WorldWideScience

Sample records for 1d structural sequences

  1. 1D camera geometry and its application to the self-calibration of circular motion sequences.

    Science.gov (United States)

    Wong, Kwan-Yee K; Zhang, Guoqiang; Liang, Chen; Zhang, Hui

    2008-12-01

    This paper proposes a novel method for robustly recovering the camera geometry of an uncalibrated image sequence taken under circular motion. Under circular motion, all the camera centers lie on a circle and the mapping from the plane containing this circle to the horizon line observed in the image can be modelled as a 1D projection. A 2 x 2 homography is introduced in this paper to relate the projections of the camera centers in two 1D views. It is shown that the two imaged circular points of the motion plane and the rotation angle between the two views can be derived directly from such a homography. This way of recovering the imaged circular points and rotation angles is intrinsically a multiple view approach, as all the sequence geometry embedded in the epipoles is exploited in the estimation of the homography for each view pair. This results in a more robust method compared to those computing the rotation angles using adjacent views only. The proposed method has been applied to self-calibrate turntable sequences using either point features or silhouettes, and highly accurate results have been achieved. PMID:18988956

  2. Sequence repeats and protein structure

    Science.gov (United States)

    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.

  3. Protein folds and families: sequence and structure alignments.

    OpenAIRE

    Holm, L.; Sander, C.

    1999-01-01

    Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). As a result, the HSSP database not only provides aligned...

  4. Protein Structure Predicted from Sequence

    CERN Document Server

    Marks, Debora S; Sheridan, Robert; Hopf, Thomas A; Pagnani, Andrea; Zecchina, Riccardo; Sander, Chris

    2011-01-01

    The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify these constraints and use them to computationally fold proteins have so far been unsuccessful. Here, we show that co-variation of residue pairs, observed in a large protein family, provides sufficient information to determine 3D protein structure. Using a data-constrained maximum entropy model of the multiple sequence alignment, we identify pairs of statistically coupled residue positions which are expected to be close in the protein fold, termed contacts inferred from evolutionary information (EICs). To assess the amount of information about the protein fold contained in these coupled pairs, we evaluate the accuracy of predicted 3D structures for proteins of 50-260 residues, from 15 diverse protein families, including a G-protein coupled receptor. These structure predictions ...

  5. Dispersive Elastodynamics of 1D Banded Materials and Structures: Design

    CERN Document Server

    Hussein, M I; Scott, R A

    2006-01-01

    Within periodic materials and structures, wave scattering and dispersion occur across constituent material interfaces leading to a banded frequency response. In an earlier paper, the elastodynamics of one-dimensional periodic materials and finite structures comprising these materials were examined with an emphasis on their frequency-dependent characteristics. In this work, a novel design paradigm is presented whereby periodic unit cells are designed for desired frequency band properties, and with appropriate scaling, these cells are used as building blocks for forming fully periodic or partially periodic structures with related dynamical characteristics. Through this multiscale dispersive design methodology, which is hierarchical and integrated, structures can be devised for effective vibration or shock isolation without needing to employ dissipative damping mechanisms. The speed of energy propagation in a designed structure can also be dictated through synthesis of the unit cells. Case studies are presented ...

  6. Comments on the Bifurcation Structure of 1D Maps

    DEFF Research Database (Denmark)

    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 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 called into attention.

  7. Formation of 1D adsorbed water structures on CaO(001)

    Science.gov (United States)

    Zhao, Xunhua; Bhattacharya, Saswata; Ghiringhelli, Luca M.; Levchenko, Sergey V.; Scheffler, Matthias

    2015-03-01

    Understanding the interaction of water with oxide surfaces is of fundamental importance for basic and engineering sciences. Recently, a spontaneous formation of one-dimensional (1D) adsorbed water structures have been observed on CaO(001). Interestingly, at other alkaline earth metal oxides, in particular MgO(001) and SrO(001), such structures have not been found experimentally. We calculate the relative stability of adsorbed water structures on the three oxides using density-functional theory combined with the ab initio atomistic thermodynamics. Low-energy structures at different coverages are obtained with a first-principles genetic algorithm. Finite-temperature vibrational spectra are calculated using ab initio molecular dynamics. We find a range of (T, p) conditions where 1D structures are thermodynamically stable on CaO(001). The orientation and vibrational spectra of the 1D structures are in agreement with the experiments. The formation of the 1D structures is found to be actuated by a symmetry breaking in the adsorbed water tetramer, as well as by a balance between water-water and water-substrate interactions, determined by the lattice constant of the oxide.

  8. Vertically integrated ZnO-Based 1D1R structure for resistive switching

    International Nuclear Information System (INIS)

    We report a ZnO-based 1D1R structure, which is formed by a vertical integration of a FeZnO/MgO switching resistor (1R) and an Ag/MgZnO Schottky diode (1D). The multifunctional ZnO and its compounds are grown through MOCVD with in situ doping. For the R element, the current ratio of the high-resistance state (HRS) over the low-resistance state (LRS) at 1 V is 2.4 × 106. The conduction mechanisms of the HRS and LRS are Poole–Frenkel emission and resistive conduction, respectively. The D element shows the forward/reverse current ratio at ±1 V to be 2.4 × 107. This 1D1R structure exhibits high RHRS/RLRS ratio, excellent rectifying characteristics and robust retention. (paper)

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

    CERN Document Server

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

    2004-01-01

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

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

    CERN Document Server

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

    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.

  11. The Array Structure of Modified Jacobi Sequences

    Directory of Open Access Journals (Sweden)

    Shenghua Li

    2013-12-01

    Full Text Available It is known that the out-of-phase autocorrelation values of modified Jacobi sequences of period $pq$, $p$, $q$ prime, are depend only on the difference between $p$ and $q$. In this paper, the array structure of modified Jacobi sequences is studied. Based on the structure, their autocorrelation functions are computed clearly, and some modifications of modified Jacobi sequences can be obtained.

  12. Resistivity structure of Sumatran Fault (Aceh segment) derived from 1-D magnetotelluric modeling

    Science.gov (United States)

    Nurhasan, Sutarno, D.; Bachtiar, H.; Sugiyanto, D.; Ogawa, Y.; Kimata, F.; Fitriani, D.

    2012-06-01

    Sumatran Fault Zone is the most active fault in Indonesia as a result of strike-slip component of Indo-Australian oblique convergence. With the length of 1900 km, Sumatran fault was divided into 20 segments starting from the southernmost Sumatra Island having small slip rate and increasing to the north end of Sumatra Island. There are several geophysical methods to analyze fault structure depending on physical parameter used in these methods, such as seismology, geodesy and electromagnetic. Magnetotelluric method which is one of geophysical methods has been widely used in mapping and sounding resistivity distribution because it does not only has the ability for detecting contras resistivity but also has a penetration range up to hundreds of kilometers. Magnetotelluric survey was carried out in Aceh region with the 12 total sites crossing Sumatran Fault on Aceh and Seulimeum segments. Two components of electric and magnetic fields were recorded during 10 hours in average with the frequency range from 320 Hz to 0,01 Hz. Analysis of the pseudosection of phase and apparent resistivity exhibit vertical low phase flanked on the west and east by high phase describing the existence of resistivity contras in this region. Having rotated the data to N45°E direction, interpretation of the result has been performed using three different methods of 1D MT modeling i.e. Bostick inversion, 1D MT inversion of TM data, and 1D MT inversion of the impedance determinant. By comparison, we concluded that the use of TM data only and the impedance determinant in 1D inversion yield the more reliable resistivity structure of the fault compare to other methods. Based on this result, it has been shown clearly that Sumatra Fault is characterized by vertical contras resistivity indicating the existence of Aceh and Seulimeum faults which has a good agreement with the geological data.

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

    Energy Technology Data Exchange (ETDEWEB)

    K.R. Maskaly

    2005-06-01

    Dielectric reflectors that are periodic in one or two dimensions, also known as 1D and 2D photonic crystals, have been widely studied for many potential applications due to the presence of wavelength-tunable photonic bandgaps. However, the unique optical behavior of photonic crystals is based on theoretical models of perfect analogues. Little is known about the practical effects of dielectric imperfections on their technologically useful optical properties. In order to address this issue, a finite-difference time-domain (FDTD) code is employed to study the effect of three specific dielectric imperfections in 1D and 2D photonic crystals. The first imperfection investigated is dielectric interfacial roughness in quarter-wave tuned 1D photonic crystals at normal incidence. This study reveals that the reflectivity of some roughened photonic crystal configurations can change up to 50% at the center of the bandgap for RMS roughness values around 20% of the characteristic periodicity of the crystal. However, this reflectivity change can be mitigated by increasing the index contrast and/or the number of bilayers in the crystal. In order to explain these results, the homogenization approximation, which is usually applied to single rough surfaces, is applied to the quarter-wave stacks. The results of the homogenization approximation match the FDTD results extremely well, suggesting that the main role of the roughness features is to grade the refractive index profile of the interfaces in the photonic crystal rather than diffusely scatter the incoming light. This result also implies that the amount of incoherent reflection from the roughened quarterwave stacks is extremely small. This is confirmed through direct extraction of the amount of incoherent power from the FDTD calculations. Further FDTD studies are done on the entire normal incidence bandgap of roughened 1D photonic crystals. These results reveal a narrowing and red-shifting of the normal incidence bandgap with 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.

  14. Reversible interconversion of a divalent vanadium bronze between ? and ? quasi-1D structures.

    Science.gov (United States)

    Marley, Peter M; Banerjee, Sarbajit

    2012-05-01

    Charge fluctuations along the quasi-1D frameworks of M(x)V(2)O(5) bronzes have evinced much recent interest owing to the manifestation of colossal metal-insulator transitions and superconductivity. Depending upon the nature of the intercalating cation (M), distinctive geometries of the V(2)O(5) framework are accessible. Herein, we demonstrate an unprecedented reversible transformation between double-layered (?) and tunnel (?) quasi-1D geometries for nanowires of a divalent vanadium bronze, Ca(x)V(2)O(5) (x ? 0.23), upon annealing-induced dehydration and hydrothermally induced hydration. Such a facile hydration/dehydration-induced interconversion between two prominent quasi-1D structures (accompanied by a change in charge-ordering motifs) has not been observed in the bulk and is posited to result from the ease of propagation of crystallographic slip processes across the confined nanowire widths for the ? ? ? conversion and the facile diffusion of water molecules within the tunnel geometries for the ? ? ? reversion. PMID:22506534

  15. Which Came First, Protein Sequence or Structure?

    Science.gov (United States)

    Mehran Kardar (Massachusetts Institute of Technology; Department of Physics)

    1996-08-02

    Access to the article is free, however registration and sign-in are required. The sequence of amino acids in a protein determines how it will eventually fold into its three-dimensional structure. One way to understand how this works is by considering the protein's "foldability"--that is, the likelihood of folding into a useful structure. Another approach, however, is that taken in the report by Li et al. (p. 666) and discussed in the Perspective by Kardar. Here, the authors consider the "designability" of proteins--the number of sequences that uniquely fold into a particular structure.

  16. Effect of copper doping on the crystal structure and morphology of 1D nanostructured manganese oxides.

    Science.gov (United States)

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

    2007-11-01

    We have tried to control the aspect ratio and physicochemical properties of 1D nanostructured manganese oxides through copper doping. Copper-doped manganese oxide nanostructures have been synthesized by one-pot hydrothermal treatment for the mixed solution of permanganate anions and copper cations. According to powder X-ray diffraction and electron microscopic analyses, all the present materials commonly crystallize with alpha-MnO2-type structure but their aspect ratio decreases significantly with increasing the content of copper. Such a variation of crystallite dimension is attributable to the limitation of crystal growth by the incorporation of copper ions. X-ray absorption spectroscopic studies at Mn K- and Cu K-edges clearly demonstrate that the average oxidation state of manganese ions is increased by the substitution of divalent copper ions. Electrochemical measurements reveal the improvement of the electrode performance of nanostructured manganate upon copper doping, which can be interpreted as a result of the decrease of aspect ratio and the increase of Mn valence state. From the present experimental findings, it becomes certain that the present Cu doping method can provide an effective way of controlling the crystal dimension and electrochemical property of 1D nanostructured manganese oxide. PMID:18047111

  17. Quadruplex DNA: sequence, topology and structure

    OpenAIRE

    Burge, S.; Parkinson, G. N.; Hazel, P.; Todd, A. K.; Neidle, S.

    2006-01-01

    G-quadruplexes are higher-order DNA and RNA structures formed from G-rich sequences that are built around tetrads of hydrogen-bonded guanine bases. Potential quadruplex sequences have been identified in G-rich eukaryotic telomeres, and more recently in non-telomeric genomic DNA, e.g. in nuclease-hypersensitive promoter regions. The natural role and biological validation of these structures is starting to be explored, and there is particular interest in them as targets for therapeutic interven...

  18. Detecting mosaic structures in DNA sequence alignments

    OpenAIRE

    Husmeier, D

    2006-01-01

    This article first provides a concise introduction to the statistical approach to phyloge- netics. It then describes a new method for detecting mosaic structures in DNA sequence alignments, which is based on combining two probabilistic graphical models: (1) a taxon graph (phylogenetic tree) representing the relationships among the taxa, and (2) a site graph (hidden Markov model) representing spatial correlations between nucleotides.

  19. Characteristics of the low frequency sequence bands observed in the vibronic emission spectra of the jet cooled p-fluorobenzyl radical in the D1?D0 transition

    International Nuclear Information System (INIS)

    The p-fluorobenzyl radical was generated from the p-fluorotoluene and vibronically excited in a corona excited supersonic expansion with inert buffer gases. The vibronic emission spectra of the jet cooled p-fluorobenzyl radical in the D1?D0 transition have been observed in the visible region. The spectra exhibit several low frequency sequence bands in the vicinity of the every strong vibronic band. The characteristics of the sequence bands have been examined by varying the experimental conditions such as carrier gas and nozzle size to identify the origin of the transition in the spectra

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

    DEFF Research Database (Denmark)

    Breinbjerg, Olav; Yaghjian, Arthur D.

    2014-01-01

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

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

    OpenAIRE

    Lee Byungkook; Kim Changhoon

    2007-01-01

    Abstract Background Accurate sequence alignments are essential for homology searches and for building three-dimensional structural models of proteins. Since structure is better conserved than sequence, structure alignments have been used to guide sequence alignments and are commonly used as the gold standard for sequence alignment evaluation. Nonetheless, as far as we know, there is no report of a systematic evaluation of pairwise structure alignment programs in terms of the sequence alignmen...

  2. Tertiary structural propensities reveal fundamental sequence/structure relationships.

    Science.gov (United States)

    Zheng, Fan; Zhang, Jian; Grigoryan, Gevorg

    2015-05-01

    Extracting useful generalizations from the continually growing Protein Data Bank (PDB) is of central importance. We hypothesize that the PDB contains valuable quantitative information on the level of local tertiary structural motifs (TERMs). We show that by breaking a protein structure into its constituent TERMs, and querying the PDB to characterize the natural ensemble matching each, we can estimate the compatibility of the structure with a given amino acid sequence through a metric we term "structure score." Considering submissions from recent Critical Assessment of Structure Prediction (CASP) experiments, we found a strong correlation (R = 0.69) between structure score and model accuracy, with poorly predicted regions readily identifiable. This performance exceeds that of leading atomistic statistical energy functions. Furthermore, TERM-based analysis of two prototypical multi-state proteins rapidly produced structural insights fully consistent with prior extensive experimental studies. We thus find that TERM-based analysis should have considerable utility for protein structural biology. PMID:25914055

  3. From 1D chain to 3D network: A theoretical study on TiO2 low dimensional structures.

    Science.gov (United States)

    Guo, Ling-Ju; Zeng, Zhi; He, Tao

    2015-06-14

    We have performed a systematic study on a series of low dimensional TiO2 nanostructures under density functional theory methods. The geometries, stabilities, growth mechanism, and electronic structures of 1D chain, 2D ring, 2D ring array, and 3D network of TiO2 nanostructures are analyzed. Based on the Ti2O4 building unit, a series of 1D TiO2 nano chains and rings can be built. Furthermore, 2D ring array and 3D network nanostructures can be constructed from 1D chains and rings. Among non-periodic TiO2 chain and ring structures, one series of ring structures is found to be more stable. The geometry model of the 2D ring arrays and 3D network structures in this work has provided a theoretical understanding on the structure information in experiments. Based on these semiconductive low dimensional structures, moreover, it can help to understand and design new hierarchical TiO2 nanostructure in the future. PMID:26071708

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

    CERN Document Server

    Strouthos, C G

    2003-01-01

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

  5. Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis.

    Science.gov (United States)

    Fell, J W; Boekhout, T; Fonseca, A; Scorzetti, G; Statzell-Tallman, A

    2000-05-01

    The molecular systematics of 337 strains of basidiomycetous yeasts and yeast-like fungi, representing 230 species in 18 anamorphic and 24 teleomorphic genera, was determined by sequence analysis of the D1/D2 region of the large-subunit rDNA. The data were compared with published sequences of other basidiomycetous fungi. The results demonstrated that the yeast species and genera are phylogenetically distributed among the Microbotryum, Sporidiobolus, Agaricostilbum and Erythrobasidium clades of the Urediniomycetes; the Tremellales, Trichosporonales ord. nov., Filobasidiales and Cystofilobasidiales clades of the Hymenomycetes; and the Ustilaginales, Microstromatales and Malasseziales clades of the Ustilaginomycetes. Genera such as Bensingtonia, Cryptococcus, Rhodotorula and Sporobolomyces are polyphyletic, i.e. they occur in two or more clades. In contrast, other genera, e.g. Bullera, Cystofilobasidium, Fellomyces, Filobasidiella, Filobasidium, Kondoa, Kurtzmanomyces, Leucosporidium, Rhodosporidium, Sporidiobolus and Udeniomyces, are monophyletic. The majority of the species can be identified using D1/D2 analyses, although the internal transcribed spacer region is required to distinguish closely related species. The intergenic spacer region is recommended for additional differentiation of species and strains. PMID:10843082

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

    OpenAIRE

    Tautz Diethard; Nolte Arne W; Sonnenberg Rainer

    2007-01-01

    Abstract Background Identification of species via DNA sequences is the basis for DNA taxonomy and DNA barcoding. Currently there is a strong focus on using a mitochondrial marker for this purpose, in particular a fragment from the cytochrome oxidase I gene (COI). While there is ample evidence that this marker is indeed suitable across a broad taxonomic range to delineate species, it has also become clear that a complementation by a nuclear marker system could be advantageous. Ribosomal RNA ge...

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

    OpenAIRE

    Huang Conrad C; Couch Gregory S; Pettersen Eric F; Meng Elaine C; Ferrin Thomas E

    2006-01-01

    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 (f...

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

    International Nuclear Information System (INIS)

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

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

    OpenAIRE

    Klau Gunnar W; Bauer Markus; Reinert Knut

    2007-01-01

    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-str...

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

    OpenAIRE

    Karabash, Illya M.

    2011-01-01

    The paper is devoted to optimization of resonances associated with 1-D wave equations in inhomogeneous media. The medium's structure is represented by a nonnegative function B. The problem is to design for a given $\\alpha \\in \\R$ a medium that generates a resonance on the line $\\alpha + \\i \\R$ with a minimal possible modulus of the imaginary part. We consider an admissible family of mediums that arises in a problem of optimal design for photonic crystals. This admissible fam...

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

    Science.gov (United States)

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

    2011-09-01

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

  12. Mechanical consequences of LOCA in PWR: Full scale coupled 1D/3D simulations with fluid–structure interaction

    Energy Technology Data Exchange (ETDEWEB)

    Faucher, V., E-mail: vincent.faucher@cea.fr [LaMSID, UMR EDF-CEA-CNRS 2832, Clamart F-92141 (France); CEA, DEN, DANS, DM2S, SEMT, DYN, Gif-sur-Yvette F-91191 (France); Crouzet, F. [LaMSID, UMR EDF-CEA-CNRS 2832, Clamart F-92141 (France); EDF R and D, Analysis in Mechanics and Acoustics, Clamart F-92141 (France); Debaud, F. [EDF SEPTEN, Nuclear Engineering Division, Villeurbanne F-69628 (France)

    2014-04-01

    Highlights: • We propose an approach to analyze the transient effects of LOCA on PWR internals. • The complete primary loop is modeled using a coupled 1D-pipe/3D strategy. • Full fluid–structure interaction is considered inside the main vessel. • Impedance relations modeling the influence of small details are precisely calibrated. • The capabilities of the 1D/3D methodology are demonstrated on a significant example. - Abstract: The present paper is dedicated to the analysis of the fast transient mechanical consequences of the Loss Of Coolant Accident (LOCA) on the internal structures of a Pressurized Water Reactor (PWR). A complete methodology is described, based on a coupled 1D/3D representation of the entire primary loop of the reactor, with a robust and accurate approach for fluid–structure interaction inside the main vessel. A special attention is given to the modeling of small geometric details, such as perforated plates in the vicinity of the reactor core, through local impedance relations acting on the flow, which must be carefully calibrated for industrial purposes. The capabilities of the proposed framework are demonstrated with the application of the complete computational scheme to the simulation of the consequences of LOCA for a French 900 MW PWR, performed with EUROPLEXUS software.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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 available for Microsoft Windows, Apple Mac OS X, Linux, and other platforms from http://www.cgl.ucsf.edu/chimera.

  15. Synthesis, crystal structure, and properties of a 1-D terbium-substituted monolacunary Keggin-type polyoxotungstate

    Science.gov (United States)

    Ma, Pengtao; Si, Yanan; Wan, Rong; Zhang, Shaowei; Wang, Jingping; Niu, Jingyang

    2015-03-01

    A new 1-D linear chainlike terbium-substituted polyoxometalate [Tb(H2O)2(?-PW11O39)]4- (1) has been synthesized in aqueous solution and characterized by elemental analysis, inductively coupled plasma atomic emission spectrometry (ICP-AES), X-ray powder diffraction (XRPD), IR spectrum, thermal analysis, electrospray ionization mass spectrometry (ESI-MS), and X-ray single-crystal diffraction. X-ray structural analysis reveals that 1 displays a 1-D linear chain containing [Tb(H2O)2(?-PW11O39)]4- moieties. The Tb(III) cation incorporated into the monolacunary Keggin-type [?-PW11O39]7- unit resides in a distorted monocapped triangular prismatic geometry and acts as a linker to join two adjacent [?-PW11O39]7- units to form a 1-D chain structure. Solid-state photoluminescent property of 1 has been investigated at room temperature and the photoluminescent emission mainly results from the synergistic effect of the TbIII cation and the Na7[?-PW11O39] precursor. The ESI-MS spectrum of 1 confirms that the polyanion [Tb(H2O)(HPW11O39)]3- is stable in aqueous solution.

  16. Synthesis, crystal structure, and properties of a 1-D terbium-substituted monolacunary Keggin-type polyoxotungstate.

    Science.gov (United States)

    Ma, Pengtao; Si, Yanan; Wan, Rong; Zhang, Shaowei; Wang, Jingping; Niu, Jingyang

    2015-03-01

    A new 1-D linear chainlike terbium-substituted polyoxometalate [Tb(H2O)2(?-PW11O39)](4-) (1) has been synthesized in aqueous solution and characterized by elemental analysis, inductively coupled plasma atomic emission spectrometry (ICP-AES), X-ray powder diffraction (XRPD), IR spectrum, thermal analysis, electrospray ionization mass spectrometry (ESI-MS), and X-ray single-crystal diffraction. X-ray structural analysis reveals that 1 displays a 1-D linear chain containing [Tb(H2O)2(?-PW11O39)](4-) moieties. The Tb(III) cation incorporated into the monolacunary Keggin-type [?-PW11O39](7-) unit resides in a distorted monocapped triangular prismatic geometry and acts as a linker to join two adjacent [?-PW11O39](7-) units to form a 1-D chain structure. Solid-state photoluminescent property of 1 has been investigated at room temperature and the photoluminescent emission mainly results from the synergistic effect of the Tb(III) cation and the Na7[?-PW11O39] precursor. The ESI-MS spectrum of 1 confirms that the polyanion [Tb(H2O)(HPW11O39)](3-) is stable in aqueous solution. PMID:25541394

  17. RSEARCH: Finding homologs of single structured RNA sequences

    OpenAIRE

    Eddy Sean R; Klein Robert J

    2003-01-01

    Abstract Background For many RNA molecules, secondary structure rather than primary sequence is the evolutionarily conserved feature. No programs have yet been published that allow searching a sequence database for homologs of a single RNA molecule on the basis of secondary structure. Results We have developed a program, RSEARCH, that takes a single RNA sequence with its secondary structure and utilizes a local alignment algorithm to search a database for homologous RNAs. For this purpose, we...

  18. Measurement of the Deuteron Spin Structure Function g1d(x) for 1 (GeV/c)2 2 2

    International Nuclear Information System (INIS)

    New measurements are reported on the deuteron spin structure function g1d. These results were obtained from deep inelastic scattering of 48.3 GeV electrons on polarized deuterons in the kinematic range 0.01 2 2. These are the first high dose electron scattering data obtained using lithium deuteride (6Li2H) as the target material. Extrapolations of the data were performed to obtain moments of g1d, including ?1d, and the net quark polarization ? ?

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

    International Nuclear Information System (INIS)

    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

  20. Computational methods in sequence and structure prediction

    Science.gov (United States)

    Lang, Caiyi

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

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

    Directory of Open Access Journals (Sweden)

    Zhou Yuan Wu

    2013-07-01

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

  2. Genetic heterogeneity of Indian field isolates of foot-and-mouth disease virus serotype O as revealed by partial sequencing of 1D gene.

    Science.gov (United States)

    Pattnaik, B; Venkataramanan, R; Tosh, C; Sanyal, A; Hemadri, D; Samuel, A R; Knowles, N J; Kitching, R P

    1998-06-01

    The sequence of 165 nucleotides at the 3' end of the 1D gene, determined from RT PCR amplified cDNA fragments, of 25 type O strains isolated from different parts/regions of India during 1987 1995 and the vaccine strain (R2/75) currently in use in India were subjected to phylogenetic analysis. One isolate from the neighbouring country Nepal was also included in the study. The virus/ field strains showed high degree of genetic heterogeneity among themselves with % divergence in nucleotide sequence ranging from 1.2 to 19.4%. The Indian strains were much away (13.3 20.6%) from the exotic type O strains of O1BFS, O1K, and O1Campos. The type O strains analyzed were classified into three genotypes basing on level of divergence observed in nucleotide sequence. The type O vaccine virus (R2/75) was > 71% divergent (7.3-15.2%) from the field strains which revealed significant ( > 5%) genetic heterogeneity between the two. The phylogenetic analysis identified three distinct lineages, viz., (i) lineage 1 represented by the exotic strains, (ii) lineage 2 represented by 25 of the field strains which clustered into seven subgroups/sublines (2a-2g), and (iii) lineage 3 represented by a unique field isolate which shared the branching/origin with the vaccine strain. The lineage 2 which comprised of 25 of the 26 type O field strains analyzed, was placed almost at equidistance from the lineages 1 and 3 in the phylogenetic tree. The vaccine strain was closer to the viruses in lineage 2. Though there was no specific distribution pattern of sequences in different geographical regions of India, the viruses/ sequences in subgroup 2f appeared to be restricted to the southern states. Comparison of deduced amino acid sequence in the immunodominant regions 133-160 and 200-208 of the 1D gene product (VP1) showed that the two viruses in lineage 3 had unique amino acid residues at the positions 138 (D), 139 (G), 144 (I), and 158 (A) compared to rest of the strains including the exotic ones. Comparison of amino acid residues at critical positions 144, 148, 149, 151, 153, 154, and 208 revealed similarity between the type O strains analyzed. The virus strains showed variation (V/L/I) at position 144. One field strain showed replacement from Q149-->E and another from P208-->L. Thus, the study revealed that the type O FMD virus populations circulating in India and causing disease outbreaks are genetically much heterogeneous but related at the immunodominant region of VP1 polypeptide, and there are more than one genetically distinct virus populations in almost every region of the country which is possible due to unrestricted animal movement in the country. The involvement of vaccine virus in disease outbreaks was ruled out as the field strains (excluding the one in lineage 3) were phylogenetically distinct from it. PMID:9725665

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

    Directory of Open Access Journals (Sweden)

    Daniels Noah M

    2012-10-01

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

  4. Structure and relaxation processes of an anisotropic molecular fluid confined into 1D nanochannels

    OpenAIRE

    Lefort, Ronan; Morineau, Denis; Guégan, Régis; Alain, Moréac; Ecolivet, Claude; Guendouz, Mohammed

    2007-01-01

    Abstract Structural order parameters of a smectic liquid crystal confined into the columnar form of porous silicon are studied using neutron scattering and optical spectroscopic techniques. It is shown that both the translational and orientational anisotropic properties of the confined phase strongly couple to the one-dimensional character of the porous silicon matrix. The influence of this confinement induced anisotropic local structure on the molecular reorientations occuring in ...

  5. Structure and relaxation processes of an anisotropic molecular fluid confined into 1D nanochannels

    CERN Document Server

    Lefort, R; Guégan, R; Alain, M; Ecolivet, C; Guendouz, M; Lefort, Ronan; Morineau, Denis; Alain, Mor\\'{e}ac; Ecolivet, Claude; Guendouz, Mohammed

    2006-01-01

    Structural order parameters of a smectic liquid crystal confined into the columnar form of porous silicon are studied using neutron scattering and optical spectroscopic techniques. It is shown that both the translational and orientational anisotropic properties of the confined phase strongly couple to the one-dimensional character of the porous silicon matrix. The influence of this confinement induced anisotropic local structure on the molecular reorientations occuring in the picosecond timescale is discussed.

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

    DEFF Research Database (Denmark)

    Breinbjerg, O.

    2012-01-01

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

  7. Integrability of and differential–algebraic structures for spatially 1D hydrodynamical systems of Riemann type

    International Nuclear Information System (INIS)

    Highlights: • A new differential–algebraic–geometric approach for testing integrability is described. • The approach is applied to a generalized Riemann type hydrodynamic system. • The approach is applied to a generalized Ostrovsky–Vakhnenko system. • The approach is applied to a new two-component Burgers type hydrodynamic system. -- Abstract: A differential–algebraic approach to studying the Lax integrability of a generalized Riemann type hydrodynamic hierarchy is revisited and a new Lax representation is constructed. The related bi-Hamiltonian integrability and compatible Poissonian structures of this hierarchy are also investigated using gradient-holonomic and geometric methods. The complete integrability of a new generalized Riemann hydrodynamic system is studied via a novel combination of symplectic and differential–algebraic tools. A compatible pair of polynomial Poissonian structures, a Lax representation and a related infinite hierarchy of conservation laws are obtained. In addition, the differential–algebraic approach is used to prove the complete Lax integrability of the generalized Ostrovsky–Vakhnenko and a new Burgers type system, and special cases are studied using symplectic and gradient-holonomic tools. Compatible pairs of polynomial Poissonian structures, matrix Lax representations and infinite hierarchies of conservation laws are derived

  8. 3D mechanical measurements with an atomic force microscope on 1D structures.

    DEFF Research Database (Denmark)

    KallesØe, Christian; Larsen, Martin Benjamin Barbour Spanget

    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 in a short time. Based on this method Young's modulus of carbon nanofibers and epitaxial grown III-V nanowires has been determined.

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

    Science.gov (United States)

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

    2009-03-23

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

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

    Science.gov (United States)

    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.

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

    CERN Document Server

    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...

  12. Synthesis, crystal structures, magnetic and luminescent properties of unique 1D p-ferrocenylbenzoate-bridged lanthanide complexes

    International Nuclear Information System (INIS)

    Treatments of p-ferrocenylbenzoate [p-NaOOCH4C6Fc, Fc=(?5-C5H5)Fe(?5-C5H4)] with Ln(NO3)3.nH2O afford seven p-ferrocenylbenzoate lanthanide complexes {[Ln(OOCH4C6Fc)2(?2-OOCH4C6Fc)2(H2O)2](H3O)}n [Ln=Ce (1), Pr (2), Sm (3), Eu (4), Gd (5), Tb (6) and Dy (7)]. X-ray crystallographic analysis reveals that the isomorphous complexes {[Ce(OOCH4C6Fc)2(?2-OOCH4C6Fc)2(H2O)2](H3O)}n (1) and {[Pr(OOCH4C6Fc)2(?2-OOCH4C6Fc)2(H2O)2](H3O)}n (2) form a unique 1D double-bridged infinite chain structure bridged by ?2-OOCH4C6Fc groups. Each Ln(III) ion adopts a dodecahedron coordination environment with eight coordinated oxygen atoms from two terminal monodentate coordinated FcC6H4COO- units, two terminal monodentate coordinated H2O molecules and four ?2--OOCH4C6Fc units. The luminescent spectra reveal that only 4 and 6 exhibit characteristic emissions of lanthanide ions, Eu(III) and Ts of lanthanide ions, Eu(III) and Tb(III) ions, respectively. The variable-temperature magnetic properties of 5 and 7 suggest that a ferromagnetic coupling between spin carriers may exist in 5. - Graphical abstract: Seven p-ferrocenylbenzoate lanthanide coordination polymers were synthesized. Given is the perspective view of a unique 1D double-bridged infinite chain structure of 1, excitation and emission spectra of 6 and plots of ?mT vs. T and ?m-1 vs. T of 5.

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

    CERN Document Server

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

    1999-01-01

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

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

    OpenAIRE

    Daniels Noah M; Nadimpalli Shilpa; Cowen Lenore J

    2012-01-01

    Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We pre...

  15. Algorithm of detecting structural variations in DNA sequences

    Science.gov (United States)

    Na?ecz-Charkiewicz, Katarzyna; Nowak, Robert

    2014-11-01

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

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

    Directory of Open Access Journals (Sweden)

    D. Yu. Klimushkin

    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.

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

    Science.gov (United States)

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

    2011-01-11

    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 mutagenesis and iterative rounds of positive antibiotic selection, we identified extensively redesigned and highly convergent resolvase and invertase populations in the context of engineered zinc-finger recombinase (ZFR) fusion proteins. Reprogrammed variants selectively catalyzed recombination of nonnative DNA sequences > 10,000-fold more effectively than their parental enzymes. Alanine-scanning mutagenesis revealed the molecular basis of resolvase and invertase DNA sequence specificity. When used as rationally designed ZFR heterodimers, the reprogrammed enzyme variants site-specifically modified unnatural and asymmetric DNA sequences. Early studies on the directed evolution of serine recombinase DNA sequence specificity produced enzymes with relaxed substrate specificity as a result of randomly incorporated mutations. In the current study, we focused our mutagenesis exclusively on DNA determinants, leading to redesigned enzymes that remained highly specific and directed transgene integration into the human genome with > 80% accuracy. These results demonstrate that unique resolvase and invertase derivatives can be developed to site-specifically modify the human genome in the context of zinc-finger recombinase fusion proteins. PMID:21187418

  18. Sequence and Structural Analyses for Functional Non-coding RNAs

    Science.gov (United States)

    Sakakibara, Yasubumi; Sato, Kengo

    Analysis and detection of functional RNAs are currently important topics in both molecular biology and bioinformatics research. Several computational methods based on stochastic context-free grammars (SCFGs) have been developed for modeling and analysing functional RNA sequences. These grammatical methods have succeeded in modeling typical secondary structures of RNAs and are used for structural alignments of RNA sequences. Such stochastic models, however, are not sufficient to discriminate member sequences of an RNA family from non-members, and hence to detect non-coding RNA regions from genome sequences. Recently, the support vector machine (SVM) and kernel function techniques have been actively studied and proposed as a solution to various problems in bioinformatics. SVMs are trained from positive and negative samples and have strong, accurate discrimination abilities, and hence are more appropriate for the discrimination tasks. A few kernel functions that extend the string kernel to measure the similarity of two RNA sequences from the viewpoint of secondary structures have been proposed. In this article, we give an overview of recent progress in SCFG-based methods for RNA sequence analysis and novel kernel functions tailored to measure the similarity of two RNA sequences and developed for use with support vector machines (SVM) in discriminating members of an RNA family from non-members.

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

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; LyngsØ, Rune B.

    2005-01-01

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

  20. A fast structural multiple alignment method for long RNA sequences

    Directory of Open Access Journals (Sweden)

    Kin Taishin

    2008-01-01

    Full Text Available Abstract Background Aligning multiple RNA sequences is essential for analyzing non-coding RNAs. Although many alignment methods for non-coding RNAs, including Sankoff's algorithm for strict structural alignments, have been proposed, they are either inaccurate or computationally too expensive. Faster methods with reasonable accuracies are required for genome-scale analyses. Results We propose a fast algorithm for multiple structural alignments of RNA sequences that is an extension of our pairwise structural alignment method (implemented in SCARNA. The accuracies of the implemented software, MXSCARNA, are at least as favorable as those of state-of-art algorithms that are computationally much more expensive in time and memory. Conclusion The proposed method for structural alignment of multiple RNA sequences is fast enough for large-scale analyses with accuracies at least comparable to those of existing algorithms. The source code of MXSCARNA and its web server are available at http://mxscarna.ncrna.org.

  1. Nucleotide sequence and secondary structure of apple scar skin viroid.

    OpenAIRE

    Hashimoto, J.; Koganezawa, H.

    1987-01-01

    The complete nucleotide sequence of apple scar skin viroid(ASSV) has been established, and a probable secondary structure is proposed. A single-stranded circular ASSV RNA consists of 330 nucleotides and can assume the rodlike conformation with extensive base-pairing characteristic of all the known viroids. ASSV shows low sequence homologies with other viroids and lacks the central conserved region. These indicate that ASSV should be allocated to a separate viroid group. However, homologous se...

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

    Directory of Open Access Journals (Sweden)

    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 predictions stem from the novel features that express collocation of the secondary structure segments in the protein sequence and that combine evolutionary and secondary structure information. Our work demonstrates that conservation and arrangement of the secondary structure segments predicted along the protein chain can successfully predict structural classes which are defined based on the spatial arrangement of the secondary structures. A web server is available at http://biomine.ece.ualberta.ca/MODAS/.

  3. Nucleotide sequence and proposed secondary structure of Columnea latent viroid: a natural mosaic of viroid sequences.

    OpenAIRE

    Hammond, R.; Smith, D. R.; Diener, T. O.

    1989-01-01

    The Columnea latent viroid (CLV) occurs latently in certain Columnea erythrophae plants grown commercially. In potato and tomato, CLV causes potato spindle tuber viroid (PSTV)-like symptoms. Its nucleotide sequence and proposed secondary structure reveal that CLV consists of a single-stranded circular RNA of 370 nucleotides which can assume a rod-like structure with extensive base-pairing characteristic of all known viroids. The electrophoretic mobility of circular CLV under nondenaturing con...

  4. Electronic structure of Cr1-dS (d=0,0.17) with NiAs-type crystal structure

    OpenAIRE

    Koyama, M; Sato, H; Ueda, Y.; Hirai, C.; Taniguchi, M.

    2002-01-01

    Valence-band and conduction-band electronic structure of CrS (d=0) and Cr5S6 (d=0.17) has been investigated by means of photoemission and inverse-photoemission spectroscopies. Bandwidth of the valence bands of Cr5S6 (8.5 eV) is wider than that of CrS (8.1 eV), though the Cr 3d partial density of states evaluated from the Cr 3p-3d resonant photoemission spectroscopy is almost unchanged between the two compounds with respect to the shapes including binding energies. The Cr 3d ...

  5. Structure and Sequence Search on Aptamer-Protein Docking

    Science.gov (United States)

    Xiao, Jiajie; Bonin, Keith; Guthold, Martin; Salsbury, Freddie

    2015-03-01

    Interactions between proteins and deoxyribonucleic acid (DNA) play a significant role in the living systems, especially through gene regulation. However, short nucleic acids sequences (aptamers) with specific binding affinity to specific proteins exhibit clinical potential as therapeutics. Our capillary and gel electrophoresis selection experiments show that specific sequences of aptamers can be selected that bind specific proteins. Computationally, given the experimentally-determined structure and sequence of a thrombin-binding aptamer, we can successfully dock the aptamer onto thrombin in agreement with experimental structures of the complex. In order to further study the conformational flexibility of this thrombin-binding aptamer and to potentially develop a predictive computational model of aptamer-binding, we use GPU-enabled molecular dynamics simulations to both examine the conformational flexibility of the aptamer in the absence of binding to thrombin, and to determine our ability to fold an aptamer. This study should help further de-novo predictions of aptamer sequences by enabling the study of structural and sequence-dependent effects on aptamer-protein docking specificity.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

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

    2014-01-01

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

  8. Sequence, Structure, and Network Evolution of Protein Phosphorylation

    Science.gov (United States)

    Chris Soon Heng Tan (Mount Sinai Hospital; Samuel Lunenfeld Research Institute REV)

    2011-07-19

    With the increasing amount of information about the phosphoproteomes of diverse organisms, it is now possible to begin to evaluate this information in the context of evolution. Work described at the inaugural Keystone Symposium on “The Evolution of Protein Phosphorylation” covered a wide range of eukaryotic and prokaryotic organisms, revealing insights into the evolution of protein phosphorylation at the sequence, network, and structural levels.

  9. Biophysical and structural considerations for protein sequence evolution

    Directory of Open Access Journals (Sweden)

    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.

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

    DEFF Research Database (Denmark)

    Kielpinski, Lukasz Jan

    2014-01-01

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

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

    CERN Document Server

    Recanati, Catherine; Bennani, Younès

    2007-01-01

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

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

    International Nuclear Information System (INIS)

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

  13. Finding Structure in Text, Genome and Other Symbolic Sequences

    OpenAIRE

    Dunning, Ted

    2012-01-01

    The statistical methods derived and described in this thesis provide new ways to elucidate the structural properties of text and other symbolic sequences. Generically, these methods allow detection of a difference in the frequency of a single feature, the detection of a difference between the frequencies of an ensemble of features and the attribution of the source of a text. These three abstract tasks suffice to solve problems in a wide variety of settings. Furthermore, the ...

  14. HSP: evolved and conserved proteins, structure and sequence studies

    OpenAIRE

    Desai N.S.; Agarwal A.A.; Uplap S.S.

    2010-01-01

    Heat shock proteins (HSPs) are the proteins which are present normally in the cell but theirexpression level increases under stress condition and are mainly divided into five groups, low molecularweight HSP (LMW HSP), HSP 60, HSP 70, HSP 90 and high molecular weight HSP (HMW HSP). All theseclasses of HSPs are highly conserved and ubiquitous in nature and hence serve as a good model forphylogenetic analysis. For the first time in this study,the sequence and structural analysis has been carried...

  15. Avocado sunblotch viroid: primary sequence and proposed secondary structure.

    OpenAIRE

    Symons, R H

    1981-01-01

    The sequence of the 247 nucleotide residues of the single strand circular RNA of avocado sunblotch viroid (ASBV) was determined using partial enzymic cleavage methods on overlapping viroid fragments obtained by partial ribonuclease digestion followed by 32p-labelling in vitro at their 5'-ends. ASBV is much smaller than potato spindle tuber viroid (PSTV; 359 residues) and chrysanthemum stunt viroid (CSV; 356 residues). A secondary structure model for ASBV is proposed and contains 67% of its re...

  16. Spectral Dependence of the Degree of Localization in a 1D Disordered System with a Complex Structural Unit

    OpenAIRE

    Kozlov, Gleb G.

    2011-01-01

    We analyze the spectral distribution of localisation in a 1D diagonally disordered chain of fragments each of which consist of m coupled two-level systems. The calculations performed by means of developed perturbation theory for joint statistics of advanced and retarded Green’s functions. We show that this distribution is rather inhomogeneous and reveals spectral regions of weakly localized states with sharp peaks of the localization degree in the centers of these regions.

  17. Exploring the sequence-structure relationship for amyloid peptides.

    Science.gov (United States)

    Morris, Kyle L; Rodger, Alison; Hicks, Matthew R; Debulpaep, Maya; Schymkowitz, Joost; Rousseau, Frederic; Serpell, Louise C

    2013-03-01

    Amyloid fibril formation is associated with misfolding diseases, as well as fulfilling a functional role. The cross-? molecular architecture has been reported in increasing numbers of amyloid-like fibrillar systems. The Waltz algorithm is able to predict ordered self-assembly of amyloidogenic peptides by taking into account the residue type and position. This algorithm has expanded the amyloid sequence space, and in the present study we characterize the structures of amyloid-like fibrils formed by three peptides identified by Waltz that form fibrils but not crystals. The structural challenge is met by combining electron microscopy, linear dichroism, CD and X-ray fibre diffraction. We propose structures that reveal a cross-? conformation with 'steric-zipper' features, giving insights into the role for side chains in peptide packing and stability within fibrils. The amenity of these peptides to structural characterization makes them compelling model systems to use for understanding the relationship between sequence, self-assembly, stability and structure of amyloid fibrils. PMID:23252554

  18. A case of Beauveria bassiana keratitis confirmed by internal transcribed spacer and LSU rDNA D1D2 sequencing

    OpenAIRE

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

    2014-01-01

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

  19. WildSpan: mining structured motifs from protein sequences

    Directory of Open Access Journals (Sweden)

    Chen Chien-Yu

    2011-03-01

    Full Text Available Abstract Background Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. Discovering such patterns is time-consuming because abundant combinations exist when long gaps (a gap consists of one or more successive wildcards are considered. Mining algorithms often employ constraints to narrow down the search space in order to increase efficiency. However, improper constraint models might degrade the sensitivity and specificity of the motifs discovered by computational methods. We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. The patterns that satisfy the proposed constraint model are called W-patterns. A W-pattern is a structured motif that groups motif symbols into pattern blocks interleaved with large irregular gaps. Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions that incorporates several pruning strategies to largely reduce the mining cost. Results WildSpan is shown to efficiently find W-patterns containing conserved residues that are far separated in sequences. We conducted experiments with two mining strategies, protein-based and family-based mining, to evaluate the usefulness of W-patterns and performance of WildSpan. The protein-based mining mode of WildSpan is developed for discovering functional regions of a single protein by referring to a set of related sequences (e.g. its homologues. The discovered W-patterns are used to characterize the protein sequence and the results are compared with the conserved positions identified by multiple sequence alignment (MSA. The family-based mining mode of WildSpan is developed for extracting sequence signatures for a group of related proteins (e.g. a protein family for protein function classification. In this situation, the discovered W-patterns are compared with PROSITE patterns as well as the patterns generated by three existing methods performing the similar task. Finally, analysis on execution time of running WildSpan reveals that the proposed pruning strategy is effective in improving the scalability of the proposed algorithm. Conclusions The mining results conducted in this study reveal that WildSpan is efficient and effective in discovering functional signatures of proteins directly from sequences. The proposed pruning strategy is effective in improving the scalability of WildSpan. It is demonstrated in this study that the W-patterns discovered by WildSpan provides useful information in characterizing protein sequences. The WildSpan executable and open source codes are available on the web (http://biominer.csie.cyu.edu.tw/wildspan.

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

    DEFF Research Database (Denmark)

    JØrgensen, Allan GrØnlund

    2010-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    Directory of Open Access Journals (Sweden)

    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 the full HOTAIR in mammals. Conclusions HOTAIR exists in mammals, has poorly conserved sequences and considerably conserved structures, and has evolved faster than nearby HoxC genes. Exons of HOTAIR show distinct evolutionary features, and a 239 bp domain in the 1804 bp exon6 is especially conserved. These features, together with the absence of some exons and sequences in mouse, rat and kangaroo, suggest ab initio generation of HOTAIR in marsupials. Structure prediction identifies two fragments in the 5' end exon1 and the 3' end domain B of exon6, with sequence and structure invariably occurring in various predicted structures of exon1, the domain B of exon6 and the full HOTAIR.

  3. Structural Correlates of Skilled Performance on a Motor Sequence Task

    Directory of Open Access Journals (Sweden)

    ChristopherJSteele

    2012-10-01

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

  4. Structural correlates of skilled performance on a motor sequence task.

    Science.gov (United States)

    Steele, Christopher J; Scholz, Jan; Douaud, Gwenaëlle; Johansen-Berg, Heidi; Penhune, Virginia B

    2012-01-01

    The brain regions functionally engaged in motor sequence performance are well-established, but the structural characteristics of these regions and the fiber pathways involved have been less well studied. In addition, relatively few studies have combined multiple magnetic resonance imaging (MRI) and behavioral performance measures in the same sample. Therefore, the current study used diffusion tensor imaging (DTI), probabilistic tractography, and voxel-based morphometry (VBM) to determine the structural correlates of skilled motor performance. Further, we compared these findings with fMRI results in the same sample. We correlated final performance and rate of improvement measures on a temporal motor sequence task (TMST) with skeletonized fractional anisotropy (FA) and whole brain gray matter (GM) volume. Final synchronization performance was negatively correlated with FA in white matter (WM) underlying bilateral sensorimotor cortex-an effect that was mediated by a positive correlation with radial diffusivity. Multi-fiber tractography indicated that this region contained crossing fibers from the corticospinal tract (CST) and superior longitudinal fasciculus (SLF). The identified SLF pathway linked parietal and auditory cortical regions that have been shown to be functionally engaged in this task. Thus, we hypothesize that enhanced synchronization performance on this task may be related to greater fiber integrity of the SLF. Rate of improvement on synchronization was positively correlated with GM volume in cerebellar lobules HVI and V-regions that showed training-related decreases in activity in the same sample. Taken together, our results link individual differences in brain structure and function to motor sequence performance on the same task. Further, our study illustrates the utility of using multiple MR measures and analysis techniques to specify the interpretation of structural findings. PMID:23125826

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

    International Nuclear Information System (INIS)

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

  6. Bulk anisotropic excitons in type-II semiconductors built with 1D and 2D low-dimensional structures

    Scientific Electronic Library Online (English)

    H.A., Coyotecatl; M. del, Castillo-Mussot; J.A., Reyes; G.J., Vázquez; J.A., Montemayor-Aldrete; J.A., Reyes-Esqueda; G.H., Cocoletzi.

    Full Text Available Utilizamos un método variacional para tomar en cuenta la diferencia entre las masas efectivas del electrón y del hueco en excitones Wannier-Mott en heteroestructuras semiconductoras tipo II en las que el electrón está constreñido en un alambre cuántico unidimensional (AC1D) y el hueco en un pozo cuá [...] ntico bidimensional (PC2D) perpendicular al alambre o viceversa. La ecuación de Schrödinger resultante es similar a la de un excitón en el bulto en 3D porque el número de variables libres (no confinadas) es tres; dos que provienen del PC2D y una del AC1D. En este sistema interacción efectiva electrón-hueco depende de los potenciales de confinamiento. Abstract in english We used a simple variational approach to account for the difference in the electron and hole effective masses in Wannier-Mott excitons in type-II semiconducting heterostructures in which the electron is constrained in an one-dimensional quantum wire (1DQW) and the hole is in a two-dimensional quantu [...] m layer (2DQL) perpendicular to the wire or viceversa. The resulting Schrödinger equation is similar to that of a 3D bulk exciton because the number of free (nonconfined) variables is three; two coming from the 2DQL and one from the 1DQW. In this system the effective electron-hole interaction depends on the confinement potentials.

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

    CERN Document Server

    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.

  8. Topological characterization of crystalline ice structures from coordination sequences

    CERN Document Server

    Herrero, Carlos P

    2013-01-01

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

  9. Systematic investigation of sequence and structural motifs that recognize ATP.

    Science.gov (United States)

    Chen, Ke; Wang, Dacheng; Kurgan, Lukasz

    2015-06-01

    Interaction between ATP, a multifunctional and ubiquitous nucleotide, and proteins initializes phosphorylation, polypeptide synthesis and ATP hydrolysis which supplies energy for metabolism. However, current knowledge concerning the mechanisms through which ATP is recognized by proteins is incomplete, scattered, and inaccurate. We systemically investigate sequence and structural motifs of proteins that recognize ATP. We identified three novel motifs and refined the known p-loop and class II aminoacyl-tRNA synthetase motifs. The five motifs define five distinct ATP-protein interaction modes which concern over 5% of known protein structures. We demonstrate that although these motifs share a common GXG tripeptide they recognize ATP through different functional groups. The p-loop motif recognizes ATP through phosphates, class II aminoacyl-tRNA synthetase motif targets adenosine and the other three motifs recognize both phosphates and adenosine. We show that some motifs are shared by different enzyme types. Statistical tests demonstrate that the five sequence motifs are significantly associated with the nucleotide binding proteins. Large-scale test on PDB reveals that about 98% of proteins that include one of the structural motifs are confirmed to bind ATP. PMID:25935117

  10. RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis

    OpenAIRE

    Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

    2012-01-01

    RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the bio...

  11. Novel 1D coordination polymer {Tm(Piv)3}n: Synthesis, structure, magnetic properties and thermal behavior

    Science.gov (United States)

    Fomina, Irina; Dobrokhotova, Zhanna; Aleksandrov, Grygory; Emelina, Anna; Bykov, Mikhail; Malkerova, Irina; Bogomyakov, Artem; Puntus, Lada; Novotortsev, Vladimir; Eremenko, Igor

    2012-01-01

    The new 1D coordination polymer {Tm(Piv)3}n (1), where Piv=OOCBut-, was synthesized in high yield (>95%) by the reaction of thulium acetate with pivalic acid in air at 100 °C. According to the X-ray diffraction data, the metal atoms in compound 1 are in an octahedral ligand environment unusual for lanthanides. The magnetic and luminescence properties of polymer 1, it's the solid-phase thermal decomposition in air and under argon, and the thermal behavior in the temperature range of -50…+50 °C were investigated. The vaporization process of complex 1 was studied by the Knudsen effusion method combined with mass-spectrometric analysis of the gas-phase composition in the temperature range of 570-680 K.

  12. Rational experiment design for sequencing-based RNA structure mapping.

    Science.gov (United States)

    Aviran, Sharon; Pachter, Lior

    2014-12-01

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

  13. Age-structured Trait Substitution Sequence Process and Canonical Equation

    CERN Document Server

    Méléard, Sylvie

    2007-01-01

    We are interested in a stochastic model of trait and age-structured population undergoing mutation and selection. We start with a continuous time, discrete individual-centered population process. Taking the large population and rare mutations limits under a well-chosen time-scale separation condition, we obtain a jump process that generalizes the Trait Substitution Sequence process describing Adaptive Dynamics for populations without age structure. Under the additional assumption of small mutations, we derive an age-dependent ordinary differential equation that extends the Canonical Equation. These evolutionary approximations have never been introduced to our knowledge. They are based on ecological phenomena represented by PDEs that generalize the Gurtin-McCamy equation in Demography. Another particularity is that they involve a fitness function, describing the probability of invasion of the resident population by the mutant one, that can not always be computed explicitly. Examples illustrate how adding an ag...

  14. Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE

    OpenAIRE

    Dandekar Thomas; Müller Tobias; Seibel Philipp N; Wolf Matthias

    2008-01-01

    Abstract Background The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural level than on the sequence level. Understanding the function of noncoding RNA sequence families requires two things: a hand-crafted or hand-improved alignment and detailed analyses of the secondary structures. There are several tools available that help performing these tasks, but all of them are...

  15. Chrysanthemum stunt viroid: primary sequence and secondary structure.

    OpenAIRE

    Haseloff, J.; Symons, R. H.

    1981-01-01

    The sequence of the 356 nucleotide residues of chrysanthemum stunt viroid (CSV) has been determined. Overlapping linear viroid fragments were obtained by partial ribonuclease digestion, radiolabelled in vitro at their 5'-ends, and sequenced using partial enzymic cleavage methods. Of the CSV sequence, 69% is contained in the published sequence of potato spindle tuber viroid (PSTV). Differences in the primary sequence of CSV and PSTV suggest that neither the positive nor putative negative stran...

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

    International Nuclear Information System (INIS)

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

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

    Directory of Open Access Journals (Sweden)

    Chen Ke

    2008-05-01

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

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

    Directory of Open Access Journals (Sweden)

    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.

  19. Iterative refinement of structure-based sequence alignments by Seed Extension

    OpenAIRE

    Lee Byungkook; Tai Chin-Hsien; Kim Changhoon

    2009-01-01

    Abstract Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available, but current structure-based sequence alignment procedures still mis-align substantial numbers of residues. In order to correct such errors, we previously explored the possibility of replacing the residue-based dynamic progra...

  20. Synthesis of 1 D, 2 D, and 3 D ZnO Polycrystalline Nano structures Using the Sol-Gel Method

    International Nuclear Information System (INIS)

    This study employed various polyol solvents to synthesize zinc oxide polycrystalline nano structures in the form of fibers (1 D), rhombic flakes (2 D), and spheres (3 D). The synthetic process primarily involved the use of zinc acetate dihydrate in polyol solutions, which were used to derive precursors of zinc alkoxides. Following hydrolysis at 160 degree C, the zinc alkoxide particles self-assembled into polycrystalline nano structures with different morphologies. Following calcination at 500 degree C for 1 h, polycrystalline ZnO with good crystallinity was obtained. FE-SEM explored variations in surface morphology; XRD was used to analyze the crystalline structures and crystallinity of the products, which were confirmed as ZnO wurtzite structures. FE-TEM verified that the ZnO nano structures were polycrystalline. Furthermore, we employed TGA/DSC to observe the phase transition. According to the results of property analyses, we proposed models of the relevant formation mechanisms. Finally, various ZnO structures were applied in the degradation of methylene blue to compare their photo catalytic efficiency.

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

    Directory of Open Access Journals (Sweden)

    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, development of protein structure and function analysis tools are a necessary endeavor. We have developed a useful application towards a solution to this problem using common structural and sequence based analysis tools. These approaches are able to find statistically significant environments in a database of protein structure, and the method is able to quantify how closely associated each environment is to a predicted functional annotation.

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

    CERN Document Server

    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.

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

    DEFF Research Database (Denmark)

    Woggon, U.; Gindele, F.

    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.

  4. Structural properties of replication origins in yeast DNA sequences

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

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

    Directory of Open Access Journals (Sweden)

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

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

    OpenAIRE

    Nemoto Wataru; Toh Hiroyuki

    2012-01-01

    Abstract Background The detection of conserved residue clusters on a protein structure is one of the effective strategies for the prediction of functional protein regions. Various methods, such as Evolutionary Trace, have been developed based on this strategy. In such approaches, the conserved residues are identified through comparisons of homologous amino acid sequences. Therefore, the selection of homologous sequences is a critical step. It is empirically known that a certain degree of sequ...

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

    Directory of Open Access Journals (Sweden)

    Kenji Nakatani

    2015-04-01

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    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. PMID:19430122

  11. Reversible switching of electronic ground state in a pentacoordinated Cu(II) 1D cationic polymer and structural diversity.

    Science.gov (United States)

    Sasmal, Ashok; Garribba, Eugenio; Rizzoli, Corrado; Mitra, Samiran

    2014-07-01

    Two copper(II) polymeric complexes {[Cu(HPymat)(MeOH)](NO3)}n (1) and {[Cu4(Pymab)4(H2O)4](NO3)4} (2) were synthesized with the carboxylate-containing Schiff-base ligands HPymat(-) and Pymab(-) [H2Pymat = (E)-2-(1-(pyridin-2-yl)methyleneamino)terephthalic acid, HPymab = (E)-2-((pyridine-2-yl)methyleneamino)benzoic acid]. Complex 1 is a one-dimensional Cu(II) cationic polymeric complex containing free protonated carboxylic groups and nitrate anions as counterions. Complex 2 is a zero-dimensional tetranuclear cationic Cu(II) complex containing nitrate anions as counterions. Complex 1 shows rhombic electron paramagnetic resonance (EPR) spectra in the solid state at room temperature (RT) and 77 K and tetragonal EPR spectra in dimethyl sulfoxide (DMSO) and dimethylformamide (DMF) and "inverse" EPR spectrum in CH3CN. Complex 2 shows rhombic EPR spectra in the solid state at RT and 77 K. But complex 2 shows tetragonal spectra in DMSO, DMF, and CH3CN. Thermogravimetric analysis was also performed for both complexes 1 and 2. Mean-square displacement amplitude analysis was carried out to detect librational disorder along the metal-ligand bonds in crystal structures. PMID:24911032

  12. RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis

    Science.gov (United States)

    Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

    2012-01-01

    RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. Availability http://www.cemb.edu.pk/sw.html Abbreviations RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language. PMID:23055611

  13. Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE

    Directory of Open Access Journals (Sweden)

    Dandekar Thomas

    2008-10-01

    Full Text Available Abstract Background The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural level than on the sequence level. Understanding the function of noncoding RNA sequence families requires two things: a hand-crafted or hand-improved alignment and detailed analyses of the secondary structures. There are several tools available that help performing these tasks, but all of them are specialized and focus on only one aspect, editing the alignment or plotting the secondary structure. The problem is both these tasks need to be performed simultaneously. Findings 4SALE is designed to handle sequence and secondary structure information of RNAs synchronously. By including a complete new method of simultaneous visualization and editing RNA sequences and secondary structure information, 4SALE enables to improve and understand RNA sequence and secondary structure evolution much more easily. Conclusion 4SALE is a step further for simultaneously handling RNA sequence and secondary structure information. It provides a complete new way of visual monitoring different structural aspects, while editing the alignment. The software is freely available and distributed from its website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de/

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

    OpenAIRE

    Dumontier Michel; Bader Gary D; Michalickova Katerina; Lieu Hao; Betel Doron; Isserlin Ruth; Wv, Hogue Christopher

    2002-01-01

    Abstract Background SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. Results SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence re...

  15. 4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

    OpenAIRE

    Schultz Jörg; Dandekar Thomas; Müller Tobias; Seibel Philipp N; Wolf Matthias

    2006-01-01

    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 ...

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

    OpenAIRE

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

    1994-01-01

    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...

  17. DNA structure influences sequence specific cleavage by bleomycin.

    OpenAIRE

    Nightingale, K. P.; Fox, K. R.

    1993-01-01

    We have examined the cleavage of several synthetic DNA sequences by iron(II)-bleomycin. We find that, although bleomycin cuts mixed sequence DNAs with a preference for GC = GT > GA >> GG, it efficiently cleaves regions of (AT)n cutting exclusively at ApT, not TpA. Isolated ApT steps show very little cleavage while blocks of three or more contiguous ATs are cut as efficiently as GpT. This cleavage is specific for (AT)n, since sequences of the type (TAA)n.(TTA)n and (ATT)n.(AAT)n are hardly cut...

  18. Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation

    DEFF Research Database (Denmark)

    Tian, Pengfei; Boomsma, Wouter

    2014-01-01

    Functional amyloid fibers, called curli, play a critical role in adhesion and invasion of many bacteria. Unlike pathological amyloids, curli structures are formed by polypeptide sequences whose amyloid structure has been selected for during evolution. This important distinction provides us with an opportunity to obtain structural insights from an unexpected source: the covariation of amino acids in sequences of different curli proteins. We used recently developed methods to extract amino acid contacts from a multiple sequence alignment of homologues of the curli subunit protein, CsgA. Together with an efficient force field, these contacts allow us to determine structural models of CsgA. We find that CsgA forms a ?-helical structure, where each turn corresponds to previously identified repeat sequences in CsgA. The proposed structure is validated by previously measured solid-state NMR, electron microscopy and X-ray diffraction data, and agrees with an earlier proposed model derived by complementary means.

  19. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

    OpenAIRE

    Ashkenazy, Haim; Erez, Elana; Martz, Eric; Pupko, Tal; Ben-Tal, Nir

    2010-01-01

    It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionary conservation of amino acid positions in proteins using an empirical Bayesian inference, starting from protein structure and sequence, respectively. Here, we present the new ver...

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

    Science.gov (United States)

    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

  1. RASS: a web server for RNA alignment in the joint sequence-structure space.

    Science.gov (United States)

    He, Gewen; Steppi, Albert; Laborde, Jose; Srivastava, Anuj; Zhao, Peixiang; Zhang, Jinfeng

    2014-07-01

    Comparison of ribonucleic acid (RNA) molecules is important for revealing their evolutionary relationships, predicting their functions and predicting their structures. Many methods have been developed for comparing RNAs using either sequence or three-dimensional (3D) structure (backbone geometry) information. Sequences and 3D structures contain non-overlapping sets of information that both determine RNA functions. When comparing RNA 3D structures, both types of information need to be taken into account. However, few methods compare RNA structures using both sequence and 3D structure information. Recently, we have developed a new method based on elastic shape analysis (ESA) that compares RNA molecules by combining both sequence and 3D structure information. ESA treats RNA structures as 3D curves with sequence information encoded on additional coordinates so that the alignment can be performed in the joint sequence-structure space. The similarity between two RNA molecules is quantified by a formal distance, geodesic distance. In this study, we implement a web server for the method, called RASS, to make it publicly available to research community. The web server is located at http://cloud.stat.fsu.edu/RASS/. PMID:24831547

  2. Thermal Solitons in 1d and 2d Anharmonic Lattices - Solectrons and the Organization of Non-Linear Fluctuations in Long-Living Dynamical Structures

    Science.gov (United States)

    Velarde, M. G.; Ebeling, W.; Chetverikov, A. P.

    2013-01-01

    We study the thermal excitation of intrinsic localized modes in the form of solitons in 1d and 2d anharmonic lattices at moderately high temperatures. Such finite-amplitude fluctuations form long-living dynamical structures with life-time in the pico-second range thus surviving a relatively long time in comparison to other thermal fluctuations. Further we discuss the influence of such long-living fluctuations on the dynamics of added excess free electrons. The atomic lattice units are treated as quasi-classical objects interacting by Morse forces and stochastically moving according to Langevin equations. In 2d the atoms are initially organized in a triangular lattice. The electron distributions are in a first estimate represented by equilibrium adiabatic distributions in the actual polarization fields. Computer simulations show that in 2d systems such excitations are moving with supersonic velocities along lattice rows oriented with the cristallographic axes. By following the electron distributions we have also been able to study the excitations of solectron type (electron-soliton dynamic bound states) and estimate their life times.

  3. Structure and Dynamics of Asymmetric Poly(styrene-b-1,4-isoprene) Diblock Copolymer under 1D and 2D Nanoconfinement.

    Science.gov (United States)

    Kipnusu, Wycliffe K; Elmahdy, Mahdy M; Mapesa, Emmanuel U; Zhang, Jianqi; Böhlmann, Winfried; Smilgies, Detlef-M; Papadakis, Christine M; Kremer, Friedrich

    2015-06-17

    The impact of 1- and 2-dimensional (2D) confinement on the structure and dynamics of poly(styrene-b-1,4-isoprene) P(S-b-I) diblock copolymer is investigated by a combination of Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), Grazing-Incidence Small-Angle X-ray Scattering (GISAXS), and Broadband Dielectric Spectroscopy (BDS). 1D confinement is achieved by spin coating the P(S-b-I) to form nanometric thin films on silicon substrates, while in the 2D confinement, the copolymer is infiltrated into cylindrical anodized aluminum oxide (AAO) nanopores. After dissolving the AAO matrix having mean pore diameter of 150 nm, the SEM images of the exposed P(S-b-I) show straight nanorods. For the thin films, GISAXS and AFM reveal hexagonally packed cylinders of PS in a PI matrix. Three dielectrically active relaxation modes assigned to the two segmental modes of the styrene and isoprene blocks and the normal mode of the latter are studied selectively by BDS. The dynamic glass transition, related to the segmental modes of the styrene and isoprene blocks, is independent of the dimensionality and the finite sizes (down to 18 nm) of confinement, but the normal mode is influenced by both factors with 2D geometrical constraints exerting greater impact. This reflects the considerable difference in the length scales on which the two kinds of fluctuations take place. PMID:25660102

  4. Structure and sequence of the gene encoding human keratocan.

    Science.gov (United States)

    Tasheva, E S; Funderburgh, J L; Funderburgh, M L; Corpuz, L M; Conrad, G W

    1999-01-01

    Keratocan is one of the three major keratan sulfate proteoglycans characteristically expressed in cornea. We have isolated cDNA and genomic clones and determined the sequence of the entire human keratocan (Kera) gene. The gene is spread over 7.65 kb of DNA and contains three exons. An open reading frame starting at the beginning of the second exon encodes a protein of 352 aa. The amino acid sequence of keratocan shows high identity among mammalian species. This evolutionary conservation between the keratocan proteins as well as the restricted expression of Kera gene in cornea suggests that this molecule might be important in developing and maintaining corneal transparency. PMID:10565548

  5. BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences

    OpenAIRE

    Piovesan, Damiano; Luigi Martelli, Pier; Fariselli, Piero; Zauli, Andrea; Rossi, Ivan; Casadio, Rita

    2011-01-01

    We introduce BAR-PLUS (BAR+), a web server for functional and structural annotation of protein sequences. BAR+ is based on a large-scale genome cross comparison and a non-hierarchical clustering procedure characterized by a metric that ensures a reliable transfer of features within clusters. In this version, the method takes advantage of a large-scale pairwise sequence comparison of 13?495?736 protein chains also including 988 complete proteomes. Available sequence annotation is derived f...

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

    Science.gov (United States)

    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

  7. Fraisse sequences: category-theoretic approach to universal homogeneous structures.

    Czech Academy of Sciences Publication Activity Database

    Kubi?, Wieslaw

    2014-01-01

    Ro?. 165, ?. 11 (2014), s. 1755-1811. ISSN 0168-0072 R&D Projects: GA ?R(CZ) GAP201/12/0290 Institutional support: RVO:67985840 Keywords : universal homogeneous object * Fraissé sequence * amalgamation Subject RIV: BA - General Mathematics Impact factor: 0.451, year: 2013 http://www.sciencedirect.com/science/article/pii/S0168007214000773

  8. The sexual inducer of Volvox carteri. Primary structure deduced from cDNA sequence

    OpenAIRE

    Mages, H. W.; Tschochner, H.; Sumper, Manfred

    1988-01-01

    The primary structure of the sexual inducer of Volvox carteri f. nagariensis has been deduced by cloning and sequence analysis of cDNA. The sexual inducer contains 208 amino acids including a signal sequence. A total of six potential N-glycosylation sites are found within the polypeptide chain. At the genomic level, the sexual inducer protein is encoded in five exons.

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

    OpenAIRE

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

    2006-01-01

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

  10. Structure and Evolution of Pre-Main Sequence Stars

    CERN Document Server

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

    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 ...

  11. Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance

    Directory of Open Access Journals (Sweden)

    Bansal Vikas

    2010-06-01

    Full Text Available Abstract Background Massively parallel DNA sequencing technologies have enabled the sequencing of several individual human genomes. These technologies are also being used in novel ways for mRNA expression profiling, genome-wide discovery of transcription-factor binding sites, small RNA discovery, etc. The multitude of sequencing platforms, each with their unique characteristics, pose a number of design challenges, regarding the technology to be used and the depth of sequencing required for a particular sequencing application. Here we describe a number of analytical and empirical results to address design questions for two applications: detection of structural variations from paired-end sequencing and estimating mRNA transcript abundance. Results For structural variation, our results provide explicit trade-offs between the detection and resolution of rearrangement breakpoints, and the optimal mix of paired-read insert lengths. Specifically, we prove that optimal detection and resolution of breakpoints is achieved using a mix of exactly two insert library lengths. Furthermore, we derive explicit formulae to determine these insert length combinations, enabling a 15% improvement in breakpoint detection at the same experimental cost. On empirical short read data, these predictions show good concordance with Illumina 200 bp and 2 Kbp insert length libraries. For transcriptome sequencing, we determine the sequencing depth needed to detect rare transcripts from a small pilot study. With only 1 Million reads, we derive corrections that enable almost perfect prediction of the underlying expression probability distribution, and use this to predict the sequencing depth required to detect low expressed genes with greater than 95% probability. Conclusions Together, our results form a generic framework for many design considerations related to high-throughput sequencing. We provide software tools http://bix.ucsd.edu/projects/NGS-DesignTools to derive platform independent guidelines for designing sequencing experiments (amount of sequencing, choice of insert length, mix of libraries for novel applications of next generation sequencing.

  12. Optimal sequence selection in proteins of known structure by simulated evolution.

    OpenAIRE

    Hellinga, H W; Richards, F. M.

    1994-01-01

    Rational design of protein structure requires the identification of optimal sequences to carry out a particular function within a given backbone structure. A general solution to this problem requires that a potential function describing the energy of the system as a function of its atomic coordinates be minimized simultaneously over all available sequences and their three-dimensional atomic configurations. Here we present a method that explicitly minimizes a semiempirical potential function s...

  13. Data mining for important amino acid residues in multiple sequence alignments and protein structures

    OpenAIRE

    Janda, Jan-oliver

    2014-01-01

    Enzymes are highly efficient bio-catalysts interesting for industries and medicine. Therefore, a goal of utmost importance in biochemical research is to understand how an enzyme catalyzes a chemical reaction. Here, the computational identification of functionally or structurally important residue positions can be of tremendous help. The datasets that are most informative for the algorithms are the 3D structure of a protein and a multiple sequence alignment (MSA) composed of homologous sequenc...

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

    Directory of Open Access Journals (Sweden)

    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 significance threshold are shown to be more accurate for TurboFold than for alternative methods that estimate base pairing probabilities. TurboFold-MEA, which uses base pairing probabilities from TurboFold in a maximum expected accuracy algorithm for secondary structure prediction, has accuracy comparable to the best performing secondary structure prediction methods. The computational and memory requirements for TurboFold are modest and, in terms of sequence length and number of sequences, scale much more favorably than joint alignment and folding algorithms. Conclusions TurboFold is an iterative probabilistic method for predicting secondary structures for multiple RNA sequences that efficiently and accurately combines the information from the comparative analysis between sequences with the thermodynamic folding model. Unlike most other multi-sequence structure prediction methods, TurboFold does not enforce strict commonality of structures and is therefore useful for predicting structures for homologous sequences that have diverged significantly. TurboFold can be downloaded as part of the RNAstructure package at http://rna.urmc.rochester.edu.

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

    CERN Document Server

    Gorban, A N; Zinovyev, A Yu

    2011-01-01

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

  16. Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.

    Science.gov (United States)

    Moncunill, Valentí; Gonzalez, Santi; Beà, Sílvia; Andrieux, Lise O; Salaverria, Itziar; Royo, Cristina; Martinez, Laura; Puiggròs, Montserrat; Segura-Wang, Maia; Stütz, Adrian M; Navarro, Alba; Royo, Romina; Gelpí, Josep L; Gut, Ivo G; López-Otín, Carlos; Orozco, Modesto; Korbel, Jan O; Campo, Elias; Puente, Xose S; Torrents, David

    2014-11-01

    The development of high-throughput sequencing technologies has advanced our understanding of cancer. However, characterizing somatic structural variants in tumor genomes is still challenging because current strategies depend on the initial alignment of reads to a reference genome. Here, we describe SMUFIN (somatic mutation finder), a single program that directly compares sequence reads from normal and tumor genomes to accurately identify and characterize a range of somatic sequence variation, from single-nucleotide variants (SNV) to large structural variants at base pair resolution. Performance tests on modeled tumor genomes showed average sensitivity of 92% and 74% for SNVs and structural variants, with specificities of 95% and 91%, respectively. Analyses of aggressive forms of solid and hematological tumors revealed that SMUFIN identifies breakpoints associated with chromothripsis and chromoplexy with high specificity. SMUFIN provides an integrated solution for the accurate, fast and comprehensive characterization of somatic sequence variation in cancer. PMID:25344728

  17. Cocompact imbeddings and structure of weakly convergent sequences

    CERN Document Server

    Tintarev, Kyril

    2008-01-01

    Concentration compactness method is a powerful techniques for establishing existence of minimizers for inequalities and of critical points of functionals in general. The paper gives a functional-analytic formulation for the method in Banach space, generalizing the Hilbert space case elaborated in \\cite{ccbook}. The key object is a dislocation space - a triple $(X,F,D)$, where $F$ is a convex functional that defines a norm on Banach space $X$, and $D$ is a group of isometries on $X$. Bounded sequences in dislocation spaces admit a decomposition into an asymptotic sum "profiles" $w^{(n)}\\in X$ dislocated by actions of $D$, that is, a sum of the form $\\sum_ng^{(n)}_kw^{(n)}$, $g^{(n)}_k\\in D$, while the remainder term converges weakly under actions of any sequence $g_k\\in D$ ({\\em $D$-weak convergence}). This decomposition allows to extend the weak convergence argument from variational problems with compactness to problems where $X$ is {\\em cocompactly} (relatively to the group $D$) imbedded into a Banach space ...

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

    Science.gov (United States)

    Zhang, Yang; Ponty, Yann; Blanchette, Mathieu; Lécuyer, Eric; Waldispühl, Jérôme

    2013-07-01

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

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

    Directory of Open Access Journals (Sweden)

    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 to current similarity search methods.

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

    International Nuclear Information System (INIS)

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

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

    Directory of Open Access Journals (Sweden)

    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 ? sheet.

  2. Chromatin structure characteristics of pre-miRNA genomic sequences

    OpenAIRE

    Teng Mingxiang; Liu Bo; Wang Guohua; Jiang Qinghua; Zhu Shijia; Wang Yadong

    2011-01-01

    Abstract Background MicroRNAs (miRNAs) are non-coding RNAs with important roles in regulating gene expression. Recent studies indicate that transcription and cleavage of miRNA are coupled, and that chromatin structure may influence miRNA transcription. However, little is known about the relationship between the chromatin structure and cleavage of pre-miRNA from pri-miRNA. Results By analysis of genome-wide nucleosome positioning data sets from human and Caenorhabditis elegans (C. elegans), we...

  3. 1D Aging

    OpenAIRE

    Fontes, L. R.; Isopi, M.; Newman, C. M.; Stein, D. L.

    2001-01-01

    We derive exact expressions for a number of aging functions that are scaling limits of non-equilibrium correlations, R(tw,tw+t) as tw --> infinity with t/tw --> theta, in the 1D homogenous q-state Potts model for all q with T=0 dynamics following a quench from infinite temperature. One such quantity is (the two-point, two-time correlation function) when n/sqrt(tw) --> z. Exact, closed-form expressions are also obtained when one or more interludes of infinite temperature dyn...

  4. Flexible structural protein alignment by a sequence of local transformations

    OpenAIRE

    Rocha, Jairo; Segura, Joan; Wilson, Richard C.; Dasgupta, Swagata

    2009-01-01

    Motivation: Throughout evolution, homologous proteins have common regions that stay semi-rigid relative to each other and other parts that vary in a more noticeable way. In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that are reliable and easy to use.

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

    Science.gov (United States)

    Pollastri, Gianluca; Martin, Alberto JM; Mooney, Catherine; Vullo, Alessandro

    2007-01-01

    Background Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to known structures is available. Structural properties are also routinely used in protein analysis even when homology is available, largely because homology modelling is lower throughput than, say, secondary structure prediction. Nonetheless, predictors of secondary structure and solvent accessibility are virtually always ab initio. Results Here we develop high-throughput machine learning systems for the prediction of protein secondary structure and solvent accessibility that exploit homology to proteins of known structure, where available, in the form of simple structural frequency profiles extracted from sets of PDB templates. We compare these systems to their state-of-the-art ab initio counterparts, and with a number of baselines in which secondary structures and solvent accessibilities are extracted directly from the templates. We show that structural information from templates greatly improves secondary structure and solvent accessibility prediction quality, and that, on average, the systems significantly enrich the information contained in the templates. For sequence similarity exceeding 30%, secondary structure prediction quality is approximately 90%, close to its theoretical maximum, and 2-class solvent accessibility roughly 85%. Gains are robust with respect to template selection noise, and significant for marginal sequence similarity and for short alignments, supporting the claim that these improved predictions may prove beneficial beyond the case in which clear homology is available. Conclusion The predictive system are publicly available at the address . PMID:17570843

  6. Evolutionary Analyses of DNA Sequences Subject to Constraints on Secondary Structure

    OpenAIRE

    Muse, S. V.

    1995-01-01

    Evolutionary models appropriate for analyzing nucleotide sequences that are subject to constraints on secondary structure are developed. The models consider the evolution of pairs of nucleotides, and they incorporate the effects of base-pairing constraints on nucleotide substitution rates by introducing a new parameter to extensions of standard models of sequence evolution. To illustrate some potential uses of the models, a likelihood-ratio test is constructed for the null hypothesis that two...

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

    OpenAIRE

    Lindblad-toh, K.; Wade, Cm; Mikkelsen, Ts; Karlsson, Ek; Jaffe, Db; Kamal, M.; Clamp, M.; Chang, Jl; Kulbokas, Ej; Zody, Mc; Mauceli, E.; Xie, X.; Breen, M.; Wayne, Rk; Ostrander, Ea

    2005-01-01

    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 geno...

  8. Structure of the baboon endogenous virus genome: nucleotide sequences of the long terminal repeat.

    OpenAIRE

    Tamura, T.; Noda, M.; Takano, T.

    1981-01-01

    The entire nucleotide sequence of the long terminal repeat (LTR) of baboon endogenous virus (BaEV) M7 was determined, which consisted of 554 base pairs (bp). At both ends of the LTR, 13 bp sequences, AAATGAAAAGTAA and TGATTCTAACATC, were detected to be inverted repeats. The structure with these inverted repeats resembles those of other retroviruses and transposable elements. a Hogness box, TATAAAA, and a putative poly(A)-addition signal, AGTAAA, were present within the right-hand half of the...

  9. Overview of PSB track on gene structure identification in large-scale genomic sequence

    Energy Technology Data Exchange (ETDEWEB)

    Uberbacher, E.C.; Xu, Y.

    1998-12-31

    The recent funding of more than a dozen major genome centers to begin community-wide high-throughput sequencing of the human genome has created a significant new challenge for the computational analysis of DNA sequence and the prediction of gene structure and function. It has been estimated that on average from 1996 to 2003, approximately 2 million bases of newly finished DNA sequence will be produced every day and be made available on the Internet and in central databases. The finished (fully assembled) sequence generated each day will represent approximately 75 new genes (and their respective proteins), and many times this number will be represented in partially completed sequences. The information contained in these is of immeasurable value to medical research, biotechnology, the pharmaceutical industry and researchers in a host of fields ranging from microorganism metabolism, to structural biology, to bioremediation. Sequencing of microorganisms and other model organisms is also ramping up at a very rapid rate. The genomes for yeast and several microorganisms such as H. influenza have recently been fully sequenced, although the significance of many genes remains to be determined.

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

    Directory of Open Access Journals (Sweden)

    Kondrashov Fyodor A

    2007-11-01

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

  11. 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...

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

    International Nuclear Information System (INIS)

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

  13. Implicit Sequence Learning: Effects of Level of Structure, Adult Age, and Extended Practice

    OpenAIRE

    Howard, Darlene V.; Howard, James H.; Japikse, Karin; Diyanni, Cara; Thompson, Amanda; Somberg, Rachel

    2004-01-01

    The influence of structure and age on sequence learning was investigated by testing 24 young and 24 older participants for 10 sessions in an alternating serial response time task in which pattern trials alternated with random trials. Individuals encountered lag-2 or lag-3 structure, and learning was measured by the difference (in response time and accuracy) between pattern and random trials. Both ages learned lag-2 structure, but the young learned more than the older participants. Only the yo...

  14. On the internal structure of main-sequence stars

    International Nuclear Information System (INIS)

    The authors present the main results of a study of the observed internal structure constants, k2, for a wide set of eclipsing binaries. From the analysis of the variations in relative positions of the eclipses and the comparison with different theoretical models, they could deduce that the discrepancy, previously reported by several authors between theory and observations, is no longer supported. Moreover, a strong correlation has been found between the evolution of the parameter k2 and the gravity at the surface of the star, g. (Auth.)

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

    DEFF Research Database (Denmark)

    Marie, Rodolphe; Pedersen, Jonas Nyvold

    2013-01-01

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

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

    OpenAIRE

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

    1991-01-01

    Polypeptide chains of 19 previously studied Escherichia coli aminoacyl-tRNA synthetases are as large as 951 amino acids and, depending on the enzyme, have quaternary structures of alpha, alpha 2, alpha 2 beta 2, and alpha 4. These enzymes have been organized into two classes which are defined by sequence motifs that are associated with specific three-dimensional structures. We isolated, cloned, and sequenced the previously uncharacterized gene for E. coli cysteine-tRNA synthetase (EC 6.1.1.16...

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

    Science.gov (United States)

    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

  18. R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

    Science.gov (United States)

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

    2015-01-01

    The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

  19. Sequence divergence of Entamoeba histolytica tubulin is responsible for its altered tertiary structure

    International Nuclear Information System (INIS)

    Atypical microtubular structures of the protozoan parasite Entamoeba histolytica (Eh) have been attributed to amino acid sequence divergence of Eh tubulin. To investigate if this sequence divergence leads to significant differences in the tertiary structure of the Eh ??-tubulin heterodimer, we have modeled ??-tubulin heterodimer of Eh based on the crystal structure of mammalian tubulin. The predicted 3D homology model exhibits an overall resemblance with the known crystal structure of mammalian tubulin except for the 16 residue long carboxy terminal region of Eh ?-tubulin. We propose that this C-terminal region may provide steric hindrance in the polymerization of Eh ??-tubulin for microtubule formation. Using docking studies, we have identified the binding sites for different microtubule specific drugs on Eh ?-tubulin. Our model provides a rational framework, both for understanding the contribution of Eh?-tubulin C-terminal region to ??-tubulin polymerization and design of new anti-protozoan drugs in order to control amoebiasis

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

    Directory of Open Access Journals (Sweden)

    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.

  1. The Continental Margin of Morocco: Seismic Sequences, Structural Elements and the Geological Development

    OpenAIRE

    Hinz, K; Dostmann, H; Fritsch, J

    1981-01-01

    Seismic sequences, structural elements and the geological development of the Moroccan continental margin, which is subdivided from the south to the north into the North Tarfaya segment, the Tafelney Plateau, the Essaouira segment the Mazagan Plateau, the Prerif segment, are discussed.

  2. Analysis of Developmental Sequences within the Structural Approach: Conceptual, Empirical, and Methodological Considerations.

    Science.gov (United States)

    Schroder, Eberhard; Edelstein, Wolfgang

    In this paper conceptual and methodological issues in the analysis of developmental sequences are discussed. Conceptually, the reconstruction of the logic of acquisition calls for the use of task or structure analysis. Methodologically, it calls for an individual-oriented approach, the use of statement calculus for formulation of the postulated…

  3. Viroids: From Genotype to Phenotype Just Relying on RNA Sequence and Structural Motifs

    OpenAIRE

    RicardoFlores; FrancescoDi Serio

    2012-01-01

    As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson–Crick pairs are flanked by apparently unstructured loops. However, comp...

  4. Three-dimensional hydrogel structures as optical sensor arrays, for the detection of specific DNA sequences

    OpenAIRE

    Kivlehan, F.; Paolucci, M.; Brennan, D.; Ragoussis, I.; Galvin, P.

    2012-01-01

    The fabrication and characterization of surface-attached PEG-diacrylate hydrogel structures and their application as sensing platforms for the detection of specific target sequences are reported. Hydrogel structures were formed by a photopolymerization process, using substrate-bound Eosin Y molecules for the production of free radicals. We have demonstrated that this fabrication process allows for control over hydrogel growth down to the micrometer scale. Confocal imaging revealed relatively ...

  5. Examining protein surface structure in highly conserved sequence variants with mass spectrometry.

    Science.gov (United States)

    Tao, Yuanqi; Julian, Ryan R

    2012-02-28

    A simple mass spectrometry-based method capable of examining protein structure called SNAPP (selective noncovalent adduct protein probing) is used to evaluate the structural consequences of point mutations in naturally occurring sequence variants from different species. SNAPP monitors changes in the attachment of noncovalent adducts to proteins as a function of structural state. Mutations that lead to perturbations to the electrostatic surface structure of a protein affect noncovalent attachment and are easily observed with SNAPP. Mutations that do not alter the tertiary structure or electrostatic surface structure yield similar results by SNAPP. For example, bovine, porcine, and human insulin all have very similar backbone structures and no basic or acidic residue mutations, and the SNAPP distributions for all three proteins are very similar. In contrast, four variants of cytochrome c (cytc) have varying degrees of sequence homology, which are reflected in the observed SNAPP distributions. Bovine and pigeon cytc have several basic or acidic residue substitutions relative to horse cytc, but the SNAPP distributions for all three proteins are similar. This suggests that these mutations do not significantly influence the protein surface structure. On the other hand, yeast cytc has the least sequence homology and exhibits a unique, though related, SNAPP distribution. Even greater differences are observed for lysozyme. Hen and human lysozyme have identical tertiary structures but significant variations in the locations of numerous basic and acidic residues. The SNAPP distributions are quite distinct for the two forms of lysozyme, suggesting significant differences in the surface structures. In summary, SNAPP experiments are relatively easy to perform, require minimal sample consumption, and provide a facile route for comparison of protein surface structure between highly homologous proteins. PMID:22320248

  6. Examining Protein Surface Structure in Highly Conserved Sequence Variants with Mass Spectrometry‡

    Science.gov (United States)

    Tao, Yuanqi; Julian, Ryan R.

    2012-01-01

    A simple mass spectrometry based method capable of examining protein structure called SNAPP (selective noncovalent adduct protein probing) is used to evaluate the structural consequences of point mutations in naturally occurring sequence variants from different species. SNAPP monitors changes in the attachment of noncovalent adducts to proteins as a function of structural state. Mutations which lead to perturbations to the electrostatic surface structure of a protein affect noncovalent attachment and are easily observed with SNAPP. Mutations which do not alter the tertiary structure or electrostatic surface structure yield similar results by SNAPP. For example, bovine, porcine, and human insulin all have very similar backbone structures and no basic or acidic residue mutations, and the SNAPP distributions for all three proteins are very similar. In contrast, four variants of cytochrome c (cytc) have varying degrees of sequence homology, which are reflected in the observed SNAPP distributions. Bovine and pigeon cytc have several basic or acidic residue substitutions relative to horse cytc, but the SNAPP distributions for all three proteins are similar. This suggests that these mutations do not significantly influence the protein surface structure. On the other hand, yeast cytc has the least sequence homology and exhibits a unique, though related, SNAPP distribution. Even greater differences are observed for lysozyme. Hen and human lysozyme have identical tertiary structures, but significant variations in the locations of numerous basic and acidic residues. The SNAPP distributions are quite distinct for the two forms of lysozyme, suggesting significant differences in the surface structures. In summary, SNAPP experiments are relatively easy to perform, require minimal sample consumption, and provide a facile route for comparison of protein surface structure between highly homologous proteins. PMID:22320248

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

    Energy Technology Data Exchange (ETDEWEB)

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

    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.

  8. 1D transfer matrices

    Energy Technology Data Exchange (ETDEWEB)

    Perez-Alvarez, R.; Garcia-Moliner, F. [University ' Jaume I' , Castellon de la Plana (Spain)]. E-mails: perez@exp.uji.es; garmol@ext.uji.es; Trallero-Herrero, C. [University ' Jaume I' , Castellon de la Plana (Spain)

    2001-07-01

    Many problems of physical interest - for instance, in statistical mechanics - are described by linear ordinary second-order differential systems for which different types of transfer matrices can be introduced and used. Focusing on heterostructures where matching at interfaces is involved, this paper discusses two of them with emphasis on one, here denoted T, which involves the linear differential form expressing the physical quantities matched at the interfaces. The mathematical background is summarized in a simple way and then T is used to study two types of heterostructures involving a large number of interfaces. Firstly, the regular periodic superlattices are studied and the role of different boundary conditions (BCs) at the end of one period is discussed. Only periodic BCs are suitable to study a simple regular superlattices but the discussion provides the background to study different approximants when the period is a largish generation of a quasi-regular heterostructure, like, for instance, a Fibonacci sequence. (author)

  9. [Sequence variation and protein structure of pipo gene in Potato virus Y].

    Science.gov (United States)

    Gao, Fang-Luan; Shen, Jian-Guo; Shi, Feng-Yang; Chang, Fei; Xie, Lian-Hui; Zhan, Jia-Sui

    2013-09-01

    The objectives of this study were to understand the sequence variation and the putative protein structure of pipo gene in the Potato virus Y (PVY) collected from Solanum tuberosum. The pipo gene in PVY was cloned using a pair of degenerate primers designed from its conserved region and its sequences were used to re-construct phylogenetic tree in Potyvirus genera by a Bayesian inference method. An expected fragment of 235 bp was amplified in all 20 samples by RT-PCR and the pipo genes in the 20 samples assayed shared more than 92% nucleotide sequence similarity with the published sequences of PVY strains. Among the 20 pipo gene sequences, 13 polymorphic sites were detected, including 4 parsimony informative sites and 9 singleton variable sites. These results indicate that PVY pipo gene is highly conserved but some sequence variations exist. Further analyses suggest that the pipo gene encodes a hydrophilic protein without signal peptide and transmembrane region. The protein has theoretical isoelectric points (pI) ranging from 11.26 to 11.62 and contains three highly conserved regions, especially between aa 10 and 59. The protein is likely located in the mitochondria and has a-helix secondary structure. Bayesian inference of phylogenetic trees reveals that PVY isolates are clustered in the same branch with high posterior probability, while Sunflower chlorotic mottle virus (SoCMoV) and Pepper severe mosaic virus (PepSMV) are closely related, consisting with the classification of Potyvirus genera using other approaches. Our analyses suggest that the pipo gene can be a new marker for phylogenetic analysis of the genera. The results reported in this paper provide useful insights in the genetic variation and the evolution of PVY and can stimulate further research on structure and function of the PIPO protein. PMID:24400487

  10. Sequence and structural analysis of two designed proteins with 88% identity adopting different folds.

    Science.gov (United States)

    Saravanan, K Mani; Balasubramanian, Harihar; Nallusamy, Saranya; Samuel, Selvaraj

    2010-12-01

    Protein folding is a natural phenomenon by which a sequence of amino acids folds into a unique functional three-dimensional structure. Although the sequence code that governs folding remains a mystery, one can identify key inter-residue contacts responsible for a given topology. In nature, there are many pairs of proteins of a given length that share little or no sequence identity. Similarly, there are many proteins that share a common topology but lack significant evidence of homology. In order to tackle this problem, protein engineering studies have been used to determine the minimal number of amino acid residues that codes for a particular fold. In recent years, the coupling of theoretical models and experiments in the study of protein folding has resulted in providing some fruitful clues. He et al. have designed two proteins with 88% sequence identity, which adopt different folds and functions. In this work, we have systematically analysed these two proteins by performing pentapeptide search, secondary structure predictions, variation in inter-residue interactions and residue-residue pair preferences, surrounding hydrophobicity computations, conformational switching and energy computations. We conclude that the local secondary structural preference of the two designed proteins at the Nand C-terminal ends to adopt either coil or strand conformation may be a crucial factor in adopting the different folds. Early on during the process of folding, both proteins may choose different energetically favourable pathways to attain the different folds. PMID:20952437

  11. Inferring Aftershock Sequence Properties and Tectonic Structure Using Empirical Signal Detectors

    Science.gov (United States)

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

    2015-02-01

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

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

    DEFF Research Database (Denmark)

    Lindgreen, Stinus

    2010-01-01

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

  13. Population structure of Lactobacillus helveticus isolates from naturally fermented dairy products based on multilocus sequence typing.

    Science.gov (United States)

    Sun, Zhihong; Liu, Wenjun; Song, Yuqin; Xu, Haiyan; Yu, Jie; Bilige, Menghe; Zhang, Heping; Chen, Yongfu

    2015-05-01

    Lactobacillus helveticus is an economically important lactic acid bacterium used in industrial dairy fermentation. In the present study, the population structure of 245 isolates of L. helveticus from different naturally fermented dairy products in China and Mongolia were investigated using an multilocus sequence typing scheme with 11 housekeeping genes. A total of 108 sequence types were detected, which formed 8 clonal complexes and 27 singletons. Results from Structure, SplitsTree, and ClonalFrame software analyses demonstrated the presence of 3 subpopulations in the L. helveticus isolates used in our study, namely koumiss, kurut-tarag, and panmictic lineages. Most L. helveticus isolates from particular ecological origins had specific population structures. PMID:25726109

  14. Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures.

    Science.gov (United States)

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

    2005-01-01

    The structure of a closely integrated data warehouse is described that is designed to link different types and varying numbers of biological networks, sequence analysis methods and experimental results such as those coming from microarrays. The data schema is inspired by a combination of graph based methods and generalised data structures and makes use of ontologies and meta-data. The core idea is to consider and store biological networks as graphs, and to use generalised data structures (GDS) for the storage of further relevant information. This is possible because many biological networks can be stored as graphs: protein interactions, signal transduction networks, metabolic pathways, gene regulatory networks etc. Nodes in biological graphs represent entities such as promoters, proteins, genes and transcripts whereas the edges of such graphs specify how the nodes are related. The semantics of the nodes and edges are defined using ontologies of node and relation types. Besides generic attributes that most biological entities possess (name, attribute description), further information is stored using generalised data structures. By directly linking to underlying sequences (exons, introns, promoters, amino acid sequences) in a systematic way, close interoperability to sequence analysis methods can be achieved. This approach allows us to store, query and update a wide variety of biological information in a way that is semantically compact without requiring changes at the database schema level when new kinds of biological information is added. We describe how this datawarehouse is being implemented by extending the text-mining framework ONDEX to link, support and complement different bioinformatics applications and research activities such as microarray analysis, sequence analysis and modelling/simulation of biological systems. The system is developed under the GPL license and can be downloaded from http://sourceforge.net/projects/ondex/ PMID:15972003

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

    CERN Document Server

    Backelin, Erik

    2009-01-01

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

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

    International Nuclear Information System (INIS)

    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.

  17. Similarity landscapes: a way to detect many structural and sequence motifs in both introns and exons.

    Science.gov (United States)

    Hultner, M; Smith, D W; Wills, C

    1994-02-01

    When investigators undertake searches of DNA databases, they normally discard large numbers of alignments that demonstrate very weak resemblances to each other, retaining only those that show statistically significant levels of resemblance. We show here that a great deal of information can be extracted from these weak alignments by examining them en masse. This is done by building three-dimensional similarity landscapes from the alignments, landscapes that reveal whether an unusual number of individually nonsignificant alignments tend to match up to a particular region of the query sequence being searched. The power of the search is increased by the use of libraries consisting entirely of introns or of exons. We show that (1) similarity landscapes with a variety of features can be generated from both intron and exon libraries, using introns or exons as query sequences; (2) the landscape features are real and not a statistical artifact; (3) well-known protein motifs used as query sequences can generate various landscape features; and (4) there is some evidence for resemblances between short regions of sequence carried by introns and exons. One possible interpretation of these results is that both introns and exons may have been built up during their evolution from short regions of sequence that as a result are now widely distributed throughout eukaryotic genomes. Such an interpretation would imply that these short regions have common ancestry. Alternatively, the wide sharing of short pieces of DNA may reflect regions with particular structural properties that have arisen through convergent evolution. The similarity-landscape approach can be used to detect such widespread structural motifs and sequence motifs in the genome that might be missed by less-global searches. It can also be used in conjunction with algorithms developed for detecting significant multiple alignments by isolating promising subsets of the databases that can be examined in more detail. PMID:8169961

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

    Directory of Open Access Journals (Sweden)

    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 structurally conserved residues is already available on request and will be soon accessible on our web server. The procedure is intended for the use of pattern database curators and of scientists interested in a specific protein family for which no specific or selective patterns are yet available.

  19. Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

    Directory of Open Access Journals (Sweden)

    Dowell Robin D

    2006-09-01

    Full Text Available Abstract Background We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. Results We use probabilistic models (pair stochastic context-free grammars, pairSCFGs as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins. These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. Conclusion Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm – this work (Consan, David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN – have comparable overall performance with different strengths and weaknesses.

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

    International Nuclear Information System (INIS)

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

  1. Can We Improve Structured Sequence Processing? Exploring the Direct and Indirect Effects of Computerized Training Using a Mediational Model

    Science.gov (United States)

    Smith, Gretchen N. L.; Conway, Christopher M.; Bauernschmidt, Althea; Pisoni, David B.

    2015-01-01

    Recent research suggests that language acquisition may rely on domain-general learning abilities, such as structured sequence processing, which is the ability to extract, encode, and represent structured patterns in a temporal sequence. If structured sequence processing supports language, then it may be possible to improve language function by enhancing this foundational learning ability. The goal of the present study was to use a novel computerized training task as a means to better understand the relationship between structured sequence processing and language function. Participants first were assessed on pre-training tasks to provide baseline behavioral measures of structured sequence processing and language abilities. Participants were then quasi-randomly assigned to either a treatment group involving adaptive structured visuospatial sequence training, a treatment group involving adaptive non-structured visuospatial sequence training, or a control group. Following four days of sequence training, all participants were assessed with the same pre-training measures. Overall comparison of the post-training means revealed no group differences. However, in order to examine the potential relations between sequence training, structured sequence processing, and language ability, we used a mediation analysis that showed two competing effects. In the indirect effect, adaptive sequence training with structural regularities had a positive impact on structured sequence processing performance, which in turn had a positive impact on language processing. This finding not only identifies a potential novel intervention to treat language impairments but also may be the first demonstration that structured sequence processing can be improved and that this, in turn, has an impact on language processing. However, in the direct effect, adaptive sequence training with structural regularities had a direct negative impact on language processing. This unexpected finding suggests that adaptive training with structural regularities might potentially interfere with language processing. Taken together, these findings underscore the importance of pursuing designs that promote a better understanding of the mechanisms underlying training-related changes, so that regimens can be developed that help reduce these types of negative effects while simultaneously maximizing the benefits to outcome measures of interest. PMID:25946222

  2. Multifractal properties of the structure factor of a class of substitutional sequences

    International Nuclear Information System (INIS)

    We show how to estimate the multifractal generating functional of the structure factor of a class of substitutional sequences. These sequences are sequences of two elements, a and b, and are generated by the repetitive application of the rules a??1(a,b) and b??2(a,b), with the ?'s consisting of strings of a's and b's. We restrict ourselves to the case in which ?1 and ?2 each contain R elements. This set includes the case of the Thue-Morse sequence. Subject to a technical assumption, we present a systematic approximation scheme for the multifractal generating functional, in which the lowest-order approximation is the generating functional of an R-scale Cantor set. As a by-product of our analysis, we demonstrate the existence of a discontinuity in the multifractal spectrum of the Thue-Morse sequence, and explain the origin of that discontinuity. We present explicit results for two examples, including the Thue-Morse case, and compare the results of our approximations for the Thue-Morse system with numerical simulations

  3. Structure of Moloney murine leukemia viral DNA: nucleotide sequence of the 5' long terminal repeat and adjacent cellular sequences.

    OpenAIRE

    Beveren, C.; Goddard, J. G.; Berns, A.; Verma, I. M.

    1980-01-01

    Some unintegrated and all integrated forms of murine leukemia viral DNA contain long terminal repeats (LTRs). The entire nucleotide sequence of the LTR and adjacent cellular sequences at the 5' end of a cloned integrated proviral DNA obtained from BALB/Mo mouse has been determined. It was compared to the nucleotide sequence of the LTR at the 3' end. The results indicate: (i) a direct 517-nucleotide repeat at the 5' and 3' termini; (ii) 145 nucleotides out of 517 nucleotides represent sequence...

  4. FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Rapacki, Kristoffer

    2006-01-01

    FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB) for structures of homologous proteins. The results are displayed both as an annotated sequence alignment, where the user-provided annotations as well as the sequence conservation between the query and the target sequence are displayed, and also as a publication-quality image of the 3D protein structure with the selected features and sequence conservation enhanced. The results are also returned in a readily parsable text format as well as a PyMol (http://pymol.sourceforge.net/) script file, which allows the user to easily modify the protein structure image to suit a specific purpose. FeatureMap3D can also be used without sequence annotation, to evaluate the quality of the alignment of the input sequences to the most homologous structures in the PDB, through the sequence conservation colored 3D structure visualization tool. FeatureMap3D is available at: http://www.cbs.dtu.dk/services/FeatureMap3D/.

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

    DEFF Research Database (Denmark)

    Welinder, K G; Jespersen, H M

    1991-01-01

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

  6. Dimension reduction for extracting geometrical structure of multidimensional phase space: Application to fast energy exchange in the reaction O(1D)+N2O?NO+NO

    International Nuclear Information System (INIS)

    One of the most fundamental problems in studying general Hamiltonian systems with many degrees of freedom is to extract a low-dimensional subsystem including the essential dynamics. In this paper, a new partial normal form (PNF) method is developed to reduce the number of coupling terms in the Hamiltonian and to simplify the dynamics analyses. The PNF method allows one to decouple many unimportant bath modes as well as the reactive mode from the system by assessing the significance of the coupling terms. The method is applied to the chemical reaction O(1D)+N2O?NO+NO, which was found to exhibit efficient energy exchange between the two NO stretching modes despite the short lifetime of the reaction intermediate [S. Kawai et al., J. Chem. Phys. 124, 184315 (2006)]. Through the analysis of the two-dimensional PNF Hamiltonian subsystem, it is found that the motion of the subsystem preserves the 'normal mode picture' of the symmetric and antisymmetric NO stretching modes despite its high energy. Then the vibrational energy, initially localized in the newly formed NO bond, is transferred to the reactants' NO bond through the beating between the symmetric and antisymmetric stretching modes. The preservation of the normal mode picture and the short period of the beating explain the fast energy exchange between the two NO bonds. This successful application proves that the PNF method can extract the essential small subspace from many-degrees-of-freedom Hasubspace from many-degrees-of-freedom Hamiltonian systems

  7. MultiSeq: unifying sequence and structure data for evolutionary analysis

    Directory of Open Access Journals (Sweden)

    Wright Dan

    2006-08-01

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

  8. Prediction of Protein Structural Features from Sequence Data Based on Shannon Entropy and Kolmogorov Complexity

    Science.gov (United States)

    Bywater, Robert Paul

    2015-01-01

    While the genome for a given organism stores the information necessary for the organism to function and flourish it is the proteins that are encoded by the genome that perhaps more than anything else characterize the phenotype for that organism. It is therefore not surprising that one of the many approaches to understanding and predicting protein folding and properties has come from genomics and more specifically from multiple sequence alignments. In this work I explore ways in which data derived from sequence alignment data can be used to investigate in a predictive way three different aspects of protein structure: secondary structures, inter-residue contacts and the dynamics of switching between different states of the protein. In particular the use of Kolmogorov complexity has identified a novel pathway towards achieving these goals. PMID:25856073

  9. Structure-Function Analysis of Diacylglycerol Acyltransferase Sequences from 70 Organisms

    Directory of Open Access Journals (Sweden)

    Cao Heping

    2011-07-01

    Full Text Available Abstract Background Diacylglycerol acyltransferase families (DGATs catalyze the final and rate-limiting step of triacylglycerol (TAG biosynthesis in eukaryotic organisms. Understanding the roles of DGATs will help to create transgenic plants with value-added properties and provide clues for therapeutic intervention for obesity and related diseases. The objective of this analysis was to identify conserved sequence motifs and amino acid residues for better understanding of the structure-function relationship of these important enzymes. Results 117 DGAT sequences from 70 organisms including plants, animals, fungi and human are obtained from database search using tung tree DGATs. Phylogenetic analysis separates these proteins into DGAT1 and DGAT2 subfamilies. These DGATs are integral membrane proteins with more than 40% of the total amino acid residues being hydrophobic. They have similar properties and amino acid composition except that DGAT1s are approximately 20 kDa larger than DGAT2s. DGAT1s and DGAT2s have 41 and 16 completely conserved amino acid residues, respectively, although only two of them are shared by all DGATs. These residues are distributed in 7 and 6 sequence blocks for DGAT1s and DGAT2s, respectively, and located at the carboxyl termini, suggesting the location of the catalytic domains. These conserved sequence blocks do not contain the putative neutral lipid-binding domain, mitochondrial targeting signal, or ER retrieval motif. The importance of conserved residues has been demonstrated by site-directed and natural mutants. Conclusions This study has identified conserved sequence motifs and amino acid residues in all 117 DGATs and the two subfamilies. None of the completely conserved residues in DGAT1s and DGAT2s is present in recently reported isoforms in the multiple sequences alignment, raising an important question how proteins with completely different amino acid sequences could perform the same biochemical reaction. The sequence analysis should facilitate studying the structure-function relationship of DGATs with the ultimate goal to identify critical amino acid residues for engineering superb enzymes in metabolic engineering and selecting enzyme inhibitors in therapeutic application for obesity and related diseases.

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

    OpenAIRE

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

    2013-01-01

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

  11. Cold dark matter, the structure of galactic haloes and the origin of the Hubble sequence

    International Nuclear Information System (INIS)

    The authors describe a simulation of a flat CDM (cold, dark matter) universe which can resolve structures of comparable scale to the luminous parts of galaxies. It is found that such a universe produces objects with the abundance and characteristic properties inferred for galaxy haloes. The results imply that merging plays an important part in galaxy formation and suggest a possible explanation for the Hubble sequence. (author)

  12. Global matrilineal population structure in sperm whales as indicated by mitochondrial DNA sequences.

    OpenAIRE

    Lyrholm, T; Gyllensten, U.

    1998-01-01

    The genetic variability and population structure of worldwide populations of the sperm whale was investigated by sequence analysis of the first 5'L 330 base pairs in the mitochondrial DNA (mtDNA) control region. The study included a total of 231 individuals from three major oceanic regions, the North Atlantic, the North Pacific and the Southern Hemisphere. Fifteen segregating nucleotide sites defined 16 mtDNA haplotypes (lineages). The most common mtDNA types were present in more than one oce...

  13. Predicting deleterious nsSNPs: an analysis of sequence and structural attributes

    OpenAIRE

    Saqi Mansoor AS; Caulfield Mark J; Munroe Patricia B; Dobson Richard J

    2006-01-01

    Abstract Background There has been an explosion in the number of single nucleotide polymorphisms (SNPs) within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs), some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learnin...

  14. Vector quantization kernels for the classification of protein sequences and structures.

    Science.gov (United States)

    Clark, Wyatt T; Radivojac, Predrag

    2014-01-01

    We propose a new kernel-based method for the classification of protein sequences and structures. We first represent each protein as a set of time series data using several structural, physicochemical, and predicted properties such as a sequence of consecutive dihedral angles, hydrophobicity indices, or predictions of disordered regions. A kernel function is then computed for pairs of proteins, exploiting the principles of vector quantization and subsequently used with support vector machines for protein classification. Although our method requires a significant pre-processing step, it is fast in the training and prediction stages owing to the linear complexity of kernel computation with the length of protein sequences. We evaluate our approach on two protein classification tasks involving the prediction of SCOP structural classes and catalytic activity according to the Gene Ontology. We provide evidence that the method is competitive when compared to string kernels, and useful for a range of protein classification tasks. Furthermore, the applicability of our approach extends beyond computational biology to any classification of time series data. PMID:24297558

  15. Nramp: from sequence to structure and mechanism of divalent metal import.

    Science.gov (United States)

    Cellier, Mathieu F M

    2012-01-01

    Mn and Fe are important for energy metabolism and oxidative stress resistance and cells maintain adequate stores for survival and prevention of toxicity. Membrane permeases of the natural resistance-associated macrophage protein (Nramp) family importing protons and divalent metals are conserved from bacteria to man. Nramp hydrophobic core relates structurally to a superfamily of cation-driven carriers with inverted symmetry. Molecular phylogeny and sequence features support Nramp pseudo-symmetric three-dimensional (3D) model, and remote ancestry to the LeuT superfamily. Genetic analyses suggest conservation of Nramp sequence marks the transition from a phylogenetic out-group and may relate to divalent metal selectivity. Three phylogroups of bacterial proton-dependent manganese transporters (MntH) demonstrate specific patterns of sequence conservation suggesting functional constraints linked to ecological or taxonomical distributions, which may contribute to bacterial virulence. Nramp 3D model is supported experimentally by transmembrane topology and structure-function studies of Escherichia coli and mouse homologs as well as peptide structure analyses. Eukaryotic Nramps are required for Mn and Fe homeostasis, contributing in multicellular organisms to subcellular and systemic metal traffic and intercellular signaling. Nramps are subjected to elaborate regulation including developmental control of gene expression, protein subcellular targeting, dynamic metallo-dependent control of messenger RNA and protein stability and trafficking. Several human pathologies may result from defects in Nramp-dependent Fe(2+) or Mn(2+) transport, including iron overload, neurodegenerative diseases and innate susceptibility to infectious diseases. PMID:23046654

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

    Directory of Open Access Journals (Sweden)

    Suzan-Monti Marie

    2009-05-01

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Agarwal, Pratul Kumar (Knoxville, TN)

    2011-07-19

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

  19. Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq.

    Science.gov (United States)

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

    2013-12-01

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

  20. DNA/RNA transverse current sequencing: intrinsic structural noise from neighboring bases

    Science.gov (United States)

    Alvarez, Jose R.; Skachkov, Dmitry; Massey, Steven E.; Kalitsov, Alan; Velev, Julian P.

    2015-01-01

    Nanopore DNA sequencing via transverse current has emerged as a promising candidate for third-generation sequencing technology. It produces long read lengths which could alleviate problems with assembly errors inherent in current technologies. However, the high error rates of nanopore sequencing have to be addressed. A very important source of the error is the intrinsic noise in the current arising from carrier dispersion along the chain of the molecule, i.e., from the influence of neighboring bases. In this work we perform calculations of the transverse current within an effective multi-orbital tight-binding model derived from first-principles calculations of the DNA/RNA molecules, to study the effect of this structural noise on the error rates in DNA/RNA sequencing via transverse current in nanopores. We demonstrate that a statistical technique, utilizing not only the currents through the nucleotides but also the correlations in the currents, can in principle reduce the error rate below any desired precision.

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

    Directory of Open Access Journals (Sweden)

    Povelones Michael

    2010-09-01

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

  2. Patterns of structural and sequence variation within isotype lineages of the Neisseria meningitidis transferrin receptor system.

    Science.gov (United States)

    Adamiak, Paul; Calmettes, Charles; Moraes, Trevor F; Schryvers, Anthony B

    2015-06-01

    Neisseria meningitidis inhabits the human upper respiratory tract and is an important cause of sepsis and meningitis. A surface receptor comprised of transferrin-binding proteins A and B (TbpA and TbpB), is responsible for acquiring iron from host transferrin. Sequence and immunological diversity divides TbpBs into two distinct lineages; isotype I and isotype II. Two representative isotype I and II strains, B16B6 and M982, differ in their dependence on TbpB for in vitro growth on exogenous transferrin. The crystal structure of TbpB and a structural model for TbpA from the representative isotype I N. meningitidis strain B16B6 were obtained. The structures were integrated with a comprehensive analysis of the sequence diversity of these proteins to probe for potential functional differences. A distinct isotype I TbpA was identified that co-varied with TbpB and lacked sequence in the region for the loop 3 ?-helix that is proposed to be involved in iron removal from transferrin. The tightly associated isotype I TbpBs had a distinct anchor peptide region, a distinct, smaller linker region between the lobes and lacked the large loops in the isotype II C-lobe. Sequences of the intact TbpB, the TbpB N-lobe, the TbpB C-lobe, and TbpA were subjected to phylogenetic analyses. The phylogenetic clustering of TbpA and the TbpB C-lobe were similar with two main branches comprising the isotype 1 and isotype 2 TbpBs, possibly suggesting an association between TbpA and the TbpB C-lobe. The intact TbpB and TbpB N-lobe had 4 main branches, one consisting of the isotype 1 TbpBs. One isotype 2 TbpB cluster appeared to consist of isotype 1 N-lobe sequences and isotype 2 C-lobe sequences, indicating the swapping of N-lobes and C-lobes. Our findings should inform future studies on the interaction between TbpB and TbpA and the process of iron acquisition. PMID:25800619

  3. Data structures and compression algorithms for high-throughput sequencing technologies

    Directory of Open Access Journals (Sweden)

    Christley Scott

    2010-10-01

    Full Text Available Abstract Background High-throughput sequencing (HTS technologies play important roles in the life sciences by allowing the rapid parallel sequencing of very large numbers of relatively short nucleotide sequences, in applications ranging from genome sequencing and resequencing to digital microarrays and ChIP-Seq experiments. As experiments scale up, HTS technologies create new bioinformatics challenges for the storage and sharing of HTS data. Results We develop data structures and compression algorithms for HTS data. A processing stage maps short sequences to a reference genome or a large table of sequences. Then the integers representing the short sequence absolute or relative addresses, their length, and the substitutions they may contain are compressed and stored using various entropy coding algorithms, including both old and new fixed codes (e.g Golomb, Elias Gamma, MOV and variable codes (e.g. Huffman. The general methodology is illustrated and applied to several HTS data sets. Results show that the information contained in HTS files can be compressed by a factor of 10 or more, depending on the statistical properties of the data sets and various other choices and constraints. Our algorithms fair well against general purpose compression programs such as gzip, bzip2 and 7zip; timing results show that our algorithms are consistently faster than the best general purpose compression programs. Conclusions It is not likely that exactly one encoding strategy will be optimal for all types of HTS data. Different experimental conditions are going to generate various data distributions whereby one encoding strategy can be more effective than another. We have implemented some of our encoding algorithms into the software package GenCompress which is available upon request from the authors. With the advent of HTS technology and increasingly new experimental protocols for using the technology, sequence databases are expected to continue rising in size. The methodology we have proposed is general, and these advanced compression techniques should allow researchers to manage and share their HTS data in a more timely fashion.

  4. Characterization of an insertion sequence (IS891) of novel structure from the cyanobacterium Anabaena sp. strain M-131.

    OpenAIRE

    Bancroft, I; Wolk, C P

    1989-01-01

    When recombinant plasmids that were transferred to the cyanobacterium Anabaena sp. strain M-131 were transferred back to Escherichia coli, some of the transformants contained inserts. One of the insertion sequences (ISs) was characterized by sequencing. This 1,351-base-pair IS contained an open reading frame that was capable of encoding a peptide of 310 amino acids and had terminal sequences with distinctive structures, but it lacked terminal inverted repeats and did not duplicate target DNA ...

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

    Science.gov (United States)

    Flores, Ricardo; Serra, Pedro; Minoia, Sofía; Di Serio, Francesco; Navarro, Beatriz

    2012-01-01

    As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson-Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunviroidae adopt multibranched conformations occasionally stabilized by kissing-loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures - either global or local - determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs. PMID:22719735

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

    Directory of Open Access Journals (Sweden)

    RicardoFlores

    2012-06-01

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

  7. [Cu2(?-Me2N-ba)2bn)I]n, 1D coordination polymer of copper(I) iodide: synthesis, characterization, and crystal structure.

    Czech Academy of Sciences Publication Activity Database

    Khalaji, A.D.; Jafari, K.; Bahramian, B.; Fejfarová, Karla; Dušek, Michal

    2013-01-01

    Ro?. 144, ?. 11 (2013), s. 1621-1626. ISSN 0026-9247 Grant ostatní: AV?R(CZ) Praemium Academiae Institutional research plan: CEZ:AV0Z10100521 Keywords : coordination polymer * Schiff base * copper * x-ray diffraction * structure analysis Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.347, year: 2013

  8. Evolutionary conservation of sequence and secondary structures inCRISPR repeats

    Energy Technology Data Exchange (ETDEWEB)

    Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

    2006-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Lees Jonathan G

    2008-01-01

    Full Text Available 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 methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

  10. SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

    Science.gov (United States)

    Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R.; Krogh, Anders; Vinther, Jeppe

    2015-01-01

    Selective 2? Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA–RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing. PMID:25805860

  11. SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

    DEFF Research Database (Denmark)

    Poulsen, Line Dahl; Kielpinski, Lukasz Jan

    2015-01-01

    Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA-RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing.

  12. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data.

    Science.gov (United States)

    Parisien, Marc; Major, François

    2008-03-01

    The classical RNA secondary structure model considers A.U and G.C Watson-Crick as well as G.U wobble base pairs. Here we substitute it for a new one, in which sets of nucleotide cyclic motifs define RNA structures. This model allows us to unify all base pairing energetic contributions in an effective scoring function to tackle the problem of RNA folding. We show how pipelining two computer algorithms based on nucleotide cyclic motifs, MC-Fold and MC-Sym, reproduces a series of experimentally determined RNA three-dimensional structures from the sequence. This demonstrates how crucial the consideration of all base-pairing interactions is in filling the gap between sequence and structure. We use the pipeline to define rules of precursor microRNA folding in double helices, despite the presence of a number of presumed mismatches and bulges, and to propose a new model of the human immunodeficiency virus-1 -1 frame-shifting element. PMID:18322526

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

    CERN Document Server

    Geroldinger, Alfred; Philipp, Andreas

    2010-01-01

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

  14. Using structural motif descriptors for sequence-based binding site prediction

    Directory of Open Access Journals (Sweden)

    Kim Wan

    2007-05-01

    Full Text Available Abstract Background Many protein sequences are still poorly annotated. Functional characterization of a protein is often improved by the identification of its interaction partners. Here, we aim to predict protein-protein interactions (PPI and protein-ligand interactions (PLI on sequence level using 3D information. To this end, we use machine learning to compile sequential segments that constitute structural features of an interaction site into one profile Hidden Markov Model descriptor. The resulting collection of descriptors can be used to screen sequence databases in order to predict functional sites. Results We generate descriptors for 740 classified types of protein-protein binding sites and for more than 3,000 protein-ligand binding sites. Cross validation reveals that two thirds of the PPI descriptors are sufficiently conserved and significant enough to be used for binding site recognition. We further validate 230 PPIs that were extracted from the literature, where we additionally identify the interface residues. Finally we test ligand-binding descriptors for the case of ATP. From sequences with Swiss-Prot annotation "ATP-binding", we achieve a recall of 25% with a precision of 89%, whereas Prosite's P-loop motif recognizes an equal amount of hits at the expense of a much higher number of false positives (precision: 57%. Our method yields 771 hits with a precision of 96% that were not previously picked up by any Prosite-pattern. Conclusion The automatically generated descriptors are a useful complement to known Prosite/InterPro motifs. They serve to predict protein-protein as well as protein-ligand interactions along with their binding site residues for proteins where merely sequence information is available.

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

    DEFF Research Database (Denmark)

    Pedersen, BjØrn Panella; Ifrim, Georgiana

    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-suited for this task. The classification of P-type ATPases, a large family of ATP-driven membrane pumps transporting essential cations, was selected as a test-case that would generate important biological information as well as provide a proof-of-concept for the application of SLR to a large scale bioinformatics problem. Results Using SLR, we have built classifiers to identify and automatically categorize P-type ATPases into one of 11 pre-defined classes. The SLR-classifiers are compared to a Hidden Markov Model approach and shown to be highly accurate and scalable. Representing the bulk of currently known sequences, we analysed 9.3 million sequences in the UniProtKB and attempted to classify a large numberof P-type ATPases. To examine the distribution of pumps on organisms, we also applied SLR to 1,123 complete genomes from the Entrez genome database. Finally, we analysed the predicted membrane topology of the identified P-type ATPases. Conclusions Using the SLR-based classification tool we are able to run a large scale study of P-type ATPases. This study provides proof-of-concept for the application of SLR to a bioinformatics problem and the analysis of P-type ATPases pinpoints new and interesting targets for further biochemical characterization and structural analysis.

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

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Menzel, Karl Peter

    2011-01-01

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

  17. Structural, electronic, and magnetic properties of quasi-1D quantum magnets [Ni(HF2)(pyz)2]X (pyz = pyrazine; X = PF6(-), SbF6(-)) exhibiting Ni-FHF-Ni and Ni-pyz-Ni spin interactions.

    Science.gov (United States)

    Manson, Jamie L; Lapidus, Saul H; Stephens, Peter W; Peterson, Peter K; Carreiro, Kimberly E; Southerland, Heather I; Lancaster, Tom; Blundell, Stephen J; Steele, Andrew J; Goddard, Paul A; Pratt, Francis L; Singleton, John; Kohama, Yoshimitsu; McDonald, Ross D; Del Sesto, Rico E; Smith, Nickolaus A; Bendix, Jesper; Zvyagin, Sergei A; Kang, Jinhee; Lee, Changhoon; Whangbo, Myung-Hwan; Zapf, Vivien S; Plonczak, Alex

    2011-07-01

    [Ni(HF(2))(pyz)(2)]X {pyz = pyrazine; X = PF(6)(-) (1), SbF(6)(-) (2)} were structurally characterized by synchrotron X-ray powder diffraction and found to possess axially compressed NiN(4)F(2) octahedra. At 298 K, 1 is monoclinic (C2/c) with unit cell parameters, a = 9.9481(3), b = 9.9421(3), c = 12.5953(4) Å, and ? = 81.610(3)° while 2 is tetragonal (P4/nmm) with a = b = 9.9359(3) and c = 6.4471(2) Å and is isomorphic with the Cu-analogue. Infinite one-dimensional (1D) Ni-FHF-Ni chains propagate along the c-axis which are linked via ?-pyz bridges in the ab-plane to afford three-dimensional polymeric frameworks with PF(6)(-) and SbF(6)(-) counterions occupying the interior sites. A major difference between 1 and 2 is that the Ni-F-H bonds are bent (?157°) in 1 but are linear in 2. Ligand field calculations (LFT) based on an angular overlap model (AOM), with comparison to the electronic absorption spectra, indicate greater ?-donation of the HF(2)(-) ligand in 1 owing to the bent Ni-F-H bonds. Magnetic susceptibility data for 1 and 2 exhibit broad maxima at 7.4 and 15 K, respectively, and ?-like peaks in d?T/dT at 6.2 and 12.2 K that are ascribed to transitions to long-range antiferromagnetic order (T(N)). Muon-spin relaxation and specific heat studies confirm these T(N)'s. A comparative analysis of ? vs T to various 1D Heisenberg/Ising models suggests moderate antiferromagnetic interactions, with the primary interaction strength determined to be 3.05/3.42 K (1) and 5.65/6.37 K (2). However, high critical fields of 19 and 37.4 T obtained from low temperature pulsed-field magnetization data indicate that a single exchange constant (J(1D)) alone is insufficient to explain the data and that residual terms in the spin Hamiltonian, which could include interchain magnetic couplings (J(?)), as mediated by Ni-pyz-Ni, and single-ion anisotropy (D), must be considered. While it is difficult to draw absolute conclusions regarding the magnitude (and sign) of J(?) and D based solely on powder data, further support offered by related Ni(II)-pyz compounds and our LFT and density-functional theory (DFT) results lead us to a consistent quasi-1D magnetic description for 1 and 2. PMID:21598910

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

    Directory of Open Access Journals (Sweden)

    Chen Ming

    2011-05-01

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

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

    Science.gov (United States)

    Grechko, Maksim; Zanni, Martin T.

    2012-01-01

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

  20. Memory Efficient Sequence Analysis Using Compressed Data Structures (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Simpson, Jared [Wellcome Trust Sanger Institute

    2011-10-13

    Wellcome Trust Sanger Institute's Jared Simpson on "Memory efficient sequence analysis using compressed data structures" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011

  1. Assembling Metal Ions Induced Cyanide-Bridged Heterometallic 1D and Ion-Pair Complexes: Synthesis, Crystal Structures and Magnetic Properties

    Energy Technology Data Exchange (ETDEWEB)

    Kong, Lingqian [Liaocheng Univ., Liaocheng (China); Zhao, Zengdian; Chen, Kexun; Wang, Ping; Zhang, Daopeng [Shandong Univ. of Technology, Zibo (China)

    2013-07-15

    We obtained a heterobimetallic one-dimensional cyanide-bridged Mn(II)-Ni(II) complex and an Co(III)-Ni(II) ion-pair complex with [Ni(CN){sub 4}]{sup 2-} as building block and M(II)-phenanthroline (M = Mn, Co) compounds as assembling segment. The different structural types of complexes 1 and 2 indicate that the property of the metal ions the assembling segment contained have obvious influence on the structure of the cyanide-bridged complex. Investigation over the magnetic properties of complex 1 reveals an overall weak antiferromagnetic coupling between the adjacent Mn(II) ions bridged by the antiferromagnetic [-NC-Ni-CN-] unit. Among of all the molecular magnetism systems, for the well known reasons, cyanide-containing complexes have been widely employed as bridges to assemble homo/hetero-metallic molecular magnetic materials by using the cyanide bridge transferring magnetic coupling between the neighboring paramagnetic ions, in whichsome showed interesting magnetic properties, such as high-Tc magnets, spin crossover materials, single-molecule magnets (SMMs) and single-chain magnets (SCMs)

  2. Syntheses and crystal structures of four 1-D or 2-D coordination polymers based on 1-((benzotriazol-1-yl)methyl)-1 H-1,3-imidazole

    Science.gov (United States)

    Zhou, Xiaoli; Li, Weiqiang; Jin, Guanghua; Zhao, Dong; Zhu, Xiaoqing; Meng, Xiangru; Hou, Hongwei

    2011-05-01

    In this paper, four coordination polymers, {[Ag(bmi)]·NO 3} n ( 1), [Co(N 3) 2(bmi) 2] n ( 2), [Cu(SCN) 2(bmi) 2] n ( 3), and {[Cu(bmi) 2(CH 3OH)(H 2O)]·(ClO 4) 2} n ( 4) have been synthesized through the reactions of an unsymmetrical ligand 1-((benzotriazol-1-yl)methyl)-1 H-1,3-imidazole (bmi) with Ag(I), Co(II) and Cu(II) salts at room temperature. X-ray diffraction analyses showed that compound 1 exhibits double-stranded helical chain. Compounds 2- 4 display 2-D rhombus grid network structure. The rhombus grid consists of 32-membered rings, and gives the dimensions of ca. 8.9 × 8.9 Å for compound 2, ca. 10.1 × 10.1 Å for compound 3, and ca. 9.7 × 9.5 Å for compound 4. In addition, the 2-D layers of compound 3 are stacked into 3-D structure via ?- ? interactions, while the 3-D architecture of compound 4 is realized through complicated hydrogen bonds and ?- ? interactions. The thermal analyses of compounds 1 and 3 indicate that they have high thermal stability and are stable up to 259 °C.

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

    Science.gov (United States)

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

    2014-07-01

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

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

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  6. Structural, electronic, and magnetic properties of quasi-1D quantum magnets [Ni(HF2)(pyz)2]X (pyz = pyrazine; X = PF6(-), SbF6(-)) exhibiting Ni-FHF-Ni and Ni-pyz-Ni spin interactions.

    OpenAIRE

    Manson, JL; Lapidus, SH; Stephens, PW; Peterson, PK; Carreiro, KE; Southerland, HI; Lancaster, T.; Blundell, SJ; Steele, AJ; Goddard, PA; Pratt, FL; Singleton, J.; Kohama, Y.; McDonald, RD; Del Sesto, RE

    2011-01-01

    [Ni(HF(2))(pyz)(2)]X {pyz = pyrazine; X = PF(6)(-) (1), SbF(6)(-) (2)} were structurally characterized by synchrotron X-ray powder diffraction and found to possess axially compressed NiN(4)F(2) octahedra. At 298 K, 1 is monoclinic (C2/c) with unit cell parameters, a = 9.9481(3), b = 9.9421(3), c = 12.5953(4) Å, and ? = 81.610(3)° while 2 is tetragonal (P4/nmm) with a = b = 9.9359(3) and c = 6.4471(2) Å and is isomorphic with the Cu-analogue. Infinite one-dimensional (1D) Ni-FHF-Ni chains ...

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

    Science.gov (United States)

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

    2011-04-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    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.

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

    CERN Document Server

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

    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.

  10. Estimating Rheological Parameters of Anhydrite from Folded Evaporite sequences: Implications for Internal Dynamics of Salt Structure

    Science.gov (United States)

    Adamuszek, Marta; Dabrowski, Marcin; Schmalholz, Stefan M.; Urai, Janos L.; Raith, Alexander

    2015-04-01

    Salt structures have been identified as a potential target for hydrocarbon, CO2, or radioactive waste storage. The most suitable locations for magazines are considered in the thick and relatively homogeneous rock salt layers. However, salt structures often consist of the evaporite sequence including rock salt intercalated with other rock types e.g.: anhydrite, gypsum, potassium and magnesium salt, calcite, dolomite, or shale. The presence of such heterogeneities causes a serious disturbance in the structure management. Detailed analysis of the internal architecture and internal dynamics of the salt structure are crucial for evaluating them as suitable repositories and also their long-term stability. The goal of this study is to analyse the influence of the presence of anhydrite layers on the internal dynamics of salt structures. Anhydrite is a common rock in evaporite sequences. Its physical and mechanical properties strongly differ from the properties of rock salt. The density of anhydrite is much higher than the density of salt, thus anhydrite is likely to sink in salt causing the disturbance of the surrounding structures. This suggestion was the starting point to the discussion about the long-term stability of the magazines in salt structures [1]. However, the other important parameter that has to be taken into account is the viscosity of anhydrite. The high viscosity ratio between salt and anhydrite can restrain the layer from sinking. The rheological behaviour of anhydrite has been studied in laboratory experiments [2], but the results only provide information about the short-term behaviour. The long-term behaviour can be best predicted using indirect methods e.g. based on the analysis of natural structures that developed over geological time scale. One of the most promising are fold structures, the shape of which is very sensitive to the rheological parameters of the deforming materials. Folds can develop in mechanically stratified materials during layer parallel shortening. Mechanical model have been developed to rigorously correlate rheological properties of rock to the fold shape. A quantitative fold shape analysis combined with the folding theory allows deciphering the rock rheology. In this study, we analyse anhydrite layers embedded in the rock salt from the Upper Permian Zechstein salt formation from Dutch offshore. The anhydrite layers are common intercalation in the sequence. Their thickness varies between few millimetres up to hundred meters. The layers are strongly deformed often forming fold structures, which can be observed on a wide range of scales: in core samples, mine galleries, and also in the seismic sections. For our analysis, we select single layer fold trains. Quantitative fold shape analysis is carried out using Fold Geometry Toolbox [3], which allows deciphering the viscosity ratio between anhydrite and salt. The results indicate that anhydrite layer is ca. 10 to 30 times more viscous than the embedding salt. Further, we use the estimated rheological parameters of anhydrite in the numerical analysis of the internal salt dynamics. We solve an incompressible Stokes equation in the presence of the gravity using the finite element method solver MILAMIN [4]. We show that the presence of denser and more viscous anhydrite layers in the tectonically stable regime is insignificant for the internal stability of the salt structures. [1] Chemia, Z., Koyi, H., Schmeling, H. 2008. Numerical modelling of rise and fall of a dense layer in salt diapirs. Geophysical Journal International, 172: 798-816. [2] Muller, W.H., Briegel, U. 1978. The rheological behaviour of polycrystalline Anhydrite. Eclogae Geol. Helv, 71(2): 397-407 [3] Adamuszek M., Schmid D.W., Dabrowski M. 2011. Fold geometry toolbox - Automated determination of fold shape, shortening, and material properties, Journal of Structural Geology, 33: 1406-1416. [4] Dabrowski, M., Krotkiewski, M., and Schmid, D. W. 2008. MILAMIN: MATLAB-based finite element method solver for large problems. Geochemistry Geophysics Geosystems, 9: Q04030.

  11. Main: 1D6R [RPSD[Archive

    Lifescience Database Archive (English)

    Full Text Available 1D6R ?? 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 ...

  12. Sequence-structure based phylogeny of GPCR Class A Rhodopsin receptors.

    Science.gov (United States)

    Kakarala, Kavita Kumari; Jamil, Kaiser

    2014-05-01

    Current methods of G protein coupled receptors (GPCRs) phylogenetic classification are sequence based and therefore inappropriate for highly divergent sequences, sharing low sequence identity. In this study, sequence structure profile based alignment generated by PROMALS3D was used to understand the GPCR Class A Rhodopsin superfamily evolution using the MEGA 5 software. Phylogenetic analysis included a combination of Neighbor-Joining method and Maximum Likelihood method, with 1000 bootstrap replicates. Our study was able to identify potential ligand association for Class A Orphans and putative/unclassified Class A receptors with no cognate ligand information: GPR21 and GPR52 with fatty acids; GPR75 with Neuropeptide Y; GPR82, GPR18, GPR141 with N-arachidonylglycine; GPR176 with Free fatty acids, GPR10 with Tachykinin & Neuropeptide Y; GPR85 with ATP, ADP & UDP glucose; GPR151 with Galanin; GPR153 and GPR162 with Adrenalin, Noradrenalin; GPR146, GPR139, GPR142 with Neuromedin, Ghrelin, Neuromedin U-25 & Thyrotropin-releasing hormone; GPR171 with ATP, ADP & UDP Glucose; GPR88, GPR135, GPR161, GPR101with 11-cis-retinal; GPR83 with Tackykinin; GPR148 with Prostanoids, GPR109b, GPR81, GPR31with ATP & UTP and GPR150 with GnRH I & GnRHII. Furthermore, we suggest that this study would prove useful in re-classification of receptors, selecting templates for homology modeling and identifying ligands which may show cross reactivity with other GPCRs as signaling via multiple ligands play a significant role in disease modulation. PMID:24503482

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-03-04

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

  15. Prediction of new high pressure structural sequence in thorium carbide: A first principles study

    Science.gov (United States)

    Sahoo, B. D.; Joshi, K. D.; Gupta, Satish C.

    2015-05-01

    In the present work, we report the detailed electronic band structure calculations on thorium monocarbide. The comparison of enthalpies, derived for various phases using evolutionary structure search method in conjunction with first principles total energy calculations at several hydrostatic compressions, yielded a high pressure structural sequence of NaCl type (B1) ? Pnma ? Cmcm ? CsCl type (B2) at hydrostatic pressures of ˜19 GPa, 36 GPa, and 200 GPa, respectively. However, the two high pressure experimental studies by Gerward et al. [J. Appl. Crystallogr. 19, 308 (1986); J. Less-Common Met. 161, L11 (1990)] one up to 36 GPa and other up to 50 GPa, on substoichiometric thorium carbide samples with carbon deficiency of ˜20%, do not report any structural transition. The discrepancy between theory and experiment could be due to the non-stoichiometry of thorium carbide samples used in the experiment. Further, in order to substantiate the results of our static lattice calculations, we have determined the phonon dispersion relations for these structures from lattice dynamic calculations. The theoretically calculated phonon spectrum reveal that the B1 phase fails dynamically at ˜33.8 GPa whereas the Pnma phase appears as dynamically stable structure around the B1 to Pnma transition pressure. Similarly, the Cmcm structure also displays dynamic stability in the regime of its structural stability. The B2 phase becomes dynamically stable much below the Cmcm to B2 transition pressure. Additionally, we have derived various thermophysical properties such as zero pressure equilibrium volume, bulk modulus, its pressure derivative, Debye temperature, thermal expansion coefficient and Gruneisen parameter at 300 K and compared these with available experimental data. Further, the behavior of zero pressure bulk modulus, heat capacity and Helmholtz free energy has been examined as a function temperature and compared with the experimental data of Danan [J. Nucl. Mater. 57, 280 (1975)].

  16. Effect of the crossing-structure sequence on mixing performance within three-dimensional micromixers

    Science.gov (United States)

    Feng, Xiangsong; Ren, Yukun; Jiang, Hongyuan

    2014-01-01

    The geometry of crossing structure formed by two-layer microchannels determines the axial and transverse movements of contact interface between two liquid streams, which gives us a new method for promoting the micromixers. Hence, we designed four different three-dimensional micromixers by selecting two different crossing structures as basic units (one unit is a crossing structure called “X” and the other is a reversed crossing structure called “rX”). In order to find out how the crossing-structure sequence affects the mixing performance within three-dimensional micromixers, we organized these four mixers in different ways, i.e., the first combination is X-rX-X-rX-…, the second is X-rX-rX-X-…, the third is X-X-rX-X-…, and the last one is X-X-X-X…. Consequently, quite distinct mixing phenomena are engendered. Furthermore, experiments were also conducted using the first and the last models to verify the simulation results. We infer that the last mixer is more likely to trigger chaos and convection by rotating the contact surface than the first one that merely swings the surface even when the flow rates and viscosities of the two liquid streams are increased. PMID:24959307

  17. Cloning, Sequencing, Purification, and Crystal Structure of Grenache (Vitis vinifera) Polyphenol Oxidase

    Energy Technology Data Exchange (ETDEWEB)

    Virador, V.; Reyes Grajeda, J; Blanco-Labra, A; Mendiola-Olaya, E; Smith, G; Moreno, A; Whitaker, J

    2010-01-01

    The full-length cDNA sequence (P93622{_}VITVI) of polyphenol oxidase (PPO) cDNA from grape Vitis vinifera L., cv Grenache, was found to encode a translated protein of 607 amino acids with an expected molecular weight of ca. 67 kDa and a predicted pI of 6.83. The translated amino acid sequence was 99%, identical to that of a white grape berry PPO (1) (5 out of 607 amino acid potential sequence differences). The protein was purified from Grenache grape berries by using traditional methods, and it was crystallized with ammonium acetate by the hanging-drop vapor diffusion method. The crystals were orthorhombic, space group C2221. The structure was obtained at 2.2 {angstrom} resolution using synchrotron radiation using the 39 kDa isozyme of sweet potato PPO (PDB code: 1BT1) as a phase donor. The basic symmetry of the cell parameters (a, b, and c and {alpha}, {beta}, and {gamma}) as well as in the number of asymmetric units in the unit cell of the crystals of PPO, differed between the two proteins. The structures of the two enzymes are quite similar in overall fold, the location of the helix bundles at the core, and the active site in which three histidines bind each of the two catalytic copper ions, and one of the histidines is engaged in a thioether linkage with a cysteine residue. The possibility that the formation of the Cys-His thioether linkage constitutes the activation step is proposed. No evidence of phosphorylation or glycoslyation was found in the electron density map. The mass of the crystallized protein appears to be only 38.4 kDa, and the processing that occurs in the grape berry that leads to this smaller size is discussed.

  18. Sequence-Based Protein Crystallization Propensity Prediction for Structural Genomics: Review and Comparative Analysis

    Directory of Open Access Journals (Sweden)

    Marcin J. Mizianty

    2009-09-01

    Full Text Available Structural genomics (SG is an international effort that aims at solving three-dimensional shapes of important biological macro-molecules with primary focus on proteins. One of the main bottlenecks in SG is the ability to produce dif-fraction quality crystals for X-ray crystallogra-phy based protein structure determination. SG pipelines allow for certain flexibility in target selection which motivates development of in- silico methods for sequence-based prediction/ assessment of the protein crystallization pro-pensity. We overview existing SG databanks that are used to derive these predictive models and we discuss analytical results concerning protein sequence properties that were discov-ered to correlate with the ability to form crystals. We also contrast and empirically compare mo- dern sequence-based predictors of crystalliza-tion propensity including OB-Score, ParCrys, XtalPred and CRYSTALP2. Our analysis shows that these methods provide useful and compli-mentary predictions. Although their average ac- curacy is similar at around 70%, we show that application of a simple majority-vote based en-semble improves accuracy to almost 74%. The best improvements are achieved by combining XtalPred with CRYSTALP2 while OB-Score and ParCrys methods overlap to a larger extend, although they still complement the other two predictors. We also demonstrate that 90% of the protein chains can be correctly predicted by at least one of these methods, which suggests that more accurate ensembles could be built in the future. We believe that current protein crystalli-zation propensity predictors could provide useful input for the target selection procedures utilized by the SG centers.

  19. Nuclear Pore Complex Protein Sequences Determine Overall Copolymer Brush Structure and Function?

    Science.gov (United States)

    Ando, David; Kim, Yongwoon; Zandi, Roya; Colvin, Michael; Rexach, Michael; Gopinathan, Ajay

    2015-03-01

    Disordered proteins are an interesting class of unfolded protein biopolymers which are functionally versatile. Their sequences are unconstrained by a sequence-structure relationship, and allow for a wide range of chemical and physical polymer properties. The Nuclear Pore Complex (NPC) contains over one hundred of such proteins (FG nups), which collectively function to regulate the exchange of all materials between the nucleus and cytoplasm. We perform coarse grained simulations of both individual FG nups and grafted rings of nups mimicking the in vivo geometry of the NPC, supplemented with polymer brush modeling. Our results indicate that different regions or ``blocks'' of an individual FG nup can have distinctly different forms of disorder, and that this property appears to be a conserved feature across eukarya. Furthermore, this block structure at the individual protein level is critical to the formation of a unique higher-order polymer brush architecture. Because the interactions between FG nups may be modulated by certain forms of transport factors, our results indicate that transitions between brush morphologies could play an important role in regulating transport across the NPC, suggesting novel forms of gated transport across membrane pores with wide biomimetic applicability.

  20. ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and their structures.

    Science.gov (United States)

    Mehta, Divya; Anand, Priya; Kumar, Vineet; Joshi, Anshika; Mathur, Deepika; Singh, Sandeep; Tuknait, Abhishek; Chaudhary, Kumardeep; Gautam, Shailendra K; Gautam, Ankur; Varshney, Grish C; Raghava, Gajendra P S

    2014-01-01

    ParaPep is a repository of antiparasitic peptides, which provides comprehensive information related to experimentally validated antiparasitic peptide sequences and their structures. The data were collected and compiled from published research papers, patents and from various databases. The current release of ParaPep holds 863 entries among which 519 are unique peptides. In addition to peptides having natural amino acids, ParaPep also consists of peptides having d-amino acids and chemically modified residues. In ParaPep, most of the peptides have been evaluated for growth inhibition of various species of Plasmodium, Leishmania and Trypanosoma. We have provided comprehensive information about these peptides that include peptide sequence, chemical modifications, stereochemistry, antiparasitic activity, origin, nature of peptide, assay types, type of parasite, mode of action and hemolytic activity. Structures of peptides consisting of natural, as well as modified amino acids have been determined using state-of-the-art software, PEPstr. To facilitate users, various user-friendly web tools, for data fetching, analysis and browsing, have been integrated. We hope that ParaPep will be advantageous in designing therapeutic peptides against parasitic diseases. Database URL: http://crdd.osdd.net/raghava/parapep/ PMID:24923818

  1. Modelling the effect of structure and base sequence on DNA molecular electronics

    International Nuclear Information System (INIS)

    DNA is a material that has the potential to be used in nanoelectronic devices as an active component. However, the electronic properties of DNA responsible for its conducting behaviour remain controversial. Here we use a self-consistent quantum molecular dynamics method to study the effect of DNA structure and base sequence on the energy involved when electrons are added or removed from isolated molecules and the transfer of the injected charge along the molecular axis when an electric field is applied. Our results show that the addition or removal of an electron from DNA molecules is most exothermic for poly(dC)-poly(dG) in its B-form and poly(dA)-poly(dT) in its A-form, and least exothermic in its Z-form. Additionally, when an electric field is applied to a charged DNA molecule along its axis, there is electron transfer through the molecule, regardless of the number and sign of the injected charge, the molecular structure and the base sequence. Results from these simulations provide useful information that is hard to obtain from experiments and needs to be considered for further modelling aiming to improve charge transport efficiency in nanoelectronic devices based on DNA

  2. LNCipedia: a database for annotated human lncRNA transcript sequences and structures.

    Science.gov (United States)

    Volders, Pieter-Jan; Helsens, Kenny; Wang, Xiaowei; Menten, Björn; Martens, Lennart; Gevaert, Kris; Vandesompele, Jo; Mestdagh, Pieter

    2013-01-01

    Here, we present LNCipedia (http://www.lncipedia.org), a novel database for human long non-coding RNA (lncRNA) transcripts and genes. LncRNAs constitute a large and diverse class of non-coding RNA genes. Although several lncRNAs have been functionally annotated, the majority remains to be characterized. Different high-throughput methods to identify new lncRNAs (including RNA sequencing and annotation of chromatin-state maps) have been applied in various studies resulting in multiple unrelated lncRNA data sets. LNCipedia offers 21 488 annotated human lncRNA transcripts obtained from different sources. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites. Our analyses suggest that, much like microRNAs, many lncRNAs have a significant secondary structure, in-line with their presumed association with proteins or protein complexes. Available literature on specific lncRNAs is linked, and users or authors can submit articles through a web interface. Protein coding potential is assessed by two different prediction algorithms: Coding Potential Calculator and HMMER. In addition, a novel strategy has been integrated for detecting potentially coding lncRNAs by automatically re-analysing the large body of publicly available mass spectrometry data in the PRIDE database. LNCipedia is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria. The database may serve as a resource to initiate small- and large-scale lncRNA studies. As an example, the LNCipedia content was used to develop a custom microarray for expression profiling of all available lncRNAs. PMID:23042674

  3. A more accurate relocation of the 2013 M s7.0 Lushan, Sichuan, China, earthquake sequence, and the seismogenic structure analysis

    Science.gov (United States)

    Long, F.; Wen, X. Z.; Ruan, X.; Zhao, M.; Yi, G. X.

    2015-07-01

    We use a combined earthquake location technique to relocate the M s7.0 Lushan, Sichuan, China, earthquake sequence of April 20, 2013. A stepwise approach, employing three existing location methods (the HYPOINVERSE method, the Minimum 1-D model, and the Double Difference method), is used to improve location precision by iteratively revising the velocity model station corrections, and hypocenter relocations throughout the process. Our stepwise approach has significantly improved the location precision of the Lushan earthquake sequence, yielding hypocenter locations with final errors of 359, 309, and 605 m in the E-W, N-S, and vertical directions, respectively, with average travel time residuals of 0.12 s. Furthermore, we analyzed the seismogenic structure surrounding the Lushan earthquake sequence by combining the results of the relocated hypocenter distribution with new focal mechanism solutions and information from regional geological and geophysical investigations. From our analysis, we conclude that the vast majority of the aftershocks of the Lushan earthquake sequence occurred at depths of 6-9 km, near the front of the southwestern segment of the NE-trending Longmenshan fault zone. Densely aligned hypocenters clearly suggest that the seismogenic structure of the mainshock consists of a set of basal thrust faults dipping to the NW at 40-50°, at a ramp of the deep basal décollement-thrust system at depths of 7-18 km. Focal mechanism solutions suggest that the seismogenic faults have produced almost pure thrusting. At least one SE-dipping back-thrust is also observed within the basement, as indicated by the hypocenter relocations, which points to either a secondary rupture plane during the mainshock or a plane of aftershock slips. A small number of minor events in the Lushan sequence are located at depths of 0-6 km, with a distribution suggesting that the three NE-trending faults with surface traces running through or passing close to the aftershock area are confined to the upper Mesozoic sedimentary cover, making them independent of the deeper thrust faults that ruptured during the mainshock. Therefore, the 2013 M s7.0 Lushan earthquake was a blind thrust fault generated on active thrust faults within the basement of the southwestern Longmenshan fault zone, with an upper limit estimation of the rupture length, average down-dip width, and rupture area of 40, 16, and 640 km2, respectively.

  4. A more accurate relocation of the 2013 M s7.0 Lushan, Sichuan, China, earthquake sequence, and the seismogenic structure analysis

    Science.gov (United States)

    Long, F.; Wen, X. Z.; Ruan, X.; Zhao, M.; Yi, G. X.

    2015-02-01

    We use a combined earthquake location technique to relocate the M s7.0 Lushan, Sichuan, China, earthquake sequence of April 20, 2013. A stepwise approach, employing three existing location methods (the HYPOINVERSE method, the Minimum 1-D model, and the Double Difference method), is used to improve location precision by iteratively revising the velocity model station corrections, and hypocenter relocations throughout the process. Our stepwise approach has significantly improved the location precision of the Lushan earthquake sequence, yielding hypocenter locations with final errors of 359, 309, and 605 m in the E-W, N-S, and vertical directions, respectively, with average travel time residuals of 0.12 s. Furthermore, we analyzed the seismogenic structure surrounding the Lushan earthquake sequence by combining the results of the relocated hypocenter distribution with new focal mechanism solutions and information from regional geological and geophysical investigations. From our analysis, we conclude that the vast majority of the aftershocks of the Lushan earthquake sequence occurred at depths of 6-9 km, near the front of the southwestern segment of the NE-trending Longmenshan fault zone. Densely aligned hypocenters clearly suggest that the seismogenic structure of the mainshock consists of a set of basal thrust faults dipping to the NW at 40-50°, at a ramp of the deep basal décollement-thrust system at depths of 7-18 km. Focal mechanism solutions suggest that the seismogenic faults have produced almost pure thrusting. At least one SE-dipping back-thrust is also observed within the basement, as indicated by the hypocenter relocations, which points to either a secondary rupture plane during the mainshock or a plane of aftershock slips. A small number of minor events in the Lushan sequence are located at depths of 0-6 km, with a distribution suggesting that the three NE-trending faults with surface traces running through or passing close to the aftershock area are confined to the upper Mesozoic sedimentary cover, making them independent of the deeper thrust faults that ruptured during the mainshock. Therefore, the 2013 M s7.0 Lushan earthquake was a blind thrust fault generated on active thrust faults within the basement of the southwestern Longmenshan fault zone, with an upper limit estimation of the rupture length, average down-dip width, and rupture area of 40, 16, and 640 km2, respectively.

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

    Scientific Electronic Library Online (English)

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

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

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

    Directory of Open Access Journals (Sweden)

    Akutsu Tatsuya

    2009-01-01

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

  7. Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps

    OpenAIRE

    Dixit, S.B.; Beveridge, D.L.; Case, D A; Cheatham, T. E.; Guidice, E.; Lankas, F.; Lavery, R; Maddocks, J.H.; Osman, R.; Sklenar, H; Thayer, K; Varnai, P.

    2005-01-01

    Molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide basepair steps are reported. The objective is to obtain the calculated dynamical structure for at least two copies of each case, use the results to examine issues with regard to convergence and dynamical stability of MD on DNA, and determine the significance of sequence context effects on all unique dinucleotide steps. This information is essential to understand seq...

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

    Scientific Electronic Library Online (English)

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

    2008-01-01

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

  9. Sequence-specific 1H NMR assignments and secondary structure of porcine motilin

    International Nuclear Information System (INIS)

    The solution structure of the 22-residue peptide hormone motilin has been studied by circular dichroism and two-dimensional 1H nuclear magnetic resonance spectroscopy. Circular dichroism spectra indicate the presence of ?-helical secondary structure in aqueous solution, and the secondary structure can be stabilized with hexafluoro-2-propanol. Sequence-specific assignments of the proton NMR spectrum of porcine motilin in 30% hexafluoro-2-propanol have been made by using two-dimensional NMR techniques. All backbone proton resonances (NH and ?CH) and most of the side-chain resonances have been assigned by using double-quantum-filtered COSY, RELAYED-COSY, and NOESY experiments. Simulations of NOESY cross-peak intensities as a function of mixing time indicate that spin diffusion has a relatively small effect in peptides the size of motilin, thereby allowing the use of long mixing times to confidently make assignments and delineate secondary structure. Sequential ?CH-NH and NH-NH NOESY connectivities were observed over a significant portion of the length of the peptide. The intensities of selected NOESY cross-peaks relative to corresponding diagonal peaks were used to estimate a rotational correlation time of approximately 2.5 ns for the peptide, indicating that the peptide exists as a monomer in solution under the conditions used here

  10. 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.

    Science.gov (United States)

    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 ?B. 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 ?0H ? 3 T is applied along the a' axis. The ?0H-T phase diagram of (pipH)CuBr3 is roughly constructed. PMID:24617285

  11. 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.

    Science.gov (United States)

    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 (?-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 ?-Fe2O3@mSiO2 nanochains possessed hollow mesoporous structure and high specific surface area (197.2m(2)g(-1)) were used as a drug carrier, which displayed a controlled release property. PMID:26119084

  12. Use of Endogenous Retroviral Sequences (ERVs and structural markers for retroviral phylogenetic inference and taxonomy

    Directory of Open Access Journals (Sweden)

    Sperber Göran O

    2005-08-01

    Full Text Available Abstract Background Endogenous retroviral sequences (ERVs are integral parts of most eukaryotic genomes and vastly outnumber exogenous retroviruses (XRVs. ERVs with a relatively complete structure were retrieved from the genetic archives of humans and chickens, diametrically opposite representatives of vertebrate retroviruses (over 3300 proviruses, and analyzed, using a bioinformatic program, RetroTector©, developed by us. This rich source of proviral information, accumulated in a local database, and a collection of XRV sequences from the literature, allowed the reconstruction of a Pol based phylogenetic tree, more extensive than previously possible. The aim was to find traits useful for classification and evolutionary studies of retroviruses. Some of these traits have been used by others, but they are here tested in a wider context than before. Results In the ERV collection we found sequences similar to the XRV-based genera: alpha-, beta-, gamma-, epsilon- and spumaretroviruses. However, the occurrence of intermediates between them indicated an evolutionary continuum and suggested that taxonomic changes eventually will be necessary. No delta or lentivirus representatives were found among ERVs. Classification based on Pol similarity is congruent with a number of structural traits. Acquisition of dUTPase occurred three times in retroviral evolution. Loss of one or two NC zinc fingers appears to have occurred several times during evolution. Nucleotide biases have been described earlier for lenti-, delta- and betaretroviruses and were here confirmed in a larger context. Conclusion Pol similarities and other structural traits contribute to a better understanding of retroviral phylogeny. "Global" genomic properties useful in phylogenies are i. translational strategy, ii. number of Gag NC zinc finger motifs, iii. presence of Pro N-terminal dUTPase (dUTPasePro, iv. presence of Pro C-terminal G-patch and v. presence of a GPY/F motif in the Pol integrase (IN C-terminal domain. "Local" retroviral genomic properties useful for delineation of lower level taxa are i. host species range, ii. nucleotide compositional bias and iii. LTR lengths.

  13. Physical organisation of simple sequence repeats (SSRs) in Triticeae: structural, functional and evolutionary implications.

    Science.gov (United States)

    Cuadrado, A; Cardoso, M; Jouve, N

    2008-01-01

    A significant fraction of the nuclear DNA of all eukaryotes is occupied by simple sequence repeats (SSRs) or microsatellites. This type of sequence has sparked great interest as a means of studying genetic variation, linkage mapping, gene tagging and evolution. Although SSRs at different positions in a gene help determine the regulation of expression and the function of the protein produced, little attention has been paid to the chromosomal organisation and distribution of these sequences, even in model species. This review discusses the main achievements in the characterisation of long-range SSR organisation in the chromosomes of Triticum aestivum L., Secale cereale L., and Hordeum vulgare L. (all members of Triticeae). We have detected SSRs using an improved FISH technique based on the random primer labelling of synthetic oligonucleotides (15-24 bases) in multi-colour experiments. Detailed information on the presence and distribution of AC, AG and all the possible classes of trinucleotide repeats has been acquired. These data have revealed the motif-dependent and non-random chromosome distributions of SSRs in the different genomes, and allowed the correlation of particular SSRs with chromosome areas characterised by specific features (e.g., heterochromatin, euchromatin and centromeres) in all three species. The present review provides a detailed comparative study of the distribution of these SSRs in each of the seven chromosomes of the genomes A, B and D of wheat, H of barley and R of rye. The importance of SSRs in plant breeding and their possible role in chromosome structure, function and evolution is discussed. PMID:18504349

  14. Unusual and strongly structured sequence variation in a complex satellite DNA family from the nematode Meloidogyne chitwoodi.

    Science.gov (United States)

    Castagnone-Sereno, P; Leroy, H; Semblat, J P; Leroy, F; Abad, P; Zijlstra, C

    1998-02-01

    An AluI satellite DNA family has been isolated in the genome of the root-knot nematode Meloidogyne chitwoodi. This repeated sequence was shown to be present at approximately 11,400 copies per haploid genome, and represents about 3.5% of the total genomic DNA. Nineteen monomers were cloned and sequenced. Their length ranged from 142 to 180 bp, and their A + T content was high (from 65.7 to 79.1%), with frequent runs of As and Ts. An unexpected heterogeneity in primary structure was observed between monomers, and multiple alignment analysis showed that the 19 repeats could be unambiguously clustered in six subfamilies. A consensus sequence has been deduced for each subfamily, within which the number of positions conserved is very high, ranging from 86.7% to 98.6%. Even though blocks of conserved regions could be observed, multiple alignment of the six consensus sequences did not enable the establishment of a general unambiguous consensus sequence. Screening of the six consensus sequences for evidence of internal repeated subunits revealed a 6-bp motif (AAATTT), present in both direct and inverted orientation. This motif was found up to nine times in the consensus sequences, also with the occurrence of degenerated subrepeats. Along with the meiotic parthenogenetic mode of reproduction of this nematode, such structural features may argue for the evolution of this satellite DNA family either (1) from a common ancestral sequence by amplification followed by mechanisms of sequence divergence, or (2) through independent mutations of the ancestral sequence in isolated amphimictic nematode populations and subsequent hybridization events. Overall, our results suggest the ancient origin of this satellite DNA family, and may reflect for M. chitwoodi a phylogenetic position close to the ancestral amphimictic forms of root-knot nematodes. PMID:9452524

  15. Cluster Segmentation of Thermal Image Sequences Using kd-Tree Structure

    Science.gov (United States)

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

    2014-12-01

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

  16. Sequence variability of bovine leukemia virus env gene and its relevance to the structure and antigenicity of the glycoproteins.

    OpenAIRE

    Mamoun, R. Z.; Morisson, M.; Rebeyrotte, N.; Busetta, B.; Couez, D.; Kettmann, R.; Hospital, M.; Guillemain, B.

    1990-01-01

    The nucleotide sequences of the env genes of seven bovine leukemia viruses and the encoded peptide sequence were compared, with the objective of (i) determining the genetic distance separating bovine leukemia virus isolates from different geographical regions, (ii) identifying particular amino acids that contribute to the sequential and conformational epitopes, and (iii) relating such epitopes to their projected position in a three-dimensional model of the structure of the gp51 surface glycop...

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

    Science.gov (United States)

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

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

    OpenAIRE

    Kudo, S.; Fukuda, M

    1989-01-01

    Glycophorins A (GPA) and B (GPB) are two major sialoglycoproteins of the human erythrocyte membrane. Here we present a comparison of the genomic structures of GPA and GPB developed by analyzing DNA clones isolated from a K562 genomic library. Nucleotide sequences of exon-intron junctions and 5' and 3' flanking sequences revealed that the GPA and GPB genes consist of 7 and 5 exons, respectively, and both genes have greater than 95% identical sequence from the 5' flanking region to the region a...

  19. Analysis of Sequence Polymorphism and Population Structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in Viroid-Infected Tomato Plants

    OpenAIRE

    Nie, Xianzhou

    2012-01-01

    The sequence polymorphism and population structure of Tomato chlorotic dwarf viroid (TCDVd) (isolate Trust) and Potato tuber spindle viroid (PSTVd) (isolate FN) in tomato plants were investigated. Of the 9 and 35 TCDVd clones sequenced from 2 different TCDVd-infected plants, 2 and 4 sequence variants were identified, respectively, leading to a total of 4 sequence variants of 360 nucleotides in length. Variant I was identical to AF162131, the first TCDVd sequence to be reported, and the rest e...

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

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus

    2010-01-01

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

  1. Comparative sequence- and structure-inspired drug design for PilF protein of Neisseria meningitidis.

    Science.gov (United States)

    Mehta, Abijeet Singh; Snigdha, Kirti; Potukuchi, M Sharada; Tsonis, Panagiotis A

    2015-01-01

    Serogroup A of Neisseria meningitidis is the organism responsible for causing epidemic diseases in developing countries by a pilus-mediated adhesion to human brain endothelial cells. Type IV pilus assembly protein (PilF) associated with bacterial adhesion, aggregation, invasion, host cell signaling, surface motility, and natural transformation can be considered as a candidate for effective anti-meningococcal drug development. Since the crystal structure of PilF was not available, in the present study, it was modeled after the Z2491 strain (CAM09255.1) using crystal structure of chain A of Vibrio cholerae putative Ntpase EpsE (Protein Data Bank (PDB) ID: 1P9R) and then we based this analysis on sequence comparisons and structural similarity using in silico methods and docking processes, to design a suitable inhibitor molecule. The ligand 3-{(4S)-5-{[(1R)-1-cyclohexylethyl]amino}-4-[(5S)-5-(prop-2-en-1-yl) cyclopent-1-en-1-yl]-1,4-dihydro-7H-pyrrolo[2,3-d] pyrimidin-7-yl}-1,2-dideoxy-b-L-erythro-hex-1-en-3-ulofuranosyl binds to the protein with a binding energy of -8.10 kcal and showed a drug likeness of 0.952 with no predicted health hazard. It can be utilized as a potent inhibitor of N. meningitidis pilus-mediated adhesion to human brain endothelial cells preventing meningeal colonization. PMID:25928839

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

    International Nuclear Information System (INIS)

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

  3. Involvement of interstitial telomeric sequences in two new cases of mosaicism for autosomal structural rearrangements.

    Science.gov (United States)

    Lévy, Jonathan; Receveur, Aline; Jedraszak, Guillaume; Chantot-Bastaraud, Sandra; Renaldo, Florence; Gondry, Jean; Andrieux, Joris; Copin, Henri; Siffroi, Jean-Pierre; Portnoï, Marie-France

    2015-02-01

    Mosaicism for an autosomal structural rearrangement that does not involve ring or marker chromosomes is rare. The mechanisms responsible for genome instability have not always been explained. Several studies have shown that interstitial telomeric sequences (ITSs), involved in some mosaic constitutional anomalies, are potent sources of genomic instability. Here we describe two cases of mosaicism for uncommon constitutional autosomal rearrangements, involving ITSs, identified by karyotyping and characterized by FISH and SNP-array analysis. The first patient, a boy with global developmental delay, had a rare type of pure distal 1q inverted duplication (1q32-qter), attached to the end of the short arm of the same chromosome 1, in approximately 35% of his cells. The second patient, a phenotypically normal man, was diagnosed as having mosaic for a balanced non-reciprocal translocation of the distal segment of 7q (7q33qter), onto the terminal region of the short arm of a whole chromosome 12, in approximately 80% of his cells. The remaining 20% of the cells showed an unbalanced state of the translocation, with only the der(7) chromosome. He was ascertained through his malformed fetus carrying a non-mosaic partial monosomy 7q, identified at prenatal diagnosis. We show that pan-telomeric and subtelomeric sequences were observed at the interstitial junction point of the inv dup(1q) and of the der(12)t(7;12), respectively. The present cases and review of the literature suggest that the presence of ITSs at internal sites of the chromosomes may explain mechanisms of the patients's mosaic structural rearrangements. PMID:25428228

  4. Predicting deleterious nsSNPs: an analysis of sequence and structural attributes

    Directory of Open Access Journals (Sweden)

    Saqi Mansoor AS

    2006-04-01

    Full Text Available Abstract Background There has been an explosion in the number of single nucleotide polymorphisms (SNPs within public databases. In this study we focused on non-synonymous protein coding single nucleotide polymorphisms (nsSNPs, some associated with disease and others which are thought to be neutral. We describe the distribution of both types of nsSNPs using structural and sequence based features and assess the relative value of these attributes as predictors of function using machine learning methods. We also address the common problem of balance within machine learning methods and show the effect of imbalance on nsSNP function prediction. We show that nsSNP function prediction can be significantly improved by 100% undersampling of the majority class. The learnt rules were then applied to make predictions of function on all nsSNPs within Ensembl. Results The measure of prediction success is greatly affected by the level of imbalance in the training dataset. We found the balanced dataset that included all attributes produced the best prediction. The performance as measured by the Matthews correlation coefficient (MCC varied between 0.49 and 0.25 depending on the imbalance. As previously observed, the degree of sequence conservation at the nsSNP position is the single most useful attribute. In addition to conservation, structural predictions made using a balanced dataset can be of value. Conclusion The predictions for all nsSNPs within Ensembl, based on a balanced dataset using all attributes, are available as a DAS annotation. Instructions for adding the track to Ensembl are at http://www.brightstudy.ac.uk/das_help.html

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-05-19

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

  6. Signatures of DNA flexibility, interactions and sequence-related structural variations in classical X-ray diffraction patterns

    OpenAIRE

    Kornyshev, A. A.; Lee, D. J.; Wynveen, A.; Leikin, S.

    2011-01-01

    The theory of X-ray diffraction from ideal, rigid helices allowed Watson and Crick to unravel the DNA structure, thereby elucidating functions encoded in it. Yet, as we know now, the DNA double helix is neither ideal nor rigid. Its structure varies with the base pair sequence. Its flexibility leads to thermal fluctuations and allows molecules to adapt their structure to optimize their intermolecular interactions. In addition to the double helix symmetry revealed by Watson and Crick, classical...

  7. GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization

    Directory of Open Access Journals (Sweden)

    Ranjan Akash

    2007-08-01

    Full Text Available Abstract Background Mycobacterium smegmatis is fast growing non-pathogenic mycobacteria. This organism has been widely used as a model organism to study the biology of other virulent and extremely slow growing species like Mycobacterium tuberculosis. Based on the homology of the N-terminal DNA binding domain, the recently sequenced genome of M. smegmatis has been shown to possess several putative GntR regulators. A striking characteristic feature of this family of regulators is that they possess a conserved N-terminal DNA binding domain and a diverse C-terminal domain involved in the effector binding and/or oligomerization. Since the physiological role of these regulators is critically dependent upon effector binding and operator sites, we have analysed and classified these regulators into their specific subfamilies and identified their potential binding sites. Results The sequence analysis of M. smegmatis putative GntRs has revealed that FadR, HutC, MocR and the YtrA-like regulators are encoded by 45, 8, 8 and 1 genes respectively. Further out of 45 FadR-like regulators, 19 were classified into the FadR group and 26 into the VanR group. All these proteins showed similar secondary structural elements specific to their respective subfamilies except MSMEG_3959, which showed additional secondary structural elements. Using the reciprocal BLAST searches, we further identified the orthologs of these regulators in Bacillus subtilis and other mycobacteria. Since the expression of many regulators is auto-regulatory, we have identified potential operator sites for a number of these GntR regulators by analyzing the upstream sequences. Conclusion This study helps in extending the annotation of M. smegmatis GntR proteins. It identifies the GntR regulators of M. smegmatis that could serve as a model for studying orthologous regulators from virulent as well as other saprophytic mycobacteria. This study also sheds some light on the nucleotide preferences in the target-motifs of GntRs thus providing important leads for initiating the experimental characterization of these proteins, construction of the gene regulatory network for these regulators and an understanding of the influence of these proteins on the physiology of the mycobacteria.

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

    Scientific Electronic Library Online (English)

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

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

  9. The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone.

    Science.gov (United States)

    Roche, Daniel Barry; Brüls, Thomas

    2015-05-01

    As the largest fraction of any proteome does not carry out enzymatic functions, and in order to leverage 3D structural data for the annotation of increasingly higher volumes of sequence data, we wanted to assess the strength of the link between coarse grained structural data (i.e., homologous superfamily level) and the enzymatic versus non-enzymatic nature of protein sequences. To probe this relationship, we took advantage of 41 phylogenetically diverse (encompassing 11 distinct phyla) genomes recently sequenced within the GEBA initiative, for which we integrated structural information, as defined by CATH, with enzyme level information, as defined by Enzyme Commission (EC) numbers. This analysis revealed that only a very small fraction (about 1%) of domain sequences occurring in the analyzed genomes was found to be associated with homologous superfamilies strongly indicative of enzymatic function. Resorting to less stringent criteria to define enzyme versus non-enzyme biased structural classes or excluding highly prevalent folds from the analysis had only modest effect on this proportion. Thus, the low genomic coverage by structurally anchored protein domains strongly associated to catalytic activities indicates that, on its own, the power of coarse grained structural information to infer the general property of being an enzyme is rather limited. PMID:25559918

  10. Lanthanide complexes in hybrid halometallate materials: interconversion between a novel 2D microporous framework and a 1D zigzag chain structure of iodoargentates templated by octakis-solvated terbium(III) cation.

    Science.gov (United States)

    Mishra, Shashank; Jeanneau, Erwann; Ledoux, Gilles; Daniele, Stéphane

    2009-07-01

    Octakis solvated terbium iodide complexes [Tb(DMSO)(8)]I(3) (1) and [Tb(DMF)(8)]I(3) (2) (DMSO = dimethylsulfoxide; DMF = dimethylformamide) were used as synthons to construct novel iodoargentate fabrics. Reaction of 1 with 6 equivalents of AgI in the presence of NH(4)I produced a novel framework compound [Tb(DMSO)(8)](2)[Ag(2)(mu-I)(3)I(2)][Ag(5)(mu(3)-I)(4)(mu-I)(4)](2infinity) (3) involving alternate layers of discrete [Tb(DMSO)(8)](3+) cation, [Ag(2)I(5)](3-) anion and a 2D microporous sheet of the composition [Ag(5)I(8)](3-), whereas similar reaction of 2 yielded [Tb(DMF)(8)][Ag(6)(mu(4)-I)(2)(mu(3)-I)(2)(mu-I)(5)](1infinity) (4) with a 1D zigzag structure. The two structural forms are completely inter-convertible on mutual exchange of DMSO and DMF ligands, the partial substitution of the former ligand in 3 yielding a mixed-ligand complex [Tb(DMF)(6.7)(DMSO)(1.3)][Ag(6)(mu(4)-I)(2)(mu(3)-I)(2)(mu-I)(5)](1infinity) (5). Single crystal X-ray structures are reported for all the complexes. Thermo-gravimetric analyses of these complexes show that thermal stability decreases in the order 4 > 2 > 3 > 1, whereas the diffuse reflectance spectra of 3 and 4 exhibit an optical band gap of about 3.7 eV, thus revealing the insulator nature of these hybrid iodoargentates. Compared to solvated terbium iodide complexes 1 and 2, the high energy transitions in the excitation spectra of the iodoargentate complexes 3 and 4 are quenched by a process which can best be attributed to the auto-ionization of the carriers in the above materials. PMID:19662287

  11. Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance

    OpenAIRE

    Bansal Vikas; Bashir Ali; Bafna Vineet

    2010-01-01

    Abstract Background Massively parallel DNA sequencing technologies have enabled the sequencing of several individual human genomes. These technologies are also being used in novel ways for mRNA expression profiling, genome-wide discovery of transcription-factor binding sites, small RNA discovery, etc. The multitude of sequencing platforms, each with their unique characteristics, pose a number of design challenges, regarding the technology to be used and the depth of sequencing required for a ...

  12. Sequence-specific size, structure, and stability of tight protein knots

    CERN Document Server

    Dzubiella, Joachim

    2008-01-01

    Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport, e.g., as in cellular threading or translocation processes through narrow biological pores. Here we investigate tigh peptide knot (TPK) characteristics in detail by pulling selected 3_1 and 4_1-knotted peptides using all-atom molecular dynamics computer simulations. We find that the 3_1 and 4_1-TPK lengths are typically Delta l~4.7 nm and 6.9 nm, respectively, for a wide range of tensions (F < 1.5 nN), pointing to a pore diameter of ~2 nm below which a translocated knotted protein might get stuck. The 4_1-knot length is in agreement with recent AFM pulling experiments. Detailed TPK characteristics however, may be sequence-specific: we find a different size and structural behavior in polyglycines, and, strikingly, a strong hydrogen bonding and water molecule trapping capabi...

  13. Analysis of sequence, structure of GAPDH of Leishmania donovani and its interactions.

    Science.gov (United States)

    Sahoo, Ganesh Chandra; Dikhit, Manas Ranjan; Rani, Mukta; Ansari, Md Yousuf; Jha, Chanda; Rana, Sindhuprava; Das, Pradeep

    2013-03-01

    Drug resistance acquired by Leishmania donovani (Ldv) is a major problem in the treatment and control of visceral leishmaniasis (VL). Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a major glycolytic enzyme has been targeted as is found in other protozoan which cause diseases like sleeping sickness. GAPDH gene of Ldv (AG83 strain) was amplified, sequenced, and modeled on the basis of crystal structure of Leishmania mexicana. The model of the Ldv GAPDH exhibited NAD-binding domain with Rossmann folding. Virtual screening of different experimentally proved compounds with the crystal and the modeled structures of GAPDH of Leishmania strains revealed diverse binding affinities of different compounds. Comparison of binding affinities (based on different programs) of compounds revealed that discovery studio v2.5 (Ligandfit) was able to predict the most hit compounds, the best hit compounds against GAPDH of Leishmania strains are hydrazine, vetrazine, and benzyl carbazate. It is predicted that patients suffering from both VL and cardiac disorders (atrial fibrillation) may benefit if they are treated with warfarin in conjunction with first-line antileishmanial therapies such as miltefosine and AmBisome. PMID:22830998

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

    Directory of Open Access Journals (Sweden)

    Manzini Giovanni

    2007-07-01

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

  15. Cellular immunostimulation by CpG-sequence-coated DNA origami structures.

    Science.gov (United States)

    Schüller, Verena J; Heidegger, Simon; Sandholzer, Nadja; Nickels, Philipp C; Suhartha, Nina A; Endres, Stefan; Bourquin, Carole; Liedl, Tim

    2011-12-27

    To investigate the potential of DNA origami constructs as programmable and noncytotoxic immunostimulants, we tested the immune responses induced by hollow 30-helix DNA origami tubes covered with up to 62 cytosine-phosphate-guanine (CpG) sequences in freshly isolated spleen cells. Unmethylated CpG sequences that are highly specific for bacterial DNA are recognized by a specialized receptor of the innate immune system localized in the endosome, the Toll-like receptor 9 (TLR9). When incubated with oligonucleotides containing CpGs, immune cells are stimulated through TLR9 to produce and secrete cytokine mediators such as interleukin-6 (IL-6) and interleukin-12p70 (IL-12p70), a process associated with the initiation of an immune response. In our studies, the DNA origami tube built from an 8634 nt long variant of the commonly used single-stranded DNA origami scaffold M13mp18 and 227 staple oligonucleotides decorated with 62 CpG-containing oligonucleotides triggered a strong immune response, characterized by cytokine production and immune cell activation, which was entirely dependent on TLR9 stimulation. Such decorated origami tubes also triggered higher immunostimulation than equal amounts of CpG oligonucleotides associated with a standard carrier system such as Lipofectamine. In the absence of CpG oligonucleotides, cytokine production induced by the origami tubes was low and was not related to TLR9 recognition. Fluorescent microscopy revealed localization of CpG-containing DNA origami structures in the endosome. The DNA constructs showed in contrast to Lipofectamine no detectable toxicity and did not affect the viability of splenocytes. We thus demonstrate that DNA origami constructs represent a delivery system for CpG oligonucleotides that is both efficient and nontoxic. PMID:22092186

  16. Structure and sequence of mutations induced by ionizing radiation at selectable loci in Chinese hamster ovary cells

    International Nuclear Information System (INIS)

    The spectrum of mutations induced by ionizing radiation at two non-essential genetic loci varies markedly. Those at the adenine phosphoribosyl transferase (aprt) locus predominantly have no detectable alterations of gene structure on Southern blots, while those at the hypoxanthine guanine phosphoribosyl transferase (hprt) locus are largely massive deletions eliminating all coding sequence. Insertion mutations were detected at both loci. To characterize the sequence alterations producing the minor changes at the aprt locus, two mutant genes were cloned from lambda genomic libraries and sequenced. One of these mutants proved to be a 20 base-pair deletion formed between two short (3 base-pair) direct repeat sequences, while the second was the result of a 58 base-pair insertion accompanied by a 13 base-pair deletion. (author)

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

    Science.gov (United States)

    Deng, Su-Ping; Huang, De-Shuang

    2014-10-01

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

  18. Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics

    Directory of Open Access Journals (Sweden)

    Brunham Robert C

    2004-07-01

    Full Text Available Abstract Background We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, maintainability and safety work to model time-to-failure of mechanical devices, mechanisms, building constructions and equipment. Results We have found that the Weibull function describes protein fold distribution within and among genomes more accurately than conventional power functions which have been used in a number of structural genomic studies reported to date. It has also been found that the Weibull reliability parameter ? for protein fold distributions varies between genomes and may reflect differences in rates of gene duplication in evolutionary history of organisms. Conclusions The results of this work demonstrate that reliability analysis can provide useful insights and testable predictions in the fields of comparative and structural genomics.

  19. Inverted repeat regions of Marek's disease virus DNA possess a structure similar to that of the a sequence of herpes simplex virus DNA and contain host cell telomere sequences.

    OpenAIRE

    Kishi, M.; Bradley, G.; Jessip, J.; Tanaka, A.; Nonoyama, M.

    1991-01-01

    The genomic structure of Marek's disease virus (MDV) is similar to those of the alphaherpesviruses herpes simplex virus (HSV) types 1 and 2. Sequence analysis of the junction region between the long component (L) and the short component (S) revealed the existence of an a-like sequence, similar in structure to the a sequence of HSV-1. Further study revealed that the MDV genome contains five copies of the a-like sequence within the long terminal repeat region as well as in the short terminal re...

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

    DEFF Research Database (Denmark)

    Mirza, Aashiq H; Kaur, Simranjeet

    2014-01-01

    Long non-coding RNAs are a new class of non-coding RNAs that are at the crosshairs in many human diseases such as cancers, cardiovascular disorders, inflammatory and autoimmune disease like Inflammatory Bowel Disease (IBD) and Type 1 Diabetes (T1D). Nearly 90% of the phenotype-associated single-nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) lie outside of the protein coding regions, and map to the non-coding intervals. However, the relationship between phenotype-associated loci and the non-coding regions including the long non-coding RNAs (lncRNAs) is poorly understood. Here, we systemically identified all annotated IBD and T1D loci-associated lncRNAs, and mapped nominally significant GWAS/ImmunoChip SNPs for IBD and T1D within these lncRNAs. Additionally, we identified tissue-specific cis-eQTLs, and strong linkage disequilibrium (LD) signals associated with these SNPs. We explored sequence and structure based attributes of these lncRNAs, and also predicted the structuraleffects of mapped SNPs within them. We also identified lncRNAs in IBD and T1D that are under recent positive selection. Our analysis identified putative lncRNA secondary structure-disruptive SNPs within and in close proximity (+/-5 kb flanking regions) of IBD and T1D loci-associated candidate genes, suggesting that these RNA conformation-altering polymorphisms might be associated with diseased-phenotype. Disruption of lncRNA secondary structure due to presence of GWAS SNPs provides valuable information that could be potentially useful for future structure-function studies on lncRNAs.

  1. Developing JSequitur to Study the Hierarchical Structure of Biological Sequences in a Grammatical Inference Framework of String Compression Algorithms.

    Science.gov (United States)

    Galbadrakh, Bulgan; Lee, Kyung-Eun; Park, Hyun-Seok

    2012-12-01

    Grammatical inference methods are expected to find grammatical structures hidden in biological sequences. One hopes that studies of grammar serve as an appropriate tool for theory formation. Thus, we have developed JSequitur for automatically generating the grammatical structure of biological sequences in an inference framework of string compression algorithms. Our original motivation was to find any grammatical traits of several cancer genes that can be detected by string compression algorithms. Through this research, we could not find any meaningful unique traits of the cancer genes yet, but we could observe some interesting traits in regards to the relationship among gene length, similarity of sequences, the patterns of the generated grammar, and compression rate. PMID:23346041

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

    Directory of Open Access Journals (Sweden)

    Eddy Sean R

    2002-07-01

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

  3. Hydrothermal syntheses, crystal structures and properties of 0-D, 1-D and 2-D organic-inorganic hybrid borotungstates constructed from Keggin-type heteropolyanion [?-BW12O40]5- and transition-metal complexes

    International Nuclear Information System (INIS)

    Three novel organic-inorganic hybrid borotungstates {[Ni(phen)2(H2O)]2H(?-BW12O40)}.4H2O (1), [CuI(2,2'-bipy)(4,4'-bipy)0.5]2{[CuI(2,2'-bipy)]2CuI(4,4'-bipy)2 (?-BW12O40)} (2) and {[CuI(4,4'-bipy)]3H2(?-BW12O40)}.3.5H2O (3) (phen=1,10-phenanthroline, 2,2'-bipy=2,2'-bipyridine, 4,4'-bipy=4,4'-bipyridine) have been hydrothermally synthesized and structurally characterized by elemental analyses, IR, UV spectra, powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA), single-crystal X-ray diffraction, X-ray photoelectron spectroscopy (XPS) and photoluminescence. The structural analysis reveals that 1 consists of a 0-D bisupporting polyoxometalate cluster where two [Ni(phen)2(H2O)]2+ cations are grafted on the polyoxoanion [?-BW12O40]5- through two terminal oxygen atoms, 2 shows a 1-D infinite chain constructed from [?-BW12O40]5- polyoxoanions and {[CuI(2,2'-bipy)]2CuI(4,4'-bipy)2}3+ cations by means of alternating fashion, and 3 displays an unprecedented 2D extended structure built by [?-BW12O40]5- polyoxoanions and -CuI-4,4'-bipy- lins and -CuI-4,4'-bipy- linear chains, in which each [?-BW12O40]5- polyoxoanion acts as a tetradentate inorganic ligand and provides three terminal oxygen atom and one two-bridging oxygen atom. The presence of NiII and WVI in 1, CuI ions and WVI in 2 and 3 are identified by XPS spectra. The photoluminescence of 2 and 3 are also investigated. - Graphical abstract: Three novel organic-inorganic hybrid borotungstates {[Ni(phen)2(H2O)]2H(?-BW12O40)}.4H2O (1), [CuI(2,2'-bipy) (4,4'-bipy)0.5]2{[CuI(2,2'-bipy)]2CuI(4,4'-bipy)2(?-BW12O40)} (2) and {[CuI(4,4'-bipy)]3H2(?-BW12O40)}.3.5H2O (3) have been hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction, thermogravimetric analyses, X-ray photoelectron spectroscopy and photoluminescence.

  4. Striking structural dynamism and nucleotide sequence variation of the transposon Galileo in the genome of Drosophila mojavensis

    Directory of Open Access Journals (Sweden)

    Marzo Mar

    2013-02-01

    Full Text Available Abstract Background Galileo is a transposable element responsible for the generation of three chromosomal inversions in natural populations of Drosophila buzzatii. Although the most characteristic feature of Galileo is the long internally-repetitive terminal inverted repeats (TIRs, which resemble the Drosophila Foldback element, its transposase-coding sequence has led to its classification as a member of the P-element superfamily (Class II, subclass 1, TIR order. Furthermore, Galileo has a wide distribution in the genus Drosophila, since it has been found in 6 of the 12 Drosophila sequenced genomes. Among these species, D. mojavensis, the one closest to D. buzzatii, presented the highest diversity in sequence and structure of Galileo elements. Results In the present work, we carried out a thorough search and annotation of all the Galileo copies present in the D. mojavensis sequenced genome. In our set of 170 Galileo copies we have detected 5 Galileo subfamilies (C, D, E, F, and X with different structures ranging from nearly complete, to only 2 TIR or solo TIR copies. Finally, we have explored the structural and length variation of the Galileo copies that point out the relatively frequent rearrangements within and between Galileo elements. Different mechanisms responsible for these rearrangements are discussed. Conclusions Although Galileo is a transposable element with an ancient history in the D. mojavensis genome, our data indicate a recent transpositional activity. Furthermore, the dynamism in sequence and structure, mainly affecting the TIRs, suggests an active exchange of sequences among the copies. This exchange could lead to new subfamilies of the transposon, which could be crucial for the long-term survival of the element in the genome.

  5. STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence

    Science.gov (United States)

    Neshich, Goran; Togawa, Roberto C.; Mancini, Adauto L.; Kuser, Paula R.; Yamagishi, Michel E. B.; Pappas, Georgios; Torres, Wellington V.; Campos, Tharsis Fonseca e; Ferreira, Leonardo L.; Luna, Fabio M.; Oliveira, Adilton G.; Miura, Ronald T.; Inoue, Marcus K.; Horita, Luiz G.; de Souza, Dimas F.; Dominiquini, Fabiana; Álvaro, Alexandre; Lima, Cleber S.; Ogawa, Fabio O.; Gomes, Gabriel B.; Palandrani, Juliana F.; dos Santos, Gabriela F.; de Freitas, Esther M.; Mattiuz, Amanda R.; Costa, Ivan C.; de Almeida, Celso L.; Souza, Savio; Baudet, Christian; Higa, Roberto H.

    2003-01-01

    STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Biologists find SMS useful because it provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. Using SMS it is now possible to analyze sequence to structure relationships, the quality of the structure, nature and volume of atomic contacts of intra and inter chain type, relative conservation of amino acids at the specific sequence position based on multiple sequence alignment, indications of folding essential residue (FER) based on the relationship of the residue conservation to the intra-chain contacts and C?–C? and C?–C? distance geometry. Specific emphasis in SMS is given to interface forming residues (IFR)—amino acids that define the interactive portion of the protein surfaces. SMS may simultaneously display and analyze previously superimposed structures. PDB updates trigger SMS updates in a synchronized fashion. SMS is freely accessible for public data at http://www.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS and http://trantor.bioc.columbia.edu/SMS. PMID:12824333

  6. Structural variability of nucleosomes detected by single-pair Förster resonance energy transfer: histone acetylation, sequence variation, and salt effects.

    Science.gov (United States)

    Gansen, Alex; Tóth, Katalin; Schwarz, Nathalie; Langowski, Jörg

    2009-03-01

    Nucleosomes were reconstituted from 170 bp long fragments of 5S rDNA and an optimal positioning sequence, the Selex 601, with recombinant histones. In free-solution single pair Förster resonance energy transfer (spFRET) measurements of the distance between fluorescently labeled bases in the nucleosomal DNA, the samples exhibited structural diversity. The structural heterogeneity correlated with the stability of the complexes and depended on the DNA sequence and histone acetylation. The stability of the nucleosomes was assessed via dilution-driven disruption: histone acetylation decreased nucleosome stability. The spFRET experiments used a new approach for data acquisition and analysis that we term "deliberately detuned detection" (D3). This permits the separation of subpopulations in the samples even for the low-FRET regime characteristic for the linker-DNA labeled nucleosomes. Thus, it became possible to study in more detail histone acetylation- and salt-dependent structural variations using either end- or internally labeled DNAs on the nucleosome. We found that the distance distribution of the fluorophore pairs on the linker DNA ends was much more sensitive to histone acetylation or sequence variation than that of labels on the internal part of the DNA, which was more tightly associated with the histone core. spFRET on freely diffusing nucleosomes allows us therefore to localize the influence of histone modifications and DNA sequence variations on the nucleosome structure and dynamics. PMID:18950220

  7. Three-dimensional simulations of near-surface convection in main-sequence stars - I. Overall structure

    OpenAIRE

    Beeck, Benjamin; Cameron, Robert H.; Reiners, Ansgar; Schu?ssler, Manfred

    2013-01-01

    The near-surface layers of cool main-sequence stars are structured by convective flows, which are overshooting into the atmosphere. The flows and the associated spatio-temporal variations of density and temperature affect spectral line profiles and thus have an impact on estimates of stellar properties such as effective temperature, gravitational acceleration, and abundances. We aim at identifying distinctive properties of the thermodynamic structure of the atmospheres of di...

  8. Structural changes induced by binding of the high-mobility group I protein to a mouse satellite DNA sequence.

    OpenAIRE

    Slama-Schwok, A; Zakrzewska, K.; Léger, G.; Leroux, Y; Takahashi, M.; Käs, E; Debey, P

    2000-01-01

    Using spectroscopic methods, we have studied the structural changes induced in both protein and DNA upon binding of the High-Mobility Group I (HMG-I) protein to a 21-bp sequence derived from mouse satellite DNA. We show that these structural changes depend on the stoichiometry of the protein/DNA complexes formed, as determined by Job plots derived from experiments using pyrene-labeled duplexes. Circular dichroism and melting temperature experiments extended in the far ultraviolet range show t...

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

    Science.gov (United States)

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

    2010-01-01

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

  10. Correlation between sequence conservation and structural thermodynamics of microRNA precursors from human, mouse, and chicken genomes

    Directory of Open Access Journals (Sweden)

    Wang Shengqi

    2010-10-01

    Full Text Available Abstract Background Previous studies have shown that microRNA precursors (pre-miRNAs have considerably more stable secondary structures than other native RNAs (tRNA, rRNA, and mRNA and artificial RNA sequences. However, pre-miRNAs with ultra stable secondary structures have not been investigated. It is not known if there is a tendency in pre-miRNA sequences towards or against ultra stable structures? Furthermore, the relationship between the structural thermodynamic stability of pre-miRNA and their evolution remains unclear. Results We investigated the correlation between pre-miRNA sequence conservation and structural stability as measured by adjusted minimum folding free energies in pre-miRNAs isolated from human, mouse, and chicken. The analysis revealed that conserved and non-conserved pre-miRNA sequences had structures with similar average stabilities. However, the relatively ultra stable and unstable pre-miRNAs were more likely to be non-conserved than pre-miRNAs with moderate stability. Non-conserved pre-miRNAs had more G+C than A+U nucleotides, while conserved pre-miRNAs contained more A+U nucleotides. Notably, the U content of conserved pre-miRNAs was especially higher than that of non-conserved pre-miRNAs. Further investigations showed that conserved and non-conserved pre-miRNAs exhibited different structural element features, even though they had comparable levels of stability. Conclusions We proposed that there is a correlation between structural thermodynamic stability and sequence conservation for pre-miRNAs from human, mouse, and chicken genomes. Our analyses suggested that pre-miRNAs with relatively ultra stable or unstable structures were less favoured by natural selection than those with moderately stable structures. Comparison of nucleotide compositions between non-conserved and conserved pre-miRNAs indicated the importance of U nucleotides in the pre-miRNA evolutionary process. Several characteristic structural elements were also detected in conserved pre-miRNAs.

  11. 1D Signal Phase Unwrapper

    International Nuclear Information System (INIS)

    Signal phase values are crucial in seismic data interpretation to enhance the analysis of amplitudes, bright spots, dim spots etc. Phase values can be zeroed in a section to enhance signal comparison which can be related to velocities and other petro-physical properties. Homomorphic signal processing and deconvolution both require exact phase value estimates. Consequently, in-depth investigations are necessary to solve problems of phase estimation in various wave propagation situations. Meanwhile, phase values are often measured modulo-2 called principal values and the amount of phase estimation in various wave propagation situations. Meanwhile, values are often measured modulo-2 called principal values and the amount of phase information is independent of any integer multiple of 2 added to the principal value phase. However, to be useful for linear processing, this principal value phase has to be unwrapped. This will result in a continuous function, the 2 discontinuities being eliminated, or at least reduced. Operations like deconvolution and homomorphic signal processing require unwrapped phase values. Phase unwrapping is applied to pre-stack data for the computation of PVA phase variation with angle of incidence attribute used to improve processing and interpretation.Conventional 1D phase unwrapping algorithms integrate the wrapped phase difference between two contiguous points. This was later improved to use adaptive integration of phase differences. Alternativelyration of phase differences. Alternatively, phase difference ambiguity due to sparse sampling can be overcome by taking samples at progressively closer intervals. These methods are often inadequate due to problems of aliasing caused by rapid phase value variations. We develop a 1D phase unwrapping technique using the amplitude of a complex trace and discrete Fourier transforms. This technique is simple, very reliable and less sensitive to aliasing. It exploits the periodicity of Fourier transform to unwind wrapped phase values. We demonstrate this technique using synthetic and real data

  12. A 1-D dusty plasma photonic crystal

    International Nuclear Information System (INIS)

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

  13. A 1-D dusty plasma photonic crystal

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-09-21

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

  14. Quantitative 1D saturation profiles on chalk by NMR.

    DEFF Research Database (Denmark)

    Olsen, Dan; Topp, Simon

    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 that strong saturation gradients exist in chalk core samples after core floods, due to capillary effects. The method is useful in analysis of corefloods, e.g., for determination of capillary pressure functions

  15. Insilico structural analysis of parasporin 2 protein sequences of non-toxic bacillus thuringiensis

    Directory of Open Access Journals (Sweden)

    Ayyasamy Mahalakshmi

    2010-04-01

    Full Text Available The unusual and remarkable property of parasporin 2 of non-insecticidal Bacillus thuringiensis is specifically recognizing and selectively targeting human leukemic cell lines. The 37-kDa inactive nascent protein is proteolytically cleaved to the 30-kDa active form that loses both the N-terminal and the C-terminal segments. Accumulated cytological and biochemical observations on parasporin-2 imply that the protein is a pore-forming toxin. To confirm the hypothesis, insilico analysis was performed using homology modeling. The resulting model of parasporin 2 protein is unusually elongated and mainly comprises long ?-strands aligned with its long axis. It is similar to aerolysin-type ?-pore-forming toxins, which strongly reinforce the pore-forming hypothesis. The molecule can be divided into three domains. Domain 1, comprising a small ?-sheet sandwiched by short ?-helices, is probably the target-binding module. Two other domains are both ?-sandwiches and thought to be involved in oligomerization and pore formation. Domain 2 has a putative channel-forming ?-hairpin characteristic of aerolysin-type toxins. The surface of the protein has an extensive track of exposed side chains of serine and threonine residues. The track might orient the molecule on the cell membrane when domain 1 binds to the target until oligomerization and pore formation are initiated. The ?-hairpin has such a tight structure that it seems unlikely to reform as postulated in a recent model of pore formation developed for aerolysin-type toxins. Parasporin 2 (Accession no: BAD35170 protein sequence analysis indicated two different domains namely, aerolysin toxin and clostridium toxin domain based on different database searches (CDD and Pfam. It showed a close similarity with the available PDB template (PDB id: 2ZTB of parasporin which has cytocidal activity against MOLT-4, HL60 and Jurkat cell lines. Based on the PSI Blast analysis, 3D structures of the domains were predicted by using Swiss model server. Accuracy of the prediction of 3D structure of different domains of parasporin protein was further validated by Ramachandran plot and PROCHECK (G-value. The structure is dominated by ?-strands (67%, S1-12, most of which are remarkably extensive, running all or most of the longer axis of the molecule. This study helped to elucidate the 3D structure of parasporin 2 (Acc. No. BAD35170 which might enable to probe further its specific mechanism of action. Though the similarity is observed in the domain architecture, there is variation in the regions of the domains even among the same group of parasporin 2. Docking of this model structure and experimental structure with specific receptors of the cancer cells will facilitate to explore mechanism of parasporin 2 action and also provide information about its evolutionary relationship with toxic Cry proteins.

  16. ITS2, 18S, 16S or any other RNA - simply aligning sequences and their individual secondary structures simultaneously by an automatic approach.

    Science.gov (United States)

    Wolf, Matthias; Koetschan, Christian; Müller, Tobias

    2014-08-10

    Secondary structures of RNA sequences are increasingly being used as additional information in reconstructing phylogenies and/or in distinguishing species by compensatory base change (CBC) analyses. However, in most cases just one secondary structure is used in manually correcting an automatically generated multiple sequence alignment and/or just one secondary structure is used in guiding a sequence alignment still completely generated by hand. With the advent of databases and tools offering individual RNA secondary structures, here we re-introduce a twelve letter code already implemented in 4SALE - a tool for synchronous sequence and secondary structure alignment and editing - that enables one to align RNA sequences and their individual secondary structures synchronously and fully automatic, while dramatically increasing the phylogenetic information content. We further introduce a scaled down non-GUI version of 4SALE particularly designed for big data analysis, and available at: http://4sale.bioapps.biozentrum.uni-wuerzburg.de. PMID:24881812

  17. Characterization of bud emergence 46 (BEM46) protein: Sequence, structural, phylogenetic and subcellular localization analyses

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Abhishek; Kollath-Leiß, Krisztina; Kempken, Frank, E-mail: fkempken@bot.uni-kiel.de

    2013-08-30

    Highlights: •All eukaryotes have at least a single copy of a bem46 ortholog. •The catalytic triad of BEM46 is illustrated using sequence and structural analysis. •We identified indels in the conserved domain of BEM46 protein. •Localization studies of BEM46 protein were carried out using GFP-fusion tagging. -- Abstract: The bud emergence 46 (BEM46) protein from Neurospora crassa belongs to the ?/?-hydrolase superfamily. Recently, we have reported that the BEM46 protein is localized in the perinuclear ER and also forms spots close by the plasma membrane. The protein appears to be required for cell type-specific polarity formation in N. crassa. Furthermore, initial studies suggested that the BEM46 amino acid sequence is conserved in eukaryotes and is considered to be one of the widespread conserved “known unknown” eukaryotic genes. This warrants for a comprehensive phylogenetic analysis of this superfamily to unravel origin and molecular evolution of these genes in different eukaryotes. Herein, we observe that all eukaryotes have at least a single copy of a bem46 ortholog. Upon scanning of these proteins in various genomes, we find that there are expansions leading into several paralogs in vertebrates. Usingcomparative genomic analyses, we identified insertion/deletions (indels) in the conserved domain of BEM46 protein, which allow to differentiate fungal classes such as ascomycetes from basidiomycetes. We also find that exonic indels are able to differentiate BEM46 homologs of different eukaryotic lineage. Furthermore, we unravel that BEM46 protein from N. crassa possess a novel endoplasmic-retention signal (PEKK) using GFP-fusion tagging experiments. We propose that three residues namely a serine 188S, a histidine 292H and an aspartic acid 262D are most critical residues, forming a catalytic triad in BEM46 protein from N. crassa. We carried out a comprehensive study on bem46 genes from a molecular evolution perspective with combination of functional analyses. The evolutionary history of BEM46 proteins is characterized by exonic indels in lineage specific manner.

  18. Sequence based residue depth prediction using evolutionary information and predicted secondary structure

    Directory of Open Access Journals (Sweden)

    Chen Ke

    2008-09-01

    Full Text Available Abstract Background Residue depth allows determining how deeply a given residue is buried, in contrast to the solvent accessibility that differentiates between buried and solvent-exposed residues. When compared with the solvent accessibility, the depth allows studying deep-level structures and functional sites, and formation of the protein folding nucleus. Accurate prediction of residue depth would provide valuable information for fold recognition, prediction of functional sites, and protein design. Results A new method, RDPred, for the real-value depth prediction from protein sequence is proposed. RDPred combines information extracted from the sequence, PSI-BLAST scoring matrices, and secondary structure predicted with PSIPRED. Three-fold/ten-fold cross validation based tests performed on three independent, low-identity datasets show that the distance based depth (computed using MSMS predicted by RDPred is characterized by 0.67/0.67, 0.66/0.67, and 0.64/0.65 correlation with the actual depth, by the mean absolute errors equal 0.56/0.56, 0.61/0.60, and 0.58/0.57, and by the mean relative errors equal 17.0%/16.9%, 18.2%/18.1%, and 17.7%/17.6%, respectively. The mean absolute and the mean relative errors are shown to be statistically significantly better when compared with a method recently proposed by Yuan and Wang [Proteins 2008; 70:509–516]. The results show that three-fold cross validation underestimates the variability of the prediction quality when compared with the results based on the ten-fold cross validation. We also show that the hydrophilic and flexible residues are predicted more accurately than hydrophobic and rigid residues. Similarly, the charged residues that include Lys, Glu, Asp, and Arg are the most accurately predicted. Our analysis reveals that evolutionary information encoded using PSSM is characterized by stronger correlation with the depth for hydrophilic amino acids (AAs and aliphatic AAs when compared with hydrophobic AAs and aromatic AAs. Finally, we show that the secondary structure of coils and strands is useful in depth prediction, in contrast to helices that have relatively uniform distribution over the protein depth. Application of the predicted residue depth to prediction of buried/exposed residues shows consistent improvements in detection rates of both buried and exposed residues when compared with the competing method. Finally, we contrasted the prediction performance among distance based (MSMS and DPX and volume based (SADIC depth definitions. We found that the distance based indices are harder to predict due to the more complex nature of the corresponding depth profiles. Conclusion The proposed method, RDPred, provides statistically significantly better predictions of residue depth when compared with the competing method. The predicted depth can be used to provide improved prediction of both buried and exposed residues. The prediction of exposed residues has implications in characterization/prediction of interactions with ligands and other proteins, while the prediction of buried residues could be used in the context of folding predictions and simulations.

  19. Two-dimensional deterministic photonic band gap structures based on the quasiperiodic sequences at millimeter wave frequencies

    Directory of Open Access Journals (Sweden)

    Y. Trabelsi

    2011-08-01

    Full Text Available Two-dimensional quasi-periodic band gap structures were investigated theoretically in microwave frequency range. Quasiperiodic photonic crystal based on the square range, arranged in a quasi-periodical fashion which follows Thue Morse or Fibonaci period substitutional sequences were obtained by the inflation rules emerging from the quasi-periodic sequence. The introduction of 2D quasi-periodicity distribution like Thue Morse or Fibonacci order and deterministic aperiodicity give some interesting microwave properties and offers amultitude of adjacent pseudo-band gap in different frequency range. The potential of photonic structures are explored by varying the structural parameters. The photonic band gap formation was explored as function of geometries of the structures such as pillar radius and parameters of quasi-periodical sequences. The electromagnetic field distribution can be described as a quasi-localized state varied by some defect carried by Thue Morse order. These structures provide interesting properties, which could be used to design novelmicrowave devices.

  20. THE INTERIOR STRUCTURE CONSTANTS AS AN AGE DIAGNOSTIC FOR LOW-MASS, PRE-MAIN-SEQUENCE DETACHED ECLIPSING BINARY STARS

    International Nuclear Information System (INIS)

    We propose a novel method for determining the ages of low-mass, pre-main-sequence stellar systems using the apsidal motion of low-mass detached eclipsing binaries. The apsidal motion of a binary system with an eccentric orbit provides information regarding the interior structure constants of the individual stars. These constants are related to the normalized stellar interior density distribution and can be extracted from the predictions of stellar evolution models. We demonstrate that low-mass, pre-main-sequence stars undergoing radiative core contraction display rapidly changing interior structure constants (greater than 5% per 10 Myr) that, when combined with observational determinations of the interior structure constants (with 5%-10% precision), allow for a robust age estimate. This age estimate, unlike those based on surface quantities, is largely insensitive to the surface layer where effects of magnetic activity are likely to be most pronounced. On the main sequence, where age sensitivity is minimal, the interior structure constants provide a valuable test of the physics used in stellar structure models of low-mass stars. There are currently no known systems where this technique is applicable. Nevertheless, the emphasis on time domain astronomy with current missions, such as Kepler, and future missions, such as LSST, has the potential to discover systems where the proposed method will be observationally feasible.

  1. Structural biology of disease-associated repetitive DNA sequences and protein-DNA complexes involved in DNA damage and repair

    Energy Technology Data Exchange (ETDEWEB)

    Gupta, G.; Santhana Mariappan, S.V.; Chen, X.; Catasti, P.; Silks, L.A. III; Moyzis, R.K.; Bradbury, E.M.; Garcia, A.E.

    1997-07-01

    This project is aimed at formulating the sequence-structure-function correlations of various microsatellites in the human (and other eukaryotic) genomes. Here the authors have been able to develop and apply structure biology tools to understand the following: the molecular mechanism of length polymorphism microsatellites; the molecular mechanism by which the microsatellites in the noncoding regions alter the regulation of the associated gene; and finally, the molecular mechanism by which the expansion of these microsatellites impairs gene expression and causes the disease. Their multidisciplinary structural biology approach is quantitative and can be applied to all coding and noncoding DNA sequences associated with any gene. Both NIH and DOE are interested in developing quantitative tools for understanding the function of various human genes for prevention against diseases caused by genetic and environmental effects.

  2. Sequence-Specific Assignment and Secondary Structure of the Catalytic Domain of Protein from Ubiquitination Pathway

    International Nuclear Information System (INIS)

    Ubiquitination is a post-translational protein modification which plays an important role in a wide variety of cellular processes including cell cycle, DNA repair and cell apoptosis. It is well known, that the ubiquitination requires sequential activity of three enzymes with different functions: activation, conjugation and ligation. Unfortunately, the three-dimensional structures of all three proteins responsible for these processes are not available at present and the process of proteins ubiquitination still is not understood in detail. In our communication, we present first, preliminary NMR data for the sequence-specific assignments for 112 amino acid residues long domain of one of the proteins from the ubiquitination pathway. The NMR samples were prepared by dissolving 1 mm either 15N-labeled or 15N, 13C-double labeled protein in 90%/10% H2O/D2O, 50 mm TRIS buffer, and 50 mm NaCl. The ph was adjusted to 6.5 (uncorrected value). All NMR measurements were performed on the Varian Unity+ 500 NMR spectrometer (11.7 T) equipped with three channels, Performa II PFG unit and 5 mm 1H, 13C, 15N-triple resonance pro behead. The 1H, 15N, and 13C backbone resonances were assigned by standard methods using 3D heteronuclear HNCACB, CBCA(CO)NH, HNCA, HN(CO)CA, HNCO, (HCA)CO(CA)NH NMR spectra collected at 303 K. The aliphatic 1H and 13C resoatic 1H and 13C resonances were assigned on the basis of C(CO)NH, HBHA(CO)NH, and H(CO)NH experiments. After finishing of assignment procedure, solution of secondary structure in studied protein has been performed. The exact position of the ?-helices and ?-strands were solved on base analysis of cross-peaks between HN and H? protons in 3D 15N-edited NOESY-HSQC spectrum, 3JNH? coupling constants evaluated from 3D HNHA experiment, and chemical shifts of backbone nuclei (TALOS software). Obtained results will be used in future for solution of three-dimensional structure of catalytic domain with high resolution by means NMR methods. (author)

  3. Uncovering the Pseudo-Subclonal Structure of Tumor Sample With Copy Number Variation Analysis of Next-Generation Sequencing Data - Yi Qiao, TCGA Scientific Symposium 2011

    Science.gov (United States)

    Home News and Events Multimedia Library Videos Uncovering the Pseudo-Subclonal Structure of Tumor Samples - Yi Qiao Uncovering the Pseudo-Subclonal Structure of Tumor Sample With Copy Number Variation Analysis of Next-Generation Sequencing Data -

  4. Structure of a human beta-actin-related pseudogene which lacks intervening sequences.

    OpenAIRE

    Moos, M.; Gallwitz, D.

    1982-01-01

    From a human genomic library we have isolated and sequenced a beta-actin-related pseudogene (Hbeta Ac-psi l) which is free of intervening sequences. Several nucleotide insertions and deletions and translational stop codons generated within the protein-coding region indicate that this gene is functionless.

  5. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

    OpenAIRE

    Müller Kirsten M; Madabusi Lakshmi V; Lin Nan; Feng Brian; Du Yushi; D'Souza Lisa M; Collett James R; Schnare Murray N; Subramanian Sankar; Cannone Jamie J; Pande Nupur; Shang Zhidi; Yu Nan; Gutell Robin R

    2002-01-01

    Abstract Background Comparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree. Underlying these accomplishments are very large, well-organized, and processed collections of RNA sequences. This data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of c...

  6. Amino-terminal amino acid sequence of the major structural polypeptides of avian retroviruses: sequence homology between reticuloendotheliosis virus p30 and p30s of mammalian retroviruses.

    Science.gov (United States)

    Hunter, E; Bhown, A S; Bennett, J C

    1978-01-01

    The major structural polypeptides, p30 of reticuloendotheliosis virus (REV) (strain T) and p27 of avian sarcoma virus B77, have been compared with regard to amino acid composition. NH2-terminal amino acid sequence, and immunological crossreactions. The amino acid composition of the two polypeptides is distinct, and a comparison of the first 30 NH2-terminal amino acids of REV p30 with that for the first 25 of B77 p27 yields only three homologous residues. In competition radioimmunoassays the polypeptides show no crossreactivity. A comparison of the amino acid composition and NH2-terminal amino acid sequence of REV p30 with those reported for several mammalian retrovirus p30s shows remarkable similarities. Both REV and mammalian p30s contain a large number of polar residues in their amino acid composition and show approximately 40% homology in the first 30 NH2-terminal amino acids. No crossreactivity could be observed, however, in competition radioimmunoassays between Rauscher murine leukemia virus p30 and that of REV. The observations reported here suggest a close evolutionary relationship between REV and the mammalian retroviruses. Images PMID:208072

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

    Directory of Open Access Journals (Sweden)

    Zuzana Ho?ejší

    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.

  8. Prediction of guide strand of microRNAs from its sequence and secondary structure

    Directory of Open Access Journals (Sweden)

    Ahmed Firoz

    2009-04-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are produced by the sequential processing of a long hairpin RNA transcript by Drosha and Dicer, an RNase III enzymes, and form transitory small RNA duplexes. One strand of the duplex, which incorporates into RNA-induced silencing complex (RISC and silences the gene expression is called guide strand, or miRNA; while the other strand of duplex is degraded and called the passenger strand, or miRNA*. Predicting the guide strand of miRNA is important for better understanding the RNA interference pathways. Results This paper describes support vector machine (SVM models developed for predicting the guide strands of miRNAs. All models were trained and tested on a dataset consisting of 329 miRNA and 329 miRNA* pairs using five fold cross validation technique. Firstly, models were developed using mono-, di-, and tri-nucleotide composition of miRNA strands and achieved the highest accuracies of 0.588, 0.638 and 0.596 respectively. Secondly, models were developed using split nucleotide composition and achieved maximum accuracies of 0.553, 0.641 and 0.602 for mono-, di-, and tri-nucleotide respectively. Thirdly, models were developed using binary pattern and achieved the highest accuracy of 0.708. Furthermore, when integrating the secondary structure features with binary pattern, an accuracy of 0.719 was seen. Finally, hybrid models were developed by combining various features and achieved maximum accuracy of 0.799 with sensitivity 0.781 and specificity 0.818. Moreover, the performance of this model was tested on an independent dataset that achieved an accuracy of 0.80. In addition, we also compared the performance of our method with various siRNA-designing methods on miRNA and siRNA datasets. Conclusion In this study, first time a method has been developed to predict guide miRNA strands, of miRNA duplex. This study demonstrates that guide and passenger strand of miRNA precursors can be distinguished using their nucleotide sequence and secondary structure. This method will be useful in understanding microRNA processing and can be implemented in RNA silencing technology to improve the biological and clinical research. A web server has been developed based on SVM models described in this study http://crdd.osdd.net:8081/RISCbinder/.

  9. A Study of Sequence Clustering on Protein’s Primary Structure using a Statistical Method

    Directory of Open Access Journals (Sweden)

    Alina Bogan-Marta

    2006-07-01

    Full Text Available The clustering of biological sequences into biologically meaningful classesdenotes two computationally complex challenges: the choice of a biologically pertinent andcomputable criterion to evaluate the clusters homogenity, and the optimal exploration ofthe solution space. Here we are analysing the clustering potential of a new method ofsequence similarity based on statistical sequence content evaluation. Applying on the samedata the popular CLUSTAL W method for sequence similarity we contrasted the results.The analysis, computational efficiency and high accuracy of the results from the newmethod is encouraging for further development that could make it an appealing alternativeto the existent methods.

  10. Sequence dependent structure and thermodynamics of DNA oligonucleotides and polynucleotides: uv melting and NMR (nuclear magnetic resonance) studies

    International Nuclear Information System (INIS)

    Thermodynamic parameters for double strand formation have been measured for the twenty-five DNA double helices made by mixing deoxyoligonucleotides of the sequence dCA3XA3G with the complement dCT3YT3G. Each of the bases A, C, G, T, and I (I = hypoxanthine) have been substituted at the positions labeled X and Y. The results are analyzed in terms of nearest neighbors. At higher temperatures the sequences containing a G/center dot/C base pair become more stable than those containing only A/center dot/T. All molecules containing mismatcher are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. Large neighboring base effects upon stability were observed. For example, when (X, Y) = (I, A), the duplex is eightfold more stable than when (X, Y) = (A, I). Independent of sequence effects the order of stabilities is: I/center dot/C /succ/ I/center dot/ A/succ/ I/center dot/T ? I/center dot/G. All of these results are discussed within the context of models for sequence dependent DNA secondary structure, replication fidelity and mechanisms of mismatch repair, and implications for probe design. The duplex deoxyoligonucleotide d(GGATGGGAG)/center dot/d(CTCCCATCC) is a portion of the gene recognition sequence of the protein transcription factor IIIA. The crystal structure of this oligonucleotide was shown to be A-form The present study employs Nuclear Magnetic Resonance, optical, chemical and enzymatic techniques to investigate the solution structure of this DNA 9-mer. (157 refs., 19 figs., 10 tabs.)

  11. Structure and organization of the mitochondrial DNA control region with tandemly repeated sequence in the Amazon ornamental fish.

    Science.gov (United States)

    Terencio, Maria Leandra; Schneider, Carlos Henrique; Gross, Maria Claudia; Feldberg, Eliana; Porto, Jorge Ivan Rebelo

    2013-02-01

    Tandemly repeated sequences are a common feature of vertebrate mitochondrial DNA control regions. However, questions still remain about their mode of evolution and function. To better understand patterns of variation in length and to explore the existence of previously described domain, we have characterized the control region structure of the Amazonian ornamental fish Nannostomus eques and Nannostomus unifasciatus. The control region ranged from 1121 to 1142 bp in length and could be separated into three domains: the domain associated with the extended terminal associated sequences, the central conserved domain, and the conserved sequence blocks domain. In the first domain, we encountered a sequence repeated 10 times in tandem (variable number tandem repeat (VNTR)) that could adopt an "inverted repetitions" type structural conformation. The results suggest that the VNTR pattern encountered in both N. eques and N. unifasciatus is consistent with the prerequisites of the illegitimate elongation model in which the unequal pairing of the chains near the 5'-end of the control region favors the formation of repetitions. PMID:22954310

  12. Bias in Ligation-Based Small RNA Sequencing Library Construction Is Determined by Adaptor and RNA Structure

    Science.gov (United States)

    Fuchs, Ryan T.; Sun, Zhiyi; Zhuang, Fanglei; Robb, G. Brett

    2015-01-01

    High-throughput sequencing (HTS) has become a powerful tool for the detection of and sequence characterization of microRNAs (miRNA) and other small RNAs (sRNA). Unfortunately, the use of HTS data to determine the relative quantity of different miRNAs in a sample has been shown to be inconsistent with quantitative PCR and Northern Blot results. Several recent studies have concluded that the major contributor to this inconsistency is bias introduced during the construction of sRNA libraries for HTS and that the bias is primarily derived from the adaptor ligation steps, specifically where single stranded adaptors are sequentially ligated to the 3’ and 5’-end of sRNAs using T4 RNA ligases. In this study we investigated the effects of ligation bias by using a pool of randomized ligation substrates, defined mixtures of miRNA sequences and several combinations of adaptors in HTS library construction. We show that like the 3’ adaptor ligation step, the 5’ adaptor ligation is also biased, not because of primary sequence, but instead due to secondary structures of the two ligation substrates. We find that multiple secondary structural factors influence final representation in HTS results. Our results provide insight about the nature of ligation bias and allowed us to design adaptors that reduce ligation bias and produce HTS results that more accurately reflect the actual concentrations of miRNAs in the defined starting material. PMID:25942392

  13. Cellular immunostimulation by CpG-sequence-coated DNA origami structures

    OpenAIRE

    Schüller, Verena J.; Heidegger, Simon; Sandholzer, Nadja; Nickels, Philipp C.; Suhartha, Nina A.; Endres, Stefan; Bourquin, Carole; Liedl, Tim

    2012-01-01

    To investigate the potential of DNA origami constructs as programmable and noncytotoxic immunostimulants, we tested the immune responses induced by hollow 30-helix DNA origami tubes covered with up to 62 cytosine-phosphate-guanine (CpG) sequences in freshly isolated spleen cells. Unmethylated CpG sequences that are highly specific for bacterial DNA are recognized by a specialized receptor of the innate immune system localized in the endosome, the Toll-like receptor 9 (TLR9). When incubated wi...

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

    OpenAIRE

    Regulapati, Rahul; Bhasi, Ashwini; Singh, Chandan Kumar; Senapathy, Periannan

    2008-01-01

    The mechanism by which protein-coding portions of eukaryotic genes came to be separated by long non-coding stretches of DNA, and the purpose for this perplexing arrangement, have remained unresolved fundamental biological problems for three decades. We report here a plausible solution to this problem based on analysis of open reading frame (ORF) length constraints in the genomes of nine diverse species. If primordial nucleic acid sequences were random in sequence, functional proteins that are...

  15. Structure-based design of conformation- and sequence-specific antibodies against amyloid ?

    OpenAIRE

    Perchiacca, Joseph M.; Ladiwala, Ali Reza A.; Bhattacharya, Moumita; Tessier, Peter M.

    2011-01-01

    Conformation-specific antibodies that recognize aggregated proteins associated with several conformational disorders (e.g., Parkinson and prion diseases) are invaluable for diagnostic and therapeutic applications. However, no systematic strategy exists for generating conformation-specific antibodies that target linear sequence epitopes within misfolded proteins. Here we report a strategy for designing conformation- and sequence-specific antibodies against misfolded proteins that is inspired b...

  16. The effect of zinc on the secondary structure of d(GA.TC)n DNA sequences of different length: a model for the formation *H-DNA.

    OpenAIRE

    Martínez-Balbás, A; Azorín, F

    1993-01-01

    Alternating d(GA.TC)n DNA sequences are known to undergo transition to *H-DNA in the presence of zinc. Here, the effect of zinc on the secondary DNA structure of d(GA.TC)n sequences of different length (n = 5, 8, 10 and 19) was determined. Short d(GA.TC)n sequences form *H-DNA with a higher difficulty than longer ones. At bacterial negative superhelical density (- sigma = 0.05), zinc still induces transition to the *H-DNA conformation at a d(GA.TC)10 sequence but shorter sequences do not form...

  17. A REVISED PARALLEL-SEQUENCE MORPHOLOGICAL CLASSIFICATION OF GALAXIES: STRUCTURE AND FORMATION OF S0 AND SPHEROIDAL GALAXIES

    International Nuclear Information System (INIS)

    We update van den Bergh's parallel-sequence galaxy classification in which S0 galaxies form a sequence S0a-S0b-S0c that parallels the sequence Sa-Sb-Sc of spiral galaxies. The ratio B/T of bulge-to-total light defines the position of a galaxy in this tuning-fork diagram. Our classification makes one major improvement. We extend the S0a-S0b-S0c sequence to spheroidal ('Sph') galaxies that are positioned in parallel to irregular galaxies in a similarly extended Sa-Sb-Sc-Im sequence. This provides a natural 'home' for spheroidals, which previously were omitted from galaxy classification schemes or inappropriately combined with ellipticals. To motivate our juxtaposition of Sph and Im galaxies, we present photometry and bulge-disk decompositions of four rare, late-type S0s that bridge the gap between the more common S0b and Sph galaxies. NGC 4762 is an edge-on SB0bc galaxy with a very small classical-bulge-to-total ratio of B/T = 0.13 ± 0.02. NGC 4452 is an edge-on SB0 galaxy with an even tinier pseudobulge-to-total ratio of PB/T = 0.017 ± 0.004. It is therefore an SB0c. VCC 2048, whose published classification is S0, contains an edge-on disk, but its 'bulge' plots in the structural parameter sequence of spheroidals. It is therefore a disky Sph. And NGC 4638 is similarly a 'missing link' between S0s and Sphs—it has a tiny bulge and an edge-on disk embedded in an Sph halo. In the Appendix, we present photometry and bulge-disk decompositions of all Hubble Space Telescopeositions of all Hubble Space Telescope Advanced Camera for Surveys Virgo Cluster Survey S0s that do not have published decompositions. We use these data to update the structural parameter correlations of Sph, S+Im, and E galaxies. We show that Sph galaxies of increasing luminosity form a continuous sequence with the disks (but not bulges) of S0c-S0b-S0a galaxies. Remarkably, the Sph-S0-disk sequence is almost identical to that of Im galaxies and spiral galaxy disks. We review published observations for galaxy transformation processes, particularly ram-pressure stripping of cold gas. We suggest that Sph galaxies are transformed, 'red and dead' Scd-Im galaxies in the same way that many S0 galaxies are transformed, red and dead Sa-Sc spiral galaxies.

  18. Effects of Carbon Structure and Mixing Sequence in an Expander on the Capacity of Negative Electrodes in a Traction Battery

    Science.gov (United States)

    Meenakorn, Somsak; Termsuksawad, Preecha; Phiboonkulsumrit, Sorraya

    2015-01-01

    Expanders were prepared by mixing barium sulfate, sodium lignosulfonate, and carbon materials by a high speed mixer. Effects of type of carbon materials and mixing sequence on electrochemical property of electrode were studied. Three different carbon materials: medium structure carbon black, high structure carbon black, and multi-wall carbon nanotube, were employed. The amount of charge and charge transfer resistance of electrode using different expanders were investigated by cyclic voltammetry and electrochemical impedance spectroscopy, respectively. Prepared expanders were characterized by a transmission electron microscope and a field emission scanning electron microscope. The capacity of the battery was tested by the high discharge rate test. Negative active materials were characterized by a field emission scanning electron microscope. The results showed that the type of carbon material and mixing sequence influenced the structure of carbon network in an expander and resulted in the change of the amount of charge and charge transfer resistance. All prepared expanders exhibited higher amount of charge and lower charge transfer resistance than those of a commercial expander. The highest amount of charge was obtained when the expander was prepared by mixing medium structure carbon black for 90 s before adding high structure carbon black. The high discharge test shows that the capacity of a battery using NAM prepared by this expander is approximately 10% higher than that using a commercial expander. The higher capacity is due to an increase of the surface area of NAM.

  19. Developing 1D nanostructure arrays for future nanophotonics

    Directory of Open Access Journals (Sweden)

    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.

  20. Structural insights into specific crRNA G-rich sequence binding by Meiothermus ruber Cse2.

    Science.gov (United States)

    Liu, Su; Yuan, Zuanning; Yuan, Y Adam

    2015-05-01

    CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats)-mediated defense against invading nucleic acids is a process recently discovered in prokaryotes, which includes recognition and incorporation of invading genetic elements, transcription and processing of CRISPR-RNA (crRNA) and targeting the invaders through base pair recognition. In the type I-E CRISPR-Cas system, Cse2 is proposed to provide a platform to facilitate the targeting of the invading dsDNA by crRNA. Here we report the crystal structure of Meiothermus ruber Cse2 at 2.8Å. M. ruber Cse2 adopts an ?-helical bundle scaffold, harbors a positive surface for nucleic acid binding and a conserved dimer interface with strikingly low buried surface area. M. ruber Cse2 selectively binds to G-rich crRNA sequence, which is stripped off from the Cse2-crRNA and Cascade-crRNA complexes by ssDNA or dsDNA with complementary sequence. Stable M. ruber Cascade is readily formed by co-expression of M. ruber Cascade proteins together with G-rich crRNA in vitro. Docking of M. ruber Cse2 structures into the Escherichia coli Cascade Cryo-EM envelope reveals a curved elongated shallow groove for ssRNA binding, which adopts a similar dimer interface discovered by high-resolution crystal structure of Cse2 within E. Coli Cascade. Taken together, our data provides the structural insights into crRNA G-rich sequence recognition by M. ruber Cse2 and reveals the potential structural mechanism for M. ruber Cascade assembly and function. PMID:25791617

  1. Internal tectonic structure of the Central American Wadati-Benioff zone based on analysis of aftershock sequences

    Science.gov (United States)

    Špi?ák, Aleš; Hanuš, Václav; Van?k, Ji?í; B?hounková, Marie

    2007-09-01

    Relocated Engdahl et al. (1998) global seismological data for 10 aftershock sequences were used to analyze the internal tectonic structure of the Central American subduction zone; the main shocks of several of these were the most destructive and often referenced earthquakes in the region (e.g., the 1970 Chiapas, 1983 Osa, 1992 Nicaragua, 1999 Quepos, 2001 El Salvador earthquakes). The spatial analysis of aftershock foci distribution was performed in a rotated Cartesian coordinate system (x, y, z) related to the Wadati-Benioff zone, and not in a standard coordinate system ($\\varphi$, ?, h are latitude, longitude, focal depth, respectively). Available fault plane solutions were also transformed into the plane approximating the Wadati-Benioff zone. The spatial distribution of earthquakes in each aftershock sequence was modeled as either a plane fit using a least squares approximation or a volume fit with a minimum thickness rectangular box. The analysis points to a quasi-planar distribution of earthquake foci in all aftershock sequences, manifesting the appurtenance of aftershocks to fracture zones. Geometrical parameters of fracture zones (strike, dip, and dimensions) hosting individual sequences were calculated and compared with the seafloor morphology of the Cocos Plate. The smooth character of the seafloor correlates with the aftershock fracture zones oriented parallel to the trench and commonly subparallel to the subducting slab, whereas subduction of the Cocos Ridge and seamounts around the Quepos Plateau coincides with steeply dipping fracture zones. Transformed focal mechanisms are almost exclusively (>90%) of normal character.

  2. Structure and nucleotide sequence of the 5' region of the human and feline c-sis proto-oncogenes

    Energy Technology Data Exchange (ETDEWEB)

    Van den Ouweland, M.W.; Roebroek, A.J.M.; Schalken, J.A.; Claesen, C.A.A.; Bloemers, H.P.J.; Van de Ven, W.J.M.

    1986-01-24

    Comparative analysis of cosmid clones containing the human and feline c-sis genetic regions revealed the similar structural organization of these areas in the two species. The areas shared seven different genetic regions in and around the c-sis locus and one of these was related to v-sis. Another region, 1.9 kbp in size and located about 8 kbp upstream of the v-sis homologous region in the human genome, also hybridized to the main c-sis transcriptional product of 3.5 kb. In this exon, the presumed initiation site of the predicted PDGF-2 containing precursor protein was located and appeared to be preceded by a large untranslated region. In the region immediately upstream of this exon, a TATA box and a consensus sequence for a potential Sp1 binding site were found at similar positions in both species. This region also exhibited promoter activity when tested in an assay in which coding sequences of bacterial chloramphenicol acetyltransferase were placed under its control. The five other DNA regions were found upstream and downstream of the human c-sis transcription unit and also in an intron. Hybridization analysis of human and feline c-sis containing cosmid clones with a mixed synthetic nucleotide probe, which corresponded to sequences encoding amino acid residues 2-7 of chain 1 of platelet-derived growth factor (PDGF-1), suggested that the c-sis cosmid clones did not include PDGF-1-specific genetic sequences.

  3. DNA topology influences p53 sequence-specific DNA binding through structural transitions within the target sites.

    Science.gov (United States)

    Jagelská, Eva B; Brázda, Václav; Pecinka, Petr; Palecek, Emil; Fojta, Miroslav

    2008-05-15

    The tumour suppressor protein p53 is one of the most important factors regulating cell proliferation, differentiation and programmed cell death in response to a variety of cellular stress signals. P53 is a nuclear phosphoprotein and its biochemical function is closely associated with its ability to bind DNA in a sequence-specific manner and operate as a transcription factor. Using a competition assay, we investigated the effect of DNA topology on the DNA binding of human wild-type p53 protein. We prepared sets of topoisomers of plasmid DNA with and without p53 target sequences, differing in their internal symmetry. Binding of p53 to DNA increased with increasing negative superhelix density (-sigma). At -sigma perfect inverted repeat sequence exhibited a more significant enhancement of p53 binding as a result of increasing levels of negative DNA supercoiling. For -sigma = 0.07, an approx. 3-fold additional increase in binding was observed for a symmetrical target site compared with a non-symmetrical target site. The p53 target sequences possessing the inverted repeat symmetry were shown to form a cruciform structure in sufficiently negative supercoiled DNA. We show that formation of cruciforms in DNA topoisomers at -sigma > or = 0.05 correlates with the extra enhancement of p53-DNA binding. PMID:18271758

  4. Sequence of the mouse XPC cDNA and genomic structure of the human XPC gene.

    OpenAIRE

    LI, L; Peterson, C.; Legerski, R

    1996-01-01

    The full length-mouse XPC cDNA contains a 2703 bp orf which encodes a polypeptide containing 900 amino acids. Overall, there is 75% identity in nucleotide sequence and 73% identity in amino acid sequence between mouse and human genes. The C-terminal half is more conserved (80%) than the N-terminal half (65%). Northern analysis has revealed a constitutive expression pattern for both human and mouse transcripts in various tissues examined. However, high level expression was observed in liver, t...

  5. Small fragments of herpesvirus DNA with transforming activity contain insertion sequence-like structures.

    OpenAIRE

    Galloway, D A; Nelson, J.A.; McDougall, J K

    1984-01-01

    A 737-base-pair fragment of herpes simplex virus type 2 DNA with morphological-transforming ability was identified by transfecting into rodent cells deleted fragments of the left-hand end of the Bgl II N fragment region (map position 0.58-0.625), which were constructed in vitro. The transforming sequences lie within the coding region for a Mr 61,000 protein, but the fragment itself does not appear to specify a viral polypeptide. Contained within the transforming fragment are sequences that ca...

  6. A cholinesterase genes server (ESTHER): a database of cholinesterase-related sequences for multiple alignments, phylogenetic relationships, mutations and structural data retrieval.

    OpenAIRE

    Cousin, X.; Hotelier, T.; Lie?vin, P.; Toutant, J. P.; Chatonnet, A.

    1996-01-01

    We have built a database of sequences phylogenetically related to cholinesterases (ESTHER) for esterases, alpha/beta hydrolase enzymes and relatives). These sequences define a homogeneous group of enzymes (carboxylesterases, lipases and hormone-sensitive lipases) with some related proteins devoid of enzymatic activity. The purpose of ESTHER is to help comparison and alignment of any new sequence appearing in the field, to favour mutation analysis of structure-function relationships and to all...

  7. Non-virulence of a recombinant shrimp nidovirus is associated with its non structural gene sequence and not a large structural gene deletion

    International Nuclear Information System (INIS)

    RT-PCR using a commercial kit for yellow head virus (YHV) detection in growth-retarded shrimp yielded an unusual 777 bp amplicon instead of expected amplicons of 277 bp for YHV type-1 (YHV-1) or 406 bp for YHV type-2 (YHV-2). Cloning and sequencing (GenBank (EU170438)) revealed approximately 80% identity to non-structural (NS) ORF1b sequences of both YHV-1 (GenBank (AA083987)) and YHV-2 (GenBank (AF227196)), indicating an atypical YHV type (A-YHV) phylogenetically equidistant from both types. An RT-PCR test specifically designed for A-YHV revealed that it was uncommon and that its occurrence in shrimp culture ponds did not correlate with growth retardation or mortality. By immunohistochemistry with YHV-specific monoclonal antibodies, the A-YHV gave positive reactions for envelope protein gp64 and capsid protein p20, but not for envelope protein gp116, even though gp116 and gp64 originate from a polyprotein of ORF3. Lack of gp116 immunoreactivity correlated with a large ORF3 deletion (GenBank (EU123854)) in the region of the protein targeted by an MAb against gp116. Transmission electron microscopy of A-YHV-infected shrimp revealed only unenveloped pre-virions. During manuscript revision, information received revealed that typing of YHV isolates based on sequences of ORF1b and ORF3 had yielded several geographical types, including one virulent type (YHV-1b) with an ORF3 deletion sequence that matched the sequence of A-YHV. Using these sequences and an additional A-YHV g these sequences and an additional A-YHV sequence ( (EU853170)) from the ORF1b typing region, A-YHV potentially represents a recombinant between type 1b and type 5. SDS-PAGE and Western blot analysis revealed that type 1b produced a gp116 deletion protein that did not bind with the MAb or polyclonal Ab to normal gp116. Overall, the information suggested that lack of A-YHV virulence was associated with the NS gene sequence linked to ORF1b rather than the deletion in ORF3

  8. Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures

    International Nuclear Information System (INIS)

    Total DNAs from various animals were transcribed in vitro in a HeLa cell extract, and it was found that one to several discrete RNAs were transcribed by RNA polymerase III. With tortoise (Geoclemys reevessi) and newt (Cynops pyrrhogaster), distinct 6.5S and 8S RNAs were transcribed from these respective DNAs. Representative phage clones carrying the 6.5S and 8S RNA genes were isolated from genomic libraries of these animals, and the sequences of these genes were determined. The 5' parts of highly repetitive and transcribable sequences of tortoise and newt were found to have close resemblance to tRNA1/sup Lys/ (rabbit) gene (78% homology) and a tRNA/sup Glu/ (Drosophila) gene (74% homology, not counting the aminoacyl stem region), respectively. The homologies extended to secondary structures, homologous nucleotides being located on similar secondary structures. It is proposed that many, if not all, highly repetitive and transcribable sequences detected by total DNA transcription have specific tRNA genes as their progenitors

  9. High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems

    Directory of Open Access Journals (Sweden)

    Yin Li

    2012-12-01

    Full Text Available Abstract Background Deep sequencing provides the basis for analysis of biodiversity of taxonomically similar organisms in an environment. While extensively applied to microbiome studies, population genetics studies of viruses are limited. To define the scope of HIV-1 population biodiversity within infected individuals, a suite of phylogenetic and population genetic algorithms was applied to HIV-1 envelope hypervariable domain 3 (Env V3 within peripheral blood mononuclear cells from a group of perinatally HIV-1 subtype B infected, therapy-naïve children. Results Biodiversity of HIV-1 Env V3 quasispecies ranged from about 70 to 270 unique sequence clusters across individuals. Viral population structure was organized into a limited number of clusters that included the dominant variants combined with multiple clusters of low frequency variants. Next generation viral quasispecies evolved from low frequency variants at earlier time points through multiple non-synonymous changes in lineages within the evolutionary landscape. Minor V3 variants detected as long as four years after infection co-localized in phylogenetic reconstructions with early transmitting viruses or with subsequent plasma virus circulating two years later. Conclusions Deep sequencing defines HIV-1 population complexity and structure, reveals the ebb and flow of dominant and rare viral variants in the host ecosystem, and identifies an evolutionary record of low-frequency cell-associated viral V3 variants that persist for years. Bioinformatics pipeline developed for HIV-1 can be applied for biodiversity studies of virome populations in human, animal, or plant ecosystems.

  10. Iterative Solvers within Sequences of Large Linear Systems in Non-linear Structural Mechanics.

    Czech Academy of Sciences Publication Activity Database

    Hartmann, S.; Duintjer Tebbens, Jurjen; Quint, K.J.; Meister, A.

    2009-01-01

    Ro?. 89, ?. 9 (2009), s. 711-728. ISSN 0044-2267 R&D Projects: GA AV ?R KJB100300703 Institutional research plan: CEZ:AV0Z10300504 Keywords : iterative solver * non-symmetric matrices * sequences of linear systems * finite strains * finite elements Subject RIV: BA - General Mathematics Impact factor: 0.866, year: 2009

  11. Structural changes induced by binding of the high-mobility group I protein to a mouse satellite DNA sequence.

    Science.gov (United States)

    Slama-Schwok, A; Zakrzewska, K; Léger, G; Leroux, Y; Takahashi, M; Käs, E; Debey, P

    2000-01-01

    Using spectroscopic methods, we have studied the structural changes induced in both protein and DNA upon binding of the High-Mobility Group I (HMG-I) protein to a 21-bp sequence derived from mouse satellite DNA. We show that these structural changes depend on the stoichiometry of the protein/DNA complexes formed, as determined by Job plots derived from experiments using pyrene-labeled duplexes. Circular dichroism and melting temperature experiments extended in the far ultraviolet range show that while native HMG-I is mainly random coiled in solution, it adopts a beta-turn conformation upon forming a 1:1 complex in which the protein first binds to one of two dA.dT stretches present in the duplex. HMG-I structure in the 1:1 complex is dependent on the sequence of its DNA target. A 3:1 HMG-I/DNA complex can also form and is characterized by a small increase in the DNA natural bend and/or compaction coupled to a change in the protein conformation, as determined from fluorescence resonance energy transfer (FRET) experiments. In addition, a peptide corresponding to an extended DNA-binding domain of HMG-I induces an ordered condensation of DNA duplexes. Based on the constraints derived from pyrene excimer measurements, we present a model of these nucleated structures. Our results illustrate an extreme case of protein structure induced by DNA conformation that may bear on the evolutionary conservation of the DNA-binding motifs of HMG-I. We discuss the functional relevance of the structural flexibility of HMG-I associated with the nature of its DNA targets and the implications of the binding stoichiometry for several aspects of chromatin structure and gene regulation. PMID:10777751

  12. The X-ray structure of a mutant eye lens beta B2-crystallin with truncated sequence extensions.

    Science.gov (United States)

    Norledge, B V; Trinkl, S; Jaenicke, R; Slingsby, C

    1997-08-01

    beta-Crystallins are oligomeric eye lens proteins that are related to monomeric gamma-crystallins by domain swapping: like gamma-crystallins, they are comprised of two similar domains but they differ in having long sequence extensions. beta B2, a major component of beta-crystallin oligomers, self-associates to a homodimer in solution. In two crystal structures of native beta B2, the protein is a 222-symmetric tetramer of eight domains. It has previously been shown that a mutant of rat beta B2-crystallin, in which the bulk of the N- and C-terminal sequence extensions has been deleted, assembles into dimers and tetramers. Here we present the 3.0 A resolution X-ray structure of the tetramer, beta B2 delta NC1. The mutant tetramer has a very similar set of domain interactions to the native structure. However, the structures differ in the relative orientation of the two sets of four domains. The paired N- and C-terminal domain interface, which is at the heart of the dimer structure, is very similar to the native structure. However, the truncation of the C-terminal extension removes an important tryptophan residue, which prevents the extension from acting as a (non-covalent) linker, as it does in native beta B2. There is a knock-on structural effect that removes a contact between extension and covalent linker, and this appears to cause a small twist in the linker that is amplified into a 20 degrees rotation between sets of paired domains. PMID:9260274

  13. Protein Classification Based on Analysis of Local Sequence-Structure Correspondence

    Energy Technology Data Exchange (ETDEWEB)

    Zemla, A T

    2006-02-13

    The goal of this project was to develop an algorithm to detect and calculate common structural motifs in compared structures, and define a set of numerical criteria to be used for fully automated motif based protein structure classification. The Protein Data Bank (PDB) contains more than 33,000 experimentally solved protein structures, and the Structural Classification of Proteins (SCOP) database, a manual classification of these structures, cannot keep pace with the rapid growth of the PDB. In our approach called STRALCP (STRucture Alignment based Clustering of Proteins), we generate detailed information about global and local similarities between given set of structures, identify similar fragments that are conserved within analyzed proteins, and use these conserved regions (detected structural motifs) to classify proteins.

  14. Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways

    International Nuclear Information System (INIS)

    The renaturation/denaturation of DNA oligonucleotides is characterized in the context of expanded ensemble (EXE) and transition path sampling (TPS) simulations. Free energy profiles have been determined from EXE for DNA sequences of varying composition, chain length, and ionic strength. TPS simulations within a Langevin dynamics formalism have been carried out to obtain further information of the transition state for renaturation. Simulation results reveal that free energy profiles are strikingly similar for the various DNA sequences considered in this work. Taking intact double-stranded DNA to have an extent of reaction ? = 1.0, the maximum of the free energy profile appears at ??0.15, corresponding to ?2 base pairs. In terms of chain length, the free energy barrier of longer oligonucleotides (30 versus 15 base pairs) is higher and slightly narrower, due to increased sharpness associated with the transition. Low ionic strength tends to decrease free energy barriers, whereby increasing strand rigidity facilitates reassociation. Two mechanisms for DNA reassociation emerge from our analysis of the transition state ensemble. Repetitive sequences tend to reassociate through a non-specific pathway involving molecular slithering. In contrast, random sequences associate through a more restrictive pathway involving the formation of specific contacts, which then leads to overall molecular zippering. In both random and repetitive sequences, the distribution of contacts suces, the distribution of contacts suggests that nucleation is favored for sites located within the middle region of the chain. The prevalent extent of reaction for the transition state is ??0.25, and the critical size of the nucleus as obtained from our analysis involves ?4 base pairs.

  15. Structure of DNA hexamer sequence d-CGATCG by two-dimensional nuclear magnetic resonance spectroscopy and restrained molecular dynamics.

    Science.gov (United States)

    Barthwal, Ritu; Monica; Awasthi, Pamita; Srivastava, Nandana; Sharma, Uma; Kaur, Manpreet; Govil, Girjesh

    2003-12-01

    Solution conformation of self-complementary DNA duplex d-CGATCG, containing 5' d-CpG 3' site for intercalation of anticancer drug, daunomycin and adriamycin, has been investigated by nuclear magnetic resonance (NMR) spectroscopy. Complete resonance assignments of all the protons (except some H5'/H5" protons) have been obtained following standard procedures based on double quantum filtered correlation spectroscopy (dQF COSY) and two-dimensional nuclear Overhauser effect (NOE) spectra. Analysis of sums of coupling constants in one-dimensional NMR spectra, cross peak patterns in dQF COSY spectra and inter proton distances shows that the DNA sequence assumes a conformation close to the B-DNA family. The deoxyribose sugar conformation is in dynamic equilibrium with predominantly S-type conformer and a minor N-type conformer with NS equilibrium varying with temperature. At 325 K, the mole fraction of the N-conformer increases for some of the residues by approximately 9%. Using a total of 10 spin-spin coupling constants and 112 NOE intensities, structural refinement has been carried out using Restrained Molecular Dynamics (rMD) with different starting structures, potential functions and rMD protocols. It is observed that pseudorotation phase angle of deoxyribose sugar for A3 and T4 residues is approximately 180 degrees and approximately 120 degrees, respectively while all other residues are close to C2'endo-conformation. A large propeller twist (approximately -18 degrees) and smallest twist angle (approximately 31 degrees) at A3pT4 step, in the middle of the sequence, a wider (12 A) and shallower (3.0 A) major groove with glycosidic bond rotation as high anti at both the ends of hexanucleotide are observed. The structure shows base-sequence dependent variations and hence strong local structural heterogeneity, which may have implications in ligand binding. PMID:14616036

  16. Functional and structural analysis of the DNA sequence conferring glucocorticoid inducibility to the mouse mammary tumor virus gene

    International Nuclear Information System (INIS)

    In the first part of my thesis I show that the DNA element conferring glucocorticoid inducibility to the Mouse Mammary Tumor Virus (HRE) has enhancer properties. It activates a heterologous promoter - that of the ?-globin gene, independently of distance, position and orientation. These properties however have to be regarded in relation to the remaining regulatory elements of the activated gene as the recombinants between HRE and the TK gene have demonstrated. In the second part of my thesis I investigated the biological significance of certain sequence motifs of the HRE, which are remarkable by their interaction with transacting factors or sequence homologies with other regulatory DNA elements. I could confirm the generally postulated modular structure of enhancers for the HRE and bring the relevance of the single subdomains for the function of the element into relationship. (orig.)

  17. Protein Ordered Sequences are Formed by Random Joining of Amino Acids in Protein 0th-Order Structure, Followed by Evolutionary Process

    Science.gov (United States)

    Ikehara, Kenji

    2014-12-01

    Only random processes should occur on the primitive Earth. In contrast, many ordered sequences are synthesized according to genetic information on the present Earth. In this communication, I have proposed an idea that protein 0th-order structures or specific amino acid compositions would mediate the transfer from random process to formation of ordered sequences, after formation of double-stranded genes.

  18. Combining Network Topological Characteristics With Sequence and Structure Based Features for Predicting Protein Stability Changes Upon Single Amino Acid Mutation

    Directory of Open Access Journals (Sweden)

    Lijun Yang

    2013-12-01

    Full Text Available It has been shown that the stability of protein structure could be significantly changed by single amino acid substitution. Accurate prediction of protein stability changes caused by single amino acid substitutions is valuable for understanding the relationship between protein structures and functions as well as designing new proteins. Currently, various computational methods have been developed to study the effect of single amino acid mutation on protein stability. In this study, by combining network topological characteristics extracted from Protein Structure Network (PSN with other physicochemical features obtained from protein sequence or structure, a Support Vector Machine (SVM model was developed to distinguish the stabilizing mutants from the destabilizing mutants. 20-fold cross-validation was implemented for performance evaluation. An accuracy of 0.88 and a Matthews Correlation Coefficient (MCC of 0.71 were obtained for the dataset with 1925 variants. Our method is superior to the existing machine learning approaches evaluated under the same datasets. It suggests that such a combining strategy should be valuable in predicting protein stability changes upon amino acid mutation. In our study, the topological parameters are informative for prediction upon substitutions. Moreover, it is indicated that the Protein Structure Network (PSN could be effectively used for representing the three-dimensional structure of protein and such network parameters are associated with the changes of protein function and structure.

  19. Preferential binding and structural distortion by Fe2+ at RGGG-containing DNA sequences correlates with enhanced oxidative cleavage at such sequences

    OpenAIRE

    Rai, Priyamvada; Wemmer, David E; Linn, Stuart

    2005-01-01

    Certain DNA sequences are known to be unusually sensitive to nicking via the Fe2+-mediated Fenton reaction. Most notable are a purine nucleotide followed by three or more G residues, RGGG, and purine nucleotides flanking a TG combination, RTGR. Our laboratory previously demonstrated that nicking in the RGGG sequences occurs preferentially 5? to a G residue with the nicking probability decreasing from the 5? to 3?end of these sequences. Using 1H NMR to characterize Fe2+ binding within th...

  20. Structure-sequence based analysis for identification of conserved regions in proteins

    Science.gov (United States)

    Zemla, Adam T; Zhou, Carol E; Lam, Marisa W; Smith, Jason R; Pardes, Elizabeth

    2013-05-28

    Disclosed are computational methods, and associated hardware and software products for scoring conservation in a protein structure based on a computationally identified family or cluster of protein structures. A method of computationally identifying a family or cluster of protein structures in also disclosed herein.

  1. Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties

    Science.gov (United States)

    Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

    2015-01-01

    Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP marker set will be useful for systematic estimation of admixture structure of citrus germplasm and for diverse genetic studies. PMID:25973611

  2. Applications of AMPS-1D for solar cell simulation

    Science.gov (United States)

    Zhu, Hong; Kalkan, Ali Kaan; Hou, Jingya; Fonash, Stephen J.

    1999-03-01

    The AMPS-1D PC computer program is now used by over 70 groups world-wide for detector and solar cell analysis. It has proved to be a very powerful tool in understanding device operation and physics for single crystal, poly-crystalline and amorphous structures. For example, AMPS-1D has been successful in explaining the "red kink" [1] and the "transient effect" in CdS/CIGS poly-crystalline solar cells. It has been used to show that thin film poly-Si structures, with reasonable light trapping, are capable of competitive solar cell conversion efficiencies. In the case of a-Si:H structures, it has been used, for example, to settle the discrepancies in bandgap measurement, to predict the effective QE>1 phenomenon later seen in these materials [2], to determine the relative roles of interface and bulk properties, and to point the direction toward 16% triple junction structures. In general AMPS-1D is used for cell and detector design, material parameter sensitivity studies, and parameter extraction. Recently we have shown that it can be used to determine optimum structure and light and voltage biasing conditions in the material parameter extraction function. Information on AMPS can be found at www.psu.edu/dept/AMPS/amps_web/AMPS.html and at other web sites set up by user groups.

  3. The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis.

    Science.gov (United States)

    Yao, Xiaohong; Tang, Ping; Li, Zuozhou; Li, Dawei; Liu, Yifei; Huang, Hongwen

    2015-01-01

    Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids. PMID:26046631

  4. Protein folding funnels: a kinetic approach to the sequence-structure relationship.

    OpenAIRE

    Leopold, P. E.; Montal, M.; Onuchic, J. N.

    1992-01-01

    A lattice model of protein folding is developed to distinguish between amino acid sequences that do and do not fold into unique conformations. Although Monte Carlo simulations provide insights into the long-time processes involved in protein folding, these simulations cannot systematically chart the conformational energy surface that enables folding. By assuming that protein folding occurs after chain collapse, a kinetic map of important pathways on this surface is constructed through the use...

  5. Analysis of DNA structural patterns and sequence organization at the larval cuticle locus in Drosophila melanogaster.

    OpenAIRE

    Eissenberg, J. C.; Elgin, S. C.

    1983-01-01

    We examined the pattern of DNA organization at the larval cuticle gene complex 44D of Drosophila melanogaster, using micrococcal nuclease and the 1,10-phenanthroline-cuprous complex. The initial cleavage patterns obtained with both reagents exhibited "gaps" at the positions of each of the genes examined, as well as at a pseudogene sequence contained within the complex. An additional gap for which no gene exists was observed for both patterns. The cleavage pattern obtained with micrococcal nuc...

  6. Baboon Carboxylesterases 1 and 2: Sequences, Structures and Phylogenetic Relationships with Human and other Primate Carboxylesterases

    OpenAIRE

    Holmes, Roger S.; Glenn, Jeremy P.; Vandeberg, John L.; Cox, Laura A.

    2009-01-01

    Carboxylesterase (CES) is predominantly responsible for the detoxification of a wide range of drugs and narcotics, and catalyze several reactions in cholesterol and fatty acid metabolism. Studies of the genetic and biochemical properties of primate CES may contribute to an improved understanding of human disease, including atherosclerosis, obesity and drug addiction, for which non-human primates serve as useful animal models. We cloned and sequenced baboon CES1 and CES2 and used in vitro and ...

  7. 1D design style implications for mask making and CEBL

    Science.gov (United States)

    Smayling, Michael C.

    2013-09-01

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

  8. The shikimate pathway: Review of amino acid sequence, function and three-dimensional structures of the enzymes.

    Science.gov (United States)

    Mir, Rafia; Jallu, Shais; Singh, T P

    2013-08-01

    Abstract The aromatic compounds such as aromatic amino acids, vitamin K and ubiquinone are important prerequisites for the metabolism of an organism. All organisms can synthesize these aromatic metabolites through shikimate pathway, except for mammals which are dependent on their diet for these compounds. The pathway converts phosphoenolpyruvate and erythrose 4-phosphate to chorismate through seven enzymatically catalyzed steps and chorismate serves as a precursor for the synthesis of variety of aromatic compounds. These enzymes have shown to play a vital role for the viability of microorganisms and thus are suggested to present attractive molecular targets for the design of novel antimicrobial drugs. This review focuses on the seven enzymes of the shikimate pathway, highlighting their primary sequences, functions and three-dimensional structures. The understanding of their active site amino acid maps, functions and three-dimensional structures will provide a framework on which the rational design of antimicrobial drugs would be based. Comparing the full length amino acid sequences and the X-ray crystal structures of these enzymes from bacteria, fungi and plant sources would contribute in designing a specific drug and/or in developing broad-spectrum compounds with efficacy against a variety of pathogens. PMID:23919299

  9. Numerical modeling of block structure dynamics: Application to the Vrancea region and study of earthquakes sequences in the synthetic catalogs

    International Nuclear Information System (INIS)

    A seismically active region is represented as a system of absolutely rigid blocks divided by infinitely thin plane faults. The interaction of the blocks along the fault planes and with the underlying medium is viscous-elastic. The system of blocks moves as a consequence of prescribed motion of boundary blocks and the underlying medium. When for some part of a fault plane the stress surpasses a certain strength level a stress-drop (''a failure'') occurs. It can cause a failure for other parts of fault planes. The failures are considered as earthquakes. As a result of the numerical simulation a synthetic earthquake catalogue is produced. This procedure is applied for numerical modeling of dynamics of the block structure approximating the tectonic structure of the Vrancea region. By numerical experiments the values of the model parameters were obtained which supplied the synthetic earthquake catalog with the space distribution of epicenters close to the real distribution of the earthquake epicenters in the Vrancea region. The frequency-magnitude relations (Gutenberg-Richter curves) obtained for the synthetic and real catalogs have some common features. The sequences of earthquakes arising in the model are studied for some artificial structures. It is found that ''foreshocks'', ''main shocks'', and ''aftershocks'' could be detected among earthquakes forming the sequences. The features of aftershocks, foreshocks, and catalogs of main shocks are analysed. (author). 5 refs, 12 figs, 16 tabs

  10. cDNA Sequence and Fab Crystal Structure of HL4E10, a Hamster IgG Lambda Light Chain Antibody Stimulatory for ?? T Cells

    OpenAIRE

    Verdino, Petra; Witherden, Deborah A; Podshivalova, Katie; Rieder, Stephanie E.; Havran, Wendy L; Wilson, Ian A.

    2011-01-01

    Hamsters are widely used to generate monoclonal antibodies against mouse, rat, and human antigens, but sequence and structural information for hamster immunoglobulins is sparse. To our knowledge, only three hamster IgG sequences have been published, all of which use kappa light chains, and no three-dimensional structure of a hamster antibody has been reported. We generated antibody HL4E10 as a probe to identify novel costimulatory molecules on the surface of ?? T cells which lack the tradit...

  11. CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure.

    Directory of Open Access Journals (Sweden)

    2006-03-01

    Full Text Available CpG island methylation plays an important role in epigenetic gene control during mammalian development and is frequently altered in disease situations such as cancer. The majority of CpG islands is normally unmethylated, but a sizeable fraction is prone to become methylated in various cell types and pathological situations. The goal of this study is to show that a computational epigenetics approach can discriminate between CpG islands that are prone to methylation from those that remain unmethylated. We develop a bioinformatics scoring and prediction method on the basis of a set of 1,184 DNA attributes, which refer to sequence, repeats, predicted structure, CpG islands, genes, predicted binding sites, conservation, and single nucleotide polymorphisms. These attributes are scored on 132 CpG islands across the entire human Chromosome 21, whose methylation status was previously established for normal human lymphocytes. Our results show that three groups of DNA attributes, namely certain sequence patterns, specific DNA repeats, and a particular DNA structure, are each highly correlated with CpG island methylation (correlation coefficients of 0.64, 0.66, and 0.49, respectively. We predicted, and subsequently experimentally examined 12 CpG islands from human Chromosome 21 with unknown methylation patterns and found more than 90% of our predictions to be correct. In addition, we applied our prediction method to analyzing Human Epigenome Project methylation data on human Chromosome 6 and again observed high prediction accuracy. In summary, our results suggest that DNA composition of CpG islands (sequence, repeats, and structure plays a significant role in predisposing CpG islands for DNA methylation. This finding may have a strong impact on our understanding of changes in CpG island methylation in development and disease.

  12. A novel suite of cyclotides from Viola odorata: sequence variation and the implications for structure, function and stability.

    Science.gov (United States)

    Ireland, David C; Colgrave, Michelle L; Craik, David J

    2006-11-15

    Cyclotides are a fascinating family of plant-derived peptides characterized by their head-to-tail cyclized backbone and knotted arrangement of three disulfide bonds. This conserved structural architecture, termed the CCK (cyclic cystine knot), is responsible for their exceptional resistance to thermal, chemical and enzymatic degradation. Cyclotides have a variety of biological activities, but their insecticidal activities suggest that their primary function is in plant defence. In the present study, we determined the cyclotide content of the sweet violet Viola odorata, a member of the Violaceae family. We identified 30 cyclotides from the aerial parts and roots of this plant, 13 of which are novel sequences. The new sequences provide information about the natural diversity of cyclotides and the role of particular residues in defining structure and function. As many of the biological activities of cyclotides appear to be associated with membrane interactions, we used haemolytic activity as a marker of bioactivity for a selection of the new cyclotides. The new cyclotides were tested for their ability to resist proteolysis by a range of enzymes and, in common with other cyclotides, were completely resistant to trypsin, pepsin and thermolysin. The results show that while biological activity varies with the sequence, the proteolytic stability of the framework does not, and appears to be an inherent feature of the cyclotide framework. The structure of one of the new cyclotides, cycloviolacin O14, was determined and shown to contain the CCK motif. This study confirms that cyclotides may be regarded as a natural combinatorial template that displays a variety of peptide epitopes most likely targeted to a range of plant pests and pathogens. PMID:16872274

  13. Structural studies of O-polysaccharide isolated from Cronobacter sakazakii Sequence Type 12 from a case of neonatal necrotizing enterocolitis.

    Science.gov (United States)

    Marszewska, Kinga; Czerwicka, Ma?gorzata; Forsythe, Stephen J; Ossowska, Karolina; Dziadziuszko, Halina; Kaczy?ski, Zbigniew

    2015-04-30

    The O-polysaccharide (OPS) of Cronobacter sakazakii NTU 696 (Sequence Type 12) from a case of neonatal necrotizing enterocolitis was isolated from the polysaccharide fraction obtained after lipopolysaccharide (LPS) hydrolysis. Purified OPS was analyzed by NMR spectroscopy ((1)H, COSY, TOCSY, NOESY, HSQC, HSQC-TOCSY and HMBC experiments) and chemical methods. Obtained monosaccharide derivatives analyzed by gas chromatography and gas chromatography-mass spectrometry allowed the identification of six sugar components. Performed experiments enabled to establish a structure of the OPS repeating unit of C. sakazakii NTU 696, as. PMID:25723620

  14. Structural similarity in the absence of sequence homology of the messenger RNA export factors Mtr2 and p15

    OpenAIRE

    Fribourg, Se?bastien; Conti, Elena

    2003-01-01

    The association between Mtr2 and Mex67 is essential for the nuclear export of bulk messenger RNA in yeast. In metazoans, the analogous function is carried out by the TAP–p15 heterodimer. Whereas Mex67 and TAP are highly conserved proteins, their binding partners, Mtr2 and p15, share no sequence similarity, but are nevertheless functionally homologous. Here, we report the 2.8-Å resolution crystal structure of Mtr2 in complex with the NTF2-like domain of Mex67. Mtr2 is a novel member of the ...

  15. The use of 2-hydroperoxytetrahydrofuran as a reagent to sequence cytosine and to probe non-Watson-Crick DNA structures.

    OpenAIRE

    Liang, G.; Gannett, P.; Gold, B.

    1995-01-01

    2-Hydroperoxytetrahydrofuran (THF-OOH) can be employed to sequence cytosine (C) and to probe for non-canonical DNA structures involving C. Using 32P-labeled oligomers and a DNA restriction fragment, it is demonstrated that THF-OOH has a strong preference for Cs in single-stranded (s-s) DNA regions, and in bulges, loops and mismatches. The reactivity of C is diminished below pH 6.0, but is not affected by substitution of 5-methylcytosine. To demonstrate the utility of the reagent, it is direct...

  16. The X-ray structure of a mutant eye lens beta B2-crystallin with truncated sequence extensions.

    OpenAIRE

    Norledge, B. V.; Trinkl, S.; Jaenicke, R.; Slingsby, C.

    1997-01-01

    beta-Crystallins are oligomeric eye lens proteins that are related to monomeric gamma-crystallins by domain swapping: like gamma-crystallins, they are comprised of two similar domains but they differ in having long sequence extensions. beta B2, a major component of beta-crystallin oligomers, self-associates to a homodimer in solution. In two crystal structures of native beta B2, the protein is a 222-symmetric tetramer of eight domains. It has previously been shown that a mutant of rat beta B2...

  17. eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.

    Science.gov (United States)

    Brylinski, Michal

    2014-09-01

    Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4-9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite. PMID:25232727

  18. One short cysteine-rich sequence pattern - two different disulfide-bonded structures - a molecular dynamics simulation study.

    Science.gov (United States)

    Dames, Sonja A

    2015-06-01

    The nematocyst walls of Hydra are formed by proteins containing small cysteine-rich domains (CRDs) of ~25 amino acids. The first CRD of nematocyst outer all antigen (NW1) and the C-terminal CRD of minicollagen-1 (Mcol1C) contain six cysteines at identical sequence positions, however adopt different disulfide bonded structures. NW1 shows the disulfide connectivities C2-C14/C6-C19/C10-C18 and Mcol1C C2-C18/C6-C14/C10-C19. To analyze if both show structural preferences in the open, non-disulfide bonded form, which explain the formation of either disulfide connectivity pattern, molecular dynamics (MD) simulations at different temperatures were performed. NW1 maintained in the 100-ns MD simulations at 283?K a rather compact fold that is stabilized by specific hydrogen bonds. The Mcol1C structure fluctuated overall more, however stayed most of the time also rather compact. The analysis of the backbone ?/? angles indicated different turn propensities for NW1 and Mcol1C, which mostly can be explained based on published data about the influence of different amino acid side chains on the local backbone conformation. Whereas a folded precursor mechanism may be considered for NW1, Mcol1C may fold according to the quasi-stochastic folding model involving disulfide bond reshuffling and conformational changes, locking the native disulfide conformations. The study further demonstrates the power of MD simulations to detect local structural preferences in rather dynamic systems such as the open, non-disulfide bonded forms of NW1 and Mcol1C, which complement published information from NMR backbone residual dipolar couplings. Because the backbone structural preferences encoded by the amino acid sequence embedding the cysteines influence which disulfide connectivities are formed, the data are generally interesting for a better understanding of oxidative folding and the design of disulfide stabilized therapeutics. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd. PMID:25781269

  19. A conditional random fields method for RNA sequence–structure relationship modeling and conformation sampling

    OpenAIRE

    Wang, Zhiyong; Xu, Jinbo

    2011-01-01

    Accurate tertiary structures are very important for the functional study of non-coding RNA molecules. However, predicting RNA tertiary structures is extremely challenging, because of a large conformation space to be explored and lack of an accurate scoring function differentiating the native structure from decoys. The fragment-based conformation sampling method (e.g. FARNA) bears shortcomings that the limited size of a fragment library makes it infeasible to represent all possible conformatio...

  20. Multidisciplinary investigation of the seismogenic structure of the Matese 2013-2014 seismic sequence (Southern Apennine, Italy)

    Science.gov (United States)

    Ferranti, Luigi; Milano, Girolamo; Burrato, Pierfrancesco; Palano, Mimmo; Cannavò, Flavio

    2014-05-01

    The December 2013 seismic sequence (ML 5.0 mainshock) of the Sannio-Matese area, one of the most seismically active segments of the Apennine Chain, struck in the internal part of the Matese massif (southern Italy), in a sector where no evidence of active faulting were recorded so far. A recent analysis of geodetic velocities suggested current strain accumulation on an array of NW-SE striking, SW-dipping high-angle normal faults (Matese Lake Fault System) which borders a >30 km long asymmetric basin nested in the interior of the massif. GPS sites straddled by the Matese Lake Fault, when resolved on a geologically constrained fault model, were found to be consistent with an horizontal extension at ~0.8±0.5 mm/yr, with a left-oblique component at ~0.7±0.4 mm/yr. As a matter of fact, if the fault is (at least partially) locked, the significant geodetic strain accumulation on the fault may be of concern, in light of its recent seismic activation. This finding is consistent with the seismicity of the Matese-Sannio area which is characterized by the occurrence of isolated events within the massif (Mseismic sequences and swarms, which mainly concentrate at the tips of seismogenic sources of destructive historical events. Spurred by the sudden activation of this "silent" fault, we used geologic-structural data, long-term morphological data, seismicity and geodetic data in order to: 1) correlate the seismic sequence with a crustal fault model; 2) provide geologic source parameters and a numerical model for the seismogenic structure; and 3) refine the current understanding of the coupling between strain accumulation and release. The projection of the relocated seismicity provide information on which part of the NW-SE striking array has activated during the sequence and the results of the computed focal mechanisms for the most energetic events of the sequence are compared with the results of the pseudo-focal mechanisms obtained from fault slip inversion from different portions of the faults. Finally, refining of the existing GPS-based analysis provided an update map of the strain-rate field, geodetic-moments and strain accumulation-rate, as well as a broad reconstruction of the spatiotemporal coseismic dislocation for the mainshock (ML 5.0).

  1. Importance of secondary structure in the signal sequence for protein secretion.

    OpenAIRE

    Emr, S. D.; Silhavy, T. J.

    1983-01-01

    Mutant Escherichia coli strains in which export of the LamB protein (coded for by the lamB gene) to the outer membrane of the cell is prevented have been described previously. One of these mutant strains contains a small (12-base pair) deletion mutation within the region of the lamB gene that codes for the NH2-terminal signal sequence. In this mutant strain, export but not synthesis of the LamB protein is blocked. We have isolated pseudorevertants that restore export of functional LamB protei...

  2. Structure- and sequence-specificity of ozone degradation of supercoiled plasmid DNA.

    OpenAIRE

    Sawadaishi, K; Miura, K.; Ohtsuka, E.; Ueda, T.; Shinriki, N; Ishizaki, K

    1986-01-01

    Ozone-reactive sites on the nucleobase moieties in supercoiled pBR322 DNA were investigated by using sequencing procedures. Ozonolysis in the absence of salt resulted in degradation of thymine residues in the A + T rich region located at 3100-3400bp. In the presence of salt, such as NaCl or MgCl2, a conformational change of plasmid DNA was induced. Subsequently the thymine and guanine residues in the loop of the cruciform located at 3120bp and 3220bp were degraded. In addition, central thymin...

  3. StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase

    Energy Technology Data Exchange (ETDEWEB)

    Zemla, A; Lang, D; Kostova, T; Andino, R; Zhou, C

    2010-11-29

    Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory - still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could overcome these difficulties and facilitate the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV, a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus and demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique or that shared structural similarity with structures that are distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position.

  4. Influence of non-B DNA structures and DNA methylations to p53 sequence specific binding.

    Czech Academy of Sciences Publication Activity Database

    Brázda, Václav; Brázdová Jagelská, Eva; Arrowsmith, Ch.

    Hilton Papagayo Resort, 2009. s. 62. [The fifth meeting on Chromatin Structure & Function. 16.11.2009-19.11.2009, Hilton Papagayo Resort] R&D Projects: GA ?R(CZ) GP301/07/P160 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : p53 * DNA structure * methylation of DNA Subject RIV: BO - Biophysics

  5. TOF-2: a large 1D channel thorium organic framework.

    OpenAIRE

    Ok, KM; Sung, J; Hu, G.; Jacobs, RM; O'Hare, D.

    2008-01-01

    A new neutral 1D channel thorium organic framework material (TOF-2) has been synthesized under hydrothermal conditions. TOF-2 exhibits a hexagonal channel structure consisting of eight-coordinate ThO6F2 polyhedra and 1,3,5-benzentricarboxylate ligands. The channels run along the c-axis and are approximately 13 A in diameter. The single-crystal X-ray structure suggests that the amount of void space is 41%. The structure is stable to ca. 400 degrees C. Gas adsorption measurements show deferenti...

  6. Social exploration of 1D games

    DEFF Research Database (Denmark)

    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 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.

  7. Intelligent Access to Sequence and Structure Databases (IASSD) ? an interface for accessing information from major web databases

    Science.gov (United States)

    Ganguli, Sayak; Gupta, Manoj Kumar; Basu, Protip; Banik, Rahul; Singh, Pankaj Kumar; Vishal, Vineet; Bera, Abhisek Ranjan; Chakraborty, Hirak Jyoti; Das, Sasti Gopal

    2014-01-01

    With the advent of age of big data and advances in high throughput technology accessing data has become one of the most important step in the entire knowledge discovery process. Most users are not able to decipher the query result that is obtained when non specific keywords or a combination of keywords are used. Intelligent access to sequence and structure databases (IASSD) is a desktop application for windows operating system. It is written in Java and utilizes the web service description language (wsdl) files and Jar files of E-utilities of various databases such as National Centre for Biotechnology Information (NCBI) and Protein Data Bank (PDB). Apart from that IASSD allows the user to view protein structure using a JMOL application which supports conditional editing. Availability The Jar file is freely available through e-mail from the corresponding author. PMID:25670880

  8. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

    OpenAIRE

    Mckernan, Kevin Judd; Peckham, Heather E.; Costa, Gina L.; Mclaughlin, Stephen F.; Fu, Yutao; Tsung, Eric F.; Clouser, Christopher R.; Duncan, Cisyla; Ichikawa, Jeffrey K.; Lee, Clarence C.; Zhang, Zheng; Ranade, Swati S.; Dimalanta, Eileen T.; Hyland, Fiona C.; Sokolsky, Tanya D.

    2009-01-01

    We describe the genome sequencing of an anonymous individual of African origin using a novel ligation-based sequencing assay that enables a unique form of error correction that improves the raw accuracy of the aligned reads to >99.9%, allowing us to accurately call SNPs with as few as two reads per allele. We collected several billion mate-paired reads yielding ?18× haploid coverage of aligned sequence and close to 300× clone coverage. Over 98% of the reference genome is covered with at l...

  9. Antimicrobial and cell-penetrating properties of penetratin analogs : effect of sequence and secondary structure

    DEFF Research Database (Denmark)

    Bahnsen, Jesper SØborg; Franzyk, Henrik

    2013-01-01

    Cell-penetrating peptides (CPPs) and antimicrobial peptides (AMPs) show great potential as drug delivery vectors and new antibiotic drug entities, respectively. The current study deals with the properties of a variety of peptide analogs derived from the well-known CPP penetratin as well as octaarginine and different Tat sequences. The effects of peptide length, guanidinium content, and sequence of non-cationic residues were assessed in mammalian and bacterial cells. The arginine (Arg) content in the penetratin analogs was found to influence eukaryotic cell uptake efficiency, antimicrobial activity towards both Gram-positive and Gram-negative bacteria as well as eukaryotic cell viability. All examined analogs retained the ability to cross eukaryotic membranes giving rise to a distribution within the vacuolar apparatus. Interestingly, a series of shuffled analogs of penetratin with the cationic residues in conserved positions, attain the same a-helical conformation as native penetratin in the presence of cholesterol-containing liposomes, while conformational differences were observed in the presence of highly anionic liposomes. While the antibacterial effect of the two groups of peptides was similar, the eukaryotic cellular uptake of the shuffled analogs was noticeably lower than for native penetratin. Moreover, a point substitution of Met to Leu in native penetratin had no influence on eukaryotic cellular uptake and antimicrobial effect, and only a minor effect on cytotoxicity, in contrast to the fact that the same substitution in the shuffled analog gave rise to reduced eukaryotic cellular uptake while increasing the antibacterial effect and cytotoxicity.

  10. Nucleolin, the major nucleolar protein of growing eukaryotic cells: an unusual protein structure revealed by the nucleotide sequence.

    Science.gov (United States)

    Lapeyre, B; Bourbon, H; Amalric, F

    1987-01-01

    Nucleolin (also called C23) is the major nucleolar protein of exponentially growing eukaryotic cells. It is found associated with intranucleolar chromatin and preribosomal particles. Through use of a polyclonal antiserum, nucleolin cDNA clones were isolated from a Chinese hamster ovary cell library constructed in the expression vector lambda gt11. The isolated cDNAs encoded a polypeptide containing 679 residues of the 713 amino acids of nucleolin. The amino acid sequence presents several unusual features: in particular, repetitive sequences are found at both ends of the molecule. A repeat, Hy-Thr-Pro-Hy-Lys-Lys-Hy-Hy, in which Hy is a nonpolar residue, is found six times in the NH2-end proximal portion, followed by three acidic stretches containing 25, 25, and 33 glutamic acid or aspartic acid residues. Four potential phosphorylation sites (serines) are also observed in this region. The COOH-terminal proximal portion of the protein carries a glycine-rich region with fairly regularly interspersed phenylalanine and dimethylarginine residues. The two terminal portions of the molecule exhibit unique potential secondary structures: alpha-helix (NH2 terminus) and extended (COOH terminus). The central region exhibits alternating hydrophobic and hydrophilic stretches. Five potential N glycosylation sites are detected. The structure of this protein may reflect two functions in preribosome biogenesis: interaction with chromatin (NH2 terminus) and with preribosomes (COOH terminus). PMID:3470736

  11. Nucleotide sequence of the structural protein-encoding region of foot-and-mouth disease virus A22-India.

    Science.gov (United States)

    Tosh, C; Venkataramanan, R; Hemadri, D; Sanyal, A; Samuel, A R; Knowles, N J; Kitching, R P

    2000-01-01

    Nucleotide sequence of the structural protein-encoding region of foot-and-mouth disease virus (FMDV) A22-India 17/77 was determined using non-radioisotopic technique. Comparison of nucleotide and deduced amino acid sequence with A22-Iraq 24/64 revealed 175 synonymous (silent) and 42 non-synonymous nucleotide changes resulting in 34 amino acid substitutions along the capsid proteins (VP1-VP4). Out of the 4 structural proteins VP4 is highly conserved. The highly variable and immunodominant protein VP1 showed 47% of the total amino acid substitutions. VP2 and VP3 contain 38.2% and 14.7% of the amino acid substitutions, respectively. The VP1-based phylogenetic analysis of 18 different type A viruses including A22-India 17/77 divided them in to two broad genetic groups (Asian and European/South American), and each group is further subdivided in to two separate genotypes. A22-India 17/77, A22-Iraq 24/64 and A22-Azerbaijan/65 formed one genotype and the 4 Chinese strains formed a separate genotype in the Asian group of viruses. In the European/South American group, A-Argentina/87 represents one genotype and the remaining 10 strains formed the second genotype in this group. PMID:10949956

  12. The Effect of Initial Inoculum Source on the Microbial Community Structure and Dynamics in Laboratory-Scale Sequencing Batch Reactors

    KAUST Repository

    Hernandez, Susana

    2011-07-01

    Understanding the factors that shapes the microbial community assembly in activated sludge wastewater treatment processes provide a conceptual foundation for improving process performance. The aim of this study was to compare two major theories (deterministic theory and neutral theory) regarding the assembly of microorganisms in activated sludge: Six lab-scale activated sludge sequencing batch reactors were inoculated with activated sludge collected from three different sources (domestic, industrial, and sugar industry WWTP). Additionally, two reactors were seeded with equal proportion of sludge from the three WWTPs. Duplicate reactors were used for each sludge source (i.e. domestic, industrial, sugar and mix). Reactors were operated in parallel for 11 weeks under identical conditions. Bacterial diversity and community structure in the eight SBRs were assessed by 16S rRNA gene pyrosequencing. The 16S rRNA gene sequences were analyzed using taxonomic and clustering analysis and by measuring diversity indices (Shannon-weaver and Chao1 indices). Cluster analysis revealed that the microbial community structure was dynamic and that replicate reactors evolved differently. Also the microbial community structure in the SBRs seeded with a different sludge did not converge after 11 weeks of operation under identical conditions. These results suggest that history and distribution of taxa in the source inoculum were stronger regulating factors in shaping bacterial community structure than environmental factors. This supports the neutral theory which states that the assembly of the local microbial community from the metacommunity is random and is regulated by the size and diversity of the metacommunity. Furthermore, sludge performance, measured by COD and ammonia removal, confirmed that broad-scale functions (e.g. COD removal) are not influenced by dynamics in the microbial composition, while specific functions (e.g. nitrification) are more susceptible to these changes.

  13. Molecular modelling of the 3-D structure of RNA tetraloops with different nucleotide sequences.

    OpenAIRE

    Kajava, A; Rüterjans, H.

    1993-01-01

    One surprisingly common element of RNA secondary structure consists of a hairpin capped by a four-base loop (or the tetraloop). Recently the 3-D structures of two RNA-tetraloops have been determined by NMR-studies. Both structures have a similar architecture: the first and the last bases of the loop form a hydrogen bonded pair which is stacked on the stem base pair. We have analysed the ability of tetraloops, with the other combinations of the first and the fourth bases, to adopt such a 'dilo...

  14. De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences

    DEFF Research Database (Denmark)

    Ruzzo, Walter L; Gorodkin, Jan

    2014-01-01

    De novo discovery of "motifs" capturing the commonalities among related noncoding ncRNA structured RNAs is among the most difficult problems in computational biology. This chapter outlines the challenges presented by this problem, together with some approaches towards solving them, with an emphasis on an approach based on the CMfinder CMfinder program as a case study. Applications to genomic screens for novel de novo structured ncRNA ncRNA s, including structured RNA elements in untranslated portions of protein-coding genes, are presented.

  15. Overview remarks on homogeneous N = 1, d = 11 supergravity cosmologies

    International Nuclear Information System (INIS)

    The dynamics of the full class of homogeneous N = 1, d = 11 supergravity world models is investigated. By using the classification of Lie algebras of Lie groups which act simply transitively on 6- and 7-dimensional compact spaces some conclusions are drawn concerning the non-existence of the chaotic regime near the singularity. This is illustrated with some new solutions having a richer structure of the microspace. The significance of known solutions is briefly discussed. 25 refs., 1 fig., 1 tab. (author)

  16. Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package

    OpenAIRE

    Meier Harald; Kipfer Peter; Westram Ralf; Kumar Yadhu; Ludwig Wolfgang

    2006-01-01

    Abstract Background Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended fo...

  17. Circular, Cryogenic Structures from the Hirnantian Deglaciation Sequence (Anti-Atlas, Morocco).

    Czech Academy of Sciences Publication Activity Database

    Nutz, A.; Ghienne, J.-F.; Štorch, Petr

    2013-01-01

    Ro?. 83, ?. 1 (2013), s. 115-131. ISSN 1527-1404 Institutional support: RVO:67985831 Keywords : Ordovician * Anti-Atlas (Morocco) * cryogenic structure Subject RIV: DB - Geology ; Mineralogy Impact factor: 1.943, year: 2013

  18. Structure Contour of the Top of the Middle Miocene Sequence, Gulf Coast

    U.S. Geological Survey, Department of the Interior — The structure contours were created using biostratigraphic data in the Paleo-Data, Inc., Tenroc Regional Geologic Database. The depths of the microfossil locations...

  19. Structure Contour of the Top of the Lower Miocene 1 Sequence, Gulf Coast

    U.S. Geological Survey, Department of the Interior — The structure contours were created using biostratigraphic data in the Paleo-Data, Inc., Tenroc Regional Geologic Database. The depths of the microfossil locations...

  20. Structure Contour of the Top of the Lower Miocene 2 Sequence, Gulf Coast

    U.S. Geological Survey, Department of the Interior — The structure contours were created using biostratigraphic data in the Paleo-Data, Inc., Tenroc Regional Geologic Database. The depths of the microfossil locations...

  1. Structure Contour of the Top of the Upper Miocene Sequence, Gulf Coast

    U.S. Geological Survey, Department of the Interior — The structure contours were created using biostratigraphic data in the Paleo-Data, Inc., Tenroc Regional Geologic Database. The depths of the microfossil locations...

  2. A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination

    OpenAIRE

    Koldobskaya, Yelena; Duguid, Erica M.; Shechner, David M; Suslov, Nikolai B.; Ye, Jingdong; Sidhu, Sachdev S; Bartel, David P; Koide, Shohei; Kossiakoff, Anthony A; Piccirilli, Joseph A.

    2010-01-01

    RNA crystallization and phasing represent major bottlenecks in RNA structure determination. Seeking to exploit antibody fragments as RNA crystallization chaperones, we have used an arginine-enriched synthetic Fab library displayed on phage to obtain Fabs against the class I ligase ribozyme. We solved the structure of a Fab–ligase complex at 3.1-Å resolution using molecular replacement with Fab coordinates, confirming the ribozyme architecture and revealing the chaperone's role in RNA recog...

  3. Sequence-specific 1H assignment and secondary structure of the bacteriocin AS-48 cyclic peptide

    International Nuclear Information System (INIS)

    The bacteriocin AS-48 is a cationic peptide (7149 Da) having a broad antimicrobial spectrum, encoded by the 68 kb conjugative plasmid pMB2 from Enterococcus faecalis S-48. It is a unique peptide since it has a cyclic structure, which is achieved by the formation of a tail-head peptide bond after ribosomal synthesis (Galvez et al., 1989; Martinez-Bueno et al., 1994; Samyn et al., 1994). Preliminary CD and calorimetric studies (data not shown) pointed towards a highly helical and very stable three dimensional structure.All the information gathered until now indicates that the target of AS-48 is the cytoplasmic membrane in which it opens channels or pores, leading to dissipation of the proton motive force and cell death, which in some cases is also followed by bacterial lysis (Galvez et al., 1991). This peptide is a suitable tool for studying protein-membrane interactions, and it also offers promising perspectives for biotechnological applications.Knowledge of the 3D structure of AS-48 is a first step in the conduct of further structure-function studies. Here we report the complete1 H NMR assignment of its proton resonances together with the resulting secondary structure pattern as prerequisites for the determination of a high-resolution 3D solution structure

  4. Hypothesis testing on the fractal structure of behavioral sequences: the Bayesian assessment of scaling methodology.

    Science.gov (United States)

    Moscoso del Prado Martín, Fermín

    2013-12-01

    I introduce the Bayesian assessment of scaling (BAS), a simple but powerful Bayesian hypothesis contrast methodology that can be used to test hypotheses on the scaling regime exhibited by a sequence of behavioral data. Rather than comparing parametric models, as typically done in previous approaches, the BAS offers a direct, nonparametric way to test whether a time series exhibits fractal scaling. The BAS provides a simpler and faster test than do previous methods, and the code for making the required computations is provided. The method also enables testing of finely specified hypotheses on the scaling indices, something that was not possible with the previously available methods. I then present 4 simulation studies showing that the BAS methodology outperforms the other methods used in the psychological literature. I conclude with a discussion of methodological issues on fractal analyses in experimental psychology. PMID:24417750

  5. Regional Implications of Ypresian Flysch Sequence From South of Marmara Sea: Structural, Stratigraphic and Paleontological Data

    Science.gov (United States)

    Ülgen, S. C.; Okay, A. I.; Özcan, E.; ?engör, A. M. C.; Akbayram, K.

    2012-04-01

    The study of a Ypresian flysch sequence, immediately southern of the Intra-Pontid suture zone and overlying the Upper Cretaceous basement rocks, permit us to comment on the late Cretaceous-early Tertiary tectonic history of the region This flysch sequence with a thickness 1500-2000 m consisting of sandstones, shales and conglomerates derived from the Upper-Cretaceous basement rocks. These clastics are intercalated with andesitic tuffs, pyroclasts, agglomerates and lenticular limestones. The flysch contains some larger foraminifera levels including Orbitoclypeus douvillei douvillei, O. douvillei yesilyurtensis, O. schopeni ex. interc. suvlukayensis-crimensis, O. schopeni crimensis, O.munieri munieri, Asterocyclina alticostata cf. gallica, , Discocyclina fortisi simferopolensis. The Ypresian flysch overlies a unit which consists of quartz conglomerate and boulders, chert, serpentinite , metamorphic rock blocks and conglomerates. Some think this unit to be a debris flow, but the range of rock types, the style of deformation and the its areal extent clearly shows it could be a mélange. Gravity flows like mudflows, slump folds and NW-SE trending anticline and synclines are observed and mapped in Ypresian flysch which suggest that it was tectonized during or soon after deposition. Anticlines, synclines and north-nortwest dipping thrust faults point SE vergance in the region. Also earlier published apatite fission track data from metamorphic rocks cropping out at south of Marmara Sea shows that nearby areas uplifted during Early Eocene (~ 52 Ma). We suggest that there are two probable sources for this tectonism in northwest Turkey; the compression related to the consumption of the Intra-Pontide Ocean in the north or the Late Cretaceous-Paleocene collision of Pontides and Taurides in the south.

  6. Lossless Compression Method for Medical Image Sequences Using Super-Spatial Structure Prediction and Inter-frame Coding

    Directory of Open Access Journals (Sweden)

    Mudassar Raza

    2012-08-01

    Full Text Available Space research organizations, hospitals and military air surveillance activities, among others, produce a huge amountof data in the form of images hence a large storage space is required to record this information. In hospitals, dataproduced during medical examination is in the form of a sequence of images and are very much correlated; becausethese images have great importance, some kind of lossless image compression technique is needed. Moreover, theseimages are often required to be transmitted over the network. Since the availability of storage and bandwidth islimited, a compression technique is required to reduce the number of bits to store these images and take less time totransmit them over the network. For this purpose, there are many state-of the-art lossless image compressionalgorithms like CALIC, LOCO-I, JPEG-LS, JPEG20000; Nevertheless, these compression algorithms take only asingle file to compress and cannot exploit the correlation among the sequence frames of MRI or CE images. Toexploit the correlation, a new algorithm is proposed in this paper. The primary goals of the proposed compressionmethod are to minimize the memory resource during storage of compressed data as well as minimize the bandwidthrequirement during transmission of compressed data. For achieving these goals, the proposed compression methodcombines the single image compression technique called super spatial structure prediction with inter-frame coding toacquire grater compression ratio. An efficient compression method requires elimination of redundancy of data duringcompression; therefore, for elimination of redundancy of data, initially, the super spatial structure prediction algorithmis applied with the fast block matching approach and later Huffman coding is applied for reducing the number of bitsrequired for transmitting and storing single pixel value. Also, to speed up the block-matching process during motionestimation, the proposed method compares those blocks that have identical sum and leave the others; therefore, thetime taken by the block-matching process is reduced by minimizing the unnecessary overhead during the blockmatchingprocess. Thus, in the proposed fast lossless compression method for medical image sequences, the twostageredundant data elimination process ultimately reduces the memory resource required for storing andtransmission. The method is tested on the sequences of MRI and CE images and produces an improved compression rate.

  7. Lossless Compression Method for Medical Image Sequences Using Super-Spatial Structure Prediction and Inter-frame Coding

    Scientific Electronic Library Online (English)

    Mudassar, Raza; Ahmed, Adnan; Muhammad, Sharif; Syed Waqas, Haider.

    2012-08-01

    Full Text Available Space research organizations, hospitals and military air surveillance activities, among others, produce a huge amount of data in the form of images hence a large storage space is required to record this information. In hospitals, data produced during medical examination is in the form of a sequence [...] of images and are very much correlated; because these images have great importance, some kind of lossless image compression technique is needed. Moreover, these images are often required to be transmitted over the network. Since the availability of storage and bandwidth is limited, a compression technique is required to reduce the number of bits to store these images and take less time to transmit them over the network. For this purpose, there are many state-of the-art lossless image compression algorithms like CALIC, LOCO-I, JPEG-LS, JPEG20000; Nevertheless, these compression algorithms take only a single file to compress and cannot exploit the correlation among the sequence frames of MRI or CE images. To exploit the correlation, a new algorithm is proposed in this paper. The primary goals of the proposed compression method are to minimize the memory resource during storage of compressed data as well as minimize the bandwidth requirement during transmission of compressed data. For achieving these goals, the proposed compression method combines the single image compression technique called super spatial structure prediction with inter-frame coding to acquire grater compression ratio. An efficient compression method requires elimination of redundancy of data during compression; therefore, for elimination of redundancy of data, initially, the super spatial structure prediction algorithm is applied with the fast block matching approach and later Huffman coding is applied for reducing the number of bits required for transmitting and storing single pixel value. Also, to speed up the block-matching process during motion estimation, the proposed method compares those blocks that have identical sum and leave the others; therefore, the time taken by the block-matching process is reduced by minimizing the unnecessary overhead during the block-matching process. Thus, in the proposed fast lossless compression method for medical image sequences, the two-stage redundant data elimination process ultimately reduces the memory resource required for storing and transmission. The method is tested on the sequences of MRI and CE images and produces an improved compression rate.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-04-24

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

  9. Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrroly-sine containing genes

    DEFF Research Database (Denmark)

    Have, Christian Theil; Zambach, Sine

    2013-01-01

    Background Pyrrolysine (the 22nd amino acid) is in certain organisms and under certain circumstances encoded by the amber stop codon, UAG. The circumstances driving pyrrolysine translation are not well understood. The involvement of a predicted mRNA structure in the region downstream UAG has been suggested, but the structure does not seem to be present in all pyrrolysine incorporating genes. Results We propose a strategy to predict pyrrolysine encoding genes in genomes of archaea and bacteria. We cluster open reading frames interrupted by the amber codon based on sequence similarity. We rank these clusters according to several features that may influence pyrrolysine translation. The ranking effects of different features are assessed and we propose a weighted combination of these features which best explains the currently known pyrrolysine incorporating genes. We devote special attention to the effect of structural conservation and provide further substantiation to support that structural conservation maybe influential – but is not a necessary factor. Finally, from the weighted ranking, we identify a number of potentially pyrrolysine incorporating genes. Conclusions We propose a method for prediction of pyrrolysine incorporating genes in genomes of bacteria and archaea leading to insights about the factors driving pyrrolysine translation and identification of new gene candidates. The method predicts known conserved genes with high recall and predicts several other promising candidates for experimental verification. The method is implemented as a computational pipeline which is available on request.

  10. Sequence, structure, and active site analyses of p38 MAP kinase: exploiting DFG-out conformation as a strategy to design new type II leads.

    Science.gov (United States)

    Badrinarayan, Preethi; Sastry, G Narahari

    2011-01-24

    A new knowledge, structure, and sequence based strategy involving the effective exploitation of the DFG-out conformation is delineated. A comprehensive analysis of the structure, sequence, cocrystals, and active sites of p38 MAP kinase crystal structures present in Protein Data Bank (PDB) and the FDA approved MAP kinase drugs has been done, and the information is used for the design of type II leads. The 98 crystal structures, 138 cocrystals, and 31 FDA drugs comprise of 7 different sequences of 2 organisms viz., Homo sapiens and Mus musculus differing in sequence length, constituting both homo- and heterochains. Multiple sequence alignment with ClustalW showed >95% sequence similarity with highly conserved domains and a high propensity for mutations in the activation loop. The bound ligands were extracted, and their interactions with DFG in and out conformations were studied. These cocrystals and FDA drugs were fragmented on the basis of their binding interactions and their affinity to ATP and allosteric sites. The fragment library thus generated contains 106 fragments with overlapping drug fragments. A blue print constituting three main parts viz., head (ATP region), linker (DFG region), and tail (allosteric region) has thus been formulated and used to design 64 type II p38 MAP kinase inhibitors. The above strategy has been employed to design potent type II p38 MAP kinase inhibitors, which are shown to be very promising. PMID:21141877

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

    Scientific Electronic Library Online (English)

    Sergio, Zamorano; Juan, Camus.

    2011-01-01

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

  12. Sequencing Rules for Sub-Gap Structures in Superconducing Point Contacts

    Science.gov (United States)

    Smith, Charles W.; Dolan, Paul J., Jr.

    2003-03-01

    Multiple Andreev reflections within a superconducting point contact result in 2n-1 quasiparticle transits across the contact that give rise to enhanced current at values of the contact potential, eV = 2?/n, where n = 1, 2, 3, ... For contacts between two different superconductors, the sub-gap structures are more complex than integer subharmonic. Measurements (Charles W. Smith, Randal C. Reinertson and Paul J. Dolan, Jr., Physica B 218, 119 (1996).) of sub-gap structures for Nb/Nb, Nb/Pb and Pb/V contacts compare well with predictions from a generalized trajectory counting model.

  13. A critique on the structural analysis of lignins and application of novel tandem mass spectrometric strategies to determine lignin sequencing.

    Science.gov (United States)

    Banoub, Joseph; Delmas, Guo-Hua; Joly, Nicolas; Mackenzie, Grahame; Cachet, Nadja; Benjelloun-Mlayah, Bouchra; Delmas, Michel

    2015-01-01

    This review is devoted to the application of MS using soft ionization methods with a special emphasis on electrospray ionization, atmospheric pressure photoionization and matrix-assisted laser desorption/ionization MS and tandem MS (MS/MS) for the elucidation of the chemical structure of native and modified lignins. We describe and critically evaluate how these soft ionization methods have contributed to the present-day knowledge of the structure of lignins. Herein, we will introduce new nomenclature concerning the chemical state of lignins, namely, virgin released lignins (VRLs) and processed modified lignins (PML). VRLs are obtained by liberation of lignins through degradation of vegetable matter by either chemical hydrolysis and/or enzymatic hydrolysis. PMLs are produced by subjecting the VRL to a series of further chemical transformations and purifications that are likely to alter their original chemical structures. We are proposing that native lignin polymers, present in the lignocellulosic biomass, are not made of macromolecules linked to cellulose fibres as has been frequently reported. Instead, we propose that the lignins are composed of vast series of linear related oligomers, having different lengths that are covalently linked in a criss-cross pattern to cellulose and hemicellulose fibres forming the network of vegetal matter. Consequently, structural elucidation of VRLs, which presumably have not been purified and processed by any other type of additional chemical treatment and purification, may reflect the structure of the native lignin. In this review, we present an introduction to a MS/MS top-down concept of lignin sequencing and how this technique may be used to address the challenge of characterizing the structure of VRLs. Finally, we offer the case that although lignins have been reported to have very high or high molecular weights, they might not exist on the basis that such polymers have never been identified by the mild ionizing techniques used in modern MS. PMID:25601673

  14. Conservative forgetful scholars: How people learn causal structure through sequences of interventions.

    Science.gov (United States)

    Bramley, Neil R; Lagnado, David A; Speekenbrink, Maarten

    2015-05-01

    Interacting with a system is key to uncovering its causal structure. A computational framework for interventional causal learning has been developed over the last decade, but how real causal learners might achieve or approximate the computations entailed by this framework is still poorly understood. Here we describe an interactive computer task in which participants were incentivized to learn the structure of probabilistic causal systems through free selection of multiple interventions. We develop models of participants' intervention choices and online structure judgments, using expected utility gain, probability gain, and information gain and introducing plausible memory and processing constraints. We find that successful participants are best described by a model that acts to maximize information (rather than expected score or probability of being correct); that forgets much of the evidence received in earlier trials; but that mitigates this by being conservative, preferring structures consistent with earlier stated beliefs. We explore 2 heuristics that partly explain how participants might be approximating these models without explicitly representing or updating a hypothesis space. (PsycINFO Database Record PMID:25329086

  15. Organocatalytic asymmetric strategies to carbocyclic structures by gamma-alkylation-annulation sequences

    DEFF Research Database (Denmark)

    Donslund, Bjarke S.; Halskov, Kim Soholm

    2014-01-01

    Attractive carbocyclic structures are accessed via a highly regio- and enantioselective aminocatalytic gamma-addition of cyclic enals to vinyl phosphonates followed by a one-pot intramolecular Horner-Wadsworth-Emmons reaction. It is also demonstrated that nitro olefins can act as electrophiles in a similar reaction concept, providing carbocycles in equally high stereoselectivity.

  16. PALLAS-1D(V3): variable-dimension version of PALLAS-1D(VII)

    International Nuclear Information System (INIS)

    The PALLAS-1D(V3) program is a variable-dimension version of the PALLAS-1D(VII) code, which is the revised version of the PALLAS-PL, SP-Br code. The PALLAS-1D(VII) code could treat transport of both neutrons and gamma rays, in particular of secondary photons including the bremsstrahlung and annihilation photons. This document gives a full description of input and output data for PALLAS-1D(V3) code, also with the input description of several sample problems. (author)

  17. Quasispecies structure, cornerstone of hepatitis B virus infection: Mass sequencing approach

    Directory of Open Access Journals (Sweden)

    Francisco Rodriguez-Frias

    2013-01-01

    Full Text Available Hepatitis B virus (HBV is a DNA virus with complex replication, and high replication and mutation rates, leading to a heterogeneous viral population. The population is comprised of genomes that are closely related, but not identical; hence, HBV is considered a viral quasispecies. Quasispecies variability may be somewhat limited by the high degree of overlapping between the HBV coding regions, which is especially important in the P and S gene overlapping regions, but is less significant in the X and preCore/Core genes. Despite this restriction, several clinically and pathologically relevant variants have been characterized along the viral genome. Next-generation sequencing (NGS approaches enable high-throughput analysis of thousands of clonally amplified regions and are powerful tools for characterizing genetic diversity in viral strains. In the present review, we update the information regarding HBV variability and present a summary of the various NGS approaches available for research in this virus. In addition, we provide an analysis of the clinical implications of HBV variants and their study by NGS.

  18. STRUCTURAL SOFTWARE TESTING: HYBRID ALGORITHM FOR OPTIMAL TEST SEQUENCE SELECTION DURING REGRESSION TESTING

    Directory of Open Access Journals (Sweden)

    J. Albert Mayan

    2015-02-01

    Full Text Available Regression testing is one of the testing methods, which is done to ensure that the changes made in fixes or any improvement changes does not affect the previously developed functionality of the software. When modification is done to an application, the newly added features had to be tested along with the already available features to ensure that the modification at one part of the program does not have any adverse effect on other parts of the application. Test coverage must be enhanced without conciliation of timelines. Thus, the test case generation and test case selection play an important role in the SUT (Software Under Test. Many techniques are proposed to overcome these issues however those techniques could not achieve complete code coverage within the less time duration. In this paper we have proposed a hybrid algorithm which is used to generate an optimal test case selection sequence as well as new test case generation technique for regression testing. The experimental results obtained by our proposed approach shows better results compared to other approaches.

  19. Structure and sequence of thrusting in deep-water sediments during ophiolite emplacement in the south-central Oman Mountains

    Science.gov (United States)

    Cooper, D. J. W.

    Sedimentological and stratigraphical investigations of the deep-water passive margin sediments of the Oman Neo-Tethys (the 'Hawasina Ocean'), when allied with structural relationships between duplexes of these units emplaced on to the Oman margin during late Cretaceous ophiolite obduction, allow the reconstruction of sediment distribution in the Hawasina Ocean. From this starting point, and the observed stacking order of duplexes, the sequence of thrusting of the oceanic sediments can be deduced. Imbrication proceeded through foreland-propagating thrusts, whilst the assembled thrust stack was modified at a late stage of emplacement by out-of-sequence thrusting related to sequential locking of thrust planes towards the hinterland, and gravity sliding off the flanks of a major anticline that developed in the underlying autochthonous shelf and basement. Two main factors governed duplex and imbricate fan formation and distribution. Firstly, two contrasting sedimentary basins were present along the central Oman margin, the 'Duru basin' distal to the 'Al Ayn basin'. Secondly, competent sedimentary successions were bulldozed ahead of the Semail Ophiolite, whilst less competent shale and chert units were overridden by the ophiolite or imbricated along its leading edge.

  20. Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes

    Directory of Open Access Journals (Sweden)

    Selvaraj S

    2011-10-01

    Full Text Available Abstract Background Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology. Methods We have developed an energy based approach for identifying the binding site residues in protein–protein complexes. The binding site residues have been analyzed with sequence and structure based parameters such as binding propensity, neighboring residues in the vicinity of binding sites, conservation score and conformational switching. Results We observed that the binding propensities of amino acid residues are specific for protein-protein complexes. Further, typical dipeptides and tripeptides showed high preference for binding, which is unique to protein-protein complexes. Most of the binding site residues are highly conserved among homologous sequences. Our analysis showed that 7% of residues changed their conformations upon protein-protein complex formation and it is 9.2% and 6.6% in the binding and non-binding sites, respectively. Specifically, the residues Glu, Lys, Leu and Ser changed their conformation from coil to helix/strand and from helix to coil/strand. Leu, Ser, Thr and Val prefer to change their conformation from strand to coil/helix. Conclusions The results obtained in this study will be helpful for understanding and predicting the binding sites in protein-protein complexes.

  1. Sequence variation and structural conservation allows development of novel function and immune evasion in parasite surface protein families.

    Science.gov (United States)

    Higgins, Matthew K; Carrington, Mark

    2014-04-01

    Trypanosoma and Plasmodium species are unicellular, eukaryotic pathogens that have evolved the capacity to survive and proliferate within a human host, causing sleeping sickness and malaria, respectively. They have very different survival strategies. African trypanosomes divide in blood and extracellular spaces, whereas Plasmodium species invade and proliferate within host cells. Interaction with host macromolecules is central to establishment and maintenance of an infection by both parasites. Proteins that mediate these interactions are under selection pressure to bind host ligands without compromising immune avoidance strategies. In both parasites, the expansion of genes encoding a small number of protein folds has established large protein families. This has permitted both diversification to form novel ligand binding sites and variation in sequence that contributes to avoidance of immune recognition. In this review we consider two such parasite surface protein families, one from each species. In each case, known structures demonstrate how extensive sequence variation around a conserved molecular architecture provides an adaptable protein scaffold that the parasites can mobilise to mediate interactions with their hosts. PMID:24442723

  2. Sequence-specific 1H-NMR assignments and identification of two small antiparallel beta-sheets in the solution structure of recombinant human transforming growth factor alpha.

    OpenAIRE

    Montelione, G. T.; Winkler, M. E.; Burton, L. E.; Rinderknecht, E.; Sporn, M. B.; Wagner, G.

    1989-01-01

    Transforming growth factor alpha (TGF alpha) is a small mitogenic protein with about 35% sequence identity with epidermal growth factor (EGF). TGF alpha-like proteins have been proposed to play a role in oncogenesis and wound healing. This report describes sequence-specific 1H-NMR resonance assignments for recombinant human TGF alpha (hTGF alpha). These assignments provide the basis for interpreting NMR data which demonstrate that the solution structure of hTGF alpha includes an antiparallel ...

  3. Coupling method of 1-d/1-d and 1-d/3-d junctions for an implict WCOBRA/TRAC

    International Nuclear Information System (INIS)

    COBRA/TRAC is an advanced thermal-hydraulic computer code, originally developed by Battelle Pacific Northwest Laboratories. The code combines a two-fluid, three-dimensional (3-d) program, COBRA-TF, with a one-dimensional (1-d) drift flux program, TRAC-PD2. COBRA-TF is designed to be used to model the pressurized water reactor (PWR), and loop components are modeled with TRAC-PD2. An implicit method was proposed for the COBRA part of the code, and some success was achieved as demonstrated by an analysis of a film-boiling experiment for a steady-state and power ascension transient. On the other hand, TRAC-PD2 includes an option to choose a semi-implicit or an implicit method in solving component equations. This implicit option improves running time somewhat, but the junctions among the components are treated semi-implicitly. So, the time step is controlled by the Courant numbers at the 1-d/3-d and 1-d/1-d component junctions. In order to speed up the code further, the solution method for the junctions must be changed to implicit. An implicit method is introduced. It is evaluated by a COBRA/TRAC model of a less-of-fluid test (LOFT) and a two-loop PWR

  4. Adaptive processing of structural data: from sequences to trees and beyond

    OpenAIRE

    Ku?chler, Andreas

    2000-01-01

    In computer science, structural (e.g. causal, topological, or hierarchical) relationships between parts of an object are commonly represented by symbolic formalisms such as graphs, terms or diagrams. Symbolic machine learning approaches can deal with these representations, but fail if the range of the intended mapping is of continuous nature. On the other hand, existing analog models of computation and learning are tailored to the processing of continuous information. However, these models as...

  5. Modelling Intermolecular Structures and Defining Ambiguity in Gene Sequences using Matrix Insertion-Deletion Systems

    OpenAIRE

    Kuppusamy, Lakshmanan; Mahendran, Anand; Villemonte La Clergerie, E?ric

    2011-01-01

    Gene insertion and deletion are considered as the basic operations in DNA processing and RNA editing. Based on these evolutionary transformations, a computing model has been formulated in formal language theory known as insertion-deletion systems. Recently, in [6], a new computing model named Matrix insertion-deletion system has been introduced to model various bio-molecular structures such as hairpin, stem and loop, pseudoknot, attenuator, cloverleaf, dumbbell that occur at intramolecular le...

  6. Oligosaccharide structure and amino acid sequence of the major glycopeptides of mature human ?-hexosaminidase

    International Nuclear Information System (INIS)

    Human ?-hexosaminidase is a lysosomal enzyme that hydrolyzes terminal N-acetylhexosamines from GM2 ganglioside, oligosaccharides, and other carbohydrate-containing macromolecules. There are two major forms of hexosaminidase: hexosaminidase A, with the structure ?(?/sub a/?/sub b/), and hexosaminidase B, 2(?/sub a/?/sub b/). Like other lysosomal proteins, hexosaminidase is targeted to its destination via glycosylation and processing in the rough endoplasmic reticulum and Golgi apparatus. Phosphorylation of specific mannose residues allows binding of the protein to the phosphomannosyl receptor and transfer to the lysosome. In order to define the structure and placement of the oligosaccharides in mature hexosaminidase and thus identify candidate mannose 6-phosphate recipient sites, the major tryptic/chymotryptic glycopeptides from each isozyme were purified by reverse-phase high-performance liquid chromatography. Two major concanavalin A binding glycopeptides, localized to the ?/sub b/f chain, and one non concanavalin A binding glycopeptide, localized to the ?/sub a/ chain, were found associated with the ?-subunit in both hexosaminidase A and hexosaminidase B. The oligosaccharide structures were determined by nuclear magnetic resonance spectrometry. The unique glycopeptide associated with the ?/sub a/ chain contained a single GlcNAc residue. Thus all three mature polypeptides comprising the ? and ? subunits of hexosaminidase contain carbohydrate, tnidase contain carbohydrate, the structures of which have the appearance of being partially degraded in the lysosome. In the ? chain they found only one possible site for in vivo phosphorylation. In the ? it is unclear if only one or all three of the sites could have contained phosphate. However, mature placental hexosaminidase A and B can be rephosphorylated in vitro. This requires the presence of an oligosaccharide containing an ?1,2-linked mannose residue

  7. Phylogeographical structure inferred from cpDNA sequence variation of Zygophyllum xanthoxylon across north-west China.

    Science.gov (United States)

    Shi, Xiao-Jun; Zhang, Ming-Li

    2015-03-01

    Zygophyllum xanthoxylon, a desert species, displaying a broad east-west continuous distribution pattern in arid Northwestern China, can be considered as a model species to investigate the biogeographical history of this region. We sequenced two chloroplast DNA spacers (psbK-psbI and rpl32-trnL) in 226 individuals from 31 populations to explore the phylogeographical structure. Median-joining network was constructed and analysis of AMOVA, SMOVA, neutrality tests and distribution analysis were used to examine genetic structure and potential range expansion. Using species distribution modeling, the geographical distribution of Z. xanthoxylon was modeled during the present and at the Last Glacial Maximum (LGM). Among 26 haplotypes, one was widely distributed, but most was restricted to either the eastern or western region. The populations with the highest levels of haplotype diversity were found in the Tianshan Mountains and its surroundings in the west, and the Helan Mountains and Alxa Plateau in the east. AMOVA and SAMOVA showed that over all populations, the species lacks phylogeographical structure, which is speculated to be the result of its specific biology. Neutrality tests and mismatch distribution analysis support past range expansions of the species. Comparing the current distribution to those cold and dry conditions in LGM, Z. xanthoxylon had a shrunken and more fragmented range during LGM. Based on the evidences from phylogeographical patterns, distribution of genetic variability, and paleodistribution modeling, Z. xanthoxylon is speculated most likely to have originated from the east and migrated westward via the Hexi Corridor. PMID:25626403

  8. Probing the structure of glucan lyases – the lytic members of GH31 - by sequence analysis, circular dichroism and proteolysis

    DEFF Research Database (Denmark)

    Ernst, Heidi; Lo Leggio, Leila

    2005-01-01

    Glucan lyase (GL) is a polysaccharide lyase with unique characteristics. It is involved in an alternative pathway for the degradation of alpha-glucans, the anhydrofructose pathway. Sequence similarity suggests that this lytic enzyme belongs to glycoside hydrolase family 31, for which until very recently no structural representative was available. In the present study, the GLs have been analysed by bioinformatics, and experimental data have been obtained for two isozymes from the red alga Gracilariopsis lemaneiformis by circular dichrosim and limited proteolysis. Based on these results, the GLs are predicted to have a central catalytic domain with (beta/alpha)(8) structure flanked by beta-rich domains at the N- and C-termini. The GLs were found to be surprisingly resistant to proteolytic degradation, requiring relatively high protease concentrations and long incubation times for cleavage to occur. Two cleavage sites have been identified in the N-terminal part of the protein, while the central domain and the C-terminal region do not seem to be susceptible to proteolytic attack. These results suggest that GLs are compact in structure, unlike many carbohydrate-modifying enzymes consisting of modules connected by long flexible linkers.

  9. On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence

    Directory of Open Access Journals (Sweden)

    Theobald Douglas L

    2011-11-01

    Full Text Available Abstract Background The universal common ancestry (UCA of all known life is a fundamental component of modern evolutionary theory, supported by a wide range of qualitative molecular evidence. Nevertheless, recently both the status and nature of UCA has been questioned. In earlier work I presented a formal, quantitative test of UCA in which model selection criteria overwhelmingly choose common ancestry over independent ancestry, based on a dataset of universally conserved proteins. These model-based tests are founded in likelihoodist and Bayesian probability theory, in opposition to classical frequentist null hypothesis tests such as Karlin-Altschul E-values for sequence similarity. In a recent comment, Koonin and Wolf (K&W claim that the model preference for UCA is "a trivial consequence of significant sequence similarity". They support this claim with a computational simulation, derived from universally conserved proteins, which produces similar sequences lacking phylogenetic structure. The model selection tests prefer common ancestry for this artificial data set. Results For the real universal protein sequences, hierarchical phylogenetic structure (induced by genealogical history is the overriding reason for why the tests choose UCA; sequence similarity is a relatively minor factor. First, for cases of conflicting phylogenetic structure, the tests choose independent ancestry even with highly similar sequences. Second, certain models, like star trees and K&W's profile model (corresponding to their simulation, readily explain sequence similarity yet lack phylogenetic structure. However, these are extremely poor models for the real proteins, even worse than independent ancestry models, though they explain K&W's artificial data well. Finally, K&W's simulation is an implementation of a well-known phylogenetic model, and it produces sequences that mimic homologous proteins. Therefore the model selection tests work appropriately with the artificial data. Conclusions For K&W's artificial protein data, sequence similarity is the predominant factor influencing the preference for common ancestry. In contrast, for the real proteins, model selection tests show that phylogenetic structure is much more important than sequence similarity. Hence, the model selection tests demonstrate that real universally conserved proteins are homologous, a conclusion based primarily on the specific nested patterns of correlations induced in genetically related protein sequences. Reviewers This article was reviewed by Rob Knight, Robert Beiko (nominated by Peter Gogarten, and Michael Gilchrist.

  10. Analysis of sequence polymorphism and population structure of tomato chlorotic dwarf viroid and potato spindle tuber viroid in viroid-infected tomato plants.

    Science.gov (United States)

    Nie, Xianzhou

    2012-06-01

    The sequence polymorphism and population structure of Tomato chlorotic dwarf viroid (TCDVd) (isolate Trust) and Potato tuber spindle viroid (PSTVd) (isolate FN) in tomato plants were investigated. Of the 9 and 35 TCDVd clones sequenced from 2 different TCDVd-infected plants, 2 and 4 sequence variants were identified, respectively, leading to a total of 4 sequence variants of 360 nucleotides in length. Variant I was identical to AF162131, the first TCDVd sequence to be reported, and the rest exhibited 1 to 3 nucleotide differences, all in the T(R) domain, from AF162131/variant I. Of the 33 and 29 PSTVd clones sequenced from 2 different PSTVd-infected plants, 8 and 9 sequence variants were found, respectively, leading to a total of 15 variants ranging in length from 356 to 359 nucleotides. The variant I was identical to EF044303, a PSTVd reported in Russia. The rest exhibited 1 to 11 nucleotide differences scattering in all five domains from EF044303/variant I. The results demonstrated for the first time that TCDVd, like many other viroids including PSTVd, exists in host plants as a collective group comprised of various sequence variants. However, in comparison to PSTVd, TCDVd is less polymorphic in tomato plants as fewer variants and lower haplotype/nucleotide diversities were observed. PMID:22816033

  11. New seismogenic source and deep structures revealed by the 1999 Chia-yi earthquake sequence in southwestern Taiwan

    Science.gov (United States)

    Chen, Yue-Gau; Kuo, Yu-Ting; Wu, Yih-Min; Chen, Hsiung-Lin; Chang, Chien-Hsin; Chen, Ron-Yu; Lo, Po-Wen; Ching, Kuo-En; Lee, Jian-Cheng

    2008-03-01

    In a tectonically active setting large earthquakes are always threats; however, they may also be useful in elucidating the subsurface geology. Instrumentally recorded seismicity is, therefore, widely utilized to extend our knowledge into the deeper crust, especially where basement is involved. It is because the earthquakes are triggered by underground stress changes that usually corresponding to the framework of geological structures. Hidden faults, therefore, can be recognized and their extension as well as orientation can be estimated. Both above are of relevance for assessment on seismic hazard of a region, since the active faults are supposed to be re-activated and cause large earthquakes. In this study, we analysed the 1999 October 22 earthquake sequence that occurred in southwestern Taiwan. Two major seismicity clusters were identified with spatial distribution between depths of 10 and 16 km. One cluster is nearly vertical and striking 032°, corresponding to the strike-slip Meishan fault (MSF) that generated the 1906 surface rupture. Another cluster strikes 190° and dips 64° to the west, which is interpreted as west-vergent reverse fault, in contrast to previous expectation of east vergence. Our analysis of the focal solutions of all the larger earthquakes in the 1999 sequence with the 3-D distribution of all the earthquakes over the period 1990-2004 allows us reinterpret the structural framework and suggest previously unreognized seismogenic sources in this area. We accordingly suggest: (1) multiple detachment faults are present in southwestern Taiwan coastal plain and (2) additional seismogenic sources consist of tear faults and backthrust faults in addition to sources associated with west-vergent fold-and-thrust belt.

  12. Extended-Range Ultrarefractive 1D Photonic Crystal Prisms

    Science.gov (United States)

    Ting, David Z.

    2007-01-01

    A proposal has been made to exploit the special wavelength-dispersive characteristics of devices of the type described in One-Dimensional Photonic Crystal Superprisms (NPO-30232) NASA Tech Briefs, Vol. 29, No. 4 (April 2005), page 10a. A photonic crystal is an optical component that has a periodic structure comprising two dielectric materials with high dielectric contrast (e.g., a semiconductor and air), with geometrical feature sizes comparable to or smaller than light wavelengths of interest. Experimental superprisms have been realized as photonic crystals having three-dimensional (3D) structures comprising regions of amorphous Si alternating with regions of SiO2, fabricated in a complex process that included sputtering. A photonic crystal of the type to be exploited according to the present proposal is said to be one-dimensional (1D) because its contrasting dielectric materials would be stacked in parallel planar layers; in other words, there would be spatial periodicity in one dimension only. The processes of designing and fabricating 1D photonic crystal superprisms would be simpler and, hence, would cost less than do those for 3D photonic crystal superprisms. As in 3D structures, 1D photonic crystals may be used in applications such as wavelength-division multiplexing. In the extended-range configuration, it is also suitable for spectrometry applications. As an engineered structure or artificially engineered material, a photonic crystal can exhibit optical properties not commonly found in natural substances. Prior research had revealed several classes of photonic crystal structures for which the propagation of electromagnetic radiation is forbidden in certain frequency ranges, denoted photonic bandgaps. It had also been found that in narrow frequency bands just outside the photonic bandgaps, the angular wavelength dispersion of electromagnetic waves propagating in photonic crystal superprisms is much stronger than is the angular wavelength dispersion obtained by use of conventional prisms and diffraction gratings and is highly nonlinear.

  13. A simple quasi-1D model of Fibonacci anyons

    Science.gov (United States)

    Aasen, David; Mong, Roger; Clarke, David; Alicea, Jason; Fendley, Paul

    2015-03-01

    There exists various ways of understanding the topological properties of Ising anyons--from simple free-fermion toy models to formal topological quantum field theory. For other types of anyons simple toy models rarely exist; their properties have to be obtained using formal self-consistency relations. We explore a family of gapped 1D local bosonic models that in a certain limit become trivial to solve and provide an intuitive picture for Fibonacci anyons. One can interpret this model as a quasi-1D wire that forms the building block of a 2D topological phase with Fibonacci anyons. With this interpretation all topological properties of the Fibonacci anyons become manifest including ground state degeneracy and braid relations. We conjecture that the structure of the model is protected by an emergent symmetry analogous to fermion parity. There exists various ways of understanding the topological properties of Ising anyons--from simple free-fermion toy models to formal topological quantum field theory. For other types of anyons simple toy models rarely exist; their properties have to be obtained using formal self-consistency relations. We explore a family of gapped 1D local bosonic models that in a certain limit become trivial to solve and provide an intuitive picture for Fibonacci anyons. One can interpret this model as a quasi-1D wire that forms the building block of a 2D topological phase with Fibonacci anyons. With this interpretation all topological properties of the Fibonacci anyons become manifest including ground state degeneracy and braid relations. We conjecture that the structure of the model is protected by an emergent symmetry analogous to fermion parity. 1) NSF Grant DMR-1341822 2) Institute for Quantum Information and Matter, an NSF physics frontier center with support from the Moore Foundation. 3) NSERC-PGSD.

  14. A structural and primary sequence comparison of the viral RNA-dependent RNA polymerases

    OpenAIRE

    Bruenn, Jeremy A.

    2003-01-01

    A systematic bioinformatic approach to identifying the evolutionarily conserved regions of proteins has verified the universality of a newly described conserved motif in RNA-dependent RNA polymerases (motif F). In combination with structural comparisons, this approach has defined two regions that may be involved in unwinding double-stranded RNA (dsRNA) for transcription. One of these is the N-terminal portion of motif F and the second is a large insertion in motif F present in the RNA-depende...

  15. Dealing with a New T1D Diagnosis in College

    Science.gov (United States)

    ... College Dealing with a New T1D Diagnosis in College A diabetes diagnosis is shocking at any point ... everything you set your heart on. T1D in College T1D in College Studying in College Handling Roommate ...

  16. Ising-model description of long-range correlations in DNA sequences

    Science.gov (United States)

    Colliva, A.; Pellegrini, R.; Testori, A.; Caselle, M.

    2015-05-01

    We model long-range correlations of nucleotides in the human DNA sequence using the long-range one-dimensional (1D) Ising model. We show that, for distances between 103 and 106 bp, the correlations show a universal behavior and may be described by the non-mean-field limit of the long-range 1D Ising model. This allows us to make some testable hypothesis on the nature of the interaction between distant portions of the DNA chain which led to the DNA structure that we observe today in higher eukaryotes.

  17. In silico Sequence Analysis, Structure Prediction and Function Annotation of Human Bcl-X Beta Protein

    Directory of Open Access Journals (Sweden)

    Anjali Singh

    2014-03-01

    Full Text Available Bcl-X proteins are the one of the best categorized member of the Bcl-2 protein families which acts as primary regulators of apoptosis in mammalian cells. The Bcl-X proteins are potential anti-cancer drug targets. In this study, the tertiary structure of the beta isoform of the apoptosis regulator Bcl-X in humans (h-Bcl-X? has been predicted by fold-recognition (threading approach. In silico assessment of the h-Bcl-X? protein revealed the characteristic structural features of anti-apoptotic Bcl-2 protein family in h-Bcl-X? protein. The predicted model was comprised of BH1-BH4 domains, seven alpha-helices and a C-terminal transmembrane domain for membrane localization and sub-cellular targeting. Quality assessment of the predict model confirmed its reliability as fairly good model. Active sites of h-Bcl-X? protein were identified using CASTp server. The future work can be directed towards drug designing for cancer treatment by regulating the activity of h-Bcl-X? proteins.

  18. The Medium-Chain Dehydrogenase/reductase Engineering Database: a systematic analysis of a diverse protein family to understand sequence-structure-function relationship.

    Science.gov (United States)

    Knoll, Michael; Pleiss, Jürgen

    2008-10-01

    The Medium-Chain Dehydrogenase/Reductase Engineering Database (MDRED, http://www.mdred.uni-stuttgart.de) has been established to serve as an analysis tool for a systematic investigation of sequence-structure-function relationships. It includes sequence and structure information of 2684 and 42 medium-chain dehydrogenases/reductases (MDRs), respectively. Although MDRs are very diverse in sequence, they have a conserved tertiary structure. MDRs are assigned to 199 homologous families and 29 superfamilies. For each family, annotated multiple sequence alignments are provided, and functionally relevant residues are annotated. Twenty-five superfamilies were classified as zinc-containing MDRs, four as non-zinc-containing MDRs. For the zinc-containing MDRs, three subclasses were identified by systematic analysis of a variable loop region, the quaternary structure determining loop (QSDL): the class of short, medium, and long QSDL, which include 11, 3, and 5 superfamilies, respectively. The length of the QSDL is predictive for tetramer (short QSDL) and dimer (long QSDL) formation. The class of medium QSDL includes both tetrameric and dimeric MDRs. The shape of the substrate-binding site is highly conserved in all zinc-containing MDRs with the exception of two variable regions, the substrate recognition sites (SRS): two residues located on the QSDL (SRS1) and, for the class of long QSDL, one residue located in the catalytic domain (SRS2). The MDRED is the first online-accessible resource of MDRs that integrates information on sequence, structure, and function. Annotation of functionally relevant residues assist the understanding of sequence-structure-function relationships. Thus, the MDRED serves as a valuable tool to identify potential hotspots for engineering properties such as substrate specificity. PMID:18614751

  19. Structural mechanisms underlying sequence-dependent variations in GAG affinities of decorin binding protein A, a Borrelia burgdorferi adhesin.

    Science.gov (United States)

    Morgan, Ashli M; Wang, Xu

    2015-05-01

    Decorin-binding protein A (DBPA) is an important surface adhesin of the bacterium Borrelia burgdorferi, the causative agent of Lyme disease. DBPA facilitates the bacteria's colonization of human tissue by adhering to glycosaminoglycan (GAG), a sulfated polysaccharide. Interestingly, DBPA sequence variation among different strains of Borrelia spirochetes is high, resulting in significant differences in their GAG affinities. However, the structural mechanisms contributing to these differences are unknown. We determined the solution structures of DBPAs from strain N40 of B. burgdorferi and strain PBr of Borrelia garinii, two DBPA variants whose GAG affinities deviate significantly from strain B31, the best characterized version of DBPA. Our structures revealed that significant differences exist between PBr DBPA and B31/N40 DBPAs. In particular, the C-terminus of PBr DBPA, unlike C-termini from B31 and N40 DBPAs, is positioned away from the GAG-binding pocket and the linker between helices one and two of PBr DBPA is highly structured and retracted from the GAG-binding pocket. The repositioning of the C-terminus allowed the formation of an extra GAG-binding epitope in PBr DBPA and the retracted linker gave GAG ligands more access to the GAG-binding epitopes than other DBPAs. Characterization of GAG ligands' interactions with wild-type (WT) PBr and mutants confirmed the importance of the second major GAG-binding epitope and established the fact that the two epitopes are independent of one another and the new epitope is as important to GAG binding as the traditional epitope. PMID:25695518

  20. Secondary structure determination for alpha-neurotoxin from Dendroaspis polylepis polylepis based on sequence-specific 1H-nuclear-magnetic-resonance assignments.

    Science.gov (United States)

    Labhardt, A M; Hunziker-Kwik, E H; Wüthrich, K

    1988-11-01

    Sequence-specific assignments are presented for the polypeptide backbone protons and a majority of the amino-acid-side-chain protons of alpha-neurotoxin from Dendroaspis polylepis polylepis, and individual amide proton-exchange rates with the solvent are reported. The secondary structure and the hydrogen-bonding patterns in the regular secondary structure elements are deduced from nuclear Overhauser effects and the sequence locations of the slowly exchanging amide protons. The molecule includes a three-stranded antiparallel beta-sheet, and there are indications that two additional short chain segments are arranged in an antiparallel beta-sheet. These structural elements are similar, but not identical, to either the secondary structure reported for erabutoxin b in single crystals, or the solution structure of cytotoxin CTXIIb from Naja mossambica mossambica. PMID:2847926

  1. Integrated sequence stratigraphy of the postimpact sediments from the Eyreville core holes, Chesapeake Bay impact structure inner basin

    Science.gov (United States)

    Browning, J.V.; Miller, K.G.; McLaughlin, P.P., Jr.; Edwards, L.E.; Kulpecz, A.A.; Powars, D.S.; Wade, B.S.; Feigenson, M.D.; Wright, J.D.

    2009-01-01

    The Eyreville core holes provide the first continuously cored record of postimpact sequences from within the deepest part of the central Chesapeake Bay impact crater. We analyzed the upper Eocene to Pliocene postimpact sediments from the Eyreville A and C core holes for lithology (semiquantitative measurements of grain size and composition), sequence stratigraphy, and chronostratigraphy. Age is based primarily on Sr isotope stratigraphy supplemented by biostratigraphy (dinocysts, nannofossils, and planktonic foraminifers); age resolution is approximately ??0.5 Ma for early Miocene sequences and approximately ??1.0 Ma for younger and older sequences. Eocene-lower Miocene sequences are subtle, upper middle to lower upper Miocene sequences are more clearly distinguished, and upper Miocene- Pliocene sequences display a distinct facies pattern within sequences. We recognize two upper Eocene, two Oligocene, nine Miocene, three Pliocene, and one Pleistocene sequence and correlate them with those in New Jersey and Delaware. The upper Eocene through Pleistocene strata at Eyreville record changes from: (1) rapidly deposited, extremely fi ne-grained Eocene strata that probably represent two sequences deposited in a deep (>200 m) basin; to (2) highly dissected Oligocene (two very thin sequences) to lower Miocene (three thin sequences) with a long hiatus; to (3) a thick, rapidly deposited (43-73 m/Ma), very fi ne-grained, biosiliceous middle Miocene (16.5-14 Ma) section divided into three sequences (V5-V3) deposited in middle neritic paleoenvironments; to (4) a 4.5-Ma-long hiatus (12.8-8.3 Ma); to (5) sandy, shelly upper Miocene to Pliocene strata (8.3-2.0 Ma) divided into six sequences deposited in shelf and shoreface environments; and, last, to (6) a sandy middle Pleistocene paralic sequence (~400 ka). The Eyreville cores thus record the fi lling of a deep impact-generated basin where the timing of sequence boundaries is heavily infl uenced by eustasy. ?? 2009 The Geological Society of America.

  2. Effects of salinity on performance and microbial community structure of an anoxic-aerobic sequencing batch reactor.

    Science.gov (United States)

    Wang, Zichao; Gao, Mengchun; Wang, Sen; Chang, Qingbo; Wang, Zhe

    2015-08-01

    The effects of salinity on the performance and microbial community structure of activated sludge were investigated in an anoxic-aerobic sequencing batch reactor (SBR). The removal efficiencies of chemical oxygen demand (COD) and [Formula: see text]-N decreased as the influent salinity increased from 0.5% to 6%. The specific oxygen utilization rate of activated sludge increased from 22.47 to 43.16?mg?O2?g(-1)?mixed liquid suspended solids (MLSS)?h(-1) with the increase in salinity from 0.5% to 4% and subsequently decreased to 18.3?mg?O2?g(-1)?MLSS?h(-1) at 6% salinity. The specific ammonium oxidation rate (SAOR) and specific nitrite oxidation rate (SNOR) decreased slowly at 0.5-1% salinity and then decreased rapidly with the increase in salinity from 1% to 6%. The SNOR diminished at a faster rate than the SAOR with the increase in salinity from 0.5% to 6%. The specific nitrate reduction rate (SNRR) decreased with the increase in salinity, whereas the SNRR was higher than the sum of SAOR and SNOR at 0.5-6% salinity. The denaturing gradient gel electrophoresis profiles revealed obvious changes in microbial community structure at different salinities. Some microbes were capable of tolerating up to 6% salinity in the SBR, such as Planomonospora sphaerica, Nitrosomonas sp. Is32, and Denitromonas sp. D2-1. PMID:25686658

  3. Structure Analysis of Aerobic Granule from a Sequencing Batch Reactor for Organic Matter and Ammonia Nitrogen Removal

    Directory of Open Access Journals (Sweden)

    Jun Li

    2014-02-01

    Full Text Available Aerobic granules were cultivated in a sequencing batch reactor (SBR. COD and ammonia nitrogen removal rate were 94% and 99%, respectively. The diameter, settling velocity and SVI10 of granules ranged from 2 to 5 mm, 80 to 110 m/h and about 40 mL/g, respectively. Freezing microtome images, DO concentration profiles by microelectrode, distribution of bacteria and EPS by confocal laser scanning microscopy (CLSM show that the aerobic granules have a three-layer structure. Each layer has different thickness, character, bacteria, and DO transfer rate. A hypothesis for granule structure is proposed: the first layer, the surface of the granule, is composed mostly of heterotrophic organisms for organic matter removal, with a thickness range from 150 to 350 ?m; the second layer, mostly composed of autotrophic organisms for ammonia nitrogen removal, with a thickness range from 250 to 450 ?m; the third layer, located in the core of the granule, has mostly an inorganic composition and contains pores and channels.

  4. Large-scale prediction of drug-target interactions using protein sequences and drug topological structures

    Energy Technology Data Exchange (ETDEWEB)

    Cao Dongsheng [Research Center of Modernization of Traditional Chinese Medicines, Central South University, Changsha 410083 (China); Liu Shao [Xiangya Hospital, Central South University, Changsha 410008 (China); Xu Qingsong [School of Mathematical Sciences and Computing Technology, Central South University, Changsha 410083 (China); Lu Hongmei; Huang Jianhua [Research Center of Modernization of Traditional Chinese Medicines, Central South University, Changsha 410083 (China); Hu Qiannan [Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071 (China); Liang Yizeng, E-mail: yizeng_liang@263.net [Research Center of Modernization of Traditional Chinese Medicines, Central South University, Changsha 410083 (China)

    2012-11-08

    Highlights: Black-Right-Pointing-Pointer Drug-target interactions are predicted using an extended SAR methodology. Black-Right-Pointing-Pointer A drug-target interaction is regarded as an event triggered by many factors. Black-Right-Pointing-Pointer Molecular fingerprint and CTD descriptors are used to represent drugs and proteins. Black-Right-Pointing-Pointer Our approach shows compatibility between the new scheme and current SAR methodology. - Abstract: The identification of interactions between drugs and target proteins plays a key role in the process of genomic drug discovery. It is both consuming and costly to determine drug-target interactions by experiments alone. Therefore, there is an urgent need to develop new in silico prediction approaches capable of identifying these potential drug-target interactions in a timely manner. In this article, we aim at extending current structure-activity relationship (SAR) methodology to fulfill such requirements. In some sense, a drug-target interaction can be regarded as an event or property triggered by many influence factors from drugs and target proteins. Thus, each interaction pair can be represented theoretically by using these factors which are based on the structural and physicochemical properties simultaneously from drugs and proteins. To realize this, drug molecules are encoded with MACCS substructure fingerings representing existence of certain functional groups or fragments; and proteins are encoded with some biochemical and physicochemical properties. Four classes of drug-target interaction networks in humans involving enzymes, ion channels, G-protein-coupled receptors (GPCRs) and nuclear receptors, are independently used for establishing predictive models with support vector machines (SVMs). The SVM models gave prediction accuracy of 90.31%, 88.91%, 84.68% and 83.74% for four datasets, respectively. In conclusion, the results demonstrate the ability of our proposed method to predict the drug-target interactions, and show a general compatibility between the new scheme and current SAR methodology. They open the way to a host of new investigations on the diversity analysis and prediction of drug-target interactions.

  5. Effect of monomer sequence distribution in poly(vinyl alcohol-co-vinyl acetate) on the hydrogen bonding structure and physical properties

    Science.gov (United States)

    Tasaka, Shun; Urakawa, Osamu; Inoue, Tadashi

    2015-03-01

    It has been well known that hydrogen (H-) bonding interaction in polymer materials strongly affects their properties. For example, glass transition temperature (Tg) and terminal relaxation time increase by introducing H-bonding sites. This is because the molecular motion is restricted due to the formation of inter- and intra-chain H-bonds. For H-bonding copolymers in which H-bonding monomer and non- bonding one are incorporated, the fraction dependence of their properties has been examined so far. However, the influence of sequence distribution on their properties has not been studied in detail. In this work, we investigated the H-bonding structure and physical properties of molten poly(vinyl alcohol-co-vinyl acetate) with different monomer sequences to clarify the effect of the sequence distribution. We found that, with increasing the randomness in monomer sequences, the number of H-bonds between carbonyl group and hydroxyl (OH) group increased. Moreover, OH groups form linearly connected structure (OH-OH-OH) and its number also increases with the sequence randomness. Tg for the samples with higher sequence randomness are higher than those with lower randomness for high VOH copolymers. These results indicate that formation of larger number of H-bonds makes Tg higher.

  6. Structural analysis of the HLA-A/HLA-F subregion: Precise localization of two new multigene families closely associated with the HLA class I sequences

    Energy Technology Data Exchange (ETDEWEB)

    Pichon, L.; Carn, G.; Bouric, P. [CNRS, Rennes (France)] [and others

    1996-03-01

    Positional cloning strategies for the hemochromatosis gene have previously concentrated on a target area restricted to a maximum genomic expanse of 400 kb around the HLA-A and HLA-F loci. Recently, the candidate region has been extended to 2-3 Mb on the distal side of the MHC. In this study, 10 coding sequences [hemochromatosis candidate genes (HCG) I to X] were isolated by cDNA selection using YACs covering the HLA-A/HLA-F subregion. Two of these (HCG II and HCG IV) belong to multigene families, as well as other sequences already described in this region, i.e., P5, pMC 6.7, and HLA class I. Fingerprinting of the four YACSs overlapping the region was performed and allowed partial localization of the different multigene family sequences on each YAC without defining their exact positions. Fingerprinting on cosmids isolated from the ICRF chromosome 6-specific cosmid library allowed more precise localization of the redundant sequences in all of the multigene families and revealed their apparent organization in clusters. Further examination of these intertwined sequences demonstrated that this structural organization resulted from a succession of complex phenomena, including duplications and contractions. This study presents a precise description of the structural organization of the HLA-A/HLA-F region and a determination of the sequences involved in the megabase size polymorphism observed among the A3, A24, and A31 haplotypes. 29 refs., 2 figs., 2 tabs.

  7. Viral genome structures, charge, and sequences are optimal for capsid assembly

    Science.gov (United States)

    Hagan, Michael

    2014-03-01

    For many viruses, the spontaneous assembly of a capsid shell around the nu-cleic acid (NA) genome is an essential step in the viral life cycle. Capsid formation is a multicomponent, out-of-equilibrium assembly process for which kinetic effects and thermodynamic constraints compete to determine the outcome. Understand-ing how viral components drive highly efficient assembly under these constraints could promote biomedical efforts to block viral propagation, and would elucidate the factors controlling assembly in a wide range of systems containing proteins and polyelectrolytes. This talk will describe coarse-grained models of capsid proteins and NAs with which we investigate the dynamics and thermodynamics of virus assembly. In con-trast to recent theoretical models, we find that capsids spontaneously `overcharge' that is, the NA length which is kinetically and thermodynamically optimal possess-es a negative charge greater than the positive charge of the capsid. When applied to specific virus capsids, the calculated optimal NA lengths closely correspond to the natural viral genome lengths. These results suggest that the features included in this model (i.e. electrostatics, excluded volume, and NA tertiary structure) play key roles in determining assembly thermodynamics and consequently exert selec-tive pressure on viral evolution. I will then discuss mechanisms by which se-quence-specific interactions between NAs and capsid proteins promote selective encapsidation of the viral genome. This work was supported by NIH R01GM108021 and the Brandeis MRSEC NSF-MRSEC-0820492.

  8. ProteinSplit: splitting of multi-domain proteins using prediction of ordered and disordered regions in protein sequences for virtual structural genomics

    International Nuclear Information System (INIS)

    The annotation of protein folds within newly sequenced genomes is the main target for semi-automated protein structure prediction (virtual structural genomics). A large number of automated methods have been developed recently with very good results in the case of single-domain proteins. Unfortunately, most of these automated methods often fail to properly predict the distant homology between a given multi-domain protein query and structural templates. Therefore a multi-domain protein should be split into domains in order to overcome this limitation. ProteinSplit is designed to identify protein domain boundaries using a novel algorithm that predicts disordered regions in protein sequences. The software utilizes various sequence characteristics to assess the local propensity of a protein to be disordered or ordered in terms of local structure stability. These disordered parts of a protein are likely to create interdomain spacers. Because of its speed and portability, the method was successfully applied to several genome-wide fold annotation experiments. The user can run an automated analysis of sets of proteins or perform semi-automated multiple user projects (saving the results on the server). Additionally the sequences of predicted domains can be sent to the Bioinfo.PL Protein Structure Prediction Meta-Server for further protein three-dimensional structure and function prediction. The program is freely accessible as a web service at http://lucjan.bioinfo.pl/proteinsplice at http://lucjan.bioinfo.pl/proteinsplit together with detailed benchmark results on the critical assessment of a fully automated structure prediction (CAFASP) set of sequences. The source code of the local version of protein domain boundary prediction is available upon request from the authors

  9. Genetic structure of five Huanghe schizothoracin Schizopygopsis pylzovi populations based on mtDNA control region sequences

    Directory of Open Access Journals (Sweden)

    QI De-Lin

    2008-12-01

    Full Text Available Huanghe schizothoracin Schizopygopsis pylzovi is a freshwater fish endemic to Qinghai-Tibetan Plateau, which distributes mainly in the Qiadam drainage and the upper reaches of Yellow River in the northern and northeastern Qinghai-Tibetan Plateau. So far little is known about the genetic diversity, radiation and population structure. In the present study, the sequence of mitochondrial control region (821bp of 99 individuals representing five populations in the distribution regions were sequenced. Within the analyzed 821 bp bases, 77 (9.37% nucleotides were variable, and a total of 53 haplotypes were identified, in which only one haplotype (DT12 was shared by two populations in the upper reaches of Yellow River. Haplotype diversity (h=0.79±0.06 and nucleotide diversity (?=0.0027±0.0017 of the populations in Qiadam drainage were lower than those of the populations in the upper reaches of Yellow River. The AMOVA analysis indicated that the genetic variation mainly occurred within populations instead of among populations. Although no geographic clustering was observed in the phylogenetic tree, significant population subdivision was supported by both of the pairwise Fst values and average pairwise differences. This result implies that the geographic barriers among the drainages were formed relatively late by the uplift of Qinghai-Tibetan Plateau. The unimodal mismatch distribution of haplotypes, based on the selective neutrality test of Tajima’s D (-1.497, P =0.058 and Fu’s Fs (-24.741, P=0.001, suggest that a recent population expansion of Huanghe schizothoracin has been occurred during the uplift of the Qinghai-Tibetan Plateau [Acta Zoologica Sinica 54(6: 972–980, 2008].

  10. Genetic structure of the Aleuts and Circumpolar populations based on mitochondrial DNA sequences: a synthesis.

    Science.gov (United States)

    Zlojutro, Mark; Rubicz, Rohina; Devor, Eric J; Spitsyn, Victor A; Makarov, Sergei V; Wilson, Kristin; Crawford, Michael H

    2006-03-01

    The mtDNA variation of 198 Aleuts, as well as North American and Asian populations drawn from the literature, were analyzed to reconstruct the Aleuts' genetic prehistory and to investigate their role in the peopling of the Circumarctic region. From median-joining network analysis, three star-like clusters were identified in the Aleuts within the following subhaplogroups: A3, A7 (an Aleut-specific subclade of A3), and D2. Mismatch analyses, neutrality test scores, and coalescent time estimates for these three components provided evidence of two expansion events, one occurring at approximately 19,900 B.P. and the other at 5,400 B.P. Based on these findings and evidence from the archaeological data, four general models for the genetic prehistory of the Aleutian Island chain are proposed: 1) biological continuity involving a kin-structured peopling of the archipelago; 2) intrusion and expansion of a non-native biface-producing population dominated by subhaplogroup D2; 3) amalgamation of Arctic Small Tool tradition peoples characterized by D2 with an older Anangula substratum; and 4) biological continuity with significant gene flow from neighboring populations of the Alaskan mainland and Kodiak Island. The Aleut mtDNAs are consistent with the Circumarctic pattern by the fixation of A3 and D2, and the exhibition of depressed diversity levels relative to Amerind and Siberian groups. The results of this study indicate a broad postglacial reexpansion of Na-Dene and Esko-Aleuts from reduced populations within northern North America, with D2 representing a later infusion of Siberian mtDNAs into the Beringian gene pool. PMID:16323192

  11. Quadrupole oscillator strengths for the helium isoelectronic sequence: n 1S-m 1D, n 3S-m 3D, n 1P-m 1P, and n 3P-m 3P transitions with n<7 and m<7

    International Nuclear Information System (INIS)

    Quadrupole oscillator strengths (QOS) for He and the isoelectronic ions from Li+ to Ne8+ are reported for all possible n 1S-m 1D, n 3S-m 3D, n 1P-m 1P and n 3P-m 3P transitions involving states with m<7 and n<7. The calculations are based upon explicitly correlated wavefunctions that lead to variational energies only nano-Hartrees above the best literature values. The results extend significantly both the accuracy and range of the QOSs available for two-electron atomic species. (author)

  12. Metal-dependent assembly of a tetranuclear copper(II) complex versus a 1D chain coordination polymer of cobalt(III) complex with N2O2-chelating Schiff-base ligand: Synthesis, characterization and crystal structures.

    Czech Academy of Sciences Publication Activity Database

    Khalaji, A.D.; Hadadzadeh, H.; Fejfarová, Karla; Dušek, Michal

    2010-01-01

    Ro?. 29, ?. 2 (2010), s. 807-812. ISSN 0277-5387 Grant ostatní: GA AV ?R(CZ) Praemium Academiae Institutional research plan: CEZ:AV0Z10100521 Keywords : Schiff bases * crystal structure * Jana2006 * coordination chemistry Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.033, year: 2010

  13. YORP torques with 1D thermal model

    CERN Document Server

    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.

  14. Preparation of 1D nanostructures using biomolecules

    Energy Technology Data Exchange (ETDEWEB)

    Pruneanu, Stela; Olenic, Liliana; Kacso, Irina [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath, 400293 Cluj-Napoca (Romania); Tudoran, Lucian Barbu [Babes-Bolyai University, Electron Microscopy Center, 1 Mihail Kogalniceanu, 400006 Cluj-Napoca (Romania); Al-Said, Said A Farha; Hassanien, Reda; Houlton, Andrew; Horrocks, Benjamin R, E-mail: stela.pruneanu@itim-cj.r [School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU (United Kingdom)

    2009-08-01

    In this paper we have shown that one-dimensional (1D) particle arrays can be obtained using biomolecules, like DNA or amino-acids. Nano-arrays of silver and gold were prepared in a single-step synthesis, by exploiting the binding abilities of {lambda}-DNA and L-Arginine. The morphology and optical properties of these nanostructures were investigated using AFM, TEM and UV-Vis absorption spectroscopy.

  15. Finite thermal conductivity in 1d lattices

    OpenAIRE

    Giardina, C; Livi, R; Politi, A; Vassalli, M.

    1999-01-01

    We discuss the thermal conductivity of a chain of coupled rotators, showing that it is the first example of a 1d nonlinear lattice exhibiting normal transport properties in the absence of an on-site potential. Numerical estimates obtained by simulating a chain in contact with two thermal baths at different temperatures are found to be consistent with those ones based on linear response theory. The dynamics of the Fourier modes provides direct evidence of energy diffusion. Th...

  16. DNA sequences of three papA genes from uropathogenic Escherichia coli strains: evidence of structural and serological conservation.

    Science.gov (United States)

    Denich, K; Blyn, L B; Craiu, A; Braaten, B A; Hardy, J; Low, D A; O'Hanley, P D

    1991-01-01

    Pyelonephritis-associated pili (Pap) are important in the pathogenesis of ascending, unobstructive Escherichia coli-caused renal infections because these surface bacterial organelles mediate digalactoside-specific binding to host uroepithelial cells. Pap are composed of many different polypeptides, of which only the tip proteins mediate specific binding. The PapA moiety polymerizes to form the bulk of the pilus structure and has been employed in vaccines despite its lack of Gal alpha(1-4)Gal receptor specificity. Animal recipients of PapA pilus-based vaccines are protected against experimental pyelonephritis caused by homologous and heterologous Gal-Gal-binding uropathogenic E. coli strains. Specific PapA immunoglobulin G antibodies in urine are correlated with protection in these infection models. The nucleotide sequences of the gene encoding PapA were determined for three E. coli clones expressing F7(1), F7(2), and F9 pili and were compared with corresponding sequences for other F serotypes. Specific rabbit antisera were employed in enzyme-linked immunosorbent assays to study the cross-reactivity between Gal-Gal pili purified from recombinant strains expressing F7(1), F7(2), F9, or F13 pili and among 60 Gal-Gal-binding wild-type strains. We present data which corroborate the concept that papA genes are highly homologous and encode proteins which exhibit greater than 70% homology among pili of different serotypes. The differences primarily occur in the cysteine-cysteine loop and variable regions and constitute the basis for serological diversity of these pili. Although there are differences in primary structures among these pili, antisera raised against pili of one serotype cross-reacted frequently with many other Gal-Gal pili of different serotypes. Furthermore, antisera raised against pili of the F13 serotype cross-reacted strongly or moderately with 52 (86%) of 60 wild-type Gal-Gal-binding E. coli strains. These data suggest that there are common immunogenic domains among these proteins. These additional data further support the hypothesis that broadly cross-protective PapA pilus vaccines for the immunoprophylaxis of pyelonephritis might be developed. PMID:1682251

  17. T1D in College (Type 1 Diabetes)

    Science.gov (United States)

    ... Life with T1D / T1D in College T1D in College College for young adults with T1D means more ... college students. Dealing with a new diagnosis in college A diabetes diagnosis is shocking at any point ...

  18. Geographic Patterns of Genetic Variation in a Broadly Distributed Marine Vertebrate: New Insights into Loggerhead Turtle Stock Structure from Expanded Mitochondrial DNA Sequences

    OpenAIRE

    Shamblin, Brian M.; Bolten, Alan B.; Abreu-grobois, F. Alberto; Bjorndal, Karen A.; Cardona, Luis; Carreras, Carlos; Clusa, Marcel; Monzo?n-argu?ello, Catalina; Nairn, Campbell J.; Nielsen, Janne T.; Nel, Ronel; Soares, Luciano S.; Stewart, Kelly R.; Vilac?a, Sibelle T.; Tu?rkozan, Oguz

    2014-01-01

    Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize availab...

  19. The three-dimensional structure of the Moorella thermoacetica selenocysteine insertion sequence RNA hairpin and its interaction with the elongation factor SelB

    OpenAIRE

    Beribisky, Alexander V.; Tavares, Tony J.; Amborski, Andrew N.; Motamed, Mina; Johnson, Anne E.; Mark, Tobi L.; Johnson, Philip E.

    2007-01-01

    Incorporation of the amino acid selenocysteine into a growing protein chain involves the interaction between a hairpin in the mRNA termed the selenocysteine insertion sequence (SECIS) and the special elongation factor SelB. Here we present the structure of the SECIS from the thermophilic organism Moorella thermoacetica (SECIS-MT) determined using nuclear magnetic resonance (NMR) spectroscopy. The SECIS-MT hairpin structure contains a pentaloop with the first and fourth nucleotides of the loop...

  20. Structural similarity between lung surfactant protein D and conglutinin. Two distinct, C-type lectins containing collagen-like sequences

    DEFF Research Database (Denmark)

    Lu, J; Wiedemann, H

    1993-01-01

    Preparations of bovine lung surfactant D (SP-D) and conglutinin were examined by electron microscopy, gel-filtration and SDS/PAGE. SP-D is composed of non-covalently linked subunits, of 160 kDa, which each contain three, disulphide-linked, 44-kDa polypeptide chains. In the electron microscope a single 160-kDa subunit of SP-D appears as a 45.8 +/- 3-nm-long rod connected to a small globular 'head'. Particles were also seen which correspond to non-covalently linked dimers, trimers and tetramers of the 160-kDa monomer subunit of SP-D. The tetramer structure contains 12 polypeptide chains and is very similar to the electron microscopy images and model reported by Strang et al. [Strang, C. J., Slayter, US., Lachmann, P. J. and Davis, A. E. (1986) Biochem. J. 236, 3811-389] for bovine conglutinin in which four 160-kDa subunits are disulphide-linked to give a molecule of expected molecular mass of 528 kDa. This study confirmed the findings by Strang et al. in the above paper for intact conglutinin and also emphasised that the rod-like structures, of length 37.6 +/- 3.7 nm, seen in the conglutinin subunits were significantly shorter than those in SP-D despite the close similarity in amino acid sequence (79% identify) and chain length between the two proteins. In addition, a truncated form of conglutinin was found in the conglutinin preparations, due to limited proteolysis of the Arg-Ala bond at position 54 in the 44-kDa chains. These truncated conglutinin chains yield a subunit composed of three shortened, non-disulphide-linked, chains and this subunit appears as a monomer with a rod length of 34.2 +/- 2.8 nm in the electron microscope. On gel-filtration, a proportion of the SP-D preparation behaved, as expected, as a molecule with an apparent molecular mass of 600 kDa. The remainder of the SP-D preparation behaved as aggregated material with a molecular mass greater than 900 kDa which yielded no distinct structures in the electron microscope. Intact conglutinin was eluted at a position greater than 900 kDa but yet provided clear electron microscopy images of the tetramer structure described above.(ABSTRACT TRUNCATED AT 400 WORDS)

  1. Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene

    DEFF Research Database (Denmark)

    Bowman, J.S.; Rasmussen, S.

    2012-01-01

    Dramatic decreases in the extent of Arctic multiyear ice (MYI) suggest this environment may disappear as early as 2100, replaced by ecologically different first-year ice. To better understand the implications of this loss on microbial biodiversity, we undertook a detailed census of the microbial community in MYI at two sites near the geographic North Pole using parallel tag sequencing of the 16S rRNA gene. Although the composition of the MYI microbial community has been characterized by previous studies, microbial community structure has not been. Although richness was lower in MYI than in underlying surface water, we found diversity to be comparable using the Simpson and Shannon's indices (for Simpson t=0.65, P=0.56; for Shannon t=0.25, P=0.84 for a Student's t-test of mean values). Cyanobacteria, comprising 6.8% of reads obtained from MYI, were observed for the first time in Arctic sea ice. In addition, several low-abundance clades not previously reported in sea ice were present, including the phylum TM7 and the classes Spartobacteria and Opitutae. Members of Coraliomargarita, a recently described genus of the class Opitutae, were present in sufficient numbers to suggest niche occupation within MYI. © 2012 International Society for Microbial Ecology All rights reserved.

  2. Identification of the amino acid sequence that targets peroxiredoxin 6 to lysosome-like structures of lung epithelial cells

    Science.gov (United States)

    Sorokina, Elena M.; Feinstein, Sheldon I.; Milovanova, Tatyana N.

    2009-01-01

    Peroxiredoxin 6 (Prdx6), an enzyme with glutathione peroxidase and PLA2 (aiPLA2) activities, is highly expressed in respiratory epithelium, where it participates in phospholipid turnover and antioxidant defense. Prdx6 has been localized by immunocytochemistry and subcellular fractionation to acidic organelles (lung lamellar bodies and lysosomes) and cytosol. On the basis of their pH optima, we have postulated that protein subcellular localization determines the balance between the two activities of Prdx6. Using green fluorescent protein-labeled protein expression in alveolar epithelial cell lines, we showed Prdx6 localization to organellar structures resembling lamellar bodies in mouse lung epithelial (MLE-12) cells and lysosomes in A549 cells. Localization within lamellar bodies/lysosomes was in the luminal compartment. Targeting to lysosome-like organelles was abolished by the deletion of amino acids 31–40 from the Prdx6 NH2-terminal region; deletion of the COOH-terminal region had no effect. A green fluorescent protein-labeled peptide containing only amino acids 31–40 showed lysosomal targeting that was abolished by mutation of S32 or G34 within the peptide. Studies with mutated protein indicated that lipid binding was not necessary for Prdx6 targeting. This peptide sequence has no homology to known organellar targeting motifs. These studies indicate that the localization of Prdx6 in acidic organelles and consequent PLA2 activity depend on a novel 10-aa peptide located at positions 31–40 of the protein. PMID:19700648

  3. Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas.

    Science.gov (United States)

    Hong, Chen; Si, Yanxiao; Xing, Yi; Li, Yang

    2015-07-01

    Mine activities leaked heavy metals into surrounding soil and may affected indigenous microbial communities. In the present study, the diversity and composition of the bacterial community in soil collected from three regions which have different pollution degree, heavy pollution, moderate pollution, and non-pollution, within the catchment of Chao River in Beijing City, were compared using the Illumina MiSeq sequencing technique. Rarefaction results showed that the polluted area had significant higher bacterial alpha diversity than those from unpolluted area. Principal component analysis (PCA) showed that microbial communities in the polluted areas had significant differences compared with the unpolluted area. Moreover, PCA at phylum level and Matastats results demonstrated that communities in locations shared similar phyla diversity, indicating that the bacterial community changes under metal pollution were not reflected on phyla structure. At genus level, the relative abundance of dominant genera changed in sites with degrees of pollution. Genera Bradyrhizobium, Rhodanobacter, Reyranella, and Rhizomicrobium significantly decreased with increasing pollution degree, and their dominance decreased, whereas several genera (e.g., Steroidobacter, Massilia, Arthrobacter, Flavisolibacter, and Roseiflexus) increased and became new dominant genera in the heavily metal-polluted area. The potential resistant bacteria, found within the genera of Thiobacillus, Pseudomonas, Arthrobacter, Microcoleus, Leptolyngbya, and Rhodobacter, are less than 2.0 % in the indigenous bacterial communities, which play an important role in soil ecosystem. This effort to profile the background diversity may set the first stage for better understanding the mechanism underlying the community structure changes under in situ mild heavy metal pollution. PMID:25761991

  4. Morphology, genome sequence, and structural proteome of type phage P335 from Lactococcus lactis

    DEFF Research Database (Denmark)

    Labrie, Simon J.; Josephsen, Jytte

    2008-01-01

    Lactococcus lactis phage P335 is a virulent type phage for the species that bears its name and belongs phage P335 is a virulent type phage for the species that bears its name and belongs to the Siphoviridae family. Morphologically, P335 resembled the L. lactis phages TP901-1 and Tuc2009, except for a shorter tail and a different collar/whisker structure. Its 33,613-bp double-stranded DNA genome had 50 open reading frames. Putative functions were assigned to 29 of them. Unlike other sequenced genomes from lactococcal phages belonging to this species, P335 did not have a lysogeny module. However, it did carry a dUTPase gene, the most conserved gene among this phage species. Comparative genomic analyses revealed a high level of identity between the morphogenesis modules of the phages P335, ul36, TP901-1, and Tuc2009 and two putative prophages of L. lactis SK11. Differences were noted in genes coding for receptor-binding proteins, in agreement with their distinct host ranges. Sixteen structural proteins of phage P335 were identified by liquid chromatography-tandem mass spectrometry. A 2.8-kb insertion was recognized between the putative genes coding for the activator of late transcription (Alt) and the small terminase subunit (TerS). Four genes within this region were autonomously late transcribed and possibly under the control of Alt. Three of the four deduced proteins had similarities with proteins from Streptococcus pyogenes prophages, suggesting that P335 acquired this module from another phage genome. The genetic diversity of the P335 species indicates that they are exceptional models for studying the modular theory of phage evolution.

  5. Development of a multilocus sequence typing scheme for the study of Anaplasma marginale population structure over space and time.

    Science.gov (United States)

    Guillemi, Eliana C; Ruybal, Paula; Lia, Verónica; Gonzalez, Sergio; Lew, Sergio; Zimmer, Patricia; Lopez Arias, Ludmila; Rodriguez, Jose L; Rodriguez, Sonia Y; Frutos, Roger; Wilkowsky, Silvina E; Farber, Marisa D

    2015-03-01

    Bovine Anaplasmosis caused by Anaplasma marginale is a worldwide disease prevalent in tropical and subtropical regions where Rhipicephalus microplus is considered the most significant biological vector. Molecular markers previously applied for A. marginale typing are efficient for isolate discrimination but they are not a suitable tool for studying population structure and dynamics. Here we report the development of an MLST scheme based on the study of seven genes: dnaA, ftsZ, groEl, lipA, recA, secY and sucB. Five annotated genomes (Saint Maries, Florida, Mississippi, Puerto Rico and Virginia) and 53 bovine blood samples from different world regions were analyzed. High nucleotide diversity and a large proportion of synonymous substitutions, indicative of negative selection resulted from DnaSP 5.00.02 package application. Recombination events were detected in almost all genes, this evidence together with the coexistence of more than one A. marginale strain in the same sample might suggest the superinfection phenomena as a potential source of variation. The allelic profile analysis performed through GoeBURST shown two main CC that did not support geography. In addition, the AMOVA test confirmed the occurrence of at least two main genetically divergent groups. The composition of the emergent groups reflected the impact of both historical and environmental traits on A. marginale population structure. Finally, a web-based platform "Galaxy MLST-Pipeline" was developed to automate DNA sequence editing and data analysis that together with the Data Base are freely available to users. The A. marginale MLST scheme developed here is a valuable tool with a high discrimination power, besides PCR based strategies are still the better choice for epidemiological intracellular pathogens studies. Finally, the allelic profile describe herein would contribute to uncover the mechanisms in how intracellular pathogens challenge virulence paradigm. PMID:25550150

  6. Amino-terminal sequence of bovine leukemia virus major internal protein: homology with mammalian type C virus p30 structural proteins.

    Science.gov (United States)

    Oroszlan, S; Copeland, T D; Henderson, L E; Stephenson, J R; Gilden, R V

    1979-01-01

    The amino acid composition, the COOH-terminal amino acid, and the NH2-terminal amino acid sequence of the first 55 residues of the major internal structural protein, p24, of bovine leukemia virus (BLV) were determined. The compositional data and the results of end-group analysis revealed that, although BLV p24 is chemically distinct, it more closely resembles the p30 structural proteins than the other gag gene products of mammalian retroviruses. It was found that BLV p24 shares the common NH2-terminal proline and COOH-terminal leucine but lacks the common prolylleucylarginine tripeptide and the larger conserved region found near the NH2 terminus of all mammalian type C viral p30s. Alignment of the amino acid sequence of BLV p24 with the previously determined sequence of feline leukemia virus p27 revealed a statistically significant sequence homology. A more distant relationship was found between BLV p24 and other mammalian p30s. The finding of a definite sequence homology between BLV p24 and mammalian type C virus p30s clearly establishes the origin of these contemporary viral proteins from common progenitor genes. Images PMID:223166

  7. Analysis of Sequence Polymorphism and Population Structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in Viroid-Infected Tomato Plants

    OpenAIRE

    Xianzhou Nie

    2012-01-01

    The sequence polymorphism and population structure of Tomato chlorotic dwarf viroid (TCDVd) (isolate Trust) and Potato tuber spindle viroid (PSTVd) (isolate FN) in tomato plants were investigated. Of the 9 and 35 TCDVd clones sequenced from 2 different TCDVd-infected plants, 2 and 4 sequence variants were identified, respectively, leading to a total of 4 sequence variants of 360 nucleotides in length. Variant I was identical to AF162131, the first TCD...

  8. Structure of the complex of calmodulin with the target sequence of calmodulin-dependent protein kinase I: studies of the kinase activation mechanism.

    Science.gov (United States)

    Clapperton, Julie A; Martin, Stephen R; Smerdon, Stephen J; Gamblin, Steven J; Bayley, Peter M

    2002-12-17

    Calcium-saturated calmodulin (CaM) directly activates CaM-dependent protein kinase I (CaMKI) by binding to a region in the C-terminal regulatory sequence of the enzyme to relieve autoinhibition. The structure of CaM in a high-affinity complex with a 25-residue peptide of CaMKI (residues 294-318) has been determined by X-ray crystallography at 1.7 A resolution. Upon complex formation, the CaMKI peptide adopts an alpha-helical conformation, while changes in the CaM domain linker enable both its N- and C-domains to wrap around the peptide helix. Target peptide residues Trp-303 (interacting with the CaM C-domain) and Met-316 (with the CaM N-domain) define the mode of binding as 1-14. In addition, two basic patches on the peptide form complementary charge interactions with CaM. The CaM-peptide affinity is approximately 1 pM, compared with 30 nM for the CaM-kinase complex, indicating that activation of autoinhibited CaMKI by CaM requires a costly energetic disruption of the interactions between the CaM-binding sequence and the rest of the enzyme. We present biochemical and structural evidence indicating the involvement of both CaM domains in the activation process: while the C-domain exhibits tight binding toward the regulatory sequence, the N-domain is necessary for activation. Our crystal structure also enables us to identify the full CaM-binding sequence. Residues Lys-296 and Phe-298 from the target peptide interact directly with CaM, demonstrating overlap between the autoinhibitory and CaM-binding sequences. Thus, the kinase activation mechanism involves the binding of CaM to residues associated with the inhibitory pseudosubstrate sequence. PMID:12475216

  9. Growth and Magnetic characterization of 1D Permalloy Nanowires using self developed AAO Templates

    Science.gov (United States)

    Singh, A. K.; Khan, G. G.; Das, B.; Mandal, K.

    2015-02-01

    1D Permalloy refers to an alloy of Ni and Fe with 80% and 20% composition respectively. 1D Permalloy nanowires are particularly attractive because of their high permeability, low coercivity, near zero magnetostriction and high anisotropic magnetoresistance. Because of low magnetostriction of Permalloy shape anisotropy plays a very important role. As a result, the nanowires show unidirectional anisotropy along their length. Because of this property, they can be used in many applications such as recording head sensors, magnetic storage devices etc. In the present work 1D Permalloy nanowires arrays were fabricated into the pores of self engineered Anodic Aluminium Oxide (AAO) templates by a simple electrodeposition technique (EDT). By varying the Anodization voltage and the parameters of the electrolytic solutions we developed various AAO templates with different average pore diameters. We developed the 1D Permalloy NW's of different diameters depending on the pore size arrangement of AAO templates by varying the deposition conditions. Structural characterization of AAO templates and 1D Permalloy NW's was performed by Transmission and Scanning Electron Microscopy (TEM & SEM). XRD studies of 1D Permalloy NW's shows their fcc crystalline structure and the AAO template was found to be amorphous in nature. Magnetic studies show the 1D Permalloy NW's arrays to have obvious anisotropy, and the easy axis was found to be parallel to the nanowires axis. We performed the angular dependence measurement of 1D Permalloy NW's. When the applied magnetic field was parallel to the nanowires, the coercivity (Hc) and the maximum remanent ratio (Mr/Ms) were considerably higher than those while the magnetic field perpendicular to the nanowires. 1D Permalloy NW's developed in this work are expected to be utilize in magnetic memory and magnetic recording devices.

  10. Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs.

    OpenAIRE

    Grosjean, H.; Nicoghosian, K.; Haumont, E.; So?ll, D.; Cedergren, R.

    1985-01-01

    We have determined the nucleotide sequence of the major species of E. coli tRNASer and of a minor species having the same GGA anticodon. These two tRNAs should recognize the UCC and UCU codons, the most widely used codons for serine in the highly expressed genes of E. coli. The two sequences differ in only one position of the D-loop. Neither tRNA has a modified adenosine in the position 3'-adjacent to the anticodon. This can be rationalized on the basis of a structural constraint in the antic...

  11. Sequence-specific 1H-NMR assignment and secondary structure of black mamba dendrotoxin I, a highly selective blocker of voltage-gated potassium channels.

    Science.gov (United States)

    Foray, M F; Lancelin, J M; Hollecker, M; Marion, D

    1993-02-01

    The secondary structure of dendrotoxin I, an important constituent of the venom of the African black mamba snake Dendroaspis polylepis polylepis, was determined in aqueous solution by two-dimensional methods. Complete sequence-specific 1H-NMR assignment was obtained with the exception of the backbone amide proton of Gly39 and Cys40. Dendrotoxin I is based on a central antiparallel beta-sheet and two small helices located at the N- and the C-terminal extremities. These secondary-structural units occur at exactly the same places in the amino acid sequence as those of bovine pancreatic trypsin inhibitor (BPTI), with which dendrotoxin I shares 33% sequence similarity. According to the disulfide-bridge positions and the long-range NOE observed these secondary-structural elements fold in a similar manner to BPTI. This similarity allows an hypothesis according to which dendrotoxin I could derive from an ancestral Künitz-type proteinase inhibitor. This ancestor would have been heavily mutated at amino acid positions not critical for gross structure. The spatial locations of the solvent-exposed amino acids concerned could therefore serve as a guideline for interpretation of the structure/activity relationship of dendrotoxin I for the blockage of voltage-sensitive potassium channels of which dendrotoxin I is a strong inhibitor. The possible connections with other polypeptide toxins that block related ion currents is discussed. PMID:7679640

  12. Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats

    Directory of Open Access Journals (Sweden)

    Eisenberg Eli

    2010-07-01

    Full Text Available Abstract Background Alu repeats in the human transcriptome undergo massive adenosine to inosine RNA editing. This process is selective, as editing efficiency varies greatly among different adenosines. Several studies have identified weak sequence motifs characterizing the editing sites, but these alone do not account for the large diversity observed. Results Here we build a dataset of 29,971 editing sites and use it to characterize editing preferences. We focus on structural aspects, studying the double-stranded RNA structure of the Alu repeats, and show the editing frequency of a given site to depend strongly on the micro-structure it resides in. Surprisingly, we find that interior loops, and especially the nucleotides at their edges, are more likely to be edited than helices. In addition, the sequence motifs characterizing editing sites vary with the micro-structure. Finally, we show that thermodynamic stability of the site is important for its editing. Conclusions Analysis of a large dataset of editing events reveals more information on sequence and structural motifs characterizing the A-to-I editing process

  13. 1-D EQUILIBRIUM DISCRETE DIFFUSION MONTE CARLO

    Energy Technology Data Exchange (ETDEWEB)

    T. EVANS; ET AL

    2000-08-01

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

  14. The structure of the yeast ribosomal RNA genes. 2. The nucleotide sequence of the initiation site for ribosomal RNA transcription.

    OpenAIRE

    Bayev, A A; Georgiev, O I; Hadjiolov, A A; Kermekchiev, M B; Nikolaev, N.; Skryabin, K.G.; Zakharyev, V M

    1980-01-01

    The 5'-terminal coding sequence for the 37 S precursor to rRNA of Saccharomyces cerevisiae is identified by reverse transcriptase extension and protection mapping with nuclease S1. The sequence of a 419 bp rDNA fragment containing the transcription initiation site and its adjacent region is determined.

  15. Distinct structural features of the ? and ? subunits of nitrogenase molybdenum-iron protein of Clostridium pasteurianum: an analysis of amino acid sequences

    International Nuclear Information System (INIS)

    Nitrogenase is composed of two separately purified proteins, a molybdenum-iron (MoFe) protein and an iron (Fe) protein. Structural genes (nifD and nifK) encoding ? and ? subunits of the MoFe protein of Clostridium pasteurianum (Cp) have been cloned and sequenced. The deduced amino acid sequences were analyzed for structures that could be related to the unique properties of the Cp protein, particularly its low capacity to form an active enzyme with a heterologous Fe protein. Cp nifK is located immediately downstream from Cp nifD, with the start codon of nifK overlapping by one base with the stop codon of nifD. An open reading frame following nifK was identified as nifE. The amino acid sequence deduced from nifK encompasses the partial amino acid sequences previously reported from the isolated ? subunit. Cp nifK encodes a polypeptide of 458 amino acid residues (M/sub r/ 50,115) whose amino-terminal region is about 50 resides shorter than the otherwise conserved corresponding polypeptides from four other organisms. In contrast, Cp ? subunit (nifD product) contains an additional stretch of 50 amino acid residues in the 380-430 region, which is unique to the Cp protein. It therefore appears that the combined size of the ? and ? subunits could be important to nitrogenase function. An analysis of the predicted secondary structure from the amino acid sequence of each subunit from three species (C. pasteurianum, Azotobacter vinelandii, and Rhizobium japonicum) further re and Rhizobium japonicum) further revealed structural features, including regions adjacent to some of the conserved cysteine resides, differentiating the Cp MoFe protein from others. These different regions may be further tested for correlation with distinct properties of Cp nitrogenase

  16. Synthesis, crystal structure and properties of two 1D nano-chain coordination polymers constructed by lanthanide with pyridine-3,4-dicarboxylic acid and 1,10-phenanthroline

    Science.gov (United States)

    Song, Hui-Hua; Li, Ya-Juan; Song, You; Han, Zhan-Gang; Yang, Fang

    2008-05-01

    The hydrothermal reactions of LnCl 3·6H 2O ( Ln=Eu, Tb), pyridine-3,4-dicarboxylic acid (3,4-pydaH 2), 1,10-phenthroline (phen) and NaOH in aqueous medium yield two metal-organic hybrid materials, [Eu 2(3,4-pyda) 3(phen)(H 2O)·H 2O] n ( 1) and [Tb 2(3,4-pyda) 3(phen)(H 2O)·H 2O] n ( 2), respectively. Both compounds have similar topology structure containing one-dimensional nano-chain, which is further assembled into a three-dimensional supramolecular network via ?- ? stacking interactions and hydrogen bonds. To the best of our knowledge, they represent the first example of nano-chain coordination polymers constructed by 3,4-pydaH 2 and chelate heterocylic ligand. Interestingly, the 3,4-pyda anion exhibits three kinds of coordination modes in these complexes. The coordination modes of 3,4-pyda in complexes 1 and 2 have not been observed in other coordination polymers containing 3,4-pyda ligands. Compounds 1 and 2 exhibit strong fluorescent emission bands in the solid state at room temperature. Their magnetic analyses show that they exhibit different magnetic interactions.

  17. Synthesis, crystal structure and properties of two 1D nano-chain coordination polymers constructed by lanthanide with pyridine-3,4-dicarboxylic acid and 1,10-phenanthroline

    International Nuclear Information System (INIS)

    The hydrothermal reactions of LnCl3.6H2O (Ln=Eu, Tb), pyridine-3,4-dicarboxylic acid (3,4-pydaH2), 1,10-phenthroline (phen) and NaOH in aqueous medium yield two metal-organic hybrid materials, [Eu2(3,4-pyda)3(phen)(H2O).H2O]n (1) and [Tb2(3,4-pyda)3(phen)(H2O).H2O]n (2), respectively. Both compounds have similar topology structure containing one-dimensional nano-chain, which is further assembled into a three-dimensional supramolecular network via ?-? stacking interactions and hydrogen bonds. To the best of our knowledge, they represent the first example of nano-chain coordination polymers constructed by 3,4-pydaH2 and chelate heterocylic ligand. Interestingly, the 3,4-pyda anion exhibits three kinds of coordination modes in these complexes. The coordination modes of 3,4-pyda in complexes 1 and 2 have not been observed in other coordination polymers containing 3,4-pyda ligands. Compounds 1 and 2 exhibit strong fluorescent emission bands in the solid state at room temperature. Their magnetic analyses show that they exhibit different magnetic interactions. - Graphical abstract: Two novel lanthanide coordination polymers [M2(pydc)3(phen)(H2O).H2O]n (M=Eu(1) and Tb(2), pydc=pyridine-3,4-dicarboxylate, phen=1,10-phenthroline) have been synthesized and characterized. ave been synthesized and characterized. Both compounds reveal a one-dimensional nano-chain, which is further assembled into a three-dimensional supramolecular network via ?-? stacking interactions and hydrogen bonds. Their luminescent and magnetic properties have been investigated

  18. Sequence-motif Detection of NAD(P)-binding Proteins: Discovery of a Unique Antibacterial Drug Target

    Science.gov (United States)

    Hua, Yun Hao; Wu, Chih Yuan; Sargsyan, Karen; Lim, Carmay

    2014-09-01

    Many enzymes use nicotinamide adenine dinucleotide or nicotinamide adenine dinucleotide phosphate (NAD(P)) as essential coenzymes. These enzymes often do not share significant sequence identity and cannot be easily detected by sequence homology. Previously, we determined all distinct locally conserved pyrophosphate-binding structures (3d motifs) from NAD(P)-bound protein structures, from which 1d sequence motifs were derived. Here, we aim to establish the precision of these 3d and 1d motifs to annotate NAD(P)-binding proteins. We show that the pyrophosphate-binding 3d motifs are characteristic of NAD(P)-binding proteins, as they are rarely found in nonNAD(P)-binding proteins. Furthermore, several 1d motifs could distinguish between proteins that bind only NAD and those that bind only NADP. They could also distinguish between NAD(P)-binding proteins from nonNAD(P)-binding ones. Interestingly, one of the pyrophosphate-binding 3d and corresponding 1d motifs was found only in enoyl-acyl carrier protein reductases, which are enzymes essential for bacterial fatty acid biosynthesis. This unique 3d motif serves as an attractive novel drug target, as it is conserved across many bacterial species and is not found in human proteins.

  19. Synthesis of magnetic 1D dichalcogenide nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Kidd, Timothy E., E-mail: tim.kidd@uni.edu; O' Shea, Aaron; Griffith, Zach; Leslie, Stroh; Shand, Paul M. [University of Northern Iowa, Physics Department (United States); Boyle, Kayla R.; Strauss, Laura H. [University of Northern Iowa, Chemistry and Biochemistry Department (United States)

    2012-06-15

    We report the first synthesis of magnetic one-dimensional transition metal dichalcogenides. Pure and Mn-doped tantalum disulfide nanotapes were synthesized using a catalyst-free single-step growth process. The sample yield of nanostructures was nearly 100 %. The nanotapes were composed of a number of smaller nanowires which appear to be open-ended nanotubes. The smaller nanowires have diameters ranging from about 30 to 300 nm. The Mn dopants were incorporated within intercalation sites between TaS{sub 2} layers. Interactions between these dopant ions induced low temperature magnetic phase transitions similar to those seen in macroscopic Mn{sub x}TaS{sub 2} compounds. The magnetic properties do not exactly correspond to their bulk counterparts, as exemplified by a higher than expected ferromagnetic transition temperature in 1D nanostructures. This indicates the magnetic properties are likely influenced by quantum size effects. The simplicity of this one-step synthesis method should allow for this technique to be extended to other dichalcogenide systems and/or magnetic dopants, opening up a new class of 1D magnetic nanostructures.

  20. Population genetic structure of skipjack tuna Katsuwonus pelamis from the Indian coast using sequence analysis of the mitochondrial DNA D-loop region.

    Science.gov (United States)

    Menezes, M R; Kumar, G; Kunal, S P

    2012-05-01

    Genetic structure of skipjack tuna Katsuwonus pelamis from the Indian region was investigated using sequence data of mitochondrial DNA (mtDNA) D-loop region. A total of 315 individuals were sampled from six major fishing grounds around the east and west coasts of India including the Andaman (Port Blair) and Lakshadweep (Minicoy) Islands. Nucleotide and gene diversities were high in all the sample collections. Significant genetic heterogeneity was observed for the mtDNA sequence data among sites (?(ST) = 0·0273, P pelamis along the Indian coast can thus be rejected. Phylogenetic analysis of the mtDNA sequence data showed the presence of four clades of K. pelamis in the Indian waters. There was no clear pattern, however, of haplotypes and geographic location among samples. The results of this study suggest the occurrence of four genetically differentiated groups of K. pelamis across the coastal waters of India. PMID:22551177

  1. Critical Structural and Functional Roles for the N-Terminal Insertion Sequence in Surfactant Protein B Analogs

    Science.gov (United States)

    Walther, Frans J.; Waring, Alan J.; Hernandez-Juviel, Jose M.; Gordon, Larry M.; Wang, Zhengdong; Jung, Chun-Ling; Ruchala, Piotr; Clark, Andrew P.; Smith, Wesley M.; Sharma, Shantanu; Notter, Robert H.

    2010-01-01

    Background Surfactant protein B (SP-B; 79 residues) belongs to the saposin protein superfamily, and plays functional roles in lung surfactant. The disulfide cross-linked, N- and C-terminal domains of SP-B have been theoretically predicted to fold as charged, amphipathic helices, suggesting their participation in surfactant activities. Earlier structural studies with Mini-B, a disulfide-linked construct based on the N- and C-terminal regions of SP-B (i.e., ?residues 8–25 and 63–78), confirmed that these neighboring domains are helical; moreover, Mini-B retains critical in vitro and in vivo surfactant functions of the native protein. Here, we perform similar analyses on a Super Mini-B construct that has native SP-B residues (1–7) attached to the N-terminus of Mini-B, to test whether the N-terminal sequence is also involved in surfactant activity. Methodology/Results FTIR spectra of Mini-B and Super Mini-B in either lipids or lipid-mimics indicated that these peptides share similar conformations, with primary ?-helix and secondary ?-sheet and loop-turns. Gel electrophoresis demonstrated that Super Mini-B was dimeric in SDS detergent-polyacrylamide, while Mini-B was monomeric. Surface plasmon resonance (SPR), predictive aggregation algorithms, and molecular dynamics (MD) and docking simulations further suggested a preliminary model for dimeric Super Mini-B, in which monomers self-associate to form a dimer peptide with a “saposin-like” fold. Similar to native SP-B, both Mini-B and Super Mini-B exhibit in vitro activity with spread films showing near-zero minimum surface tension during cycling using captive bubble surfactometry. In vivo, Super Mini-B demonstrates oxygenation and dynamic compliance that are greater than Mini-B and compare favorably to full-length SP-B. Conclusion Super Mini-B shows enhanced surfactant activity, probably due to the self-assembly of monomer peptide into dimer Super Mini-B that mimics the functions and putative structure of native SP-B. PMID:20084172

  2. Prospects for detection of ?(1D)??(1S)?? via ?(3S)??(1D)+X

    International Nuclear Information System (INIS)

    At least one state in the first family of D-wave bb(bar sign) quarkonium levels has been discovered near the predicted mass of 10.16 GeV/c2. This state is probably the one with J=2. This state and the ones with J=1 and J=3 may contribute a detectable amount to the decay ?(1D)??(1S)??, depending on the partial widths for these decays for which predictions vary considerably. The prospects for detection of the chain ?(3S)??(1D)+X????+X are discussed

  3. Yeast Identification by DNA Sequencing in an Undergraduate Mycology Laboratory

    OpenAIRE

    Safranek, William W.

    2014-01-01

    A yeast identification procedure based on the sequencing of the D1/D2 region of the yeast 26S ribosomal DNA was presented in an undergraduate general mycology laboratory. Extracted genomic DNA of environmental yeasts collected by the students was used to PCR-amplify the D1/D2 region of the isolates. Agarose gel electrophoresis confirmed the presence of the expected amplicon which was purified for sequencing by a spincolumn method then submitted to a commercial sequencing laboratory.  The stu...

  4. Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures

    OpenAIRE

    Gerstein Mark; Alexandrov Vadim

    2004-01-01

    Abstract Background Hidden Markov Models (HMMs) have proven very useful in computational biology for such applications as sequence pattern matching, gene-finding, and structure prediction. Thus far, however, they have been confined to representing 1D sequence (or the aspects of structure that could be represented by character strings). Results We develop an HMM formalism that explicitly uses 3D coordinates in its match states. The match states are modeled by 3D Gaussian distributions centered...

  5. Thermally activated polymorphic transition from a 1D ribbon to a 2D carpet: squaric acid on Au(111).

    Science.gov (United States)

    Ueji, Kan; Jung, Jaehoon; Oh, Junepyo; Miyamura, Kazuo; Kim, Yousoo

    2014-10-01

    Polymorphic transition from the 1D ribbon to the 2D carpet superstructure of squaric acid molecules on Au(111) was achieved through a thermally activated process. Our combined STM and DFT study revealed that the molecular arrangements in 1D and 2D superstructures are determined by the stability of their conformational isomers and assembled structures, respectively. PMID:25116868

  6. Fine-structured multi-scaling long-range correlations in completely sequenced genomes - features, origin and classification.

    OpenAIRE

    Knoch, T. A.; Go?cker, M.; Lohner, R.; Abuseiris, A.; Grosveld, F. G.

    2009-01-01

    The sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. Long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 9 106 to 3.0 9 107 bp from Archaea, Bacteria, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pom...

  7. Fine-structured multi-scaling long-range correlations in completely sequenced genomes—features, origin, and classification

    OpenAIRE

    Knoch, Tobias A.; Go?ker, Markus; Lohner, Rudolf; Abuseiris, Anis; Grosveld, Frank G.

    2009-01-01

    The sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. Long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 × 106 to 3.0 × 107 bp from Archaea, Bacteria, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomy...

  8. Multilocus Sequence Typing of Lactobacillus casei Reveals a Clonal Population Structure with Low Levels of Homologous Recombination? †

    OpenAIRE

    Diancourt, Laure; Passet, Virginie; Chervaux, Christian; Garault, Peggy; Smokvina, Tamara; Brisse, Sylvain

    2007-01-01

    Robust genotyping methods for Lactobacillus casei are needed for strain tracking and collection management, as well as for population biology research. A collection of 52 strains initially labeled L. casei or Lactobacillus paracasei was first subjected to rplB gene sequencing together with reference strains of Lactobacillus zeae, Lactobacillus rhamnosus, and other species. Phylogenetic analysis showed that all 52 strains belonged to a single compact L. casei-L. paracasei sequence cluster, tog...

  9. 1D fast coded aperture camera

    Science.gov (United States)

    Haw, Magnus; Bellan, Paul

    2015-04-01

    A fast (100 MHz) 1D coded aperture visible light camera has been developed as a prototype for imaging plasma experiments in the EUV/X-ray bands. The system uses printed patterns on transparency sheets as the masked aperture and an 80 channel photodiode array (9 V reverse bias) as the detector. In the low signal limit, the system has demonstrated 40-fold increase in throughput and a signal-to-noise gain of ?7 over that of a pinhole camera of equivalent parameters. In its present iteration, the camera can only image visible light; however, the only modifications needed to make the system EUV/X-ray sensitive are to acquire appropriate EUV/X-ray photodiodes and to machine a metal masked aperture.

  10. Universal nature of collective plasmonic excitations in finite 1-D carbon-based nanostructures

    CERN Document Server

    Polizzi, Eric

    2015-01-01

    Tomonaga-Luttinger (T-L) theory predicts collective plasmon resonances in 1-D nanostructure conductors of finite length, that vary roughly in inverse proportion to the length of the structure. Yet, such resonances have not been clearly identified in experiments so far. Here we provide evidence of the T-L plasmon resonances using first-principle computational real-time spectroscopy studies of representative finite 1-D carbon-based nanostructures ranging from atom and benzene-like chain structures to short carbon nanotubes. Our all-electron Time-Dependent Density-Functional Theory (TDDFT) real-time simulation framework is capable to accurately capture the relevant nanoscopic effects including correct frequencies for known optical transitions, and various collective plasmon excitations. The presence of 1-D T-L plasmons is universally predicted by the various numerical experiments, which also demonstrate a phenomenon of resonance splitting. Extending these simulations to longer structures will allow the accurate ...

  11. Cloning of the VASP (Vasodilator-Stimulated Phosphoprotein) genes in human and mouse: Structure, sequence, and chromosomal localization

    Energy Technology Data Exchange (ETDEWEB)

    Zimmer, M.; Fischer, L.; Hauser, W. [Medizinische Universitaetsklinik, Wuerzburg (Germany)] [and others

    1996-09-01

    The genes encoding the vasodilator-stimulated phosphoprotein (VASP) in human and mouse were isolated, and major parts were sequenced. In both species the gene is composed of 13 exons with conserved exon-intron positions. The mouse VASP cDNA sequence was deduced from the genomic sequence. The predicted amino acid sequence is 89% identical to the human protein. The high nucleotide sequence homology extends not only over the coding regions but also into the 3{prime}-UTRs, indicating a possible function in mRNA targeting or regulation of translation. Prominent 5{prime} CpG islands including multiple SP1 sites indicate a housekeeping function of VASP. Using cosmid DNA as a probe for fluorescence in situ hybridization, the human VASP gene was assigned to chromosome 19q13.2-q13.3, an extended region with homology to mouse chromosome 7. A sequence overlap of the VASP 5{prime}-region with the telomeric end of a cosmid contig physically links the VASP gene with ERCC1. VASP is located about 92 kb distal to ERCC1 and about 300 kb proximal to the myotonic dystrophy protein kinase gene. 43 refs., 6 figs.

  12. Numerical shock instability on 1D Euler equations

    Science.gov (United States)

    Wahi, Nadihah; Ismail, Farzad

    2013-04-01

    Numerical shock instabilities are deficiencies that may occur when predicting a shockwave in compressible flow computations. These deficiencies are usually present in shock capturing schemes with minimal numerical diffusion (i.e. Roe flux) when computing slowly moving shock problems, the hypersonic wall heating problem (Noh's problem) and even when simply predicting a steady state supersonic flow past a circular cylinder. For the supersonic flow past a cylinder, the predicted solution would normally consist of a pair of oblique shocks as opposed to the correct solution which is a bow-shock. Thus, the predicted thermodynamic quantities behind the shockwave are incorrect, compromising the overall flow predictions around the cylinder. This problem is also infamously known as the carbuncle phenomenon. The carbuncle problem has been around for more than 20 years yet there is no consensus within the literature of its true 'cause'. Recent studies have pointed out that the carbuncle may manifest itself in 2D, 1 1/2 D and even 1D shock structures. The current study will investigate the stability of 1D shock profiles based on the scalar and isothermal Euler equations using a numerical method based on Roe-flux. The results of this study will hopefully pave the way to better understand the root of the carbuncle phenomenon.

  13. The seismogenic structure of the 2013-2014 Matese seismic sequence, Southern Italy: implication for the geometry of the Apennines active extensional belt

    Science.gov (United States)

    Ferranti, L.; Milano, G.; Burrato, P.; Palano, M.; Cannavò, F.

    2015-05-01

    Seismological, geological and geodetic data have been integrated to characterize the seismogenic structure of the late 2013-early 2014 moderate energy (maximum local magnitude MLmax = 4.9) seismic sequence that struck the interior of the Matese Massif, part of the Southern Apennines active extensional belt. The sequence, heralded by a ML = 2.7 foreshock, was characterized by two main shocks with ML = 4.9 and ML = 4.2, respectively, which occurred at a depth of ˜17-18 km. The sequence was confined in the 10-20 km depth range, significantly deeper than the 1997-1998 sequence which occurred few km away on the northeastern side of the massif above ˜15 km depth. The depth distribution of the 2013-14 sequence is almost continuous, albeit a deeper (16-19 km) and a shallower (11-15 km) group of events can be distinguished, the former including the main shocks and the foreshock. The epicentral distribution formed a ˜10 km long NNW-SSE trending alignment, which almost parallels the surface trace of late Pliocene-Quaternary southwest-dipping normal faults with a poor evidence of current geological and geodetic deformation. We built an upper crustal model profile for the eastern Matese massif through integration of geological data, oil exploration well logs and seismic tomographic images. Projection of hypocentres on the profile suggests that the seismogenic volume falls mostly within the crystalline crust and subordinately within the Mesozoic sedimentary cover of Apulia, the underthrust foreland of the Southern Apennines fold and thrust belt. Geological data and the regional macroseismic field of the sequence suggest that the southwest-dipping nodal plane of the main shocks represents the rupture surface that we refer to here as the Matese fault. The major lithological discontinuity between crystalline and sedimentary rocks of Apulia likely confined upward the rupture extent of the Matese fault. Repeated coseismic failure represented by the deeper group of events in the sequence, activated in a passive fashion the overlying ˜11-15 km deep section of the upper crustal normal faults. We consider the southwest-dipping Matese fault representative of a poorly known type of seismogenic structures in the Southern Apennines, where extensional seismogenesis and geodetic strain accumulation occur more frequently on NE-dipping, shallower-rooted faults. This is the case of the Boiano Basin fault located on the northern side of the massif, to which the 1997-1998 sequence is related. The close proximity of the two types of seismogenic faults at the Matese Massif is related to the complex crustal architecture generated by the Pliocene-early Pleistocene contractional and transpressional tectonics.

  14. Comparative Sequence, Structure and Redox Analyses of Klebsiella pneumoniae DsbA Show That Anti-Virulence Target DsbA Enzymes Fall into Distinct Classes

    Science.gov (United States)

    Kurth, Fabian; Rimmer, Kieran; Premkumar, Lakshmanane; Mohanty, Biswaranjan; Duprez, Wilko; Halili, Maria A.; Shouldice, Stephen R.; Heras, Begoña; Fairlie, David P.; Scanlon, Martin J.; Martin, Jennifer L.

    2013-01-01

    Bacterial DsbA enzymes catalyze oxidative folding of virulence factors, and have been identified as targets for antivirulence drugs. However, DsbA enzymes characterized to date exhibit a wide spectrum of redox properties and divergent structural features compared to the prototypical DsbA enzyme of Escherichia coli DsbA (EcDsbA). Nonetheless, sequence analysis shows that DsbAs are more highly conserved than their known substrate virulence factors, highlighting the potential to inhibit virulence across a range of organisms by targeting DsbA. For example, Salmonella enterica typhimurium (SeDsbA, 86 % sequence identity to EcDsbA) shares almost identical structural, surface and redox properties. Using comparative sequence and structure analysis we predicted that five other bacterial DsbAs would share these properties. To confirm this, we characterized Klebsiella pneumoniae DsbA (KpDsbA, 81 % identity to EcDsbA). As expected, the redox properties, structure and surface features (from crystal and NMR data) of KpDsbA were almost identical to those of EcDsbA and SeDsbA. Moreover, KpDsbA and EcDsbA bind peptides derived from their respective DsbBs with almost equal affinity, supporting the notion that compounds designed to inhibit EcDsbA will also inhibit KpDsbA. Taken together, our data show that DsbAs fall into different classes; that DsbAs within a class may be predicted by sequence analysis of binding loops; that DsbAs within a class are able to complement one another in vivo and that compounds designed to inhibit EcDsbA are likely to inhibit DsbAs within the same class. PMID:24244651

  15. Genetic structure of the high dispersal Atlanto-Mediterreanean sea star Astropecten aranciacus revealed by mitochondrial DNA sequences and microsatellite loci

    OpenAIRE

    Zulliger, D. E.; Tanner, S.; Ruch, M.; Ribi, G.

    2009-01-01

    To investigate the impact of potential marine barriers on gene-flow in high dispersal marine invertebrates, we assessed the population genetic structure of the sea star Astropecten aranciacus. Samples were obtained from nine locations within the Atlantic and the Mediterranean Sea including populations east of the Siculo-Tunisian Strait. We obtained both DNA sequence data of the mitochondrial control region and genotype data at four microsatellite loci. Both markers were highly polymorphic and...

  16. Structure-specific nuclease activity of RAGs is modulated by sequence, length and phase position of flanking double-stranded DNA.

    Science.gov (United States)

    Kumari, Rupa; Raghavan, Sathees C

    2015-01-01

    RAGs (recombination activating genes) are responsible for the generation of antigen receptor diversity through the process of combinatorial joining of different V (variable), D (diversity) and J (joining) gene segments. In addition to its physiological property, wherein RAG functions as a sequence-specific nuclease, it can also act as a structure-specific nuclease leading to genomic instability and cancer. In the present study, we investigate the factors that regulate RAG cleavage on non-B DNA structures. We find that RAG binding and cleavage on heteroduplex DNA is dependent on the length of the double-stranded flanking region. Besides, the immediate flanking double-stranded region regulates RAG activity in a sequence-dependent manner. Interestingly, the cleavage efficiency of RAGs at the heteroduplex region is influenced by the phasing of DNA. Thus, our results suggest that sequence, length and phase positions of the DNA can affect the efficiency of RAG cleavage when it acts as a structure-specific nuclease. These findings provide novel insights on the regulation of the pathological functions of RAGs. PMID:25327637

  17. Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences.

    Science.gov (United States)

    Shamblin, Brian M; Bolten, Alan B; Abreu-Grobois, F Alberto; Bjorndal, Karen A; Cardona, Luis; Carreras, Carlos; Clusa, Marcel; Monzón-Argüello, Catalina; Nairn, Campbell J; Nielsen, Janne T; Nel, Ronel; Soares, Luciano S; Stewart, Kelly R; Vilaça, Sibelle T; Türkozan, Oguz; Yilmaz, Can; Dutton, Peter H

    2014-01-01

    Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (?800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology. PMID:24465810

  18. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  19. VES/TEM 1D joint inversion by using Controlled Random Search (CRS) algorithm

    Science.gov (United States)

    Bortolozo, Cassiano Antonio; Porsani, Jorge Luís; Santos, Fernando Acácio Monteiro dos; Almeida, Emerson Rodrigo

    2015-01-01

    Electrical (DC) and Transient Electromagnetic (TEM) soundings are used in a great number of environmental, hydrological, and mining exploration studies. Usually, data interpretation is accomplished by individual 1D models resulting often in ambiguous models. This fact can be explained by the way as the two different methodologies sample the medium beneath surface. Vertical Electrical Sounding (VES) is good in marking resistive structures, while Transient Electromagnetic sounding (TEM) is very sensitive to conductive structures. Another difference is VES is better to detect shallow structures, while TEM soundings can reach deeper layers. A Matlab program for 1D joint inversion of VES and TEM soundings was developed aiming at exploring the best of both methods. The program uses CRS - Controlled Random Search - algorithm for both single and 1D joint inversions. Usually inversion programs use Marquadt type algorithms but for electrical and electromagnetic methods, these algorithms may find a local minimum or not converge. Initially, the algorithm was tested with synthetic data, and then it was used to invert experimental data from two places in Paraná sedimentary basin (Bebedouro and Pirassununga cities), both located in São Paulo State, Brazil. Geoelectric model obtained from VES and TEM data 1D joint inversion is similar to the real geological condition, and ambiguities were minimized. Results with synthetic and real data show that 1D VES/TEM joint inversion better recovers simulated models and shows a great potential in geological studies, especially in hydrogeological studies.

  20. Quasi-1D excitons in lateral induced superlattices.

    Science.gov (United States)

    Cocoletzi, Gregorio H.; Hernández de La Luz, Alvaro D.; Ulloa, Sergio E.

    1998-03-01

    Effects of electrostatic-potential-induced lateral superlattices on the optical properties of quasi-1D excitons in GaAs-AlGaAs quantum wells are investigated. Variational estimations are presented, in the tight binding limit, of minibands, binding energies E_ex and absorption coefficients ?_ex of the ground state and first excited state of heavy-hole excitonic transitions as functions of the applied electrostatic potentials and the period of induced superlattices. The limit of small periods and high electrostatic potential produces strong confinement, and consequently, this polarizes the excitons, resembling a type II superlattice where electrons and holes are spatially separated in different potential wells. The variations of the period induce strongh oscillations on E_ex and ?_ex as a result of a competition between quantum structural confinement and Coulomb interactions.

  1. Magnetic structure in cool stars. III - CA II H and K emission and rotation of main-sequence stars

    Science.gov (United States)

    Middelkoop, F.

    1981-09-01

    Ca II H and K fluxes were measured in 31 rapidly rotating main-sequence stars of type F and in seven single-line main-sequence spectroscopic binaries with periods less than 10 days. Most of the rapidly rotating stars observed appear to have relatively high fluxes compared to the slowly rotating stars of the same spectral type. Calculations show that the effect of rotational broadening is negligible and that the fluxes greater than normal measured in these stars must be a result of the increased Ca II H and K emission. All main-sequence binaries with periods less than nine days show eccentricities smaller than 0.1, which indicates that in these systems the rotational and orbital motions are probably synchronized.

  2. Magnetic structure in cool stars. IV - Rotation and CA II H and K emission of main-sequence stars

    Science.gov (United States)

    Middelkoop, F.

    1982-03-01

    The measured Ca II H and K emission indices of stars are converted to surface fluxes (FH + FK). This conversion largely eliminates the dependence on spectral type in the relation between the uncorrected Ca II H and K emission and the rotational velocity of a star which has been found by Vaughan et al. This relation holds for single main-sequence stars as well as for short-period binaries indicating that the enhanced emission in short-period binaries is a result of rapid rotation enforced by tidal coupling. A plot of surface fluxes against ? sin i values suggests a color-dependent discontinuity in the relation. This discontinuity may explain the two branches in (FH + FK) for (B-V) < 1.00 among main-sequence stars. From the relation between (FH + FK) and rotational velocity it is deduced that the average rotational velocity of late-type main-sequence Hyades decreases with decreasing effective temperature.

  3. Sequence characterization of S100A8 gene reveals structural differences of protein and transcriptional factor binding sites in water buffalo and yak.

    Science.gov (United States)

    Kathiravan, P; Goyal, S; Kataria, R S; Mishra, B P; Jayakumar, S; Joshi, B K

    2011-01-01

    The present study was undertaken to characterize the structure of S100A8 gene and its promoter in water buffalo and yak. Sequence data of 2.067 kb, 2.071 kb, and 2.052 kb with respect to complete S100A8 gene including 5' flanking region was generated in river buffalo, swamp buffalo, and yak, respectively. BLAST analysis of coding DNA sequences (CDS) of S100A8 gene revealed 95% homology of buffalo sequence with cattle, 85% with pig and horse, 83% with dog, 72-73% with murines, and around 79% with primates and humans. Phylogenetic analysis of predicted CDS revealed distinct clustering of murines, primates, and domestic animals with bovines and bubalines forming a subcluster among farm animals. In silico translation of predicted CDS revealed a sequence of 89 amino acids with 7 amino acid changes between cattle and buffalo and 2 changes between cattle and yak. The search for Pfam fam