarbide. The comparison of enthalpies, derived for various phases using evolutionary structure search method in conjunction with first principles total energy calculations at several hydrostatic compressions, yielded a high pressure structural sequence of NaCl type (B1) → Pnma → Cmcm → CsCl type (B2) at hydrostatic pressures of ˜19 GPa, 36 GPa, and 200 GPa, respectively. However, the two high pressure experimental studies by Gerward et al. [J. Appl. Crystallogr. 19, 308 (1986); J. Less-Common Met. 161, L11 (1990)] one up to 36 GPa and other up to 50 GPa, on substoichiometric thorium carbide samples with carbon deficiency of ˜20%, do not report any structural transition. The discrepancy between theory and experiment could be due to the non-stoichiometry of thorium carbide samples used in the experiment. Further, in order to substantiate the results of our static lattice calculations, we have determined the phonon dispersion relations for these structures from lattice dynamic calculations. The theoretically calculated phonon spectrum reveal that the B1 phase fails dynamically at ˜33.8 GPa whereas the Pnma phase appears as dynamically stable structure around the B1 to Pnma transition pressure. Similarly, the Cmcm structure also displays dynamic stability in the regime of its structural stability. The B2 phase becomes dynamically stable much below the Cmcm to B2 transition pressure. Additionally, we have derived various thermophysical properties such as zero pressure equilibrium volume, bulk modulus, its pressure derivative, Debye temperature, thermal expansion coefficient and Gruneisen parameter at 300 K and compared these with available experimental data. Further, the behavior of zero pressure bulk modulus, heat capacity and Helmholtz free energy has been examined as a function temperature and compared with the experimental data of Danan [J. Nucl. Mater. 57, 280

  6. Diagnostic SNPs for inferring population structure in American mink (Neovison vison) identified through RAD sequencing

    DEFF Research Database (Denmark)


    Data from: "Diagnostic SNPs for inferring population structure in American mink (Neovison vison) identified through RAD sequencing" in Genomic Resources Notes accepted 1 October 2014 to 30 November 2014....

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

    KAUST Repository

    Deng, Dong


    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.

  8. Structure-templated predictions of novel protein interactions from sequence information.

    Directory of Open Access Journals (Sweden)

    Doron Betel


    Full Text Available The multitude of functions performed in the cell are largely controlled by a set of carefully orchestrated protein interactions often facilitated by specific binding of conserved domains in the interacting proteins. Interacting domains commonly exhibit distinct binding specificity to short and conserved recognition peptides called binding profiles. Although many conserved domains are known in nature, only a few have well-characterized binding profiles. Here, we describe a novel predictive method known as domain-motif interactions from structural topology (D-MIST for elucidating the binding profiles of interacting domains. A set of domains and their corresponding binding profiles were derived from extant protein structures and protein interaction data and then used to predict novel protein interactions in yeast. A number of the predicted interactions were verified experimentally, including new interactions of the mitotic exit network, RNA polymerases, nucleotide metabolism enzymes, and the chaperone complex. These results demonstrate that new protein interactions can be predicted exclusively from sequence information.

  9. Structure-templated predictions of novel protein interactions from sequence information. (United States)

    Betel, Doron; Breitkreuz, Kevin E; Isserlin, Ruth; Dewar-Darch, Danielle; Tyers, Mike; Hogue, Christopher W V


    The multitude of functions performed in the cell are largely controlled by a set of carefully orchestrated protein interactions often facilitated by specific binding of conserved domains in the interacting proteins. Interacting domains commonly exhibit distinct binding specificity to short and conserved recognition peptides called binding profiles. Although many conserved domains are known in nature, only a few have well-characterized binding profiles. Here, we describe a novel predictive method known as domain-motif interactions from structural topology (D-MIST) for elucidating the binding profiles of interacting domains. A set of domains and their corresponding binding profiles were derived from extant protein structures and protein interaction data and then used to predict novel protein interactions in yeast. A number of the predicted interactions were verified experimentally, including new interactions of the mitotic exit network, RNA polymerases, nucleotide metabolism enzymes, and the chaperone complex. These results demonstrate that new protein interactions can be predicted exclusively from sequence information.

  10. Large-scale oscillation of structure-related DNA sequence features in human chromosome 21 (United States)

    Li, Wentian; Miramontes, Pedro


    Human chromosome 21 is the only chromosome in the human genome that exhibits oscillation of the (G+C) content of a cycle length of hundreds kilobases (kb) ( 500kb near the right telomere). We aim at establishing the existence of a similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi- and tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10- or 11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting or unwinding, stiffness, and a putative tendency for nucleosome formation.

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

    Energy Technology Data Exchange (ETDEWEB)

    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)


    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.

  12. Structural features of conopeptide genes inferred from partial sequences of the Conus tribblei genome. (United States)

    Barghi, Neda; Concepcion, Gisela P; Olivera, Baldomero M; Lluisma, Arturo O


    The evolvability of venom components (in particular, the gene-encoded peptide toxins) in venomous species serves as an adaptive strategy allowing them to target new prey types or respond to changes in the prey field. The structure, organization, and expression of the venom peptide genes may provide insights into the molecular mechanisms that drive the evolution of such genes. Conus is a particularly interesting group given the high chemical diversity of their venom peptides, and the rapid evolution of the conopeptide-encoding genes. Conus genomes, however, are large and characterized by a high proportion of repetitive sequences. As a result, the structure and organization of conopeptide genes have remained poorly known. In this study, a survey of the genome of Conus tribblei was undertaken to address this gap. A partial assembly of C. tribblei genome was generated; the assembly, though consisting of a large number of fragments, accounted for 2160.5 Mb of sequence. A large number of repetitive genomic elements consisting of 642.6 Mb of retrotransposable elements, simple repeats, and novel interspersed repeats were observed. We characterized the structural organization and distribution of conotoxin genes in the genome. A significant number of conopeptide genes (estimated to be between 148 and 193) belonging to different superfamilies with complete or nearly complete exon regions were observed, ~60 % of which were expressed. The unexpressed conopeptide genes represent hidden but significant conotoxin diversity. The conotoxin genes also differed in the frequency and length of the introns. The interruption of exons by long introns in the conopeptide genes and the presence of repeats in the introns may indicate the importance of introns in facilitating recombination, evolution and diversification of conotoxins. These findings advance our understanding of the structural framework that promotes the gene-level molecular evolution of venom peptides.

  13. 1D-1D Coulomb drag in a 6 Million Mobility Bi-layer Heterostructure (United States)

    Bilodeau, Simon; Laroche, Dominique; Xia, Jian-Sheng; Lilly, Mike; Reno, John; Pfeiffer, Loren; West, Ken; Gervais, Guillaume

    We report Coulomb drag measurements in vertically-coupled quantum wires. The wires are fabricated in GaAs/AlGaAs bilayer heterostructures grown from two different MBE chambers: one at Sandia National Laboratories (1.2M mobility), and the other at Princeton University (6M mobility). The previously observed positive and negative drag signals are seen in both types of devices, demonstrating the robustness of the result. However, attempts to determine the temperature dependence of the drag signal in the 1D regime proved challenging in the higher mobility heterostructure (Princeton), in part because of difficulties in aligning the wires within the same transverse subband configuration. Nevertheless, this work, performed at the Microkelvin laboratory of the University of Florida, is an important proof-of-concept for future investigations of the temperature dependence of the 1D-1D drag signal down to a few mK. Such an experiment could confirm the Luttinger charge density wave interlocking predicted to occur in the wires. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94AL8500.

  14. Relocation and seismogenic structure of the 1998 Zhangbei-Shangyi earthquake sequence

    Institute of Scientific and Technical Information of China (English)

    杨智娴; 陈运泰; 张宏志


    On January 10, 1998, an earthquake of ML=6.2 occurred in the border region between the Zhangbei County and Shangyi County of Hebei Province. This earthquake has been the most significant event occurred in the northern China in the recent years. Historical seismicity in the Zhangbei-Shangyi region was very low. In the epicentral area no active fault capable of generating a moderate earthquake like this event was found. The earthquake locations of the main shock and its aftershocks of the Zhangbei-Shangyi earthquake sequence given by several agencies and authors were diverse and the resulted hypocentral distribution revealed no any dominant horizontal lineation. To study the seismogenic structure of the Zhangbei-Shangyi earthquake, in this paper the main shock and its aftershocks with ML≥3.0 of the Zhangbei-Shangyi earthquake sequence were relocated using the master event relative relocation algorithm. The relocated results show that the epicentral location of the main shock was 41.145°N, 114.462°E, which was located 4 km to the NE of the macro-epicenter of the main shock. The relocated focal depth of the main shock was 15 km. The hypocenters of the aftershocks distributed in a nearly vertical N20°E-striking plane and its vicinity. The relocated results of the Zhangbei-Shangyi earthquake sequence clearly indicated that the seismogenic structure of this event was a nearly N-S- to NNE-SSW-striking fault with right-lateral and reverse slip, and that the occurrence of this event was associated with the horizontal and ENE-oriented compressive tectonic stress, which was compatible with the tectonic stress field in the northern China.

  15. Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

    Directory of Open Access Journals (Sweden)

    Masfique Mehedi

    Full Text Available 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.

  16. Cloning, Sequencing, Purification, and Crystal Structure of Grenache (Vitis vinifera) Polyphenol Oxidase

    Energy Technology Data Exchange (ETDEWEB)

    Virador, V.; Reyes Grajeda, J; Blanco-Labra, A; Mendiola-Olaya, E; Smith, G; Moreno, A; Whitaker, J


    The full-length cDNA sequence (P93622{_}VITVI) of polyphenol oxidase (PPO) cDNA from grape Vitis vinifera L., cv Grenache, was found to encode a translated protein of 607 amino acids with an expected molecular weight of ca. 67 kDa and a predicted pI of 6.83. The translated amino acid sequence was 99%, identical to that of a white grape berry PPO (1) (5 out of 607 amino acid potential sequence differences). The protein was purified from Grenache grape berries by using traditional methods, and it was crystallized with ammonium acetate by the hanging-drop vapor diffusion method. The crystals were orthorhombic, space group C2221. The structure was obtained at 2.2 {angstrom} resolution using synchrotron radiation using the 39 kDa isozyme of sweet potato PPO (PDB code: 1BT1) as a phase donor. The basic symmetry of the cell parameters (a, b, and c and {alpha}, {beta}, and {gamma}) as well as in the number of asymmetric units in the unit cell of the crystals of PPO, differed between the two proteins. The structures of the two enzymes are quite similar in overall fold, the location of the helix bundles at the core, and the active site in which three histidines bind each of the two catalytic copper ions, and one of the histidines is engaged in a thioether linkage with a cysteine residue. The possibility that the formation of the Cys-His thioether linkage constitutes the activation step is proposed. No evidence of phosphorylation or glycoslyation was found in the electron density map. The mass of the crystallized protein appears to be only 38.4 kDa, and the processing that occurs in the grape berry that leads to this smaller size is discussed.

  17. Synthetic CpG islands reveal DNA sequence determinants of chromatin structure (United States)

    Wachter, Elisabeth; Quante, Timo; Merusi, Cara; Arczewska, Aleksandra; Stewart, Francis; Webb, Shaun; Bird, Adrian


    The mammalian genome is punctuated by CpG islands (CGIs), which differ sharply from the bulk genome by being rich in G + C and the dinucleotide CpG. CGIs often include transcription initiation sites and display ‘active’ histone marks, notably histone H3 lysine 4 methylation. In embryonic stem cells (ESCs) some CGIs adopt a ‘bivalent’ chromatin state bearing simultaneous ‘active’ and ‘inactive’ chromatin marks. To determine whether CGI chromatin is developmentally programmed at specific genes or is imposed by shared features of CGI DNA, we integrated artificial CGI-like DNA sequences into the ESC genome. We found that bivalency is the default chromatin structure for CpG-rich, G + C-rich DNA. A high CpG density alone is not sufficient for this effect, as A + T-rich sequence settings invariably provoke de novo DNA methylation leading to loss of CGI signature chromatin. We conclude that both CpG-richness and G + C-richness are required for induction of signature chromatin structures at CGIs. DOI: PMID:25259796

  18. Functional and Structural Overview of G-Protein-Coupled Receptors Comprehensively Obtained from Genome Sequences

    Directory of Open Access Journals (Sweden)

    Makiko Suwa


    Full Text Available An understanding of the functional mechanisms of G-protein-coupled receptors (GPCRs is very important for GPCR-related drug design. We have developed an integrated GPCR database (SEVENS that includes 64,090 reliable GPCR genes comprehensively identified from 56 eukaryote genome sequences, and overviewed the sequences and structure spaces of the GPCRs. In vertebrates, the number of receptors for biological amines, peptides, etc. is conserved in most species, whereas the number of chemosensory receptors for odorant, pheromone, etc. significantly differs among species. The latter receptors tend to be single exon type or a few exon type and show a high ratio in the numbers of GPCRs, whereas some families, such as Class B and Class C receptors, have long lengths due to the presence of many exons. Statistical analyses of amino acid residues reveal that most of the conserved residues in Class A GPCRs are found in the cytoplasmic half regions of transmembrane (TM helices, while residues characteristic to each subfamily found on the extracellular half regions. The 69 of Protein Data Bank (PDB entries of complete or fragmentary structures could be mapped on the TM/loop regions of Class A GPCRs covering 14 subfamilies.

  19. Analyses of the Sequence and Structural Properties Corresponding to Pentapeptide and Large Palindromes in Proteins.

    Directory of Open Access Journals (Sweden)

    Settu Sridhar

    Full Text Available The analyses of 3967 representative proteins selected from the Protein Data Bank revealed the presence of 2803 pentapeptide and large palindrome sequences with known secondary structure conformation. These represent 2014 unique palindrome sequences. 60% palindromes are not associated with any regular secondary structure and 28% are in helix conformation, 11% in strand conformation and 1% in the coil conformation. The average solvent accessibility values are in the range between 0-155.28 Å2 suggesting that the palindromes in proteins can be either buried, exposed to the solvent or share an intermittent property. The number of residue neighborhood contacts defined by interactions ≤ 3.2 Ǻ is in the range between 0-29 residues. Palindromes of the same length in helix, strand and coil conformation are associated with different amino acid residue preferences at the individual positions. Nearly, 20% palindromes interact with catalytic/active site residues, ligand or metal ions in proteins and may therefore be important for function in the corresponding protein. The average hydrophobicity values for the pentapeptide and large palindromes range between -4.3 to +4.32 and the number of palindromes is almost equally distributed between the negative and positive hydrophobicity values. The palindromes represent 107 different protein families and the hydrolases, transferases, oxidoreductases and lyases contain relatively large number of palindromes.

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

    Directory of Open Access Journals (Sweden)

    Akutsu Tatsuya


    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Adachi, Motoyasu, E-mail:; Shimizu, Rumi; Kuroki, Ryota [Japan Atomic Energy Agency, Shirakatashirane 2-4, Nakagun Tokaimura, Ibaraki 319-1195 (Japan); Blaber, Michael [Japan Atomic Energy Agency, Shirakatashirane 2-4, Nakagun Tokaimura, Ibaraki 319-1195 (Japan); Florida State University, Tallahassee, FL 32306-4300 (United States)


    An artificial protein with three complete sequence repeats was created and the structure was determined by X-ray crystallography. The structure showed threefold symmetry even though there is an amino- and carboxy-terminal. The artificial protein with threefold symmetry may be useful as a scaffold to capture small materials with C3 symmetry. Symfoil-4P is a de novo protein exhibiting the threefold symmetrical β-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

  2. Modeling atrazine transport in soil columns with HYDRUS-1D

    Directory of Open Access Journals (Sweden)



    Full Text Available Both physical and chemical processes affect the fate and transport of herbicides. It is useful to simulate these processes with computer programs to predict solute movement. Simulations were run with HYDRUS-1D to identify the sorption and degradation parameters of atrazine through calibration from the breakthrough curves (BTCs. Data from undisturbed and disturbed soil column experiments were compared and analyzed using the dual-porosity model. The study results show that the values of dispersivity are slightly lower in disturbed columns, suggesting that the more heterogeneous the structure is, the higher the dispersivity. Sorption parameters also show slight variability, which is attributed to the differences in soil properties, experimental conditions and methods, or other ecological factors. For both of the columns, the degradation rates were similar. Potassium bromide was used as a conservative non-reactive tracer to characterize the water movement in columns. Atrazine BTCs exhibited significant tailing and asymmetry, indicating non-equilibrium sorption during solute transport. The dual-porosity model was verified to best fit the BTCs of the column experiments. Greater or lesser concentration of atrazine spreading to the bottom of the columns indicated risk of groundwater contamination. Overall, HYDRUS-1D successfully simulated the atrazine transport in soil columns.

  3. Nucleotide sequence of a crustacean 18S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs. (United States)

    Nelles, L; Fang, B L; Volckaert, G; Vandenberghe, A; De Wachter, R


    The primary structure of the gene for 18 S rRNA of the crustacean Artemia salina was determined. The sequence has been aligned with 13 other small ribosomal subunit RNA sequences of eukaryotic, archaebacterial, eubacterial, chloroplastic and plant mitochondrial origin. Secondary structure models for these RNAs were derived on the basis of previously proposed models and additional comparative evidence found in the alignment. Although there is a general similarity in the secondary structure models for eukaryotes and prokaryotes, the evidence seems to indicate a different topology in a central area of the structures.

  4. Growth and Magnetic Characterization of 1D Permalloy Nanowires Using Self Developed Anodic Aluminium Oxide Templates. (United States)

    Singh, Ashutosh K; Mandal, Kalyan


    1D Permalloy refers to arrays of nanowires (NWs) made of an alloy of Ni and Fe with 80 and 20 at% composition respectively. In the present work 1 D Permalloy NWs arrays were fabricated into the pores of self engineered Anodic Aluminium Oxide (AAO) templates by a simple electrodeposition technique (EDT). By varying the anodization voltage and parameters of the electrolyte solutions we developed AAO templates with different average pore diameters (40 nm to 70 nm) and developed 1D Permalloy NWs within them. Structural characterization of AAO templates and 1D Permalloy NWs were performed by Transmission and Scanning Electron Microscopy (TEM and SEM respectively). X-ray diffraction (XRD) studies of 1D Permalloy NWs showed their fcc crystalline structure and the AAO template was found to be amorphous in nature. Magnetic studies showed the 1D Permalloy NWs arrays to have strong shape anisotropy, and the easy axis was found to be parallel to the NWs axis. We studied the angular dependence of magnetic properties of the NWs. Coercivity (Hc) and remanence (Mr/Ms) measured along the NWs axis were found to be higher than those measured in a direction perpendicular to the NWs axis. 1D Permalloy NWs developed in this work have the potential to be used in magnetic recording devices.

  5. The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles). (United States)

    Bhattacharyya, A; Lilley, D M


    We have studied the structure and reactivities of two kinds of mismatched DNA sequences--unopposed bases, or bulges, and multiple mismatched pairs of bases. These were generated in a constant sequence environment, in relatively long DNA fragments, using a technique based on heteroduplex formation between sequences cloned into single-stranded M13 phage. The mismatched sequences were studied from two points of view, viz 1. The mobility of the fragments on gel electrophoresis in polyacrylamide was studied in order to examine possible bending of the DNA due to the presence of the mismatch defect. Such bending would constitute a global effect on the conformation of the molecule. 2. Sequences in and around the mismatches were studied using enzyme and chemical probes of DNA structure. This would reveal more local structural effects of the mismatched sequences. We observed that the structures of the bulges and the multiple mismatches appear to be fundamentally different. The bulged sequences exhibited a large gel retardation, consistent with a significant bending of the DNA at the bulge, and whose magnitude depends on the number of mismatched bases. The larger bulges were sensitive to cleavage by single-strand specific nucleases, and modified by diethyl pyrocarbonate (adenines) or osmium tetroxide (thymines) in a non-uniform way, suggesting that the bulges have a precise structure that leads to exposure of some, but not all, of the bases. In contrast the multiple mismatches ('bubbles') cause very much less bending of the DNA fragment in which they occur, and uniform patterns of chemical reactivity along the length of the mismatched sequences, suggesting a less well defined, and possibly flexible, structure. The precise structure of the bulges suggests that such features may be especially significant for recognition by proteins.

  6. The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ruiying; Zheng, Han; Preamplume, Gan; Shao, Yaming; Li, Hong [FSU


    The repeat-associated mysterious proteins (RAMPs) comprise the most abundant family of proteins involved in prokaryotic immunity against invading genetic elements conferred by the clustered regularly interspaced short palindromic repeat (CRISPR) system. Cas6 is one of the first characterized RAMP proteins and is a key enzyme required for CRISPR RNA maturation. Despite a strong structural homology with other RAMP proteins that bind hairpin RNA, Cas6 distinctly recognizes single-stranded RNA. Previous structural and biochemical studies show that Cas6 captures the 5' end while cleaving the 3' end of the CRISPR RNA. Here, we describe three structures and complementary biochemical analysis of a noncatalytic Cas6 homolog from Pyrococcus horikoshii bound to CRISPR repeat RNA of different sequences. Our study confirms the specificity of the Cas6 protein for single-stranded RNA and further reveals the importance of the bases at Positions 5-7 in Cas6-RNA interactions. Substitutions of these bases result in structural changes in the protein-RNA complex including its oligomerization state.

  7. In Silico sequence analysis and molecular modeling of the three-dimensional structure of DAHP synthase from Pseudomonas fragi. (United States)

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


    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 (β/α)(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.

  8. Fast Large Scale Structure Perturbation Theory using 1D FFTs

    CERN Document Server

    Schmittfull, Marcel; McDonald, Patrick


    The usual fluid equations describing the large-scale evolution of mass density in the universe can be written as local in the density, velocity divergence, and velocity potential fields. As a result, the perturbative expansion in small density fluctuations, usually written in terms of convolutions in Fourier space, can be written as a series of products of these fields evaluated at the same location in configuration space. Based on this, we establish a new method to numerically evaluate the 1-loop power spectrum (i.e., Fourier transform of the 2-point correlation function) with one-dimensional Fast Fourier Transforms. This is exact and a few orders of magnitude faster than previously used numerical approaches. Numerical results of the new method are in excellent agreement with the standard quadrature integration method. This fast model evaluation can in principle be extended to higher loop order where existing codes become painfully slow. Our approach follows by writing higher order corrections to the 2-point...

  9. The primary structure of the hemoglobin of Malayan sun bear (Helarctos malayanus, Carnivora) and structural comparison to other hemoglobin sequences. (United States)

    Hofmann, O; Braunitzer, G; Göltenboth, R


    The complete primary structure of the alpha- and beta-chains of the hemoglobin of Malayan Sun Bear (Helarctos malayanus) is presented. After cleavage of the heme-protein link and chain separation by RP-HPLC, amino-acid sequences were determined by Edman degradation in liquid- and gas-phase sequenators. An interesting result of this work is the demonstration that the hemoglobin of Malayan Sun Bear is identical to the hemoglobins of Polar Bear (Ursus maritimus) and Asiatic Black Bear (Ursus tibetanus). The paper gives an updated table of identical hemoglobin chains from different species. This paper may be considered as a compilation of work on the genetic relationship of Pandas.

  10. Analysis list: Nr1d2 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Nr1d2 Liver + mm9 ...

  11. In vivo 1D and 2D correlation MR spectroscopy of the soleus muscle at 7T (United States)

    Ramadan, Saadallah; Ratai, Eva-Maria; Wald, Lawrence L.; Mountford, Carolyn E.


    AimThis study aims to (1) undertake and analyse 1D and 2D MR correlation spectroscopy from human soleus muscle in vivo at 7T, and (2) determine T1 and T2 relaxation time constants at 7T field strength due to their importance in sequence design and spectral quantitation. MethodSix healthy, male volunteers were consented and scanned on a 7T whole-body scanner (Siemens AG, Erlangen, Germany). Experiments were undertaken using a 28 cm diameter detunable birdcage coil for signal excitation and an 8.5 cm diameter surface coil for signal reception. The relaxation time constants, T1 and T2 were recorded using a STEAM sequence, using the 'progressive saturation' method for the T1 and multiple echo times for T2. The 2D L-Correlated SpectroscopY (L-COSY) method was employed with 64 increments (0.4 ms increment size) and eight averages per scan, with a total time of 17 min. ResultsT1 and T2 values for the metabolites of interest were determined. The L-COSY spectra obtained from the soleus muscle provided information on lipid content and chemical structure not available, in vivo, at lower field strengths. All molecular fragments within multiple lipid compartments were chemically shifted by 0.20-0.26 ppm at this field strength. 1D and 2D L-COSY spectra were assigned and proton connectivities were confirmed with the 2D method. ConclusionIn vivo 1D and 2D spectroscopic examination of muscle can be successfully recorded at 7T and is now available to assess lipid alterations as well as other metabolites present with disease. T1 and T2 values were also determined in soleus muscle of male healthy volunteers.

  12. Periodic Properties of 1D FE Discrete Models in High Frequency Dynamics

    Directory of Open Access Journals (Sweden)

    A. Żak


    Full Text Available Finite element discrete models of various engineering 1D structures may be considered as structures of certain periodic characteristics. The source of this periodicity comes from the discontinuity of stress/strain field between the elements. This behaviour remains unnoticeable, when low frequency dynamics of these structures is investigated. At high frequency regimes, however, its influence may be strong enough to dominate calculated structural responses distorting or even falsifying them completely. In this paper, certain computational aspects of structural periodicity of 1D FE discrete models are discussed by the authors. In this discussion, the authors focus their attention on an exemplary problem of 1D rod modelled according to the elementary theory.

  13. Analysis list: Nr1d1 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available Nr1d1 Adipocyte,Cardiovascular,Liver,Neural + mm9,,,http://dbarchive.biosc

  14. A rostro-caudal gradient of structured sequence processing in the left inferior frontal gyrus. (United States)

    Uddén, Julia; Bahlmann, Jörg


    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.

  15. Star formation along the Hubble sequence: Radial structure of the star formation of CALIFA galaxies

    CERN Document Server

    Delgado, R M González; Pérez, E; García-Benito, R; Fernández, R López; Lacerda, E A D; Cortijo-Ferrero, C; de Amorim, A L; Asari, N Vale; Sánchez, S F; Walcher, C J; Wisotzki, L; Mast, D; Alves, J; Ascasibar, Y; Bland-Hawthorn, J; Galbany, L; Kennicutt, R C; Márquez, I; Masegosa, J; Mollá, M; Sánchez-Blázquez, P; Vílchez, J M


    The aim of this paper is to characterize the radial structure of the star formation rate (SFR) in galaxies in the nearby Universe as represented by the CALIFA survey. The sample under study contains 416 galaxies observed with IFS, covering a wide range of Hubble types and stellar masses. Spectral synthesis techniques are applied to obtain radial profiles of the intensity of the star formation rate in the recent past, and the local sSFR. To emphasize the behavior of these properties for galaxies that are on and off the main sequence of star formation (MSSF) we stack the individual radial profiles in bins of galaxy morphology and stellar masses. Our main results are: a) The intensity of SFR shows declining profiles that exhibit very little differences between spirals. The dispersion between the profiles is significantly smaller in late type spirals. This confirms that the MSSF is a sequence of galaxies with nearly constant intensity of SFR b) sSFR values scale with Hubble type and increase radially outwards, wi...

  16. Geographical and Temporal Structures of Legionella pneumophila Sequence Types in Comunitat Valenciana (Spain), 1998 to 2013. (United States)

    Sánchez-Busó, Leonor; Coscollà, Mireia; Palero, Ferran; Camaró, María Luisa; Gimeno, Ana; Moreno, Pilar; Escribano, Isabel; López Perezagua, María Mar; Colomina, Javier; Vanaclocha, Herme; González-Candelas, Fernando


    Legionella pneumophila is an accidental human pathogen associated with aerosol formation in water-related sources. High recombination rates make Legionella populations genetically diverse, and nearly 2,000 different sequence types (STs) have been described to date for this environmental pathogen. The spatial distribution of STs is extremely heterogeneous, with some variants being present worldwide and others being detected at only a local scale. Similarly, some STs have been associated with disease outbreaks, such as ST578 or ST23. Spain is among the European countries with the highest incidences of reported legionellosis cases, and specifically, Comunitat Valenciana (CV) is the second most affected area in the country. In this work, we aimed at studying the overall diversity of Legionella pneumophila populations found in the period from 1998 to 2013 in 79 localities encompassing 23 regions within CV. To do so, we performed sequence-based typing (SBT) on 1,088 L. pneumophila strains detected in the area from both environmental and clinical sources. A comparison with the genetic structuring detected in a global data set that included 20 European and 7 non-European countries was performed. Our results reveal a level of diversity in CV that can be considered representative of the diversity found in other countries worldwide.

  17. CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles. (United States)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole; Petersen, Thomas Nordahl


    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 web server is available at

  18. Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics

    Directory of Open Access Journals (Sweden)

    Brunham Robert C


    Full Text Available Abstract Background We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, maintainability and safety work to model time-to-failure of mechanical devices, mechanisms, building constructions and equipment. Results We have found that the Weibull function describes protein fold distribution within and among genomes more accurately than conventional power functions which have been used in a number of structural genomic studies reported to date. It has also been found that the Weibull reliability parameter β for protein fold distributions varies between genomes and may reflect differences in rates of gene duplication in evolutionary history of organisms. Conclusions The results of this work demonstrate that reliability analysis can provide useful insights and testable predictions in the fields of comparative and structural genomics.

  19. Recursive organizer (ROR): an analytic framework for sequence-based association analysis. (United States)

    Zhao, Lue Ping; Huang, Xin


    The advent of next-generation sequencing technologies affords the ability to sequence thousands of subjects cost-effectively, and is revolutionizing the landscape of genetic research. With the evolving genotyping/sequencing technologies, it is not unrealistic to expect that we will soon obtain a pair of diploidic fully phased genome sequences from each subject in the near future. Here, in light of this potential, we propose an analytic framework called, recursive organizer (ROR), which recursively groups sequence variants based upon sequence similarities and their empirical disease associations, into fewer and potentially more interpretable super sequence variants (SSV). As an illustration, we applied ROR to assess an association between HLA-DRB1 and type 1 diabetes (T1D), discovering SSVs of HLA-DRB1 with sequence data from the Wellcome Trust Case Control Consortium. Specifically, ROR reduces 36 observed unique HLA-DRB1 sequences into 8 SSVs that empirically associate with T1D, a fourfold reduction of sequence complexity. Using HLA-DRB1 data from Type 1 Diabetes Genetics Consortium as cases and data from Fred Hutchinson Cancer Research Center as controls, we are able to validate associations of these SSVs with T1D. Further, SSVs consist of nine nucleotides, and each associates with its corresponding amino acids. Detailed examination of these selected amino acids reveals their potential functional roles in protein structures and possible implication to the mechanism of T1D.

  20. Variable structure multiple model for articulated human motion tracking from monocular video sequences

    Institute of Scientific and Technical Information of China (English)

    HAN Hong; TONG MingLei; CHEN ZhiChao; FAN YouJian


    A new model-based human body tracking framework with learning-based theory is introduced inthis paper.We propose a variable structure multiple model (VSMM) framework to address challenging problems such as uncertainty of motion styles,imprecise detection of feature points,and ambiguity of joint locations.Key human joint points are detected automatically and the undetected points are estimated with Kalman filters.Multiple motion models are learned from motion capture data using a ridge regression method.The model set that covers the total motion set is designed on the basis of topological and compatibility relationships,while the VSMM algorithm is used to estimate quaternion vectors of joint rotation.Experiments using real image sequences and simulation videos demonstrate the high efficiency of our proposed human tracking framework.

  1. Inferring action structure and causal relationships in continuous sequences of human action. (United States)

    Buchsbaum, Daphna; Griffiths, Thomas L; Plunkett, Dillon; Gopnik, Alison; Baldwin, Dare


    In the real world, causal variables do not come pre-identified or occur in isolation, but instead are embedded within a continuous temporal stream of events. A challenge faced by both human learners and machine learning algorithms is identifying subsequences that correspond to the appropriate variables for causal inference. A specific instance of this problem is action segmentation: dividing a sequence of observed behavior into meaningful actions, and determining which of those actions lead to effects in the world. Here we present a Bayesian analysis of how statistical and causal cues to segmentation should optimally be combined, as well as four experiments investigating human action segmentation and causal inference. We find that both people and our model are sensitive to statistical regularities and causal structure in continuous action, and are able to combine these sources of information in order to correctly infer both causal relationships and segmentation boundaries.

  2. Analysis of cDNA sequence, protein structure and expression of parotid secretory protein in pig

    Institute of Scientific and Technical Information of China (English)

    YIN Haifang; FAN Baoliang; ZHAO Zhihui; LIU Zhaoliang; FEI Jing; LI Ning


    Parotid secretory protein (PSP) secreted abundantly in saliva, whose function is related with the anti-bacterial effect. The PSP cDNA has been isolated from pig parotid glands by 3′ and 5′ rapid amplification of cDNA end (RACE),based on the conserved signal peptide region among the known mammalian PSP. Theresult of homologous comparison shows that pig PSP and human PSP shares the high identity at the level of the primary, secondary and tertiary protein structure. A search for functionally significant protein motifs revealed a unique amino acid sequence pattern consisting of the residues Leu-X(6)-Leu-X(6)-Leu- X(7)-Leu-X(6)-Leu-X(6)-Leu near the amino-terminal portion of the protein, which is important to its function. RT-PCR, Dot blot and Northern blot analysis demonstrated that PSP was strongly expressed in parotid glands, but not in other tissues.

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

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole;


    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.......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...

  4. Involvement of interstitial telomeric sequences in two new cases of mosaicism for autosomal structural rearrangements. (United States)

    Lévy, Jonathan; Receveur, Aline; Jedraszak, Guillaume; Chantot-Bastaraud, Sandra; Renaldo, Florence; Gondry, Jean; Andrieux, Joris; Copin, Henri; Siffroi, Jean-Pierre; Portnoï, Marie-France


    Mosaicism for an autosomal structural rearrangement that does not involve ring or marker chromosomes is rare. The mechanisms responsible for genome instability have not always been explained. Several studies have shown that interstitial telomeric sequences (ITSs), involved in some mosaic constitutional anomalies, are potent sources of genomic instability. Here we describe two cases of mosaicism for uncommon constitutional autosomal rearrangements, involving ITSs, identified by karyotyping and characterized by FISH and SNP-array analysis. The first patient, a boy with global developmental delay, had a rare type of pure distal 1q inverted duplication (1q32-qter), attached to the end of the short arm of the same chromosome 1, in approximately 35% of his cells. The second patient, a phenotypically normal man, was diagnosed as having mosaic for a balanced non-reciprocal translocation of the distal segment of 7q (7q33qter), onto the terminal region of the short arm of a whole chromosome 12, in approximately 80% of his cells. The remaining 20% of the cells showed an unbalanced state of the translocation, with only the der(7) chromosome. He was ascertained through his malformed fetus carrying a non-mosaic partial monosomy 7q, identified at prenatal diagnosis. We show that pan-telomeric and subtelomeric sequences were observed at the interstitial junction point of the inv dup(1q) and of the der(12)t(7;12), respectively. The present cases and review of the literature suggest that the presence of ITSs at internal sites of the chromosomes may explain mechanisms of the patients's mosaic structural rearrangements.

  5. Predicting deleterious nsSNPs: an analysis of sequence and structural attributes

    Directory of Open Access Journals (Sweden)

    Saqi Mansoor AS


    Full Text Available Abstract Background There has been an explosion in the number of single nucleotide polymorphisms (SNPs within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs, some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learning methods. We also address the common problem of balance within machine learning methods and show the effect of imbalance on nsSNP function prediction. We show that nsSNP function prediction can be significantly improved by 100% undersampling of the majority class. The learnt rules were then applied to make predictions of function on all nsSNPs within Ensembl. Results The measure of prediction success is greatly affected by the level of imbalance in the training dataset. We found the balanced dataset that included all attributes produced the best prediction. The performance as measured by the Matthews correlation coefficient (MCC varied between 0.49 and 0.25 depending on the imbalance. As previously observed, the degree of sequence conservation at the nsSNP position is the single most useful attribute. In addition to conservation, structural predictions made using a balanced dataset can be of value. Conclusion The predictions for all nsSNPs within Ensembl, based on a balanced dataset using all attributes, are available as a DAS annotation. Instructions for adding the track to Ensembl are at

  6. Structural organization, nucleotide sequence, and regulation of the Haemophilus influenzae rec-1+ gene. (United States)

    Zulty, J J; Barcak, G J


    The Haemophilus influenzae rec-1+ protein plays a central role in DNA metabolism, participating in general homologous recombination, recombinational (postreplication) DNA repair, and prophage induction. Although many H. influenzae rec-1 mutants have been phenotypically characterized, little is known about the rec-1+ gene at the molecular level. In this study, we present the genetic organization of the rec-1+ locus, the DNA sequence of rec-1+, and studies of the transcriptional regulation of rec-1+ during cellular assault by DNA-damaging agents and during the induction of competence for genetic transformation. Although little is known about promoter structure in H. influenzae, we identified a potential rec-1+ promoter that is identical in 11 of 12 positions to the bacterial sigma 70-dependent promoter consensus sequence. Results from a primer extension analysis revealed that the start site of rec-1+ transcription is centered 6 nucleotides downstream of this promoter. We identified potential DNA binding sites in the rec-1+ gene for LexA, integration host factor, and cyclic AMP receptor protein. We obtained evidence that at least one of the proposed cyclic AMP receptor protein binding sites is active in modulating rec-1+ transcription. This finding makes rec-1+ control circuitry novel among recA+ homologs. Two H. influenzae DNA uptake sequences that may function as a transcription termination signal were identified in inverted orientations at the end of the rec-1+ coding sequence. In addition, we report the first use of the Escherichia coli lacZ operon fusion technique in H. influenzae to study the transcriptional control of rec-1+. Our results indicate that rec-1+ is transcriptionally induced about threefold during DNA-damaging events. Furthermore, we show that rec-1+ can substitute for recA+ in E. coli to modulate SOS induction of dinB1 expression. Surprisingly, although 5% of the H. influenzae genome is in the form of single-stranded DNA during competence for

  7. FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Rapacki, Krzysztof; Stærfeldt, Hans Henrik;


    FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB) f...

  8. Pleurotus ostreatus heme peroxidases: an in silico analysis from the genome sequence to the enzyme molecular structure. (United States)

    Ruiz-Dueñas, Francisco J; Fernández, Elena; Martínez, María Jesús; Martínez, Angel T


    An exhaustive screening of the Pleurotus ostreatus genome was performed to search for nucleotide sequences of heme peroxidases in this white-rot fungus, which could be useful for different biotechnological applications. After sequence identification and manual curation of the corresponding genes and cDNAs, the deduced amino acid sequences were converted into structural homology models. A comparative study of these sequences and their structural models with those of known fungal peroxidases revealed the complete inventory of heme peroxidases of this fungus. This consists of cytochrome c peroxidase and ligninolytic peroxidases, including manganese peroxidase and versatile peroxidase but not lignin peroxidase, as representative of the "classical" superfamily of plant, fungal, and bacterial peroxidases; and members of two relatively "new" peroxidase superfamilies, namely heme-thiolate peroxidases, here described for the first time in a fungus from the genus Pleurotus, and dye-decolorizing peroxidases, already known in P. ostreatus but still to be thoroughly explored and characterized.

  9. Camps 2.0: exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins. (United States)

    Neumann, Sindy; Hartmann, Holger; Martin-Galiano, Antonio J; Fuchs, Angelika; Frishman, Dmitrij


    Structural bioinformatics of membrane proteins is still in its infancy, and the picture of their fold space is only beginning to emerge. Because only a handful of three-dimensional structures are available, sequence comparison and structure prediction remain the main tools for investigating sequence-structure relationships in membrane protein families. Here we present a comprehensive analysis of the structural families corresponding to α-helical membrane proteins with at least three transmembrane helices. The new version of our CAMPS database (CAMPS 2.0) covers nearly 1300 eukaryotic, prokaryotic, and viral genomes. Using an advanced classification procedure, which is based on high-order hidden Markov models and considers both sequence similarity as well as the number of transmembrane helices and loop lengths, we identified 1353 structurally homogeneous clusters roughly corresponding to membrane protein folds. Only 53 clusters are associated with experimentally determined three-dimensional structures, and for these clusters CAMPS is in reasonable agreement with structure-based classification approaches such as SCOP and CATH. We therefore estimate that ∼1300 structures would need to be determined to provide a sufficient structural coverage of polytopic membrane proteins. CAMPS 2.0 is available at

  10. Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences. (United States)

    Lemesle-Varloot, L; Henrissat, B; Gaboriaud, C; Bissery, V; Morgat, A; Mornon, J P


    Hydrophobic cluster analysis (HCA) [15] is a very efficient method to analyse and compare protein sequences. Despite its effectiveness, this method is not widely used because it relies in part on the experience and training of the user. In this article, detailed guidelines as to the use of HCA are presented and include discussions on: the definition of the hydrophobic clusters and their relationships with secondary and tertiary structures; the length of the clusters; the amino acid classification used for HCA; the HCA plot programs; and the working strategies. Various procedures for the analysis of a single sequence are presented: structural segmentation, structural domains and secondary structure evaluation. Like most sequence analysis methods, HCA is more efficient when several homologous sequences are compared. Procedures for the detection and alignment of distantly related proteins by HCA are described through several published examples along with 2 previously unreported cases: the beta-glucosidase from Ruminococcus albus is clearly related to the beta-glucosidases from Clostridum thermocellum and Hansenula anomala although they display a reverse organization of their constitutive domains; the alignment of the sequence of human GTPase activating protein with that of the Crk oncogene is presented. Finally, the pertinence of HCA in the identification of important residues for structure/function as well as in the preparation of homology modelling is discussed.

  11. Sequence Analysis and Structural Prediction of the Severe Acute Respiratory Syndrome Coronavirus nsp5

    Institute of Scientific and Technical Information of China (English)

    Jia-Hai LU; Nan-Shan ZHONG; Ding-Mei ZHANG; Guo-Ling WANG; Zhong-Min GUO; Juan LI; Bing-Yan TAN; Li-Ping OU-YANG; Wen-Hua LING; Xin-Bing YU


    The non-structural proteins (nsp or replicase proteins) of coronaviruses are relatively conserved and can be effective targets for drugs. Few studies have been conducted into the function of the severe acute respiratory syndrome coronavirus (SARS-CoV) nsp5. In this study, bioinformatics methods were employed to predict the secondary structure and construct 3-D models of the SARS-CoV GD strain nsp5. Sequencing and sequential comparison was performed to analyze the mutation trend of the polymerase nsp5 gene during the epidemic process using a nucleotide-nucleotide basic local alignment search tool (BLASTN) and a protein-protein basic local alignment search tool (BLASTP). The results indicated that the nsp5 gene was steady during the epidemic process and the protein was homologous with other coronavirus nsp5 proteins. The protein encoded by the nsp5 gene was expressed in COS-7 cells and analyzed by sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE). This study provided the foundation for further exploration of the protein's biological function, and contributed to the search for anti-SARS-CoV drugs.

  12. Sequence-specific size, structure, and stability of tight protein knots

    CERN Document Server

    Dzubiella, Joachim


    Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport, e.g., as in cellular threading or translocation processes through narrow biological pores. Here we investigate tigh peptide knot (TPK) characteristics in detail by pulling selected 3_1 and 4_1-knotted peptides using all-atom molecular dynamics computer simulations. We find that the 3_1 and 4_1-TPK lengths are typically Delta l~4.7 nm and 6.9 nm, respectively, for a wide range of tensions (F < 1.5 nN), pointing to a pore diameter of ~2 nm below which a translocated knotted protein might get stuck. The 4_1-knot length is in agreement with recent AFM pulling experiments. Detailed TPK characteristics however, may be sequence-specific: we find a different size and structural behavior in polyglycines, and, strikingly, a strong hydrogen bonding and water molecule trapping capabi...

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

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

  14. The Pollino Seismic Sequence: Activated Graben Structures in a Seismic Gap (United States)

    Rößler, Dirk; Passarelli, Luigi; Govoni, Aladino; Bindi, Dino; Cesca, Simone; Hainzl, Sebatian; Maccaferri, Francesco; Rivalta, Eleonora; Woith, Heiko; Dahm, Torsten


    The Mercure Basin (MB) and the Castrovillari Fault (CF) in the Pollino range (Southern Apennines, Italy) represent one of the most prominent seismic gaps in the Italian seismic catalogue, with no M>5.5 earthquakes during the last centuries. In historical times several swarm-like seismic sequences occurred in the area including two intense swarms within the past two decades. The most energetic one started in 2010 and has been still active in 2014. The seismicity culminated in autumn 2012 with a M=5 event on 25 October. The range hosts a number of opposing normal faults forming a graben-like structure. Their rheology and their interactions are unclear. Current debates include the potential of the MB and the CF to host large earthquakes and the style of deformation. Understanding the seismicity and the behaviour of the faults is necessary to assess the tectonics and the seismic hazard. The GFZ German Research Centre for Geosciences and INGV, Italy, have jointly monitored the ongoing seismicity using a small-aperture seismic array, integrated in a temporary seismic network. Based on this installation, we located more than 16,000 local earthquakes that occurred between November 2012 and September 2014. Here we investigate quantitatively all the phases of the seismic sequence starting from January 2010. Event locations along with moment tensor inversion constrain spatially the structures activated by the swarm and the migration pattern of the seismicity. The seismicity forms clusters concentrated within the southern part of the MB and along the Pollino Fault linking MB and CF. Most earthquakes are confined to the upper 10 km of the crust in an area of ~15x15 km2. However, sparse seismicity at depths between 15 and 20 km and moderate seismicity further north with deepening hypocenters also exist. In contrast, the CF appears aseismic; only the northern part has experienced micro-seismicity. The spatial distribution is however more complex than the major tectonic structures

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

    Directory of Open Access Journals (Sweden)

    Manzini Giovanni


    (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

  16. An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment

    NARCIS (Netherlands)

    Bauer, M.; Klau, G.W.; Reinert, K.


    One of the main tasks in computational biology is the computation of alignments of genomic sequences to reveal their commonalities. In case of DNA or protein sequences, sequence information alone is usually sufficient to compute reliable alignments. RNA molecules, however, build spatial confor

  17. Complete plastid genome sequence of Primula sinensis (Primulaceae: structure comparison, sequence variation and evidence for accD transfer to nucleus

    Directory of Open Access Journals (Sweden)

    Tong-Jian Liu


    Full Text Available Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp were separated by a large single-copy region (82,064 bp and a small single-copy region (17,725 bp. The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36–rps8, rps16–trnQ, trnH–psbA and ndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis.

  18. Elucidation of the structural determinants responsible for the specific formation of heterodimeric Mxd1/Max b-HLH-LZ and its binding to E-box sequences. (United States)

    Montagne, Martin; Naud, Jean-François; Lavigne, Pierre


    The proteins of the Mxd family (formally known as Mad) are antagonists of the oncoprotein c-Myc. They compete with c-Myc for their obligate partner Max to prevent the c-Myc/Max heterodimer from binding to E-box sequences in the target gene promoters. In cancer cells, where Myc is overexpressed, the expression of Mxd proteins is usually insufficient or abrogated. However, the reintroduction of Mxd1 expression in these cells prevents growth and proliferation. While the antagonism of c-Myc functions by Mxd proteins is of potential relevance for the development of cancer treatment strategies, the structural determinants responsible for the specific heterodimerization between the Mxd and the Max b-helix-loop-helix-leucine zippers are not fully understood. Moreover, whether the heterodimer is assembled on DNA or in the nucleoplasm prior to DNA binding is under debate. In this article, we demonstrate that Mxd1 D112a and Max N78a and H81d, which are located in the leucine zippers of the proteins, can dictate the specificity of heterodimerization and whether or not the Mxd1/Max/DNA complex forms. Our results also indicate that additional specific determinants exist in the helix-loop-helix domains of Max and Mxd1. Finally, we provide evidence that heterodimerization must precede DNA binding in vivo.

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

    Directory of Open Access Journals (Sweden)

    Christian Huhn

    Full Text Available 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

  20. Cellular immunostimulation by CpG-sequence-coated DNA origami structures. (United States)

    Schüller, Verena J; Heidegger, Simon; Sandholzer, Nadja; Nickels, Philipp C; Suhartha, Nina A; Endres, Stefan; Bourquin, Carole; Liedl, Tim


    To investigate the potential of DNA origami constructs as programmable and noncytotoxic immunostimulants, we tested the immune responses induced by hollow 30-helix DNA origami tubes covered with up to 62 cytosine-phosphate-guanine (CpG) sequences in freshly isolated spleen cells. Unmethylated CpG sequences that are highly specific for bacterial DNA are recognized by a specialized receptor of the innate immune system localized in the endosome, the Toll-like receptor 9 (TLR9). When incubated with oligonucleotides containing CpGs, immune cells are stimulated through TLR9 to produce and secrete cytokine mediators such as interleukin-6 (IL-6) and interleukin-12p70 (IL-12p70), a process associated with the initiation of an immune response. In our studies, the DNA origami tube built from an 8634 nt long variant of the commonly used single-stranded DNA origami scaffold M13mp18 and 227 staple oligonucleotides decorated with 62 CpG-containing oligonucleotides triggered a strong immune response, characterized by cytokine production and immune cell activation, which was entirely dependent on TLR9 stimulation. Such decorated origami tubes also triggered higher immunostimulation than equal amounts of CpG oligonucleotides associated with a standard carrier system such as Lipofectamine. In the absence of CpG oligonucleotides, cytokine production induced by the origami tubes was low and was not related to TLR9 recognition. Fluorescent microscopy revealed localization of CpG-containing DNA origami structures in the endosome. The DNA constructs showed in contrast to Lipofectamine no detectable toxicity and did not affect the viability of splenocytes. We thus demonstrate that DNA origami constructs represent a delivery system for CpG oligonucleotides that is both efficient and nontoxic.

  1. The Interior Structure Constants as an Age Diagnostic for Low-Mass, Pre-Main Sequence Detached Eclipsing Binary Stars

    CERN Document Server

    Feiden, Gregory A


    We propose a novel method for determining the ages of low-mass, pre-main sequence stellar systems using the apsidal motion of low-mass detached eclipsing binaries. The apsidal motion of a binary system with an eccentric orbit provides information regarding the interior structure constants of the individual stars. These constants are related to the normalized stellar interior density distribution and can be extracted from the predictions of stellar evolution models. We demonstrate that low-mass, pre-main sequence stars undergoing radiative core contraction display rapidly changing interior structure constants (greater than 5% per 10 Myr) that, when combined with observational determinations of the interior structure constants (with 5 -- 10% precision), allow for a robust age estimate. This age estimate, unlike those based on surface quantities, is largely insensitive to the surface layer where effects of magnetic activity are likely to be most pronounced. On the main sequence, where age sensitivity is minimal,...

  2. The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone. (United States)

    Roche, Daniel Barry; Brüls, Thomas


    As the largest fraction of any proteome does not carry out enzymatic functions, and in order to leverage 3D structural data for the annotation of increasingly higher volumes of sequence data, we wanted to assess the strength of the link between coarse grained structural data (i.e., homologous superfamily level) and the enzymatic versus non-enzymatic nature of protein sequences. To probe this relationship, we took advantage of 41 phylogenetically diverse (encompassing 11 distinct phyla) genomes recently sequenced within the GEBA initiative, for which we integrated structural information, as defined by CATH, with enzyme level information, as defined by Enzyme Commission (EC) numbers. This analysis revealed that only a very small fraction (about 1%) of domain sequences occurring in the analyzed genomes was found to be associated with homologous superfamilies strongly indicative of enzymatic function. Resorting to less stringent criteria to define enzyme versus non-enzyme biased structural classes or excluding highly prevalent folds from the analysis had only modest effect on this proportion. Thus, the low genomic coverage by structurally anchored protein domains strongly associated to catalytic activities indicates that, on its own, the power of coarse grained structural information to infer the general property of being an enzyme is rather limited.

  3. The investigation of the secondary structures of various peptide sequences of β-casein by the multicanonical simulation method (United States)

    Yaşar, F.; Çelik, S.; Köksel, H.


    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 β-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 β-turn, γ-turn and helical structures. Structural predictions of these sequences of β-casein molecule indicate the presence of high level of helical structures and βIII-turns. The occurrence probabilities of inverse and classical β-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.

  4. eProS--a database and toolbox for investigating protein sequence-structure-function relationships through energy profiles. (United States)

    Heinke, Florian; Schildbach, Stefan; Stockmann, Daniel; Labudde, Dirk


    Gaining information about structural and functional features of newly identified proteins is often a difficult task. This information is crucial for understanding sequence-structure-function relationships of target proteins and, thus, essential in comprehending the mechanisms and dynamics of the molecular systems of interest. Using protein energy profiles is a novel approach that can contribute in addressing such problems. An energy profile corresponds to the sequence of energy values that are derived from a coarse-grained energy model. Energy profiles can be computed from protein structures or predicted from sequences. As shown, correspondences and dissimilarities in energy profiles can be applied for investigations of protein mechanics and dynamics. We developed eProS (energy profile suite, freely available at, a database that provides ∼76 000 pre-calculated energy profiles as well as a toolbox for addressing numerous problems of structure biology. Energy profiles can be browsed, visualized, calculated from an uploaded structure or predicted from sequence. Furthermore, it is possible to align energy profiles of interest or compare them with all entries in the eProS database to identify significantly similar energy profiles and, thus, possibly relevant structural and functional relationships. Additionally, annotations and cross-links from numerous sources provide a broad view of potential biological correspondences.

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

    Directory of Open Access Journals (Sweden)

    Olfa Siala


    Full Text Available 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 software. 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.

  6. Theoretical Study of Interesting Fine-Structure Splittings for 23P0,1,2 States along Helium Isoelectronic Sequence

    Institute of Scientific and Technical Information of China (English)

    QING Bo; CHEN Shao-Hao; GAO Xiang; LI Jia-Ming


    Using the multi-configuration Dirac-Fock method including the Breit interactions and QED corrections, we calculate the fine-structure energy levels of the 23P,0,1,2 states along the helium isoelectronic sequence with atomic number up to Z=36, where LS-coupling is appropriate. Our calculation results agree with the experimental results within about 1%. We elucidate the mechanism of the interesting fine-structure splittings for the 23P,0,1,2 states along the helium isoelectronic sequence, I. E. The competitions between the spin-orbit interactions and the Breit interactions which represent the relativistic retardation effect of electromagnetic interactions.

  7. Using DNA sequencing electrophoresis compression artifacts as reporters of stable mRNA structures affecting gene expression. (United States)

    Kapoor, Divya; Chandrayan, Sanjeev Kumar; Ahmed, Shubbir; Guptasarma, Purnananda


    The formation of secondary structure in oligonucleotide DNA is known to lead to "compression" artifacts in electropherograms produced through DNA sequencing. Separately, the formation of secondary structure in mRNA is known to suppress translation; in particular, when such structures form in a region covered by the ribosome either during, or shortly after, initiation of translation. Here, we demonstrate how a DNA sequencing compression artifact provides important clues to the location(s) of translation-suppressing secondary structural elements in mRNA. Our study involves an engineered version of a gene sourced from Rhodothermus marinus encoding an enzyme called Cel12A. We introduced this gene into Escherichia coli with the intention of overexpressing it, but found that it expressed extremely poorly. Intriguingly, the gene displayed a remarkable compression artifact during DNA sequencing electrophoresis. Selected "designer" silent mutations destroyed the artifact. They also simultaneously greatly enhanced the expression of the cel12A gene, presumably by destroying stable mRNA structures that otherwise suppress translation. We propose that this method of finding problem mRNA sequences is superior to software-based analyses, especially if combined with low-temperature CE.

  8. Optimizing texture measures quantifying bone structures as well as MR-sequences at 3 Tesla: an integrative statistical approach (United States)

    Raeth, Christoph W.; Mueller, Dirk; Rummeny, Ernst J.; Link, Thomas M.; Vogel, Mika; Koenig, Hartmut; Boehm, Holger; Monetti, Roberto


    High resolution MR-scanners working with magnetic field strengths of 3 Tesla are clinically available nowadays. They offer the possibility to obtain 3D images with unprecedented spatial resolution and/or signal-to-noise-ratio (SNR) allowing for an accurate visualization of the trabecular bone structure. It has been demonstrated that scaling indices are well suited to quantify these structures, especially to discriminate between plate-like and rod-like structural elements, which is crucial for the diagnosis of osteoporosis. Until now image quality has mainly been assessed by visual impression or by measures based on the SNR. In this work we present a methodology to assess different MR-sequences with respect to the texture measure that is used later in the image analysis. We acquired for a bone specimen HR-MR-sequences with different spatial resolution and signal to noise ratio. For these data sets we selected two volumes of interest (VOI) of same size located in the trabecular bone and in the background of the image. For both VOIs the scaling indices are calculated for different scale parameters. Subsequently the 'texture contrast' between structure and background is calculated by comparing the probability distributions of the scaling indices using a quadratic distance measure. By means of the contrast the optimal set of scale parameters is determined. By comparing the contrast for the different MR sequences the best suited ones are determined. It turns out that sequences with slightly lower spatial resolution but better signal to noise ration yield a better texture contrast than sequences with the best spatial resolution. The presented methodology offers the possibility to optimize simultaneously texture measures and MR-sequences, which will allow for an adapted and thus optimized analysis of image structures, e.g. trabecular bone, in the HR-MR data.

  9. VES/TEM 1D joint inversion by using Controlled Random Search (CRS) algorithm (United States)

    Bortolozo, Cassiano Antonio; Porsani, Jorge Luís; Santos, Fernando Acácio Monteiro dos; Almeida, Emerson Rodrigo


    Electrical (DC) and Transient Electromagnetic (TEM) soundings are used in a great number of environmental, hydrological, and mining exploration studies. Usually, data interpretation is accomplished by individual 1D models resulting often in ambiguous models. This fact can be explained by the way as the two different methodologies sample the medium beneath surface. Vertical Electrical Sounding (VES) is good in marking resistive structures, while Transient Electromagnetic sounding (TEM) is very sensitive to conductive structures. Another difference is VES is better to detect shallow structures, while TEM soundings can reach deeper layers. A Matlab program for 1D joint inversion of VES and TEM soundings was developed aiming at exploring the best of both methods. The program uses CRS - Controlled Random Search - algorithm for both single and 1D joint inversions. Usually inversion programs use Marquadt type algorithms but for electrical and electromagnetic methods, these algorithms may find a local minimum or not converge. Initially, the algorithm was tested with synthetic data, and then it was used to invert experimental data from two places in Paraná sedimentary basin (Bebedouro and Pirassununga cities), both located in São Paulo State, Brazil. Geoelectric model obtained from VES and TEM data 1D joint inversion is similar to the real geological condition, and ambiguities were minimized. Results with synthetic and real data show that 1D VES/TEM joint inversion better recovers simulated models and shows a great potential in geological studies, especially in hydrogeological studies.

  10. Structural variation discovery in the cancer genome using next generation sequencing: Computational solutions and perspectives (United States)

    Liu, Biao; Conroy, Jeffrey M.; Morrison, Carl D.; Odunsi, Adekunle O.; Qin, Maochun; Wei, Lei; Trump, Donald L.; Johnson, Candace S.; Liu, Song; Wang, Jianmin


    Somatic Structural Variations (SVs) are a complex collection of chromosomal mutations that could directly contribute to carcinogenesis. Next Generation Sequencing (NGS) technology has emerged as the primary means of interrogating the SVs of the cancer genome in recent investigations. Sophisticated computational methods are required to accurately identify the SV events and delineate their breakpoints from the massive amounts of reads generated by a NGS experiment. In this review, we provide an overview of current analytic tools used for SV detection in NGS-based cancer studies. We summarize the features of common SV groups and the primary types of NGS signatures that can be used in SV detection methods. We discuss the principles and key similarities and differences of existing computational programs and comment on unresolved issues related to this research field. The aim of this article is to provide a practical guide of relevant concepts, computational methods, software tools and important factors for analyzing and interpreting NGS data for the detection of SVs in the cancer genome. PMID:25849937

  11. Research on time structure characteristic of gas concentration sequence in the working face

    Institute of Scientific and Technical Information of China (English)

    HE Li-wen; SONG Yi; SHI Shi-liang; LI Xi-bin


    In the procedure of coal industry production,the losses of the persons and economy caused by the gas explosion accidents are most serious,therefore,prevention and control of the gas explosion accident of the coal mines is an important issue needed to be solved urgently in the safety production work of our coal mines.The characteristic of time structure variation index characteristic was analyzed about gas concentration sequence of three measure points in the NO.II1024 working face.It was found that the value of time variation about three measure points was mostly 1<δ≤ 1.5,and gas emission presented consistently strong-clustering state twice,and the value of time variation presented continuous variation state in the active stage of gas concentration.Complex characteristics of the value indicated gas emission was continuously variable in time or space and presented the complex nonlinear characteristics.So the characteristic about gas emission system was correctly depicted and analyzed to gas emission system according to the relation of its state variation and essential of nonlinear system.The result also provided reliable warranty for its continued nonlinear research on gas emission.

  12. How are exons encoding transmembrane sequences distributed in the exon-intron structure of genes? (United States)

    Sawada, Ryusuke; Mitaku, Shigeki


    The exon-intron structure of eukaryotic genes raises a question about the distribution of transmembrane regions in membrane proteins. Were exons that encode transmembrane regions formed simply by inserting introns into preexisting genes or by some kind of exon shuffling? To answer this question, the exon-per-gene distribution was analyzed for all genes in 40 eukaryotic genomes with a particular focus on exons encoding transmembrane segments. In 21 higher multicellular eukaryotes, the percentage of multi-exon genes (those containing at least one intron) within all genes in a genome was high (>70%) and with a mean of 87%. When genes were grouped by the number of exons per gene in higher eukaryotes, good exponential distributions were obtained not only for all genes but also for the exons encoding transmembrane segments, leading to a constant ratio of membrane proteins independent of the exon-per-gene number. The positional distribution of transmembrane regions in single-pass membrane proteins showed that they are generally located in the amino or carboxyl terminal regions. This nonrandom distribution of transmembrane regions explains the constant ratio of membrane proteins to the exon-per-gene numbers because there are always two terminal (i.e., the amino and carboxyl) regions - independent of the length of sequences.

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

    Directory of Open Access Journals (Sweden)

    Dybowski J Nikolaj


    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.

  14. RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps. (United States)

    Drory Retwitzer, Matan; Polishchuk, Maya; Churkin, Elena; Kifer, Ilona; Yakhini, Zohar; Barash, Danny


    Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular-no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence. Here, we introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods. RNAPattMatch service is available at A standalone version of the search tool is also available to download at the site.

  15. One-Dimensional (1D) ZnS Nanomaterials and Nanostructures

    Institute of Scientific and Technical Information of China (English)

    Xiaosheng FANG; Lide ZHANG


    One-dimensional (1D) nanomaterials and nanostructures have received much attention due to their potential interest for understanding fundamental physical concepts and for applications in constructing nanoscale electric and optoelectronic devices. Zinc sulfide (ZnS) is an important semiconductor compound of Ⅱ-Ⅵ group,and the synthesis of 1D ZnS nanomaterials and nanostructures has been of growing interest owing to their promising application in nanoscale optoelectronic devices. This paper reviews the recent progress on 1D ZnS nanomaterials and nanostructures, including nanowires, nanowire arrays, nanorods, nanobelts or nanoribbons,nanocables, and hierarchical nanostructures etc. This article begins with a survey of various methods that have been developed for generating 1D nanomaterials and nanostructures, and then mainly focuses on structures,synthesis, characterization, formation mechanisms and optical property tuning, and luminescence mechanisms of 1D ZnS nanomaterials and nanostructures. Finally, this review concludes with personal views towards future research on 1D ZnS nanomaterials and nanostructures.

  16. Dynamical Models of SAURON and CALIFA Galaxies: 1D and 2D Rotational Curves (United States)

    Kalinova, Veselina; van de Ven, G.; Lyubenova, M.; Falcon-Barroso, J.; van den Bosch, R.


    The mass of a galaxy is the most important parameter to understand its structure and evolution. The total mass we can infer by constructing dynamical models that fit the motion of the stars and gas in the galaxy. The dark matter content then follows after subtracting the luminous matter inferred from colors and/or spectra. Here, we present the mass distribution of a sample of 18 late-type spiral (Sb-Sd) galaxies, using two-dimensional stellar kinematics obtained with the integral-field spectrograph SAURON. The observed second order velocity moments of these galaxies are fitted with solutions of the Axisymmetric Jeans equations and give us an accurate estimation of the mass-to-light ratio profiles and rotational curves. The rotation curves of the galaxies are obtained by the Asymmetric Drift Correction (ADC) and Multi-Gaussian Expansion (MGE) methods, corresponding to one- and two-dimensional mass distribution. Their comparison shows that the mass distribution based on the 2D stellar kinematics is much more reliable than 1D one. SAURON integral field of view looks at the inner parts of the galaxies in contrast with CALIFA survey. CALIFA survey provides PMAS/PPAK integral-field spectroscopic data of ~ 600 nearby galaxies as part of the Calar Alto Legacy Integral Field Area. We show the first CALIFA dynamical models of different morphological type of galaxies, giving the clue about the mass distribution of galaxies through the whole Hubble sequence and their evolution from the blue cloud to the red sequence.

  17. Structural parameterization and functional prediction of antigenic polypeptome sequences with biological activity through quantitative sequence-activity models (QSAM) by molecular electronegativity edge-distance vector (VMED)

    Institute of Scientific and Technical Information of China (English)

    LI; ZhiLiang; WU; ShiRong; CHEN; ZeCong; YE; Nancy; YANG; ShengXi; LIAO; ChunYang; ZHANG; MengJun; YANG; Li; MEI; Hu; YANG; Yan; ZHAO; Na; ZHOU; Yuan; ZHOU; Ping; XIONG; Qing; XU; Hong; LIU; ShuShen; LING; ZiHua; CHEN; Gang; LI; GenRong


    Only from the primary structures of peptides, a new set of descriptors called the molecular electronegativity edge-distance vector (VMED) was proposed and applied to describing and characterizing the molecular structures of oligopeptides and polypeptides, based on the electronegativity of each atom or electronic charge index (ECI) of atomic clusters and the bonding distance between atom-pairs. Here, the molecular structures of antigenic polypeptides were well expressed in order to propose the automated technique for the computerized identification of helper T lymphocyte (Th) epitopes. Furthermore, a modified MED vector was proposed from the primary structures of polypeptides, based on the ECI and the relative bonding distance of the fundamental skeleton groups. The side-chains of each amino acid were here treated as a pseudo-atom. The developed VMED was easy to calculate and able to work. Some quantitative model was established for 28 immunogenic or antigenic polypeptides (AGPP) with 14 (1―14) Ad and 14 other restricted activities assigned as "1"(+) and "0"(-), respectively. The latter comprised 6 Ab(15-20), 3 Ak(21-23), 2 Ek(24-26), 2 H-2k(27 and 28) restricted sequences. Good results were obtained with 90% correct classification (only 2 wrong ones for 20 training samples) and 100% correct prediction (none wrong for 8 testing samples); while contrastively 100% correct classification (none wrong for 20 training samples) and 88% correct classification (1 wrong for 8 testing samples). Both stochastic samplings and cross validations were performed to demonstrate good performance. The described method may also be suitable for estimation and prediction of classes I and II for major histocompatibility antigen (MHC) epitope of human. It will be useful in immune identification and recognition of proteins and genes and in the design and development of subunit vaccines. Several quantitative structure activity relationship (QSAR) models were developed for various

  18. Common interruptions in the repeating tripeptide sequence of non-fibrillar collagens: sequence analysis and structural studies on triple-helix peptide models. (United States)

    Thiagarajan, Geetha; Li, Yingjie; Mohs, Angela; Strafaci, Christopher; Popiel, Magdalena; Baum, Jean; Brodsky, Barbara


    Interruptions in the repeating (Gly-X1-X2)(n) amino acid sequence pattern are found in the triple-helix domains of all non-fibrillar collagens, and perturbations to the triple-helix at such sites are likely to play a role in collagen higher-order structure and function. This study defines the sequence features and structural consequences of the most common interruption, where one residue is missing from the tripeptide pattern, Gly-X1-X2-Gly-AA(1)-Gly-X1-X2, designated G1G interruptions. Residues found within G1G interruptions are predominantly hydrophobic (70%), followed by a significant amount of charged residues (16%), and the Gly-X1-X2 triplets flanking the interruption are atypical. Studies on peptide models indicate the degree of destabilization is much greater when Pro is in the interruption, GP, than when hydrophobic residues (GF, GY) are present, and a rigid Gly-Pro-Hyp tripeptide adjacent to the interruption leads to greater destabilization than a flexible Gly-Ala-Ala sequence. Modeling based on NMR data indicates the Phe residue within a GF interruption is located on the outside of the triple helix. The G1G interruptions resemble a previously studied collagen interruption GPOGAAVMGPO, designated G4G-type, in that both are destabilizing, but allow continuation of rod-like triple helices and maintenance of the single residue stagger throughout the imperfection, with a loss of axial register of the superhelix on both sides. Both kinds of interruptions result in a highly localized perturbation in hydrogen bonding and dihedral angles, but the hydrophobic residue of a G4G interruption packs near the central axis of the superhelix, while the hydrophobic residue of a G1G interruption is located on the triple-helix surface. The different structural consequences of G1G and G4G interruptions in the repeating tripeptide sequence pattern suggest a physical basis for their differential susceptibility to matrix metalloproteinases in type X collagen.

  19. Sequence and structure-based prediction of fructosyltransferase activity for functional subclassification of fungal GH32 enzymes. (United States)

    Trollope, Kim M; van Wyk, Niël; Kotjomela, Momo A; Volschenk, Heinrich


    Sucrolytic enzymes catalyse sucrose hydrolysis or the synthesis of fructooligosaccharides (FOSs), a prebiotic in human and animal nutrition. FOS synthesis capacity differs between sucrolytic enzymes. Amino-acid-sequence-based classification of FOS synthesizing enzymes would greatly facilitate the in silico identification of novel catalysts, as large amounts of sequence data lie untapped. The development of a bioinformatics tool to rapidly distinguish between high-level FOSs synthesizing predominantly sucrose hydrolysing enzymes from fungal genomic data is presented. Sequence comparison of functionally characterized enzymes displaying low- and high-level FOS synthesis revealed conserved motifs unique to each group. New light is shed on the sequence context of active site residues in three previously identified conserved motifs. We characterized two enzymes predicted to possess low- and high-level FOS synthesis activities based on their conserved motif sequences. FOS data for the enzymes confirmed our successful prediction of their FOS synthesis capacity. Structural comparison of enzymes displaying low- and high-level FOS synthesis identified steric hindrance between nystose and a long loop region present only in low-level FOS synthesizers. This loop is proposed to limit the synthesis of FOS species with higher degrees of polymerization, a phenomenon observed among enzymes displaying low-level FOS synthesis. Conserved sequence motifs surrounding catalytic residues and a distant structural determinant were identifiers of FOS synthesis capacity and allow for functional annotation of sucrolytic enzymes directly from amino acid sequence. The tool presented may also be useful to study the structure-function relationships of β-fructofuranosidases by identifying mutations present in a group of closely related enzymes displaying similar function.

  20. Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Abhishek; Kollath-Leiß, Krisztina; Kempken, Frank, E-mail:


    Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the α/β-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional

  1. Cytochrome P450 1D1: A novel CYP1A-related gene that is not transcriptionally activated by PCB126 or TCDD

    DEFF Research Database (Denmark)

    Goldstone, J.V.; Jönsson, M.E.; Behrendt, Lars;


    Enzymes in the cytochrome P450 1 family oxidize many common environmental toxicants. We identified a new CYP1, termed CYP1D1, in zebrafish. Phylogenetically, CYP1D1 is paralogous to CYP1A and the two share 45% amino acid identity and similar gene structure. In adult zebrafish, CYP1D1 is most high...

  2. The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.

    Directory of Open Access Journals (Sweden)

    Leila do Nascimento Vieira

    Full Text Available BACKGROUND: Podocarpus lambertii (Podocarpaceae is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. METHODOLOGY/PRINCIPAL FINDINGS: The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR. It contains 118 unique genes and one duplicated tRNA (trnN-GUU, which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi and Araucariaceae (Agathis dammara. Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. CONCLUSION: The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of

  3. Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Charles K Lee

    Full Text Available Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.

  4. Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing. (United States)

    Lee, Charles K; Herbold, Craig W; Polson, Shawn W; Wommack, K Eric; Williamson, Shannon J; McDonald, Ian R; Cary, S Craig


    Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.

  5. The Complete Chloroplast Genome Sequence of Podocarpus lambertii: Genome Structure, Evolutionary Aspects, Gene Content and SSR Detection (United States)

    Vieira, Leila do Nascimento; Faoro, Helisson; Rogalski, Marcelo; Fraga, Hugo Pacheco de Freitas; Cardoso, Rodrigo Luis Alves; de Souza, Emanuel Maltempi; de Oliveira Pedrosa, Fábio; Nodari, Rubens Onofre; Guerra, Miguel Pedro


    Background Podocarpus lambertii (Podocarpaceae) is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp) genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. Methodology/Principal Findings The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR). It contains 118 unique genes and one duplicated tRNA (trnN-GUU), which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi) and Araucariaceae (Agathis dammara). Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. Conclusion The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of this genus. PMID

  6. STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence (United States)

    Neshich, Goran; Togawa, Roberto C.; Mancini, Adauto L.; Kuser, Paula R.; Yamagishi, Michel E. B.; Pappas, Georgios; Torres, Wellington V.; Campos, Tharsis Fonseca e; Ferreira, Leonardo L.; Luna, Fabio M.; Oliveira, Adilton G.; Miura, Ronald T.; Inoue, Marcus K.; Horita, Luiz G.; de Souza, Dimas F.; Dominiquini, Fabiana; Álvaro, Alexandre; Lima, Cleber S.; Ogawa, Fabio O.; Gomes, Gabriel B.; Palandrani, Juliana F.; dos Santos, Gabriela F.; de Freitas, Esther M.; Mattiuz, Amanda R.; Costa, Ivan C.; de Almeida, Celso L.; Souza, Savio; Baudet, Christian; Higa, Roberto H.


    STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Biologists find SMS useful because it provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. Using SMS it is now possible to analyze sequence to structure relationships, the quality of the structure, nature and volume of atomic contacts of intra and inter chain type, relative conservation of amino acids at the specific sequence position based on multiple sequence alignment, indications of folding essential residue (FER) based on the relationship of the residue conservation to the intra-chain contacts and Cα–Cα and Cβ–Cβ distance geometry. Specific emphasis in SMS is given to interface forming residues (IFR)—amino acids that define the interactive portion of the protein surfaces. SMS may simultaneously display and analyze previously superimposed structures. PDB updates trigger SMS updates in a synchronized fashion. SMS is freely accessible for public data at, and PMID:12824333

  7. RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins.

    Directory of Open Access Journals (Sweden)

    Hilal Kazan

    Full Text Available Metazoan genomes encode hundreds of RNA-binding proteins (RBPs. These proteins regulate post-transcriptional gene expression and have critical roles in numerous cellular processes including mRNA splicing, export, stability and translation. Despite their ubiquity and importance, the binding preferences for most RBPs are not well characterized. In vitro and in vivo studies, using affinity selection-based approaches, have successfully identified RNA sequence associated with specific RBPs; however, it is difficult to infer RBP sequence and structural preferences without specifically designed motif finding methods. In this study, we introduce a new motif-finding method, RNAcontext, designed to elucidate RBP-specific sequence and structural preferences with greater accuracy than existing approaches. We evaluated RNAcontext on recently published in vitro and in vivo RNA affinity selected data and demonstrate that RNAcontext identifies known binding preferences for several control proteins including HuR, PTB, and Vts1p and predicts new RNA structure preferences for SF2/ASF, RBM4, FUSIP1 and SLM2. The predicted preferences for SF2/ASF are consistent with its recently reported in vivo binding sites. RNAcontext is an accurate and efficient motif finding method ideally suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RBPs for a wide range of RNA sequences and structures.

  8. Interaction of environmental contaminants with zebrafish organic anion transporting polypeptide, Oatp1d1 (Slco1d1)

    Energy Technology Data Exchange (ETDEWEB)

    Popovic, Marta; Zaja, Roko [Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Rudjer Boskovic Institute, Bijenicka 54, 10 000 Zagreb (Croatia); Fent, Karl [University of Applied Sciences Northwestern Switzerland, School of Life Sciences, Gründenstrasse 40, CH-4132 Muttenz (Switzerland); Swiss Federal Institute of Technology (ETH Zürich), Department of Environmental System Sciences, Institute of Biogeochemistry and Pollution Dynamics, CH-8092 Zürich (Switzerland); Smital, Tvrtko, E-mail: [Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Rudjer Boskovic Institute, Bijenicka 54, 10 000 Zagreb (Croatia)


    Polyspecific transporters from the organic anion transporting polypeptide (OATP/Oatp) superfamily mediate the uptake of a wide range of compounds. In zebrafish, Oatp1d1 transports conjugated steroid hormones and cortisol. It is predominantly expressed in the liver, brain and testes. In this study we have characterized the transport of xenobiotics by the zebrafish Oatp1d1 transporter. We developed a novel assay for assessing Oatp1d1 interactors using the fluorescent probe Lucifer yellow and transient transfection in HEK293 cells. Our data showed that numerous environmental contaminants interact with zebrafish Oatp1d1. Oatp1d1 mediated the transport of diclofenac with very high affinity, followed by high affinity towards perfluorooctanesulfonic acid (PFOS), nonylphenol, gemfibrozil and 17α-ethinylestradiol; moderate affinity towards carbaryl, diazinon and caffeine; and low affinity towards metolachlor. Importantly, many environmental chemicals acted as strong inhibitors of Oatp1d1. A strong inhibition of Oatp1d1 transport activity was found by perfluorooctanoic acid (PFOA), chlorpyrifos-methyl, estrone (E1) and 17β-estradiol (E2), followed by moderate to low inhibition by diethyl phthalate, bisphenol A, 7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4 tetrahydronapthalene and clofibrate. In this study we identified Oatp1d1 as a first Solute Carrier (SLC) transporter involved in the transport of a wide range of xenobiotics in fish. Considering that Oatps in zebrafish have not been characterized before, our work on zebrafish Oatp1d1 offers important new insights on the understanding of uptake processes of environmental contaminants, and contributes to the better characterization of zebrafish as a model species. - Highlights: • We optimized a novel assay for determination of Oatp1d1 interactors • Oatp1d1 is the first SLC characterized fish xenobiotic transporter • PFOS, nonylphenol, diclofenac, EE2, caffeine are high affinity Oatp1d1substrates • PFOA, chlorpyrifos

  9. A study of optical reflectance and localization modes of 1-D Fibonacci photonic quasicrystals using different graded dielectric materials (United States)

    Singh, Bipin K.; Pandey, Praveen C.


    In this paper, we present an analytical study on the reflection properties of light through one-dimensional (1-D) quasi-periodic multilayer structures. The considered structures are as follows: F7, F8, F9, (F2)10, (F3)10 and some combinations such as: [(F2)10 (F7) (F2)10], [(F2)10 (F8) (F2)10], [(F3)10 (F7) (F3)10], [(F3)10 (F8) (F3)10], [(F2)10(F3)10], [(F2)10 (F7) (F3)10] and [(F2)10 (F8) (F3)10], where (Fj)n represents n period of the Fibonacci sequence of jth generation. These multilayer structures are considered of two types of layers. One type of layer is considered of graded material like normal, linear or exponential graded material, and the second type of layer is considered of constant refractive index material. Transfer matrix method is utilized to calculate the reflection spectra and localization modes of such structures in the frequency range 150-450 THz. This work would provide the basis of understanding of the effect of graded materials on the reflection and localization modes in Fibonacci photonic quasicrystal structures and obtained spectra can be used in the recognition of grading of materials. The considered heterostructures provide the broad reflection band and some localization modes in the calculated region.


    Institute of Scientific and Technical Information of China (English)


    A series of thermotropic liquid crystalline polyesteramides with different sequence structure based on dimethylbenzidine (DMBD), bisphenol-A(BPA) and pterephthalyl chloride (TPC) was synthesized by changing the feeding order of monomers in low temperature solution polycondensation system. By means of NMR and a computer program the sequence structure parameters were measured. The effect of sequence structure on liquid crystalline phase transition temperature of PEAs obtained was investigated.

  11. Correlation between sequence conservation and structural thermodynamics of microRNA precursors from human, mouse, and chicken genomes

    Directory of Open Access Journals (Sweden)

    Wang Shengqi


    Full Text Available Abstract Background Previous studies have shown that microRNA precursors (pre-miRNAs have considerably more stable secondary structures than other native RNAs (tRNA, rRNA, and mRNA and artificial RNA sequences. However, pre-miRNAs with ultra stable secondary structures have not been investigated. It is not known if there is a tendency in pre-miRNA sequences towards or against ultra stable structures? Furthermore, the relationship between the structural thermodynamic stability of pre-miRNA and their evolution remains unclear. Results We investigated the correlation between pre-miRNA sequence conservation and structural stability as measured by adjusted minimum folding free energies in pre-miRNAs isolated from human, mouse, and chicken. The analysis revealed that conserved and non-conserved pre-miRNA sequences had structures with similar average stabilities. However, the relatively ultra stable and unstable pre-miRNAs were more likely to be non-conserved than pre-miRNAs with moderate stability. Non-conserved pre-miRNAs had more G+C than A+U nucleotides, while conserved pre-miRNAs contained more A+U nucleotides. Notably, the U content of conserved pre-miRNAs was especially higher than that of non-conserved pre-miRNAs. Further investigations showed that conserved and non-conserved pre-miRNAs exhibited different structural element features, even though they had comparable levels of stability. Conclusions We proposed that there is a correlation between structural thermodynamic stability and sequence conservation for pre-miRNAs from human, mouse, and chicken genomes. Our analyses suggested that pre-miRNAs with relatively ultra stable or unstable structures were less favoured by natural selection than those with moderately stable structures. Comparison of nucleotide compositions between non-conserved and conserved pre-miRNAs indicated the importance of U nucleotides in the pre-miRNA evolutionary process. Several characteristic structural elements were

  12. Cavitation Influence in 1D Part-load Vortex Models (United States)

    Dörfler, P. K.


    Residual swirl in the draft tube of Francis turbines may cause annoying low- frequency pulsation of pressure and power output, in particular during part-load operation. A 1D analytical model for these dynamic phenomena would enable simulation by some conventional method for computing hydraulic transients. The proper structure of such a model has implications for the prediction of prototype behaviour based on laboratory tests. The source of excitation as well as the dynamic transmission behaviour of the draft tube flow may both be described either by lumped or distributed parameters. The distributed version contains more information and, due to limited possibilities of identification, some data must be estimated. The distributed cavitation compliance is an example for this dilemma. In recent publications, the customary assumption of a constant wave speed has produced dubious results. The paper presents a more realistic model for distributed compressibility. The measured influence of the Thoma number is applied with the local cavitation factor. This concept is less sensitive to modelling errors and explains both the Thoma and Froude number influence. The possible effect of the normally unknown non-condensable gas content in the vortex cavity is shortly commented. Its measurement in future tests is recommended. It is also recommended to check the available analytical vortex models for possible dispersion effects.

  13. Sulfur chemistry: 1D modeling in massive dense cores

    CERN Document Server

    Wakelam, V; Herpin, F


    The main sulfur-bearing molecules OCS, H2S, SO, SO2, and CS have been observed in four high mass dense cores (W43-MM1, IRAS 18264, IRAS 05358, and IRAS 18162). Our goal is to put some constraints on the relative evolutionary stage of these sources by comparing these observations with time-dependent chemical modeling. We used the chemical model Nahoon, which computes the gas-phase chemistry and gas-grain interactions of depletion and evaporation. Mixing of the different chemical compositions shells in a 1D structure through protostellar envelope has been included since observed lines suggest nonthermal supersonic broadening. Observed radial profiles of the temperature and density are used to compute the chemistry as a function of time. With our model, we underproduce CS by several orders of magnitude compared to the other S-bearing molecules, which seems to contradict observations, although some uncertainties in the CS abundance observed at high temperature remain. The OCS/SO2, SO/SO2, and H2S/SO2 abundance ra...

  14. 1D and 2D assembly structures by imidazole···chloride hydrogen bonds of iron(II) complexes [Fe(II)(HL(n-Pr))3]Cl·Y (HL(n-Pr) = 2-methylimidazol-4-yl-methylideneamino-n-propyl; Y = AsF6, BF4) and their spin states. (United States)

    Fujinami, Takeshi; Nishi, Koshiro; Matsumoto, Naohide; Iijima, Seiichiro; Halcrow, Malcolm A; Sunatsuki, Yukinari; Kojima, Masaaki


    Two Fe(II) complexes fac-[Fe(II)(HL(n-Pr))(3)]Cl·Y (Y = AsF(6) (1) and BF(4) (2)) were synthesized, where HL(n-Pr) is 2-methylimidazole-4-yl-methylideneamino-n-propyl. Each complex-cation has the same octahedral N(6) geometry coordinated by three bidentate ligands and assumes facial-isomerism, fac-[Fe(II)(HL(n-Pr))(3)](2+) with Δ- and Λ-enantiomorphs. Three imidazole groups per Δ- or Λ-fac-[Fe(II)(HL(n-Pr))(3)](2+) are hydrogen-bonded to three Cl(-) ions or, from the viewpoint of the Cl(-) ion, one Cl(-) ion is hydrogen-bonded to three neighbouring fac-[Fe(II)(HL(n-Pr))(3)](2+) cations. The 3 : 3 NH···Cl(-) hydrogen bonds between Δ- or Λ-fac-[Fe(II)(HL(n-Pr))(3)](2+) and Cl(-) generate two kinds of assembly structures. The directions of the 3 : 3 NH···Cl(-) hydrogen bonds and hence the resulting assembly structures are determined by the size of the anion Y, though Y is not involved into the network structure and just accommodated in the cavity. Compound 1 has a 1D ladder structure giving a larger cavity, in which the Δ- and Λ-fac-[Fe(II)(HL(n-Pr))(3)](2+) enantiomorphs are bridged by two NH···Cl(-) hydrogen bonds. Compound 2 has a 2D network structure with a net unit of a cyclic trimer of {fac-[Fe(II)(HL(n-Pr))(3)](2+)···Cl(-)}(3) giving a smaller cavity, in which Δ- or Λ-fac-[Fe(II)(HL(n-Pr))(3)](2+) species with the same chirality are linked by NH···Cl(-) hydrogen bonds to give a homochiral 2D network structure. Magnetic susceptibility and Mössbauer spectral measurements demonstrated that compound 1 showed an abrupt one-step spin crossover with 4.0 K thermal hysteresis of T(c↓) = 125.5 K and T(c↑) = 129.5 K and compound 2 showed no spin transition and stayed in the high-spin state over the 5-300 K temperature range.

  15. Local descriptors of protein structure: a systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions. (United States)

    Hvidsten, Torgeir R; Kryshtafovych, Andriy; Fidelis, Krzysztof


    Local protein structure representations that incorporate long-range contacts between residues are often considered in protein structure comparison but have found relatively little use in structure prediction where assembly from single backbone fragments dominates. Here, we introduce the concept of local descriptors of protein structure to characterize local neighborhoods of amino acids including short- and long-range interactions. We build a library of recurring local descriptors and show that this library is general enough to allow assembly of unseen protein structures. The library could on average re-assemble 83% of 119 unseen structures, and showed little or no performance decrease between homologous targets and targets with folds not represented among domains used to build it. We then systematically evaluate the descriptor library to establish the level of the sequence signal in sets of protein fragments of similar geometrical conformation. In particular, we test whether that signal is strong enough to facilitate correct assignment and alignment of these local geometries to new sequences. We use the signal to assign descriptors to a test set of 479 sequences with less than 40% sequence identity to any domain used to build the library, and show that on average more than 50% of the backbone fragments constituting descriptors can be correctly aligned. We also use the assigned descriptors to infer SCOP folds, and show that correct predictions can be made in many of the 151 cases where PSI-BLAST was unable to detect significant sequence similarity to proteins in the library. Although the combinatorial problem of simultaneously aligning several fragments to sequence is a major bottleneck compared with single fragment methods, the advantage of the current approach is that correct alignments imply correct long range distance constraints. The lack of these constraints is most likely the major reason why structure prediction methods fail to consistently produce adequate

  16. Statistical aspects of discerning indel-type structural variation via DNA sequence alignment

    Directory of Open Access Journals (Sweden)

    Wilson Richard K


    Full Text Available Abstract Background Structural variations in the form of DNA insertions and deletions are an important aspect of human genetics and especially relevant to medical disorders. Investigations have shown that such events can be detected via tell-tale discrepancies in the aligned lengths of paired-end DNA sequencing reads. Quantitative aspects underlying this method remain poorly understood, despite its importance and conceptual simplicity. We report the statistical theory characterizing the length-discrepancy scheme for Gaussian libraries, including coverage-related effects that preceding models are unable to account for. Results Deletion and insertion statistics both depend heavily on physical coverage, but otherwise differ dramatically, refuting a commonly held doctrine of symmetry. Specifically, coverage restrictions render insertions much more difficult to capture. Increased read length has the counterintuitive effect of worsening insertion detection characteristics of short inserts. Variance in library insert length is also a critical factor here and should be minimized to the greatest degree possible. Conversely, no significant improvement would be realized in lowering fosmid variances beyond current levels. Detection power is examined under a straightforward alternative hypothesis and found to be generally acceptable. We also consider the proposition of characterizing variation over the entire spectrum of variant sizes under constant risk of false-positive errors. At 1% risk, many designs will leave a significant gap in the 100 to 200 bp neighborhood, requiring unacceptably high redundancies to compensate. We show that a few modifications largely close this gap and we give a few examples of feasible spectrum-covering designs. Conclusion The theory resolves several outstanding issues and furnishes a general methodology for designing future projects from the standpoint of a spectrum-wide constant risk.

  17. Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats. (United States)

    Shen, Z J; Ma, R J; Cai, Z X; Yu, M L; Zhang, Z


    The fruit peach originated in China and has a history of domestication of more than 4000 years. Numerous local cultivars were selected during the long course of cultivation, and a great morphological diversity exists. To study the diversity and genetic background of local peach cultivars in China, a set of 158 accessions from different ecological regions, together with 27 modern varieties and 10 wild accessions, were evaluated using 49 simple sequence repeats (SSRs) covering the peach genome. Broad diversity was also observed in local cultivars at the SSR level. A total of 648 alleles were amplified with an average of 13.22 observed alleles per locus. The number of genotypes detected ranged from 9 (UDP96015) to 58 (BPPCT008) with an average of 27.00 genotypes per marker. Eight subpopulations divided by STRUCTURE basically coincided with the dendrogram of genetic relationships and could be explained by the traditional groups. The 8 subpopulations were juicy honey peach, southwestern peach I, wild peach, Buddha peach + southwestern peach II, northern peach, southern crisp peach, ornamental peach, and Prunus davidiana + P. kansuensis. Most modern varieties carried the genetic backgrounds of juicy honey peach and southwestern peach I, while others carried diverse genetic backgrounds, indicating that local cultivars were partly used in modern breeding programs. Based on the traditional evolution pathway, a modified pathway for the development of local peach cultivars in China was proposed using the genetic background of subpopulations that were identified by SSRs. Current status and prospects of utilization of Chinese local peach cultivars were also discussed according to the SSR information.

  18. Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a "horned" bacteriophage of marine synechococcus. (United States)

    Pope, Welkin H; Weigele, Peter R; Chang, Juan; Pedulla, Marisa L; Ford, Michael E; Houtz, Jennifer M; Jiang, Wen; Chiu, Wah; Hatfull, Graham F; Hendrix, Roger W; King, Jonathan


    Marine Synechococcus spp and marine Prochlorococcus spp are numerically dominant photoautotrophs in the open oceans and contributors to the global carbon cycle. Syn5 is a short-tailed cyanophage isolated from the Sargasso Sea on Synechococcus strain WH8109. Syn5 has been grown in WH8109 to high titer in the laboratory and purified and concentrated retaining infectivity. Genome sequencing and annotation of Syn5 revealed that the linear genome is 46,214 bp with a 237 bp terminal direct repeat. Sixty-one open reading frames (ORFs) were identified. Based on genomic organization and sequence similarity to known protein sequences within GenBank, Syn5 shares features with T7-like phages. The presence of a putative integrase suggests access to a temperate life cycle. Assignment of 11 ORFs to structural proteins found within the phage virion was confirmed by mass-spectrometry and N-terminal sequencing. Eight of these identified structural proteins exhibited amino acid sequence similarity to enteric phage proteins. The remaining three virion proteins did not resemble any known phage sequences in GenBank as of August 2006. Cryo-electron micrographs of purified Syn5 virions revealed that the capsid has a single "horn", a novel fibrous structure protruding from the opposing end of the capsid from the tail of the virion. The tail appendage displayed an apparent 3-fold rather than 6-fold symmetry. An 18 A resolution icosahedral reconstruction of the capsid revealed a T=7 lattice, but with an unusual pattern of surface knobs. This phage/host system should allow detailed investigation of the physiology and biochemistry of phage propagation in marine photosynthetic bacteria.

  19. Population genetic structure of the ark shell Scapharca broughtonii Schrenck from Korea, China, and Russia based on COI gene sequences. (United States)

    Cho, Eun-Seob; Jung, Choon-Goon; Sohn, Sang-Gyu; Kim, Chul-Won; Han, Seock-Jung


    Haplotype distribution, gene flow, and population genetic structure of the ark shell (Scapharca broughtonii) were studied using a partial sequence of a mitochondrial COI gene. The sequence analysis of 100 specimens obtained from a total of seven localities-five in Korea, one in China, and one in Russia- revealed 29 haplotypes, ranging in sequence divergence from 0.1% to 2.1%. Among these, the most frequent haplotype, SB16, was extensively distributed over study areas, especially in all Korean localities. This extensive distribution consequently resulted in the near absence of statistically significant genetic distance. Also, a high rate of gene flow was characteristic among localities in Korea. A test of genetic population structure showed that the ark shell in Korea formed a large genetic group. Moreover, an AMOVA test to determine the allocation of the genetic variance showed that most of the variance was distributed between localities, instead of within localities. However, a significant population differentiation was found between geographic populations [i.e., Jinhae (locality 6) in Korea and Sangdong (locality 5) in China and Vladivostok (locality 7) in Russia] based on geographic distance and population structure. These distinct groups may be associated with geographic characteristics and barriers. The results suggest that most of the ark shell populations in Korea caused considerable distribution to form a genetically homogeneous and intermixing structure, whereas some of the Korean and Chinese and Russian populations had a significantly different genetic structure.

  20. Two-dimensional deterministic photonic band gap structures based on the quasiperiodic sequences at millimeter wave frequencies

    Directory of Open Access Journals (Sweden)

    Y. Trabelsi


    Full Text Available Two-dimensional quasi-periodic band gap structures were investigated theoretically in microwave frequency range. Quasiperiodic photonic crystal based on the square range, arranged in a quasi-periodical fashion which follows Thue Morse or Fibonaci period substitutional sequences were obtained by the inflation rules emerging from the quasi-periodic sequence. The introduction of 2D quasi-periodicity distribution like Thue Morse or Fibonacci order and deterministic aperiodicity give some interesting microwave properties and offers amultitude of adjacent pseudo-band gap in different frequency range. The potential of photonic structures are explored by varying the structural parameters. The photonic band gap formation was explored as function of geometries of the structures such as pillar radius and parameters of quasi-periodical sequences. The electromagnetic field distribution can be described as a quasi-localized state varied by some defect carried by Thue Morse order. These structures provide interesting properties, which could be used to design novelmicrowave devices.

  1. Structural biology of disease-associated repetitive DNA sequences and protein-DNA complexes involved in DNA damage and repair

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, G.; Santhana Mariappan, S.V.; Chen, X.; Catasti, P.; Silks, L.A. III; Moyzis, R.K.; Bradbury, E.M.; Garcia, A.E.


    This project is aimed at formulating the sequence-structure-function correlations of various microsatellites in the human (and other eukaryotic) genomes. Here the authors have been able to develop and apply structure biology tools to understand the following: the molecular mechanism of length polymorphism microsatellites; the molecular mechanism by which the microsatellites in the noncoding regions alter the regulation of the associated gene; and finally, the molecular mechanism by which the expansion of these microsatellites impairs gene expression and causes the disease. Their multidisciplinary structural biology approach is quantitative and can be applied to all coding and noncoding DNA sequences associated with any gene. Both NIH and DOE are interested in developing quantitative tools for understanding the function of various human genes for prevention against diseases caused by genetic and environmental effects.

  2. Self-assembled decanuclear Na(I)2Mn(II)4Mn(III)4 complexes: from discrete clusters to 1-D and 2-D structures, with the Mn(II)4Mn(III)4 unit displaying a large spin ground state and probable SMM behaviour. (United States)

    Langley, Stuart K; Chilton, Nicholas F; Moubaraki, Boujemaa; Murray, Keith S


    The synthesis, magnetic characterization and X-ray crystal structures are reported for five new manganese compounds, [Mn(III)(teaH(2))(sal)]·(1/2)H(2)O (1), [Na(I)(2)Mn(II)(4)Mn(III)(4)(teaH)(6)(sal)(4)(N(3))(2)(MeOH)(4)]·6MeOH (2), [Na(I)(2)Mn(II)(4)Mn(III)(4)(teaH)(6)(sal)(4)(N(3))(2)(MeOH)(2)](n)·7MeOH (3), [Na(I)(2)Mn(II)(4)Mn(III)(4)(teaH)(6)(sal)(4)(N(3))(2)(MeOH)(2)](n)·2MeOH·Et(2)O (4) and [K(I)(2)Mn(II)(4)Mn(III)(4)(teaH)(6)(sal)(4)(N(3))(2)(H(2)O)(2)](n)·5MeOH (5). Complex 1 is a mononuclear compound, formed via the reaction of Mn(NO(3))(2)·4H(2)O, triethanolamine (teaH(3)) and salicylic acid (salH(2)) in a basic methanolic solution. Compound 2 is a mixed-valent hetero-metallic cluster made up of a Mn(8)Na(2) decanuclear core and is formed via the reaction of sodium azide (NaN(3)) with 1. Compounds 3-5 are isolated as 1- or 2-D coordination polymers, each containing the decanuclear Mn(8)M(2) (M = Na(+) or K(+)) core building block as the repeating unit. Compound 3 is isolated when 1 is reacted with NaN(3) over a very short reaction time and forms a 1-D coordination polymer. Each unit displays inter-cluster bridges via the O-atoms of teaH(2-) ligands bonding to the sodium ions of an adjacent cluster. Increasing the reaction time appears to drive the formation of 4 which forms 2-D polymeric sheets and is a packing polymorph of 3. The addition of KMnO(4) and NaN(3) to 1 resulted in compound 5, which also forms a 1-D coordination polymer of the decanuclear core unit. The 1-D chains are now linked via inter-cluster potassium and salicylate bridges. Solid state DC susceptibility measurements were performed on compounds 1-5. The data for 1 are as expected for an S = 2 Mn(III) ion, with the isothermal M vs. H data being fitted by matrix diagonalization methods to give values of g and the axial (D) and rhombic (E) zero field splitting parameters of 2.02, -2.70 cm(-1) and 0.36 cm(-1) respectively. The data for 2-5, each with an identical Mn(II)(4)Mn(III)(4

  3. Microbial community structure of surface sediments from a tropical estuarine environment using next generation sequencing

    Digital Repository Service at National Institute of Oceanography (India)

    Khandeparker, L.; Kuchi, N.; Kale, D.; Anil, A.C.

    analyses using 16s rRNA gene with an emphasis on the AamoA gene in the sediments of these estuaries. Despite their ubiquity, relatively less is known about micro-organisms, largely because more than 99% of prokaryotes in the environment cannot... to unravel the uncultivable novel microbial communities. The capability of high throughput sequencing of 16S rRNA gene sequences by means of Next Generation Sequencing (NGS) technologies has been pivotal in facilitating the discovery of micro biota...

  4. The first complete sequence and genome structure of daphne virus Y. (United States)

    Igori, Davaajargal; Hwang, Un Sun; Lim, Seungmo; Zhao, Fumei; Kwon, Suk-Yoon; Moon, Jae Sun


    From Daphne odora Thunb., an ornamental shrub in the Republic of Korea, a potyvirus was identified that has an RNA genome of 9,448 nucleotides (excluding the 3'-terminal poly(A) tail) encoding a polyprotein of 3,065 amino acids, with nine putative protease cleavage sites producing ten proteins. Since this potyvirus shared the highest nucleotide sequence identity (91 %; query coverage 5 %) with the available partial sequence of daphne virus Y (DVY) from New Zealand (EU179854), it was considered a Korean isolate of DVY. This is the first molecular characterization of the complete genome sequence of a DVY isolate.

  5. Severe Hypertriglyceridemia in Glut1D on Ketogenic Diet. (United States)

    Klepper, Joerg; Leiendecker, Baerbel; Heussinger, Nicole; Lausch, Ekkehart; Bosch, Friedrich


    High-fat ketogenic diets are the only treatment available for Glut1 deficiency (Glut1D). Here, we describe an 8-year-old girl with classical Glut1D responsive to a 3:1 ketogenic diet and ethosuximide. After 3 years on the diet a gradual increase of blood lipids was followed by rapid, severe asymptomatic hypertriglyceridemia (1,910 mg/dL). Serum lipid apheresis was required to determine liver, renal, and pancreatic function. A combination of medium chain triglyceride-oil and a reduction of the ketogenic diet to 1:1 ratio normalized triglyceride levels within days but triggered severe myoclonic seizures requiring comedication with sultiam. Severe hypertriglyceridemia in children with Glut1D on ketogenic diets may be underdiagnosed and harmful. In contrast to congenital hypertriglyceridemias, children with Glut1D may be treated effectively by dietary adjustments alone.

  6. Determining structure and function of steroid dehydrogenase enzymes by sequence analysis, homology modeling, and rational mutational analysis. (United States)

    Duax, William L; Thomas, James; Pletnev, Vladimir; Addlagatta, Anthony; Huether, Robert; Habegger, Lukas; Weeks, Charles M


    The short-chain oxidoreductase (SCOR) family of enzymes includes over 6,000 members identified in sequenced genomes. Of these enzymes, approximately 300 have been characterized functionally, and the three-dimensional crystal structures of approximately 40 have been reported. Since some SCOR enzymes are steroid dehydrogenases involved in hypertension, diabetes, breast cancer, and polycystic kidney disease, it is important to characterize the other members of the family for which the biological functions are currently unknown and to determine their three-dimensional structure and mechanism of action. Although the SCOR family appears to have only a single fully conserved residue, it was possible, using bioinformatics methods, to determine characteristic fingerprints composed of 30-40 residues that are conserved at the 70% or greater level in SCOR subgroups. These fingerprints permit reliable prediction of several important structure-function features including cofactor preference, catalytic residues, and substrate specificity. Human type 1 3beta-hydroxysteroid dehydrogenase isomerase (3beta-HSDI) has 30% sequence identity with a human UDP galactose 4-epimerase (UDPGE), a SCOR family enzyme for which an X-ray structure has been reported. Both UDPGE and 3-HSDI appear to trace their origins back to bacterial 3alpha,20beta-HSD. Combining three-dimensional structural information and sequence data on the 3alpha,20beta-HSD, UDPGE, and 3beta-HSDI subfamilies with mutational analysis, we were able to identify the residues critical to the dehydrogenase function of 3-HSDI. We also identified the residues most probably responsible for the isomerase activity of 3beta-HSDI. We test our predictions by specific mutations based on sequence analysis and our structure-based model.

  7. Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA



    Background Epstein-Barr virus (EBV) is a human herpesvirus implicated in cancer and autoimmune disorders. Little is known concerning the roles of RNA structure in this important human pathogen. This study provides the first comprehensive genome-wide survey of RNA and RNA structure in EBV. Results Novel EBV RNAs and RNA structures were identified by computational modeling and RNA-Seq analyses of EBV. Scans of the genomic sequences of four EBV strains (EBV-1, EBV-2, GD1, and GD2) and of the clo...

  8. Probing the dispersion properties of 1D nanophotonic waveguides with far-field Fourier optics

    DEFF Research Database (Denmark)

    Le Thomas, N.; Jágerská, J.; Houdré, R.;


    We present an advanced Fourier space imaging technique to probe guided light in nanophotonic structures with an effective numerical aperture of 2.5. This superresolution technique allows us to successfully investigate the dispersive properties of 1D nanowaveguides such as photonic crystal W1 wave...

  9. Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. (United States)

    Mashiyama, Susan T; Malabanan, M Merced; Akiva, Eyal; Bhosle, Rahul; Branch, Megan C; Hillerich, Brandan; Jagessar, Kevin; Kim, Jungwook; Patskovsky, Yury; Seidel, Ronald D; Stead, Mark; Toro, Rafael; Vetting, Matthew W; Almo, Steven C; Armstrong, Richard N; Babbitt, Patricia C


    The cytosolic glutathione transferase (cytGST) superfamily comprises more than 13,000 nonredundant sequences found throughout the biosphere. Their key roles in metabolism and defense against oxidative damage have led to thousands of studies over several decades. Despite this attention, little is known about the physiological reactions they catalyze and most of the substrates used to assay cytGSTs are synthetic compounds. A deeper understanding of relationships across the superfamily could provide new clues about their functions. To establish a foundation for expanded classification of cytGSTs, we generated similarity-based subgroupings for the entire superfamily. Using the resulting sequence similarity networks, we chose targets that broadly covered unknown functions and report here experimental results confirming GST-like activity for 82 of them, along with 37 new 3D structures determined for 27 targets. These new data, along with experimentally known GST reactions and structures reported in the literature, were painted onto the networks to generate a global view of their sequence-structure-function relationships. The results show how proteins of both known and unknown function relate to each other across the entire superfamily and reveal that the great majority of cytGSTs have not been experimentally characterized or annotated by canonical class. A mapping of taxonomic classes across the superfamily indicates that many taxa are represented in each subgroup and highlights challenges for classification of superfamily sequences into functionally relevant classes. Experimental determination of disulfide bond reductase activity in many diverse subgroups illustrate a theme common for many reaction types. Finally, sequence comparison between an enzyme that catalyzes a reductive dechlorination reaction relevant to bioremediation efforts with some of its closest homologs reveals differences among them likely to be associated with evolution of this unusual reaction

  10. Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere.

    Directory of Open Access Journals (Sweden)

    Susan T Mashiyama


    Full Text Available The cytosolic glutathione transferase (cytGST superfamily comprises more than 13,000 nonredundant sequences found throughout the biosphere. Their key roles in metabolism and defense against oxidative damage have led to thousands of studies over several decades. Despite this attention, little is known about the physiological reactions they catalyze and most of the substrates used to assay cytGSTs are synthetic compounds. A deeper understanding of relationships across the superfamily could provide new clues about their functions. To establish a foundation for expanded classification of cytGSTs, we generated similarity-based subgroupings for the entire superfamily. Using the resulting sequence similarity networks, we chose targets that broadly covered unknown functions and report here experimental results confirming GST-like activity for 82 of them, along with 37 new 3D structures determined for 27 targets. These new data, along with experimentally known GST reactions and structures reported in the literature, were painted onto the networks to generate a global view of their sequence-structure-function relationships. The results show how proteins of both known and unknown function relate to each other across the entire superfamily and reveal that the great majority of cytGSTs have not been experimentally characterized or annotated by canonical class. A mapping of taxonomic classes across the superfamily indicates that many taxa are represented in each subgroup and highlights challenges for classification of superfamily sequences into functionally relevant classes. Experimental determination of disulfide bond reductase activity in many diverse subgroups illustrate a theme common for many reaction types. Finally, sequence comparison between an enzyme that catalyzes a reductive dechlorination reaction relevant to bioremediation efforts with some of its closest homologs reveals differences among them likely to be associated with evolution of this

  11. 1D photonic crystal sensor integrated in a microfluidic system

    DEFF Research Database (Denmark)

    Nunes, Pedro; Mortensen, Asger; Kutter, Jörg Peter


    A refractive index sensor was designed as a 1D resonator incorporated in a microfluidic channel, where aqueous solutions were injected. A sensitivity of 480 nm/RIU and a minimum difference of Deltan = 0.002 were determined.......A refractive index sensor was designed as a 1D resonator incorporated in a microfluidic channel, where aqueous solutions were injected. A sensitivity of 480 nm/RIU and a minimum difference of Deltan = 0.002 were determined....

  12. Supported plasma-made 1D heterostructures: perspectives and applications


    Borras, Ana; Macias-Montero, Manuel; Romero-Gomez, Pablo; Gonzalez-Elipe, Agustin R.


    Abstract Plasma related methods have been widely used in the fabrication of carbon nanotubes and nanofibres and semiconducting inorganic nanowires. A natural progression of the research in the field of 1D nanostructures is the synthesis of multicomponent nanowires and nanofibres. In this article we review the state of the art of the fabrication by plasma methods of 1D heterostructures including applications and perspectives. Furthermore, recent developments on the use of metal seeds (Ag, A...

  13. Formation of pentacyclic structures by a domino sequence on cyclic enamides. (United States)

    Satyanarayana, Gedu; Maichle-Mössmer, Caecilia; Maier, Martin E


    Novel spiropentacyclic compounds were obtained from cyclic enamides of type , featuring a (2-bromophenyl)propyl substituent in the 5-position, through a Pd-mediated domino sequence taking place via Heck insertion and C-H activation.

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

    DEFF Research Database (Denmark)

    Welinder, K G; Jespersen, H M; Walther-Rasmussen, J;


    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...... 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...

  15. seeMotif: exploring and visualizing sequence motifs in 3D structures



    Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation. As increasing numbers of motifs are detected experimentally or predicted computationally, characterizing the functional roles of motifs and identifying the potential synergetic relationships between them are important next steps. A good way to investigate novel motifs is to utilize the abundant 3D st...

  16. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). (United States)

    Rambaut, Andrew; Lam, Tommy T; Max Carvalho, Luiz; Pybus, Oliver G


    Gene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the sequences in question undergo measurable amounts of evolutionary change between sampling times. Data sets with this property are termed heterochronous and have become increasingly common in several fields of biology, most notably the molecular epidemiology of rapidly evolving viruses. Here we introduce the cross-platform software tool, TempEst (formerly known as Path-O-Gen), for the visualization and analysis of temporally sampled sequence data. Given a molecular phylogeny and the dates of sampling for each sequence, TempEst uses an interactive regression approach to explore the association between genetic divergence through time and sampling dates. TempEst can be used to (1) assess whether there is sufficient temporal signal in the data to proceed with phylogenetic molecular clock analysis, and (2) identify sequences whose genetic divergence and sampling date are incongruent. Examination of the latter can help identify data quality problems, including errors in data annotation, sample contamination, sequence recombination, or alignment error. We recommend that all users of the molecular clock models implemented in BEAST first check their data using TempEst prior to analysis.

  17. Star formation along the Hubble sequence. Radial structure of the star formation of CALIFA galaxies (United States)

    González Delgado, R. M.; Cid Fernandes, R.; Pérez, E.; García-Benito, R.; López Fernández, R.; Lacerda, E. A. D.; Cortijo-Ferrero, C.; de Amorim, A. L.; Vale Asari, N.; Sánchez, S. F.; Walcher, C. J.; Wisotzki, L.; Mast, D.; Alves, J.; Ascasibar, Y.; Bland-Hawthorn, J.; Galbany, L.; Kennicutt, R. C.; Márquez, I.; Masegosa, J.; Mollá, M.; Sánchez-Blázquez, P.; Vílchez, J. M.


    The spatially resolved stellar population content of today's galaxies holds important information for understanding the different processes that contribute to the star formation and mass assembly histories of galaxies. The aim of this paper is to characterize the radial structure of the star formation rate (SFR) in galaxies in the nearby Universe as represented by a uniquely rich and diverse data set drawn from the CALIFA survey. The sample under study contains 416 galaxies observed with integral field spectroscopy, covering a wide range of Hubble types and stellar masses ranging from M⋆ ~ 109 to 7 × 1011 M⊙. Spectral synthesis techniques are applied to the datacubes to derive 2D maps and radial profiles of the intensity of the star formation rate in the recent past (ΣSFR), as well as related properties, such as the local specific star formation rate (sSFR), defined as the ratio between ΣSFR and the stellar mass surface density (μ⋆). To emphasize the behavior of these properties for galaxies that are on and off the main sequence of star formation (MSSF), we stack the individual radial profiles in seven bins of galaxy morphology (E, S0, Sa, Sb, Sbc, Sc, and Sd), and several stellar masses. Our main results are: (a) the intensity of the star formation rate shows declining profiles that exhibit very small differences between spirals with values at R = 1 half light radius (HLR) within a factor two of ΣSFR ~ 20 M⊙Gyr-1pc-2. The dispersion in the ΣSFR(R) profiles is significantly smaller in late type spirals (Sbc, Sc, Sd). This confirms that the MSSF is a sequence of galaxies with nearly constant ΣSFR. (b) sSFR values scale with Hubble type and increase radially outward with a steeper slope in the inner 1 HLR. This behavior suggests that galaxies are quenched inside-out and that this process is faster in the central, bulge-dominated part than in the disks. (c) As a whole and at all radii, E and S0 are off the MSSF with SFR much smaller than spirals of the

  18. Benchmarks and models for 1-D radiation transport in stochastic participating media

    Energy Technology Data Exchange (ETDEWEB)

    Miller, D S


    Benchmark calculations for radiation transport coupled to a material temperature equation in a 1-D slab and 1-D spherical geometry binary random media are presented. The mixing statistics are taken to be homogeneous Markov statistics in the 1-D slab but only approximately Markov statistics in the 1-D sphere. The material chunk sizes are described by Poisson distribution functions. The material opacities are first taken to be constant and then allowed to vary as a strong function of material temperature. Benchmark values and variances for time evolution of the ensemble average of material temperature energy density and radiation transmission are computed via a Monte Carlo type method. These benchmarks are used as a basis for compar