WorldWideScience

Sample records for 1d structural sequences

  1. Novel 1-D Sandwich Photonic Bandgap Structure

    庞云波; 高葆新

    2004-01-01

    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. Significance of flow clustering and sequencing on sediment transport: 1D sediment transport modelling

    Hassan, Kazi; Allen, Deonie; Haynes, Heather

    2016-04-01

    This paper considers 1D hydraulic model data on the effect of high flow clusters and sequencing on sediment transport. Using observed flow gauge data from the River Caldew, England, a novel stochastic modelling approach was developed in order to create alternative 50 year flow sequences. Whilst the observed probability density of gauge data was preserved in all sequences, the order in which those flows occurred was varied using the output from a Hidden Markov Model (HMM) with generalised Pareto distribution (GP). In total, one hundred 50 year synthetic flow series were generated and used as the inflow boundary conditions for individual flow series model runs using the 1D sediment transport model HEC-RAS. The model routed graded sediment through the case study river reach to define the long-term morphological changes. Comparison of individual simulations provided a detailed understanding of the sensitivity of channel capacity to flow sequence. Specifically, each 50 year synthetic flow sequence was analysed using a 3-month, 6-month or 12-month rolling window approach and classified for clusters in peak discharge. As a cluster is described as a temporal grouping of flow events above a specified threshold, the threshold condition used herein is considered as a morphologically active channel forming discharge event. Thus, clusters were identified for peak discharges in excess of 10%, 20%, 50%, 100% and 150% of the 1 year Return Period (RP) event. The window of above-peak flows also required cluster definition and was tested for timeframes 1, 2, 10 and 30 days. Subsequently, clusters could be described in terms of the number of events, maximum peak flow discharge, cumulative flow discharge and skewness (i.e. a description of the flow sequence). The model output for each cluster was analysed for the cumulative flow volume and cumulative sediment transport (mass). This was then compared to the total sediment transport of a single flow event of equivalent flow volume

  3. Comments on the Bifurcation Structure of 1D Maps

    Belykh, V.N.; Mosekilde, Erik

    1997-01-01

    The paper presents a complementary view on some of the phenomena related to the bifurcation structure of unimodal maps. An approximate renormalization theory for the period-doubling cascade is developed, and a mapping procedure is established that accounts directly for the box-within-a-box struct......The paper presents a complementary view on some of the phenomena related to the bifurcation structure of unimodal maps. An approximate renormalization theory for the period-doubling cascade is developed, and a mapping procedure is established that accounts directly for the box......-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, are...

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

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

    2005-01-01

    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.

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

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

    2005-01-01

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

  6. Investigation of 1-D crustal velocity structure beneath Izmir Gulf and surroundings by using local earthquakes

    Polat, Orhan; Özer, Ćaglar

    2016-04-01

    In this study; we examined one dimensional crustal velocity structure of Izmir gulf and surroundings. We used nearly one thousand high quality (A and B class) earthquake data which recorded by Disaster and Emergency Management Presidency (AFAD) [1], Bogazici University (BU-KOERI) [2] and National Observatory of Athens (NOA) [3,4]. We tried several synthetic tests to understand power of new velocity structure, and examined phase residuals, RMS values and shifting tests. After evaluating these tests; we decided one dimensional velocity structure and minimum 1-D P wave velocities, hypocentral parameter and earthquake locations from VELEST algorithm. Distribution of earthquakes was visibly improved by using new minimum velocity structure.

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

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

  8. Uranium(VI) coordination polymers with pyromellitate ligand: Unique 1D channel structures and diverse fluorescence

    Zhang, Yingjie, E-mail: yzx@ansto.gov.au [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia); Bhadbhade, Mohan [Mark Wainwright Analytical Centre, University of New South Wales, Kensington, NSW 2052 (Australia); Karatchevtseva, Inna [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia); Price, Jason R. [Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168 (Australia); Liu, Hao [Centre for Clean Energy Technology, School of Chemistry and Forensic Science, University of Technology Sydney, PO Box 123, Broadway, Sydney, NSW 2007 (Australia); Zhang, Zhaoming; Kong, Linggen [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia); Čejka, Jiří [Department of Mineralogy, National Museum, Václavské náměstí, 68, Prague 1, 115 79-CZ (Czech Republic); Lu, Kim; Lumpkin, Gregory R. [Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232 (Australia)

    2015-03-15

    Three new coordination polymers of uranium(VI) with pyromellitic acid (H{sub 4}btca) have been synthesized and structurally characterized. (ED)[(UO{sub 2})(btca)]·(DMSO)·3H{sub 2}O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH{sub 4}){sub 2}[(UO{sub 2}){sub 6}O{sub 2}(OH){sub 6}(btca)]·~6H{sub 2}O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO{sub 2}){sub 2}(H{sub 2}O)(btca)]·4H{sub 2}O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ{sub 5}-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5 Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated. - Graphical abstract: Table of content: three new uranium(VI) coordination polymers with pyromellitic acid (H{sub 4}btca) have been synthesized via room temperature and hydrothermal synthesis methods, and structurally characterized. Two to three dimensional (3D) frameworks are revealed. All 3D frameworks have unique 1D large channels. Their vibrational modes, thermal stabilities and photoluminescence properties have been investigated. - Highlights: • Three new coordination polymers of U(VI) with pyromellitic acid (H{sub 4}btca). • Structures from a 2D layer to 3D frameworks with unique 1D channels. • Unusual µ{sub 5}-(η{sub 1}:η{sub 2}:η{sub 1}:η{sub 2:}η{sub 1}) coordination mode of btca ligand. • Vibrational modes, thermal stabilities and luminescent properties reported.

  9. Uranium(VI) coordination polymers with pyromellitate ligand: Unique 1D channel structures and diverse fluorescence

    Three new coordination polymers of uranium(VI) with pyromellitic acid (H4btca) have been synthesized and structurally characterized. (ED)[(UO2)(btca)]·(DMSO)·3H2O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH4)2[(UO2)6O2(OH)6(btca)]·~6H2O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO2)2(H2O)(btca)]·4H2O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ5-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5 Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated. - Graphical abstract: Table of content: three new uranium(VI) coordination polymers with pyromellitic acid (H4btca) have been synthesized via room temperature and hydrothermal synthesis methods, and structurally characterized. Two to three dimensional (3D) frameworks are revealed. All 3D frameworks have unique 1D large channels. Their vibrational modes, thermal stabilities and photoluminescence properties have been investigated. - Highlights: • Three new coordination polymers of U(VI) with pyromellitic acid (H4btca). • Structures from a 2D layer to 3D frameworks with unique 1D channels. • Unusual µ5-(η1:η2:η1:η2:η1) coordination mode of btca ligand. • Vibrational modes, thermal stabilities and luminescent properties reported

  10. From GPE to KPZ: finite temperature dynamical structure factor of the 1D Bose gas

    Kulkarni, Manas; Lamacraft, Austen

    2012-01-01

    We study the finite temperature dynamical structure factor $S(k,\\omega)$ of a 1D Bose gas using numerical simulations of the Gross--Pitaevskii equation appropriate to a weakly interacting system. The lineshape of the phonon peaks in $S(k,\\omega)$ has a width $\\propto |k|^{3/2}$ at low wavevectors. This anomalous width arises from resonant three-phonon interactions, and reveals a remarkable connection to the Kardar--Parisi--Zhang universality class of dynamical critical phenomena.

  11. Thermodynamic nature of vitrification in a 1D model of a structural glass former

    We propose a new spin-glass model with no positional quenched disorder which is regarded as a coarse-grained model of a structural glass-former. The model is analyzed in the 1D case when the number N of states of a primary cell is large. For N → ∞, the model exhibits a sharp freezing transition of the thermodynamic origin. It is shown both analytically and numerically that the glass transition is accompanied by a significant growth of a static length scale ξ pointing to the structural (equilibrium) nature of dynamical slowdown effects in supercooled liquids

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

    K.R. Maskaly

    2005-06-01

    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.

  13. Complete Genome Sequence of Herbinix luporum SD1D, a New Cellulose-Degrading Bacterium Isolated from a Thermophilic Biogas Reactor

    Koeck, Daniela E.; Maus, Irena; Wibberg, Daniel; Winkler, Anika; Zverlov, Vladimir V.; Liebl, Wolfgang; Pühler, Alfred; Schwarz, Wolfgang H.

    2016-01-01

    A novel cellulolytic bacterial strain was isolated from an industrial-scale biogas plant. The 16S rRNA gene sequence of the strain SD1D showed 96.4% similarity to Herbinix hemicellulosilytica T3/55T, indicating a novel species within the genus Herbinix (family Lachnospiraceae). Here, the complete genome sequence of Herbinix luporum SD1D is reported. PMID:27445379

  14. Complete Genome Sequence of Herbinix luporum SD1D, a New Cellulose-Degrading Bacterium Isolated from a Thermophilic Biogas Reactor.

    Koeck, Daniela E; Maus, Irena; Wibberg, Daniel; Winkler, Anika; Zverlov, Vladimir V; Liebl, Wolfgang; Pühler, Alfred; Schwarz, Wolfgang H; Schlüter, Andreas

    2016-01-01

    A novel cellulolytic bacterial strain was isolated from an industrial-scale biogas plant. The 16S rRNA gene sequence of the strain SD1D showed 96.4% similarity to Herbinix hemicellulosilytica T3/55(T), indicating a novel species within the genus Herbinix (family Lachnospiraceae). Here, the complete genome sequence of Herbinix luporum SD1D is reported. PMID:27445379

  15. Study of phase space structures in driven 1D Vlasov poisson model

    Electrostatic waves in a collisionless, unmagnetized plasma are known to interact with particles that stream with velocities close to the wave phase speed to produce damping effects, particle trapping and interesting nonlinear coherent structures. For example, it is well known that if the initial amplitude of the wave is large enough, the damping effects can be overcome to form BGK structures. In the present work, we consider a 1D driven Vlasov-Poisson plasma model. It is demonstrated that by a careful choice of drive phase and for drive amplitudes smaller than or comparable to the linear limit, it is possible to generate surprisingly large amplitude coherent structures in phase space. This and other details will be presented. (author)

  16. Uranium(VI) coordination polymers with pyromellitate ligand: Unique 1D channel structures and diverse fluorescence

    Zhang, Yingjie; Bhadbhade, Mohan; Karatchevtseva, Inna; Price, Jason R.; Liu, Hao; Zhang, Zhaoming; Kong, Linggen; Čejka, Jiří; Lu, Kim; Lumpkin, Gregory R.

    2015-03-01

    Three new coordination polymers of uranium(VI) with pyromellitic acid (H4btca) have been synthesized and structurally characterized. (ED)[(UO2)(btca)]·(DMSO)·3H2O (1) (ED=ethylenediammonium; DMSO=dimethylsulfoxide) has a lamellar structure with intercalation of ED and DMSO. (NH4)2[(UO2)6O2(OH)6(btca)]·~6H2O (2) has a 3D framework built from 7-fold coordinated uranyl trinuclear units and btca ligands with 1D diamond-shaped channels (~8.5 Å×~8.6 Å). [(UO2)2(H2O)(btca)]·4H2O (3) has a 3D network constructed by two types of 7-fold coordinated uranium polyhedron. The unique μ5-coordination mode of btca in 3 enables the formation of 1D olive-shaped large channels (~4.5 Å×~19 Å). Vibrational modes, thermal stabilities and fluorescence properties have been investigated.

  17. Sequence repeats and protein structure

    Hoang, Trinh X.; Trovato, Antonio; Seno, Flavio; Banavar, Jayanth R.; Maritan, Amos

    2012-11-01

    Repeats are frequently found in known protein sequences. The level of sequence conservation in tandem repeats correlates with their propensities to be intrinsically disordered. We employ a coarse-grained model of a protein with a two-letter amino acid alphabet, hydrophobic (H) and polar (P), to examine the sequence-structure relationship in the realm of repeated sequences. A fraction of repeated sequences comprises a distinct class of bad folders, whose folding temperatures are much lower than those of random sequences. Imperfection in sequence repetition improves the folding properties of the bad folders while deteriorating those of the good folders. Our results may explain why nature has utilized repeated sequences for their versatility and especially to design functional proteins that are intrinsically unstructured at physiological temperatures.

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

    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.

  19. 1D crustal structure from quality seismological data for the Cyprus subduction zone

    Perk, Şükran; Deǧer, Ali; Özbakır, Karabulut, Hayrullah

    2013-04-01

    The eastern Mediterranean is a tectonically complex region, where long-term subduction and accretion processes have shaped the overall evolution. Recently, many seismic tomography studies have shown subducted slabs of the Neo-Tethyan lithosphere, continuing its subduction in the Hellenic trench, stalled in the Cyprus trench and being torn near the intersection between them. Antalya bay is a key region located on the western flank of the Cyprus Subduction Zone (CSZ), close to the junction between the Hellenic and Cyprus Arcs. Here deep earthquakes are nucleated, which otherwise cannot be seen anywhere else along the CSZ. For this reason, we focus our attention specifically to the Antalya Bay area but also the remaining parts of the CSZ. Several regional studies have been carried out to define the velocity structure beneath the region but none have been able to locate the CSZ. One of the main reasons for this was the lack of incorporation of a wide seismic network in those regional studies. We compile a large catalog of seismicity and relocate earthquakes to infer 1D local crustal structure using the clusters of seismicity. We used seismic data between 2005 - 2011 which are recorded at more than 335 seismic stations operated by several agencies and portable deployments. The data-set is composed of over 10,000 events and earthquakes can be grouped in several distinct clusters. We defined five of these clusters, where the total number of events is more than 4500, among which we selected over 2000 events with the highest data quality. 1-D local P-wave velocity models are developed using this high quality data-set and the earthquakes are relocated using the local velocity models. The compiled and reanalyzed data will contribute to perform local earthquake tomography. Moreover, obtained local velocity models represent a fundamental step towards an improved seismic tomography studies in a very crucial region in the eastern Mediterranean.

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

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

    2009-01-01

    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.

  1. A zwitterionic 1D/2D polymer co-crystal and its polymorphic sub-components: a highly selective sensing platform for HIV ds-DNA sequences.

    Zhao, Hai-Qing; Yang, Shui-Ping; Ding, Ni-Ni; Qin, Liang; Qiu, Gui-Hua; Chen, Jin-Xiang; Zhang, Wen-Hua; Chen, Wen-Hua; Hor, T S Andy

    2016-03-15

    Polymorphic compounds {[Cu(dcbb)2(H2O)2]·10H2O}n (, 1D chain), [Cu(dcbb)2]n (, 2D layer) and their co-crystal {[Cu(dcbb)2(H2O)][Cu(dcbb)2]2}n () have been prepared from the coordination reaction of a 2D polymer [Na(dcbb)(H2O)]n (, H2dcbbBr = 1-(3,5-dicarboxybenzyl)-4,4'-bipyridinium bromide) with Cu(NO3)2·3H2O at different temperatures in water. Compounds have an identical metal-to-ligand stoichiometric ratio of 1 : 2, but absolutely differ in structure. Compound features a 2D layer structure with aromatic rings, positively charged pyridinium and free carboxylates on its surface, promoting electrostatic, π-stacking and/or hydrogen-bonding interactions with the carboxyfluorescein (FAM) labeled probe single-stranded DNA (probe ss-DNA, delineates as P-DNA). The resultant P-DNA@ system facilitated fluorescence quenching of FAM via a photoinduced electron transfer process. The P-DNA@ system functions as an efficient fluorescent sensor selective for HIV double-stranded DNA (HIV ds-DNA) due to the formation of a rigid triplex structure with the recovery of FAM fluorescence. The system reported herein also distinguishes complementary HIV ds-DNA from mismatched target DNA sequences with the detection limit of 1.42 nM. PMID:26883749

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

    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......-Bloch space harmonics. We discuss how space harmonic permittivity and permeability can be expressed in seemingly different though equivalent forms, and we investigate these parameters of the zeroeth order space harmonic for a particular 1D periodic structure that is based on a previously reported 3D periodic...

  3. Simulation of unsteady state performance of a secondary air system by the 1D-3D-Structure coupled method

    Wu, Hong; Li, Peng; Li, Yulong

    2016-02-01

    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.

  4. Sequence-structure relations of biopolymers

    Barrett, Christopher; Reidys, Christian M

    2015-01-01

    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 ...

  5. Complete Genome Sequence of a Classical Swine Fever Virus Isolate Belonging to New Subgenotype 2.1d from Henan Province, Central China.

    Lv, Chaochao; Yang, Qingyuan; Gao, Xiaojing; Yao, Yali; Li, Xiangdong; Xiao, Yan; Tian, Kegong

    2016-01-01

    We report here the complete genome sequence of HeN1505, a field isolate of classical swine fever virus belonging to the new subgenotype 2.1d. HeN1505 distinguishes itself from other classical swine fever virus (CSFVs) by 1 amino acid substitution in position 159 (threonine by isoleucine), which led to the loss of one N-glycosylation site in the N(pro) protein. PMID:27174260

  6. Complete Genome Sequence of Classical Swine Fever Virus Strain JSZL, Belonging to a New Subgenotype, 2.1d, Isolated in China in 2014.

    Zhang, Hongliang; Feng, Liping; Liu, Chunxiao; Chen, Jiazeng; Leng, Chaoliang; Bai, Yun; Peng, Jinmei; An, Tongqing; Cai, Xuehui; Yang, Xufu; Tian, Zhijun; Tong, Guangzhi

    2015-01-01

    The complete genome sequence of classic swine fever virus (CSFV) strain JSZL was determined in this study. JSZL was originally isolated from an immune pig farm in Jiangsu Province, China. JSZL is more closely related to subgenotype 2.1b than to 2.1a and 2.1c. Importantly, JSZL was classified into a new subgenotype, 2.1d. PMID:26294620

  7. Complete Genome Sequence of a Classical Swine Fever Virus Isolate Belonging to New Subgenotype 2.1d from Henan Province, Central China

    Lv, Chaochao; Yang, Qingyuan; Gao, Xiaojing; Yao, Yali; Li, Xiangdong; Xiao, Yan; Tian, Kegong

    2016-01-01

    We report here the complete genome sequence of HeN1505, a field isolate of classical swine fever virus belonging to the new subgenotype 2.1d. HeN1505 distinguishes itself from other classical swine fever virus (CSFVs) by 1 amino acid substitution in position 159 (threonine by isoleucine), which led to the loss of one N-glycosylation site in the Npro protein.

  8. Structure, electrochemical properties and capacitance performance of polypyrrole electrodeposited onto 1-D crystals of iridium complex

    Wysocka-Żołopa, Monika; Winkler, Krzysztof

    2015-12-01

    Composites of polypyrrole and one-dimensional iridium complex crystals [(C2H5)4N]0.55[IrCl2(CO)2] were prepared by in situ two-step electrodeposition. Initially, iridium complex crystals were formed during [IrCl2(CO)2]- complex oxidation. Next, pyrrole was electropolymerized on the surface of the iridium needles. The morphology of the composite was investigated by scanning and transmission electron microscopy. At positive potentials, the iridium complex crystals and the polypyrrole were oxidized. In aprotic solvents, oxidation of the iridium complex crystals resulted in their dissolution. In water containing tetra(n-butyl)ammonium chlorides, the 1-D iridium complex crystals were reversibly oxidized. The product of the iridium complex oxidation remained on the electrode surface in crystalline form. The iridium complex needles significantly influenced the redox properties of the polymer. The polypyrrole involved electrode processes become more reversible in presence of crystals of iridium complex. The current of polypyrrole oxidation was higher compared to that of pure polypyrrole and the capacitance properties of the polymer were significantly enhanced. A specific capacitance as high as 590 F g-1 was obtained for a composite of polypyrrole and 1-D crystals of the iridium complex in water containing tetra(n-butyl)ammonium chloride. This value is approximately twice as high as the capacitance of the pure polymer deposited onto the electrode surface.

  9. Development of input structure software for MARS 1D-3D graphic user interface

    A user-friendly Input Software for MARS 1D-3D GUI called MARA (MARS Adjunct Reactor Assembler) has been developed. Extension of the current MARA to the overall input system for MARS will result in an integrated commercial GUI comparable to those for computational analysis codes ANSYS, ABAQUS, FLUENT and CFX. MARA will help accelerate marketing of MARS and other potential system analysis codes to developing countries in Southeast Asia planning to put nuclear power in their electrical grids. MARS code and associated developmental technology are in the process of being disseminated to twenty-two organizations spanning the industry, academia and laboratories across the country. MARA will find its way to practical applications in a variety of engineering problems

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

    Freimuth, Paul I.

    2010-04-06

    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.

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

    Breinbjerg, O.

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

  12. Mapping of the serotonin 5-HT{sub 1D{beta}} autoreceptor gene on chromosome 6 and direct analysis for sequence variants

    Lappalainen, J.; Dean, M.; Virkkunen, M. [National Cancer Institute, Fredrick, MD (United States)] [and others

    1995-04-24

    Abnormal brain serotonin function may be characteristic of several neuropsychiatric disorders. Thus, it is important to identify polymorphic genes and screen for functional variants at loci coding for genes that control normal serotonin functions. 5-HT{sub 1D{beta}} is a terminal serotonin autoreceptor which may play a role in regulating serotonin synthesis and release. Using an SSCP technique we screened for 5-HT{sub 1D{beta}} coding sequence variants in psychiatrically interviewed populations, which included controls, alcoholics, and alcoholic arsonists and alcoholic violent offenders with low CSF concentrations of the main serotonin metabolite 5-HIAA. A common polymorphism was identified in the 5-HT{sub 1D{beta}} gene with allele frequencies of 0.72 and 0.28. The SSCP variant was caused by a silent G to C substitution at nucleotide 861 of the coding region. This polymorphism could also be detected as a HincII RFLP of amplified DNA. DNAs from informative CEPH families were typed for the HincII RFLP and analyzed with respect to 20 linked markers on chromosome 6. Multipoint analysis placed the 5-HT{sub 1D{beta}} receptor gene between markers D6S286 and D6S275. A maximum two-point lod score of 10.90 was obtained to D6S26, which had been previously localized on 6q14-15. Chromosomal aberrations involving this region have been previously shown to cause retinal anomalies, developmental delay, and abnormal brain development. This region also contains the gene for North Carolina-type macular dystrophy. 34 refs., 3 figs., 1 tab.

  13. Overcoming Sequence Misalignments with Weighted Structural Superposition

    Khazanov, Nickolay A.; Damm-Ganamet, Kelly L.; Quang, Daniel X.; Carlson, Heather A.

    2012-01-01

    An appropriate structural superposition identifies similarities and differences between homologous proteins that are not evident from sequence alignments alone. We have coupled our Gaussian-weighted RMSD (wRMSD) tool with a sequence aligner and seed extension (SE) algorithm to create a robust technique for overlaying structures and aligning sequences of homologous proteins (HwRMSD). HwRMSD overcomes errors in the initial sequence alignment that would normally propagate into a standard RMSD ov...

  14. Electrophysiological and Structural Remodeling in Heart Failure Modulate Arrhythmogenesis. 1D Simulation Study

    Gómez García, Juan Francisco; Romero Pérez, Lucia; Ferrero De Loma-Osorio, José María; Trenor Gomis, Beatriz Ana

    2014-01-01

    Background: Heart failure is a final common pathway or descriptor for various cardiac pathologies. It is associated with sudden cardiac death, which is frequently caused by ventricular arrhythmias. Electrophysiological remodeling, intercellular uncoupling, fibrosis and autonomic imbalance have been identified as major arrhythmogenic factors in heart failure etiology and progression. Objective: In this study we investigate in silico the role of electrophysiological and structur...

  15. Bifurcation Structures in a Family of 1D Discontinuous Linear-Hyperbolic Invertible Maps

    Makrooni, Roya; Gardini, Laura; Sushko, Iryna

    2015-12-01

    We consider a family of one-dimensional discontinuous invertible maps from an application in engineering. It is defined by a linear function and by a hyperbolic function with real exponent. The presence of vertical and horizontal asymptotes of the hyperbolic branch leads to particular codimension-two border collision bifurcation (BCB) such that if the parameter point approaches the bifurcation value from one side then the related cycle undergoes a regular BCB, while if the same bifurcation value is approached from the other side then a nonregular BCB occurs, involving periodic points at infinity, related to the asymptotes of the map. We investigate the bifurcation structure in the parameter space. Depending on the exponent of the hyperbolic branch, different period incrementing structures can be observed, where the boundaries of a periodicity region are related either to subcritical, or supercritical, or degenerate flip bifurcations of the related cycle, as well as to a regular or nonregular BCB. In particular, if the exponent is positive and smaller than one, then the period incrementing structure with bistability regions is observed and the corresponding flip bifurcations are subcritical, while if the exponent is larger than one, then the related flip bifurcations are supercritical and, thus, also the regions associated with cycles of double period are involved into the incrementing structure.

  16. 3D mechanical measurements with an atomic force microscope on 1D structures

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

    2012-01-01

    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...

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

    Topcu, Gulacti; Ulubelen, Ayhan

    2007-05-01

    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.

  18. Fibonacci Sequence and Supramolecular Structure of DNA.

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

    2016-05-01

    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. PMID:27265133

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

    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). - Graphical abstract: Two novel cobalt complexes have been prepared. Compound 1 consists of tetranuclear (Co3IINa) 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

  20. Structural Basis of the Interaction between Tuberous Sclerosis Complex 1 (TSC1) and Tre2-Bub2-Cdc16 Domain Family Member 7 (TBC1D7).

    Qin, Jiayue; Wang, Zhizhi; Hoogeveen-Westerveld, Marianne; Shen, Guobo; Gong, Weimin; Nellist, Mark; Xu, Wenqing

    2016-04-15

    Mutations in TSC1 or TSC2 cause tuberous sclerosis complex (TSC), an autosomal dominant disorder characterized by the occurrence of benign tumors in various vital organs and tissues. TSC1 and TSC2, the TSC1 and TSC2 gene products, form the TSC protein complex that senses specific cellular growth conditions to control mTORC1 signaling. TBC1D7 is the third subunit of the TSC complex, and helps to stabilize the TSC1-TSC2 complex through its direct interaction with TSC1. Homozygous inactivation of TBC1D7 causes intellectual disability and megaencephaly. Here we report the crystal structure of a TSC1-TBC1D7 complex and biochemical characterization of the TSC1-TBC1D7 interaction. TBC1D7 interacts with the C-terminal region of the predicted coiled-coil domain of TSC1. The TSC1-TBC1D7 interface is largely hydrophobic, involving the α4 helix of TBC1D7. Each TBC1D7 molecule interacts simultaneously with two parallel TSC1 helices from two TSC1 molecules, suggesting that TBC1D7 may stabilize the TSC complex by tethering the C-terminal ends of two TSC1 coiled-coils. PMID:26893383

  1. 1D nanorod-planted 3D inverse opal structures for use in dye-sensitized solar cells

    Park, Yesle; Lee, Jung Woo; Ha, Su-Jin; Moon, Jun Hyuk

    2014-02-01

    The effectiveness of the 1D nanorod (NR)-planted 3D inverse opal (IO) structure as an electrode for dye-sensitized solar cells (DSSCs) is demonstrated here. The NRs were grown on the surface of a macroporous IO structure and their longitudinal growth increased the surface area of the structure proportional to the growth duration. NR/IO electrodes with various NR growth times were compared. A remarkable JSC was obtained for the DSSCs utilizing a NR/IO electrode. The improvement of the JSC was analyzed in terms of its efficiency in light harvesting and electron transport. The growth of the NRs improved the dye adsorption density and scattering property of the electrode, resulting in an improvement in the light harvesting efficiency. Electrochemical impedance analysis revealed that the NRs also improved its electron transport properties. Further growth of the NRs tended to limit the increase of the JSC, which could be attributed to an overlap between them.The effectiveness of the 1D nanorod (NR)-planted 3D inverse opal (IO) structure as an electrode for dye-sensitized solar cells (DSSCs) is demonstrated here. The NRs were grown on the surface of a macroporous IO structure and their longitudinal growth increased the surface area of the structure proportional to the growth duration. NR/IO electrodes with various NR growth times were compared. A remarkable JSC was obtained for the DSSCs utilizing a NR/IO electrode. The improvement of the JSC was analyzed in terms of its efficiency in light harvesting and electron transport. The growth of the NRs improved the dye adsorption density and scattering property of the electrode, resulting in an improvement in the light harvesting efficiency. Electrochemical impedance analysis revealed that the NRs also improved its electron transport properties. Further growth of the NRs tended to limit the increase of the JSC, which could be attributed to an overlap between them. Electronic supplementary information (ESI) available. See DOI

  2. Whole-exome sequencing identifies mutations of TBC1D1 encoding a Rab-GTPase-activating protein in patients with congenital anomalies of the kidneys and urinary tract (CAKUT).

    Kosfeld, Anne; Kreuzer, Martin; Daniel, Christoph; Brand, Frank; Schäfer, Anne-Kathrin; Chadt, Alexandra; Weiss, Anna-Carina; Riehmer, Vera; Jeanpierre, Cécile; Klintschar, Michael; Bräsen, Jan Hinrich; Amann, Kerstin; Pape, Lars; Kispert, Andreas; Al-Hasani, Hadi; Haffner, Dieter; Weber, Ruthild G

    2016-01-01

    Congenital anomalies of the kidneys and urinary tract (CAKUT) are genetically highly heterogeneous leaving most cases unclear after mutational analysis of the around 30 causative genes known so far. Assuming that phenotypes frequently showing dominant inheritance, such as CAKUT, can be caused by de novo mutations, de novo analysis of whole-exome sequencing data was done on two patient-parent-trios to identify novel CAKUT genes. In one case, we detected a heterozygous de novo frameshift variant in TBC1D1 encoding a Rab-GTPase-activating protein regulating glucose transporter GLUT4 translocation. Sequence analysis of 100 further CAKUT cases yielded three novel or rare inherited heterozygous TBC1D1 missense variants predicted to be pathogenic. TBC1D1 mutations affected Ser237-phosphorylation or protein stability and thereby act as hypomorphs. Tbc1d1 showed widespread expression in the developing murine urogenital system. A mild CAKUT spectrum phenotype, including anomalies observed in patients carrying TBC1D1 mutations, was found in kidneys of some Tbc1d1 (-/-) mice. Significantly reduced Glut4 levels were detected in kidneys of Tbc1d1 (-/-) mice and the dysplastic kidney of a TBC1D1 mutation carrier versus controls. TBC1D1 and SLC2A4 encoding GLUT4 were highly expressed in human fetal kidney. The patient with the truncating TBC1D1 mutation showed evidence for insulin resistance. These data demonstrate heterozygous deactivating TBC1D1 mutations in CAKUT patients with a similar renal and ureteral phenotype, and provide evidence that TBC1D1 mutations may contribute to CAKUT pathogenesis, possibly via a role in glucose homeostasis. PMID:26572137

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

    Karabash, Illya M

    2011-01-01

    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...

  4. An approach to jointly invert hypocenters and 1D velocity structure and its application to the Lushan earthquake series

    Qian, Hui; Mechie, James; Li, Haibing; Xue, Guangqi; Su, Heping; Cui, Xiang

    2016-01-01

    Earthquake location is essential when defining fault systems and other geological structures. Many methods have been developed to locate hypocenters within a 1D velocity model. In this study, a new approach, named MatLoc, has been developed which can simultaneously invert for the locations and origin times of the hypocenters and the velocity structure, from the arrival times of local earthquakes. Moreover, it can invert for layer boundary depths, such as Moho depths, which can be well constrained by the Pm and Pn phases. For this purpose, the package was developed to take into account reflected phases, e.g., the Pm phase. The speed of the inversion is acceptable due to the use of optimized matrix calculations. The package has been used to re-locate the Lushan earthquake series which occurred in Sichuan, China, from April 20 to April 22, 2013. The results obtained with the package show that the Lushan earthquake series defines the dip of the Guankou fault, on which most of the series occurred, to be 39° toward the NW. Further, the surface projection of the Lushan earthquake series is consistent with the regional tectonic strike which is about N45° E.

  5. 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

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

    2011-01-01

    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.

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

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

    2009-01-01

    @@ 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].

  7. Gold-induced nanowires on the Ge(100) surface yield a 2D and not a 1D electronic structure

    de Jong, N.; Heimbuch, R.; Eliëns, S.; Smit, S.; Frantzeskakis, E.; Caux, J.-S.; Zandvliet, H. J. W.; Golden, M. S.

    2016-06-01

    Atomic nanowires on semiconductor surfaces induced by the adsorption of metallic atoms have attracted a lot of attention as possible hosts of the elusive, one-dimensional Tomonaga-Luttinger liquid. The Au/Ge(100) system in particular is the subject of controversy as to whether the Au-induced nanowires do indeed host exotic, 1D (one-dimensional) metallic states. In light of this debate, we report here a thorough study of the electronic properties of high quality nanowires formed at the Au/Ge(100) surface. The high-resolution ARPES data show the low-lying Au-induced electronic states to possess a dispersion relation that depends on two orthogonal directions in k space. Comparison of the E (kx,ky) surface measured using high-resolution ARPES to tight-binding calculations yields hopping parameters in the two different directions that differ by approximately factor of two. Additionally, by pinpointing the Au-induced surface states in the first, second, and third surface Brillouin zones and analyzing their periodicity in k||, the nanowire propagation direction seen clearly in STM can be imported into the ARPES data. We find that the larger of the two hopping parameters corresponds, in fact, to the direction perpendicular to the nanowires (tperp). This proves that the Au-induced electron pockets possess a two-dimensional, closed Fermi surface, and this firmly places the Au/Ge(100) nanowire system outside potential hosts of a Tomonaga-Luttinger liquid. We combine these ARPES data with scanning tunneling spectroscopic measurements of the spatially resolved electronic structure and find that the spatially straight—wirelike—conduction channels observed up to energies of order one electron volt below the Fermi level do not originate from the Au-induced states seen in the ARPES data. The former are rather more likely to be associated with bulk Ge states that are localized to the subsurface region. Despite our proof of the 2D (two-dimentional) nature of the Au

  8. ITS SEQUENCE AND ELECTROPHORETIC KARYOTYPE COMPARISONS OF THE ASCOMYCETOUS YEAST SPECIES WITH IDENTICAL OR SIMILAR LSU RRNA GENE D1/D2 DOMAIN SEQUENCES%大亚基rRNA基因D1/D2区序列相同或相似的子囊菌酵母ITS序列比较和核型分析

    吴作为; 白逢彦

    2005-01-01

    The species in each of the following groups: Ⅰ) Candida aaseri and Candida butyri; Ⅱ) Candida boleticola, Candida laureliae and Candida ralunensis; Ⅲ) Candida zeylanoides and Candida krissii and Ⅳ)Pichiafarinosa and Candida cacaoi were considered to be conspecific because of their identical or similar (only 1 base difference) large subunit (26S) RNA gene D1/D2 domain sequences. The present study indicated that the internal transcribed spacer (ITS) sequences of the species in each of the groups were also identical or had only 1 base difference. The electrophorefic karyotyping showed that the chromosomal DNA banding profiles of the species in groups Ⅱ and Ⅳ were identical or similar. The conspecificity of the species in each of the two groups was thus confirmed. However, remarkably different electrophoretic karyotypes were found between the species in each of groups Ⅰ and Ⅲ. The taxonomic relationships of them remain to be clarified.%下面每个组内的酵母菌:Ⅰ)Candida aaseri和Candida butyri;Ⅱ)Candida boleticola,Candida laureliae和Candida ralunensis;Ⅲ) Candida zeylanoides和Candida krissii以及Ⅳ)Pichia farinosa和Candida cacaoi因具有相同或只有一个碱基差异的大亚基(26S)rRNA基因D1/D2区序列,而被认为属于同一个种.本研究对其ITS序列和电泳核型进行了比较分析.结果表明前3个组内的种具有完全相同的ITS序列,第Ⅳ组的两个种只有1个碱基差异,但是各组内的核型并不完全一致.第Ⅳ组内的两个种具有完全相同的核型,证实他们属于同一个种.第Ⅱ组内的C. laureliae和C. ralunensis也具有完全相同的核型,可以肯定二者也属于同一个种,该组内的C. boleticola的核型与前二者不完全一样,但染色体分子量范围相似,也可能与前二者属于同一个种.第Ⅰ和Ⅲ组内各种的核型具有明显差异,对组内种间的同物异名关系未提供支持.

  9. Structural protein descriptors in 1-dimension and their sequence-based predictions.

    Kurgan, Lukasz; Disfani, Fatemeh Miri

    2011-09-01

    The last few decades observed an increasing interest in development and application of 1-dimensional (1D) descriptors of protein structure. These descriptors project 3D structural features onto 1D strings of residue-wise structural assignments. They cover a wide-range of structural aspects including conformation of the backbone, burying depth/solvent exposure and flexibility of residues, and inter-chain residue-residue contacts. We perform first-of-its-kind comprehensive comparative review of the existing 1D structural descriptors. We define, review and categorize ten structural descriptors and we also describe, summarize and contrast over eighty computational models that are used to predict these descriptors from the protein sequences. We show that the majority of the recent sequence-based predictors utilize machine learning models, with the most popular being neural networks, support vector machines, hidden Markov models, and support vector and linear regressions. These methods provide high-throughput predictions and most of them are accessible to a non-expert user via web servers and/or stand-alone software packages. We empirically evaluate several recent sequence-based predictors of secondary structure, disorder, and solvent accessibility descriptors using a benchmark set based on CASP8 targets. Our analysis shows that the secondary structure can be predicted with over 80% accuracy and segment overlap (SOV), disorder with over 0.9 AUC, 0.6 Matthews Correlation Coefficient (MCC), and 75% SOV, and relative solvent accessibility with PCC of 0.7 and MCC of 0.6 (0.86 when homology is used). We demonstrate that the secondary structure predicted from sequence without the use of homology modeling is as good as the structure extracted from the 3D folds predicted by top-performing template-based methods. PMID:21787299

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

    SHYAMAPADA SHIT; MADHUSUDAN NANDY; CORRADO RIZZOLI; CÉDRIC DESPLANCHES; SAMIRAN MITRA

    2016-06-01

    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.

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

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

  12. Four 1-D metal-organic polymers self-assembled from semi-flexible benzimidazole-based ligand: Syntheses, structures and fluorescent properties

    Zhou, Chun-lin; Wang, Shi-min; Liu, Sai-nan; Yu, Tian-tian; Li, Rui-ying; Xu, Hong; Liu, Zhong-yi; Sun, Huan; Cheng, Jia-jia; Li, Jin-peng; Hou, Hong-wei; Chang, Jun-biao

    2016-08-01

    Four one-dimensional (1-D) metal-organic polymers based on methylene-bis(1,1‧-benzimidazole)(mbbz), namely, {[Hg(mbbz)(SCN)2]·1/3H2O}n (1), [Co(mbbz)(Cl)2]n (2), {[Co(mbbz)(SO4)]·CH3OH}n (3) and {[Zn(mbbz)(SO4)]·CH3OH}n (4) have been successfully synthesized and structurally characterized. Single-crystal X-ray diffraction reveals that polymers 1 and 2 exhibit interesting 1-D double helical chain structures, while polymers 3 and 4 are 1-D double chain structures due to the bridging effect of mbbz ligands and sulfate anions. These polymers containing the mbbz-based ligand have a high degree of dependence on the corresponding counter anions. Furthermore, the fluorescence properties of the four polymers were also investigated in the solid state, showing the fluorescence signal changes in comparing with that of free ligand mbbz.

  13. An Integrated Sequence-Structure Database incorporating matching mRNA sequence, amino acid sequence and protein three-dimensional structure data.

    Adzhubei, I A; Adzhubei, A. A.; Neidle, S.

    1998-01-01

    We have constructed a non-homologous database, termed the Integrated Sequence-Structure Database (ISSD) which comprises the coding sequences of genes, amino acid sequences of the corresponding proteins, their secondary structure and straight phi,psi angles assignments, and polypeptide backbone coordinates. Each protein entry in the database holds the alignment of nucleotide sequence, amino acid sequence and the PDB three-dimensional structure data. The nucleotide and amino acid sequences for ...

  14. Structure Prediction of Partial-Length Protein Sequences

    Ram Samudrala; Adrian Laurenzi; Ling-Hong Hung

    2013-01-01

    Protein structure information is essential to understand protein function. Computational methods to accurately predict protein structure from the sequence have primarily been evaluated on protein sequences representing full-length native proteins. Here, we demonstrate that top-performing structure prediction methods can accurately predict the partial structures of proteins encoded by sequences that contain approximately 50% or more of the full-length protein sequence. We hypothesize that stru...

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

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

  16. Synthesis and Crystal Structure of a 1-D Chain Coordination Complex {[Mn2(HCAM)3(H2bipy)]·5H2O}n

    SUN Ya-Guang; RONG Shu-Ting; WU Yong-Li; YU Wan; WANG Chuan-Sheng; ZHANO Wan-Zhong; GAO En-Jun

    2009-01-01

    The 1-D chain coordination complex of {[Mn2(HCAM)3(H2bipy)]·5H2O}n (H3CAM = 4-hydroxypyridine-2,6-dicarboxylic acid, bipy = 4,4'-bipyridine) has been synthesized by the reaction of 4-hydroxypyridine-2,6-dicarboxylic acid, 4,4'-bipyridine and manganese carbonate under hydrothermal conditions, and its crystal structure was determined by X-ray diffraction method. The crystal belongs to the monoclinie system, space group P21/n with a = 10.110(2), b = 20.159(4), c = 17.861(4) A, β = 99.67(3)°, V= 3.5884(12) nm3, Mr= 901.47, Z = 4, Dc= 1.669 g·cm-3, μ= 0.798 mm-1, F(000) = 1840, the final R = 0.0713 and wR = 0.1853. The complex forms a 1-D chain bridged by HCAM, protonated 4,4-bipyridines link the 1-D chains to construct 2-D networks via N-H…O hydrogen bonds, and networks are further extended via π-π stacking and hydrogen bonds into 3-D supramolecular framework.

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

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

  18. New method for computation of band structures in 1D photonic crystals based on the Fresnel equations

    Roshan Entezar, S.

    2013-02-01

    In this paper, we present a new method for calculation of band structure in one-dimensional bilayer photonic crystals, based on the Fresnel equations. We derive a new relation to obtain the band structure without using the Floquet theorem. It is shown that this relation can be simplified under the assumption that the single-path phase-shift acquired through the individual layers of the photonic crystal be equal to ? . The results obtained by our method are compared with the ones obtained from the transfer matrix method to show that they are exactly identical.

  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

    2010-01-01

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

    Bellingeri, Michele

    2014-01-01

    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.

  1. 3D versus 1D quantum confinement in coherently strained CdS/ZnS quantum structures

    Woggon, U.; Gindele, F.; Petri, W.; Hetterich, M.; Grün, M.; Klingshirn, C.; Langbein, Wolfgang Werner; Hvam, Jørn Märcher; Kümmel, T; Bacher, G.; Forchel, A.

    1998-01-01

    Monolayer fluctuations in ultrathin, coherently strained CdS/ZnS quantum structures result in a very strong localization of excitons. The deepest localized excitons can be considered as individual, decoupled and three-dimensionally confined. Consequently, fingerprints of zero-dimensionality are...... found in the optical spectra like single, ultranarrow luminescence lines in micro-photoluminescence and spectrally broad optical gain in the deep blue spectral range. The exchange splitting is proven and a strong enhancement over the bulk value is observed....

  2. Structural characterization of Kraft lignins from different spent cooking liquors by 1D and 2D Nuclear Magnetic Resonance spectroscopy

    Three Kraft lignins isolated from black liquors of several paper pulp mills of the North of Spain and Portugal were structurally characterized by using monodimensional (1H and 13C) and bidimensional Nuclear Magnetic Resonance (NMR) spectrometry. From the latter, 13C–1H heteronuclear single quantum correlation (HSQC) and heteronuclear multiple bond correlation (HMBC) were employed. Lignins from black liquors are usually burned for power generation. Nevertheless, they could become high value added products within a biorefinery context. In that case, a good understanding of their structure is a prior step to transform them. From all the NMR techniques studied, HSQC has risen as the most powerful tool in lignin characterization. Kraft cooking conditions and the type of wood seem to be the main factors that determine the differences observed in the lignins. All the samples have shown an important decrease in the number of β–O–4′ linkages, due to the Kraft process, and resinol has become the most resistant linkage to the process. Moreover, all samples seem to be mainly linked to a one polysaccharide: xylan. Several parameters like S/G ratio, portion of phenolic and aliphatic hydroxyls, amount of aromatic protons and other structural aspects were also estimated. - Highlights: • Lignins from three Kraft spent liquors were obtained by acid precipitation. • Structural characterization of the dissolved lignins was performed by NMR. • Wood source and pulping conditions determine the lignin characteristics. • Kraft process implies cleavage of β–O–4 linkages and survival of resinol linkages. • Comparison of the samples would aid decisions on its future revalorization

  3. Statistical analysis of Sequence-Structure Alignment Scores

    Brunnert, Marcus; Thiele, Ralf; Mevissen, Heinz-Theodor; Urfer, Wolfgang

    2002-01-01

    The structural analysis of proteins is fundamental to the analysis of protein functions. In this context, sequence-structure alignment methods are important among the different empirical methods. In order to assess the quality of sequence-structure alignments, a statistical method using a Bayesian approach proposed by Lathrop et al. (1998) will be presented. Finally, the results of a developed statistical analysis of scores of RDP(recursive dynamic programming)-sequence-structure alignments (...

  4. A time series generalized functional model based method for vibration-based damage precise localization in structures consisting of 1D, 2D, and 3D elements

    Sakaris, C. S.; Sakellariou, J. S.; Fassois, S. D.

    2016-06-01

    This study focuses on the problem of vibration-based damage precise localization via data-based, time series type, methods for structures consisting of 1D, 2D, or 3D elements. A Generalized Functional Model Based method is postulated based on an expanded Vector-dependent Functionally Pooled ARX (VFP-ARX) model form, capable of accounting for an arbitrary structural topology. The FP model's operating parameter vector elements are properly constrained to reflect any given topology. Damage localization is based on operating parameter vector estimation within the specified topology, so that the location estimate and its uncertainty bounds are statistically optimal. The method's effectiveness is experimentally demonstrated through damage precise localization on a laboratory spatial truss structure using various damage scenarios and a single pair of random excitation - vibration response signals in a low and limited frequency bandwidth.

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

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

  6. 1D 13C-NMR Data as Molecular Descriptors in Spectra — Structure Relationship Analysis of Oligosaccharides

    Florbela Pereira

    2012-03-01

    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.

  7. Histone and histone fold sequences and structures: a database.

    Baxevanis, A. D.; Landsman, D

    1997-01-01

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

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

    Huang Conrad C

    2006-07-01

    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

  9. Structure-guided reprogramming of serine recombinase DNA sequence specificity

    Gaj, Thomas; Mercer, Andrew C.; Gersbach, Charles A; Gordley, Russell M.; Barbas III, Carlos F.

    2010-01-01

    Routine manipulation of cellular genomes is contingent upon the development of proteins and enzymes with programmable DNA sequence specificity. Here we describe the structure-guided reprogramming of the DNA sequence specificity of the invertase Gin from bacteriophage Mu and Tn3 resolvase from Escherichia coli. Structure-guided and comparative sequence analyses were used to predict a network of amino acid residues that mediate resolvase and invertase DNA sequence specificity. Using saturation ...

  10. Synthesis, Crystal Structure, and Antimicrobial Properties of a Novel 1-D Cobalt Coordination Polymer with Dicyanamide and 2-Aminopyridine

    Amah Colette Benedicta Yuoh

    2015-01-01

    Full Text Available A novel one-dimensional coordination polymer bis(2-aminopyridine-μ-bis(dicyanamido cobaltate(II has been synthesized and characterized by elemental analyses and infrared and ultraviolet visible spectroscopies and the structure has been determined by single crystal X-ray diffraction. Co(II ion in the complex is coordinated to two axial 2-aminopyridine ligands through the pyridine N-atom and four equatorial dicyanamide ligands to give a CoN6 slightly distorted octahedral coordination environment around the metal ion. The amino N-atom forms intrachain hydrogen bonds. Antimicrobial screening of the complex against eight pathogenic microorganisms (four bacteria and four fungi isolated from humans, indicates that the complex is moderately active.

  11. Use of a structural alphabet to find compatible folds for amino acid sequences.

    Mahajan, Swapnil; de Brevern, Alexandre G; Sanejouand, Yves-Henri; Srinivasan, Narayanaswamy; Offmann, Bernard

    2015-01-01

    The structural annotation of proteins with no detectable homologs of known 3D structure identified using sequence-search methods is a major challenge today. We propose an original method that computes the conditional probabilities for the amino-acid sequence of a protein to fit to known protein 3D structures using a structural alphabet, known as "Protein Blocks" (PBs). PBs constitute a library of 16 local structural prototypes that approximate every part of protein backbone structures. It is used to encode 3D protein structures into 1D PB sequences and to capture sequence to structure relationships. Our method relies on amino acid occurrence matrices, one for each PB, to score global and local threading of query amino acid sequences to protein folds encoded into PB sequences. It does not use any information from residue contacts or sequence-search methods or explicit incorporation of hydrophobic effect. The performance of the method was assessed with independent test datasets derived from SCOP 1.75A. With a Z-score cutoff that achieved 95% specificity (i.e., less than 5% false positives), global and local threading showed sensitivity of 64.1% and 34.2%, respectively. We further tested its performance on 57 difficult CASP10 targets that had no known homologs in PDB: 38 compatible templates were identified by our approach and 66% of these hits yielded correctly predicted structures. This method scales-up well and offers promising perspectives for structural annotations at genomic level. It has been implemented in the form of a web-server that is freely available at http://www.bo-protscience.fr/forsa. PMID:25297700

  12. Assembly and Crystal Structure of a Novel 1-D Coordination Polymer of Copper(Ⅱ) with Thiocyanate and 4-Cyanopyridine

    LI,Xiu-Yan(李秀艳); WANG,Ping(王平); WANG,Zhe-Ming(王哲明); YAN,Chun-Hua(严纯华); ZHANG,Li-Dan(张丽丹); GUO,Hong-You(郭洪猷)

    2002-01-01

    A novel one-dimensional coordination polymer, Catena-poly [bis(4-cyano-pyridyl) copper(Ⅱ)-di-thiocyanate ], 1∞[CuⅡ-(cypy)2(μN,s-SCN)2] (cypy=4-cyano-pyridyl), was synthe sized in a solution reaction of Cu(NO3)2@3H2O, 4-cyano-pyri dine and KSCN in mole ratio of 1:2:2 at room temperature.Its crystal structure was determined by single-crystal X-ray diffraction. The crystal belongs to monoclinic crystal system,space group P21/c with cell parameters a = 1.0719(2), b =1.8441(4), c =0.9144(2) nm, β= 110.49(3)° and Z=4. Afull-matrix least-squares refinement gave Ri = 0. 0393 and wR2 = 0. 0916 for 1554 reflections having Ⅰ> 2σ (Ⅰ). The crystal is thermally stable up to approximately 170 ℃.

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

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

    2005-01-01

    @@ 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.

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

    2002-01-01

    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.

  15. 1D Nano materials 2012

    We witnessed an initial hyped period and enthusiasm on carbon nano tubes in the 1990s later went through a significant expansion into nano tubes of other materials (metal di chalcogenides, boron nitride, etc.) as well as various nano wires and nano rods. While much of the hype might have gone, the research on one-dimensional (1D) nano materials has matured as one of the most active research areas within the nano science and nano technology community, flourishing with ample, exciting, and new research opportunities. Just like any other research frontier, researchers working in the 1D nano materials field are constantly striving to develop new fundamental science as well as potential applications. It remains a common belief that versatility and tunability of 1D nano materials would challenge many new rising tasks coming from our resource and energy demanding modern society. The traditional semiconductor industry has produced so many devices and systems from transistors, sensors, lasers, and LEDs to more sophisticated solar panels, which are now part of our daily lives. By down sizing the core components or parts to 1D form, one might wonder how fundamentally the dimensionality and morphology would impact the device performance, this is, as always, requiring us to fully understand the structure-property relationship in 1D nano materials. It may be equally crucial in connecting discovery-driven fundamental science to market-driven technology industry concerning potentially relevant findings derived from these novel materials. The importance of a platform that allows active researchers in this field to present their new development in a timely and efficient manner is therefore self-evident. Following the success of two early special issues devoted to 1D nano materials, this is the third one in a row organized by the same group of guest editors, attesting that such a platform has been well received by the readers

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

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

    maintains tractability by constructing multi-sequence alignments for pairwise comparisons. The overall method has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. Example solutions, and...... comparisons with other approaches, are provided. The solutions include finding consensus structure identical to published ones....

  17. Visualizing and Clustering Protein Similarity Networks: Sequences, Structures, and Functions.

    Mai, Te-Lun; Hu, Geng-Ming; Chen, Chi-Ming

    2016-07-01

    Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visualize the sequence-structure-function relationship of protein networks, and investigate possible causes for inconsistency in the protein classifications based on sequences, structures, and functions. Such visualization of protein networks could facilitate our understanding of the overall relationship among proteins and help researchers comprehend various protein databases. As a demonstration, we clustered 1437 enzymes by their sequences and structures using the minimum span clustering (MSC) method. The general structure of this protein network was delineated at two clustering resolutions, and the second level MSC clustering was found to be highly similar to existing enzyme classifications. The clustering of these enzymes based on sequence, structure, and function information is consistent with each other. For proteases, the Jaccard's similarity coefficient is 0.86 between sequence and function classifications, 0.82 between sequence and structure classifications, and 0.78 between structure and function classifications. From our clustering results, we discussed possible examples of divergent evolution and convergent evolution of enzymes. Our clustering approach provides a panoramic view of the sequence-structure-function network of proteins, helps visualize the relation between related proteins intuitively, and is useful in predicting the structure and function of newly determined protein sequences. PMID:27267620

  18. Measuring control structure complexity through execution sequence grammars

    MacLennan, Bruce J.

    1981-01-01

    A method for measuring the complexity of control structures is presented. It is based on the size of a grammar describing the possible execution sequences of the control structure. This method is applied to a number of control structures, including Pascal's control structures, Dijkstra's operators, and a structure recently proposed by Parnas. The verification of complexity measures is briefly discussed. (Author)

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

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

    2005-01-01

    ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy as......Motivation: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding todya as these often are conserved in structure rather than in sequence. Even though the number of available methods is growing, it is still of interest to pairwise...... detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Results: Here we present such an approach for pairwise local alignment which is based on FILDALIGN and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include the...

  20. Evolutionary optimization of biopolymers and sequence structure maps

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

    1996-06-01

    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. Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

    Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

    2012-09-01

    Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. PMID:22676903

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

    Guozhen SHEN; Di CHEN; Yoshio BANDO; Dmitri GOLBERG

    2008-01-01

    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.

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

    D. Yu. Klimushkin

    2006-09-01

    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.

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

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

    2005-01-01

    , 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...... 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...

  5. Massively Parallel Sequencing Approaches for Characterization of Structural Variation

    Koboldt, Daniel C.; Larson, David E.; Chen, Ken; Ding, Li; Wilson, Richard K.

    2012-01-01

    The emergence of next-generation sequencing (NGS) technologies offers an incredible opportunity to comprehensively study DNA sequence variation in human genomes. Commercially available platforms from Roche (454), Illumina (Genome Analyzer and Hiseq 2000), and Applied Biosystems (SOLiD) have the capability to completely sequence individual genomes to high levels of coverage. NGS data is particularly advantageous for the study of structural variation (SV) because it offers the sensitivity to de...

  6. Microsatellite Length Scoring by Single Molecule Real Time Sequencing - Effects of Sequence Structure and PCR Regime.

    Liljegren, Mikkel Meyn; de Muinck, Eric Jacques; Trosvik, Pål

    2016-01-01

    Microsatellites are DNA sequences consisting of repeated, short (1-6 bp) sequence motifs that are highly mutable by enzymatic slippage during replication. Due to their high intrinsic variability, microsatellites have important applications in population genetics, forensics, genome mapping, as well as cancer diagnostics and prognosis. The current analytical standard for microsatellites is based on length scoring by high precision electrophoresis, but due to increasing efficiency next-generation sequencing techniques may provide a viable alternative. Here, we evaluated single molecule real time (SMRT) sequencing, implemented in the PacBio series of sequencing apparatuses, as a means of microsatellite length scoring. To this end we carried out multiplexed SMRT sequencing of plasmid-carried artificial microsatellites of varying structure under different pre-sequencing PCR regimes. For each repeat structure, reads corresponding to the target length dominated. We found that pre-sequencing amplification had large effects on scoring accuracy and error distribution relative to controls, but that the effects of the number of amplification cycles were generally weak. In line with expectations enzymatic slippage decreased proportionally with microsatellite repeat unit length and increased with repetition number. Finally, we determined directional mutation trends, showing that PCR and SMRT sequencing introduced consistent but opposing error patterns in contraction and expansion of the microsatellites on the repeat motif and single nucleotide level. PMID:27414800

  7. Microsatellite Length Scoring by Single Molecule Real Time Sequencing - Effects of Sequence Structure and PCR Regime.

    Mikkel Meyn Liljegren

    Full Text Available Microsatellites are DNA sequences consisting of repeated, short (1-6 bp sequence motifs that are highly mutable by enzymatic slippage during replication. Due to their high intrinsic variability, microsatellites have important applications in population genetics, forensics, genome mapping, as well as cancer diagnostics and prognosis. The current analytical standard for microsatellites is based on length scoring by high precision electrophoresis, but due to increasing efficiency next-generation sequencing techniques may provide a viable alternative. Here, we evaluated single molecule real time (SMRT sequencing, implemented in the PacBio series of sequencing apparatuses, as a means of microsatellite length scoring. To this end we carried out multiplexed SMRT sequencing of plasmid-carried artificial microsatellites of varying structure under different pre-sequencing PCR regimes. For each repeat structure, reads corresponding to the target length dominated. We found that pre-sequencing amplification had large effects on scoring accuracy and error distribution relative to controls, but that the effects of the number of amplification cycles were generally weak. In line with expectations enzymatic slippage decreased proportionally with microsatellite repeat unit length and increased with repetition number. Finally, we determined directional mutation trends, showing that PCR and SMRT sequencing introduced consistent but opposing error patterns in contraction and expansion of the microsatellites on the repeat motif and single nucleotide level.

  8. Nuclear shadowing in polarized DIS on ^6LiD at small x and its effect on the extraction of the deuteron spin structure function g_{1}^{d}(x,Q^2)

    Guzey, V.

    2000-01-01

    We consider the effect of nuclear shadowing in polarized deep inelastic scattering (DIS) on ^6LiD at small Bjorken x and its relevance to the extraction of the deuteron spin structure function g_{1}^{d}(x,Q^2). Using models, which describe nuclear shadowing in unpolarized DIS, we demonstrate that the nuclear shadowing correction to g_{1}^{d}(x,Q^2) is significant.

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

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

    2015-11-01

    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.

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

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

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

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

    2015-11-01

    Foliar emissions of biogenic volatile organic compounds (BVOC)-important precursors of tropospheric ozone and secondary organic aerosols-vary widely by vegetation type. Modeling studies to date typically 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 variation, we compare two 1-D canopy model simulations in which BVOC emission potentials are homogeneous 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 foliage (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.

  12. Synthesis, crystal structures and magnetic properties of mer-cyanideiron(III)-based 1D heterobimetallic cyanide-bridged chiral coordination polymers.

    Zhang, Daopeng; Zhuo, Shuping; Zhang, Hongyan; Wang, Ping; Jiang, Jianzhuang

    2015-03-14

    Two pairs of cyanide-bridged Fe(III)–Mn(III)/Cu(II) chiral enantiomer coordination polymers {[Mn(S,S/R,R-Salcy)(CH3OH)2]{[Mn(S,S/R,R-Salcy)][Fe(bbp)(CN)3]}}2n (1,2) (bbp = bis(2-benzimidazolyl)pyridine dianion) and {[Cu(S,S/R,R-Chxn)2]2[Fe2(tbbp)(CN)6]}n (3,4) (tbbp = tetra(3-benzimidazolyl)-4,4′-bipyridine tetraanion) have been successfully prepared by employing mer-tricyanometallate [PPh4]2[Fe(bbp)(CN)3] or the newly bimetallic mer-cyanideiron(III) precursor K4[Fe2(tbbp)(CN)6] as building blocks and with chiral manganese(III)/copper(II) compounds as assemble segments. The four complexes have been characterized by elemental analysis, IR spectroscopy, circular dichroism (CD) and magnetic circular dichroism (MCD) spectra. Single X-ray diffraction reveals that complexes 1 and 2 possess a single anionic chain structure consisting of the asymmetric chiral {[Mn(S,S/R,R-Salcy)][Fe(bbp)(CN)3]}2(2−) unit with free [Mn(S,S/R,R-Salcy)](+) as balanced cations. The cyanide-bridged Fe(III)–Cu(II) complexes 3 and 4 can be structurally characterized as neutral ladder-like double chains composed of the alternating cyanide-bridged Fe–Cu units. Our investigation of magnetic susceptibilities reveals the antiferromagnetic coupling between the cyanide-bridged Fe(III) and Mn(III)/Cu(II) ions for complexes 1–4. These results have been further confirmed by theoretical simulation through numerical matrix diagonalization techniques using a Fortran program or a uniform chain model, leading to the coupling constants J = −7.36 cm(−1), D = −1.52 cm(−1) (1) and J = −4.35 cm(−1) (3), respectively. PMID:25661782

  13. Sequence structure of Lowary/Widom clones forming strong nucleosomes.

    Trifonov, Edward N

    2016-04-01

    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. PMID:26208855

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

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

    2011-08-15

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

  15. Methods for optimizing the structure alphabet sequences of proteins.

    Dong, Qi-wen; Wang, Xiao-long; Lin, Lei

    2007-11-01

    Protein structure prediction based on fragment assemble has made great progress in recent years. Local protein structure prediction is receiving increased attention. One essential step of local protein structure prediction method is that the three-dimensional conformations must be compressed into one-dimensional series of letters of a structural alphabet. The traditional method assigns each structure fragment the structure alphabet that has the best local structure similarity. However, such locally optimal structure alphabet sequence does not guarantee to produce the globally optimal structure. This study presents two efficient methods trying to find the optimal structure alphabet sequence, which can model the native structures as accuracy as possible. First, a 28-letter structure alphabet is derived by clustering fragment in Cartesian space with fragment length of seven residues. The average quantization error of the 28 letters is 0.82 A in term of root mean square deviation. Then, two efficient methods are presented to encode the protein structures into series of structure alphabet letters, that is, the greedy and dynamic programming algorithm. They are tested on PDB database using the structure alphabet developed in Cartesian coordinates space (our structure alphabet) and in torsion angles space (the PB structure alphabet), respectively. The experimental results show that these two methods can find the approximately optimal structure alphabet sequences by searching a small fraction of the modeling space. The traditional local-optimization method achieves 26.27 A root mean square deviations between the reconstructed structures and the native one, while the modeling accuracy is improved to 3.28 A by the greedy algorithm. The results are helpful for local protein structure prediction. PMID:17493604

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

    Jianghua Li; Chi Zhang

    2015-11-01

    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.

  17. Correlated mutations in protein sequences: Phylogenetic and structural effects

    Lapedes, A.S. [Los Alamos National Lab., NM (United States). Theoretical Div.]|[Santa Fe Inst., NM (United States); Giraud, B.G. [C.E.N. Saclay, Gif/Yvette (France). Service Physique Theorique; Liu, L.C. [Los Alamos National Lab., NM (United States). Theoretical Div.; Stormo, G.D. [Univ. of Colorado, Boulder, CO (United States). Dept. of Molecular, Cellular and Developmental Biology

    1998-12-01

    Covariation analysis of sets of aligned sequences for RNA molecules is relatively successful in elucidating RNA secondary structure, as well as some aspects of tertiary structure. Covariation analysis of sets of aligned sequences for protein molecules is successful in certain instances in elucidating certain structural and functional links, but in general, pairs of sites displaying highly covarying mutations in protein sequences do not necessarily correspond to sites that are spatially close in the protein structure. In this paper the authors identify two reasons why naive use of covariation analysis for protein sequences fails to reliably indicate sequence positions that are spatially proximate. The first reason involves the bias introduced in calculation of covariation measures due to the fact that biological sequences are generally related by a non-trivial phylogenetic tree. The authors present a null-model approach to solve this problem. The second reason involves linked chains of covariation which can result in pairs of sites displaying significant covariation even though they are not spatially proximate. They present a maximum entropy solution to this classic problem of causation versus correlation. The methodologies are validated in simulation.

  18. Triple helix structures: sequence dependence, flexibility and mismatch effects.

    Sun, J S; Mergny, J L; Lavery, R; Montenay-Garestier, T; Hélène, C

    1991-12-01

    By means of molecular modelling, electrostatic interactions are shown to play an important role in the sequence-dependent structure of triple helices formed by a homopyrimidine oligonucleotide bound to a homopurine. homopyrimidine sequence on DNA. This is caused by the presence of positive charges due to the protonation of cytosines in the Hoogsteen-bonded strand, required in order to form C.GxC+ triplets. Energetic and conformational characteristics of triple helices with different sequences are analyzed and discussed. The effects of duplex mismatches on the triple helix stability are investigated via thermal dissociation using UV absorption. PMID:1815635

  19. Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization

    Klau Gunnar W

    2007-07-01

    Full Text Available Abstract Background The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. Results We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP. We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. Conclusion The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

  20. RNA secondary structure prediction from multi-aligned sequences

    Hamada, Michiaki

    2013-01-01

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

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

    Tillmann, Barbara

    2012-10-01

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

  2. Informational structure of genetic sequences and nature of gene splicing

    Trifonov, E. N.

    1991-10-01

    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.

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

    Kurgan Lukasz

    2009-12-01

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

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

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

    2008-02-08

    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.

  5. Quaternion representation of RNA sequences and tertiary structures.

    Magarshak, Y

    1993-01-01

    A quaternion representation of nucleotides is proposed, with representation of RNA sequences by vectors whose elements are quaternions. Structure and transition matrices in quaternion representation are defined. Correspondence between diagrammatic technique in complex-number and quaternion representation of nucleotides is delineated. PMID:7690609

  6. Quantifying sequence and structural features of protein-RNA interactions.

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

    2014-09-01

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

  7. Protein Function Prediction Based on Sequence and Structure Information

    Smaili, Fatima Z.

    2016-05-25

    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.

  8. PredyFlexy: flexibility and local structure prediction from sequence

    de Brevern, Alexandre G.; Bornot, Aurélie; Craveur, Pierrick; Etchebest, Catherine; Gelly, Jean-Christophe

    2012-01-01

    Protein structures are necessary for understanding protein function at a molecular level. Dynamics and flexibility of protein structures are also key elements of protein function. So, we have proposed to look at protein flexibility using novel methods: (i) using a structural alphabet and (ii) combining classical X-ray B-factor data and molecular dynamics simulations. First, we established a library composed of structural prototypes (LSPs) to describe protein structure by a limited set of recurring local structures. We developed a prediction method that proposes structural candidates in terms of LSPs and predict protein flexibility along a given sequence. Second, we examine flexibility according to two different descriptors: X-ray B-factors considered as good indicators of flexibility and the root mean square fluctuations, based on molecular dynamics simulations. We then define three flexibility classes and propose a method based on the LSP prediction method for predicting flexibility along the sequence. This method does not resort to sophisticate learning of flexibility but predicts flexibility from average flexibility of predicted local structures. The method is implemented in PredyFlexy web server. Results are similar to those obtained with the most recent, cutting-edge methods based on direct learning of flexibility data conducted with sophisticated algorithms. PredyFlexy can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/predyflexy/. PMID:22689641

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

    Mirzaei Masoud; Eshtiagh-Hosseini Hossein; Hassanpoor Azam; Barba Victor

    2012-01-01

    The new 1D-coordination polymer of CuII ion, {(2- apymH)2[Cu(pyzdc)2] .6H2O}n, (2-apym = 2-aminopyrimidine, pyzdcH2 = 1,4- pyrazine-2,3-dicarboxylic acid), was synthesized based on proton transfer mechanism and characterized by elemental analysis, infrared spectroscopy, and single crystal X-ray diffraction. The coordination polymer consists of infinite anionic chains of [Cu(pyzdc)2]2- anion bridged crossing double chain running along a-axis and discrete (2-apymH)+ fragment. The CuII ion...

  10. Biophysical and structural considerations for protein sequence evolution

    Grahnen Johan A

    2011-12-01

    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.

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

    Adrián Angulo-Ibáñez

    2016-01-01

    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.

  12. The Chaotic Structure of Bacterial Virulence Protein Sequences

    Sevdanur Genc

    2015-01-01

    Full Text Available Bacterial virulence proteins, which have been class ified on structure of virulence, causes several diseases. For instance, Adhesins play an important role in th e host cells. They are inserted DNA sequences for a variety of virulence properties. Several important methods conducted for the prediction of bacterial virulence proteins for finding new drugs or vaccines. In this study, we propose a method for feature sele ction about classification of bacterial virulence protein. The features are constituted dir ectly from the amino acid sequence of a given protein. Amino acids form proteins, which are criti cal to life, and have many important functions in living cells. They occurring with diff erent physicochemical properties by a vector of 20 numerical values, and collected in AAIndex datab ases of known 544 indices. For all that, this approach have two steps. Firstly , the amino acid sequence of a given protein analysed with Lyapunov Exponents that they have a chaotic structure in accordance wi th the chaos theory. After that, if the results show chara cterization over the complete distribution in the phase space from the point of deterministic sys tem, it means related protein will show a chaotic structure. Empirical results revealed that generated feature v ectors give the best performance with chaotic structure of physicochemical features of amino acid s with Adhesins and non-Adhesins data sets.

  13. Sequence-derived structural features driving proteolytic processing.

    Belushkin, Alexander A; Vinogradov, Dmitry V; Gelfand, Mikhail S; Osterman, Andrei L; Cieplak, Piotr; Kazanov, Marat D

    2014-01-01

    Proteolytic signaling, or regulated proteolysis, is an essential part of many important pathways such as Notch, Wnt, and Hedgehog. How the structure of the cleaved substrate regions influences the efficacy of proteolytic processing remains underexplored. Here, we analyzed the relative importance in proteolysis of various structural features derived from substrate sequences using a dataset of more than 5000 experimentally verified proteolytic events captured in CutDB. Accessibility to the solvent was recognized as an essential property of a proteolytically processed polypeptide chain. Proteolytic events were found nearly uniformly distributed among three types of secondary structure, although with some enrichment in loops. Cleavages in α-helices were found to be relatively abundant in regions apparently prone to unfolding, while cleavages in β-structures tended to be located at the periphery of β-sheets. Application of the same statistical procedures to proteolytic events divided into separate sets according to the catalytic classes of proteases proved consistency of the results and confirmed that the structural mechanisms of proteolysis are universal. The estimated prediction power of sequence-derived structural features, which turned out to be sufficiently high, presents a rationale for their use in bioinformatic prediction of proteolytic events. PMID:24227478

  14. Elongation method for electronic structure calculations of random DNA sequences.

    Orimoto, Yuuichi; Liu, Kai; Aoki, Yuriko

    2015-10-30

    We applied ab initio order-N elongation (ELG) method to calculate electronic structures of various deoxyribonucleic acid (DNA) models. We aim to test potential application of the method for building a database of DNA electronic structures. The ELG method mimics polymerization reactions on a computer and meets the requirements for linear scaling computational efficiency and high accuracy, even for huge systems. As a benchmark test, we applied the method for calculations of various types of random sequenced A- and B-type DNA models with and without counterions. In each case, the ELG method maintained high accuracy with small errors in energy on the order of 10(-8) hartree/atom compared with conventional calculations. We demonstrate that the ELG method can provide valuable information such as stabilization energies and local densities of states for each DNA sequence. In addition, we discuss the "restarting" feature of the ELG method for constructing a database that exhaustively covers DNA species. PMID:26337429

  15. ProSAT+: visualizing sequence annotations on 3D structure.

    Stank, Antonia; Richter, Stefan; Wade, Rebecca C

    2016-08-01

    PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org. PMID:27284084

  16. Structural basis of sequence-specific collagen recognition by SPARC

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

    2008-01-01

    Protein interactions with the collagen triple helix play a critical role in collagen fibril formation, cell adhesion, and signaling. However, structural insight into sequence-specific collagen recognition is limited to an integrin-peptide complex. A GVMGFO motif in fibrillar collagens (O denotes 4-hydroxyproline) binds 3 unrelated proteins: von Willebrand factor (VWF), discoidin domain receptor 2 (DDR2), and the extracellular matrix protein SPARC/osteonectin/BM-40. We report the crystal struc...

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

    Mirzaei Masoud

    2012-01-01

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

  18. Statistical mechanics of secondary structures formed by random RNA sequences

    Bundschuh, Ralf

    2003-03-01

    In addition to its importance for the biological function of RNA molecules RNA secondary structure formation is an interesting system from the statistical physics point of view. The ensemble of secondary structures of random RNA sequences shows a rich phase diagram with distinct native, denatured, molten, and glassy phases separated by thermodynamical phase transitions. These phase transitions are driven by the competition between thermal fluctuations, the disorder frozen into the specific sequence of a given RNA molecule, and the evolutionary bias towards the formation of some biologically relevant structure. Yet, in contrast to the protein folding problem which is driven by very similar principles and shows a similar phase diagram RNA secondary structure formation can be represented by a simple diagrammatic language which allows the application of various analytical and numerical methods. This makes RNA secondary structure formation an ideal model system for heteropolymer folding. In the talk, I will characterize and explain the complex behaviour of RNA folding using several simple models and discuss possible implications to biological processes.

  19. RNAstrand: reading direction of structured RNAs in multiple sequence alignments

    Stadler Peter F

    2007-05-01

    Full Text Available Abstract Motivation Genome-wide screens for structured ncRNA genes in mammals, urochordates, and nematodes have predicted thousands of putative ncRNA genes and other structured RNA motifs. A prerequisite for their functional annotation is to determine the reading direction with high precision. Results While folding energies of an RNA and its reverse complement are similar, the differences are sufficient at least in conjunction with substitution patterns to discriminate between structured RNAs and their complements. We present here a support vector machine that reliably classifies the reading direction of a structured RNA from a multiple sequence alignment and provides a considerable improvement in classification accuracy over previous approaches. Software RNAstrand is freely available as a stand-alone tool from http://www.bioinf.uni-leipzig.de/Software/RNAstrand and is also included in the latest release of RNAz, a part of the Vienna RNA Package.

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

    Kielpinski, Lukasz Jan

    In this thesis we describe the development of four related methods for RNA structure probing that utilize massive parallel sequencing. Using them, we were able to gather structural data for multiple, long molecules simultaneously. First, we have established an easy to follow experimental and...... RTTS-Seq to detect antisense oligonucleotide binding sites within a transcriptome. In this case, we applied an enrichment strategy to greatly reduce the background. Finally, we have modified the RTTS-Seq to study the secondary structure of 3’ untranslated regions. In the course of this thesis we...... computational protocol for detecting the reverse transcription termination sites (RTTS-Seq). This protocol was subsequently applied to hydroxyl radical footprinting of three dimensional RNA structures to give a probing signal that correlates well with the RNA backbone solvent accessibility. Moreover, we applied...

  1. Sequence and structural analyses of interleukin-8-like chemokine superfamily.

    Kanagarajadurai, Karuppiah; Sowdhamini, Ramanathan

    2008-01-01

    Interleukin-8 and related chemokines are small proteins that bind to receptors belonging to the large family of G-protein-coupled receptors. They can cause migration of cells like neutrophils and eosinophils and some of them are implicated in angiogenic diseases. More than 40 subfamilies of these ligands are known that share poor sequence similarity and display receptor specificity. There is very little structural information about the mode of binding between ligands and the receptors. We have employed multi-fold sensitive sequence search methods to provide a repertoire of 252 putative interleukin-8 proteins and homologues, which are shared across humans, aves and fish. The sequences can be organized into five major known clusters. The propensity of occurrence of certain amino acid alphabets is found to be specific in different locations of the polypeptide fold. The sequence dispersion is also observed to be cluster-specific when examined by Evolutionary Trace procedure. Amino acid alphabet analysis and Evolutionary Trace procedure reveal cluster-specific amino acid distribution that provide clues about how the small fold of the ligand could display remarkable receptor specificity. We notice regions, like the beta1-beta2 loop of the fold, that are potentially involved in receptor recognition and specificity that could be potential sites for residue mutations. Systematic studies of the distribution patterns enable better understanding of the evolution and molecular recognition of this important and diverse protein superfamily. PMID:19032164

  2. WildSpan: mining structured motifs from protein sequences

    Chen Chien-Yu

    2011-03-01

    Full Text Available Abstract Background Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. Discovering such patterns is time-consuming because abundant combinations exist when long gaps (a gap consists of one or more successive wildcards are considered. Mining algorithms often employ constraints to narrow down the search space in order to increase efficiency. However, improper constraint models might degrade the sensitivity and specificity of the motifs discovered by computational methods. We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. The patterns that satisfy the proposed constraint model are called W-patterns. A W-pattern is a structured motif that groups motif symbols into pattern blocks interleaved with large irregular gaps. Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions that incorporates several pruning strategies to largely reduce the mining cost. Results WildSpan is shown to efficiently find W-patterns containing conserved residues that are far separated in sequences. We conducted experiments with two mining strategies, protein-based and family-based mining, to evaluate the usefulness of W-patterns and performance of WildSpan. The protein-based mining mode

  3. Structure and sequence analysis of influenza A virus nucleoprotein

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

    2009-01-01

    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.

  4. Structure and sequence analysis of influenza A virus nucleoprotein

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

    2009-01-01

    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.

  5. The sequence, structure and evolutionary features of HOTAIR in mammals

    Zhu Hao

    2011-04-01

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

  6. Effect of the band structure in a rigorous two-body model with long-range interactions in 1D optical lattices

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

    2016-05-01

    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).

  7. Dicynamide bridged two new zig-zag 1-D Zn(II) coordination polymers of pyrimidine derived Schiff base ligands: Synthesis, crystal structures and fluorescence studies

    Konar, Saugata

    2015-07-01

    Two new zigzag 1-D polymeric Zn(II) coordination polymers {[Zn(L1)(μ1,5-dca)](H2O)}n (1), {[Zn(L2)(μ1,5-dca)](ClO4)}n (2) of two potentially tridentate NNO-, NNN-, donor Schiff base ligands [2-(2-(4,6-dimethylpyrimidin-2-yl)hydrazono)methyl)phenol] (L1), [1-(4,6-dimethylpyrimidin-2-yl)-2-(dipyridin-2ylmethylene)hydrazine] (L2) have been synthesized and characterized by elemental analyses, IR and 1H NMR, fluorescence spectroscopy and single crystal X-ray crystallography. The dicyanamide ions act as linkers (μ1,5 mode) in the formation of these coordination polymers. Both the complexes 1 and 2 have same distorted square pyramidal geometry around the Zn(II) centres. The weak forces like π⋯π, Csbnd H⋯π, anion⋯π interactions lead to various supramolecular architectures. Complex 1 shows high chelation enhanced fluorescence compared to that of 2. The fluorescence spectral changes observed high selectivity towards Zn(II) over other metal ions such as Mn(II), Co(II), Ni(II), Cu(II).

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

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

    2007-01-01

    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.

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

    Yang Julie

    2007-05-01

    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

  10. Control of coupling in 1D photonic crystal coupled-cavity nano-wire structures via hole diameter and position variation

    Zain, A. R. Md; De La Rue, R. M.

    2015-12-01

    We have successfully demonstrated close experimental control of the resonance splitting/free spectral range of a coupled micro-cavity one-dimensional photonic crystal/photonic wire device structure based on silicon-on-insulator. Clear splitting of the resonances, with FSR values ranging from 8 nm to 48 nm, was obtained through the use of different hole arrangements within the middle section of the device structures, between the coupled cavities. The results show good agreement with calculations obtained using a finite-difference time-domain simulation approach.

  11. Analyzing the sequence-structure relationship of a library of local structural prototypes.

    Benros, Cristina; de Brevern, Alexandre G; Hazout, Serge

    2009-01-21

    We present a thorough analysis of the relation between amino acid sequence and local three-dimensional structure in proteins. A library of overlapping local structural prototypes was built using an unsupervised clustering approach called "hybrid protein model" (HPM). The HPM carries out a multiple structural alignment of local folds from a non-redundant protein structure databank encoded into a structural alphabet composed of 16 protein blocks (PBs). Following previous research focusing on the HPM protocol, we have considered gaps in the local structure prototype. This methodology allows to have variable length fragments. Hence, 120 local structure prototypes were obtained. Twenty-five percent of the protein fragments learnt by HPM had gaps. An investigation of tight turns suggested that they are mainly derived from three PB series with precise locations in the HPM. The amino acid information content of the whole conformational classes was tackled by multivariate methods, e.g., canonical correlation analysis. It points out the presence of seven amino acid equivalence classes showing high propensities for preferential local structures. In the same way, definition of "contrast factors" based on sequence-structure properties underline the specificity of certain structural prototypes, e.g., the dependence of Gly or Asn-rich turns to a limited number of PBs, or, the opposition between Pro-rich coils to those enriched in Ser, Thr, Asn and Glu. These results are so useful to analyze the sequence-structure relationships, but could also be used to improve fragment-based method for protein structure prediction from sequence. PMID:18977232

  12. Structural studies of an arabinan from the stems of Ephedra sinica by methylation analysis and 1D and 2D NMR spectroscopy.

    Xia, Yong-Gang; Liang, Jun; Yang, Bing-You; Wang, Qiu-Hong; Kuang, Hai-Xue

    2015-05-01

    Plant arabinan has important biological activity. In this study, a water-soluble arabinan (Mw∼6.15kDa) isolated from the stems of Ephedra sinica was found to consist of (1→5)-Araƒ, (1→3,5)-Araƒ, T-Araƒ, (1→3)-Araƒ and (1→2,5)-Araƒ residues at proportions of 10:2:3:2:1. A tentative structure was proposed by methylation analysis, nuclear magnetic resonance (NMR) spectroscopy ((1)H NMR, (13)C NMR, DEPT-135, (1)H-(1)H COSY, HSQC, HMBC and ROESY) and literature. The structure proposed includes a branched (1→5)-α-Araf backbone where branching occurs at the O-2 and O-3 positions of the residues with 7.7% and 15.4% of the 1,5-linked α-Araf substituted at the O-2 and O-3 positions. The presence of a branched structure was further observed by atomic force microscopy. This polymer was characterized as having a much longer linear (1→5)-α-Araf backbone as a repeating unit. In particular, the presence of α-Araf→3)-α-Araf-(1→3)-α-Araf-(1→ attached at the O-2 is a new finding. This study may facilitate a deeper understanding of structure-activity relationships of biological polysaccharides from the stems of E. sinica. PMID:25659720

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

    Fei Chen; Yuan-Ting Zhang

    2003-01-01

    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 s...

  14. Structural determination of prunusins A and B, new C-alkylated flavonoids from Prunus domestica, by 1D and 2D NMR spectroscopy.

    Mahmood, Azhar; Fatima, Itrat; Kosar, Shaheen; Ahmed, Rehana; Malik, Abdul

    2010-02-01

    Prunusins A (1) and B (2), the new C-alkylated flavonoids, have been isolated from the seed kernels of Prunus domestica. Their structures were assigned from (1)H and (13)C nuclear magnetic resonating spectra, DEPT and by correlation spectroscopy, HMQC and HMBC experiments. 3, 5, 7, 4'-Tetrahydroxyflavone (3) and 3, 5, 7-trihydroxy-8, 4'-dimethoxyflavone (4) have also been reported from this species. Both compounds (1) and (2) showed significant antifungal activity against pathogenic fungus Trichophyton simmi. PMID:19918802

  15. Synthesis, structure, and electrochemistry and magnetic properties of a novel 1D homochiral MnIII(5-Brsalen) coordination polymer with left-handed helical character

    Dong, Dapeng; Yu, Naisen; Zhao, Haiyan; Liu, Dedi; Liu, Jia; Li, Zhenghua; Liu, Dongping

    2016-01-01

    A novel homochiral manganese (III) Mn(5-Brsalen) coordination polymer with left-handed helical character by spontaneous resolution on crystallization by using Mn(5-Brsalen) and 4,4-bipyridine, [MnIII(5-Brsalen)(4,4-bipy)]·ClO4·CH3OH (1) (4,4-bipy = 4,4-bipyridine) has been synthesized and structurally characterized by X-ray single-crystal diffraction, elemental analysis and infrared spectroscopy. In compound 1, each manganese(III) anion is six-coordinate octahedral being bonded to four atoms of 5-Brsalen ligand in an equatorial plane and two nitrogen atoms from a 4,4-bipyridine ligand in axial positions. The structure of compound 1 can be described a supramolecular 2D-like structure which was formed by the intermolecular π-stacking interactions between the neighboring chains of the aromatic rings of 4,4-bipyridine and 5-Brsalen molecules. UV-vis absorption spectrum, electrochemistry and magnetic properties of the compound 1 have also been studied.

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

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

    2012-05-01

    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.

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

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

    2008-01-01

    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'.

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

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

    2011-11-01

    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).

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

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

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

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

    2008-01-01

    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.

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

    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

    2009-02-01

    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.

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

    Heiland Randy

    2006-03-01

    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 http://www.sblest.org/ 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

  3. Syntheses, structures, and IR spectroscopic characterization of new uranyl sulfate/selenate 1D-chain, 2D-sheet and 3D-framework

    Three uranyl sulfates, (C6H20N4)[(UO2)2 . (SO4)4(H2O)2](H2O)6 (TETAUS), (C15H14N3)[(UO2) . (SO4)2](NO3)(H2O)2 (TPUS), and K2[(UO2)(SO4)2(H2O)] . H2O (KUS), and two uranyl selenates, K(H3O)[(UO2)2 . (SeO4)3(H2O)](H2O)6 (KUSe) and (H3O)2[(UO2)2(SeO4)3 . (H2O)] (USe), were synthesized by slow evaporation of aqueous solutions at room temperature. TETAUS crystallizes in space group P anti 1, a = 6.7186(5) A, b = 9.2625(7) A, c = 13.1078(9) A, α = 72.337(2) , β = 89.198(2) , γ = 70.037(1) , V = 726.89(9) A3, Z = 1. TPUS is triclinic, P anti 1, a = 6.9732(7) A, b = 13.569(1) A, c = 13.641(1) A, α = 111.809(2) , β = 102.386(2) , γ = 93.833(2) , V = 1150.0(2) A3, Z = 2. KUS is orthorhombic, Cmca, a = 12.171(2) A, b = 16.689(3) A, c = 10.997(2) A, V = 2233.8(6) A3, Z = 8. These uranyl sulfates are built from infinite one-dimensional uranyl sulfate chains with different topologies. KUSe is monoclinic, P21/n, a = 14.715(1) A, b = 10.1557(7) A, c = 15.833(1) A, β = 114.415(1) , V = 2154.5(3) A3, Z = 4. Its structure is based on a two-dimensional uranyl selenate sheet. USe crystallizes in space group P21/c, a = 10.6124(2) A, b = 14.7717(3) A, c = 13.7139(3) A, β = 96.989(1) , V = 2133.86(8) A3, Z = 4, with a complex three-dimensional uranyl selenate framework containing channels extending in three directions. (orig.)

  4. Structural properties of replication origins in yeast DNA sequences

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

  5. Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences

    Tahi Fariza

    2007-11-01

    Full Text Available Abstract Background The secondary structure of an RNA must be known before the relationship between its structure and function can be determined. One way to predict the secondary structure of an RNA is to identify covarying residues that maintain the pairings (Watson-Crick, Wobble and non-canonical pairings. This "comparative approach" consists of identifying mutations from homologous sequence alignments. The sequences must covary enough for compensatory mutations to be revealed, but comparison is difficult if they are too different. Thus the choice of homologous sequences is critical. While many possible combinations of homologous sequences may be used for prediction, only a few will give good structure predictions. This can be due to poor quality alignment in stems or to the variability of certain sequences. This problem of sequence selection is currently unsolved. Results This paper describes an algorithm, SSCA, which measures the suitability of sequences for the comparative approach. It is based on evolutionary models with structure constraints, particularly those on sequence variations and stem alignment. We propose three models, based on different constraints on sequence alignments. We show the results of the SSCA algorithm for predicting the secondary structure of several RNAs. SSCA enabled us to choose sets of homologous sequences that gave better predictions than arbitrarily chosen sets of homologous sequences. Conclusion SSCA is an algorithm for selecting combinations of RNA homologous sequences suitable for secondary structure predictions with the comparative approach.

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

    Fei Chen

    2003-01-01

    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.

  7. An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment

    Bauer, M.; Klau, Gunnar; Reinert, K.

    2008-01-01

    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 conformations, which can be represented by graph-like secondary structures. Often, secondary structures are more conserved than the actual sequence. Hence, computing reliable alignments of RNA molecules ...

  8. A New Hidden Markov Model for Protein Quality Assessment Using Compatibility Between Protein Sequence and Structure

    He, Zhiquan; Ma, Wenji; Zhang, Jingfen; Xu, Dong

    2014-01-01

    Protein structure Quality Assessment (QA) is an essential component in protein structure prediction and analysis. The relationship between protein sequence and structure often serves as a basis for protein structure QA. In this work, we developed a new Hidden Markov Model (HMM) to assess the compatibility of protein sequence and structure for capturing their complex relationship. More specifically, the emission of the HMM consists of protein local structures in angular space, secondary struct...

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

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

    2013-12-01

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

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

    Aydın, Zafer; AYDIN, Zafer; Altunbaşak, Yücel; Altunbasak, Yucel; Pakatcı, Kemal İsa; Pakatci, Kemal Isa; Erdoğan, Hakan; Erdogan, Hakan

    2007-01-01

    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...

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

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

    2016-02-28

    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. PMID:26811117

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

    2003-01-01

    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.

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

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

    2009-03-01

    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.

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

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

    2000-01-01

    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, ...

  15. Structure and thermodynamic properties of (C5H12N)CuBr3: a new weakly coupled antiferromagnetic spin-1/2 chain complex lying in the 1D-3D dimensional cross-over regime.

    Pan, Bingying; Wang, Yang; Zhang, Lijuan; Li, Shiyan

    2014-04-01

    Single crystals of a metal organic complex (C5H12N)CuBr3 (C5H12N = piperidinium, pipH for short) have been synthesized, and the structure was determined by single-crystal X-ray diffraction. (pipH)CuBr3 crystallizes in the monoclinic group C2/c. Edging-sharing CuBr5 units link to form zigzag chains along the c axis, and the neighboring Cu(II) ions with spin-1/2 are bridged by bibromide ions. Magnetic susceptibility data down to 1.8 K can be well fitted by the Bonner-Fisher formula for the antiferromagnetic spin-1/2 chain, giving the intrachain magnetic coupling constant J ≈ -17 K. At zero field, (pipH)CuBr3 shows three-dimensional (3D) order below TN = 1.68 K. Calculated by the mean-field theory, the interchain coupling constant J' = -0.91 K is obtained and the ordered magnetic moment m0 is about 0.23 μB. This value of m0 makes (pipH)CuBr3 a rare compound suitable to study the 1D-3D dimensional cross-over problem in magnetism, since both 3D order and one-dimensional (1D) quantum fluctuations are prominent. In addition, specific heat measurements reveal two successive magnetic transitions with lowering temperature when external field μ0H ≥ 3 T is applied along the a' axis. The μ0H-T phase diagram of (pipH)CuBr3 is roughly constructed. PMID:24617285

  16. Synthesis of 1D Fe₃O₄/P(MBAAm-co-MAA) nanochains as stabilizers for Ag nanoparticles and templates for hollow mesoporous structure, and their applications in catalytic reaction and drug delivery.

    Zhang, Wei; Si, Xiaowei; Liu, Bin; Bian, Guomin; Qi, Yonglin; Yang, Xinlin; Li, Chenxi

    2015-10-15

    One-dimensional (1D) magnetic Fe3O4/P(MBAAm-co-MAA) nanochains were prepared by distillation-precipitation polymerization of MBAAm and MAA in the presence of Fe3O4 nanoparticles as building blocks under a magnetic heating stirrer, which played two critical roles: serving as magnetic field to induce the self-assembly of Fe3O4 nanoparticles into 1D nanochains and providing thermal energy to induce the polymerization of MAA and MBAAm on the surface of the Fe3O4 nanoparticles. The thickness of the P(MBAAm-co-MAA) layer can be easily tuned by adjusting the successive polymerization steps. The polymer layer that contained carboxyl groups was used as stabilizers for loading Ag nanoparticles and the reaction locus for deposition of outer silica layer via a sol-gel method in presence of C18TMS as the pore directing agent for tri-layer nanochains. The corresponding hollow mesoporous silica nanochains with movable maghemite cores (γ-Fe2O3@mSiO2) were produced after removal of the polymer mid-layer and the alkyl groups of the pore directing agent via calcination of the tri-layer nanochains at high temperature. The Fe3O4/P(MBAAm-co-MAA)/Ag nanochains exhibited a highly catalytic efficiency and well reusable property toward the reduction of nitrophenol. Furthermore, the γ-Fe2O3@mSiO2 nanochains possessed hollow mesoporous structure and high specific surface area (197.2 m(2) g(-1)) were used as a drug carrier, which displayed a controlled release property. PMID:26119084

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

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

    2015-09-01

    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 http://metagenomics.atc.tcs.com/compression/fastr.

  18. Quantitative 1D saturation profiles on chalk by NMR

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

    1996-01-01

    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...

  19. 4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

    Schultz Jörg

    2006-11-01

    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 http://4sale.bioapps.biozentrum.uni-wuerzburg.de

  20. 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.

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

    2016-05-14

    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

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

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

    2005-06-01

    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.

  2. Synthesis, structures and magnetic properties of two 3D 3,4-pyridinedicarboxylate bridged manganese(II) coordination polymers incorporating 1D helical Mn(carboxylate)2 chain or Mn3(OH)2 chain

    The hydrothermal reactions of MnCl2.4H2O, 3,4-pyridinedicarboxylic acid (3,4-pydaH2) and triethylamine in aqueous medium yield two 3D metal-organic hybrid materials, [Mn(3,4-pyda)] (1) and [Mn3(OH)2(3,4-pyda)2(H2O)2] (2), respectively. In both complexes, each 3,4-pyda acts as a pentadentate ligand to connect five Mn(II) atoms via the pyridyl group and the two μ2-carboxylate groups (one in syn,anti-mode and one in syn-syn mode for 1 and both in syn,anti-mode for 2). Complex 1 possesses an interesting 3D coordination polymeric structure incorporating 1D helical Mn(μ2-carboxylate)2 chain units, in which each Mn(II) atom is coordinated in less common square pyramidal geometry to four carboxylato oxygen atoms and one pyridyl nitrogen atom. Each 3,4-pyda links three helical Mn(μ2-carboxylate)2 chains and each Mn(μ2-carboxylate)2 chain is linked by other eight helical Mn(μ2-carboxylate)2 chains via sharing 3,4-pyda bridges. Complex 2 is a 3D coordination network consisting of 1D Mn3(OH)2 chains and 3,4-pyda bridges. The repeating trimeric structural unit in the manganese(II) hydroxide chain consists of two edge-sharing symmetry-related manganese octahedra linked via μ3-OH to a vertex of Mn2 octahedron. Each 3,4-pyda links three Mn3(OH)2 chains and each Mn3(OH)2 chain is linked by other six Mn3(OH)2 chains via 3,4-pyda bridges, resulting in a 3D coordination solid. Magnetic measurements reveal that a weak antiferromagnetic interaction between the MnII ions occurs in complex 1 and a 3D magnetic ordering at about 7.0K in complex 2

  3. 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

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

    2016-05-01

    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

  4. TBC1D24 genotype–phenotype correlation

    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

    2016-01-01

    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 (http://lovd.nl/TBC1D24). 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

  5. Structure is three to ten times more conserved than sequence--a study of structural response in protein cores.

    Illergård, Kristoffer; Ardell, David H; Elofsson, Arne

    2009-11-15

    Protein structures change during evolution in response to mutations. Here, we analyze the mapping between sequence and structure in a set of structurally aligned protein domains. To avoid artifacts, we restricted our attention only to the core components of these structures. We found that on average, using different measures of structural change, protein cores evolve linearly with evolutionary distance (amino acid substitutions per site). This is true irrespective of which measure of structural change we used, whether RMSD or discrete structural descriptors for secondary structure, accessibility, or contacts. This linear response allows us to quantify the claim that structure is more conserved than sequence. Using structural alphabets of similar cardinality to the sequence alphabet, structural cores evolve three to ten times slower than sequences. Although we observed an average linear response, we found a wide variance. Different domain families varied fivefold in structural response to evolution. An attempt to categorically analyze this variance among subgroups by structural and functional category revealed only one statistically significant trend. This trend can be explained by the fact that beta-sheets change faster than alpha-helices, most likely due to that they are shorter and that change occurs at the ends of the secondary structure elements. PMID:19507241

  6. Structure and Evolution of Pre-Main Sequence Stars

    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

    2009-01-01

    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 ...

  7. A fast sequence assembly method based on compressed data structures.

    Liang, Peifeng; Zhang, Yancong; Lin, Kui; Hu, Jinglu

    2014-01-01

    Assembling a large genome using next generation sequencing reads requires large computer memory and a long execution time. To reduce these requirements, a memory and time efficient assembler is presented from applying FM-index in JR-Assembler, called FMJ-Assembler, where FM stand for FMR-index derived from the FM-index and BWT and J for jumping extension. The FMJ-Assembler uses expanded FM-index and BWT to compress data of reads to save memory and jumping extension method make it faster in CPU time. An extensive comparison of the FMJ-Assembler with current assemblers shows that the FMJ-Assembler achieves a better or comparable overall assembly quality and requires lower memory use and less CPU time. All these advantages of the FMJ-Assembler indicate that the FMJ-Assembler will be an efficient assembly method in next generation sequencing technology. PMID:25569963

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

    Andrew Kuziemko

    2011-10-01

    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.

  9. Quantification of tertiary structural conservation despite primary sequence drift in the globin fold.

    Aronson, H E; Royer, W E; Hendrickson, W A

    1994-10-01

    The globin family of protein structures was the first for which it was recognized that tertiary structure can be highly conserved even when primary sequences have diverged to a virtually undetectable level of similarity. This principle of structural inertia in molecular evolution is now evident for many other protein families. We have performed a systematic comparison of the sequences and structures of 6 representative hemoglobin subunits as diverse in origin as plants, clams, and humans. Our analysis is based on a 97-residue helical core in common to all 6 structures. Amino acid sequence identities range from 12.4% to 42.3% in pairwise comparisons, and, despite these variations, the maximal RMS deviation in alpha-carbon positions is 3.02 A. Overall, sequence similarity and structural deviation are significantly anticorrelated, with a correlation coefficient of -0.71, but for a set of structures having under 20% pairwise identity, this anticorrelation falls to -0.38, which emphasizes the weak connection between a specific sequence and the tertiary fold. There is substantial variability in structure outside the helical core, and functional characteristics of these globins also differ appreciably. Nevertheless, despite variations in detail that the sequence dissimilarities and functional differences imply, the core structures of these globins remain remarkably preserved. PMID:7849587

  10. Human insulin genome sequence map, biochemical structure of insulin for recombinant DNA insulin.

    Chakraborty, Chiranjib; Mungantiwar, Ashish A

    2003-08-01

    Insulin is a essential molecule for type I diabetes that is marketed by very few companies. It is the first molecule, which was made by recombinant technology; but the commercialization process is very difficult. Knowledge about biochemical structure of insulin and human insulin genome sequence map is pivotal to large scale manufacturing of recombinant DNA Insulin. This paper reviews human insulin genome sequence map, the amino acid sequence of porcine insulin, crystal structure of porcine insulin, insulin monomer, aggregation surfaces of insulin, conformational variation in the insulin monomer, insulin X-ray structures for recombinant DNA technology in the synthesis of human insulin in Escherichia coli. PMID:12769691

  11. Sense-antisense gene pairs: sequence, transcription, and structure are not conserved between human and mouse

    Wood, Emily J.; Chin-Inmanu, Kwanrutai; Jia, Hui; Lipovich, Leonard

    2013-01-01

    Previous efforts to characterize conservation between the human and mouse genomes focused largely on sequence comparisons. These studies are inherently limited because they don't account for gene structure differences, which may exist despite genomic sequence conservation. Recent high-throughput transcriptome studies have revealed widespread and extensive overlaps between genes, and transcripts, encoded on both strands of the genomic sequence. This overlapping gene organization, which produce...

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

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

    2013-01-01

    Protein sequence alignment is essential for template-based protein structure prediction and function annotation. We collect 20 sequence alignment algorithms, 10 published and 10 newly developed, which cover all representative sequence- and profile-based alignment approaches. These algorithms are benchmarked on 538 non-redundant proteins for protein fold-recognition on a uniform template library. Results demonstrate dominant advantage of profile-profile based methods, which generate models wit...

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

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

    2014-01-01

    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...

  14. Graph Theory In Protein Sequence Clustering And Tertiary Structural Matching

    Abdullah, Rosni; Rashid, Nur'Aini Abdul; Othman, Fazilah

    2008-01-01

    The principle of graph theory which has been widely used in computer networks is now being adopted for work in protein clustering, protein structural matching, and protein folding and modeling. In this work, we present two case studies on the use of graph theory for protein clustering and tertiary structural matching. In protein clustering, we extended a clustering algorithm based on a maximal clique while in the protein tertiary structural matching we explored the bipartite graph matching algorithm. The results obtained in both the case studies will be presented.

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

    Folia, Vasiliki; Petersson, Karl Magnus

    2014-01-01

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

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

    Vasiliki eFolia

    2014-02-01

    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.

  17. Structure and sequence variation of mink interleukin-6 gene

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

  18. Structure of fault zones in cohesive volcanic sequences

    Holland, Marc

    2011-01-01

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

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

    GUO Jifeng; WANG Ping; CUI Naigang

    2006-01-01

    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.

  20. Combined sequence and sequence-structure based methods for analyzing FGF23, CYP24A1 and VDR genes.

    Nagamani, Selvaraman; Singh, Kh Dhanachandra; Muthusamy, Karthikeyan

    2016-09-01

    FGF23, CYP24A1 and VDR altogether play a significant role in genetic susceptibility to chronic kidney disease (CKD). Identification of possible causative mutations may serve as therapeutic targets and diagnostic markers for CKD. Thus, we adopted both sequence and sequence-structure based SNP analysis algorithm in order to overcome the limitations of both methods. We explore the functional significance towards the prediction of risky SNPs associated with CKD. We assessed the performance of four widely used pathogenicity prediction methods. We compared the performances of the programs using Mathews correlation Coefficient ranged from poor (MCC = 0.39) to reasonably good (MCC = 0.42). However, we got the best results for the combined sequence and structure based analysis method (MCC = 0.45). 4 SNPs from FGF23 gene, 8 SNPs from VDR gene and 13 SNPs from CYP24A1 gene were predicted to be the causative agents for human diseases. This study will be helpful in selecting potential SNPs for experimental study from the SNP pool and also will reduce the cost for identification of potential SNPs as a genetic marker. PMID:27114920

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

    Giulio Pavesi; Giancarlo Mauri; Graziano Pesole

    2004-01-01

    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

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

    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

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

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

    2010-07-06

    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

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

    Jørgensen, Allan Grønlund

    terms of hardware performance and money in the design of todays high speed memory technologies. Hardware, power failures, and environmental conditions such as cosmic rays and alpha particles can all alter the memory in unpredictable ways. In applications where large memory capacities are needed at low...... 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...... cost, it makes sense to assume that the algorithms themselves are in charge for dealing with memory faults. We investigate searching, sorting and counting algorithms and data structures that provably returns sensible information in spite of memory corruptions....

  5. TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

    Sharma Gaurav

    2011-04-01

    Full Text Available Abstract Background The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented. Results TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold. TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a

  6. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island.

    Ashton, Philip M; Nair, Satheesh; Dallman, Tim; Rubino, Salvatore; Rabsch, Wolfgang; Mwaigwisya, Solomon; Wain, John; O'Grady, Justin

    2015-03-01

    Short-read, high-throughput sequencing technology cannot identify the chromosomal position of repetitive insertion sequences that typically flank horizontally acquired genes such as bacterial virulence genes and antibiotic resistance genes. The MinION nanopore sequencer can produce long sequencing reads on a device similar in size to a USB memory stick. Here we apply a MinION sequencer to resolve the structure and chromosomal insertion site of a composite antibiotic resistance island in Salmonella Typhi Haplotype 58. Nanopore sequencing data from a single 18-h run was used to create a scaffold for an assembly generated from short-read Illumina data. Our results demonstrate the potential of the MinION device in clinical laboratories to fully characterize the epidemic spread of bacterial pathogens. PMID:25485618

  7. Using evolutionary sequence variation to make inferences about protein structure and function

    Colwell, Lucy

    2015-03-01

    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. The explosive growth in the number of available protein sequences raises the possibility of using the natural variation present in homologous protein sequences to infer these constraints and thus identify residues that control different protein phenotypes. Because in many cases phenotypic changes are controlled by more than one amino acid, the mutations that separate one phenotype from another may not be independent, requiring us to understand the correlation structure of the data. To address this we build a maximum entropy probability model for the protein sequence. The parameters of the inferred model are constrained by the statistics of a large sequence alignment. Pairs of sequence positions with the strongest interactions accurately predict contacts in protein tertiary structure, enabling all atom structural models to be constructed. We describe development of a theoretical inference framework that enables the relationship between the amount of available input data and the reliability of structural predictions to be better understood.

  8. Probing the circumstellar structure of pre-main sequence stars

    Vink, J S; Harries, T J; Oudmaijer, R D; Oudmaijer, Rene D.

    2003-01-01

    We present Halpha spectropolarimetry of a large sample of pre-main sequence (PMS) stars of low and intermediate mass, and argue that the technique is a powerful tool in studying the circumstellar geometry around these objects. For the intermediate mass (2 -- 15 Msun) Herbig Ae/Be stars we find that 16 out of 23 show a line effect, which immediately implies that flattening is common among these objects. Furthermore, we find a significant difference in Halpha spectropolarimetry behaviour between the Herbig Be and Ae groups. For the Herbig Be stars, the concept of an electron scattering disc is shown to be a useful concept to explain the depolarizations seen in this spectral range. At lower masses, more complex Halpha polarimetry behaviour starts to appear. The concept of a compact source of Halpha emission that is formed close to the stellar surface, for instance by hot spots due to magnetospheric accretion, is postulated as a working hypothesis to qualitatively explain the Halpha spectropolarimetry behaviour a...

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

    Kosinski, Jan

    2013-02-08

    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 http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

  10. Assessing a novel approach for predicting local 3D protein structures from sequence.

    Benros, Cristina; de Brevern, Alexandre G; Etchebest, Catherine; Hazout, Serge

    2006-03-01

    We developed a novel approach for predicting local protein structure from sequence. It relies on the Hybrid Protein Model (HPM), an unsupervised clustering method we previously developed. This model learns three-dimensional protein fragments encoded into a structural alphabet of 16 protein blocks (PBs). Here, we focused on 11-residue fragments encoded as a series of seven PBs and used HPM to cluster them according to their local similarities. We thus built a library of 120 overlapping prototypes (mean fragments from each cluster), with good three-dimensional local approximation, i.e., a mean accuracy of 1.61 A Calpha root-mean-square distance. Our prediction method is intended to optimize the exploitation of the sequence-structure relations deduced from this library of long protein fragments. This was achieved by setting up a system of 120 experts, each defined by logistic regression to optimize the discrimination from sequence of a given prototype relative to the others. For a target sequence window, the experts computed probabilities of sequence-structure compatibility for the prototypes and ranked them, proposing the top scorers as structural candidates. Predictions were defined as successful when a prototype structure was found among those proposed. Our strategy yielded a prediction rate of 51.2% for an average of 4.2 candidates per sequence window. We also proposed a confidence index to estimate prediction quality. Our approach predicts from sequence alone and will thus provide valuable information for proteins without structural homologs. Candidates will also contribute to global structure prediction by fragment assembly. PMID:16385557

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

    Borodovsky Mark

    2006-03-01

    Full Text Available 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 to studies of proteins with no detected homologs, however the accuracy of protein secondary structure prediction from a single-sequence is not as high as when the additional evolutionary information is present. Results In this paper, we further refine and extend the hidden semi-Markov model (HSMM initially considered in the BSPSS algorithm. We introduce an improved residue dependency model by considering the patterns of statistically significant amino acid correlation at structural segment borders. We also derive models that specialize on different sections of the dependency structure and incorporate them into HSMM. In addition, we implement an iterative training method to refine estimates of HSMM parameters. The three-state-per-residue accuracy and other accuracy measures of the new method, IPSSP, are shown to be comparable or better than ones for BSPSS as well as for PSIPRED, tested under the single-sequence condition. Conclusions We have shown that new dependency models and training methods bring further improvements to single-sequence protein secondary structure prediction. The results are obtained under cross-validation conditions using a dataset with no pair of sequences having significant sequence similarity. As new sequences are added to the database it is possible to augment the dependency structure and obtain even higher accuracy. Current and future advances should contribute to the improvement of function prediction for orphan proteins inscrutable

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

    Guo-Bing Chen; Ji-Hong Meng

    2004-01-01

    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.

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

    Abolhasan Rezaei

    2012-03-01

    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.

  14. Optical properties of LEDs with patterned 1D photonic crystal

    Hronec, P.; Kuzma, A.; Å kriniarová, J.; Kováč, J.; Benčurová, A.; Haščík, Å.; Nemec, P.

    2015-08-01

    In this paper we focus on the application of the one-dimensional photonic crystal (1D PhC) structures on the top of Al0.295Ga0.705As/GaAs multi-quantum well light emitting diode (MQW LED). 1D PhC structures with periods of 600 nm, 700 nm, 800 nm, and 900 nm were fabricated by the E-Beam Direct Write (EBDW) Lithography. Effect of 1D PhC period on the light extraction enhancement was studied. 1D PhC LED radiation profiles were obtained from Near Surface Light Emission Images (NSLEI). Measurements showed the strongest light extraction enhancement using 800 nm period of PhC. Investigation of PhC LED radiation profiles showed strong light decoupling when light reaches PhC structure. Achieved LEE was from 22.6% for 600 nm PhC LED to 47.0% for 800 nm PhC LED. LED with PhC structure at its surface was simulated by FDTD simulation method under excitation of appropriate launch field.

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

    Samah G. Babiker

    2012-03-01

    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

  16. Main: 1D6R [RPSD[Archive

    Full Text Available 1D6R 大豆 Soybean Glycine max (L.) Merrill Bowman-Birk Type Proteinase Inhibitor Precursor Glyci ... Warkentin, G.Wenzl, P.Flecker Crystal Structure Of Cancer ... Chemopreventive Bowman-Birk Inhibitor In Ternary C ...

  17. 杯[4]芳烃衍生物一维超分子的晶体结构研究%Crystal Structure of a Novel Supramolecular Calix[4]arene Derivative with 1D Structure

    邢彦军; 杜晨霞; 周稚仙; 吴养洁

    2001-01-01

    A new calix[4]arene derivative, 5,11,17,23-tetra-tert-butyl-25,27-dihydroxy-26,28-bis[2-(methoxycarbonyl)benzyloxy]calix[4]arene was synthesized. The X-ray crystal structure of the title compound has been determined. It crystallizes in the monoclinic with space group C2/c, a=1.262 8(3) nm, b=2.535 0(5) nm, c=2.095 7(4) nm,  β=103.36(3)°, V=6.528(2) nm3, Z=4, Dc=1.203 g/cm3, F(000)=2 488, R=0.114 3, wR2=0.297 9, Δρmax=0.329×103 e/nm3, Δρmin=-0.256×103 e/nm3. The crystal structure of the title compound shows that in the molecule there are hydrogen bonds between proximal hydroxyl and ether functional groups [O(H)—O: 0.300 4 nm]. The benzoic ether site in the title molecule may be considered as a π-conjugated system, therefore, the intermolecular π-π interaction exists between two benzoic ether site of the adjacent molecules, which caused the formation of a one-dimensional saw-toothed supramolecule.

  18. Multilocus Sequence Typing Analysis of Staphylococcus lugdunensis Implies a Clonal Population Structure

    Chassain, Benoît; Lemée, Ludovic; Didi, Jennifer; Thiberge, Jean-Michel; Brisse, Sylvain; Pons, Jean-Louis; Pestel-Caron, Martine

    2012-01-01

    Staphylococcus lugdunensis is recognized as one of the major pathogenic species within the genus Staphylococcus, even though it belongs to the coagulase-negative group. A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 87 S. lugdunensis isolates from various clinical and geographic sources by DNA sequence analysis of seven housekeeping genes (aroE, dat, ddl, gmk, ldh, recA, and yqiL). The number of alleles ranged from four ...

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

    Borodovsky Mark; Altunbasak Yucel; Aydin Zafer

    2006-01-01

    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...

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

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

    2006-02-01

    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.)

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

    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.)

  2. Of sequence and structure: Strategies of protein thermostability in evolutionary perspective

    Berezovsky, Igor N; Shakhnovich, Eugene I.

    2004-01-01

    In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic adaptation: (i) General, non-specific, structure-based, when proteomes of certain thermophilic organisms show significant structural bias toward proteins of higher compactness. In this case thermostability is achieved by greater overall number of stabilizing ...

  3. Sequence-Structure Alignment Using a Statistical Analysis of Core Models and Dynamic Programming

    Brunnert, Marcus; Fischer, Paul; Urfer, Wolfgang

    2002-01-01

    The expanding availability of protein data enforces the application of empirical methods necessary to recognize protein structures. In this paper a sequence-structure alignment method is described and applied to various Ubiquitin-like folded Ras-binding domains. On the basis of two probability functions that evaluate similarities between the occurrence of amino-acids in the primary and secondary protein structure, different versions of simple scoring functions are proposed. The application of...

  4. Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content and rearrangements revealed by next generation sequencing

    The complete plastid genome sequence of the American cranberry was reconstructed using next-generation sequencing data by in silico procedures. We used Roche 454 shotgun sequence data to isolate cranberry plastid-specific sequences of the cultivar ‘HyRed’ via homology comparisons with complete seque...

  5. libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny

    Roger Andrew J

    2005-06-01

    Full Text Available Background An increasing number of bioinformatics methods are considering the phylogenetic relationships between biological sequences. Implementing new methodologies using the maximum likelihood phylogenetic framework can be a time consuming task. Results The bioinformatics library libcov is a collection of C++ classes that provides a high and low-level interface to maximum likelihood phylogenetics, sequence analysis and a data structure for structural biological methods. libcov can be used to compute likelihoods, search tree topologies, estimate site rates, cluster sequences, manipulate tree structures and compare phylogenies for a broad selection of applications. Conclusion Using this library, it is possible to rapidly prototype applications that use the sophistication of phylogenetic likelihoods without getting involved in a major software engineering project. libcov is thus a potentially valuable building block to develop in-house methodologies in the field of protein phylogenetics.

  6. Developing 1D nanostructure arrays for future nanophotonics

    Cooke DG

    2006-01-01

    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.

  7. Intermediate divergence levels maximize the strength of structure-sequence correlations in enzymes and viral proteins.

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

    2016-07-01

    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. PMID:26971720

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

    Jiang Du

    2009-07-01

    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

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

    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...

  10. A study of slow light in 1D photonic crystals

    Yudistira, D.; Hoekstra, H.J.W.M.; Hammer, M; Marpaung, D.A.I.

    2005-01-01

    Slow light (SL) states corresponding to wavelength regions near the bandgap edge of grating structure are known to show strong field enhancement. Such states may be excited efficiently by well-optimised adiabatic transitions in such structures, e.g., by slowly turning on the modulation depth. To study adiabatic excitations, a detailed research in 1D is performed to obtain insight into the relation between the device parameters and properties like enhancement and modal reflection. The results ...

  11. Theory of slow light excitation in 1D photonic crystals

    Yudistira, D.; Marpaung, D.A.I.; Handoyo, H.P.; Hoekstra, H.J.W.M.; Hammer, M; Tjia, M.O.; Iskandar, A.A.

    2004-01-01

    Slow light (SL) states corresponding to wavelength regions near the bandgap edge of grated structures are known to show strong eld enhancement. Such states may be excited efciently by well-optimised adiabatic transitions in grating structures, e.g., by slowly turning on the modulation depth. To study adiabatic excitations, a detailed investigation in 1D is performed to obtain insight into the relation between the device parameters and properties like eld enhancement and modal reection. The re...

  12. Synthesis, structural characterization, and solid-state NMR spectroscopy of [Ga(phen)(H1.5PO4)2].H2O and [Ga(phen)(HPO4)(H2PO4)].1.5H2O (phen=1, 10-phenanthroline), two organic-inorganic hybrid compounds with 1-D chain structures

    Two new organic-inorganic hybrid compounds, [Ga(phen)(H1.5PO4)2].H2O (1) and [Ga(phen)(HPO4)(H2PO4)].1.5H2O (2) (phen=1,10-phenanthroline), have been synthesized by hydrothermal methods and structurally characterized by single-crystal X-ray diffraction, infrared spectroscopy, thermogravimetric analysis, and solid-state NMR spectroscopy. Their structures consist of 1-D chains of strictly alternating GaO4N2 octahedra and phosphate tetrahedra. The phen ligands in both compounds bind in a bidentate fashion to the gallium atoms and the 1-D structures extend into 3-D supramolecular arrays via π-π stacking interactions of phen ligands and hydrogen bonds. 2H MAS NMR spectroscopy was applied to study the deuterated sample of 1 which contains very short hydrogen bonds with an O-O distance of 2.406(2) A. Crystal data for 1: monoclinic, space group C2/c (No. 15), a=11.077(1) A, b=21.496(2) A, c=7.9989(7) A, β=127.211(2)o, and Z=4. The crystal symmetry is the same for 2 as for 1 except a=27.555(2) A, b=6.3501(5) A, c=21.327(2) A, β=122.498(1)o, and Z=8

  13. Independent premotor encoding of the sequence and structure of birdsong in avian cortex.

    Basista, Mark J; Elliott, Kevin C; Wu, Wei; Hyson, Richard L; Bertram, Richard; Johnson, Frank

    2014-12-10

    How the brain coordinates rapid sequences of learned behavior, such as human speech, remains a fundamental problem in neuroscience. Birdsong is a model of such behavior, which is learned and controlled by a neural circuit that spans avian cortex, basal ganglia, and thalamus. The songs of adult male zebra finches (Taeniopygia guttata), produced as rapid sequences of vocal gestures (syllables), are encoded by the cortical premotor region HVC (proper name). While the motor encoding of song within HVC has traditionally been viewed as unitary and distributed, we used an ablation technique to ask whether the sequence and structure of song are processed independently within HVC. Results revealed a functional topography across the medial-lateral axis of HVC. Bilateral ablation of medial HVC induced a positive disruption of song (increase in atypical syllable sequences), whereas bilateral ablation of lateral HVC induced a negative disruption (omission of individual syllables). Bilateral ablation of central HVC either had no effect on song or induced syllable omission, similar to lateral HVC ablation. We then investigated HVC connectivity and found parallel afferent and efferent pathways that transit medial and lateral HVC and converge at vocal motor cortex. In light of recent evidence that syntactic and lexical components of human speech are processed independently by neighboring regions of cortex (Menenti et al., 2012), our demonstration of anatomically distinct pathways that differentially process the sequence and structure of birdsong in parallel suggests that the vertebrate brain relies on a common approach to encode rapid sequences of vocal gestures. PMID:25505334

  14. Biological sequence classification with multivariate string kernels.

    Kuksa, Pavel P

    2013-01-01

    String kernel-based machine learning methods have yielded great success in practical tasks of structured/sequential data analysis. They often exhibit state-of-the-art performance on many practical tasks of sequence analysis such as biological sequence classification, remote homology detection, or protein superfamily and fold prediction. However, typical string kernel methods rely on the analysis of discrete 1D string data (e.g., DNA or amino acid sequences). In this paper, we address the multiclass biological sequence classification problems using multivariate representations in the form of sequences of features vectors (as in biological sequence profiles, or sequences of individual amino acid physicochemical descriptors) and a class of multivariate string kernels that exploit these representations. On three protein sequence classification tasks, the proposed multivariate representations and kernels show significant 15-20 percent improvements compared to existing state-of-the-art sequence classification methods. PMID:24384708

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

    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: http://www.embnet.qb.fcen.uba.ar/ in the subpage "Protein and nucleic acid structure and sequence analysis".

  16. 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

    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. - - 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 compared with X-ray data

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

    Ali Mehmanparast

    2016-01-01

    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.

  18. Social exploration of 1D games

    Valente, Andrea; Marchetti, Emanuela

    2013-01-01

    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....

  19. STUDY ON THE SEQUENCE STRUCTURE OF BUTADIENE-STYRENE RUBBER BY 13C-NMR METHOD Ⅲ. QUANTITATIVE CHARACTERIZATION OF SEQUENCE STRUCTURE

    CHEN Xiaonong; HU Liping; YAN Baozhen; JIAO Shuke

    1990-01-01

    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.

  20. Recognition of a sequence as a structure containing series of recurring vectors from an alphabet

    Kel'manov, A. V.; Mikhailova, L. V.

    2013-07-01

    A polynomial-time algorithm is designed for finding an optimal solution of a discrete optimization problem to which a pattern recognition problem is reduced, namely, the noise-proof recognition of a sequence as a structure consisting of contiguous subsequences in the form of series of identical nonzero vectors from an alphabet of vectors in the Euclidean space that alternate with zero vectors.

  1. Multiple Sequence Alignments as Tools for Protein Structure and Function Prediction

    Alfonso Valencia

    2006-04-01

    Full Text Available Multiple sequence alignments have much to offer to the understanding of protein structure, evolution and function. We are developing approaches to use this information in predicting protein-binding specificity, intra-protein and protein-protein interactions, and in reconstructing protein interaction networks.

  2. Didactical Structures as an Outcome of Research on Teaching-Learning Sequences? Special Issue

    Lijnse, Piet; Klaassen, Kees

    2004-01-01

    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…

  3. Multiple Sequence Alignments as Tools for Protein Structure and Function Prediction

    2003-01-01

    Multiple sequence alignments have much to offer to the understanding of protein structure, evolution and function. We are developing approaches to use this information in predicting protein-binding specificity, intra-protein and protein-protein interactions, and in reconstructing protein interaction networks.

  4. Reproducible analysis of sequencing-based RNA structure probing data with user-friendly tools

    Kielpinski, Lukasz Jan; Sidiropoulos, Nikos; Vinther, Jeppe

    2015-01-01

    time also made analysis of the data challenging for scientists without formal training in computational biology. Here, we discuss different strategies for data analysis of massive parallel sequencing-based structure-probing data. To facilitate reproducible and standardized analysis of this type of data...

  5. What Makes Reforms Likely?: Timing and Sequencing of Structural Reforms in Latin America

    Lora, Eduardo

    2000-01-01

    The wave of structural reforms in Latin America and elsewhere has stimulated the development of a wide body of theoretical literature on the political economy of reform, i. e. , the study of the political constraints that condition the timing, speed and sequencing of reforms. This paper tests some of the hypotheses associated with these theoretical models, using a set of structural reform indicators for approximately twenty Latin American countries for the period 1985-1995. Although there is ...

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

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

  7. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

    Lees Jonathan G; Janes Robert W

    2008-01-01

    Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction method...

  8. Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight?

    Fetrow, Jacquelyn S.; Siew, Naomi; Di Gennaro, Jeannine A.; Martinez-Yamout, Maria; Dyson, H. Jane; Skolnick, Jeffrey

    2001-01-01

    A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified. Three of the 27 predictions are probable false-positives. Three novel predictions, which subsequently have been experimentally validated, are presented. Two additional novel predictions suggest a disulfide oxidoreductase regulatory mechanism for two subunits (OST3 and OST6) of the yeast oligosaccharyltransferase complex. Based on homology, this prediction can be extended to a potential tumor suppressor gene, N33, in humans, whose biochemical function was not previously known. Attempts to obtain a folded, active N33 construct to test the prediction were unsuccessful. The results show that structure prediction coupled with biochemically relevant structural motifs is a powerful method for the function annotation of genome sequences and can provide more detailed, robust predictions than function prediction methods that rely on sequence comparison alone. PMID:11316881

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

    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.

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

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

    2008-04-03

    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.

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

    Whitaker, Katherine E.; 3D-HST Collaboration

    2016-01-01

    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.

  12. The amino acid alphabet and the architecture of the protein sequence-structure map. I. Binary alphabets.

    Ferrada, Evandro

    2014-12-01

    The correspondence between protein sequences and structures, or sequence-structure map, relates to fundamental aspects of structural, evolutionary and synthetic biology. The specifics of the mapping, such as the fraction of accessible sequences and structures, or the sequences' ability to fold fast, are dictated by the type of interactions between the monomers that compose the sequences. The set of possible interactions between monomers is encapsulated by the potential energy function. In this study, I explore the impact of the relative forces of the potential on the architecture of the sequence-structure map. My observations rely on simple exact models of proteins and random samples of the space of potential energy functions of binary alphabets. I adopt a graph perspective and study the distribution of viable sequences and the structures they produce, as networks of sequences connected by point mutations. I observe that the relative proportion of attractive, neutral and repulsive forces defines types of potentials, that induce sequence-structure maps of vastly different architectures. I characterize the properties underlying these differences and relate them to the structure of the potential. Among these properties are the expected number and relative distribution of sequences associated to specific structures and the diversity of structures as a function of sequence divergence. I study the types of binary potentials observed in natural amino acids and show that there is a strong bias towards only some types of potentials, a bias that seems to characterize the folding code of natural proteins. I discuss implications of these observations for the architecture of the sequence-structure map of natural proteins, the construction of random libraries of peptides, and the early evolution of the natural amino acid alphabet. PMID:25473967

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

    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.

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

    Cui, Xuefeng

    2016-06-15

    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.

  15. Development of 1D Liner Compression Code for IDL

    Shimazu, Akihisa; Slough, John; Pancotti, Anthony

    2015-11-01

    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.

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

    Zuzana Hořejší

    2014-04-01

    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.

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

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

    2014-01-01

    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 http://prody.csb.pitt.edu/. Contact: bahar@pitt.edu PMID:24849577

  18. Clonal genotype and population structure inference from single-cell tumor sequencing.

    Roth, Andrew; McPherson, Andrew; Laks, Emma; Biele, Justina; Yap, Damian; Wan, Adrian; Smith, Maia A; Nielsen, Cydney B; McAlpine, Jessica N; Aparicio, Samuel; Bouchard-Côté, Alexandre; Shah, Sohrab P

    2016-07-01

    Single-cell DNA sequencing has great potential to reveal the clonal genotypes and population structure of human cancers. However, single-cell data suffer from missing values and biased allelic counts as well as false genotype measurements owing to the sequencing of multiple cells. We describe the Single Cell Genotyper (https://bitbucket.org/aroth85/scg), an open-source software based on a statistical model coupled with a mean-field variational inference method, which can be used to address these problems and robustly infer clonal genotypes. PMID:27183439

  19. Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

    Andreas Martin Lisewski

    Full Text Available The transmission of genomic information from coding sequence to protein structure during protein synthesis is subject to stochastic errors. To analyze transmission limits in the presence of spurious errors, Shannon's noisy channel theorem is applied to a communication channel between amino acid sequences and their structures established from a large-scale statistical analysis of protein atomic coordinates. While Shannon's theorem confirms that in close to native conformations information is transmitted with limited error probability, additional random errors in sequence (amino acid substitutions and in structure (structural defects trigger a decrease in communication capacity toward a Shannon limit at 0.010 bits per amino acid symbol at which communication breaks down. In several controls, simulated error rates above a critical threshold and models of unfolded structures always produce capacities below this limiting value. Thus an essential biological system can be realistically modeled as a digital communication channel that is (a sensitive to random errors and (b restricted by a Shannon error limit. This forms a novel basis for predictions consistent with observed rates of defective ribosomal products during protein synthesis, and with the estimated excess of mutual information in protein contact potentials.

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

    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

    1993-09-01

    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.

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

    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.

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

    Salahuddin, Parveen; Khan, Asad U

    2014-01-01

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

  3. Blind Detection of Severely Blurred 1D Barcode

    Dridi, Noura; Delignon, Yves; Sawaya, Wadih; Septier, François

    2010-01-01

    In this paper, we present a joint blind channel estimation and symbol detection for decoding a blurred and noisy 1D barcode captured image. From an information transmission point of view, we show that the channel impulse response, the noise power and the symbols can be efficiently estimated by taking into account the signal structure such as the cyclostationary property of the hidden Markov process to estimate. Based on the Expectation-Maximisation method, we show that the new algorithm offer...

  4. Sequences with high propensity to form G-quartet structures in kinetoplast DNA from Phytomonas serpens.

    Sá-Carvalho, D; Traub-Cseko, Y M

    1995-06-01

    Naturally occurring sequences containing repetitive guanine motifs have the potential to form tetraplex DNA. Phytomonas serpens minicircle DNA shows some regions where one strand is composed mainly of G and T (GT regions). These regions contain several stretches of contiguous guanines. An oligonucleotide was constructed with the sequence corresponding to one of these regions (Phyto-GT). It was demonstrated by native gel electrophoresis and methylation protection that Phyto-GT forms tetramolecular (G4), bimolecular (G'2) and unimolecular (G4') structures stabilized through G-quartets. Tetraplex DNA formation by this sequence could have biological relevance as it can be formed in physiological conditions and GT regions comprise approximately one-third of P. serpens and Crithidia oncopelti minicircles. PMID:8538680

  5. Genome sequence, comparative analysis and haplotype structure of the domestic dog.

    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

    2005-12-01

    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. PMID:16341006

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

    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.

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

    Helmer-Citterich Manuela

    2004-04-01

    Full Text Available Abstract Background A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that – at least in some cases – the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more, functional and/or structural key residues are not represented in the pattern. Multiple sequence alignments are commonly used to build functional sequence patterns. If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure. Results Here we present a new procedure aimed at improving the sensitivity and/ or specificity of poorly-performing patterns. The procedure can be summarised as follows: 1. residues structurally conserved in different proteins, that are true positives for a pattern, are identified by means of a computational technique and by visual inspection. 2. the sequence positions of the structurally conserved residues falling outside the pattern are used to build extended sequence patterns. 3. the extended patterns are optimised on the SWISS-PROT database for their sensitivity and specificity. The method was applied to eight PROSITE patterns. Whenever structurally conserved residues are found in the surface region close to the pattern (seven out of eight cases, the addition of information inferred from structural analysis is shown to improve pattern selectivity and in some cases selectivity and sensitivity as well. In some of the cases considered the procedure allowed the identification of functionally interesting residues, whose biological role is also discussed. Conclusion Our method can be applied to any type of functional motif or pattern (not only PROSITE ones which is not able to select all and only the true positive hits and for which at least two true positive structures are available. The computational technique for the identification of

  8. The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication.

    Oldenburg, Delene J; Bendich, Arnold J

    2016-05-01

    The structure of a chromosomal DNA molecule may influence the way in which it is replicated and inherited. For decades plastid DNA (ptDNA) was believed to be circular, with breakage invoked to explain linear forms found upon extraction from the cell. Recent evidence indicates that ptDNA in vivo consists of linear molecules with discrete termini, although these ends were not characterized. We report the sequences of two terminal regions, End1 and End2, for maize (Zea mays L.) ptDNA. We describe structural features of these terminal regions and similarities found in other plant ptDNAs. The terminal sequences are within inverted repeat regions (leading to four genomic isomers) and adjacent to origins of replication. Conceptually, stem-loop structures may be formed following melting of the double-stranded DNA ends. Exonuclease digestion indicates that the ends in maize are unobstructed, but tobacco (Nicotiana tabacum L.) ends may have a 5'-protein. If the terminal structure of ptDNA molecules influences the retention of ptDNA, the unprotected molecular ends in mature leaves of maize may be more susceptible to degradation in vivo than the protected ends in tobacco. The terminal sequences and cumulative GC skew profiles are nearly identical for maize, wheat (Triticum aestivum L.) and rice (Oryza sativa L.), with less similarity among other plants. The linear structure is now confirmed for maize ptDNA and inferred for other plants and suggests a virus-like recombination-dependent replication mechanism for ptDNA. Plastid transformation vectors containing the terminal sequences may increase the chances of success in generating transplastomic cereals. PMID:26650613

  9. YORP torques with 1D thermal model

    Breiter, Slawomir; Czekaj, Maria

    2010-01-01

    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.

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

    S Balaji; N Srinivasan

    2007-01-01

    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.