WorldWideScience

Sample records for 1d structural sequences

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

    Directory of Open Access Journals (Sweden)

    Janda Jan-Oliver

    2012-04-01

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

  2. 𝒩-Structures Applied to Closed Ideals in BCH-Algebras

    Directory of Open Access Journals (Sweden)

    Mehmet Ali Öztürk

    2010-01-01

    Full Text Available The notions of 𝒩-subalgebras and 𝒩-closed ideals in BCH-algebras are introduced, and the relation between 𝒩-subalgebras and 𝒩-closed ideals is considered. Characterizations of 𝒩-subalgebras and 𝒩-closed ideals are provided. Using special subsets, 𝒩-subalgebras and 𝒩-closed ideals are constructed. A condition for an 𝒩-subalgebra to be an 𝒩-closed ideal is discussed. Given an 𝒩-structure, the greatest 𝒩-closed ideal which is contained in the 𝒩-structure is established.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Tautz Diethard

    2007-02-01

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

  6. Sequence-structure relations of biopolymers

    CERN Document Server

    Barrett, Christopher; Reidys, Christian M

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-10-15

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

  8. 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.

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

    OpenAIRE

    Kulkarni, Manas; Lamacraft, Austen

    2012-01-01

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

  10. Local RNA structure alignment with incomplete sequence

    OpenAIRE

    Kolbe, Diana L.; Eddy, Sean R

    2009-01-01

    Motivation: Accuracy of automated structural RNA alignment is improved by using models that consider not only primary sequence but also secondary structure information. However, current RNA structural alignment approaches tend to perform poorly on incomplete sequence fragments, such as single reads from metagenomic environmental surveys, because nucleotides that are expected to be base paired are missing.

  11. 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.

  12. Quark-hadron duality in spin structure functions g1p and g1d

    International Nuclear Information System (INIS)

    New measurements of the spin structure functions of the proton and deuteron g1p(x,Q2) and g1d(x,Q2) in the nucleon resonance region are compared with extrapolations of target-mass-corrected next-to-leading-order (NLO) QCD fits to higher energy data. Averaged over the entire resonance region (W2 dependence for Q2>1.7 GeV2/c2. This ''global'' duality appears to result from cancellations among the prominent ''local'' resonance regions: in particular strong ?3/2 contributions in the ?(1232) region appear to be compensated by strong ?1/2 contributions in the resonance region centered on 1.5 GeV. These results are encouraging for the extension of NLO QCD fits to lower W and Q2 than have been used previously

  13. 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.

  14. The Role of the Impedivity in the Magnetotelluric Response of 1D and 2D Structures

    Science.gov (United States)

    Esposito, Roberta; Giulia Di Giuseppe, Maria; Troiano, Antonio; Patella, Domenico; Mariano Castelo Branco, Raimundo

    2014-05-01

    The influence of the resistivity dispersion on the magnetotelluric (MT) response is analyzed. MT uses the natural electromagnetic (EM) field to determine the electrical resistivity of the subsoil and retrieve the geometry of lithospheric structures, revealing the presence of bodies as metallic deposits, hydrocarbons reservoirs, geothermal fluids. The frequency range of the EM field used varies from 10-4 to 104 Hz. If the soil is polarizable, the dispersion of the resistivity, whose characteristic frequency interval is between 10-2 and 102 Hz, may affect MT responses. Resistivity dispersion is a known phenomenology, which constitutes the basis of the Induced Polarization (IP) prospecting method. In the frequency domain (FD), the dispersion consists in a variation of the resistivity parameter as the frequency of the exciting current is changed. The dispersive resistivity, called impedivity, is a complex function of the frequency. At vanishing frequency, however, the impedivity is real and coincides with the classical resistivity parameter used in DC geoelectrical methods. A real asymptote is also approached as the frequency tends to infinity. The complex physical and chemical fluid-metal-rock interactions may produce induced polarization effects, which are related to the dispersion in rocks. This is manifested on the MT response, creating a distortion on the experimental curves. Disregarding the distortion effect may lead to misleading interpretation of the surveyed structures. We show the results from simulation of the MT responses, when dispersion is assumed to characterize the electrical properties of a region of the explored half-space. Initially, a 1D-layered earth is considered, with intermediate layer assumed to be dispersive. The influence of the dispersion amplitude on the shape of the MT responses is evaluated. The dispersion alters the shape of the curves in a way that, without any external constraints, may make the interpretation of the curves quite ambiguous. Successively, a 2D case is considered, consisting in a magma chamber at a depth of 1 km, buried into a soil. The synthetic responses were performed considering both the non-dispersive and the dispersive case and the differences of the modelled MT curves are compared. As for the 1D case, the dispersion alters the resistivity values, particularly at the boundary of the buried body, leading to an ambiguous interpretation. MT data alone are not sufficient to distinguish polarization effects or can induce to see dispersion where is not present. An approach to solve this problem consists of the combined interpretation of DC geoelectrical and MT data collected at the same site. Review of real cases is also shown.

  15. Sequence and structure of yeast phosphoglycerate kinase.

    OpenAIRE

    Watson, H.C.; Walker, N P; Shaw, P.J.; Bryant, T. N.; Wendell, P L; Fothergill, L A; Perkins, R E; Conroy, S. C.; Dobson, M. J.; Tuite, M. F.

    1982-01-01

    The structure of yeast phosphoglycerate kinase has been determined with data obtained from amino acid sequence, nucleotide sequence, and X-ray crystallographic studies. The substrate binding sites, as deduced from electron density maps, are compatible with known substrate specificity and the stereochemical requirements for the enzymic reaction. A carboxyl-imidazole interaction appears to be involved in controlling the transition between the open and closed forms of the enzyme.

  16. MAGNETIC CORE SHELL STRUCTURES: from 0D to 1D assembling.

    Science.gov (United States)

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

    2015-01-01

    Material research and development studies are focused on different techniques of bringing out nanomaterials with desired characteristics and properties. From the point of view of materials development, nowadays scientists are strongly focused on obtaining materials with predefined characteristics and properties. The morphology control seems to be a determinant factor and increasing attention is devoted to this aspect. At this moment it is possible to engineer the material's features by using different methods and materials combination for both medical and industrial applications. In the applications of chemistry and synthesis, biology, mechanics, optics solar cells and microelectronics tailoring the adjustable parameters of stoichiometry, chemical structure, shape and segregation are evaluated and opens new fields. Because of the magnetic features of nanoparticles and durable particle size, less than 100 nm, this study is aiming to describe their uses in practical applications. That's why the whole hydrodynamic magnetic core shell topic will be reviewed on this paper. Additionally, the properties acting in general sight in solid-state physics are utilized for material selection and for defining issue connecting the core, shell structure and their producing properties. Here, in the study of core/shell nanoparticle various physical and chemical synthesis routes and the effect of electrospun method are briefly discussed. Starting from a real void of the scientific literature, the existent data related to the 1D magnetic electrospun materials are reviewed. The perspectives in the medical, environmental or energetic sector is great and bring some real advantages related to the 0D core@shell structures because both mechanical and biological properties are dependent on the morphology of the materials. PMID:26377653

  17. 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.

  18. Is the extraction by Whatman FTA filter matrix technology and sequencing of large ribosomal subunit D1-D2 region sufficient for identification of clinical fungi?

    Science.gov (United States)

    Kiraz, Nuri; Oz, Yasemin; Aslan, Huseyin; Erturan, Zayre; Ener, Beyza; Arikan Akdagli, Sevtap; Muslumanoglu, Hamza; Cetinkaya, Zafer

    2015-10-01

    Although conventional identification of pathogenic fungi is based on the combination of tests evaluating their morphological and biochemical characteristics, they can fail to identify the less common species or the differentiation of closely related species. In addition these tests are time consuming, labour-intensive and require experienced personnel. We evaluated the feasibility and sufficiency of DNA extraction by Whatman FTA filter matrix technology and DNA sequencing of D1-D2 region of the large ribosomal subunit gene for identification of clinical isolates of 21 yeast and 160 moulds in our clinical mycology laboratory. While the yeast isolates were identified at species level with 100% homology, 102 (63.75%) clinically important mould isolates were identified at species level, 56 (35%) isolates at genus level against fungal sequences existing in DNA databases and two (1.25%) isolates could not be identified. Consequently, Whatman FTA filter matrix technology was a useful method for extraction of fungal DNA; extremely rapid, practical and successful. Sequence analysis strategy of D1-D2 region of the large ribosomal subunit gene was found considerably sufficient in identification to genus level for the most clinical fungi. However, the identification to species level and especially discrimination of closely related species may require additional analysis. PMID:26293550

  19. 5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy

    OpenAIRE

    Puffer, Barbara; Kreutz, Christoph; Rieder, Ulrike; Ebert, Marc-Olivier; Konrat, Robert; Micura, Ronald

    2009-01-01

    19F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondary structure equilibria were chosen as model systems and analyzed by 1D 19F and 1H NMR spectroscopy. A comparison with the unmodified analogs revealed that the equilibrium character...

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

    International Nuclear Information System (INIS)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-01

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

  2. 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...

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

    International Nuclear Information System (INIS)

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

  4. The structure and electronic properties of copper iodide 1D nanocrystals within single walled carbon nanotubes

    International Nuclear Information System (INIS)

    Copper iodide one-dimensional nanocrystals within single walled carbon nanotubes (1D CuI@SWCNTs), i.e. meta-nanotubes [1], were investigated by high resolution electron microscopy (HRTEM). In meta-nanotubes of diameter Dm = 1.3-1.4 nm produced by arc-discharge (AD) method close-packed hexagonal or deformed cubic 1D crystal anion sublattices were observed with cations in octahedral or tetrahedral positions. These two sublattices reversibly transform to one another. In catalysed chemical vapour deposition (CCVD) meta-nanotubes of diameters Dm = 1.5-2.0 nm cubic anion sublattices are formed. For diameters ?2.0 nm three-dimensional (3D) crystallization is observed

  5. 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.

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

    Science.gov (United States)

    Wysocka-?o?opa, Monika; Winkler, Krzysztof

    2015-12-01

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

  7. 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.

  8. 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

  9. 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...

  10. 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 ? ?

  11. 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.

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

    OpenAIRE

    Zhou Yuan Wu; Han, Ray P. S.

    2013-01-01

    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 pape...

  13. 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.

  14. 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.

  15. Impetus for solvothermal synthesis technique: synthesis and structure of a novel 1-D borophosphate using ionic liquid as medium

    International Nuclear Information System (INIS)

    A novel borophosphate compound has been synthesized under solvothermal conditions using ionic liquid as a medium and structurally characterized by single-crystal X-ray diffractions. The compound crystallizes in the monoclinic, space group P2(1)/n, a=8.089(8) A, b=13.977(12) A, c=8.441(8) A, ?=112.517(11) deg. , Z=2, V=881.7(14) A3, R1=0.03, wR2=0.079 and S=1.01. Its structure consists of a 1-D straight chain that is built of the alternative linkage of mutually perpendicular four-member rings. Other characterizations by IR and thermal and elemental analyses are also described

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

    DEFF Research Database (Denmark)

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

    1997-01-01

    We present a computational scheme to search for the most common motif, composed of a combination of sequence and structure constraints, among a collection of RNA sequences. The method uses a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments for pairwise comparisons. The overall method has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwi...

  17. 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

  18. Protein sequence and structure alignments within one framework

    Directory of Open Access Journals (Sweden)

    Margraf Thomas

    2008-04-01

    Full Text Available Abstract Background Protein structure alignments are usually based on very different techniques to sequence alignments. We propose a method which treats sequence, structure and even combined sequence + structure in a single framework. Using a probabilistic approach, we calculate a similarity measure which can be applied to fragments containing only protein sequence, structure or both simultaneously. Results Proof-of-concept results are given for the different problems. For sequence alignments, the methodology is no better than conventional methods. For structure alignments, the techniques are very fast, reliable and tolerant of a range of alignment parameters. Combined sequence and structure alignments may provide a more reliable alignment for pairs of proteins where pure structural alignments can be misled by repetitive elements or apparent symmetries. Conclusion The probabilistic framework has an elegance in principle, merging sequence and structure descriptors into a single framework. It has a practical use in fast structural alignments and a potential use in finding those examples where sequence and structural similarities apparently disagree.

  19. 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.

  20. 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%.

  1. Quark-Hadron Duality in Spin Structure Functions $g_1^p$ and $g_1^d$

    Energy Technology Data Exchange (ETDEWEB)

    P.E. Bosted; K.V. Dharmawardane; G.E. Dodge; T.A. Forest; S.E. Kuhn; Y. Prok

    2006-07-25

    New measurements of the spin structure functions of the proton and deuteron g{sub 1}{sup p}(x, Q{sup 2}) and g{sub 1}{sup d}(x, Q{sup 2}) in the nucleon resonance region are compared with extrapolations of target-mass-corrected next-to-leading-order (NLO) QCD fits to higher energy data. Averaged over the entire resonance region (W < 2 GeV), the data and QCD fits are in good agreement in both magnitude and Q{sup 2} dependence for Q{sup 2} > 1.7 GeV{sup 2}/c{sup 2}. This ''global'' duality appears to result from cancellations among the prominent ''local'' resonance regions: in particular strong {sigma}{sub 3/2} contributions in the {Delta}(1232) region appear to be compensated by strong {sigma}{sub 1/2} contributions in the resonance region centered on 1.5 GeV. These results are encouraging for the extension of NLO QCD fits to lower W and Q{sup 2} than have been used previously.

  2. RNA secondary structure: a comparison of real and random sequences

    OpenAIRE

    Higgs, Paul

    1993-01-01

    A sample of transfer RNA molecules is compared to a sample of random sequences having the same length and same percentage composition of the different bases. For each sequence all possible secondary structures are constructed and a distribution of free energies for the states is obtained. It is found that the ground state free energies of tRNA molecules are significantly lower than for random sequences, and that tRNA molecules have significantly fewer alternative secondary structures at energ...

  3. Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction

    OpenAIRE

    Li, Qiwei; Dahl, David B.; Vannucci, Marina; Hyun Joo,; Tsai, Jerry W.

    2014-01-01

    Determining the primary structure (i.e., amino acid sequence) of a protein has become cheaper, faster, and more accurate. Higher order protein structure provides insight into a protein’s function in the cell. Understanding a protein’s secondary structure is a first step towards this goal. Therefore, a number of computational prediction methods have been developed to predict secondary structure from just the primary amino acid sequence. The most successful methods use machine learning approach...

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

    CERN Document Server

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

    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.

  5. Human renin gene: structure and sequence analysis.

    OpenAIRE

    Hobart, P M; Fogliano, M; O'Connor, B A; Schaefer, I M; Chirgwin, J.M.

    1984-01-01

    The complete protein precursor of human kidney renin has been determined from the sequence of cloned genomic DNA. The gene spans 12 kilobases of DNA and is interrupted by eight intervening sequences. The nine regions (exons) encoding the protein were mapped with a mouse renin cDNA probe, synthetic oligonucleotide probes, and by hybridization of genomic restriction fragments to a 1600-nucleotide human kidney mRNA. The predicted 403-amino acid preprorenin consists of mature renin and a 66-resid...

  6. Evolutionary optimization of biopolymers and sequence structure maps

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-06-01

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

  7. Dissecting the relationship between protein structure and sequence variation

    Science.gov (United States)

    Shahmoradi, Amir; Wilke, Claus; Wilke Lab Team

    2015-03-01

    Over the past decade several independent works have shown that some structural properties of proteins are capable of predicting protein evolution. The strength and significance of these structure-sequence relations, however, appear to vary widely among different proteins, with absolute correlation strengths ranging from 0 . 1 to 0 . 8 . Here we present the results from a comprehensive search for the potential biophysical and structural determinants of protein evolution by studying more than 200 structural and evolutionary properties in a dataset of 209 monomeric enzymes. We discuss the main protein characteristics responsible for the general patterns of protein evolution, and identify sequence divergence as the main determinant of the strengths of virtually all structure-evolution relationships, explaining ~ 10 - 30 % of observed variation in sequence-structure relations. In addition to sequence divergence, we identify several protein structural properties that are moderately but significantly coupled with the strength of sequence-structure relations. In particular, proteins with more homogeneous back-bone hydrogen bond energies, large fractions of helical secondary structures and low fraction of beta sheets tend to have the strongest sequence-structure relation. BEACON-NSF center for the study of evolution in action.

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

    Science.gov (United States)

    Pindera, Marek-Jerzy; Aboudi, Jacob

    1998-01-01

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

  9. Massively Parallel Sequencing Approaches for Characterization of Structural Variation

    OpenAIRE

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

    2012-01-01

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

  10. Language as structured sequences: a causal role of Broca's region in sequence processing

    OpenAIRE

    Uddén, Julia

    2012-01-01

    In this thesis I approach language as a neurobiological system. I defend a sequence processing perspective on language and on the function of Broca's region in the left inferior frontal gyrus (LIFG). This perspective provides a way to express common structural aspects of language, music and action, which all engage the LIFG. It also facilitates the comparison of human language and structured sequence processing in animals. Research on infants, song-birds and non-human primates suggests ...

  11. RSEARCH: Finding homologs of single structured RNA sequences

    Directory of Open Access Journals (Sweden)

    Eddy Sean R

    2003-09-01

    Full Text Available 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 have developed a series of base pair and single nucleotide substitution matrices for RNA sequences called RIBOSUM matrices. RSEARCH reports the statistical confidence for each hit as well as the structural alignment of the hit. We show several examples in which RSEARCH outperforms the primary sequence search programs BLAST and SSEARCH. The primary drawback of the program is that it is slow. The C code for RSEARCH is freely available from our lab's website. Conclusion RSEARCH outperforms primary sequence programs in finding homologs of structured RNA sequences.

  12. Occurrence of protein structure elements in conserved sequence regions

    Directory of Open Access Journals (Sweden)

    Pietrokovski Shmuel

    2007-01-01

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

  13. CAMP: Collection of sequences and structures of antimicrobial peptides

    Science.gov (United States)

    Waghu, Faiza Hanif; Gopi, Lijin; Barai, Ram Shankar; Ramteke, Pranay; Nizami, Bilal; Idicula-Thomas, Susan

    2014-01-01

    Antimicrobial peptides (AMPs) are gaining importance as anti-infective agents. Here we describe the updated Collection of Antimicrobial Peptide (CAMP) database, available online at http://www.camp.bicnirrh.res.in/. The 3D structures of peptides are known to influence antimicrobial activity. Although there exists databases of AMPs, information on structures of AMPs is limited in these databases. CAMP is manually curated and currently holds 6756 sequences and 682 3D structures of AMPs. Sequence and structure analysis tools have been incorporated to enhance the usefulness of the database. PMID:24265220

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

    Directory of Open Access Journals (Sweden)

    Lee Byungkook

    2007-09-01

    Full Text Available Abstract Background Accurate sequence alignments are essential for homology searches and for building three-dimensional structural models of proteins. Since structure is better conserved than sequence, structure alignments have been used to guide sequence alignments and are commonly used as the gold standard for sequence alignment evaluation. Nonetheless, as far as we know, there is no report of a systematic evaluation of pairwise structure alignment programs in terms of the sequence alignment accuracy. Results In this study, we evaluate CE, DaliLite, FAST, LOCK2, MATRAS, SHEBA and VAST in terms of the accuracy of the sequence alignments they produce, using sequence alignments from NCBI's human-curated Conserved Domain Database (CDD as the standard of truth. We find that 4 to 9% of the residues on average are either not aligned or aligned with more than 8 residues of shift error and that an additional 6 to 14% of residues on average are misaligned by 1–8 residues, depending on the program and the data set used. The fraction of correctly aligned residues generally decreases as the sequence similarity decreases or as the RMSD between the C? positions of the two structures increases. It varies significantly across CDD superfamilies whether shift error is allowed or not. Also, alignments with different shift errors occur between proteins within the same CDD superfamily, leading to inconsistent alignments between superfamily members. In general, residue pairs that are more than 3.0 Å apart in the reference alignment are heavily (>= 25% on average misaligned in the test alignments. In addition, each method shows a different pattern of relative weaknesses for different SCOP classes. CE gives relatively poor results for ?-sheet-containing structures (all-?, ?/?, and ?+? classes, DaliLite for "others" class where all but the major four classes are combined, and LOCK2 and VAST for all-? and "others" classes. Conclusion When the sequence similarity is low, structure-based methods produce better sequence alignments than by using sequence similarities alone. However, current structure-based methods still mis-align 11–19% of the conserved core residues when compared to the human-curated CDD alignments. The alignment quality of each program depends on the protein structural type and similarity, with DaliLite showing the most agreement with CDD on average.

  15. Identifying Hierarchical Structure in Sequences A linear-time algorithm

    CERN Document Server

    Nevill-Manning, C G

    1997-01-01

    SEQUITUR is an algorithm that infers a hierarchical structure from a sequence of discrete symbols by replacing repeated phrases with a grammatical rule that generates the phrase, and continuing this process recursively. The result is a hierarchical representation of the original sequence, which offers insights into its lexical structure. The algorithm is driven by two constraints that reduce the size of the grammar, and produce structure as a by-product. SEQUITUR breaks new ground by operating incrementally. Moreover, the method's simple structure permits a proof that it operates in space and time that is linear in the size of the input. Our implementation can process 50,000 symbols per second and has been applied to an extensive range of real world sequences.

  16. Implicit transfer of reversed temporal structure in visuomotor sequence learning.

    Science.gov (United States)

    Tanaka, Kanji; Watanabe, Katsumi

    2014-04-01

    Some spatio-temporal structures are easier to transfer implicitly in sequential learning. In this study, we investigated whether the consistent reversal of triads of learned components would support the implicit transfer of their temporal structure in visuomotor sequence learning. A triad comprised three sequential button presses ([1][2][3]) and seven consecutive triads comprised a sequence. Participants learned sequences by trial and error, until they could complete it 20 times without error. Then, they learned another sequence, in which each triad was reversed ([3][2][1]), partially reversed ([2][1][3]), or switched so as not to overlap with the other conditions ([2][3][1] or [3][1][2]). Even when the participants did not notice the alternation rule, the consistent reversal of the temporal structure of each triad led to better implicit transfer; this was confirmed in a subsequent experiment. These results suggest that the implicit transfer of the temporal structure of a learned sequence can be influenced by both the structure and consistency of the change. PMID:24215394

  17. 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 an...

  18. 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...

  19. A tale of two ferredoxins: sequence similarity and structural differences

    Directory of Open Access Journals (Sweden)

    Sadreyev Ruslan I

    2006-04-01

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

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

    Science.gov (United States)

    Tillmann, Barbara

    2012-10-01

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

  1. 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...

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

    International Nuclear Information System (INIS)

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

  3. From 2D graphene to 1D graphene nanoribbons: dimensional crossover signals in the structural thermal fluctuations

    Science.gov (United States)

    Dobry, Ariel; Costamagna, Sebastián

    2011-03-01

    I this work, by analyzing the thermal excited rippling in the graphene honeycomb lattice, we find clear signals of an existing dimensional crossover from 2D to 1D while reducing one of the dimensions of the graphene layer. Trough a joint study, using montecarlo atomistic simulations and analytical calculation based, we find that the normal-normal correlation function G (q) does not change the power law behavior valid on the long wavelength limit, however the system size dependency of the quadratic out of plane displacement h2 shows a breakdown of its corresponding scaling law. In this case we show that a new scaling law appear which correspond to a truly 1D system. On the basis of these results, and having explored a wide number of realistic systems size, we conclude that narrow nanoribbons presents strongest corrugations than the square graphene sheets. This result could have important consequences on the electron transport properties of freestanding graphene systems.

  4. From the 2D graphene honeycomb lattice to 1D nanoribbons: dimensional crossover signals in the structural thermal fluctuations

    OpenAIRE

    Costamagna, S.; Dobry, A.

    2011-01-01

    We study the dimensional crossover from 2D to 1D type behavior, which takes place in the thermal excited rippling of a graphene honeycomb lattice, when one of the dimensions of the layer is reduced. Through a joint study, by Monte Carlo (MC) atomistic simulations using a quasi-harmonic potential and analytical calculations, we find that the normal-normal correlation function does not change its power law behavior in the long wavelength limit. However the system size dependen...

  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. 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

  8. Versatile structures of group 13 metal halide complexes with 4,4'-bipy: from 1D coordination polymers to 2D and 3D metal-organic frameworks.

    Science.gov (United States)

    Sevastianova, Tatiana N; Bodensteiner, Michael; Maulieva, Albina F; Davydova, Elena I; Virovets, Alexander V; Peresypkina, Eugenia V; Balázs, Gábor; Graßl, Christian; Seidl, Michael; Scheer, Manfred; Frenking, Gernot; Berezovskaya, Ekaterina A; Kazakov, Igor V; Khoroshilova, Olesya V; Timoshkin, Alexey Y

    2015-12-21

    A systematic structural study of complexes formed by aluminium and gallium trihalides with 4,4'-bipyridine (bipy) in 2?:?1, 1?:?1, and 1?:?2 stoichiometric ratios has been performed. Molecular structures of 11 complexes in the solid state have been determined for the first time. Complexes of 2?:?1 composition are molecular, while complexes of 1?:?1 composition form metal-organic frameworks of different kinds: an ionic 3D network (three interpenetrated lvt nets for AlCl3bipy), an ionic 2D network for AlBr3bipy and GaBr3bipy and a 1D coordination polymer in the case of GaCl3bipy. Thus, the nature of the Lewis acid plays a critical role in the structural type of the complex in the solid state. Incorporation of excess bipy molecules into (GaCl3bipy)? (formation of crystallosolvate) leads to an unprecedented change of the molecular structure from a non-ionic 1D coordination polymer to an ionic 2D metal organic framework [GaCl2bipy2](+)[GaCl4](-)·2bipy. As indicated by the temperature-dependent XRD study, removal of bipy by heating in a vacuum restores the non-ionic 1D structure. Quantum chemical computations for simple cluster model systems (up to eight Al and Ga atoms) reveal that ionic forms are slightly favourable, although the energy differences between the ionic and non-ionic structures are not large. These theoretical predictions are in good agreement with experimental findings. Thus, even relatively simple cluster models may be used to indicate the structural preferences in the solid state. Both experimental and computational IR frequency shifts of the in-plane ring bending mode of bipy upon complexation correlate well with the M-N bond distances in the complexes. PMID:26564471

  9. Recursive dynamic programming for adaptive sequence and structure alignment.

    Science.gov (United States)

    Thiele, R; Zimmer, R; Lengauer, T

    1995-01-01

    We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each level of the hierarchy, identifies locally optimal solutions and assembles them into partial alignments of sequences and/or structures. In contrast to classical dynamic programming, RDP can also handle alignment problems that use objective functions not obeying the principle of prefix optimality, e.g. scoring schemes derived from energy potentials of mean force. For such alignment problems, RDP aims at computing solutions that are near-optimal with respect to the involved cost function and biologically meaningful at the same time. Towards this goal, RDP maintains a dynamic balance between different factors governing alignment fitness such as evolutionary relationships and structural preferences. As in the RDP method gaps are not scored explicitly, the problematic assignment of gap cost parameters is circumvented. In order to evaluate the RDP approach we analyse whether known and accepted multiple alignments based on structural information can be reproduced with the RDP method. For this purpose, we consider the family of ferredoxins as our prime example. Our experiments show that, if properly tuned, the RDP method can outperform methods based on classical sequence alignment algorithms as well as methods that take purely structural information into account. PMID:7584462

  10. 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.

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

    Directory of Open Access Journals (Sweden)

    M. Ligozzi

    2014-05-01

    Full Text Available 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.

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

    International Nuclear Information System (INIS)

    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 °S. 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 °S 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. - Graphical Abstract: Novel 1D coordination polymer {Tm(Piv)3}n was synthesized and studied by X-ray diffraction. The magnetic, luminescence properties, the thermal behavior and the volatility for the compound {Tm(Piv)3}n were investigated.? Highlights: ? We synthesized the coordination polymer {Tm(Piv)3}n. ? Tm atoms in polymer have the coordination number 6. ? Polymer exhibits blue-color emission at room temperature. ? Polymer shows high thermal stability and volatility. ? Polymer has no phase transitions in the range of ?50…+50 °S.

  13. 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.

  14. 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.

  15. 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.

  16. Studying the Venus terminator thermal structure observed by SOIR/VEx with a 1D radiative transfer model

    Science.gov (United States)

    Mahieux, A.; Erwin, J. T.; Chamberlain, S.; Robert, S.; Thomas, I.; Vandaele, A. C.; Trompet, L.; Wilquet, V.; Yelle, R. V.

    2015-10-01

    The SOIR instrument on board Venus Express routinely measures the CO2 number density profiles in the mesosphere and thermosphere region at the Venus terminator using the solar occultation technique. Assuming the hydrostatic equilibrium, we derive temperature profiles, which show a permanent cold layer at 125 km, surrounded by two warmer layers at 100 km and 140 km. We developed a 1D conductive radiative transfer model to study the mean SOIR thermal profile, considering the main species, and carefully modelling the radiative terms. In order to correctly reproduce the thermal profile, aerosols cooling and heating terms are added. We describe how aerosols number density profiles can be calculated to have a good match of the thermal profiles.

  17. Sequence and structural conservation in RNA ribose zippers

    Energy Technology Data Exchange (ETDEWEB)

    Tamura, Makio; Holbrook, Stephen R.

    2002-03-01

    The ribose zipper, an important element of RNA tertiary structure, is characterized by consecutive hydrogen-bonding interactions between ribose 20-hydroxyls from different regions of an RNA chain or between RNA chains. These tertiary contacts have previously been observed to also involve base backbone and base base interactions (A-minor type). We searched for ribose zipper tertiary interactions in the crystal structures of the large ribosomal subunit RNAs of Haloarcula marismortui and Deinococcus radiodurans, and the small ribosomal subunit RNA of Thermus thermophilus and identified a total of 97 ribose zippers. Of these, 20 were found in T. thermophilus 16 S rRNA, 44 in H. marismortui 23 S rRNA (plus 2 bridging 5 S and 23 S rRNAs) and 30 in D. radiodurans 23 S rRNA (plus 1 bridging 5 S and 23 S rRNAs). These were analyzed in terms of sequence conservation, structural conservation and stability, location in secondary structure, and phylogenetic conservation. Eleven types of ribose zippers were defined based on ribose base interactions. Of these 11, seven were observed in the ribosomal RNAs. The most common of these is the canonical ribose zipper, originally observed in the P4 P6 group I intron fragment. All ribose zippers were formed by antiparallel chain interactions and only a single example extended beyond two residues, forming an overlapping ribose zipper of three consecutive residues near the small subunit A-site. Almost all ribose zippers link stem (Watson Crick duplex) or stem-like (base-paired), with loop (external, internal, or junction) chain segments. About two-thirds of the observed ribose zippers interact with ribosomal proteins. Most of these ribosomal proteins bridge the ribose zipper chain segments with basic amino acid residues hydrogen bonding to the RNA backbone. Proteins involved in crucial ribosome function and in early stages of ribosomal assembly also stabilize ribose zipper interactions. All ribose zippers show strong sequence conservation both within these three ribosomal RNA structures and in a large database of aligned prokaryotic sequences. The physical basis of the sequence conservation is stacked base triples formed between consecutive base-pairs on the stem or stem-like segment with bases (often adenines) from the loop-side segment. These triples have previously been characterized as Type I and Type II A-minor motifs and are stabilized by base base and base ribose hydrogen bonds. The sequence and structure conservation of ribose zippers can be directly used in tertiary structure prediction and may have applications in molecular modeling and design.

  18. 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.

  19. Sequence homology and structural analysis of the clostridial neurotoxins.

    Science.gov (United States)

    Lacy, D B; Stevens, R C

    1999-09-01

    The clostridial neurotoxins (CNTs), comprised of tetanus neurotoxin (TeNT) and the seven serotypes of botulinum neurotoxin (BoNT A-G), specifically bind to neuronal cells and disrupt neurotransmitter release by cleaving proteins involved in synaptic vesicle membrane fusion. In this study, multiple CNT sequences were analyzed within the context of the 1277 residue BoNT/A crystal structure to gain insight into the events of binding, pore formation, translocation, and catalysis that are required for toxicity. A comparison of the TeNT-binding domain structure to that of BoNT/A reveals striking differences in their surface properties. Further, the solvent accessibility of a key tryptophan in the C terminus of the BoNT/A-binding domain refines the location of the ganglioside-binding site. Data collected from a single frozen crystal of BoNT/A are included in this study, revealing slight differences in the binding domain orientation as well as density for a previously unobserved translocation domain loop. This loop and the conservation of charged residues with structural proximity to putative pore-forming sequences lend insight into the CNT mechanism of pore formation and translocation. The sequence analysis of the catalytic domain revealed an area near the active-site likely to account for specificity differences between the CNTs. It revealed also a tertiary structure, highly conserved in primary sequence, which seems critical to catalysis but is 30 A from the active-site zinc ion. This observation, along with an analysis of the 54 residue "belt" from the translocation domain are discussed with respect to the mechanism of catalysis. PMID:10518945

  20. 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...

  1. 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.

  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. 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

  4. Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA

    OpenAIRE

    Dong, Fang; Allawi, Hatim T.; Anderson, Todd; Neri, Bruce P.; LYAMICHEV, VICTOR I.

    2001-01-01

    DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5?-nucleases with an energy minimization algorithm that utilizes the 5?-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor seq...

  5. 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.

  6. Sequence physical properties encode the global organization of protein structure space

    OpenAIRE

    Rackovsky, S.

    2009-01-01

    It is demonstrated that, properly represented, the amino acid composition of protein sequences contains the information necessary to delineate the global properties of protein structure space. A numerical representation of amino acid sequence in terms of a set of property factors is used, and the values of those property factors are averaged over individual sequences and then over sets of sequences belonging to structurally defined groups. These sequence sets then can be viewed as points in a...

  7. Two extensions of 1D Toda hierarchy

    International Nuclear Information System (INIS)

    The extended Toda hierarchy of Carlet, Dubrovin and Zhang is reconsidered in light of a 2 + 1D extension of the 1D Toda hierarchy constructed by Ogawa. These two extensions of the 1D Toda hierarchy turn out to have a very similar structure, and the former may be thought of as a kind of dimensional reduction of the latter. In particular, this explains an origin of the mysterious structure of the bilinear formalism proposed by Milanov.

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

    International Nuclear Information System (INIS)

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

  9. Synthesis and structural characterization of uranium-doped Ca2CuO3, a 1D quantum antiferromagnet

    OpenAIRE

    Hoang, Nam Nhat; Huynh, Dang Chinh; Nguyen, Duc Tho; Nguyen, Thuy Trang; Ngo, Duc The; Finnie, Michael; Nguyen, Chau

    2008-01-01

    The technological settings of a modified sol-gel method for preparation of highly fine homogeneous powder Ca2CuO3 doped with uranium 238 (x=0-0.05) is presented. The analysis of structure, purity of phases and the justification for the role of uranium in the given compounds are provided together with almost complete classification of observed optical phonons by means of the Raman, IR measurements and ab initio calculation. The significant reduction in particle size was achie...

  10. Combining multiple structure and sequence alignments to improve sequence detection and alignment: Application to the SH2 domains of Janus kinases

    OpenAIRE

    Al-Lazikani, Bissan; Sheinerman, Felix B.; Honig, Barry

    2001-01-01

    In this paper, an approach is described that combines multiple structure alignments and multiple sequence alignments to generate sequence profiles for protein families. First, multiple sequence alignments are generated from sequences that are closely related to each sequence of known three-dimensional structure. These alignments then are merged through a multiple structure alignment of family members of known structure. The merged alignment is used to generate a Hi...

  11. 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...

  12. 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)

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

    Science.gov (United States)

    Orimoto, Yuuichi; Liu, Kai; Aoki, Yuriko

    2015-10-30

    We applied ab initio order-N elongation (ELG) method to calculate electronic structures of various deoxyribonucleic acid (DNA) models. We aim to test potential application of the method for building a database of DNA electronic structures. The ELG method mimics polymerization reactions on a computer and meets the requirements for linear scaling computational efficiency and high accuracy, even for huge systems. As a benchmark test, we applied the method for calculations of various types of random sequenced A- and B-type DNA models with and without counterions. In each case, the ELG method maintained high accuracy with small errors in energy on the order of 10(-8) hartree/atom compared with conventional calculations. We demonstrate that the ELG method can provide valuable information such as stabilization energies and local densities of states for each DNA sequence. In addition, we discuss the "restarting" feature of the ELG method for constructing a database that exhaustively covers DNA species. © 2015 Wiley Periodicals, Inc. PMID:26337429

  14. 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.

  15. 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)

  16. 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.

  17. What is the impact of the sequence structure on implicit learning in children?

    OpenAIRE

    Lejeune, Caroline; Schmitz, Xavier; Lempereur, Stéphanie; Maillart, Christelle; Meulemans, Thierry; Gabriel, Audrey

    2010-01-01

    It is generally admitted that implicit learning abilities are efficient early in childhood. However, few studies have explored the impact of the structure of the sequence on children’s performance in implicit learning tasks. The current research was intended to examine sequence learning abilities in children by comparing sequences of different structural characteristics.

  18. 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...

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

    Directory of Open Access Journals (Sweden)

    Nemoto Wataru

    2012-05-01

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

  20. 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.

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

    Science.gov (United States)

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

    2013-06-28

    The reaction of the phosphate monoester {(ArO)PO(OH)2} (Ar = 2,6-i-Pr2C6H3) with BiPh3 in a 1 : 1 ratio in refluxing toluene afforded a tetradecabismuth-oxo-phosphate cage [{(ArO)PO3}10{(ArO)PO2OH}2(Bi14O10)·2(CH3OH)]·3C6H12·3CH3OH·2H2O (Ar = 2,6-i-Pr2C6H3) (1). On the other hand the reaction of the phosphate diester {((t)BuO)2PO(OH)} with BiPh3 in a 1 : 1 ratio at room temperature in ethanol afforded the 1D-coordination polymer [Bi(C6H5)2((t)BuO)2PO2]n (2). The molecular structure of 1 reveals that the cage is comprised of a central planar Bi6 rim and two Bi4 poles. The entire aggregate is held together by multiple coordination of O(2-), [(ArO)P(O)(OH)](-), [(ArO)PO3](2-) and methanol ligands. 2 is a 1D-coordination polymer where adjacent bismuth is bridged by isobidentate [((t)BuO)2PO2](-) ligands. In solution, however, 2 decomposes into the monomeric repeat unit [Ph2Bi{((t)BuO)2PO2}] which is indicated by ESI-MS studies. Thermolysis of 1 and 2 at 700 °C affords a pure phase of BiPO4. PMID:23632600

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

    Indian Academy of Sciences (India)

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

    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.

  4. The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.

    Science.gov (United States)

    Gabanyi, Margaret J; Adams, Paul D; Arnold, Konstantin; Bordoli, Lorenza; Carter, Lester G; Flippen-Andersen, Judith; Gifford, Lida; Haas, Juergen; Kouranov, Andrei; McLaughlin, William A; Micallef, David I; Minor, Wladek; Shah, Raship; Schwede, Torsten; Tao, Yi-Ping; Westbrook, John D; Zimmerman, Matthew; Berman, Helen M

    2011-07-01

    The Protein Structure Initiative's Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org ) is an open web resource designed to turn the products of the structural genomics and structural biology efforts into knowledge that can be used by the biological community to understand living systems and disease. Here we will present examples on how to use the SBKB to enable biological research. For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models, structural genomics protein target status, experimental protocols, and the ability to order available DNA clones from the PSI:Biology-Materials Repository. A text search will find publication and technology reports resulting from the PSI's high-throughput research efforts. Web tools that aid in research, including a system that accepts protein structure requests from the community, will also be described. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events calendar to present a broader view of structural genomics and structural biology. PMID:21472436

  5. Structure and neural expression of a zebrafish homeobox sequence.

    Science.gov (United States)

    Njølstad, P R; Molven, A; Eiken, H G; Fjose, A

    1988-12-15

    A genomic library of zebrafish was constructed and screened with homeobox-containing probes. One of the positive clones contains a transcribed region which shares extensive sequence homology with the murine Hox-1.4 and Hox-2.6 genes and the human HHO.c13 gene. Characterization of this zebrafish homologue (ZF-13) with respect to expression demonstrated that it is transcribed during embryogenesis where a major RNA species of 2.5 kb and a minor transcript of 4.6 kb are detected. The highest concentration of both transcripts was found in embryos at the stage of somite formation. By in situ hybridization the spatial localization of expression was analysed in hatching embryos. Hybridization signals were mainly detected throughout the neural tube and in the brain. A small amount of RNA derived from ZF-13 was localized in differentiated muscle cells. Our results suggest that homeobox genes of distantly related vertebrate species are very similar with respect to structure and function. PMID:2468579

  6. A tale of two ferredoxins: sequence similarity and structural differences

    OpenAIRE

    Sadreyev Ruslan I; Krishna S Sri; Grishin Nick V

    2006-01-01

    Abstract Background Sequence similarity between proteins is usually considered a reliable indicator of homology. Pyruvate-ferredoxin oxidoreductase and quinol-fumarate reductase contain ferredoxin domains that bind [Fe-S] clusters and are involved in electron transport. Profile-based methods for sequence comparison, such as PSI-BLAST and HMMer, suggest statistically significant similarity between these domains. Results The sequence similarity between these ferredoxin domains resides in the ar...

  7. Inferring Social Network Structure from Bacterial Sequence Data

    OpenAIRE

    Pluci?ski, Mateusz M.; Starfield, Richard; Almeida, Rodrigo P. P.

    2011-01-01

    Using DNA sequence data from pathogens to infer transmission networks has traditionally been done in the context of epidemics and outbreaks. Sequence data could analogously be applied to cases of ubiquitous commensal bacteria; however, instead of inferring chains of transmission to track the spread of a pathogen, sequence data for bacteria circulating in an endemic equilibrium could be used to infer information about host contact networks. Here, we show—using simulated data—that multilocus DN...

  8. 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.

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

    Science.gov (United States)

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

    2015-11-01

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

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

    Science.gov (United States)

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

    2015-09-01

    Given the importance of RNA secondary structures in defining their biological role, it would be convenient for researchers seeking RNA data if both sequence and structural information pertaining to RNA molecules are made available together. Current nucleotide data repositories archive only RNA sequence data. Furthermore, storage formats which can frugally represent RNA sequence as well as structure data in a single file, are currently unavailable. This article proposes a novel storage format, 'FASTR', for concomitant representation of RNA sequence and structure. The storage efficiency of the proposed FASTR format has been evaluated using RNA data from various microorganisms. Results indicate that the size of FASTR formatted files (containing both RNA sequence as well as structure information) are equivalent to that of FASTA-format files, which contain only RNA sequence information. RNA secondary structure is typically represented using a combination of a string of nucleotide characters along with the corresponding dot-bracket notation indicating structural attributes. 'FASTR' - the novel storage format proposed in the present study enables a frugal representation of both RNA sequence and structural information in the form of a single string. In spite of having a relatively smaller storage footprint, the resultant 'fastr' string(s) retain all sequence as well as secondary structural information that could be stored using a dot-bracket notation. An implementation of the 'FASTR' methodology is available for download at http://metagenomics.atc.tcs.com/compression/fastr. PMID:26333403

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

    Indian Academy of Sciences (India)

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

    2015-09-01

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

  12. 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; Hogue Christopher WV

    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...

  13. Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases

    OpenAIRE

    Wang, Yi-Ting; Yang, Wei-Jen; Li, Chia-Lung; Doudeva, Lyudmila G.; Yuan, Hanna S.

    2006-01-01

    Nonspecific endonucleases hydrolyze DNA without sequence specificity but with sequence preference, however the structural basis for cleavage preference remains elusive. We show here that the nonspecific endonuclease ColE7 cleaves DNA with a preference for making nicks after (at 3?O-side) thymine bases but the periplasmic nuclease Vvn cleaves DNA more evenly with little sequence preference. The crystal structure of the ‘preferred complex’ of the nuclease domain of ColE7 bound to an 18 bp DNA w...

  14. Using Structure to Explore the Sequence Alignment Space of Remote Homologs

    OpenAIRE

    Kuziemko, Andrew; Honig, Barry; Petrey, Donald

    2011-01-01

    Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is “optimal” in terms of the DP score does not necessarily correspond to the alignment that produces the most ac...

  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. Iterative multi-task sequence labeling for predicting structural properties of proteins

    OpenAIRE

    Maes, Francis; Becker, Julien; Wehenkel, Louis

    2011-01-01

    Developing computational tools for predicting protein structural information given their amino acid sequence is of primary importance in protein science. Problems, such as the prediction of secondary structures, of solvent accessibility, or of disordered regions, can be expressed as sequence labeling problems and could be solved independently by existing machine learning based sequence labeling approaches. But, since these problems are closely related, we propose to rather approach them joint...

  17. Implicit transfer of spatial structure in visuomotor sequence learning.

    Science.gov (United States)

    Tanaka, Kanji; Watanabe, Katsumi

    2014-11-01

    Implicit learning and transfer in sequence learning are essential in daily life. Here, we investigated the implicit transfer of visuomotor sequences following a spatial transformation. In the two experiments, participants used trial and error to learn a sequence consisting of several button presses, known as the m×n task (Hikosaka et al., 1995). After this learning session, participants learned another sequence in which the button configuration was spatially transformed in one of the following ways: mirrored, rotated, and random arrangement. Our results showed that even when participants were unaware of the transformation rules, accuracy of transfer session in the mirrored and rotated groups was higher than that in the random group (i.e., implicit transfer occurred). Both those who noticed the transformation rules and those who did not (i.e., explicit and implicit transfer instances, respectively) showed faster performance in the mirrored sequences than in the rotated sequences. Taken together, the present results suggest that people can use their implicit visuomotor knowledge to spatially transform sequences and that implicit transfers are modulated by a transformation cost, similar to that in explicit transfer. PMID:25261739

  18. Structural (and sequence-based) analysis of transcriptional regulation

    OpenAIRE

    Contreras-Moreira, Bruno; Lozada-Chávez, Irma; Espinosa Angarica, Vladimir

    2008-01-01

    Most computational approaches to transcriptional regulation use sequence-based methodologies, that aim to discover regulatory motifs in genomic segments. Here we argue that the current content of the Protein Data Bank (PDB) can provide invaluable data that drive the prediction of regulatory interactions within genomes. First, we dissect protein-DNA interfaces and find atomic interactions that contribute to sequence-specific recognition, mainly hydrogen bonds and Van derWaals contacts. Thes...

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

    Indian Academy of Sciences (India)

    Jianghua Li; Chi Zhang

    2015-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Madej Tom

    2009-05-01

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

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

    DEFF Research Database (Denmark)

    Tian, Pengfei; Boomsma, Wouter

    2015-01-01

    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.

  2. A protein short motif search tool using amino acid sequence and their secondary structure assignment

    OpenAIRE

    Venkataraman, Arun; Chew, Teong Han; Hussein, Zeti Azura Mohamed; Shamsir, Mohd Shahir

    2011-01-01

    We present the development of a web server, a protein short motif search tool that allows users to simultaneously search for a protein sequence motif and its secondary structure assignments. The web server is able to query very short motifs searches against PDB structural data from the RCSB Protein Databank, with the users defining the type of secondary structures of the amino acids in the sequence motif. The output utilises 3D visualisation ability that highlights the position of ...

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

    DEFF Research Database (Denmark)

    Tian, Pengfei; Boomsma, Wouter; Wang, Yong; Otzen, Daniel; Jensen, Mogens H; Lindorff-Larsen, Kresten

    2015-01-01

    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 co...

  4. Cloning of soybean leghemoglobin structural gene sequences synthesized in vitro

    DEFF Research Database (Denmark)

    Truelsen, E; Gausing, K; Jochimsen, B; Jørgensen, Poul; Marcker, K A

    1979-01-01

    Double-stranded soybean leghemoglobin DNA was synthesized from leghemoglobin mRNA isolated from soybean nodules. The dsDNA was inserted into the Bam H1 site of plasmid pBR322 using the poly-dAT-joiner method. A cloned DNA fragment of one recombinant plasmid was isolated and characterized by restriction endonuclease digestion. The restriction cleavage map and the DNA sequence of a selected part of the inserted DNA are in complete accordance with the amino-acid sequence of soybean leghemoglobin.

  5. The chemical structure of DNA sequence signals for RNA transcription

    Science.gov (United States)

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

    1982-01-01

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

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

    CERN Document Server

    Li, W

    1997-01-01

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

  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: 0.548, year: 2014 http://www.sciencedirect.com/science/article/pii/S0168007214000773

  8. Sequence and structure of the dopa decarboxylase gene of Drosophila: evidence for novel RNA splicing variants.

    OpenAIRE

    Eveleth, D D; Gietz, R. D.; Spencer, C. A.; Nargang, F. E.; Hodgetts, R B; Marsh, J L

    1986-01-01

    In Drosophila, dopa decarboxylase (DDC) serves a dual role in neurotransmitter production and sclerotization of the cuticle. The Ddc gene is under complex hormonal and tissue-specific control and several sizes of Ddc RNA are observed at embryonic hatching, pupariation and adult eclosion. We present here the complete nucleotide sequence of the Drosophila dopa decarboxylase gene and the partial sequence of two corresponding Ddc cDNAs. The sequence allows us to account for the detailed structure...

  9. Effects of Template Sequence and Secondary Structure on DNA-Templated Reactivity

    OpenAIRE

    Snyder, Thomas M.; Tse, Brian N.; Liu, David R.

    2008-01-01

    DNA-templated organic synthesis enables the translation, selection, and amplification of DNA sequences encoding synthetic small-molecule libraries. As the size of DNA-templated libraries increases, the possibility of forming intramolecularly base-paired structures within templates that impede templated reactions increases as well. In order to achieve uniform reactivity across many template sequences and to computationally predict and remove any problematic sequences from DNA-templated librari...

  10. Allelic diversity and population structure of Bacillus sphaericus as revealed by multilocus sequence typing.

    Science.gov (United States)

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

    2011-08-01

    The genetic diversity of 35 Bacillus sphaericus strains was analyzed by a newly developed multilocus sequence typing (MLST) scheme, toxin gene pool survey, and mosquito bioassay. The results demonstrated that strains assigned to the same sequence type (ST) had the same occurrence of toxin genes. Further sequence analysis revealed that toxic strains presented a nearly clonal population structure, whereas nontoxic strains had a high level of heterogeneity and were significantly distinct from toxic strains. PMID:21685170

  11. Allelic Diversity and Population Structure of Bacillus sphaericus as Revealed by Multilocus Sequence Typing ? †

    OpenAIRE

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

    2011-01-01

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

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

    DEFF Research Database (Denmark)

    Worning, Peder; Jensen, Lars Juhl

    2000-01-01

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

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

    Science.gov (United States)

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

    2006-04-01

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

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

    Science.gov (United States)

    Mulder, Bruce E.

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

  15. 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 ...

  16. A model of evolution and structure for multiple sequence alignment

    OpenAIRE

    Löytynoja, Ari; Goldman, Nick

    2008-01-01

    We have developed a phylogeny-aware progressive alignment method that recognizes insertions and deletions as distinct evolutionary events and thus avoids systematic errors created by traditional alignment methods. We now extend this method to simultaneously model regional heterogeneity and evolution. This novel method can be flexibly adapted to alignment of nucleotide or amino acid sequences evolving under processes that vary over genomic regions and, being fully probabilistic, provides an es...

  17. Structure and Evolution of Pre-Main Sequence Stars

    OpenAIRE

    Norbert S. Schulz; Allen, Glenn; 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

    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 resolvi...

  18. Structural and Sequence Motifs of Protein (Histone) Methylation Enzymes

    OpenAIRE

    Cheng, Xiaodong; Collins, Robert E.; Zhang, Xing

    2005-01-01

    With genome sequencing nearing completion for the model organisms used in biomedical research, there is a rapidly growing appreciation that proteomics, the study of covalent modification to proteins, and transcriptional regulation will likely dominate the research headlines in the next decade. Protein methylation plays a central role in both of these fields, as several different residues (Arg, Lys, Gln) are methylated in cells and methylation plays a central role in the “histone code” that re...

  19. 1D Aging

    CERN Document Server

    Fontes, L R; 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 dynamics occur. Our derivations express the scaling limit via coalescing Brownian paths and a ``Brownian space-time spanning tree,'' which also yields other aging functions, such as the persistence probability of no spin flip at 0 between tw and tw+t.

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

    OpenAIRE

    Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; De Brevern, Alexandre

    2012-01-01

    Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein...

  1. The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information

    OpenAIRE

    Banerjee-Basu, Sharmila; Sink, Daniel W.; Baxevanis, Andreas D.

    2001-01-01

    The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures and genomic information for the homeodomain protein family. Release 3.0 contains 795 full-length homeodomain-containing sequences, 32 experimentally-derived structures and 143 homeo­box loci implicated in human genetic disorders. Entries are fully hyperlinked to facilitate easy retrieval of the original records from source databases. A simple search engi...

  2. 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...

  3. Interfacing sequences and structures of proteins: applications to protein annotation and sequence feature visualization

    OpenAIRE

    David, Fabrice Pierre André

    2009-01-01

    L’annotation présente dans UniProtKB (UniProt Knowledgebase) et les structures 3D dans PDB (Protein Data Bank) sont des sources de données importantes et complémentaires pour décrire la fonction et les caractéristiques des protéines. D’une part, une fraction de l’annotation séquentielle présente dans UniProtKB est générée à partir de données structurales. D’autre part, le transfert d’annotations séquentielles sur les structures peut souvent fournir un niveau supérieur de compréhension quant à...

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

    Directory of Open Access Journals (Sweden)

    Karl MagnusPetersson

    2014-02-01

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

  5. Human and Tree Shrew Alpha-synuclein: Comparative cDNA Sequence and Protein Structure Analysis.

    Science.gov (United States)

    Wu, Zheng-Cun; Huang, Zhang-Qiong; Jiang, Qin-Fang; Dai, Jie-Jie; Zhang, Ying; Gao, Jia-Hong; Sun, Xiao-Mei; Chen, Nai-Hong; Yuan, Yu-He; Li, Cong; Han, Yuan-Yuan; Li, Yun; Ma, Kai-Li

    2015-10-01

    The synaptic protein alpha-synuclein (?-syn) is associated with a number of neurodegenerative diseases, and homology analyses among many species have been reported. Nevertheless, little is known about the cDNA sequence and protein structure of ?-syn in tree shrews, and this information might contribute to our understanding of its role in both health and disease. We designed primers to the human ?-syn cDNA sequence; then, tree shrew ?-syn cDNA was obtained by RT-PCR and sequenced. Based on the acquired tree shrew ?-syn cDNA sequence, both the amino acid sequence and the spatial structure of ?-syn were predicted and analyzed. The homology analysis results showed that the tree shrew cDNA sequence matches the human cDNA sequence exactly except at nucleotide positions 45, 60, 65, 69, 93, 114, 147, 150, 157, 204, 252, 270, 284, 298, 308, and 324. Further protein sequence analysis revealed that the tree shrew ?-syn protein sequence is 97.1 % identical to that of human ?-syn. The secondary protein structure of tree shrew ?-syn based on random coils and ?-helices is the same as that of the human structure. The phosphorylation sites are highly conserved, except the site at position 103 of tree shrew?-syn. The predicted spatial structure of tree shrew ?-syn is identical to that of human ?-syn. Thus, ?-syn might have a similar function in tree shrew and in human, and tree shrew might be a potential animal model for studying the pathogenesis of ?-synucleinopathies. PMID:26265394

  6. 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.

  7. Genome-Wide Probing of RNA Structures In Vitro Using Nucleases and Deep Sequencing.

    Science.gov (United States)

    Wan, Yue; Qu, Kun; Ouyang, Zhengqing; Chang, Howard Y

    2016-01-01

    RNA structure probing is an important technique that studies the secondary and tertiary conformations of an RNA. While it was traditionally performed on one RNA at a time, recent advances in deep sequencing has enabled the secondary structure mapping of thousands of RNAs simultaneously. Here, we describe the method Parallel Analysis for RNA Structures (PARS), which couples double and single strand specific nuclease probing to high throughput sequencing. Upon cloning of the cleavage sites into a cDNA library, deep sequencing and mapping of reads to the transcriptome, the position of paired and unpaired bases along cellular RNAs can be identified. PARS can be performed under diverse solution conditions and on different organismal RNAs to provide genome-wide RNA structural information. This information can also be further used to constrain computational predictions to provide better RNA structure models under different conditions. PMID:26483021

  8. 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

    2013-01-01

    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

  9. 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.

  10. Sequence based characterization of structural variation in the mouse genome

    OpenAIRE

    Yalcin, B.; Wong, K.; Agam, A; Goodson, M; Keane, TM; Gan, X; Nellåker, C; Goodstadt, L; Nicod, J; Bhomra, A.; Hernandez-Pliego, P; Whitley, H; Cleak, J; Dutton, R; Janowitz, D

    2011-01-01

    Structural variation is widespread in mammalian genomes and is an important cause of disease, but just how abundant and important structural variants (SVs) are in shaping phenotypic variation remains unclear. Without knowing how many SVs there are, and how they arise, it is difficult to discover what they do. Combining experimental with automated analyses, we identified 711,920 SVs at 281,243 sites in the genomes of thirteen classical and four wild-derived inbred mouse strains. The majority o...

  11. Structure of fault zones in cohesive volcanic sequences

    OpenAIRE

    Holland, Marc

    2004-01-01

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

  12. CATH: comprehensive structural and functional annotations for genome sequences

    OpenAIRE

    Sillitoe, Ian; Lewis, Tony E.; Cuff, Alison; Das, Sayoni; Ashford, Paul; Dawson, Natalie L.; Furnham, Nicholas; Laskowski, Roman A; Lee, David; Lees, Jonathan G; Lehtinen, Sonja; Studer, Romain A.; Thornton, Janet; Orengo, Christine A.

    2014-01-01

    The latest version of the CATH-Gene3D protein structure classification database (4.0, http://www.cathdb.info) provides annotations for over 235 000 protein domain structures and includes 25 million domain predictions. This article provides an update on the major developments in the 2 years since the last publication in this journal including: significant improvements to the predictive power of our functional families (FunFams); the release of our ‘current’ putative domain assignments (CATH-B)...

  13. Biological Sequence Analysis with Multivariate String Kernels.

    Science.gov (United States)

    Kuksa, Pavel P

    2013-03-01

    String kernel-based machine learning methods have yielded great success in practical tasks of structured/sequential data analysis. They often exhibit state-of-the-art performance on many practical tasks of sequence analysis such as biological sequence classification, remote homology detection, or protein superfamily and fold prediction. However, typical string kernel methods rely on analysis of discrete one-dimensional (1D) string data (e.g., DNA or amino acid sequences). In this work we address the multi-class biological sequence classification problems using multivariate representations in the form of sequences of features vectors (as in biological sequence profiles, or sequences of individual amino acid physico-chemical descriptors) and a class of multivariate string kernels that exploit these representations. On a number of protein sequence classification tasks proposed multivariate representations and kernels show significant 15-20\\% improvements compared to existing state-of-the-art sequence classification methods. PMID:23509193

  14. Biological sequence classification with multivariate string kernels.

    Science.gov (United States)

    Kuksa, Pavel P

    2013-01-01

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

  15. From Sequence to Structure- Characterizing Human and Plant Aquaporins

    OpenAIRE

    Nordén, Kristina

    2012-01-01

    Aquaporins constitute a class of membrane proteins that create pores through the lipid bilayer of biological membranes, facilitating the passage of water and other small solutes. Nearly all living organisms possess a more or less intricate set up of aquaporin proteins and the importance of these channels has been implicated in many aspects of health and disease. The aim of the projects summarized in this thesis was to increase the knowledge about the structure and function of aquaporins. A me...

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

    OpenAIRE

    Kim Wan; Winter Christof; Henschel Andreas; Schroeder Michael

    2007-01-01

    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...

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

    DEFF Research Database (Denmark)

    Rosendahl, Søren; Holtgrewe-Stukenbrock, Eva

    2004-01-01

    Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with plant roots and are found in most ecosystems. In this study the community structure of AMF in a clade of the genus Glomus was examined in undisturbed costal grassland using LSU rDNA sequences amplified from roots of Hieracium pilosella. Roots were sampled from May to November along eight 30-m transects, 30–120 m apart. Phylogenetic analysis of the sequences revealed 11 phylogenetic clusters within the clade of Glomus. The phylo...

  18. 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...

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

    OpenAIRE

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

    2012-01-01

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

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

    DEFF Research Database (Denmark)

    Pedersen, Bjørn Panella; Ifrim, Georgiana; Liboriussen, Poul; Axelsen, Kristian B.; Palmgren, Michael G.; Nissen, Poul; Wiuf, Carsten Henrik; Pedersen, Christian Nørgaard Storm

    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 ...

  1. A Java applet for multiple linked visualization of protein structure and sequence.

    Science.gov (United States)

    Oldfield, Thomas J

    2004-04-01

    The amount of biological data available from experimental techniques is huge, and rapidly expanding. The ability to make sense of this vast amount of data requires that we make correlations between distinct biological disciplines using visualization techniques to highlight the critical information. This article describes the visualization techniques of dynamic data brushing, view context maintenance, fisheye sequence view, and a magic lens that have been developed to display protein structure and sequence information. PMID:15562987

  2. 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 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.)

  3. MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information

    OpenAIRE

    Pei, Jimin; Grishin, Nick V.

    2006-01-01

    We have developed MUMMALS, a program to construct multiple protein sequence alignment using probabilistic consistency. MUMMALS improves alignment quality by using pairwise alignment hidden Markov models (HMMs) with multiple match states that describe local structural information without exploiting explicit structure predictions. Parameters for such models have been estimated from a large library of structure-based alignments. We show that (i) on remote homologs, MUMMALS achieves statistically...

  4. 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...

  5. 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; Backofen, Rolf; Gorodkin, Jan

    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 Thermo...

  6. Collation and analyses of DNA-binding protein domain families from sequence and structural databanks.

    Science.gov (United States)

    Malhotra, Sony; Sowdhamini, Ramanathan

    2015-04-01

    DNA-protein interactions govern several high fidelity cellular processes like DNA-replication, transcription, DNA repair, etc. Proteins that have the ability to recognise and bind DNA sequences can be classified either according to their DNA-binding motif or based on the sequence of the target nucleotides. We have collated the DNA-binding families by integrating information from both protein sequence family and structural databases. This resulted in a dataset of 1057 DNA-binding protein domain families. Their family properties (the number of members, percent identity distribution and length of members) and domain architectures were examined. Further, sequence domain families were mapped to structures in the protein databank (PDB) and the protein domain structure classification database (SCOP). The DNA-binding families, with no structural information, were clustered together into potential superfamilies based on sequence associations. On the basis of functions attributed to DNA-binding protein folds, we observe that a majority of the DNA-binding proteins follow divergent evolution. This study can serve as a basis for annotation and distribution of DNA-binding proteins in genome(s) of interest. The entire collated set of DNA-binding protein domains is available for download as Hidden Markov Models. PMID:25656606

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

    Directory of Open Access Journals (Sweden)

    Dumontier Michel

    2002-10-01

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

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

    OpenAIRE

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

    2014-01-01

    This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a ...

  9. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-08-10

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

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

    OpenAIRE

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

    2011-01-01

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

  12. Computational design of the sequence and structure of a protein-binding peptide.

    Science.gov (United States)

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

    2011-03-30

    The de novo design of protein-binding peptides is challenging because it requires the identification of both a sequence and a backbone conformation favorable for binding. We used a computational strategy that iterates between structure and sequence optimization to redesign the C-terminal portion of the RGS14 GoLoco motif peptide so that it adopts a new conformation when bound to G?(i1). An X-ray crystal structure of the redesigned complex closely matches the computational model, with a backbone root-mean-square deviation of 1.1 Å. PMID:21388199

  13. Implicit sequence learning: effects of level of structure, adult age, and extended practice.

    Science.gov (United States)

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

    2004-03-01

    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 young people learned lag-3 structure, and they did so more slowly and to a lesser degree than they learned lag-2 structure. These age deficits in higher order sequence learning after extended practice are consistent with simultaneity theory and with theories positing that age-related deficits in neuromodulation lead to less distinctive representations. PMID:15065933

  14. DESIGN PACKAGE 1D SYSTEM SAFETY ANALYSIS

    Energy Technology Data Exchange (ETDEWEB)

    L.R. Eisler

    1995-02-02

    The purpose of this analysis is to systematically identify and evaluate hazards related to the Yucca Mountain Project Exploratory Studies Facility (ESF) Design Package 1D, Surface Facilities, (for a list of design items included in the package 1D system safety analysis see section 3). This process is an integral part of the systems engineering process; whereby safety is considered during planning, design, testing, and construction. A largely qualitative approach was used since a radiological System Safety analysis is not required. The risk assessment in this analysis characterizes the accident scenarios associated with the Design Package 1D structures/systems/components in terms of relative risk and includes recommendations for mitigating all identified risks. The priority for recommending and implementing mitigation control features is: (1) Incorporate measures to reduce risks and hazards into the structure/system/component (S/S/C) design, (2) add safety devices and capabilities to the designs that reduce risk, (3) provide devices that detect and warn personnel of hazardous conditions, and (4) develop procedures and conduct training to increase worker awareness of potential hazards, on methods to reduce exposure to hazards, and on the actions required to avoid accidents or correct hazardous conditions. The scope of this analysis is limited to the Design Package 1D structures/systems/components (S/S/Cs) during normal operations excluding hazards occurring during maintenance and ''off normal'' operations.

  15. 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

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

    International Nuclear Information System (INIS)

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

  17. 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 Hamiltonian systems

  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

    2015-07-01

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

    OpenAIRE

    Lees Jonathan G; Janes Robert W

    2008-01-01

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

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

    CERN Document Server

    Broglia, R A

    2000-01-01

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

  1. 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

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

    OpenAIRE

    Alfonso Valencia

    2003-01-01

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

  4. 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.

  5. 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.

  6. Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing

    OpenAIRE

    Zichner, Thomas; Garfield, David A; Rausch, Tobias; Stütz, Adrian M; Cannavó, Enrico; Braun, Martina; Furlong, Eileen E. M.; Korbel, Jan O.

    2013-01-01

    Genomic structural variation (SV) is a major determinant for phenotypic variation. Although it has been extensively studied in humans, the nucleotide resolution structure of SVs within the widely used model organism Drosophila remains unknown. We report a highly accurate, densely validated map of unbalanced SVs comprising 8962 deletions and 916 tandem duplications in 39 lines derived from short-read DNA sequencing in a natural population (the “Drosophila melanogaster Genetic Reference Panel,”...

  7. PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach

    OpenAIRE

    Yoon Byung-Jun; Sahraeian Sayed Mohammad Ebrahim

    2011-01-01

    Abstract Background Accurate and efficient structural alignment of non-coding RNAs (ncRNAs) has grasped more and more attentions as recent studies unveiled the significance of ncRNAs in living organisms. While the Sankoff style structural alignment algorithms cannot efficiently serve for multiple sequences, mostly progressive schemes are used to reduce the complexity. However, this idea tends to propagate the early stage errors throughout the entire process, thereby degrading the quality of t...

  8. 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, compel...

  9. Protein-Protein Interactions in the Membrane: Sequence, Structural, and Biological Motifs

    OpenAIRE

    Moore, David T.; Berger, Bryan W; DeGrado, William F

    2008-01-01

    Single-span transmembrane (TM) helices have structural and functional roles well beyond serving as mere anchors to tether water-soluble domains in the vicinity of the membrane. They frequently direct the assembly of protein complexes and mediate signal transduction in ways analogous to small modular domains in water-soluble proteins. This review highlights different sequence and structural motifs that direct TM assembly and discusses their roles in diverse biological processes. We believe tha...

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

    Directory of Open Access Journals (Sweden)

    Waack Stephan

    2008-09-01

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

  11. 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.

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

    Science.gov (United States)

    Yoon, Gwonchan; Lee, Myeongsang; Kim, Jae In; Na, Sungsoo; Eom, Kilho

    2014-01-01

    Amyloid fibrils playing a critical role in disease expression, have recently been found to exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is comparable to that of other mechanical proteins such as microtubule, actin filament, and spider silk. These remarkable mechanical properties of amyloid fibrils are correlated with their functional role in disease expression. This suggests the importance in understanding how these excellent mechanical properties are originated through self-assembly process that may depend on the amino acid sequence. However, the sequence-structure-property relationship of amyloid fibrils has not been fully understood yet. In this work, we characterize the mechanical properties of human islet amyloid polypeptide (hIAPP) fibrils with respect to their molecular structures as well as their amino acid sequence by using all-atom explicit water molecular dynamics (MD) simulation. The simulation result suggests that the remarkable bending rigidity of amyloid fibrils can be achieved through a specific self-aggregation pattern such as antiparallel stacking of ? strands (peptide chain). Moreover, we have shown that a single point mutation of hIAPP chain constituting a hIAPP fibril significantly affects the thermodynamic stability of hIAPP fibril formed by parallel stacking of peptide chain, and that a single point mutation results in a significant change in the bending rigidity of hIAPP fibrils formed by antiparallel stacking of ? strands. This clearly elucidates the role of amino acid sequence on not only the equilibrium conformations of amyloid fibrils but also their mechanical properties. Our study sheds light on sequence-structure-property relationships of amyloid fibrils, which suggests that the mechanical properties of amyloid fibrils are encoded in their sequence-dependent molecular architecture. PMID:24551113

  13. Molecular structures of mitochondrial-DNA-like sequences in human nuclear DNA.

    OpenAIRE

    Nomiyama, H.; Fukuda, M.; Wakasugi, S; Tsuzuki, T.; Shimada, K.

    1985-01-01

    Two lambda phage clones carrying mitochondrial-DNA-like (mtDNA-like) sequences isolated from a human gene library were named Lm E-1 and Lm C-2, and their DNA structures were characterized. Lm E-1 contains about 0.4 kb DNA homologous to the 5' portion of the mitochondrial 16S ribosomal RNA (rRNA) gene and Lm C-2, a 1.6 kb DNA homologous to the 3' portion of the 12S rRNA gene and to almost all of the 16S rRNA gene. Comparisons of their nucleotide sequences with those of the corresponding region...

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

    Science.gov (United States)

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

    2014-01-01

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

  15. 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.

  16. 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

  17. In Silico Analysis of Sequence-Structure-Function Relationship of the Escherichia coli Methionine Synthase.

    Science.gov (United States)

    Kumar, Shiv; Bhagabati, Puja; Sachan, Reena; Kaushik, Aman Chandra; Dwivedi, Vivek Dhar

    2015-12-01

    The molecular evolution of various metabolic pathways in the organisms can be employed for scrutinizing the molecular aspects behind origin of life. In the present study, we chiefly concerned about the sequence-structure-function relationship between the Escherichia coli methionine synthase and their respective animal homologs by in silico approach. Using homology prediction technique, it was observed that only 79 animal species showed similarity with the E. coli methionine synthase. Also, multiple sequence alignment depicted only 25 conserved patterns between the E. coli methionine synthase and their respective animal homologs. Based on that, Pfam analysis identified the protein families of 22 conserved patterns among the attained 25 conserved patterns. Furthermore, the 3D structure was generated by HHpred and evaluated by corresponding Ramachandran plot specifying 93 % of the ? and ? residues angles in the most ideal regions. Hence, the designed structure was established as a good quality model for the full length of E. coli methionine synthase. PMID:26223547

  18. [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

  19. DNA sequences of the D-serine deaminase control region and N-terminal portion of the structural gene.

    OpenAIRE

    McFall, E; Runkel, L

    1983-01-01

    We determined the DNA sequence of the D-serine deaminase promoter region and of the N-terminal region of the structural gene. There are possibilities in the promoter for secondary structure and for initiation recognition sequences, and there is an open reading frame. The N-terminal sequence for the structural gene confirms that part of the amino acid sequence previously determined by E. Schlitz and W. Schmitt (FEBS Lett. 134:57-62, 1981), including the active site of the enzyme, and spans the...

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

    Indian Academy of Sciences (India)

    S Balaji; N Srinivasan

    2007-01-01

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

  1. 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

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

    Science.gov (United States)

    Shen, Xiaojuan; Huang, Tongcheng; Wang, Guanyu; Li, Guanglin

    2015-01-01

    Internal symmetry is commonly observed in the majority of fundamental protein folds. Meanwhile, sufficient evidence suggests that nascent polypeptide chains of proteins have the potential to start the co-translational folding process and this process allows mRNA to contain additional information on protein structure. In this paper, we study the relationship between gene sequences and protein structures from the viewpoint of symmetry to explore how gene sequences code for structural symmetry in proteins. We found that, for a set of two-fold symmetric proteins from left-handed beta-helix fold, intragenic symmetry always exists in their corresponding gene sequences. Meanwhile, codon usage bias and local mRNA structure might be involved in modulating translation speed for the formation of structural symmetry: a major decrease of local codon usage bias in the middle of the codon sequence can be identified as a common feature; and major or consecutive decreases in local mRNA folding energy near the boundaries of the symmetric substructures can also be observed. The results suggest that gene duplication and fusion may be an evolutionarily conserved process for this protein fold. In addition, the usage of rare codons and the formation of higher order of secondary structure near the boundaries of symmetric substructures might have coevolved as conserved mechanisms to slow down translation elongation and to facilitate effective folding of symmetric substructures. These findings provide valuable insights into our understanding of the mechanisms of translation and its evolution, as well as the design of proteins via symmetric modules. PMID:26641668

  3. Adapter la structure mésoscopique et l'orientation des polymères semi-cristallins et des polymères de cristaux liquides : confinement à 1D et 2D

    OpenAIRE

    Odarchenko, Yaroslav

    2012-01-01

    Le contrôle de la microstructure des matériaux organiques est crucial pour des applications pratiques telles que la photonique, la biomédecine ou encore le domaine très dynamique de l'électronique organique. Les études récentes ont montré une possibilité de contrôler la structure des polymères à l'échelle nanométrique en utilisant l'auto-assemblage supramoléculaire sous confinement spatial. Bien que de nombreuses études ont déjà été effectuées dans ce domaine, plusieurs questions essentielles...

  4. Superfluidity of the 1D Bose gas

    OpenAIRE

    Carusotto, Iacopo; Castin, Yvan

    2003-01-01

    We have investigated the superfluid properties of a ring of weakly interacting and degenerate 1D Bose gas at thermal equilibrium with a rotating vessel. The conventional definition of superfluidity predicts that the gas has a significant superfluid fraction only in the Bose condensed regime. In the opposite regime, it is found that a superfluid behaviour can still be identified when the probability distribution of the total momentum of the gas has a multi-peaked structure, r...

  5. 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.

  6. A hexanucleotide sequence (dC1dC6 tract) restricts the dC-specific cleavage of single-stranded DNA by endonuclease IV of bacteriophage T4

    OpenAIRE

    Ohshima, Hiroyuki; Hirano, Nobutaka; Takahashi, Hideo

    2007-01-01

    Endonuclease (Endo) IV encoded by denB of bacteriophage T4 is an enzyme that cleaves single-stranded (ss) DNA in a dC-specific manner. Previously we have demonstrated that a dTdCdA is most preferable for Endo IV when an oligonucleotide substrate having a single dC residue is used. Here we demonstrate that Endo IV cleaves ssDNAs exclusively at the 5?-proximal dC where a sequence comprises dC residues both at the 5? proximal and 3? proximal positions (a dCs tract-dependent cleavage). The dCs tr...

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

    Science.gov (United States)

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

    2016-01-01

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

  8. A comprehensive update of the sequence and structure classification of kinases

    Directory of Open Access Journals (Sweden)

    Zhang Hong

    2005-03-01

    Full Text Available Abstract Background A comprehensive update of the classification of all available kinases was carried out. This survey presents a complete global picture of this large functional class of proteins and confirms the soundness of our initial kinase classification scheme. Results The new survey found the total number of kinase sequences in the protein database has increased more than three-fold (from 17,310 to 59,402, and the number of determined kinase structures increased two-fold (from 359 to 702 in the past three years. However, the framework of the original two-tier classification scheme (in families and fold groups remains sufficient to describe all available kinases. Overall, the kinase sequences were classified into 25 families of homologous proteins, wherein 22 families (~98.8% of all sequences for which three-dimensional structures are known fall into 10 fold groups. These fold groups not only include some of the most widely spread proteins folds, such as the Rossmann-like fold, ferredoxin-like fold, TIM-barrel fold, and antiparallel ?-barrel fold, but also all major classes (all ?, all ?, ?+?, ?/? of protein structures. Fold predictions are made for remaining kinase families without a close homolog with solved structure. We also highlight two novel kinase structural folds, riboflavin kinase and dihydroxyacetone kinase, which have recently been characterized. Two protein families previously annotated as kinases are removed from the classification based on new experimental data. Conclusion Structural annotations of all kinase families are now revealed, including fold descriptions for all globular kinases, making this the first large functional class of proteins with a comprehensive structural annotation. Potential uses for this classification include deduction of protein function, structural fold, or enzymatic mechanism of poorly studied or newly discovered kinases based on proteins in the same family.

  9. Cloning and sequencing of the structural gene for the porin protein of Bordetella pertussis.

    Science.gov (United States)

    Li, Z M; Hannah, J H; Stibitz, S; Nguyen, N Y; Manclark, C R; Brennan, M J

    1991-07-01

    Bordetella pertussis produces a porin protein which is a prominent outer membrane component found in both virulent and avirulent strains. N-terminal amino acid analysis of purified B. pertussis porin was performed and this amino acid sequence was used to design an oligonucleotide that was then utilized to screen a lambda gt11 library containing randomly sheared fragments of DNA from B. pertussis strain 347. One clone, lambda BpPor, was identified and subcloned into pUC18. A portion of the DNA insert in this subclone, pBpPor1, was sequenced and shown to contain the N-terminal region of the structural porin gene. This truncated gene sequence was used to design an additional oligonucleotide that was used to identify a clone, pBpPor2, which overlapped with pBpPor1 and contained a termination codon. The structural gene deduced from this sequence would encode a 365-amino-acid polypeptide with a predicted mass of 39,103 daltons. The predicted product also contains a signal sequence of 20 residues that is similar to that found in other porin genes. The predicted B. pertussis porin protein sequence contains regions that are homologous to regions found in porins expressed by Neisseria species and Escherichia coli, including the presence of phenylalanine as the carboxy-terminal amino acid. DNA hybridization studies indicated that both virulent and avirulent strains of B. pertussis contain only one copy of this gene and that Bordetella bronchiseptica and Bordetella parapertussis contain a similar gene. PMID:1658537

  10. 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.

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

    OpenAIRE

    Van 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...

  12. High-resolution NMR structure of an AT-rich DNA sequence

    International Nuclear Information System (INIS)

    We have determined, by proton NMR and complete relaxation matrix methods, the high-resolution structure of a DNA oligonucleotide in solution with nine contiguous AT base pairs. The stretch of AT pairs, TAATTATAA.TTATAATTA, is imbedded in a 27-nucleotide stem-and-loop construct, which is stabilized by terminal GC base pairs and an extraordinarily stable DNA loop GAA (Hirao et al., 1994, Nucleic Acids Res.22, 576-582). The AT-rich sequence has three repeated TAA.TTA motifs, one in the reverse orientation. Comparison of the local conformations of the three motifs shows that the sequence context has a minor effect here: atomic RMSD between the three TAA.TTA fragments is 0.4-0.5 A, while each fragment is defined within the RMSD of 0.3-0.4 A. The AT-rich stem also contains a consensus sequence for the Pribnow box, TATAAT. The TpA, ApT, and TpT.ApA steps have characteristic local conformations, a combination of which determines a unique sequence-dependent pattern of minor groove width variation. All three TpA steps are locally bent in the direction compressing the major groove of DNA. These bends, however, compensate each other, because of their relative position in the sequence, so that the overall helical axis is essentially straight

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

    Indian Academy of Sciences (India)

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

    2012-05-01

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

  14. 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)

  15. 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/

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-01-01

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

  17. SARSA: a web tool for structural alignment of RNA using a structural alphabet

    OpenAIRE

    Chang, Yen-Fu; Huang, Yen-Lin; Lu, Chin Lung

    2008-01-01

    SARSA is a web tool that can be used to align two or more RNA tertiary structures. The basic idea behind SARSA is that we use the vector quantization approach to derive a structural alphabet (SA) of 23 nucleotide conformations, via which we transform RNA 3D structures into 1D sequences of SA letters and then utilize classical sequence alignment methods to compare these 1D SA-encoded sequences and determine their structural similarities. In SARSA, we provide two RNA structural alignment tools,...

  18. Structure and Dynamics of DNA-dendrimer complexation: Role of counterions, water and base pair sequence

    CERN Document Server

    Maiti, P K; Maiti, Prabal K.; Bagchi, Biman

    2006-01-01

    We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by free energy calculations and inherent structure determination. Simulations reveal formation of a stable complex and provide a detailed molecular level understanding of the structure and dynamics of such a complexation. The reaction free energy surface in the initial stage is found to be funnel-like with a significant barrier arising in the late stage due to the occurrence of misfolded states of DNA. Complexation shows surprisingly strong sensitivity to the ssDNA sequence which is found to arise from a competition between enthalpic versus entropic rigidity of ssDNA.

  19. A molecular phylogeny of Hypnales (Bryophyta inferred from ITS2 sequence-structure data

    Directory of Open Access Journals (Sweden)

    Wolf Matthias

    2010-11-01

    Full Text Available Abstract Background Hypnales comprise over 50% of all pleurocarpous mosses. They provide a young radiation complicating phylogenetic analyses. To resolve the hypnalean phylogeny, it is necessary to use a phylogenetic marker providing highly variable features to resolve species on the one hand and conserved features enabling a backbone analysis on the other. Therefore we used highly variable internal transcribed spacer 2 (ITS2 sequences and conserved secondary structures, as deposited with the ITS2 Database, simultaneously. Findings We built an accurate and in parts robustly resolved large scale phylogeny for 1,634 currently available hypnalean ITS2 sequence-structure pairs. Conclusions Profile Neighbor-Joining revealed a possible hypnalean backbone, indicating that most of the hypnalean taxa classified as different moss families are polyphyletic assemblages awaiting taxonomic changes.

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

    Indian Academy of Sciences (India)

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

    2011-11-01

    An equimolar mixture of Ni(NO3)2·6H2O and pyridine-2-aldehyde with two equivalents of NaN3 in methanol in the presence of NaOMe resulted in the formation of light green precipitate which upon crystallization from dimethylformamide (DMF) yielded light green single crystals [{Ni2Na2(pic)4(N3)2(H2O)2(MeOH)}· MeOH·3H2O]$_n$ (1) and [{Ni2Na2(pic)4(N3)2(H2O)4}$\\cdot$2DMF$\\cdot$H2O]$_n$ (2) (pic = pyridine-2-carboxylate) at room temperature and high temperature (100°C), respectively. Variable temperature magnetic studies revealed the existence of overall ferromagnetic behaviour with $J \\approx +10$ cm-1 and $D \\approx ?2$ to ?7 cm-1 for 1 and 2, respectively. Negative values as well as variation of upon slight distortion of structure by varying reaction temperature were observed. The X-band Electron Paramagnetic Resonance (EPR) spectra of both 2 and 3 were recorded below 50 K. The structural distortion was also implicated from the EPR spectra. Density Functional Theory (DFT) calculations on both complexes were performed in two different ways to corroborate the magnetic results. Considering only Ni$^{\\text{II}}_2$ dimeric unit, results were $J = +20.65$ cm-1 and $D = ?3.16$ cm-1 for 1, and $J =+24.56$ cm-1 and $D =?4.67$ cm-1 for 2. However, considering Ni$^{\\text{II}}_2$Na$^I_2$ cubane as magnetic core the results were $J =+16.35$ cm-1 (1), +19.54 cm-1 (2); $D =?3.05$ cm-1 (1), ?4.25 cm-1 (2).

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

    OpenAIRE

    Uddén, Julia; Bahlmann, Jörg

    2012-01-01

    In this paper, we present two novel perspectives on the function of the left inferior frontal gyrus (LIFG). First, a structured sequence processing perspective facilitates the search for functional segregation within the LIFG and provides a way to express common aspects across cognitive domains including language, music and action. Converging evidence from functional magnetic resonance imaging and transcranial magnetic stimulation studies suggests that the LIFG is engaged in sequential proces...

  2. An integrative probabilistic model for identification of structural variation in sequencing data

    OpenAIRE

    Sindi, Suzanne S.; Önal, Selim; Peng, Luke C; Wu, Hsin-Ta; Raphael, Benjamin J.

    2012-01-01

    Paired-end sequencing is a common approach for identifying structural variation (SV) in genomes. Discrepancies between the observed and expected alignments indicate potential SVs. Most SV detection algorithms use only one of the possible signals and ignore reads with multiple alignments. This results in reduced sensitivity to detect SVs, especially in repetitive regions. We introduce GASVPro, an algorithm combining both paired read and read depth signals into a probabilistic model that can an...

  3. Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species

    OpenAIRE

    Yamaguchi, Akihiro; Iwadate, Mitsuo; Suzuki, Ei-ichiro; Yura, Kei; Kawakita, Shigetsugu; Umeyama, Hideaki; Go, Mitiko

    2003-01-01

    Enlarged FAMSBASE is a relational database of comparative protein structure models for the whole genome of 41 species, presented in the GTOP database. The models are calculated by Full Automatic Modeling System (FAMS). Enlarged FAMSBASE provides a wide range of query keys, such as name of ORF (open reading frame), ORF keywords, Protein Data Bank (PDB) ID, PDB heterogen atoms and sequence similarity. Heterogen atoms in PDB include cofactors, ligands and other factors that interact with protein...

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

    OpenAIRE

    Ramos, Marta M. D.; Correia, Helena M. G.

    2008-01-01

    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 de molecular axis when an electric field i...

  5. Capturing “attrition intensifying” structural traits from didactic interaction sequences of MOOC learners

    OpenAIRE

    Sinha, Tanmay; Li, Nan; Jermann, Patrick; Dillenbourg, Pierre

    2014-01-01

    This work is an attempt to discover hidden structural configurations in learning activity sequences of students in Massive Open Online Courses (MOOCs). Leveraging combined representations of video click- stream interactions and forum activities, we seek to fundamentally understand traits that are predictive of decreasing engagement over time. Grounded in the inter- disciplinary field of network science, we follow a graph based approach to success- fully extract indicators of active and passiv...

  6. The Transmembrane Domain Sequence Affects the Structure and Function of the Newcastle Disease Virus Fusion Protein ?

    OpenAIRE

    Gravel, Kathryn A.; McGinnes, Lori W.; Reitter, Julie; Morrison, Trudy G.

    2011-01-01

    The role of specific sequences in the transmembrane (TM) domain of Newcastle disease virus (NDV) fusion (F) protein in the structure and function of this protein was assessed by replacing this domain with the F protein TM domains from two other paramyxoviruses, Sendai virus (SV) and measles virus (MV), or the TM domain of the unrelated glycoprotein (G) of vesicular stomatitis virus (VSV). Mutant proteins with the SV or MV F protein TM domains were expressed, transported to cell surfaces, and ...

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

    OpenAIRE

    Wright Dan; Eargle John; Roberts Elijah; Luthey-Schulten Zaida

    2006-01-01

    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...

  8. Nucleotide sequences and mutational analysis of the structural genes for nitrogenase 2 of Azotobacter vinelandii.

    OpenAIRE

    Joerger, R D; Loveless, T M; Pau, R N; Mitchenall, L A; Simon, B H; Bishop, P E

    1990-01-01

    The nucleotide sequence (6,559 base pairs) of the genomic region containing the structural genes for nitrogenase 2 (V nitrogenase) from Azotobacter vinelandii was determined. The open reading frames present in this region are organized into two transcriptional units. One contains vnfH (encoding dinitrogenase reductase 2) and a ferredoxinlike open reading frame (Fd). The second one includes vnfD (encoding the alpha subunit of dinitrogenase 2), vnfG (encoding a product similar to the delta subu...

  9. Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors

    OpenAIRE

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

    2012-01-01

    TAL (transcription activator–like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair by using two hypervariable residues [known as repeat variable diresidues (RVDs)] at positions 12 and 13. Here, we report the crystal structures of an 11.5-repeat TAL effector in both DNA-free and DNA-bound states. Each TAL repeat comprises two helices co...

  10. Structural variation discovery in the cancer genome using next generation sequencing: Computational solutions and perspectives

    OpenAIRE

    Liu, Biao; Conroy, Jeffrey M; Morrison, Carl D.; Odunsi, Adekunle O; Qin, Maochun; Wei, Lei; Donald L. Trump; Johnson, Candace S.; Liu, Song; Wang, JianMin

    2015-01-01

    Somatic Structural Variations (SVs) are a complex collection of chromosomal mutations that could directly contribute to carcinogenesis. Next Generation Sequencing (NGS) technology has emerged as the primary means of interrogating the SVs of the cancer genome in recent investigations. Sophisticated computational methods are required to accurately identify the SV events and delineate their breakpoints from the massive amounts of reads generated by a NGS experiment. In this review, we provide an...

  11. From DNA to Fitness Differences: Sequences and Structures of Adaptive Variants of Colias Phosphoglucose Isomerase (PGI)

    OpenAIRE

    Wheat, Christopher W.; Watt, Ward B.; POLLOCK, DAVID D.; Patricia M. Schulte

    2005-01-01

    Colias eurytheme butterflies display extensive allozyme polymorphism in the enzyme phosphoglucose isomerase (PGI). Earlier studies on biochemical and fitness effects of these genotypes found evidence of strong natural selection maintaining this polymorphism in the wild. Here we analyze the molecular features of this polymorphism by sequencing multiple alleles and modeling their structures. PGI is a dimer with rotational symmetry. Each monomer provides a critical residue to the other monomer’s...

  12. A molecular phylogeny of Hypnales (Bryophyta) inferred from ITS2 sequence-structure data

    OpenAIRE

    Wolf Matthias; Merget Benjamin

    2010-01-01

    Abstract Background Hypnales comprise over 50% of all pleurocarpous mosses. They provide a young radiation complicating phylogenetic analyses. To resolve the hypnalean phylogeny, it is necessary to use a phylogenetic marker providing highly variable features to resolve species on the one hand and conserved features enabling a backbone analysis on the other. Therefore we used highly variable internal transcribed spacer 2 (ITS2) sequences and conserved secondary structures, as deposited with th...

  13. Structural Elements And Formation Parameters For Some Lower Cretaceous Sequences In The Western Desert, Egypt

    OpenAIRE

    El Dairy, M. D. [????? ????? ??????

    1987-01-01

    The Lower Cretaceous sequences in the northern part of the Western Desert has been penetrated by many of drilled bore—holes adopted by different oil companies. It was encountered at depths ranging from 1200 to 3500 m. The seismic data obtained for the study area have been interpreted. However, two structural elements are depicted. On the other hand, 11 core samples belonging to the Kharita Formation were used for studying some formation parameters such as rock porosity and permeability. Both ...

  14. De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts

    OpenAIRE

    Kosciolek, Tomasz; Jones, David T

    2014-01-01

    The advent of high accuracy residue-residue intra-protein contact prediction methods enabled a significant boost in the quality of de novo structure predictions. Here, we investigate the potential benefits of combining a well-established fragment-based folding algorithm – FRAGFOLD, with PSICOV, a contact prediction method which uses sparse inverse covariance estimation to identify co-varying sites in multiple sequence alignments. Using a comprehensive set of 150 diverse globular target protei...

  15. Kinetic and Sequence-Structure-Function Analysis of LinB Enzyme Variants with ?- and ?-Hexachlorocyclohexane

    OpenAIRE

    Pandey, Rinku; Lucent, Del; Kumari, Kirti; Sharma, Pooja; Lal, Rup; Oakeshott, John G.; Pandey, Gunjan

    2014-01-01

    Organochlorine insecticide hexachlorocyclohexane (HCH) has recently been classified as a ‘Persistent Organic pollutant’ by the Stockholm Convention. The LinB haloalkane dehalogenase is a key upstream enzyme in the recently evolved Lin pathway for the catabolism of HCH in bacteria. Here we report a sequence-structure-function analysis of ten naturally occurring and thirteen synthetic mutants of LinB. One of the synthetic mutants was found to have ?80 fold more activity for ?- and ?-hexachloroc...

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

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Richter, Andreas S.

    2011-01-01

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

  17. 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.

  18. 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.

  19. 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.

  20. High evolutionary conservation of the secondary structure and of certain nucleotide sequences of U5 RNA.

    OpenAIRE

    Branlant, C.; Krol, A., van der; Lazar, E.; Haendler, B; Jacob, M; Galego-Dias, L; Pousada, C

    1983-01-01

    The nucleotide sequence of chicken, pheasant, duck and Tetrahymena pyriformis U5 RNAs as well as that of new mammalian variant U5 RNAs was determined and compared to that of rat and HeLa cells U5 RNAs. Primary structure conservation is about 95% between rat and human cells, 82% between mammals and birds and 57% between the Protozoan and mammals. The same model of secondary structure, a free single-stranded region flanked by two hairpins can be constructed from all RNAs and is identical to the...

  1. 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.

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

    Science.gov (United States)

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

    2015-09-01

    It is well established that (1) star-forming galaxies follow a relation between their star formation rate (SFR) and stellar mass ({M}\\star ), the “star formation sequence,” and (2) the SFRs of galaxies correlate with their structure, where star-forming galaxies are less concentrated than quiescent galaxies at fixed mass. Here, we consider whether the scatter and slope of the star formation sequence is correlated with systematic variations in the Sérsic indices, n, of galaxies across the SFR-{M}\\star plane. We use a mass-complete sample of 23,848 galaxies at 0.5 photometric catalogs. Galaxy light profiles parameterized by n are based on Hubble Space Telescope Cosmic Assembly Near-IR Deep Extragalactic Legacy Survey near-infrared imaging. We use a single SFR indicator empirically calibrated from stacks of Spitzer/MIPS 24 ?m imaging, adding the unobscured and obscured star formation. We find that the scatter of the star formation sequence is related in part to galaxy structure; the scatter due to variations in n at fixed mass for star-forming galaxies ranges from 0.14 ± 0.02 dex at z ˜ 2 to 0.30 ± 0.04 dex at z 2 (implying more dominant bulges) have significantly lower {SFR}/{M}\\star than the main ridgeline of the star formation sequence. These results suggest that bulges in massive z ˜ 2 galaxies are actively building up, where the stars in the central concentration are relatively young. At z < 1, the presence of older bulges within star-forming galaxies lowers global {SFR}/{M}\\star , decreasing the slope and contributing significantly to the scatter of the star formation sequence.

  3. A large 1D retroreflective autostereoscopic display

    Science.gov (United States)

    Smithwick, Quinn Y. J.; Ranieri, Nicola

    2015-03-01

    We aim to produce a wide field-of view large autostereoscopic display for multiple viewers based on a 1D retroreflective screen and overheard microprojectors. The 1D retroreflective screen consists of retroreflector, anisotropic diffuser, and embedded fiber-optic array with optical sensors. Microprojectors modified with wide angle converter lenses are mounted unobtrusively over each viewing location. Each projector's structured lighting is detected by the screen's sensor array for calibration. Pin-cushion distortion correction, rectification and cross-talk reduction are implemented for proper stereo fusion. We examine common viewing scenarios of single viewer autostereoscopic projection, multiprojector automultiscopic projection, side by side multiviewer common and independent autostereoscopic projection, and frontback autostereoscopic projection.

  4. 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 ...

  5. 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.

  6. 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

  7. 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.

  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. Functional and immunological relevance of Anaplasma marginale major surface protein 1a sequence and structural analysis.

    Science.gov (United States)

    Cabezas-Cruz, Alejandro; Passos, Lygia M F; Lis, Katarzyna; Kenneil, Rachel; Valdés, James J; Ferrolho, Joana; Tonk, Miray; Pohl, Anna E; Grubhoffer, Libor; Zweygarth, Erich; Shkap, Varda; Ribeiro, Mucio F B; Estrada-Peña, Agustín; Kocan, Katherine M; de la Fuente, José

    2013-01-01

    Bovine anaplasmosis is caused by cattle infection with the tick-borne bacterium, Anaplasma marginale. The major surface protein 1a (MSP1a) has been used as a genetic marker for identifying A. marginale strains based on N-terminal tandem repeats and a 5'-UTR microsatellite located in the msp1a gene. The MSP1a tandem repeats contain immune relevant elements and functional domains that bind to bovine erythrocytes and tick cells, thus providing information about the evolution of host-pathogen and vector-pathogen interactions. Here we propose one nomenclature for A. marginale strain classification based on MSP1a. All tandem repeats among A. marginale strains were classified and the amino acid variability/frequency in each position was determined. The sequence variation at immunodominant B cell epitopes was determined and the secondary (2D) structure of the tandem repeats was modeled. A total of 224 different strains of A. marginale were classified, showing 11 genotypes based on the 5'-UTR microsatellite and 193 different tandem repeats with high amino acid variability per position. Our results showed phylogenetic correlation between MSP1a sequence, secondary structure, B-cell epitope composition and tick transmissibility of A. marginale strains. The analysis of MSP1a sequences provides relevant information about the biology of A. marginale to design vaccines with a cross-protective capacity based on MSP1a B-cell epitopes. PMID:23776456

  10. Genetic structure of Florida green turtle rookeries as indicated by mitochondrial DNA control region sequences

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

    Straub, John

    2013-03-01

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

  13. 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.

  14. The Candida albicans agglutinin-like sequence family of adhesins: functional insights gained from structural analysis.

    Science.gov (United States)

    Cota, Ernesto; Hoyer, Lois L

    2015-10-01

    Candida albicans colonizes many host sites suggesting its interaction with diverse ligands. Candida albicans adhesion is mediated by a number of proteins including those in the Als (agglutinin-like sequence) family, which have been studied intensively. The recent solution of the Als binding domain structure ended years of speculation regarding the molecular mechanism for Als adhesive function. Als adhesins bind flexible C termini from a broad collection of proteins, providing the basis for adhesion to various cell types and perhaps for C. albicans broad tissue tropism. Understanding adhesive functions at the molecular level will reveal the sequence of events in C. albicans pathogenesis, from host recognition to complex interactions such as development of polymicrobial biofilms or disseminated disease. PMID:26438189

  15. Testing statistical significance scores of sequence comparison methods with structure similarity

    Directory of Open Access Journals (Sweden)

    Leunissen Jack AM

    2006-10-01

    Full Text Available Abstract Background In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical significance testing for an alignment. The e-value is the most commonly used statistical validation method for sequence database searching. The CluSTr database and the Protein World database have been created using an alternative statistical significance test: a Z-score based on Monte-Carlo statistics. Several papers have described the superiority of the Z-score as compared to the e-value, using simulated data. We were interested if this could be validated when applied to existing, evolutionary related protein sequences. Results All experiments are performed on the ASTRAL SCOP database. The Smith-Waterman sequence comparison algorithm with both e-value and Z-score statistics is evaluated, using ROC, CVE and AP measures. The BLAST and FASTA algorithms are used as reference. We find that two out of three Smith-Waterman implementations with e-value are better at predicting structural similarities between proteins than the Smith-Waterman implementation with Z-score. SSEARCH especially has very high scores. Conclusion The compute intensive Z-score does not have a clear advantage over the e-value. The Smith-Waterman implementations give generally better results than their heuristic counterparts. We recommend using the SSEARCH algorithm combined with e-values for pairwise sequence comparisons.

  16. 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 number of P-type ATPases. To examine the distribution of pumps on organisms, we also applied SLR to 1,123 complete genomes from the Entrez genome database. Finally, we analysed the predicted membrane topology of the identified P-type ATPases. Conclusions Using the SLR-based classification tool we are able to run a large scale study of P-type ATPases. This study provides proof-of-concept for the application of SLR to a bioinformatics problem and the analysis of P-type ATPases pinpoints new and interesting targets for further biochemical characterization and structural analysis.

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

    Directory of Open Access Journals (Sweden)

    Wu Cathy H

    2006-06-01

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

  18. Synthesis of 1D Fe?O?/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 (197.2 m(2) g(-1)) were used as a drug carrier, which displayed a controlled release property. PMID:26119084

  19. 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.

  20. Sequence-specific 1H NMR assignments and secondary structure of eglin c

    International Nuclear Information System (INIS)

    Sequence-specific nuclear magnetic resonance assignments were obtained for eglin c, a polypeptide inhibitor of the granulocytic proteinases elastase and cathepsin G and some other proteinases. The protein consists of a single polypeptide chain of 70 residues. All proton resonances were assigned except for some labile protons of arginine side chains. The patterns of nuclear Overhauser enhancements and coupling constants and the observation of slow hydrogen exchange were used to characterize the secondary structure of the protein. The results indicate that the solution structure of the free inhibitor is very similar to the crystal structure reported for the same protein in the complex with subtilisin Carlsberg. However, a part of the binding loop seems to have a significantly different conformation in the free protein

  1. Sequence composition and environment effects on residue fluctuations in protein structures

    CERN Document Server

    Ruvinsky, Anatoly M

    2009-01-01

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

  2. Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a ?-trefoil

    OpenAIRE

    Brych, Stephen R.; Blaber, Sachiko I.; Logan, Timothy M.; Blaber, Michael

    2001-01-01

    Human acidic fibroblast growth factor (FGF-1) is a member of the ?-trefoil hyperfamily and exhibits a characteristic threefold symmetry of the tertiary structure. However, evidence of this symmetry is not readily apparent at the level of the primary sequence. This suggests that while selective pressures may exist to retain (or converge upon) a symmetric tertiary structure, other selective pressures have resulted in divergence of the primary sequence during evolution. Using intra-chain and hom...

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

    OpenAIRE

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole; Petersen, Thomas Nordahl

    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 identi...

  4. Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence

    OpenAIRE

    2010-01-01

    FoxM1 is a member of the Forkhead family of transcription factors and is implicated in inducing cell proliferation and some forms of tumorigenesis. It binds promoter regions with a preference for tandem repeats of a consensus ‘TAAACA’ recognition sequence. The affinity of the isolated FoxM1 DNA-binding domain for this site is in the micromolar range, lower than observed for other Forkhead proteins. To explain these FoxM1 features, we determined the crystal structure of its DNA-binding domain ...

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

    CERN Document Server

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

    2015-01-01

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

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

    OpenAIRE

    Folia, Vasiliki; Petersson, Karl Magnus

    2014-01-01

    In this event-related fMRI study we investigated the effect of 5 days of implicit acquisition on preference classification by means of an artificial grammar learning (AGL) paradigm based on the structural mere-exposure effect and preference classification using a simple right-linear unification grammar. This allowed us to investigate implicit AGL in a proper learning design by including baseline measurements prior to grammar exposure. After 5 days of implicit acquisition, the fMRI results sho...

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

    OpenAIRE

    Karl MagnusPetersson

    2014-01-01

    In this event-related FMRI study we investigated the effect of five days of implicit acquisition on preference classification by means of an artificial grammar learning (AGL) paradigm based on the structural mere-exposure effect and preference classification using a simple right-linear unification grammar. This allowed us to investigate implicit AGL in a proper learning design by including baseline measurements prior to grammar exposure. After 5 days of implicit acquisition, the FMRI results ...

  8. 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.

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

    Science.gov (United States)

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

    2014-02-01

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

  10. 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.

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

    KAUST Repository

    Deng, Dong

    2012-01-05

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

  12. Large-scale oscillation of structure-related DNA sequence features in human chromosome 21

    Science.gov (United States)

    Li, Wentian; Miramontes, Pedro

    2006-08-01

    Human chromosome 21 is the only chromosome in the human genome that exhibits oscillation of the (G+C) content of a cycle length of hundreds kilobases (kb) ( 500kb near the right telomere). We aim at establishing the existence of a similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi- and tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10- or 11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting or unwinding, stiffness, and a putative tendency for nucleosome formation.

  13. Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors

    Science.gov (United States)

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

    2013-01-01

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

  14. 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)

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

    International Nuclear Information System (INIS)

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

    Energy Technology Data Exchange (ETDEWEB)

    Sahoo, B. D., E-mail: bdsahoo@barc.gov.in; Joshi, K. D.; Gupta, Satish C. [Applied Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)

    2015-05-14

    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)].

  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. Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

    Science.gov (United States)

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

    2013-01-01

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

  19. 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.

  20. 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.

  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. Functional and Structural Overview of G-Protein-Coupled Receptors Comprehensively Obtained from Genome Sequences

    Directory of Open Access Journals (Sweden)

    Makiko Suwa

    2011-04-01

    Full Text Available An understanding of the functional mechanisms of G-protein-coupled receptors (GPCRs is very important for GPCR-related drug design. We have developed an integrated GPCR database (SEVENS http://sevens.cbrc.jp/ that includes 64,090 reliable GPCR genes comprehensively identified from 56 eukaryote genome sequences, and overviewed the sequences and structure spaces of the GPCRs. In vertebrates, the number of receptors for biological amines, peptides, etc. is conserved in most species, whereas the number of chemosensory receptors for odorant, pheromone, etc. significantly differs among species. The latter receptors tend to be single exon type or a few exon type and show a high ratio in the numbers of GPCRs, whereas some families, such as Class B and Class C receptors, have long lengths due to the presence of many exons. Statistical analyses of amino acid residues reveal that most of the conserved residues in Class A GPCRs are found in the cytoplasmic half regions of transmembrane (TM helices, while residues characteristic to each subfamily found on the extracellular half regions. The 69 of Protein Data Bank (PDB entries of complete or fragmentary structures could be mapped on the TM/loop regions of Class A GPCRs covering 14 subfamilies.

  3. PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL

    OpenAIRE

    Bramucci Emanuele; Paiardini Alessandro; Bossa Francesco; Pascarella Stefano

    2012-01-01

    Abstract Background In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. Despite the vast majority of these tools have been released as open source software, their deep learning curves often discourages even the most experienced users. Results A simple and intuitive interface, PyMod, between the popular molecular graphics system PyMOL and several other tools (i.e., [PSI-]BLA...

  4. 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.

  5. 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.

  6. 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.

  7. IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences.

    Science.gov (United States)

    McGuffin, Liam J; Atkins, Jennifer D; Salehe, Bajuna R; Shuid, Ahmad N; Roche, Daniel B

    2015-07-01

    IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/. PMID:25820431

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

    Czech Academy of Sciences Publication Activity Database

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

    2007-01-01

    Ro?. 112, B9 (2007), B09304/1-B09304/18. ISSN 0148-0227 R&D Projects: GA ?R GA205/03/1203 Institutional research plan: CEZ:AV0Z30120515 Keywords : Wadati-Benioff zone * aftershocks sequences * internal tectonic structure Subject RIV: DC - Siesmology, Volcanology, Earth Structure Impact factor: 2.953, year: 2007

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

    Science.gov (United States)

    Uddén, Julia; Bahlmann, Jörg

    2012-07-19

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

  10. Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches

    OpenAIRE

    Abel, Haley J; Duncavage, Eric

    2013-01-01

    Next generation sequencing (NGS), or massively paralleled sequencing, refers to a collective group of methods in which numerous sequencing reactions take place simultaneously, resulting in enormous amounts of sequencing data for a small fraction of the cost of Sanger sequencing. Typically short (50–250 bp), NGS reads are first mapped to a reference genome, and then variants are called from the mapped data. While most NGS applications focus on the detection of single nucleotide variants (SNVs)...

  11. 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.

  12. 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...

  13. A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution

    OpenAIRE

    Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

    2013-01-01

    Motivations: The design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e. a random seed is progressively adapted to acquire the desired folding properties) and more importantly do not allow the user to control explicitly the nucleotide distribution such as the GC-content in their sequences. However, the latter is an important criterion for lar...

  14. Enzyme-free translation of DNA into sequence-defined synthetic polymers structurally unrelated to nucleic acids

    Science.gov (United States)

    Niu, Jia; Hili, Ryan; Liu, David R.

    2013-04-01

    The translation of DNA sequences into corresponding biopolymers enables the production, function and evolution of the macromolecules of life. In contrast, methods to generate sequence-defined synthetic polymers with similar levels of control have remained elusive. Here, we report the development of a DNA-templated translation system that enables the enzyme-free translation of DNA templates into sequence-defined synthetic polymers that have no necessary structural relationship with nucleic acids. We demonstrate the efficiency, sequence-specificity and generality of this translation system by oligomerizing building blocks including polyethylene glycol, ?-(D)-peptides, and ?-peptides in a DNA-programmed manner. Sequence-defined synthetic polymers with molecular weights of 26 kDa containing 16 consecutively coupled building blocks and 90 densely functionalized ?-amino acid residues were translated from DNA templates using this strategy. We integrated the DNA-templated translation system developed here into a complete cycle of translation, coding sequence replication, template regeneration and re-translation suitable for the iterated in vitro selection of functional sequence-defined synthetic polymers unrelated in structure to nucleic acids.

  15. Molecular cloning, sequencing, and overexpression of the structural gene encoding the delta subunit of Escherichia coli DNA polymerase III holoenzyme.

    OpenAIRE

    Carter, J. R.; Franden, M A; Aebersold, R.; McHenry, C S

    1992-01-01

    Using an oligonucleotide hybridization probe, we have mapped the structural gene for the delta subunit of Escherichia coli DNA polymerase III holoenzyme to 14.6 centisomes of the chromosome. This gene, designated holA, was cloned and sequenced. The sequence of holA matches precisely four amino acid sequences obtained for the amino terminus of delta and three internal tryptic peptides. A holA-overproducing plasmid that directs the expression of delta up to 4% of the soluble protein was constru...

  16. Quantized conductance through reconfigurable 1D channels

    Science.gov (United States)

    Lu, Shicheng; Annadi, Anil; Cheng, Guanglei; Tomczyk, Michelle; Huang, Mengchen; Lee, Hyungwoo; Ryu, Sangwoo; Eom, Chang-Beom; Irvin, Patrick; Levy, Jeremy

    2015-03-01

    In recent years, a high mobility two-dimensional electron gas LaAlO3/SrTiO3 (LAO/STO) system has become a model system to investigate various exotic ground states of condensed matter physics. This system can co-host superconductivity, magnetism, and strong spin-orbit coupling at 2D interfaces which led to predictions of exotic phenomena such as unconventional superconductivity, helical/chiral modes, and Majorana phases in these interfaces. In order to explore these exotic phases high quality 1D devices are desirable. We demonstrate the realization of a gate tunable quantum point contact (QPC) structure embedded in a LAO/STO nanowire created using conductive AFM lithography. We observe integer quantized conductance in the units of e2 / h at high magnetic fields (B = 9 Tesla, T = 50 mK),a signature of the existence of 1D quantum channels. Significantly, we observe quantized conduction for nanowires as long as 1 ?m, implying that transport is ballistic along the magnetic-field induced chiral edge states in these devices. We gratefully acknowledge financial support from the following agencies and Grants: AFOSR (FA9550-10-1-0524 and FA9550-12-1-0268), NSF (DMR-1124131 and DMR-1104191). AFOSR FA9550-12-1-0342 (CBE) and DMR-1234096 (CBE).

  17. Anti-Interference Receiver Structures for Direct Sequence Spread Spectrum Signals

    Science.gov (United States)

    Jeng, Li-Der; Ueng, Fang-Biau

    Conventional narrowband interference (NBI) rejection algorithms often assumed perfect pseudo-noise (PN) code synchronization. The functions of NBI rejection and code tracking are performed separately and independently by an adaptive filter and a code tracking loop, respectively. This paper presents two new receiver structures for direct sequence spread spectrum (DS/SS) systems, one operates in coherent mode and the other operates in noncoherent mode. Both receivers are designed to suppress NBI and minimize tracking jitter. Numerical results show that the proposed coherent receiver performs as good as the conventional receiver that uses an LMS NBI rejection filter with zero tracking jitter. The noncoherent receiver, when compared with the coherent one, suffers less than 3dB degradation for bit error probability smaller than 10-3.

  18. 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

  19. Estimation of genetic structure of a Mycosphaerella musicola population using inter-simple sequence repeat markers.

    Science.gov (United States)

    Peixouto, Y S; Dórea Bragança, C A; Andrade, W B; Ferreira, C F; Haddad, F; Oliveira, S A S; Darosci Brito, F S; Miller, R N G; Amorim, E P

    2015-01-01

    Among the diseases affecting banana (Musa sp), yellow Sigatoka, caused by the fungal pathogen Mycosphaerella musicola Leach, is considered one of the most important in Brazil, causing losses throughout the year. Understanding the genetic structure of pathogen populations will provide insight into the life history of pathogens, including the evolutionary processes occurring in agrosystems. Tools for estimating the possible emergence of pathogen variants with altered pathogenicity, virulence, or aggressiveness, as well as resistance to systemic fungicides, can also be developed from such data. The objective of this study was to analyze the genetic diversity and population genetics of M. musicola in the main banana-producing regions in Brazil. A total of 83 isolates collected from different banana cultivars in the Brazilian states of Bahia, Rio Grande do Norte, and Minas Gerais were evaluated using inter-simple sequence repeat markers. High variability was detected between the isolates, and 85.5% of the haplotypes were singletons in the populations. The highest source of genetic diversity (97.22%) was attributed to variations within populations. Bayesian cluster analysis revealed the presence of 2 probable ancestral groups, however, showed no relationship to population structure in terms of collection site, state of origin, or cultivar. Similarly, we detected noevidence of genetic recombination between individuals within different states, indicating that asexual cycles play a major role in M. musicola reproduction and that long-distance dispersal of the pathogen is the main factor contributing to the lack of population structure in the fungus. PMID:26214487

  20. 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

  1. 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.

  2. 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

  3. 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.

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

    CERN Document Server

    Roald, C B

    1999-01-01

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

  5. 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.

  6. Quantitative 1D saturation profiles on chalk by NMR

    DEFF Research Database (Denmark)

    Olsen, Dan; Topp, Simon; Stensgaard, Anders; Nørgaard, Jens Vinther; Reffstrup, Jens

    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 ...

  7. Structured diffuse scattering and the fundamental 1-d dipolar unit in PLZT (Pb1-yLay)1-?(Zr1-xTix)1-?O3 (7.5/65/35 and 7.0/60/40) transparent ferroelectric ceramics

    International Nuclear Information System (INIS)

    The observation via electron diffraction of relatively sharp, G±{111}* sheets of diffuse intensity arising from the large amplitude excitation of inherently polar, transverse optical modes of distortion in [(Pb1-yLay)1-???][(Zr1-xTix)1-???]O3 (PLZT), 7.5/65/35 and 7.0/60/40, samples close to the morphotropic phase boundary in this system shows that the fundamental dipolar units in these materials correspond to highly anisotropic chain dipoles formed from off-centre Pb/La and coupled Ti/Zr displacements. The correlation length along the chain of these 1-d dipoles can, in principle, be determined from the width of the observed {111}* diffuse sheets in reciprocal space and is estimated to be at least 2-3 nm. The primary role of the dopant La ions appears to be to set up random local strain fields preventing the condensation of long wavelength homogeneous strain distortions of the unit cell thereby suppressing transverse correlations of the fundamental chain dipoles and the development of macro-, or even nano-scale, ordered ferroelectric domain state/s in the absence of an applied external electric field. - Graphical abstract: Shows a plausible model for the nano-scale polar ordering of the PLZT (7.5/65/35 and 7.0/60/40) transparent ferroelectric samples in a single layer of the average cubic structure normal to a [110] direction. The fundamental dipolar units in these materials correspond to highly anisotropic chain dipoles formed from off-centre Pb and coupled Ti/Zr displacements

  8. Structural plays in Ellesmerian sequence and correlative strata of the National Petroleum Reserve, Alaska

    Science.gov (United States)

    Moore, Thomas E.; Potter, Christopher J.

    2003-01-01

    Reservoirs in deformed rocks of the Ellesmerian sequence in southern NPRA are assigned to two hydrocarbon plays, the Thrust-Belt play and the Ellesmerian Structural play. The two plays differ in that the Thrust-Belt play consists of reservoirs located in allochthonous strata in the frontal part of the Brooks Range fold-and-thrust belt, whereas those of the Ellesmerian Structural play are located in autochthonous or parautochthonous strata at deeper structural levels north of the Thrust-Belt play. Together, these structural plays are expected to contain about 3.5 TCF of gas but less than 6 million barrels of oil. These two plays are analyzed using a two-stage deformational model. The first stage of deformation occurred during the Neocomian, when distal strata of the Ellesmerian sequence were imbricated and assembled into deformational wedges emplaced northward onto regionally south-dipping authochon at 140-120 Ma. In the mid-Cretaceous following cessation of the deformation, the Colville basin, the foreland basin to the orogen, was filled with a thick clastic succession. During the second stage of deformation at about 60 Ma (early Tertiary), the combined older orogenic belt-foreland basin system was involved in another episode of north-vergent contractional deformation that deformed pre-existing stratigraphic and structurally trapped reservoir units, formed new structural traps, and caused significant amounts of uplift, although the amount of shortening was relatively small in comparison to the first episode of deformation. Hydrocarbon generation from source strata (Shublik Formation, Kingak Shale, and Otuk Formation) and migration into stratigraphic traps occurred primarily by sedimentary burial principally between 100-90 Ma, between the times of the two episodes of deformation. Subsequent burial caused deep stratigraphic traps to become overmature, cracking oil to gas, and some new generation to begin progressively higher in the section. Structural disruption of the traps in the Early Tertiary is hypothesized to have released sequestered hydrocarbons and caused remigration into newly formed structural traps formed at higher structural levels. Because of the generally high maturation of the Colville basin at the time of the deformation and remigration, most of the hydrocarbons available to fill traps were gas. In the the Thrust-Belt play, the primary reservoir lithology is expected to be dolomitic carbonate rocks of the Lisburne Group, which contain up to 15% porosity. Antiformal stacks of imbricated Lisburne Group strata form the primary trapping configuration, with chert and shale of the overlying Etivluk Group forming seals on closures. Traps are expected to have been charged primarily with remigrated gas, but oil generated from local sources in the Otuk Formation may have filled some traps at high structural levels. The timing for migration of gas into traps is excellent, but only moderate for oil because peak oil generation for the play as a whole occurred 30 to 40 m.y. before trap formation. Reservoir and seal quality in the play are questionable, reducing the likelyhood of hydrocarbon accumulations being present in the play. Our analysis suggests that the play will hold 5.7 million barrels of technically recoverable oil and 1.5 TCF gas (mean values). In the Ellesmerian Stuctural play, the primary reservoir lithologies will be dolomitic carbonate rocks of the Lisburne Group and, less likely, clastic units in the Ellesmerian sequence. Traps in the play are anticlinal closures caused by small amounts of strain in the footwall below the basal detachment for most early Tertiary thrusting. Because these traps lie beneath the main source rock units (Shublik, Kingak, lower Brookian sequence), reservoirs that are juxtaposed by faulting against source-rock units are expected to have the most favorable migration pathways. The charge will be primarily remigrated gas; no oil is expected because of the great depths (15,000 to 26,000 ft) and consequent high thermal maturity of this play. Although the the probability of charge an

  9. 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.

  10. Crystallization and preliminary X-ray data analysis of a DJ-1 homologue from Arabidopsis thaliana (AtDJ-1D).

    Science.gov (United States)

    Seo, Kyung Hye; Zhuang, Ningning; Cha, Joon-Yung; Son, Daeyoung; Lee, Kon Ho

    2012-01-01

    A DJ-1 homologue protein from Arabidopsis thaliana (AtDJ-1D) belongs to the DJ-1/ThiJ/Pfpl superfamily and contains two tandem arrays of DJ-1-like sequences, but no structural information is available to date for this protein. AtDJ-1D was expressed in Escherichia coli, purified and crystallized for structural analysis. A crystal of AtDJ-1D was obtained by the hanging-drop vapour-diffusion method using 0.22 M NaCl, 0.1 M bis-tris pH 6.5, 21% polyethylene glycol 3350. AtDJ-1D crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 56.78, b = 75.21, c = 141.68 Å, ? = 96.87°, and contained a trimer in the asymmetric unit. Diffraction data were collected to 2.05 Å resolution. The structure of AtDJ-1D has been determined using the multiple-wavelength anomalous dispersion (MAD) method. PMID:22232184

  11. Sequences of three molluscan 5 S ribosomal RNAs confirm the validity of a dynamic secondary structure model.

    OpenAIRE

    Fang, B L; DE BAERE, R.; VANDENBERGHE, A; De Wachter, R.

    1982-01-01

    The collection of known 5 S rRNA primary structures is enriched with the sequences from three mollusca, the snails Helix pomatia and Arion rufus, and the mussel Mytilus edulis. The three sequences can be fitted in a five-helix secondary structure model previously shown (De Wachter et al. (1982) Biochimie 64, 311-329) to apply to all 5 S RNAs regardless of their origin. One of the helices in this model can undergo a bulge-internal loop transition. Within the metazoan kingdom, the dimensions of...

  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. Transcriptome sequencing of purple petal spot region in tree peony reveals differentially expressed anthocyanin structural genes

    Science.gov (United States)

    Zhang, Yanzhao; Cheng, Yanwei; Ya, Huiyuan; Xu, Shuzhen; Han, Jianming

    2015-01-01

    The pigmented cells in defined region of a petal constitute the petal spots. Petal spots attract pollinators and are found in many angiosperm families. Several cultivars of tree peony contain a single red or purple spot at the base of petal that makes the flower more attractive for the ornamental market. So far, the understanding of the molecular mechanism of spot formation is inadequate. In this study, we sequenced the transcriptome of the purple spot and the white non-spot of tree peony flower. We assembled and annotated 67,892 unigenes. Comparative analyses of the two transcriptomes showed 1,573 differentially expressed genes, among which 933 were up-regulated, and 640 were down-regulated in the purple spot. Subsequently, we examined four anthocyanin structural genes, including PsCHS, PsF3?H, PsDFR, and PsANS, which expressed at a significantly higher level in the purple spot than in the white non-spot. We further validated the digital expression data using quantitative real-time PCR. Our result uncovered transcriptome variance between the spot and non-spot of tree peony flower, and revealed that the co-expression of four anthocyanin structural genes was responsible for spot pigment in tree peony. The data will further help to unravel the genetic mechanism of peony flower spot formation. PMID:26583029

  14. The Pollino Seismic Sequence: Activated Graben Structures in a Seismic Gap

    Science.gov (United States)

    Rößler, Dirk; Passarelli, Luigi; Govoni, Aladino; Bindi, Dino; Cesca, Simone; Hainzl, Sebatian; Maccaferri, Francesco; Rivalta, Eleonora; Woith, Heiko; Dahm, Torsten

    2015-04-01

    The Mercure Basin (MB) and the Castrovillari Fault (CF) in the Pollino range (Southern Apennines, Italy) represent one of the most prominent seismic gaps in the Italian seismic catalogue, with no M>5.5 earthquakes during the last centuries. In historical times several swarm-like seismic sequences occurred in the area including two intense swarms within the past two decades. The most energetic one started in 2010 and has been still active in 2014. The seismicity culminated in autumn 2012 with a M=5 event on 25 October. The range hosts a number of opposing normal faults forming a graben-like structure. Their rheology and their interactions are unclear. Current debates include the potential of the MB and the CF to host large earthquakes and the style of deformation. Understanding the seismicity and the behaviour of the faults is necessary to assess the tectonics and the seismic hazard. The GFZ German Research Centre for Geosciences and INGV, Italy, have jointly monitored the ongoing seismicity using a small-aperture seismic array, integrated in a temporary seismic network. Based on this installation, we located more than 16,000 local earthquakes that occurred between November 2012 and September 2014. Here we investigate quantitatively all the phases of the seismic sequence starting from January 2010. Event locations along with moment tensor inversion constrain spatially the structures activated by the swarm and the migration pattern of the seismicity. The seismicity forms clusters concentrated within the southern part of the MB and along the Pollino Fault linking MB and CF. Most earthquakes are confined to the upper 10 km of the crust in an area of ~15x15 km2. However, sparse seismicity at depths between 15 and 20 km and moderate seismicity further north with deepening hypocenters also exist. In contrast, the CF appears aseismic; only the northern part has experienced micro-seismicity. The spatial distribution is however more complex than the major tectonic structures mapped for the area. Consistent with mapped faults, the seismicity interested both eastwards and westwards dipping normal faults that define the geometry of seismically active graben-like structures. At least one cluster shows an additional spatio-temporal migration with spreading hypocentres similar to other swarm areas with fluid-triggering mechanisms. The static Coulomb stress change transferred by the largest shock onto the swarm area and on the CF cannot explain the observed high seismicity rate. We study the evolution of the frequency-size distribution of the events and the seismicity rate changes. We find that the majority of the earthquakes cannot be justified as aftershocks (directly related to the tectonics or to earthquake-earthquake interaction) and are best explained by an additional forcing active over the entire sequence. Our findings are consistent with the action of fluids (e.g. pore-pressure diffusion) triggering seismicity on pre-loaded faults. Additional aseismic release of tectonic strain by transient, slow slip is also consistent with our analysis. Analysis of deformation time series may clarify this point in future studies.

  15. 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

  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. Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA.

    Science.gov (United States)

    Lavender, Christopher A; Lorenz, Ronny; Zhang, Ge; Tamayo, Rita; Hofacker, Ivo L; Weeks, Kevin M

    2015-05-01

    Discovery and characterization of functional RNA structures remains challenging due to deficiencies in de novo secondary structure modeling. Here we describe a dynamic programming approach for model-free sequence comparison that incorporates high-throughput chemical probing data. Based on SHAPE probing data alone, ribosomal RNAs (rRNAs) from three diverse organisms--the eubacteria E. coli and C. difficile and the archeon H. volcanii--could be aligned with accuracies comparable to alignments based on actual sequence identity. When both base sequence identity and chemical probing reactivities were considered together, accuracies improved further. Derived sequence alignments and chemical probing data from protein-free RNAs were then used as pseudo-free energy constraints to model consensus secondary structures for the 16S and 23S rRNAs. There are critical differences between these experimentally-informed models and currently accepted models, including in the functionally important neck and decoding regions of the 16S rRNA. We infer that the 16S rRNA has evolved to undergo large-scale changes in base pairing as part of ribosome function. As high-quality RNA probing data become widely available, structurally-informed sequence alignment will become broadly useful for de novo motif and function discovery. PMID:25992778

  18. A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution

    Science.gov (United States)

    Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

    2013-01-01

    Motivations: The design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e. a random seed is progressively adapted to acquire the desired folding properties) and more importantly do not allow the user to control explicitly the nucleotide distribution such as the GC-content in their sequences. However, the latter is an important criterion for large-scale applications as it could presumably be used to design sequences with better transcription rates and/or structural plasticity. Results: In this article, we introduce IncaRNAtion, a novel algorithm to design RNA sequences folding into target secondary structures with a predefined nucleotide distribution. IncaRNAtion uses a global sampling approach and weighted sampling techniques. We show that our approach is fast (i.e. running time comparable or better than local search methods), seedless (we remove the bias of the seed in local search heuristics) and successfully generates high-quality sequences (i.e. thermodynamically stable) for any GC-content. To complete this study, we develop a hybrid method combining our global sampling approach with local search strategies. Remarkably, our glocal methodology overcomes both local and global approaches for sampling sequences with a specific GC-content and target structure. Availability: IncaRNAtion is available at csb.cs.mcgill.ca/incarnation/ Contact: jeromew@cs.mcgill.ca or yann.ponty@lix.polytechnique.fr Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:23812999

  19. 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.

  20. Influence of the sequence on the ab initio band structures of single and double stranded DNA models

    Science.gov (United States)

    Bogár, Ferenc; Bende, Attila; Ladik, János

    2014-06-01

    The solid state physical approach is widely used for the characterization of electronic properties of DNA. In the simplest case the helical symmetry is explicitly utilized with a repeat unit containing only a single nucleotide or nucleotide pair. This model provides a band structure that is easily interpretable and reflects the main characteristic features of the single nucleotide or a nucleotide pair chain, respectively. The chemical variability of the different DNA chains is, however, almost completely neglected in this way. In the present work we have investigated the effect of the different sequences on the band structure of periodic DNA models. For this purpose we have applied the Hartree-Fock crystal orbital method for single and double stranded DNA chains with two different subsequent nucleotides in the repeat unit of former and two different nucleotide pairs in the latter case, respectively. These results are compared to simple helical models with uniform sequences. The valence and conduction bands related to the stacked nucleotide bases of single stranded DNA built up only from guanidine as well as of double stranded DNA built up only from guanidine-cytidine pairs showed special properties different from the other cases. Namely, they had higher conduction and lower valence band positions and this way larger band gaps and smaller widths of these bands. With the introduction of non-uniform guanidine containing sequences band structures became more similar to each other and to the band structures of other sequences without guanidine. The maximal bandwidths of the non-uniform sequences are considerably smaller than in the case of uniform sequences implying smaller charge carrier mobilities both in the conduction and valence bands.

  1. 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.

  2. 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

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

    OpenAIRE

    Beeck, Benjamin; Cameron, Robert H.; Reiners, Ansgar; Schüssler, 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...

  4. Structural variation discovery in the cancer genome using next generation sequencing: computational solutions and perspectives.

    Science.gov (United States)

    Liu, Biao; Conroy, Jeffrey M; Morrison, Carl D; Odunsi, Adekunle O; Qin, Maochun; Wei, Lei; Trump, Donald L; Johnson, Candace S; Liu, Song; Wang, Jianmin

    2015-03-20

    Somatic Structural Variations (SVs) are a complex collection of chromosomal mutations that could directly contribute to carcinogenesis. Next Generation Sequencing (NGS) technology has emerged as the primary means of interrogating the SVs of the cancer genome in recent investigations. Sophisticated computational methods are required to accurately identify the SV events and delineate their breakpoints from the massive amounts of reads generated by a NGS experiment. In this review, we provide an overview of current analytic tools used for SV detection in NGS-based cancer studies. We summarize the features of common SV groups and the primary types of NGS signatures that can be used in SV detection methods. We discuss the principles and key similarities and differences of existing computational programs and comment on unresolved issues related to this research field. The aim of this article is to provide a practical guide of relevant concepts, computational methods, software tools and important factors for analyzing and interpreting NGS data for the detection of SVs in the cancer genome. PMID:25849937

  5. A comparison of genomic coding sequences for feather and scale keratins: structural and evolutionary implications.

    OpenAIRE

    Gregg, K; Wilton, S D; Parry, D A; Rogers, G E

    1984-01-01

    DNA sequences have been obtained for embryonic chick feather and scale keratin genes. Strong homologies exist between the protein coding regions of the two gene types and between the deduced amino acid sequences of the keratin proteins. Scale keratins are larger than feather keratins and the size difference is mainly attributable to four 13-amino acid repeats between residues 77 and 128 which compose a peptide sequence rich in glycine and tyrosine. The strong similarities between the two pept...

  6. Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

    DEFF Research Database (Denmark)

    McCormack, John E.; Maley, James M.; Hird, Sarah M.; Derryberry, Elizabeth P.; Graves, Gary R.; Brumfield, Robb T.

    2012-01-01

    Next generation sequencing (NGS) technologies are revolutionizing many biological disciplines but have been slow to take root in phylogeography. This is partly due to the difficulty of using NGS to sequence orthologous DNA fragments for many individuals at low cost. We explore cases of recent divergence in four phylogenetically diverse avian systems using a method for quick and cost-effective generation of primary DNA sequence data using pyrosequencing. NGS data were processed using an analytica...

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

    OpenAIRE

    Samah. G. Babiker; Yong Shuai

    2012-01-01

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

  8. Single-chain structure of human ceruloplasmin: the complete amino acid sequence of the whole molecule.

    OpenAIRE

    Takahashi, N; Ortel, T.L.; Putnam, F. W.

    1984-01-01

    We have determined the amino acid sequence of the amino-terminal 67,000-dalton (67-kDa) fragment of human ceruloplasmin and have established overlapping sequences between the 67-kDa and 50-kDa fragments and between the 50-kDa and 19-kDa fragments. The 67-kDa fragment contains 480 amino acid residues and three glucosamine oligosaccharides. These results together with our previous sequence data for the 50-kDa and 19-kDa fragments complete the amino acid sequence of human ceruloplasmin. The poly...

  9. 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.

  10. Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment-based local and energy-based nonlocal profiles.

    Science.gov (United States)

    Li, Zhixiu; Yang, Yuedong; Faraggi, Eshel; Zhan, Jian; Zhou, Yaoqi

    2014-10-01

    Locating sequences compatible with a protein structural fold is the well-known inverse protein-folding problem. While significant progress has been made, the success rate of protein design remains low. As a result, a library of designed sequences or profile of sequences is currently employed for guiding experimental screening or directed evolution. Sequence profiles can be computationally predicted by iterative mutations of a random sequence to produce energy-optimized sequences, or by combining sequences of structurally similar fragments in a template library. The latter approach is computationally more efficient but yields less accurate profiles than the former because of lacking tertiary structural information. Here we present a method called SPIN that predicts Sequence Profiles by Integrated Neural network based on fragment-derived sequence profiles and structure-derived energy profiles. SPIN improves over the fragment-derived profile by 6.7% (from 23.6 to 30.3%) in sequence identity between predicted and wild-type sequences. The method also reduces the number of residues in low complex regions by 15.7% and has a significantly better balance of hydrophilic and hydrophobic residues at protein surface. The accuracy of sequence profiles obtained is comparable to those generated from the protein design program RosettaDesign 3.5. This highly efficient method for predicting sequence profiles from structures will be useful as a single-body scoring term for improving scoring functions used in protein design and fold recognition. It also complements protein design programs in guiding experimental design of the sequence library for screening and directed evolution of designed sequences. The SPIN server is available at http://sparks-lab.org. PMID:24898915

  11. Direct prediction of profiles of sequences compatible to a protein structure by neural networks with fragment-based local and energy-based nonlocal profiles

    Science.gov (United States)

    Li, Zhixiu; Yang, Yuedong; Faraggi, Eshel; Zhan, Jian; Zhou, Yaoqi

    2014-01-01

    Locating sequences compatible to a protein structural fold is the well-known inverse protein-folding problem. While significant progress has been made, the success rate of protein design remains low. As a result, a library of designed sequences or profile of sequences is currently employed for guiding experimental screening or directed evolution. Sequence profiles can be computationally predicted by iterative mutations of a random sequence to produce energy-optimized sequences, or by combining sequences of structurally similar fragments in a template library. The latter approach is computationally more efficient but yields less accurate profiles than the former because of lacking tertiary structural information. Here we present a method called SPIN that predicts Sequence Profiles by Integrated Neural network based on fragment-derived sequence profiles and structure-derived energy profiles. SPIN improves over the fragment-derived profile by 6.7% (from 23.6% to 30.3%) in sequence identity between predicted and wild-type sequences. The method also reduces the number of residues in low complex regions by 15.7% and has a significant better balance of hydrophilic and hydrophobic residues at protein surfaces. The accuracy of sequence profiles obtained is comparable to those generated from the protein design program RosettaDesign 3.5. This highly efficient method for predicting sequence profiles from structures will be useful as a single-body scoring term for improving scoring functions used in protein design and fold recognition. It also complements protein design programs in guiding experimental design of the sequence library for screening and directed evolution of designed sequences. The SPIN server is available at http://sparks-lab.org. PMID:24898915

  12. 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.

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

    International Nuclear Information System (INIS)

    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

  14. RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins

    OpenAIRE

    Kazan, Hilal; Morris, Quaid

    2013-01-01

    RBPmotif web server (http://www.rnamotif.org) implements tools to identify binding preferences of RNA-binding proteins (RBPs). Given a set of sequences that are known to be bound and unbound by the RBP of interest, RBPmotif provides two types of analysis: (i) de novo motif finding when there is no a priori knowledge on RBP’s binding preferences and (ii) analysis of structure preferences when there is a previously identified sequence motif for the RBP. De novo motif finding is performed with t...

  15. 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 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)

  16. 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.

  17. Next-generation-sequencing-based risk stratification and identification of new genes involved in structural and sequence variations in near haploid lymphoblastic leukemia.

    Science.gov (United States)

    Chen, Cai; Bartenhagen, Christoph; Gombert, Michael; Okpanyi, Vera; Binder, Vera; Röttgers, Silja; Bradtke, Jutta; Teigler-Schlegel, Andrea; Harbott, Jochen; Ginzel, Sebastian; Thiele, Ralf; Fischer, Ute; Dugas, Martin; Hu, Jianda; Borkhardt, Arndt

    2013-06-01

    Near haploidy (23-29 chromosomes) is a numerical cytogenetic aberration in childhood acute lymphoblastic leukemia (ALL) associated with particularly poor outcome. In contrast, high hyperdiploidy (51-67 chromosomes) has a favorable prognosis. Correct classification and appropriate risk stratification of near haploidy is frequently hampered by the presence of apparently high hyperdiploid clones that arise by endoreduplication of the original near haploid clone. We evaluated next-generation-sequencing (NGS) to distinguish between "high hyperdiploid" leukemic clones of near haploid and true high hyperdiploid origin. Five high hyperdiploid ALL cases and the "high hyperdiploid" cell line MHH-CALL-2, derived from a near haploid clone, were tested for uniparental isodisomy. NGS showed that all disomic chromosomes of MHH-CALL-2, but none of the patients, were of uniparental origin, thus reliably discriminating these subtypes. Whole-exome- and whole-genome-sequencing of MHH-CALL-2 revealed homozygous non-synonymous coding mutations predicted to be deleterious for the protein function of 63 genes, among them known cancer-associated genes, such as FANCA, NF1, TCF7L2, CARD11, EP400, histone demethylases, and transferases (KDM6B, KDM1A, PRDM11). Only eight of these were also, but heterozygously, mutated in the high hyperdiploid patients. Structural variations in MHH-CALL-2 include a homozygous deletion (MTAP/CDKN2A/CDKN2B/ANRIL), a homozygous inversion (NCKAP5), and an unbalanced translocation (FAM189A1). Together, the sequence variations provide MHH-CALL-2 with capabilities typically acquired during cancer development, e.g., loss of cell cycle control, enhanced proliferation, lack of DNA repair, cell death evasion, and disturbance of epigenetic gene regulation. Poorer prognosis of near haploid ALL most likely results from full penetrance of a large array of detrimental homozygous mutations. PMID:23508829

  18. The Chinese hamster Alu-equivalent sequence: a conserved highly repetitious, interspersed deoxyribonucleic acid sequence in mammals has a structure suggestive of a transposable element.

    OpenAIRE

    Haynes, S R; Toomey, T. P.; Leinwand, L; Jelinek, W R

    1981-01-01

    A consensus sequence has been determined for a major interspersed deoxyribonucleic acid repeat in the genome of Chinese hamster ovary cells (CHO cells). This sequence is extensively homologous to (i) the human Alu sequence (P. L. Deininger et al., J. Mol. Biol., in press), (ii) the mouse B1 interspersed repetitious sequence (Krayev et al., Nucleic Acids Res. 8:1201-1215, 1980) (iii) an interspersed repetitious sequence from African green monkey deoxyribonucleic acid (Dhruva et al., Proc. Natl...

  19. Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats.

    Science.gov (United States)

    Shen, Z J; Ma, R J; Cai, Z X; Yu, M L; Zhang, Z

    2015-01-01

    The fruit peach originated in China and has a history of domestication of more than 4000 years. Numerous local cultivars were selected during the long course of cultivation, and a great morphological diversity exists. To study the diversity and genetic background of local peach cultivars in China, a set of 158 accessions from different ecological regions, together with 27 modern varieties and 10 wild accessions, were evaluated using 49 simple sequence repeats (SSRs) covering the peach genome. Broad diversity was also observed in local cultivars at the SSR level. A total of 648 alleles were amplified with an average of 13.22 observed alleles per locus. The number of genotypes detected ranged from 9 (UDP96015) to 58 (BPPCT008) with an average of 27.00 genotypes per marker. Eight subpopulations divided by STRUCTURE basically coincided with the dendrogram of genetic relationships and could be explained by the traditional groups. The 8 subpopulations were juicy honey peach, southwestern peach I, wild peach, Buddha peach + southwestern peach II, northern peach, southern crisp peach, ornamental peach, and Prunus davidiana + P. kansuensis. Most modern varieties carried the genetic backgrounds of juicy honey peach and southwestern peach I, while others carried diverse genetic backgrounds, indicating that local cultivars were partly used in modern breeding programs. Based on the traditional evolution pathway, a modified pathway for the development of local peach cultivars in China was proposed using the genetic background of subpopulations that were identified by SSRs. Current status and prospects of utilization of Chinese local peach cultivars were also discussed according to the SSR information. PMID:25729941

  20. Statistical aspects of discerning indel-type structural variation via DNA sequence alignment

    Directory of Open Access Journals (Sweden)

    Wilson Richard K

    2009-08-01

    Full Text Available Abstract Background Structural variations in the form of DNA insertions and deletions are an important aspect of human genetics and especially relevant to medical disorders. Investigations have shown that such events can be detected via tell-tale discrepancies in the aligned lengths of paired-end DNA sequencing reads. Quantitative aspects underlying this method remain poorly understood, despite its importance and conceptual simplicity. We report the statistical theory characterizing the length-discrepancy scheme for Gaussian libraries, including coverage-related effects that preceding models are unable to account for. Results Deletion and insertion statistics both depend heavily on physical coverage, but otherwise differ dramatically, refuting a commonly held doctrine of symmetry. Specifically, coverage restrictions render insertions much more difficult to capture. Increased read length has the counterintuitive effect of worsening insertion detection characteristics of short inserts. Variance in library insert length is also a critical factor here and should be minimized to the greatest degree possible. Conversely, no significant improvement would be realized in lowering fosmid variances beyond current levels. Detection power is examined under a straightforward alternative hypothesis and found to be generally acceptable. We also consider the proposition of characterizing variation over the entire spectrum of variant sizes under constant risk of false-positive errors. At 1% risk, many designs will leave a significant gap in the 100 to 200 bp neighborhood, requiring unacceptably high redundancies to compensate. We show that a few modifications largely close this gap and we give a few examples of feasible spectrum-covering designs. Conclusion The theory resolves several outstanding issues and furnishes a general methodology for designing future projects from the standpoint of a spectrum-wide constant risk.

  1. 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.

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

    DEFF Research Database (Denmark)

    Welinder, K G; Jespersen, H M; Walther-Rasmussen, J; Skjødt, K

    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 r...

  3. Structural repertoire in VH pseudogenes of immunoglobulins: comparison with human germline genes and human amino acid sequences.

    Science.gov (United States)

    Vargas-Madrazo, E; Almagro, J C; Lara-Ochoa, F

    1995-02-10

    In the pool of human immunoglobulin VH gene segments, pseudogenes amount to roughly 30% of the total number of genes. Some of them are highly conserved among unrelated individuals. These facts suggest a possible functional role for pseudogenes in the human immune response diversity. This paper intends to provide additional information about the structure of VH pseudogene sequences to evaluate the possible role of pseudogenes in the immune response. Mutations capable of altering framework stability in human VH pseudogenes were analyzed. Results indicate that VH pseudogenes are about 14 times as divergent as human VH functional germline genes on the one hand, and four times as divergent in the case of human VH amino acid sequences on the other. The high number of disruptive mutations in pseudogenes is an expected result because of the lack of functionality of these genes. In the second part of the work we analyze whether or not the same takes place in the positions that determine the existence of canonical structures in the hypervariable loops in VH pseudogenes. An extension of such analysis is applied to all species with reported VH pseudogenes. In contrast with results concerning framework positions, 69% of known human VH pseudogenes have canonical structures in the first hypervariable loop, while 48% do so in the second one. Comparison of these results with those found in human VH functional germline genes and human VH amino acid sequences shows that in the former as many as 100% and in the latter 96% have canonical structures. In VH amino acid sequences the result is similar to pseudogenes for H1. For H2, such value lies between the percentage of germline genes (96%) and the percentage of pseudogenes (48%). The possible significance of the existence of canonical structures in the hypervariable loops of VH pseudogenes is discussed. PMID:7853406

  4. Blood flow quantification using 1D CFD parameter identification

    Science.gov (United States)

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

    2014-03-01

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

  5. 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.)

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

    Energy Technology Data Exchange (ETDEWEB)

    Aboul-ela, F.M.

    1987-12-01

    Thermodynamic parameters for double strand formation have been measured for the twenty-five DNA double helices made by mixing deoxyoligonucleotides of the sequence dCA/sub 3/XA/sub 3/G with the complement dCT/sub 3/YT/sub 3/G. 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)centerreverse arrowdot)C base pair become more stable than those containing only A)centerreverse arrowdot)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)centerreverse arrowdot)C )succ) I)centerreverse arrowdot) A)succ) I)centerreverse arrowdot)T approx. I)centerreverse arrowdot)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))centerreverse arrowdot)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.

  7. Sequence and secondary structure of the colicin fragment of Bacillus stearothermophilus 16S ribosomal RNA.

    OpenAIRE

    Van Charldorp, R; Van Kimmenade, A M; Van Knippenberg, P H

    1981-01-01

    The sequence and the position of post-transcriptionally modified residues of the 3' -terminal end of Bacillus stearothermophilus 16S ribosomal RNA have been determined from the fragment that is cleaved off by bacteriocin treatment. The fragment contains 52 nucleotides, as compared to the 49 nucleotides of the corresponding fragment from E. coli ribosomes, The additional nucleotides are present in the sequence UCU very next to the 3' -terminus as was published earlier (1). The remainder of the...

  8. Genetic structuring and differentiation of Echinococcus multilocularis in Slovakia assessed by sequencing and isoenzyme studies

    DEFF Research Database (Denmark)

    Snabel, V.; Miterpakova, M.; D'Amelio, S.; Busi, M.; Bartkova, D.; Turcekova, L.; Maddox-Hyttel, Charlotte; Skuce, P.; Dubinsky, P.

    2006-01-01

    Nucleotide sequencing of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene and isoenzyme analysis were used to survey the genetic variability in Echinococcus multilocularis populations from Slovakia. A sample of 12 isolates acquired from 10 different districts from red foxes exhibited identical sequences. Compared with the previously described E. multilocularis variants, one base substitution was consistently observed relative to the M 1 variant (detected in China, Alaska, North Americ...

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

    OpenAIRE

    Manzini Giovanni; Greco Valentina; Giancarlo Raffaele; Ferragina Paolo; Valiente Gabriel

    2007-01-01

    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 ...

  10. Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes

    OpenAIRE

    Selvaraj S; Jayaram B; Saranya N; Gromiha M; Fukui Kazuhiko

    2011-01-01

    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...

  11. Sequence and structural determinants of strand swapping in cadherin domains: Do all cadherins bind through the same adhesive interface?

    OpenAIRE

    Posy, Shoshana; Shapiro, Lawrence; Honig, Barry

    2008-01-01

    Cadherins are cell surface adhesion proteins important for tissue development and integrity. Type I and type II, or “classical”, cadherins form adhesive dimers via an interface formed through the exchange, or “swapping”, of the N-terminal ?-strands from their membrane-distal EC1 domains. Here we ask which sequence and structural features in EC1 domains are responsible for ?-strand swapping and whether members of other cadherin families also form similar strand-swapped binding interfaces. We f...

  12. Structural Analysis of HMGD-DNA Complexes Reveal Influence of Intercalation on Sequence Selectivity and DNA Bending

    OpenAIRE

    Churchill, Mair E. A.; Klass, Janet; Zoetewey, David L.

    2010-01-01

    The ubiquitous eukaryotic High-Mobility-Group-Box (HMGB) chromosomal proteins promote many chromatin-mediated cellular activities through their non-sequence-specific binding and bending of DNA. Minor groove DNA binding by the HMG box results in substantial DNA bending toward the major groove owing to electrostatic interactions, shape complementarity and DNA intercalation that occurs at two sites. Here, the structures of the complexes formed with DNA by a partially DNA intercalation-deficient ...

  13. 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; Yu, Shukun; Finnie, Christine; Svensson, Birte; Larsen, Sine

    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 Gracila...

  14. Intelligent Access to Sequence and Structure Databases (IASSD) ? an interface for accessing information from major web databases

    OpenAIRE

    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 descr...

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

    OpenAIRE

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

    2007-01-01

    Abstract Background Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to known structures is available. Structural properties are also routinely used in protein analysis even when homology is available, largely because homology modelling is lower throughput than, say, secondary structure prediction. Nonetheless, predictors of secondary s...

  16. Multidimensional Inversion of MT data from Krýsuvík High Temperature Geothermal Field, SW Iceland, and study of how 1D and 2D inversion can reproduce a given 2D/3D resistivity structure using synthetic MT data

    OpenAIRE

    Lemma Didana, Yohannes, 1972-

    2010-01-01

    Electromagnetic (EM) methods are frequently used in the exploration of geothermal resources for determining the spatial distribution of electrical conductivity. Of the various EM methods, magnetotelluric (MT) method was found to be the most effective in defining a conductive reservoir at a depth exceeding 1 km overlain by a larger and more conductive clay cap. The two main objectives of this study are: firstly to explore how 1D and 2D inversion can reproduce a given 2D and 3D resistivity stru...

  17. High throughput sequencing analysis of the joint effects of BDE209-Pb on soil bacterial community structure.

    Science.gov (United States)

    Zhang, Wei; Chen, Lei; Zhang, Rong; Lin, Kuangfei

    2016-01-15

    Decabromodiphenyl ether (BDE209) and Lead (Pb) are the main pollutants at e-waste recycling sites (EWRSs). However, the impact on soil microorganism of joint exposure to the two chemicals remains almost unknown. Therefore, the indoor incubation tests were performed to determine the response of soil microbial biomass and activity as well as bacterial community structure in the presence of the two chemicals during 60 d incubation period. The results indicated that after Pb alone or BDE209-Pb exposure, soil microbial biomass C (Cmic) was significantly lower (psoil basal respiration (SBR) and metabolic quotient (qCO2) were enhanced, while BDE209 barely resulted in significant influence (p>0.05). 16S rRNA gene sequencing on the Illumina MiSeq platform demonstrated that a total 49,405 valid sequences widely represented the diversity of microbial community. Sequence analyses at phylum and genus taxonomic levels illustrated that 11 identified phyla and 297 genera were observed among all the soil samples, and the contaminants input had affected bacterial community structure, suggesting that Proteobacteria, Actinobacteria and Acidobacteria were the dominant phyla, and the genera Massilia and Bacillus were enriched in contaminated soil. BDE209 exposure alone in all the samples indicated a more similar community structure compared to the control. The results of these observations have provided a better understanding of ecotoxicological effects of BDE209 and Pb joint exposure on indigenous microorganisms in soil at EWRSs. PMID:26342145

  18. Sequence and structure comparison suggest that methionine aminopeptidase, prolidase, aminopeptidase P, and creatinase share a common fold.

    OpenAIRE

    Bazan, J F; Weaver, L H; Roderick, S L; R. Huber; Matthews, B. W.

    1994-01-01

    Amino acid sequence comparison suggests that the structure of Escherichia coli methionine aminopeptidase (EC 3.4.11.18) and the C-terminal domain of Pseudomonas putida creatinase (EC 3.5.3.3) are related. A detailed comparison of the three-dimensional folds of the two enzymes confirms this homology: with an approximately 260-residue chain segment, 218 C alpha atoms of the structures superimpose within 2.5 A; only 41 of these overlapping positions (i.e., 19%) feature identical amino acids in t...

  19. 1D WCIP and FEM hybridization

    OpenAIRE

    Girard, Caroline; Raveu, Nathalie; Perrussel, Ronan; Li, Jia; Lanteri, Stéphane

    2012-01-01

    The hybridization between two numerical methods, the 1D Wave Concept Iterative Procedure (WCIP) and the 2D Finite Element Method (FEM), is introduced. Preliminary numerical results are also presented.

  20. GTPase domains of ras p21 oncogene protein and elongation factor Tu: analysis of three-dimensional structures, sequence families, and functional sites.

    OpenAIRE

    Valencia, A.; Kjeldgaard, M.; Pai, E.F.; Sander, C

    1991-01-01

    GTPase domains are functional and structural units employed as molecular switches in a variety of important cellular functions, such as growth control, protein biosynthesis, and membrane traffic. Amino acid sequences of more than 100 members of different subfamilies are known, but crystal structures of only mammalian ras p21 and bacterial elongation factor Tu have been determined. After optimal superposition of these remarkably similar structures, careful multiple sequence alignment, and calc...

  1. 75 FR 11072 - Airworthiness Directives; Turbomeca Arriel 1B, 1D, 1D1, and 1S1 Turboshaft Engines

    Science.gov (United States)

    2010-03-10

    ...Arriel 1B, 1D, 1D1, and 1S1 Turboshaft Engines AGENCY: Federal Aviation Administration...Arriel 1B, 1D, 1D1, and 1S1 turboshaft engines. That AD requires initial and repetitive...Arriel 1D, 1D1, and 1S1 turboshaft engines that do not incorporate mod TU 347....

  2. Hfqs in Bacillus anthracis: Role of protein sequence variation in the structure and function of proteins in the Hfq family.

    Science.gov (United States)

    Vrentas, Catherine; Ghirlando, Rodolfo; Keefer, Andrea; Hu, Zonglin; Tomczak, Aurelie; Gittis, Apostolos G; Murthi, Athulaprabha; Garboczi, David N; Gottesman, Susan; Leppla, Stephen H

    2015-11-01

    Hfq proteins in Gram-negative bacteria play important roles in bacterial physiology and virulence, mediated by binding of the Hfq hexamer to small RNAs and/or mRNAs to post-transcriptionally regulate gene expression. However, the physiological role of Hfqs in Gram-positive bacteria is less clear. Bacillus anthracis, the causative agent of anthrax, uniquely expresses three distinct Hfq proteins, two from the chromosome (Hfq1, Hfq2) and one from its pXO1 virulence plasmid (Hfq3). The protein sequences of Hfq1 and 3 are evolutionarily distinct from those of Hfq2 and of Hfqs found in other Bacilli. Here, the quaternary structure of each B. anthracis Hfq protein, as produced heterologously in Escherichia coli, was characterized. While Hfq2 adopts the expected hexamer structure, Hfq1 does not form similarly stable hexamers in vitro. The impact on the monomer-hexamer equilibrium of varying Hfq C-terminal tail length and other sequence differences among the Hfqs was examined, and a sequence region of the Hfq proteins that was involved in hexamer formation was identified. It was found that, in addition to the distinct higher-order structures of the Hfq homologs, they give rise to different phenotypes. Hfq1 has a disruptive effect on the function of E. coli Hfq in vivo, while Hfq3 expression at high levels is toxic to E. coli but also partially complements Hfq function in E. coli. These results set the stage for future studies of the roles of these proteins in B. anthracis physiology and for the identification of sequence determinants of phenotypic complementation. PMID:26271475

  3. DNA sequence, structure, and tyrosine kinase activity of the Drosophila melanogaster Abelson proto-oncogene homolog.

    OpenAIRE

    Henkemeyer, M J; Bennett, R. L.; Gertler, F B; Hoffmann, F M

    1988-01-01

    We report our molecular characterization of the Drosophila melanogaster Abelson gene (abl), a gene in which recessive loss-of-function mutations result in lethality at the pupal stage of development. This essential gene consists of 10 exons extending over 26 kilobase pairs of genomic DNA. The DNA sequence encodes a protein of 1,520 amino acids with strong sequence similarity to the human c-abl proto-oncogene beginning in the type lb 5' exon and extending through the region essential for tyros...

  4. The structural organization and DNA sequence of a wheat histone H4 gene.

    OpenAIRE

    Tabata, T.; Sasaki, K.; Iwabuchi, M

    1983-01-01

    Some wheat histone H4 genes have been cloned from a Charon 4 wheat genomic DNA library using sea urchin histone H4 DNA as a probe. DNA sequence analysis of a cloned gene showed that the deduced amino acid sequence of wheat histone H4 protein was identical to that of pea. The 5' end of wheat histone H4 mRNA was mapped on the cloned gene by the S1-procedure. Southern blotting analysis of the genomic DNA indicated that histone H4 genes were reiterated 100 to 125 times per hexaploid wheat genome.

  5. 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

  6. A three-layered cortical network encodes identity and abstract categorical structure of behavioral sequences as in the primate lateral prefrontal cortex

    OpenAIRE

    Hinaut, Xavier; Dominey, Peter

    2010-01-01

    Categorical encoding is crucial for mastering large bodies of related sensory experiences. Recent single-unit recording studies in the macaque prefrontal cortex have demonstrated two characteristic forms of neural encoding of the sequential structure of the animal's behaviour. One population of neurons encodes the specific behavioural sequences. A second population of neurons encodes the sequence category (e.g. ABAB, AABB or AAAA) and does not differentiate sequences within the category [1]. ...

  7. ``Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence

    Indian Academy of Sciences (India)

    A G De Brevern; C Etchebest; C Benros; S Hazout

    2007-01-01

    The description of protein 3D structures can be performed through a library of 3D fragments, named a structural alphabet. Our structural alphabet is composed of 16 small protein fragments of 5 C in length, called protein blocks (PBs). It allows an efficient approximation of the 3D protein structures and a correct prediction of the local structure. The 72 most frequent series of 5 consecutive PBs, called structural words (SWs) are able to cover more than 90% of the 3D structures. PBs are highly conditioned by the presence of a limited number of transitions between them. In this study, we propose a new method called “pinning strategy” that used this specific feature to predict long protein fragments. Its goal is to define highly probable successions of PBs. It starts from the most probable SW and is then extended with overlapping SWs. Starting from an initial prediction rate of 34.4%, the use of the SWs instead of the PBs allows a gain of 4.5%. The pinning strategy simply applied to the SWs increases the prediction accuracy to 39.9%. In a second step, the sequence-structure relationship is optimized, the prediction accuracy reaches 43.6%.

  8. 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 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.

  9. 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.

  10. NMR study of the structures of repeated sequences, GAGXGA (X = S, Y, V), in Bombyx mori liquid silk.

    Science.gov (United States)

    Suzuki, Yu; Yamazaki, Toshimasa; Aoki, Akihiro; Shindo, Heisaburo; Asakura, Tetsuo

    2014-01-13

    The silk fibroin stored in the silk gland of the Bombyx mori silkworm, called "liquid silk", is spun out and converted into the silk fiber with extremely high strength and high toughness. Therefore it is important to determine the silk structure before spinning called Silk I at an atomic level to clarify the fiber formation mechanism. We proposed the repeated type II ?-turn structure as Silk I in the solid state with the model peptide (AG)15 and several solid state NMR techniques previously. In this paper, the solution structure of native "liquid silk" was determined with solution NMR, especially for tandem repeated sequences with (GAGXGA)n (X = S, Y, V) and GAASGA motifs in the B. mori silk fibroin. The assignment of the (13)C, (15)N, and (1)H solution NMR spectra for the repetitive sequence motifs was achieved, and the chemical shifts were obtained. The program, TALOS-N, to predict the backbone torsion angles from the chemical shifts of proteins was applied to these motifs with (13)C?, (13)C?, (13)CO, (1)H?, (1)HN, and (15)N chemical shifts. The twenty-five best matches of torsion angles (?, ?) were well populated and mainly fell into the regions for typical type II ?-turn structures in the (?, ?) map for the GAGXGA (X = S, Y, V) motifs. In contrast, (?, ?) plots for motif GAASGA were scattered, indicating that the motif is in a disordered structure. Furthermore, inter-residue HN-H? NOE cross peaks between i-th and (i+2)th residues in GAGXGA (X = S, Y, V) motifs were observed, supporting the repeated type II ?-turn structure. Thus, we could show the presence of the repeated type II ?-turn structure in "liquid silk". PMID:24266784

  11. Sequence and structure prediction of RNA-dependent RNA polymerase of lily symptomless virus isolated from L. × 'Casablanca'.

    Science.gov (United States)

    Xu, Pinsan; Li, Huangai; Liu, Jiwen; Luan, Yushi; Yin, Yalei; Bai, Jianfang

    2011-06-01

    The DNA sequence of the RNA-dependent RNA polymerase (RdRp) gene of lily symptomless virus (LSV), a lily-infecting member of the genus Carlavirus, was determined from nine overlapping cDNA fragments of different sizes. The complete sequence of this RdRp gene (HM070294) consisted of 5,847 nucleotides coding for a protein of 220 kDa. It had 97-98% sequence identity with RdRps of other known isolates at both the DNA and the amino acid level. Phylogenetic analysis indicated that this RdRp (designated as RdRp-DL) was closely related to the RdRp of the Korean isolate (AM516059), as well as to the RdRps from Passiflora latent virus (PLV) and Kalanchoe latent virus (KLV) of the genus Carlavirus. Hydrophobic analysis of RdRp-DL revealed a hydrophobic N-terminus and a hydrophilic C-terminus. Helices and Loops were the major secondary structures of RdRp-DL. In addition, RdRp-DL also had three coil structures. Four conserved domains were identified: typoviral methyltransferase, RNA-dependent RNA polymerase, P-loop-containing nucleoside triphosphate hydrolases and carlavirus endopeptidase. A model of the tertiary structure predicted by I-TASSER was obtained for each of these conserved domains. This is the first report of a detailed phylogenetic analysis of LSV RdRp with those of other members of the genus Carlavirus, and the first to predict the domain structures of LSV RdRp. PMID:21409447

  12. Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries

    Directory of Open Access Journals (Sweden)

    Okimoto Ron

    2011-02-01

    Full Text Available Abstract Background Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs to kilobase, and even megabase, sized structural variants (SVs, such as deletions, insertions, inversions, and more complex rearrangements. Although much is known about the extent of SVs in humans and mice, species in which they exert significant effects on phenotypes, very little is known about the extent of SVs in the 2.5-times smaller and less repetitive genome of the chicken. Results We identified hundreds of shared and divergent SVs in four commercial chicken lines relative to the reference chicken genome. The majority of SVs were found in intronic and intergenic regions, and we also found SVs in the coding regions. To identify the SVs, we combined high-throughput short read paired-end sequencing of genomic reduced representation libraries (RRLs of pooled samples from 25 individuals and computational mapping of DNA sequences from a reference genome. Conclusion We provide a first glimpse of the high abundance of small structural genomic variations in the chicken. Extrapolating our results, we estimate that there are thousands of rearrangements in the chicken genome, the majority of which are located in non-coding regions. We observed that structural variation contributes to genetic differentiation among current domesticated chicken breeds and the Red Jungle Fowl. We expect that, because of their high abundance, SVs might explain phenotypic differences and play a role in the evolution of the chicken genome. Finally, our study exemplifies an efficient and cost-effective approach for identifying structural variation in sequenced genomes.

  13. 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.)

  14. 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.

  15. 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.

  16. 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 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

  17. 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

  18. Sequence dependence of ?-hairpin structure: Comparison of a salt bridge and an aromatic interaction

    OpenAIRE

    Kiehna, Sarah E.; Waters, Marcey L.

    2003-01-01

    A comparison of the contributions and position dependence of cross-strand electrostatic and aromatic side-chain interactions to ?-sheet stability has been performed by using nuclear magnetic resonance in a well-folded ?-hairpin peptide of the general sequence XRTVXVdPGOXITQX. Phe–Phe and Glu–Lys pairs were varied at the internal and terminal non–hydrogen-bonded position, and the resulting stability was measured by the effects on ?-hydrogen and aromatic hydrogen chemical shifts. It was determi...

  19. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription

    OpenAIRE

    Kilpinen H; Waszak SM; Gschwind AR; Raghav SK; Witwicki RM; Orioli A; Migliavacca E; Wiederkehr M; Gutierrez-Arcelus M; Panousis NI; Yurovsky A; Lappalainen T; Romano-Palumbo L; Planchon A; Bielser D

    2013-01-01

    DNA sequence variation has been associated with quantitative changes in molecular phenotypes such as gene expression, but its impact on chromatin states is poorly characterized. To understand the interplay between chromatin and genetic control of gene regulation, we quantified allelic variability in transcription factor binding, histone modifications, and gene expression within humans. We found abundant allelic specificity in chromatin and extensive local, short-range, and long-range allelic ...

  20. Developing digital test sequences for through-silicon vias within 3D structures

    OpenAIRE

    Gulbins, M.; Hopsch, F.; Schneider, P.; Straube, B; Vermeiren, W.

    2010-01-01

    Through-silicon vias (TSVs) present new, essential elements within 3D stacked Integrated Circuits (IC). Since they connect different layers of 3D stacks, their proper operation is an essential prerequisite for the system function. In this paper a procedure for deriving local digital test sequences for TSVs is presented. The behavior of TSVs including their typical surrounding circuitry is investigated under the impact of assumed faults using fault simulation. Since a purely digital considerat...

  1. 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.

  2. Quasi-1D parahydrogen in nanopores

    CERN Document Server

    Omiyinka, Tokunbo

    2015-01-01

    The low temperature physics of parahydrogen (ph2) confined in cylindrical channels of diameter of the order of 1 nm is studied theoretically by Quantum Monte Carlo simulations. On varying the attractive strength of the wall of the cylindrical pore, as well as its diameter, the equilibrium phase evolves from a single quasi-1D channel along the axis, to a concentric cylindrical shell. It is found that the quasi-1D system retains a strong propensity to crystallization, even though on weakly attractive substrates quantum fluctuations reduce somewhat such a tendency compared to the purely 1D system. No evidence of a topologically protected superfluid phase (in the Luttinger sense) is observed. Implications on the possible existence of a bulk superfluid phase of parahydrogen are discussed

  3. 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

  4. Molecular evolution and diversity of Conus peptide toxins, as revealed by gene structure and intron sequence analyses.

    Science.gov (United States)

    Wu, Yun; Wang, Lei; Zhou, Maojun; You, Yuwen; Zhu, Xiaoyan; Qiang, Yuanyuan; Qin, Mengying; Luo, Shaonan; Ren, Zhenghua; Xu, Anlong

    2013-01-01

    Cone snails, which are predatory marine gastropods, produce a cocktail of venoms used for predation, defense and competition. The major venom component, conotoxin, has received significant attention because it is useful in neuroscience research, drug development and molecular diversity studies. In this study, we report the genomic characterization of nine conotoxin gene superfamilies from 18 Conus species and investigate the relationships among conotoxin gene structure, molecular evolution and diversity. The I1, I2, M, O2, O3, P, S, and T superfamily precursors all contain three exons and two introns, while A superfamily members contain two exons and one intron. The introns are conserved within a certain gene superfamily, and also conserved across different Conus species, but divergent among different superfamilies. The intronic sequences contain many simple repeat sequences and regulatory elements that may influence conotoxin gene expression. Furthermore, due to the unique gene structure of conotoxins, the base substitution rates and the number of positively selected sites vary greatly among exons. Many more point mutations and trinucleotide indels were observed in the mature peptide exon than in the other exons. In addition, the first example of alternative splicing in conotoxin genes was found. These results suggest that the diversity of conotoxin genes has been shaped by point mutations and indels, as well as rare gene recombination or alternative splicing events, and that the unique gene structures could have made a contribution to the evolution of conotoxin genes. PMID:24349297

  5. Structural properties and evolutionary relationships of PspA, a surface protein of Streptococcus pneumoniae, as revealed by sequence analysis.

    OpenAIRE

    Yother, J; Briles, D E

    1992-01-01

    Analysis of the sequence for the gene encoding PspA (pneumococcal surface protein A) of Streptococcus pneumoniae revealed the presence of four distinct domains in the mature protein. The structure of the N-terminal half of PspA was highly consistent with that of an alpha-helical coiled-coil protein. The alpha-helical domain was followed by a proline-rich domain (with two regions in which 18 of 43 and 5 of 11 of the residues are prolines) and a repeat domain consisting of 10 highly conserved 2...

  6. Differential binding of quadruplex structures of muscle-specific genes regulatory sequences by MyoD, MRF4 and myogenin

    OpenAIRE

    Yafe, Anat; Shklover, Jeny; Weisman-Shomer, Pnina; Bengal, Eyal; Fry, Michael

    2008-01-01

    Four myogenic regulatory factors (MRFs); MyoD, Myf-5, MRF4 and Myogenin direct muscle tissue differentiation. Heterodimers of MRFs with E-proteins activate muscle-specific gene expression by binding to E-box motifs d(CANNTG) in their promoters or enhancers. We showed previously that in contrast to the favored binding of E-box by MyoD-E47 heterodimers, homodimeric MyoD associated preferentially with quadruplex structures of regulatory sequences of muscle-specific genes. To inquire whether othe...

  7. DNA breaks and repair in interstitial telomere sequences: Influence of chromatin structure; Etude des cassures de l'ADN et des mecanismes de reparation dans les sequences telomeriques interstitielles: Influence de la structure chromatinienne

    Energy Technology Data Exchange (ETDEWEB)

    Revaud, D.

    2009-06-15

    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)

  8. Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

    Directory of Open Access Journals (Sweden)

    Leitner Dietmar

    2005-04-01

    Full Text Available Abstract Background A reliable prediction of the Xaa-Pro peptide bond conformation would be a useful tool for many protein structure calculation methods. We have analyzed the Protein Data Bank and show that the combined use of sequential and structural information has a predictive value for the assessment of the cis versus trans peptide bond conformation of Xaa-Pro within proteins. For the analysis of the data sets different statistical methods such as the calculation of the Chou-Fasman parameters and occurrence matrices were used. Furthermore we analyzed the relationship between the relative solvent accessibility and the relative occurrence of prolines in the cis and in the trans conformation. Results One of the main results of the statistical investigations is the ranking of the secondary structure and sequence information with respect to the prediction of the Xaa-Pro peptide bond conformation. We observed a significant impact of secondary structure information on the occurrence of the Xaa-Pro peptide bond conformation, while the sequence information of amino acids neighboring proline is of little predictive value for the conformation of this bond. Conclusion In this work, we present an extensive analysis of the occurrence of the cis and trans proline conformation in proteins. Based on the data set, we derived patterns and rules for a possible prediction of the proline conformation. Upon adoption of the Chou-Fasman parameters, we are able to derive statistically relevant correlations between the secondary structure of amino acid fragments and the Xaa-Pro peptide bond conformation.

  9. High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans.

    Science.gov (United States)

    Lipovich, Leonard; Hou, Zhuo-Cheng; Jia, Hui; Sinkler, Christopher; McGowen, Michael; Sterner, Kirstin N; Weckle, Amy; Sugalski, Amara B; Pipes, Lenore; Gatti, Domenico L; Mason, Christopher E; Sherwood, Chet C; Hof, Patrick R; Kuzawa, Christopher W; Grossman, Lawrence I; Goodman, Morris; Wildman, Derek E

    2016-02-01

    The human brain and human cognitive abilities are strikingly different from those of other great apes despite relatively modest genome sequence divergence. However, little is presently known about the interspecies divergence in gene structure and transcription that might contribute to these phenotypic differences. To date, most comparative studies of gene structure in the brain have examined humans, chimpanzees, and macaque monkeys. To add to this body of knowledge, we analyze here the brain transcriptome of the western lowland gorilla (Gorilla gorilla gorilla), an African great ape species that is phylogenetically closely related to humans, but with a brain that is approximately one-third the size. Manual transcriptome curation from a sample of the planum temporale region of the neocortex revealed 12 protein-coding genes and one noncoding-RNA gene with exons in the gorilla unmatched by public transcriptome data from the orthologous human loci. These interspecies gene structure differences accounted for a total of 134 amino acids in proteins found in the gorilla that were absent from protein products of the orthologous human genes. Proteins varying in structure between human and gorilla were involved in immunity and energy metabolism, suggesting their relevance to phenotypic differences. This gorilla neocortical transcriptome comprises an empirical, not homology- or prediction-driven, resource for orthologous gene comparisons between human and gorilla. These findings provide a unique repository of the sequences and structures of thousands of genes transcribed in the gorilla brain, pointing to candidate genes that may contribute to the traits distinguishing humans from other closely related great apes. J. Comp. Neurol. 524:288-308, 2016. © 2015 Wiley Periodicals, Inc. PMID:26132897

  10. Sandia reactor kinetics codes: SAK and PK1D

    International Nuclear Information System (INIS)

    The Sandia Kinetics code (SAK) is a one-dimensional coupled thermal-neutronics transient analysis code for use in simulation of reactor transients. The time-dependent cross section routines allow arbitrary time-dependent changes in material properties. The one-dimensional heat transfer routines are for cylindrical geometry and allow arbitrary mesh structure, temperature-dependent thermal properties, radiation treatment, and coolant flow and heat-transfer properties at the surface of a fuel element. The Point Kinetics 1 Dimensional Heat Transfer Code (PK1D) solves the point kinetics equations and has essentially the same heat-transfer treatment as SAK. PK1D can address extended reactor transients with minimal computer execution time

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

    OpenAIRE

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

    2012-01-01

    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...

  12. 1d WCIP and FEM hybridization

    OpenAIRE

    Girard, Caroline; Raveu, Nathalie; Lanteri, Stéphane; Perrussel, Ronan

    2012-01-01

    An hybridization between two numerical methods, the 1d Wave Concept Iterative Procedure (WCIP) and the 2d Finite Element Method (FEM), is developed. Using two examples, comparisons are provided between the new hybrid method and an analytic solution, when available, or the WCIP alone.

  13. 1-D equations of radiation hydrodynamics

    International Nuclear Information System (INIS)

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

  14. 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.

  15. 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.

  16. In vivo 1D and 2D correlation MR spectroscopy of the soleus muscle at 7T

    Science.gov (United States)

    Ramadan, Saadallah; Ratai, Eva-Maria; Wald, Lawrence L.; Mountford, Carolyn E.

    2010-05-01

    AimThis study aims to (1) undertake and analyse 1D and 2D MR correlation spectroscopy from human soleus muscle in vivo at 7T, and (2) determine T1 and T2 relaxation time constants at 7T field strength due to their importance in sequence design and spectral quantitation. MethodSix healthy, male volunteers were consented and scanned on a 7T whole-body scanner (Siemens AG, Erlangen, Germany). Experiments were undertaken using a 28 cm diameter detunable birdcage coil for signal excitation and an 8.5 cm diameter surface coil for signal reception. The relaxation time constants, T1 and T2 were recorded using a STEAM sequence, using the 'progressive saturation' method for the T1 and multiple echo times for T2. The 2D L-Correlated SpectroscopY (L-COSY) method was employed with 64 increments (0.4 ms increment size) and eight averages per scan, with a total time of 17 min. ResultsT1 and T2 values for the metabolites of interest were determined. The L-COSY spectra obtained from the soleus muscle provided information on lipid content and chemical structure not available, in vivo, at lower field strengths. All molecular fragments within multiple lipid compartments were chemically shifted by 0.20-0.26 ppm at this field strength. 1D and 2D L-COSY spectra were assigned and proton connectivities were confirmed with the 2D method. ConclusionIn vivo 1D and 2D spectroscopic examination of muscle can be successfully recorded at 7T and is now available to assess lipid alterations as well as other metabolites present with disease. T1 and T2 values were also determined in soleus muscle of male healthy volunteers.

  17. Genetic variation and population structure of hair crab (Erimacrus isenbeckii ) in Japan inferred from mitochondrial DNA sequence analysis.

    Science.gov (United States)

    Azuma, Noriko; Kunihiro, Yasushi; Sasaki, Jun; Mihara, Eiji; Mihara, Yukio; Yasunaga, Tomoaki; Jin, Deuk-Hee; Abe, Syuiti

    2008-01-01

    Genetic variation and population structure of hair crab (Erimacrus isenbeckii) were examined using nucleotide sequence analysis of 580 base pairs (bp) in the 3' portion of the mitochondrial cytochrome c oxidase subunit I gene (COI) of 20 samples collected from 16 locales in Japan (the Hokkaido and Honshu Islands) and one in Korea. A total of 27 haplotypes was defined by 23 variable nucleotide sites in the examined COI region. Pairwise population F (ST) estimates and neighbor-joining tree inferred distinct genetic differentiation between the representative samples from the Pacific Ocean off the Eastern Hokkaido Island and the Sea of Japan, while others were intermediate between these two groups. AMOVA also showed a weak but significant differentiation among these three groups. The present results suggest a moderate population structure of hair crab, probably influenced by high gene flow between regional populations due to sea current dependent larval dispersal of this species. PMID:17955293

  18. Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast

    Science.gov (United States)

    Tsai, Zing Tsung-Yeh; Shiu, Shin-Han; Tsai, Huai-Kuang

    2015-01-01

    Transcription factor (TF) binding is determined by the presence of specific sequence motifs (SM) and chromatin accessibility, where the latter is influenced by both chromatin state (CS) and DNA structure (DS) properties. Although SM, CS, and DS have been used to predict TF binding sites, a predictive model that jointly considers CS and DS has not been developed to predict either TF-specific binding or general binding properties of TFs. Using budding yeast as model, we found that machine learning classifiers trained with either CS or DS features alone perform better in predicting TF-specific binding compared to SM-based classifiers. In addition, simultaneously considering CS and DS further improves the accuracy of the TF binding predictions, indicating the highly complementary nature of these two properties. The contributions of SM, CS, and DS features to binding site predictions differ greatly between TFs, allowing TF-specific predictions and potentially reflecting different TF binding mechanisms. In addition, a "TF-agnostic" predictive model based on three DNA “intrinsic properties” (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy) that can be calculated from genomic sequences alone has performance that rivals the model incorporating experiment-derived data. This intrinsic property model allows prediction of binding regions not only across TFs, but also across DNA-binding domain families with distinct structural folds. Furthermore, these predicted binding regions can help identify TF binding sites that have a significant impact on target gene expression. Because the intrinsic property model allows prediction of binding regions across DNA-binding domain families, it is TF agnostic and likely describes general binding potential of TFs. Thus, our findings suggest that it is feasible to establish a TF agnostic model for identifying functional regulatory regions in potentially any sequenced genome. PMID:26291518

  19. Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes.

    Science.gov (United States)

    Zhuang, Jiali; Weng, Zhiping

    2015-09-30

    Genomic structural variations (SVs) are pervasive in many types of cancers. Characterizing their underlying mechanisms and potential molecular consequences is crucial for understanding the basic biology of tumorigenesis. Here, we engineered a local assembly-based algorithm (laSV) that detects SVs with high accuracy from paired-end high-throughput genomic sequencing data and pinpoints their breakpoints at single base-pair resolution. By applying laSV to 97 tumor-normal paired genomic sequencing datasets across six cancer types produced by The Cancer Genome Atlas Research Network, we discovered that non-allelic homologous recombination is the primary mechanism for generating somatic SVs in acute myeloid leukemia. This finding contrasts with results for the other five types of solid tumors, in which non-homologous end joining and microhomology end joining are the predominant mechanisms. We also found that the genes recursively mutated by single nucleotide alterations differed from the genes recursively mutated by SVs, suggesting that these two types of genetic alterations play different roles during cancer progression. We further characterized how the gene structures of the oncogene JAK1 and the tumor suppressors KDM6A and RB1 are affected by somatic SVs and discussed the potential functional implications of intergenic SVs. PMID:26283183

  20. Cloning and sequence analysis of D-erythrulose reductase from chicken: its close structural relation to tetrameric carbonyl reductases.

    Science.gov (United States)

    Maeda, Miki; Kaku, Hanae; Shimada, Mikio; Nishioka, Takaaki

    2002-07-01

    Sequence analysis of a cDNA for D-erythrulose reductase from chicken liver showed that the deduced open reading frame encodes the protein with a molecular mass of 26 kDa consisting of 246 amino acids. Although the reductase shares more than 60% identity in the amino acid sequence with the mouse tetrameric carbonyl reductase, these two enzymes have many biochemical differences; their substrate specificity, subcellular localization, organ distribution, etc. A three-dimensional structure of D-erythrulose reductase was predicted by comparative modeling based on the structure of the tetrameric carbonyl reductase (PDB entry = 1CYD). Most of the residues at the active site (within 4 A from the ligand) of the carbonyl reductase were also conserved in the D-erythrulose reductase. Nevertheless, Val190 and Leu146 in the active site of the tetrameric carbonyl reductase were substituted in the D-erythrulose reductase by Asn192 and His148, respectively. The substitutions in the active sites may be related to the difference in substrate specificity of the two enzymes. The phylogenic analysis of D-erythrulose reductase and the other related proteins suggests that the protein described as a carbonyl reductase D-erythrulose reductase. PMID:12200544

  1. 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.

  2. Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM.

    Science.gov (United States)

    Sung, Rou-Jia; Zhang, Michael; Qi, Yan; Verdine, Gregory L

    2012-05-25

    MutM, a bacterial DNA-glycosylase, plays a critical role in maintaining genome integrity by catalyzing glycosidic bond cleavage of 8-oxoguanine (oxoG) lesions to initiate base excision DNA repair. The task faced by MutM of locating rare oxoG residues embedded in an overwhelming excess of undamaged bases is especially challenging given the close structural similarity between oxoG and its normal progenitor, guanine (G). MutM actively interrogates the DNA to detect the presence of an intrahelical, fully base-paired oxoG, whereupon the enzyme promotes extrusion of the target nucleobase from the DNA duplex and insertion into the extrahelical active site. Recent structural studies have begun to provide the first glimpse into the protein-DNA interactions that enable MutM to distinguish an intrahelical oxoG from G; however, these initial studies left open the important question of how MutM can recognize oxoG residues embedded in 16 different neighboring sequence contexts (considering only the 5'- and 3'-neighboring base pairs). In this study we set out to understand the manner and extent to which intrahelical lesion recognition varies as a function of the 5'-neighbor. Here we report a comprehensive, systematic structural analysis of the effect of the 5'-neighboring base pair on recognition of an intrahelical oxoG lesion. These structures reveal that MutM imposes the same extrusion-prone ("extrudogenic") backbone conformation on the oxoG lesion irrespective of its 5'-neighbor while leaving the rest of the DNA relatively free to adjust to the particular demands of individual sequences. PMID:22465958

  3. Structure Contour of the Top of the Lower Miocene 2 Sequence, Gulf Coast

    Data.gov (United States)

    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...

  4. Structure Contour of the Top of the Upper Miocene Sequence, Gulf Coast

    Data.gov (United States)

    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...

  5. Structure Contour of the Top of the Middle Miocene Sequence, Gulf Coast

    Data.gov (United States)

    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...

  6. Structure Contour of the Top of the Lower Miocene 1 Sequence, Gulf Coast

    Data.gov (United States)

    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...

  7. 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

  8. Underwound DNA under Tension: Structure, Elasticity, and Sequence-Dependent Behaviors

    OpenAIRE

    Sheinin, Maxim Y.; Forth, Scott; Marko, John F.; Michelle D. Wang

    2011-01-01

    DNA melting under torsion plays an important role in a wide variety of cellular processes. In the present Letter, we have investigated DNA melting at the single-molecule level using an angular optical trap. By directly measuring force, extension, torque, and angle of DNA, we determined the structural and elastic parameters of torsionally melted DNA. Our data reveal that under moderate forces, the melted DNA assumes a left-handed structure as opposed to an open bubble conformation and is highl...

  9. 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

  10. Sequence to Sequence -- Video to Text

    OpenAIRE

    Venugopalan, Subhashini; Rohrbach, Marcus; Donahue, Jeff; Mooney, Raymond; Darrell, Trevor; Saenko, Kate

    2015-01-01

    Real-world videos often have complex dynamics; methods for generating open-domain video descriptions should be senstive to temporal structure and allow both input (sequence of frames) and output (sequence of words) of variable length. To approach this problem we propose a novel end-to-end sequence-to-sequence model to generate captions for videos. For this we exploit recurrent neural networks, specifically LSTMs, which have demonstrated state-of-the-art performance in image ...

  11. Complete genome sequence and structural characterization of a novel iflavirus isolated from Opsiphanes invirae (Lepidoptera: Nymphalidae).

    Science.gov (United States)

    Silva, Leonardo A; Ardisson-Araujo, Daniel M P; Tinoco, Ricardo S; Fernandes, Odair A; Melo, Fernando L; Ribeiro, Bergmann M

    2015-09-01

    Opsiphanes invirae (Lepidopera: Nymphalidae) is a common pest of the African oil palm tree (Elaeis guineensis) in Brazil. Dead larvae were collected in canopy of oil palm trees cultivated in the amazon region (Para State) and analyzed for viral infection. Electron microscopy of caterpillar extracts showed an icosahedral picorna-like virus particle with 30nm in diameter. Total RNA extracted from partially purified virus particles was sequenced. A contig of 10,083 nucleotides (nt) was identified and showed to encode one single predicted polyprotein with 3185 amino acid residues. Phylogenetic analysis showed that the new virus was closely related to another lepidopteran infective virus Spodoptera exigua iflavirus 1(SeIV-1), with 35% amino acid pairwise identity. The novel virus fulfils all ICTV requirements for a new iflavirus species and was named Opsiphanes invirae Iflavirus 1 (OilV-1). PMID:26254043

  12. 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

  13. Sequence and structural diversity of transferrin receptors in Gram-negative porcine pathogens.

    Science.gov (United States)

    Curran, David M; Adamiak, Paul J; Fegan, Jamie E; Qian, Chenzhe; Yu, Rong-Hua; Schryvers, Anthony B

    2015-10-13

    Actinobacillus pleuropneumoniae, Actinobacillus suis, and Haemophilus parasuis are bacterial pathogens from the upper respiratory tract that are responsible for a substantial burden of porcine disease. Although reduction of disease has been accomplished by intensive management practices, immunization remains an important strategy for disease prevention, particularly when intensive management practices are not feasible or suitable. An attractive target for vaccine development is the surface receptor involved in acquiring iron from host transferrin, since it is common to all three pathogenic species and has been shown to be essential for survival and disease causation. It has also recently been demonstrated that an engineered antigen derived from the lipoprotein component of the receptor, transferrin-binding protein B (TbpB), was more effective at preventing infection by H. parasuis than a commercial vaccine product. This study was initiated to explore the genetic and immunogenic diversity of the transferrin receptor system from these species. Nucleic acid sequences were obtained from a geographically and temporally diverse collection of isolates, consisting of 41 A. pleuropneumoniae strains, 30 H. parasuis strains, and 2 A. suis strains. Phylogenetic analyses demonstrated that the receptor protein sequences cluster independently of species, suggesting that there is genetic exchange between these species such that receptor-based vaccines should logically target all three species. To evaluate the cross-reactive response of TbpB-derived antigens, pigs were immunized with the intact TbpB, the TbpB N-lobe and the TbpB C-lobe from A. pleuropneumoniae strain H49 and the resulting sera were tested against a representative panel of TbpBs; demonstrating that the C-lobe induces a broadly cross-reactive response. Overall our results indicate that there is a common reservoir for transferrin receptor antigenic variation amongst these pathogens. While this could present a challenge to future vaccine development, our results suggest a rationally designed TbpB-based vaccine may provide protection against all three pathogens. PMID:26263196

  14. Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package

    Directory of Open Access Journals (Sweden)

    Meier Harald

    2006-05-01

    Full Text Available 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 for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. Results Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. Conclusion Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information in real-time environment. The extended ARB software package is made freely available for the scientific community via http://www.arb-home.de.

  15. 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.

  16. 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.

  17. 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.

  18. Structural and biophysical analysis of sequence insertions in the Venezuelan Equine Encephalitis Virus macro domain.

    Science.gov (United States)

    Guillén, Jaime; Lichière, Julie; Rabah, Nadia; Beitzel, Brett F; Canard, Bruno; Coutard, Bruno

    2015-04-01

    Random transposon insertions in viral genomes can be used to reveal genomic regions important for virus replication. We used these genomic data to evaluate at the protein level the effect of such insertions on the Venezuelan Equine Encephalitis Virus nsP3 macro domain. The structural analysis showed that transposon insertions occur mainly in loops connecting the secondary structure elements. Some of the insertions leading to a temperature sensitive viral phenotype (ts) are close to the cleavage site between nsP2 and nsP3 or the ADP-ribose binding site, two important functions of the macro domain. Using four mutants mimicking the transposon insertions, we confirmed that these insertions can affect the macro domain properties without disrupting the overall structure of the protein. PMID:25725151

  19. Hierarchical structure for audio-video based semantic classification of sports video sequences

    Science.gov (United States)

    Kolekar, M. H.; Sengupta, S.

    2005-07-01

    A hierarchical structure for sports event classification based on audio and video content analysis is proposed in this paper. Compared to the event classifications in other games, those of cricket are very challenging and yet unexplored. We have successfully solved cricket video classification problem using a six level hierarchical structure. The first level performs event detection based on audio energy and Zero Crossing Rate (ZCR) of short-time audio signal. In the subsequent levels, we classify the events based on video features using a Hidden Markov Model implemented through Dynamic Programming (HMM-DP) using color or motion as a likelihood function. For some of the game-specific decisions, a rule-based classification is also performed. Our proposed hierarchical structure can easily be applied to any other sports. Our results are very promising and we have moved a step forward towards addressing semantic classification problems in general.

  20. Entanglement teleportation through 1D Heisenberg chain

    International Nuclear Information System (INIS)

    Information transmission of two qubits through two independent 1D Heisenberg chains as a quantum channel is analyzed. It is found that the entanglement of two spin-12 quantum systems is decreased during teleportation via the thermal mixed state in 1D Heisenberg chain. The entanglement teleportation will be realized if the minimal entanglement of the thermal mixed state is provided in such quantum channel. High average fidelity of teleportation with values larger than 2/3 is obtained when the temperature T is very low. The mutual information I of the quantum channel declines with the increase of the temperature and the external magnetic field. The entanglement quality of input signal states cannot enhance mutual information of the quantum channel

  1. Crystal structure of 1?-(?-D-glucopyranosyloxy)-1,4a?,5,6,7,7a?-hexahydro-7?-methyl-5 -oxocyclopenta[c]pyran-4-carboxylic acid methyl ester (verbenalin)

    International Nuclear Information System (INIS)

    The crystal structure of verbenalin (C17H24O10) is determined by X-ray diffraction analysis (diffractometer, ?CuK?=1.5418 A, number of observed reflections=1881, R=0.035). The crystals are monoclinic, a=5.765(1), b=8.215(1), and c=19.538(4) A; ?=91.1(1) deg.; V=916.1 A3; sp. gr. P21; and Z=2. Conformation of various rings of the molecule is worked out. The molecules in the structure are linked together by intra- and intermolecular O-H···O and C-H···O hydrogen bonds

  2. 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; L. V. Bauer, David; Rasmussen, Kristian Hagsted; Yusuf, Mohammed; Volpi, Emanuela; Flyvbjerg, Henrik; Kristensen, Anders; U. Mirb, Kalim

    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...

  3. Chaos in 1d edge plasmas

    International Nuclear Information System (INIS)

    Radiative instabilities that can develop in plasmas subjected to external heating and radiative cooling are of great importance in edge plasmas of tokamaks and stellarators. They will be analyzed in this paper on the basis of the 1d heat conduction equation. Bifurcation and time evolution of temperature profiles along magnetic field lines between two target plates have been reported. The simple model functions used there are applied here together with methods proved to be useful in nonlinear theories of dynamical systems in order to investigate stable, unstable and chaotic solutions of the 1d heat conduction equation. We consider the model of a radiative plasma with periodically (period ?) injected impurities. In order to show the basic mechanism we discuss at first the time-dependent problem which leads to an equation that can be integrated piecewise exactly analogous to the equation of motion for the periodically kicked rotator. Solution and Lyapunov stability analysis of that one-dimensional radiative map show the existence of stable and unstable solutions. Calculating attractors and Lyapunov exponents in dependence of parameters like power input or period ? shows the appearance of periodical solutions followed by period doubling and finally resulting in chaos in the radiative plasma. Second, we consider 1d and time-dependent problems by calculating profiles and attractors. Enhancing the period ? starting from ? = 0 (stationary problem) rediscovers the known routes to chaos in spatial extension like period doubling or intermittence. (orig.)

  4. Binding of pixantrone to DNA at CpA dinucleotide sequences and bulge structures.

    Science.gov (United States)

    Konda, Shyam K; Wang, Haiqiang; Cutts, Suzanne M; Phillips, Don R; Collins, J Grant

    2015-06-01

    The binding of the anti-cancer drug pixantrone to three oligonucleotide sequences, d(TCATATGA)2, d(CCGAGAATTCCGG)2 {double bulge = DB} and the non-self complementary d(TACGATGAGTA)?:?d(TACCATCGTA) {single bulge = SB}, has been studied by NMR spectroscopy and molecular modelling. The upfield shifts observed for the aromatic resonances of pixantrone upon addition of the drug to each oligonucleotide confirmed the drug bound by intercalation. For the duplex sequence d(TCATATGA)2, NOEs were observed from the pixantrone aromatic H7/8 and aliphatic Ha/Hb protons to the H6/H8 and H1' protons of the C2, A3, T6 and G7 nucleotides, demonstrating that pixantrone preferentially binds at the symmetric CpA sites. However, weaker NOEs observed to various protons from the T4 and A5 residues indicated alternative minor binding sites. NOEs from the H7/H8 and Ha/Hb protons to both major (H6/H8) and minor groove (H1') protons indicated approximately equal proportions of intercalation was from the major and minor groove at the CpA sites. Intermolecular NOEs were observed between the H7/H8 and H4 protons of pixantrone and the A4H1' and G3H1' protons of the oligonucleotide that contains two symmetrically related bulge sites (DB), indicative of binding at the adenine bulge sites. For the oligonucleotide that only contains a single bulge site (SB), NOEs were observed from pixantrone protons to the SB G7H1', A8H1' and G9H1' protons, confirming that the drug bound selectively at the adenine bulge site. A molecular model of pixantrone-bound SB could be constructed with the drug bound from the minor groove at the A8pG9 site that was consistent with the observed NMR data. The results demonstrate that pixantrone preferentially intercalates at adenine bulge sites, compared to duplex DNA, and predominantly from the minor groove. PMID:25929194

  5. 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

  6. Acquisition and manipulation of mental structures : Investigations on artificial grammar learning and implicit sequence processing

    OpenAIRE

    Forkstam, Christian

    2010-01-01

    This thesis introduces repetitive artificial grammar learning as a paradigm in the investigation of sequential implicit learning, in particular as a model for language acquisition and processing. Implicit learning of sequential structure captures an essential cognitive processing capacity of interest from a larger cognitive neuroscience perspective. We investigate in this thesis the underlying neural processing architecture for implicit learning/acquisition to acquire and ...

  7. 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.

  8. CYP1D1, pseudogenized in human, is expressed and encodes a functional drug-metabolizing enzyme in cynomolgus monkey.

    Science.gov (United States)

    Uno, Yasuhiro; Uehara, Shotaro; Murayama, Norie; Yamazaki, Hiroshi

    2011-02-01

    Cytochrome P450 (P450 or CYP) 1 family consists of the CYP1A, CYP1B, CYP1C, and CYP1D subfamilies. In the human genome, CYP1A1, CYP1A2, and CYP1B1 are expressed and encode functional enzymes, whereas CYP1D1P (formerly known as CYP1A8P) is present as a pseudogene due to five nonsense mutations in the putative coding region. In this study, we identified CYP1D1 cDNA, highly identical (nearly 95%) to human CYP1D1P sequence, in cynomolgus monkey, a species frequently used in drug metabolism studies due to its evolutionary closeness to human. The amino acid sequence deduced from cynomolgus monkey CYP1D1 cDNA shared the high sequence identity (91%) with human CYP1D1P (postulated from the gene sequence), and the highest sequence identity (44-45%) with CYP1A1 and CYP1A2 among cynomolgus monkey P450s. CYP1D1 mRNA was most abundantly expressed in liver, followed by kidney, and jejunum. The hepatic expression level of CYP1D1 mRNA was comparable to that of CYP1A1 mRNA and much higher than that of CYP1A2 mRNA. CYP1D1 was barely detectable in immunoblots of cynomolgus monkey liver. Cynomolgus monkey CYP1D1 mRNA was induced in primary hepatocytes with omeprazole. Cynomolgus monkey CYP1D1 protein heterologously expressed in Escherichia coli catalyzed ethoxyresorufin O-deethylation and caffeine 8-hydroxylation, which CYP1As also catalyze. Finally, no nonsense mutations, corresponding to those found in human CYP1D1P, were found in the 20 cynomolgus monkeys and 10 rhesus monkeys used in this study. These results suggest that CYP1D1 plays a role as a functional, drug-metabolizing enzyme in cynomolgus monkey liver. PMID:21070747

  9. Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V

    2008-10-01

    Full Text Available Abstract Background Proteins show a broad range of evolutionary rates. Understanding the factors that are responsible for the characteristic rate of evolution of a given protein arguably is one of the major goals of evolutionary biology. A long-standing general assumption used to be that the evolution rate is, primarily, determined by the specific functional constraints that affect the given protein. These constrains were traditionally thought to depend both on the specific features of the protein's structure and its biological role. The advent of systems biology brought about new types of data, such as expression level and protein-protein interactions, and unexpectedly, a variety of correlations between protein evolution rate and these variables have been observed. The strongest connections by far were repeatedly seen between protein sequence evolution rate and the expression level of the respective gene. It has been hypothesized that this link is due to the selection for the robustness of the protein structure to mistranslation-induced misfolding that is particularly important for highly expressed proteins and is the dominant determinant of the sequence evolution rate. Results This work is an attempt to assess the relative contributions of protein domain structure and function, on the one hand, and expression level on the other hand, to the rate of sequence evolution. To this end, we performed a genome-wide analysis of the effect of the fusion of a pair of domains in multidomain proteins on the difference in the domain-specific evolutionary rates. The mistranslation-induced misfolding hypothesis would predict that, within multidomain proteins, fused domains, on average, should evolve at substantially closer rates than the same domains in different proteins because, within a mutlidomain protein, all domains are translated at the same rate. We performed a comprehensive comparison of the evolutionary rates of mammalian and plant protein domains that are either joined in multidomain proteins or contained in distinct proteins. Substantial homogenization of evolutionary rates in multidomain proteins was, indeed, observed in both animals and plants, although highly significant differences between domain-specific rates remained. The contributions of the translation rate, as determined by the effect of the fusion of a pair of domains within a multidomain protein, and intrinsic, domain-specific structural-functional constraints appear to be comparable in magnitude. Conclusion Fusion of domains in a multidomain protein results in substantial homogenization of the domain-specific evolutionary rates but significant differences between domain-specific evolution rates remain. Thus, the rate of translation and intrinsic structural-functional constraints both exert sizable and comparable effects on sequence evolution. Reviewers This article was reviewed by Sergei Maslov, Dennis Vitkup, Claus Wilke (nominated by Orly Alter, and Allan Drummond (nominated by Joel Bader. For the full reviews, please go to the Reviewers' Reports section.

  10. Characterization of the mouse dihydrolipoamide dehydrogenase (Dld) gene: Genomic structure, promoter sequence, and chromosomal localization

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, M.; Johanning, G.L. [Case Western Univ. School of Medicine, Cleveland, OH (United States); Yang, Hsin-Sheng [State Univ. of New York, Buffalo, NY (United States)] [and others

    1997-05-01

    The mouse dihydrolipoamide dehydrogenase (Dld) gene has been cloned, characterized, and mapped. This nuclear gene encodes a mitochondrial protein that is shared among several {alpha}-keto acid dehydrogenase complexes and the glycine cleavage system. The Dld gene is contained within an approximately 21-kb region and consists of 14 exons ranging in size from 69 to 521 nucleotides. The open reading frame codes for a preprotein of 509 amino acids with a predicted mature protein of 474 amino acids that is highly conserved among mammalian species (>90% identical). Primer extension analyses have shown the gene to have transcription initiation sites with tissue-specific differences in relative utilization. The 5{prime} flanking region is G+C rich and lacks a TATA box, but does contain initiator element and multiple transcription factor-binding consensus sequences. Northern blot analysis shows that the Dld mRNA in various tissues is approximately 2.4 kb in size. The Dld gene has been localized to the proximal region of chromosome 12, approximately 21 cM from the centromere. 32 refs., 5 figs., 1 tab.

  11. Massively parallel sequencing-based survey of eukaryotic community structures in Hiroshima Bay and Ishigaki Island.

    Science.gov (United States)

    Nagai, Satoshi; Hida, Kohsuke; Urusizaki, Shingo; Takano, Yoshihito; Hongo, Yuki; Kameda, Takahiko; Abe, Kazuo

    2016-02-01

    In this study, we compared the eukaryote biodiversity between Hiroshima Bay and Ishigaki Island in Japanese coastal waters by using the massively parallel sequencing (MPS)-based technique to collect preliminary data. The relative abundance of Alveolata was highest in both localities, and the second highest groups were Stramenopiles, Opisthokonta, or Hacrobia, which varied depending on the samples considered. For microalgal phyla, the relative abundance of operational taxonomic units (OTUs) and the number of MPS were highest for Dinophyceae in both localities, followed by Bacillariophyceae in Hiroshima Bay, and by Bacillariophyceae or Chlorophyceae in Ishigaki Island. The number of detected OTUs in Hiroshima Bay and Ishigaki Island was 645 and 791, respectively, and 15.3% and 12.5% of the OTUs were common between the two localities. In the non-metric multidimensional scaling analysis, the samples from the two localities were plotted in different positions. In the dendrogram developed using similarity indices, the samples were clustered into different nodes based on localities with high multiscale bootstrap values, reflecting geographic differences in biodiversity. Thus, we succeeded in demonstrating biodiversity differences between the two localities, although the read numbers of the MPSs were not high enough. The corresponding analysis showed a clear seasonal change in the biodiversity of Hiroshima Bay but it was not clear in Ishigaki Island. Thus, the MPS-based technique shows a great advantage of high performance by detecting several hundreds of OTUs from a single sample, strongly suggesting the effectiveness to apply this technique to routine monitoring programs. PMID:26476293

  12. The role of nucleotide sequence in the immune-active structure photochemically induced in double-stranded DNA by ultraviolet irradiation

    International Nuclear Information System (INIS)

    Pyrimidine, purine, and mixed sequence oligonucleotides from ultraviolet-irradiated DNA were tested for their inhibitory activities on the interaction of [3H]ultraviolet-irradiated DNA with its antibody raised in rabbit. Thymine dimer containing pyrimidine oligonucleotides from irradiated DNA failed to inhibit the interaction, while mixed sequence oligonucleotides, especially those with 8 or more nucleotides, exhibited potent inhibition. Purine clusters from irradiated DNA and mixed sequence oligomers from unirradiated DNA showed no inhibition. Dimerized thymine, which appears to be a critical part of the antigenic determinant, did not inhibit the interaction by itself. The same observations were made for ultraviolet-irradiated thymidine and thymidylic acid. The results suggest that a structure composed of a mixed pyrimidine and purine sequence with a certain chain length seems to be essential for the antigenicity induced in the irradiated DNA. On this nucleotide chain backbone, photochemically modified bases (mostly thymine dimer) can form an immune-active structure. (author)

  13. Bioinformatics Analysis the Complete Sequences of Cytochrome b of Takydromus sylvaticus and Modeling the Tertiary Structure of Encoded Protein

    Directory of Open Access Journals (Sweden)

    Qi-Long CHEN, Xin-Sheng TANG, Wen-Juan YAO, Shun-Qing LU

    2009-01-01

    Full Text Available Cytochrome b (cyt b gene complete sequences (1143bp of Takydromus sylvaticus were sequenced. In order to clarify the phylogenetic position of the Takydromus sylvaticus, we investigated the phylogeny of 15 Takydromus spp. distributed in East-Asia by Maximum Parsimony (MP, Bayesian Inference (BI, and Maximum Likelihood (ML methods using DNA fragments of cyt b genes. The results supported that the Platyplacopus merged into Takydromus and negated the validity of Platyplacopus. Furthermore, the prediction of tertiary structures of cyt b exhibited the CD loop region contain two short helices forming a hairpin arrangement, namely cd1 and cd2. Thermostability analysis shows that the CD-loop region is unstable thermodynamically and may provide mobility to amino acids located at the heme, and might provide high flexibility to the top of ISP (iron-sulfur protein and the cavity region of Qo binding site. It suggested that the two short helices of CD loop region of cyt b was a dominating portion for ISP binding site.

  14. 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.

  15. A Structured Evolutionary Algorithm for Identification of Transcription Factor Binding Sites in Unaligned DNA Sequences

    Directory of Open Access Journals (Sweden)

    Shripal Vijayvargiya

    2011-01-01

    Full Text Available Identification of Transcription Factor Binding Sites (TFBS also called as motifs, from the upstream region of genes remains a highly important and unsolved problem particularly in higher eukaryotic genomes. In this paper, we propose an evolutionary approach to identify transcription factor binding sites. This approach is based on the structured genetic algorithm. In this approach an individual is represented as a structured tree that help us to find variable length motifs. A simple GA can find only fix length motif where as proposed method can find variable length motifs. We applied this approach on various data sets and the results show that it can find correct result both effective and efficient for binding sites.

  16. Comparative genomic analysis of equilibrative nucleoside transporters suggests conserved protein structure despite limited sequence identity

    OpenAIRE

    Sankar, Narendra; Machado, Jerry; Abdulla, Parween; Hilliker, Arthur J.; Coe, Imogen R.

    2002-01-01

    Equilibrative nucleoside transporters (ENTs) are a recently characterized and poorly understood group of membrane proteins that are important in the uptake of endogenous nucleosides required for nucleic acid and nucleoside triphosphate synthesis. Despite their central importance in cellular metabolism and nucleoside analog chemotherapy, no human ENT gene has been described and nothing is known about gene structure and function. To gain insight into the ENT gene family, we used experimental an...

  17. Content-based inference of hierarchical structural grammar for recurrent TV programs using multiple sequence alignment

    OpenAIRE

    Qu, Bingqing; Vallet, Félicien; Carrive, Jean; Gravier, Guillaume

    2014-01-01

    Recently, unsupervised approaches were introduced to analyze the structure of TV programs, relying on the discovery of repeated elements within a program or across multiple episodes of the same program. These methods can discover key repeating elements, such as jingles and separators, however they cannot infer the entire struc- ture of a program. In this paper, we propose a hierarchical use of grammatical inference to yield a temporal grammar of a program from a collection of episodes, discov...

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

    OpenAIRE

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

    2013-01-01

    Ebolavirus (EBOV), the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. I...

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

    OpenAIRE

    Chen Ming; Ma Gwo-Chin; Kou Guang-Hsiung; Lo Chu-Fang; Tsai Shih-Feng; Wu Keh-Ming; Shu Hung-Yu; Liu Tze-Tze; You En-Min; Lin You-Yu; Huang Shiao-Wei; Wu Dongying; Aoki Takashi; Hirono Ikuo; Yu Hon-Tsen

    2011-01-01

    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. Approxi...

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

    OpenAIRE

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

    2014-01-01

    Deletion of tumor-suppressor genes as well as other genomic rearrangements pervade cancer genomes across numerous types of solid tumor and hematologic malignancies. However, even for a specific rearrangement, the breakpoints may vary between individuals, such as the recurrent CDKN2A deletion. Characterizing the exact breakpoints for structural variants (SVs) is useful for designating patient-specific tumor biomarkers. We propose AmBre (Amplification of Breakpoints), a method to target SV brea...

  1. Molecular Characterization of Buffalo Haptoglobin: Sequence Based Structural Comparison Indicates Convergent Evolution Between Ruminants and Human.

    Science.gov (United States)

    Niranjan, S K; Goyal, S; Dubey, P K; Vohra, V; Singh, S; Kathiravan, P; Kataria, R S

    2016-01-01

    Haptoglobin (Hp) protein has high affinity for hemoglobin (Hb) binding during intravascular hemolysis and scavenges the hemoglobin induced free radicals. Earlier reports indicate about uniqueness of Hp molecule in human and cattle, but in other animals, it is not much studied. In this paper, we characterized buffalo Hp molecule and determined its molecular structure, evolutionary importance, and tissue expression. Comparative analysis and predicted domain structure indicated that the buffalo Hp has an internal duplicated region in ?-chain only similar to an alternate Hp2 allele in human. This duplicated part encoded for an extra complement control protein CCP domain. Phylogenetic analysis revealed that buffalo and other ruminants were found to group together separated from all other non-ruminants, including human. The key amino acid residues involved in Hp and Hb as well as Hp and macrophage scavenger receptor, CD163 interactions in buffalo, depicted a significant variation in comparison to other non-ruminant species. Constitutive expression of Hp was also confirmed across all the vital tissues of buffalo, for the first time. Results revealed that buffalo Hp is both structurally and functionally conserved, having internal duplication in ?-chain similar to human Hp2 and other ruminant species, which might have evolved separately as a convergent evolutionary process. Furthermore, the presence of extra Hp CCP domain possibly in all ruminants may have an effect during dimerization of molecule in these species. PMID:26646629

  2. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons

    OpenAIRE

    Yao, Fei; Ariyaratne, Pramila N; Hillmer, Axel M.; Lee, Wah Heng; Li, Guoliang; Teo, Audrey S. M.; Woo, Xing Yi; Zhang, Zhenshui; Chen, Jieqi P.; Poh, Wan Ting; Zawack, Kelson F. B.; Chan, Chee Seng; Leong, See Ting; Neo, Say Chuan; Choi, Poh Sum D.

    2012-01-01

    Structural variations (SVs) contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET) sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET s...

  3. C. elegans RNA-binding protein GLD-1 recognizes its multiple targets using sequence, context, and structural information to repress translation.

    Science.gov (United States)

    Doh, Jung H; Jung, Yuchae; Reinke, Valerie; Lee, Min-Ho

    2013-10-01

    Caenorhabditis elegans GLD-1, a maxi-KH motif containing RNA-binding protein, has various functions mainly during female germ cell development, suggesting that it likely controls the expression of a selective group of maternal mRNAs. To gain an insight into how GLD-1 specifically recognizes these mRNA targets, we identified 38 biochemically proven GLD-1 binding regions from multiple mRNA targets that are among over 100 putative targets co-immunoprecipitated with GLD-1. The sequence information of these regions revealed three over-represented and phylogenetically conserved sequence motifs. We found that two of the motifs, one of which is novel, are important for GLD-1 binding in several GLD-1 binding regions but not in other regions. Further analyses indicate that the importance of one of the sequence motifs is dependent on two aspects: (1) surrounding sequence information, likely acting as an accessory feature for GLD-1 to efficiently select the sequence motif and (2) RNA secondary structural environment where the sequence motif resides, which likely provides "binding-site accessibility" for GLD-1 to effectively recognize its targets. Our data suggest some mRNAs recruit GLD-1 by a distinct mechanism, which involves more than one sequence motif that needs to be embedded in the correct context and structural environment. PMID:24744981

  4. 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.

  5. 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.

  6. Geophysical modeling of the structural relationships between the Precambrian Reading Prong rocks and the Paleozoic sedimentary sequence, Easton quadrangle, PA

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, D.M.; Malinconico, L.L. Jr. (Lafayette Coll., Easton, PA (United States). Dept. of Geology)

    1993-03-01

    This project involves the geophysical modeling of the structural relationships between the Precambrian Reading Prong rocks and the Paleozoic sedimentary cover rocks near Easton, Pennsylvania. The Precambrian rocks have generally been assumed to have been emplaced on the Paleozoic sequence along a shallow thrust fault. However, at present time the attitude of the faults bordering the Precambrian terranes are all very steeply dipping. This was explained by the subsequent folding of the whole sequence during later orogenic activity. The objective of this work is to determine the attitude and depth of the fault contact between the Precambrian crystalline rocks and the Paleozoic sedimentary rocks. A series of traverses (each separated by approximately one mile) were established perpendicular to the strike of the Precambrian rocks. Along each traverse both gravity and magnetic readings were taken at 0.2 kilometer intervals. The data were reduced and presented as profiles and contour maps. Both the magnetic and gravity data show positive anomalies that correlate spatially with the location of the Precambrian rocks. The gravity data have a long wavelength regional trend increasing to the north with a shorter wavelength anomaly of 2 milligals which coincides with the Precambrian rocks. The magnetic data have a single positive anomaly of almost 1,000 gammas which also coincides with the Precambrian terrane. These data will now be used to develop two dimensional density and susceptibility models of the area. From these models, the thickness of each formation and the structural relationships between them, as well as the attitude and depth of the fault contact will be determined.

  7. 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

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

    Directory of Open Access Journals (Sweden)

    Müller Kirsten M

    2002-01-01

    Full Text Available 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 conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields. Results We have prepared a large web site that disseminates our comparative sequence and structure models and data. The four major types of comparative information and systems available for the three ribosomal RNAs (5S, 16S, and 23S rRNA, transfer RNA (tRNA, and two of the catalytic intron RNAs (group I and group II are: (1 Current Comparative Structure Models; (2 Nucleotide Frequency and Conservation Information; (3 Sequence and Structure Data; and (4 Data Access Systems. Conclusions This online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at our Comparative RNA Web (CRW Site http://www.rna.icmb.utexas.edu. In the future, more data and information will be added to these existing categories, new categories will be developed, and additional RNAs will be studied and presented at the CRW Site.

  9. Human thrombopoietin: gene structure, cDNA sequence, expression, and chromosomal localization.

    OpenAIRE

    Foster, D C; Sprecher, C A; Grant, F J; Kramer, J M; Kuijper, J L; Holly, R D; Whitmore, T E; Heipel, M D; Bell, L A; Ching, A F

    1994-01-01

    Thrombopoietin (TPO), a lineage-specific cytokine affecting the proliferation and maturation of megakaryocytes from committed progenitor cells, is believed to be the major physiological regulator of circulating platelet levels. Recently we have isolated a cDNA encoding a ligand for the murine c-mpl protooncogene and shown it to be TPO. By employing a murine cDNA probe, we have isolated a gene encoding human TPO from a human genomic library. The TPO locus spans over 6 kb and has a structure si...

  10. Influence of manure age and sunlight on the community structure of cattle fecal bacteria as revealed by Illumina sequencing

    Science.gov (United States)

    Wong, K.; Shaw, T. I.; Oladeinde, A.; Molina, M.

    2013-12-01

    Fecal pollution of environmental waters is a major concern for the general public because exposure to fecal-associated pathogens can have severe impacts on human health. Stream and river impairment due to fecal pollution is largely the result of agricultural activities in the United States. In the last few years, numerous metagenomic studies utilized next generation sequencing to develop microbial community profiles by massively sequencing the 16sRNA hypervariable region. This technology supports the application of water quality assessment such as pathogen detection and fecal source tracking. The bacteria communities of samples in these studies were determined when they were freshly collected; therefore, little is known about how feces age or how environmental stress influences the microbial ecology of fecal materials. In this study we monitored bacteria community changes in cattle feces for 57 days after excretion (day 0, 2, 4 8, 15, 22, 29, 43, 57) by sequencing the 16s variable region 4, using Illumnia MiSeq. Twelve cattle feces were studied; half of the samples were directly exposed to sunlight (unshaded) and half were shaded. Results indicate that the relative abundance (RA) profile in both shaded and unshaded samples rapidly changed from day 0 to 15, but stabilized from day 22 to 57. Firmcutes were the most abundant phylum (~40%) at day 0, but were reduced to <10% by day 57. The RA of Proteobacteria was only 1% at day 0, but increased to ~50% by day 57in both shaded and unshaded samples. By the end of the study, shaded and unshaded samples had a similar RA of Firmcutes and Proteobacteria but the RA of Bacteroidetes and Actinobacteria was, respectively, about 7% lower and 10% higher for unshaded samples. UV intensity, moisture, and temperature were significantly different between shaded and unshaded plots, indicating that these environmental stresses could influence the structure of fecal bacteria community in the natural environment. According to the rarefaction curve analysis, richness of bacteria diversity in feces decreased as time progressed. Some pathogens such as Campylobacter were detected only at the beginning, meaning they substantially decayed during the course of our study. Overall, this study indicated: (1) sunlight can influence the community structure and (2) after excretion the fecal bacteria diversity can be significantly changed over time. Future studies should therefore use not only the microbial signature of fresh but also moderately aged fecal samples to develop more accurate community profiles for fecal source tracking.

  11. 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.

  12. A Sequence of Qubit-Qudit Pauli Groups as a Nested Structure of Doilies

    CERN Document Server

    Saniga, Metod

    2011-01-01

    Following the spirit of a recent work of one of the authors (J. Phys. A: Math. Theor. 44 (2011) 045301), the essential structure of the generalized Pauli group of a qubit-qu$d$it, where $d = 2^{k}$ and an integer $k \\geq 2$, is recast in the language of a finite geometry. A point of such geometry is represented by the maximum set of mutually commuting elements of the group and two distinct points are regarded as collinear if the corresponding sets have exactly $2^{k} - 1$ elements in common. The geometry comprises $2^{k} - 1$ copies of the generalized quadrangle of order two ("the doily") that form $2^{k-1} - 1$ pencils arranged into a remarkable nested configuration. This nested structure reflects the fact that maximum sets of mutually commuting elements are of two different kinds (ordinary and exceptional) and exhibits an intriguing alternating pattern: the subgeometry of the exceptional points of the $(k+2)$-case is found to be isomorphic to the full geometry of the $k$-case. It should be stressed, however...

  13. Population structure of the Indonesian giant tiger shrimp Penaeus monodon: a window into evolutionary similarities between paralogous mitochondrial DNA sequences and their genomes.

    Science.gov (United States)

    Abdul-Aziz, Muslihudeen A; Schöfl, Gerhard; Mrotzek, Grit; Haryanti, Haryanti; Sugama, Ketut; Saluz, Hans Peter

    2015-09-01

    Here we used both microsatellites and mtCR (mitochondrial DNA control region) sequences as genetic markers to examine the genetic diversity and population structure of Penaeus monodon shrimp from six Indonesian regions. The microsatellite data showed that shrimp from the Indian and the Pacific Ocean were genetically distinct from each other. It has been reported previously that P. monodon mtCR sequences from the Indo-Pacific group into two major paralogous clades of unclear origin. Here we show that the population structure inferred from mtCR sequences matches the microsatellite-based population structure for one of these clades. This is consistent with the notion that this mtCR clade shares evolutionary history with nuclear DNA and may thus represent nuclear mitochondrial pseudogenes (Numts). PMID:26380687

  14. Large-scale prediction of drug–target interactions using protein sequences and drug topological structures

    International Nuclear Information System (INIS)

    Highlights: ? Drug–target interactions are predicted using an extended SAR methodology. ? A drug–target interaction is regarded as an event triggered by many factors. ? Molecular fingerprint and CTD descriptors are used to represent drugs and proteins. ? 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.

  15. 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

  16. The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured

    Directory of Open Access Journals (Sweden)

    Keeling Patrick J

    2006-04-01

    Full Text Available Abstract Background Loss of photosynthesis has occurred independently in several plant and algal lineages, and represents a major metabolic shift with potential consequences for the content and structure of plastid genomes. To investigate such changes, we sequenced the complete plastid genome of the parasitic, non-photosynthetic green alga, Helicosporidium. Results The Helicosporidium plastid genome is among the smallest known (37.5 kb, and like other plastids from non-photosynthetic organisms it lacks all genes for proteins that function in photosynthesis. Its reduced size results from more than just loss of genes, however; it has little non-coding DNA, with only one intron and tiny intergenic spaces, and no inverted repeat (no duplicated genes at all. It encodes precisely the minimal complement of tRNAs needed to translate the universal genetic code, and has eliminated all redundant isoacceptors. The Helicosporidium plastid genome is also highly structured, with each half of the circular genome containing nearly all genes on one strand. Helicosporidium is known to be related to trebouxiophyte green algae, but the genome is structured and compacted in a manner more reminiscent of the non-photosynthetic plastids of apicomplexan parasites. Conclusion Helicosporidium contributes significantly to our understanding of the evolution of plastid DNA because it illustrates the highly ordered reduction that occurred following the loss of a major metabolic function. The convergence of plastid genome structure in Helicosporidium and the Apicomplexa raises the interesting possibility that there are common forces that shape plastid genomes, subsequent to the loss of photosynthesis in an organism.

  17. Quantum Cable as transport spectroscopy of 1D DOS of cylindrical quantum wires

    OpenAIRE

    Z. Y. Zeng; Xiang, Y; L. D. Zhang

    2001-01-01

    We considered the proposed Quantum Cable as a kind of transport spectroscopy of one-dimensional (1D) density of states (DOS) of cylindrical quantum wires. By simultaneously detecting the direct current through the cylindrical quantum wire and the leaked tunneling current into the neighboring wire at desired temperatures, one can obtain detailed information about 1D DOS and subband structure of cylindrical quantum wires.

  18. 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.

  19. Superlattice structures observed in the extraordinary phase sequence and analyzed by the phenomenological Landau model and the partially molecular model.

    Science.gov (United States)

    Sandhya, K L; Chandani, A D L; Fukuda, Atsuo; Kumar, S; Vij, Jagdish K

    2013-06-01

    We draw several electric-field-temperature (E-T) phase diagrams with electric-field-induced birefringence contours in the nOHFBBB1M7 (n=10) and nOTBBB1M7 (n=11) (C11) mixture system by changing the C11 concentration carefully; some of the mixtures show the unusual extraordinary phase sequence where subphases with the four-, five-, and six-layer superlattice structures emerge above the smectic-C(*) main phase. We try to understand the results in terms of two complementary models that have so far been proposed: the phenomenological Landau model of phase transitions by Dolganov et al. [P. V. Dolganov et al., Phys. Rev. E 86, 020701(R) (2012)] and the partially molecular Emelyanenko-Osipov model [A. V. Emelyanenko and M. A. Osipov, Phys. Rev. E 68, 051703 (2003)]. The observed E-T phase diagram can be well reproduced by the phenomenological model. An emergence of the subphase with the four-layer superlattice structure above smectic-C(*) is also understandable in terms of the partially molecular model. We discuss the pros and cons of the two models as well. PMID:23848704

  20. Generation of deviation parameters for amino acid singlets, doublets and triplets from three-dimensional structures of proteins and its implications for secondary structure prediction from amino acid sequences

    Indian Academy of Sciences (India)

    S A Mugilan; K Veluraja

    2000-03-01

    We present a new method, secondary structure prediction by deviation parameter (SSPDP) for predicting the secondary structure of proteins from amino acid sequence. Deviation parameters (DP) for amino acid singlets, doublets and triplets were computed with respect to secondary structural elements of proteins based on the dictionary of secondary structure prediction (DSSP)-generated secondary structure for 408 selected non-homologous proteins. To the amino acid triplets which are not found in the selected dataset, a DP value of zero is assigned with respect to the secondary structural elements of proteins. The total number of parameters generated is 15,432, in the possible parameters of 25,260. Deviation parameter is complete with respect to amino acid singlets, doublets, and partially complete with respect to amino acid triplets. These generated parameters were used to predict secondary structural elements from amino acid sequence. The secondary structure predicted by our method (SSPDP) was compared with that of single sequence (NNPREDICT) and multiple sequence (PHD) methods. The average value of the percentage of prediction accuracy for ?-helix by SSPDP, NNPREDICT and PHD methods was found to be 57%, 44% and 69% respectively for the proteins in the selected dataset. For -strand the prediction accuracy is found to be 69%, 21% and 53% respectively by SSPDP, NNPREDICT and PHD methods. This clearly indicates that the secondary structure prediction by our method is as good as PHD method but much better than NNPREDICT method.

  1. Structural aspects of the metal-insulator transition in BaVS3

    OpenAIRE

    Fagot, S.; Foury-Leylekian, P.; Ravy, S.; Pouget, J. P.; Anne, M.; Popov, G.; Lobanov, M. V.; Greenblatt, M.

    2004-01-01

    A sequence of structural transitions occurring in the quasi-one-dimensional (1D) 3d1 system BaVS3 at low temperature was investigated by high resolution synchrotron X-ray diffraction. The orthorhombic Cmc21 structure of the intermediate-temperature (70K

  2. The structure set of an arbitrary space, the algebraic surgery exact sequence and the total surgery obstruction

    International Nuclear Information System (INIS)

    The algebraic theory of surgery gives a necessary and sufficient chain level condition for a space with n-dimensional Poincare duality to be homotopy equivalent to an n-dimensional topological manifold. A relative version gives a necessary and sufficient chain level condition for a simple homotopy equivalence of n-dimensional topological manifolds to be homotopic to a homeomorphism. The chain level obstructions come from a chain level interpretation of the fibre of the assembly map in surgery. The assembly map A : Hn(X; L.) ? Ln(Z[?1(X)]) is a natural transformation from the generalized homology groups of a space X with coefficients in the 1-connective simply-connected surgery spectrum L. to the non-simply-connected surgery obstruction groups L*(Z[?1(X)]). The (Z,X)-category has objects based f.g. free Z-modules with an X-local structure. The assembly maps A are induced by a functor from the (Z, X)-category to the category of based f.g. free Z[?1(X)]- modules. The generalized homology groups H*(X;L.) are the cobordism groups of quadratic Poincare complexes over (Z,X). The relative groups S*(X) in the algebraic surgery exact sequence of X, ... ? Hn(X;L.) A-vector Ln(Z[?1(X)]) ? Sn(X) ? Hn-1(X;L.) ? ... are the cobordism groups of quadratic Poincare complexes over (Z,X) which assemble to contractible quadratic Poincare complexes over Z[?1(X)]. The total surgery obstruction s(X) is an element of Sn(X) of an n-dimensional simple Poincare complex X is the cobordism class of a quadratic Poincare complex over (Z, X) with contractible assembly over Z[?1(X)], which measures the homotopy invariant part of the failure of the link of each simplex in X to be a homology sphere. The total surgery obstruction is s(X) 0 if (and for n ? 5 only if) X is simple homotopy equivalent to an n-dimensional topological manifold. The Browder-Novikov-Sullivan-Wall surgery exact sequence for an n-dimensional topological manifold M with n ? 5, ... ? Ln+1(Z[?1(M)]) ?STOP(M) ? [M,G/TOP] ? Ln(Z[?1(M)]) is identified with the corresponding portion of the algebraic surgery exact sequence ... ? Ln+1(Z[?1(M)]) ? Sn+1(M) ? Hn(M;L.) A-vector Ln(Z[?1(M)]). The structure invariant s(h) is an element of STOP(M) = Sn+1(M) of a simple homotopy equivalence of n-dimensional topological manifolds h : N ? M is the cobordism class of an n-dimensional quadratic Poincare complex in (Z, M) with contractible assembly over Z[?1(M)], which measures the homotopy invariant part of the failure of the point inverses h-1(x) (x is an element of M) to be acyclic. The structure invariant is s(h) = 0 if (and for n ? 5 only if) h is homotopic to a homeomorphism. (author)

  3. The FC-1D: The profitable alternative Flying Circus Commercial Aviation Group

    Science.gov (United States)

    Meza, Victor J.; Alvarez, Jaime; Harrington, Brook; Lujan, Michael A.; Mitlyng, David; Saroughian, Andy; Silva, Alex; Teale, Tim

    1994-01-01

    The FC-1D was designed as an advanced solution for a low cost commercial transport meeting or exceeding all of the 1993/1994 AIAA/Lockheed request for proposal requirements. The driving philosophy behind the design of the FC-1D was the reduction of airline direct operating costs. Every effort was made during the design process to have the customer in mind. The Flying Circus Commercial Aviation Group targeted reductions in drag, fuel consumption, manufacturing costs, and maintenance costs. Flying Circus emphasized cost reduction throughout the entire design program. Drag reduction was achieved by implementation of the aft nacelle wing configuration to reduce cruise drag and increase cruise speeds. To reduce induced drag, rather than increasing the wing span of the FC-1D, spiroids were included in the efficient wing design. Profile and friction drag are reduced by using riblets in place of paint around the fuselage and empennage of the FC-1D. Choosing a single aisle configuration enabled the Flying Circus to optimize the fuselage diameter. Thus, reducing fuselage drag while gaining high structural efficiency. To further reduce fuel consumption a weight reduction program was conducted through the use of composite materials. An additional quality of the FC-1D is its design for low cost manufacturing and assembly. As a result of this design attribute, the FC-1D will have fewer parts which reduces weight as well as maintenance and assembly costs. The FC-1D is affordable and effective, the apex of commercial transport design.

  4. String Matching and 1d Lattice Gases

    CERN Document Server

    Mungan, M

    2004-01-01

    In a recent paper, Bilge et al. (q-bio.GN/0409023) have derived a set of recursion relations for the probability of encountering (matching) a given binary string of length $l$ at least once in a random string of length $k$. Using the method introduced in Mungan et al. (q-bio.MN/0406049), we obtain a closed form solution for the matching probability in the general case where the letters of the string are derived from an alphabet of $r$ letters. We show that the problem of determining string matching probabilities can be recast into a problem of calculating the partition function of a 1d lattice gas with interacting particles. We extract the large $k$ behavior of the matching probability and also calculate the probability that a given string is matched precisely $n$ times. The case of allowing imperfect matches is also considered.

  5. 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. 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.

  6. Universal nature of collective plasmonic excitations in finite 1D carbon-based nanostructures

    Science.gov (United States)

    Polizzi, Eric; Yngvesson, Sigfrid K.

    2015-08-01

    We provide evidence of the plasmon resonances in a number of representative 1D finite carbon-based nanostructures using first-principle computational electronic spectroscopy studies. Our special purpose real-space/real-time all-electron time-dependent density-functional theory simulator can perform excited-states calculations to obtain correct frequencies for known optical transitions, and capture various nanoscopic effects including collective plasmon excitations. The presence of 1D plasmons is universally predicted by the various numerical experiments, which also demonstrate a phenomenon of resonance splitting. For the metallic carbon nanotubes under study, the plasmons are expected to be related to the Tomonaga-Luttinger plasmons of infinitely long 1D structures. In-depth quantitative understanding of such resonances which have not been clearly identified in experiments so far, would be invaluable for future generations of nano-photonic and nano-electronic devices that employ 1D conductors.

  7. Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): impact on sequence alignment and phylogeny estimation.

    Science.gov (United States)

    Gillespie, Joseph J; Yoder, Matthew J; Wharton, Robert A

    2005-07-01

    We utilize the secondary structural properties of the 28S rRNA D2-D10 expansion segments to hypothesize a multiple sequence alignment for major lineages of the hymenopteran superfamily Ichneumonoidea (Braconidae, Ichneumonidae). The alignment consists of 290 sequences (originally analyzed in Belshaw and Quicke, Syst Biol 51:450-477, 2002) and provides the first global alignment template for this diverse group of insects. Predicted structures for these expansion segments as well as for over half of the 18S rRNA are given, with highly variable regions characterized and isolated within conserved structures. We demonstrate several pitfalls of optimization alignment and illustrate how these are potentially addressed with structure-based alignments. Our global alignment is presented online at (http://hymenoptera.tamu.edu/rna) with summary statistics, such as basepair frequency tables, along with novel tools for parsing structure-based alignments into input files for most commonly used phylogenetic software. These resources will be valuable for hymenopteran systematists, as well as researchers utilizing rRNA sequences for phylogeny estimation in any taxon. We explore the phylogenetic utility of our structure-based alignment by examining a subset of the data under a variety of optimality criteria using results from Belshaw and Quicke (2002) as a benchmark. PMID:16059751

  8. 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.

  9. Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene.

    DEFF Research Database (Denmark)

    Bowman, Jeff S.; Rasmussen, Simon

    2011-01-01

    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.

  10. Genetic diversity and population structure of black Dahe pig based on DNA sequences analyses of mitochondrial and nuclear genes.

    Science.gov (United States)

    Tang, Lizhou; Yu, Long; Wang, Junjie; Liu, Chao; Shi, Xiaodong; Ding, Wei; Zhu, Lei; Guo, Songchang

    2016-01-01

    To investigate the genetic diversity and population structure of black Dahe pigs, we collected 175 samples from 5 local populations and sequenced them using a combination of two selected molecular markers for mitochondrial cytochrome b and Major Histocompatibility Complex (MHC) DRB. Overall, the results of AMOVA and phylogenetic tree and gene flow analyses detected high levels of gene flow among the five populations, particularly individual pigs from Dahe town (Pop1) or Yingshang town (Pop2) to other populations (Pop3, Pop4, and Pop5). The genetic diversity analyses showed that the diversity indices of the five populations did not vary significantly, but they were much lower than those of other Chinese pig species. These results suggest that distinct gene flow, unstable population pattern, and lower genetic diversity have been influenced mainly by human introductions for economic ends. These findings provide genetic information that could be used for the preservation and further genetic improvement of the black Dahe pig, as well as an important reference for the evaluation, conservation, and utilization of the genetic resources of this breed. PMID:24617464

  11. 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.

  12. 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

  13. 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

  14. Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression

    OpenAIRE

    Qiu, Jie; Wang, Yu; Wu, Sanling; Wang, Ying-ying; Ye, Chu-Yu; Bai, Xuefei; Li, Zefeng; Yan, Chenghai; Wang, Weidi; Wang, ZiQiang; Shu, Qingyao; Xie, Jiahua; Lee, Suk-Ha; Fan, Longjiang

    2014-01-01

    Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no indep...

  15. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

    Science.gov (United States)

    Lewis, Tony E.; Sillitoe, Ian; Andreeva, Antonina; Blundell, Tom L.; Buchan, Daniel W.A.; Chothia, Cyrus; Cuff, Alison; Dana, Jose M.; Filippis, Ioannis; Gough, Julian; Hunter, Sarah; Jones, David T.; Kelley, Lawrence A.; Kleywegt, Gerard J.; Minneci, Federico; Mitchell, Alex; Murzin, Alexey G.; Ochoa-Montaño, Bernardo; Rackham, Owen J. L.; Smith, James; Sternberg, Michael J. E.; Velankar, Sameer; Yeats, Corin; Orengo, Christine

    2013-01-01

    Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on sequence–structure–function relationships. Leading structure prediction resources (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) provide annotations for UniProt sequences to indicate the locations of structural domains (structural annotations) and their 3D structures (structural models). Structural annotations and 3D model predictions are currently available for three model genomes (Homo sapiens, E. coli and baker’s yeast), and the project will extend to other genomes in the near future. As these resources exploit different strategies for predicting structures, the main aim of Genome3D is to enable comparisons between all the resources so that biologists can see where predictions agree and are therefore more trusted. Furthermore, as these methods differ in whether they build their predictions using CATH or SCOP, Genome3D also contains the first official mapping between these two databases. This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs). PMID:23203986

  16. [Sequence and Structural Analyses of the Complete Genome of Bovine Papillomavirus 2 Genotype Aks-01 Strain from Skin Samples of Cows in Southern Xinjiang, China].

    Science.gov (United States)

    Zhang, Wanqi; Hu, Jianjun; Yan, Shilei; Huang, Yaojie; Xu, Jianping; Huang, Zhongwu; Zheng, Maoliang; Meng, Ziyan; Li, Yuanyuan; Wang, Na; Wang, Qingqing

    2015-07-01

    To study the complete genomic sequence, genomic characteristics, and genetic variation of the bovine papillomavirus 2 genotype (BPV-2) Aks-01 strain at the molecular level, genotyping of this strain from the skin samples of cows in southern Xinjiang (China) was first detected by the polymerase chain reaction with FAP59/FAP64 primers. Based on the complete genome of the BPV-2 reference strain, specific primers and sequencing primers were designed, and the complete genome of the Aks-01 strain amplified and sequenced. Sequence analyses showed that genotyping of the Aks-01 strain belonged to BPV-2. The Aks-01 strain had the structural characteristics of BPV-2. The 7944-bp full-length genomic sequence of the Aks-01 strain was compiled using DNAStar™. The sequence of the Aks-01 strain had 98% similarity to the reference strain from GenBank. The Aks-01 strain was most closely related to BPV-1 and BPV-13. BPV-2, BPV-1 and BPV-13 were grouped within the genus Deltapapillomavirus. The Aks-01 strain is the first BPV-2 strain reported in southern Xinjiang. PMID:26524909

  17. 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 ...

  18. Implicit structured sequence learning

    OpenAIRE

    Folia, Vasiliki

    2013-01-01

    A simple question: Do you know how you manage to speak your native language without making grammatical errors despite the fact that you probably do not know how to describe the grammatical rules you use? Sometimes such simple questions do not have simple answers. The amazing capacity to effectively communicate complex information and thoughts through the medium of language is the result of the way language, and more specifically, linguistic rules are learned: in an implicit manner. ...

  19. Gap Sequence of Factors of Fibonacci Sequence

    OpenAIRE

    Huang, Yuke; Wen, Zhiying

    2014-01-01

    Let w be a factor of Fibonacci sequence F=x_1x_2..., then it appears in the sequence infinitely many times. Let w_p be the p-th appearance of w and v_{w,p} be the gap between w_p and w_{p+1}. In this paper, we discuss the structure of the gap sequence {v_{w,p}}, we first introduce the singular kernel word sk(w) for any factor w of F and give a decomposition of w with respect to sk(w). Using the singular kernel and the decomposition, we prove the gap sequence {v_{w,p}} has ex...

  20. 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...

  1. 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

  2. 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

  3. Nucleotide sequence of metF, the E. coli structural gene for 5-10 methylene tetrahydrofolate reductase and of its control region.

    Science.gov (United States)

    Saint-Girons, I; Duchange, N; Zakin, M M; Park, I; Margarita, D; Ferrara, P; Cohen, G N

    1983-10-11

    The nucleotide sequence of the E.coli metF gene (888 nucleotides), coding for 5-10 methylene tetrahydrofolate reductase, has been determined. The metF gene product was identified in maxicells and found to be a protein of subunit molecular weight 33,000, in agreement with the size of the coding region. The starting point for metF transcription was determined by S1 nuclease mapping. No structural evidence was found for an attenuation mechanism regulating the independent metF transcriptional unit. Comparison of the regulatory region preceding the metF structural gene with the 5' flanking region of the metBL operon shows some homology spanning 24 nucleotides. These homologous sequences could be operator structures belonging to the two transcriptional units, metF and metBL, and recognized by the same regulatory protein. PMID:6356036

  4. 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.

  5. AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome

    Directory of Open Access Journals (Sweden)

    Mei Lingling

    2011-11-01

    Full Text Available Abstract Background To complement next-generation sequencing technologies, there is a pressing need for efficient pre-sequencing capture methods with reduced costs and DNA requirement. The Alu family of short interspersed nucleotide elements is the most abundant type of transposable elements in the human genome and a recognized source of genome instability. With over one million Alu elements distributed throughout the genome, they are well positioned to facilitate genome-wide sequence amplification and capture of regions likely to harbor genetic variation hotspots of biological relevance. Results Here we report on the use of inter-Alu PCR with an enhanced range of amplicons in conjunction with next-generation sequencing to generate an Alu-anchored scan, or 'AluScan', of DNA sequences between Alu transposons, where Alu consensus sequence-based 'H-type' PCR primers that elongate outward from the head of an Alu element are combined with 'T-type' primers elongating from the poly-A containing tail to achieve huge amplicon range. To illustrate the method, glioma DNA was compared with white blood cell control DNA of the same patient by means of AluScan. The over 10 Mb sequences obtained, derived from more than 8,000 genes spread over all the chromosomes, revealed a highly reproducible capture of genomic sequences enriched in genic sequences and cancer candidate gene regions. Requiring only sub-micrograms of sample DNA, the power of AluScan as a discovery tool for genetic variations was demonstrated by the identification of 357 instances of loss of heterozygosity, 341 somatic indels, 274 somatic SNVs, and seven potential somatic SNV hotspots between control and glioma DNA. Conclusions AluScan, implemented with just a small number of H-type and T-type inter-Alu PCR primers, provides an effective capture of a diversity of genome-wide sequences for analysis. The method, by enabling an examination of gene-enriched regions containing exons, introns, and intergenic sequences with modest capture and sequencing costs, computation workload and DNA sample requirement is particularly well suited for accelerating the discovery of somatic mutations, as well as analysis of disease-predisposing germline polymorphisms, by making possible the comparative genome-wide scanning of DNA sequences from large human cohorts.

  6. Molecular cloning, sequencing and structural studies of granulocyte-macrophage colony-stimulating factor (GM-CSF) from Indian water buffalo (Bubalus bubalis)

    KAUST Repository

    Sugumar, Thennarasu

    2013-06-25

    Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a cytokine that is essential for growth and development of progenitors of granulocytes and monocytes/macrophages. In this study, we report molecular cloning, sequencing and characterization of GM-CSF from Indian water buffalo, Bubalus bubalis. In addition, we performed sequence and structural analysis for buffalo GM-CSF. Buffalo GM-CSF has been compared with 17 mammalian GM-CSFs using multiple sequence alignment and phylogenetic tree. Three-dimensional model for buffalo GM-CSF and human receptor complex was built using homology modelling to study cross-reactivity between two species. Detailed analysis was performed to study GM-CSF interface and various interactions at the interface. © 2013 John Wiley & Sons Ltd.

  7. MSLICE Sequencing

    Science.gov (United States)

    Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Norris, Jeffrey S.; Morris, John R.

    2011-01-01

    MSLICE Sequencing is a graphical tool for writing sequences and integrating them into RML files, as well as for producing SCMF files for uplink. When operated in a testbed environment, it also supports uplinking these SCMF files to the testbed via Chill. This software features a free-form textural sequence editor featuring syntax coloring, automatic content assistance (including command and argument completion proposals), complete with types, value ranges, unites, and descriptions from the command dictionary that appear as they are typed. The sequence editor also has a "field mode" that allows tabbing between arguments and displays type/range/units/description for each argument as it is edited. Color-coded error and warning annotations on problematic tokens are included, as well as indications of problems that are not visible in the current scroll range. "Quick Fix" suggestions are made for resolving problems, and all the features afforded by modern source editors are also included such as copy/cut/paste, undo/redo, and a sophisticated find-and-replace system optionally using regular expressions. The software offers a full XML editor for RML files, which features syntax coloring, content assistance and problem annotations as above. There is a form-based, "detail view" that allows structured editing of command arguments and sequence parameters when preferred. The "project view" shows the user s "workspace" as a tree of "resources" (projects, folders, and files) that can subsequently be opened in editors by double-clicking. Files can be added, deleted, dragged-dropped/copied-pasted between folders or projects, and these operations are undoable and redoable. A "problems view" contains a tabular list of all problems in the current workspace. Double-clicking on any row in the table opens an editor for the appropriate sequence, scrolling to the specific line with the problem, and highlighting the problematic characters. From there, one can invoke "quick fix" as described above to resolve the issue. Once resolved, saving the file causes the problem to be removed from the problem view.

  8. Structural organization and expression of human DNA sequences related to the transforming gene of avian myeloblastosis virus.

    OpenAIRE

    Franchini, G; wong-Staal, F; Baluda, M. A.; Lengel, C; Tronick, S R

    1983-01-01

    Bacteriophage libraries of human DNA were screened for sequences homologous to the transforming gene (v-myb) of avian myeloblastosis virus. The three overlapping clones isolated were shown to contain a total of 1.0 kilobase pair (kbp) of sequence related to v-myb distributed over 6.2 kbp. Restriction enzyme mapping and heteroduplex analysis revealed the presence of five myb-related domains interrupted by four stretches of non-homology. To study the extent of human DNA coding sequences that co...

  9. Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.

    Science.gov (United States)

    Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

    2015-09-01

    The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. PMID:26073648

  10. 4-Hydroxybenzoate hydroxylase from Pseudomonas sp. CBS3. Purification, characterization, gene cloning, sequence analysis and assignment of structural features determining the coenzyme specificity.

    Science.gov (United States)

    Seibold, B; Matthes, M; Eppink, M H; Lingens, F; Van Berkel, W J; Müller, R

    1996-07-15

    4-Hydroxybenzoate hydroxylase from Pseudomonas sp. CBS3 was purified by five consecutive steps to apparent homogeneity. The enrichment was 50-fold with a yield of about 20%. The enzyme is a homodimeric flavoprotein monooxygenase with each 44-kDa polypeptide chain containing one FAD molecule as a rather weakly bound prosthetic group. In contrast to other 4-hydroxybenzoate hydroxylases of known primary structure, the enzyme preferred NADH over NADPH as electron donor. The pH optimum for catalysis was pH 8.0 with a maximum turnover rate around 45 degrees C. Chloride ions were inhibitory, and competitive with respect to NADH. 4-Hydroxybenzoate hydroxylase from Pseudomonas sp. CBS3 has a narrow substrate specificity. In addition to the transformation of 4-hydroxybenzoate to 3,4-dihydroxybenzoate, the enzyme converted 2-fluoro-4-hydroxybenzoate, 2-chloro-4-hydroxybenzoate, and 2,4-dihydroxybenzoate. With all aromatic substrates, no uncoupling of hydroxylation was observed. The gene encoding 4-hydroxybenzoate hydroxylase from Pseudomonas sp. CBS3 was cloned in Escherichia coli. Nucleotide sequence analysis revealed an open reading frame of 1182 bp that corresponded to a protein of 394 amino acid residues. Upstream of the pobA gene, a sequence resembling an E. coli promoter was identified, which led to constitutive expression of the cloned gene in E. coli TG1. The deduced amino acid sequence of Pseudomonas sp. CBS3 4-hydroxybenzoate hydroxylase revealed 53% identity with that of the pobA enzyme from Pseudomonas fluorescens for which a three-dimensional structure is known. The active-site residues and the fingerprint sequences associated with FAD binding are strictly conserved. This and the conservation of secondary structures implies that the enzymes share a similar three-dimensional fold. Based on an isolated region of sequence divergence and site-directed mutagenesis data of 4-hydroxybenzoate hydroxylase from P. fluorescens, it is proposed that helix H2 is involved in determining the coenzyme specificity. PMID:8706756

  11. Allergens in Hymenoptera venom. XXV: The amino acid sequences of antigen 5 molecules and the structural basis of antigenic cross-reactivity.

    Science.gov (United States)

    Hoffman, D R

    1993-11-01

    The complete amino acid sequences have been determined by solid-phase protein sequencing for eight different vespid venom antigen 5 molecules. These include five species of yellow jackets, Vespula squamosa, V. flavopilosa, V. germanica, V. pensylvanica and V. vidua, representing all three species groups; two variants from the European hornet, Vespa crabro; and a species of paper wasp, Polistes fuscatus, from a second subgenus. The new sequences were compared with the seven previously published sequences from yellow jackets, hornets, and wasps, and to that of Solenopsis invicta 3 allergen from imported fire ant venom. These comparisons provided structural evidence to support the observed high degree of cross-reactivity among the antigens of the common group of yellow jackets and among those of the two common North American subgenera of paper wasps studied. The antigen 5 of V. squamosa and of V. vidua were significantly different from those of the vulgaris group. Common features that could generate immunologic cross-reactivity were seen among the antigen 5 molecules of hornets of both genera and among those of yellow jackets, hornets, and paper wasps. The imported fire ant allergen has only minimal conserved areas in common with the vespid allergens, which explains the lack of observed IgE cross-reactivity. These results provide the structural basis for the cross-reactivity patterns observed in clinical practice and suggest that the commercial extracts of yellow jacket and paper wasp could be prepared with fewer carefully selected species. PMID:8227862

  12. Identification and hydropathic characterization of structural features affecting sequence specificity for doxorubicin intercalation into DNA double-stranded polynucleotides.

    OpenAIRE

    Kellogg, G. E.; Scarsdale, J N; Fornari, F A

    1998-01-01

    The computer molecular modeling program HINT (Hydropathic INTeractions), an empirical hydropathic force field function that includes hydrogen bonding, coulombic and hydrophobic terms, was used to study sequence-selective doxorubicin binding/intercalation in the 64 unique CAxy, CGxy, TAxy, TGxy base pair quartet combinations. The CAAT quartet sequence is shown to have the highest binding score of the 64 combinations. Of the two regularly alternating polynucleotides, d(CGCGCG)2and d(TATATA)2, t...

  13. Multilocus Sequence Typing Reveals that the Population Structure of Candida dubliniensis Is Significantly Less Divergent than That of Candida albicans? †

    OpenAIRE

    McManus, Brenda A.; Coleman, David C.; Moran, Gary; Pinjon, Emmanuelle; Diogo, Dorothée; Bougnoux, Marie-Elisabeth; Borecká-Melkusova, Silvia; Bujdákova, Helena; Murphy, Philip; D'Enfert, Christophe; Sullivan, Derek J.

    2007-01-01

    The pathogenic yeast Candida dubliniensis is phylogenetically very closely related to Candida albicans, and both species share many phenotypic and genetic characteristics. DNA fingerprinting using the species-specific probe Cd25 and sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal gene cluster previously showed that C. dubliniensis is comprised of three major clades comprising four distinct ITS genotypes. Multilocus sequence typing (MLST) has been shown to be...

  14. Multilocus sequence typing reveals that the population structure of Candida dubliniensis is significantly less divergent than that of Candida albicans.

    OpenAIRE

    Murphy, Philip; MC MANUS, BRENDA

    2008-01-01

    The pathogenic yeast Candida dubliniensis is phylogenetically very closely related to Candida albicans, and both species share many phenotypic and genetic characteristics. DNA fingerprinting using the species-specific probe Cd25 and sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal gene cluster previously showed that C. dubliniensis is comprised of three major clades comprising four distinct ITS genotypes. Multilocus sequence typing (MLST) has been shown to be...

  15. MULTILOCUS SEQUENCE TYPING REVEALS THAT THE POPULATION STRUCTURE OF Candida dubliniensis IS SIGNIFICANTLY LESS DIVERGENT THAN THAT OF Candida albicans

    OpenAIRE

    SULLIVAN, DEREK; Moran, Gary; Coleman, David; MC MANUS, BRENDA ANN

    2008-01-01

    he pathogenic yeast Candida dubliniensis is phylogenetically very closely related to Candida albicans, and both species share many phenotypic and genetic characteristics. DNA fingerprinting using the species-specific probe Cd25 and sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal gene cluster previously showed that C. dubliniensis is comprised of three major clades comprising four distinct ITS genotypes. Multilocus sequence typing (MLST) has been shown to be ...

  16. Phonon multiplexing through 1D chains

    Scientific Electronic Library Online (English)

    A., Avila; D., Reyes.

    2008-12-01

    Full Text Available Recently, phonon propagation through atomic structures has become a relevant study issue. The most important applications arise in the thermal field, since phonons can carry thermal and acoustic energy. It is expected that technological advances will make possible the engineering of thermal paths ac [...] cording to convenience. A simple phonon multiplexer was analyzed as a spring-mass model. It consists of mono-atomic chains of atoms with a coupling structure between them. Forces between atoms follow Hooke's law and are restricted to be first nearest neighbor interaction. It was possible to establish simple rules on constitutive parameters such as atom masses and bonding forces that enable one to select a wavelength of transmission. The method used enables the study of structures of much greater complexity than the one presented here.

  17. Genotyping-by-sequencing approach indicates geographic distance as the main factor affecting genetic structure and gene flow in Brazilian populations of Grapholita molesta (Lepidoptera, Tortricidae)

    OpenAIRE

    Silva-Brandão, Karina Lucas; Oscar Arnaldo Batista Neto E Silva; Brandão, Marcelo Mendes; Omoto, Celso; Sperling, Felix A. H.

    2015-01-01

    The oriental fruit moth Grapholita molesta is one of the major pests of stone and pome fruit species in Brazil. Here, we applied 1226 SNPs obtained by genotyping-by-sequencing to test whether host species associations or other factors such as geographic distance structured populations of this pest. Populations from the main areas of occurrence of G. molesta were sampled principally from peach and apple orchards. Three main clusters were recovered by neighbor-joining analysis, all defined by g...

  18. Stock Structure and Homing Fidelity in Gulf of Mexico Sturgeon (Acipenser Oxyrinchus Desotoi) Based on Restriction Fragment Length Polymorphism and Sequence Analyses of Mitochondrial DNA

    OpenAIRE

    Stabile, J.; Waldman, J. R.; Parauka, F.; Wirgin, I.

    1996-01-01

    Efforts have been proposed worldwide to restore sturgeon populations through the use of hatcheries to supplement natural reproduction and to reintroduce sturgeon where they have become extinct. We examined the population structure and inferred the extent of homing in the anadromous Gulf of Mexico (Gulf) sturgeon (Acipenser oxyrinchus desotoi). Restriction fragment length polymorphism and control region sequence analyses of mitochondrial DNA (mtDNA) were used to identify haplotypes of Gulf stu...

  19. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    Energy Technology Data Exchange (ETDEWEB)

    Storrs, R.W.

    1992-08-01

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by {sup 31}P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 {Angstrom} of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an {alpha}-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  20. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    Energy Technology Data Exchange (ETDEWEB)

    Storrs, R.W.

    1992-08-01

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by [sup 31]P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 [Angstrom] of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an [alpha]-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.