Sample records for sequence backbone composition

  1. Solution rheology of hydrophobically modified associative polymers: Effects of backbone composition

    E-print Network

    Khan, Saad A.

    Solution rheology of hydrophobically modified associative polymers: Effects of backbone composition of polymer molecular structure on the solution rheology of a hydrophobically modified associative polymer ethoxylate urethane polymers, forming transient networks through mo- lecular associations. Due

  2. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.

    PubMed

    Lapidoth, Gideon D; Baran, Dror; Pszolla, Gabriele M; Norn, Christoffer; Alon, Assaf; Tyka, Michael D; Fleishman, Sarel J

    2015-08-01

    Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function-essential to exert control over all polypeptide degrees of freedom-remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root-mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti-lysozyme antibodies, complementarity-determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity. Proteins 2015; 83:1385-1406. © 2015 Wiley Periodicals, Inc. PMID:25670500

  3. De novo Backbone and Sequence Design of an Idealized ?\\/?-barrel Protein: Evidence of Stable Tertiary Structure

    Microsoft Academic Search

    F. Offredi; F. Dubail; P. Kischel; K. Sarinski; A. S. Stern; C. Van de Weerdt; J. C. Hoch; C. Prosperi; J. M. Francois; S. L. Mayo; J. A. Martial

    2003-01-01

    We have designed, synthesized, and characterized a 216 amino acid residue sequence encoding a putative idealized ?\\/?-barrel protein. The design was elaborated in two steps. First, the idealized backbone was defined with geometric parameters representing our target fold: a central eight parallel-stranded ?-sheet surrounded by eight parallel ?-helices, connected together with short structural turns on both sides of the barrel.

  4. Comparative experimental investigation on the actuation mechanisms of ionic polymer–metal composites with different backbones and water contents

    SciTech Connect

    Zhu, Zicai; Chang, Longfei; Wang, Yanjie; Chen, Hualing, E-mail: hlchen@mail.xjtu.edu.cn [State Key Laboratory of Mechanical Structure Strength and Vibration, Xi'an Jiaotong University, Xi'an 710049 (China); School of Mechanical Engineering, Xi'an Jiaotong University, Xi'an 710049 (China); Asaka, Kinji [Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Osaka 563-8577 (Japan); Zhao, Hongxia [Niumag Corporation, Shanghai 200333 (China); Li, Dichen [School of Mechanical Engineering, Xi'an Jiaotong University, Xi'an 710049 (China); State Key Laboratory for Manufacturing Systems Engineering, Xi'an Jiaotong University, Xi'an 710049 (China)

    2014-03-28

    Water-based ionic polymer–metal composites (IPMCs) exhibit complex deformation properties, especially when the water content changes. To explore the general actuation mechanisms, both Nafion and Flemion membranes are used as the polymer backbones. IPMC deformation includes three stages: fast anode deformation, relaxation deformation, and slow anode deformation, which is mainly dependent on the water content and the backbone. When the water content decreases from 21 to 14?wt.?%, Nafion–IPMC exhibits a large negative relaxation deformation, zero deformation, a positive relaxation deformation, and a positive steady deformation without relaxation in sequence. Despite the slow anode deformation, Flemion–IPMC also shows a slight relaxation deformation, which disappears when the water content is less than 13?wt.?%. The different water states are investigated at different water contents using nuclear magnetic resonance spectroscopy. The free water, which decreases rapidly at the beginning through evaporation, is proven to be critical for relaxation deformation. For the backbone, indirect evidence from the steady current response is correlated with the slow anode deformation of Flemion-IPMC. The latter is explained by the secondary dissociation of the weak acid group –COOH. Finally, we thoroughly explain not only the three deformations by swelling but also their evolvement with decreasing water content. A fitting model is also presented based on a multi-diffusion equation to reveal the deformation processes more clearly, the results from which are in good agreement with the experimental results.

  5. HPLC purification of synthetic oligodeoxyribonucleotides containing base- and backbone-modified sequences.

    PubMed

    Green, A P; Burzynski, J; Helveston, N M; Prior, G M; Wunner, W H; Thompson, J A

    1995-11-01

    Applications for a new polymer resin, PolyFlo, are described for both the small-scale and large-scale purification of synthetic oligodeoxyribonucleotides varying in length from 18-41 bases. The unique properties of this innovative resin provide > 95% purified full-length oligodeoxyribonucleotides with greater than 90% yield starting from either crude trityl-on or trityl-off unmodified as well as base (biotin)- or backbone (e.g., phosphorothioate)-modified products. Full biological activity of recovered nucleic acid is retained, and the resin is capable of removing contaminating endotoxins during purification. The resin performance is predictable and reliable. The resin can be regenerated easily and is particularly economic when employed directly in ammonia or with the trityl-off option. PolyFlo meets the requirements of current Good Manufacturing Practices. PMID:8588925

  6. T-DNA vector backbone sequences are frequently integrated into the genome of transgenic plants obtained by Agrobacterium-mediated transformation

    Microsoft Academic Search

    Sylvie De Buck; Chris De Wilde; Marc Van Montagu; Ann Depicker

    2000-01-01

    Transgenic Arabidopsis and tobacco plants (125) derived from seven Agrobacterium-mediated transformation experiments were screened by polymerase chain reaction and DNA gel blot analysis for the presence of vector `backbone' sequences. The percentage of plants with vector DNA not belonging to the T-DNA varied between 20% and 50%. Neither the plant species, the explant type used for transformation, the replicon type

  7. Modeling backbone flexibility to achieve sequence diversity: The design of novel alpha-helical ligands for Bcl -xL

    E-print Network

    of the designed solutions experimentally and found that this approach worked well when normal mode calculations to the anti-apoptotic protein Bcl-xL, a member of the Bcl-2 protein family. We demonstrate how normal mode or impossible to achieve using only a fixed backbone. Thus, introducing backbone flexibility via normal mode

  8. Composition for nucleic acid sequencing

    Microsoft Academic Search

    Jonas Korlach; Watt W. Webb; Michael Levene; Stephen Turner; Harold G. Craighead; Mathieu Foquet

    2008-01-01

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is

  9. Arbitrarily accurate narrowband composite pulse sequences

    NASA Astrophysics Data System (ADS)

    Vitanov, Nikolay V.

    2011-12-01

    Narrowband composite pulse sequences containing an arbitrary number N of identical pulses are presented. The composite phases are given by a very simple analytic formula and the transition probability is merely sin2N(A/2), where A is the pulse area. These narrowband sequences can be made accurate to any order with respect to variations in A for sufficiently many constituent pulses, i.e., excitation can be suppressed below any desired value for any pulse area but ?.

  10. Loss of Internal Backbone Carbonyls: Additional Evidence for Sequence-Scrambling in Collision-Induced Dissociation of y-Type Ions

    NASA Astrophysics Data System (ADS)

    Harper, Brett; Miladi, Mahsan; Solouki, Touradj

    2014-10-01

    It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAH AA-NH2 heptapeptide and des-acetylated-?-melanocyte-stimulating hormone (d?-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MSn), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/ z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/ z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-"like" ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.

  11. The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation.

    PubMed

    Vedler, Eve; Vahter, Merle; Heinaru, Ain

    2004-11-01

    The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium Achromobacter xylosoxidans subsp. denitrificans strain EST4002 contains plasmid pEST4011. This plasmid ensures its host a stable 2,4-D(+) phenotype. We determined the complete 76,958-bp nucleotide sequence of pEST4011. This plasmid is a deletion and duplication derivative of pD2M4, the 95-kb highly unstable laboratory ancestor of pEST4011, and was self-generated during different laboratory manipulations performed to increase the stability of the 2,4-D(+) phenotype of the original strain, strain D2M4(pD2M4). The 47,935-bp catabolic region of pEST4011 forms a transposon-like structure with identical copies of the hybrid insertion element IS1071::IS1471 at the two ends. The catabolic regions of pEST4011 and pJP4, the best-studied 2,4-D-degradative plasmid, both contain homologous, tfd-like genes for complete 2,4-D degradation, but they have little sequence similarity other than that. The backbone genes of pEST4011 are most similar to the corresponding genes of broad-host-range self-transmissible IncP1 plasmids. The backbones of the other three IncP1 catabolic plasmids that have been sequenced (the 2,4-D-degradative plasmid pJP4, the haloacetate-catabolic plasmid pUO1, and the atrazine-catabolic plasmid pADP-1) are nearly identical to the backbone of R751, the archetype plasmid of the IncP1 beta subgroup. We show that despite the overall similarity in plasmid organization, the pEST4011 backbone is sufficiently different (51 to 86% amino acid sequence identity between individual backbone genes) from the backbones of members of the three IncP1 subgroups (the alpha, beta, and gamma subgroups) that it belongs to a new IncP1subgroup, the delta subgroup. This conclusion was also supported by a phylogenetic analysis of the trfA2, korA, and traG gene products of different IncP1 plasmids. PMID:15489427

  12. Fractal dimensions of oligonucleotide compositions of DNA sequences

    SciTech Connect

    Korolev, S.V.; Tumanyan, V.G. [Russian Academy of Sciences, Moscow (Russian Federation). Engelhardt Inst. of Molecular Biology

    1993-12-31

    Fractal dimension (FD) of oligonucleotide composition is presented as an analog of genetic text complexity. FD for prokaryotic and eukaryotic sequences are estimated. Reliable differences between FD of coding and non-coding sequences in higher organisms are demonstrated. At the same time similar value of coding regions from different sources illustrate stability of such sequences against evolutionary processes. The proposed method provides a fast calculation of FD value for sequences of any length.

  13. Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences

    E-print Network

    Nowak, Martin A.

    Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences of life, the biological information of nucleic acid polymers must have increased to encode functional work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization

  14. Spines, backbones and orthopedic surgery. Spines, backbones and orthopedic surgery.

    E-print Network

    1/ 17 Spines, backbones and orthopedic surgery. Spines, backbones and orthopedic surgery. Simon;2/ 17 Spines, backbones and orthopedic surgery. Motivation #12;2/ 17 Spines, backbones and orthopedic motion with a near critical drift towards an absorbing barrier at the origin. #12;3/ 17 Spines, backbones

  15. Sea Lion Skeleton - Backbone

    NSDL National Science Digital Library

    Ketan Patel (California State University, Fullerton; Student, Biological Sciences)

    2007-07-27

    Sea lions are vertebrates with both backbones and ribs. The backbone is a gliding joint, allowing the animal to be flexible, while the ribs main function is to protect it's inner organs. The short tail helps to balance the animal while walking on land.

  16. RNA backbone is rotameric

    PubMed Central

    Murray, Laura J. W.; Arendall, W. Bryan; Richardson, David C.; Richardson, Jane S.

    2003-01-01

    Despite the importance of local structural detail to a mechanistic understanding of RNA catalysis and binding functions, RNA backbone conformation has been quite recalcitrant to analysis. There are too many variable torsion angles per residue, and their raw empirical distributions are poorly clustered. This study applies quality-filtering techniques (using resolution, crystallographic B factor, and all-atom steric clashes) to the backbone torsion angle distributions from an 8,636-residue RNA database. With noise levels greatly reduced, clear signal appears for the underlying angle preferences. Half-residue torsion angle distributions for ?-?-? and for ?-?-? are plotted and contoured in 3D; each shows about a dozen distinct peaks, which can then be combined in pairs to define complete RNA backbone conformers. Traditional nucleic acid residues are defined from phosphate to phosphate, but here we use a base-to-base (or sugar-to-sugar) division into “suites” to parse the RNA backbone repeats, both because most backbone steric clashes are within suites and because the relationship of successive bases is both reliably determined and conformationally important. A suite conformer has seven variables, with sugar pucker specified at both ends. Potential suite conformers were omitted if not represented by at least a small cluster of convincing data points after application of quality filters. The final result is a small library of 42 RNA backbone conformers, which should provide valid conformations for nearly all RNA backbone encountered in experimental structures. PMID:14612579

  17. A nucleotide composition constraint of genome sequences.

    PubMed

    Zhang, Chun-Ting; Zhang, Ren

    2004-04-01

    Let a, c, g and t denote the occurrence frequencies of A, C, G and T, respectively, in a genome. We calculated the statistical quantity S = a2 + c2 + g2 + t2 for each of 809 genomes (11 archaea, 42 bacteria, 3 eukaryota, 90 phages, 36 viroids and 627 viruses) and 236 plasmids. We found that S < 1/3 is strictly valid for almost all of the above genomes or plasmids. As a direct deduction of the above observation, it is shown that (i) the statistical quantity S is a kind of genome order index, which is negatively correlated with the Shannon H function; (ii) S < 1/3 suggests that a minimal value of the Shannon H function is required for each genome; (iii) S defined above would be a new biological statistical quantity, useful to describe the composition features of genomes; (iv) By jointly considering the Chargaff Parity Rule 2, it is shown that the genomic G + C content should be in between 0.211 and 0.789. PMID:15130543

  18. Optimized control of multistate quantum systems by composite pulse sequences

    NASA Astrophysics Data System (ADS)

    Genov, G. T.; Torosov, B. T.; Vitanov, N. V.

    2011-12-01

    We introduce a technique for derivation of high-fidelity composite pulse sequences for two types of multistate quantum systems: systems with the SU(2) and Morris-Shore dynamic symmetries. For the former type, we use the Majorana decomposition to reduce the dynamics to an effective two-state system, which allows us to find the propagator analytically and use the pool of available composite pulses for two-state systems. For the latter type of multistate systems, we use the Morris-Shore decomposition, which reduces the multistate dynamics to a set of two-state systems. We present examples which demonstrate that the multistate composite sequences open a variety of possibilities for coherent control of quantum systems with multiple states.

  19. hNCOcanH pulse sequence and a robust protocol for rapid and unambiguous assignment of backbone ((1)H(N), (15)N and (13)C') resonances in (15)N/(13)C-labeled proteins.

    PubMed

    Kumar, Dinesh; Hosur, Ramakrishna V

    2011-09-01

    A three-dimensional nuclear magnetic resonance (NMR) pulse sequence named as hNCOcanH has been described to aid rapid sequential assignment of backbone resonances in (15)N/(13)C-labeled proteins. The experiment has been derived by a simple modification of the previously described HN(C)N pulse sequence [Panchal et al., J. Biomol. NMR 20 (2001) 135-147]; t2 evolution is used to frequency label (13)C' rather than (15)N (similar trick has also been used in the design of hNCAnH pulse sequence from hNcaNH [Frueh et al., JACS, 131 (2009) 12880-12881]). The modification results in a spectrum equivalent to HNCO, but in addition to inter-residue correlation peaks (i.e. Hi , Ci-1), the spectrum also contains additional intra-residue correlation peaks (i.e. Hi-1 , Ci-1) in the direct proton dimension which has maximum resolution. This is the main strength of the experiment and thus, even a small difference in amide (1) H chemical shifts (5-6 Hz) can be used for establishing a sequential connectivity. This experiment in combination with the HNN experiment described previously [Panchal et al., J. Biomol. NMR 20 (2001) 135-147] leads to a more robust assignment protocol for backbone resonances ((1) H(N) , (15)N) than could be derived from the combination of HNN and HN(C)N experiments [Bhavesh et al., Biochemistry, 40 (2001) 14727-14735]. Further, this new protocol enables assignment of (13)C' resonances as well. We believe that the experiment and the protocol presented here will be of immense value for structural-and functional-proteomics research by NMR. Performance of this experiment has been demonstrated using (13)C/(15)N labeled ubiquitin. PMID:21818779

  20. Dolphin Skeleton - Backbone

    NSDL National Science Digital Library

    Ketan Patel (California State University, Fullerton; Student, Biological Sciences)

    2007-07-27

    The dolphin is built to be sleek. Its body is made of almost entirely backbone (a gliding joint) which makes it very flexible under water. The ribs protect the inner organs of the dolphin and the tail beats from side to side, thrusting the animal forward.

  1. Engineering Protein Structure: Backbone Relaxation, Electrostatics, Specificity

    NASA Astrophysics Data System (ADS)

    Harbury, Pehr

    2001-03-01

    Successful design of hyperthermophilic proteins has given hope of rationally engineering the shapes and functions of novel polypeptide sequences. Nevertheless, formidable technical challenges remain. First, existing design methods require prior knowledge of a naturally-occurring, fixed-backbone conformation. An enormous gap exists between fixed-backbone approaches and true de novo design. Second, current design methods use empirical potential energy functions that cannot describe the physical chemistry of enzymatic reactions. Finally, a conceptual basis for engineering specificity into molecular interactions is lacking. We are addressing these limitations within the context of the simplest of all protein folds, the coiled coil. We use parametric backbone models to generate and test novel protein backbone structures. We have developed and are characterizing a physically-based molecular mechanics potential that treats solvent as a dielectric continuum. The analytical form of the electrostatic potential is evaluated rapidly, allowing us to model the electrostatic effects of dynamic protein side-chain rearrangements. Finally, we are developing a general framework for sequence selection that specifies a sequence for a target structure by taking into consideration a large ensemble of competing conformational states. If successful, this approach will be applicable to almost any protein engineering problem.

  2. Predicting membrane protein types by fusing composite protein sequence features into pseudo amino acid composition.

    PubMed

    Hayat, Maqsood; Khan, Asifullah

    2011-02-21

    Membrane proteins are vital type of proteins that serve as channels, receptors, and energy transducers in a cell. Prediction of membrane protein types is an important research area in bioinformatics. Knowledge of membrane protein types provides some valuable information for predicting novel example of the membrane protein types. However, classification of membrane protein types can be both time consuming and susceptible to errors due to the inherent similarity of membrane protein types. In this paper, neural networks based membrane protein type prediction system is proposed. Composite protein sequence representation (CPSR) is used to extract the features of a protein sequence, which includes seven feature sets; amino acid composition, sequence length, 2 gram exchange group frequency, hydrophobic group, electronic group, sum of hydrophobicity, and R-group. Principal component analysis is then employed to reduce the dimensionality of the feature vector. The probabilistic neural network (PNN), generalized regression neural network, and support vector machine (SVM) are used as classifiers. A high success rate of 86.01% is obtained using SVM for the jackknife test. In case of independent dataset test, PNN yields the highest accuracy of 95.73%. These classifiers exhibit improved performance using other performance measures such as sensitivity, specificity, Mathew's correlation coefficient, and F-measure. The experimental results show that the prediction performance of the proposed scheme for classifying membrane protein types is the best reported, so far. This performance improvement may largely be credited to the learning capabilities of neural networks and the composite feature extraction strategy, which exploits seven different properties of protein sequences. The proposed Mem-Predictor can be accessed at http://111.68.99.218/Mem-Predictor. PMID:21110985

  3. Throughput Optimization in Mobile Backbone Networks

    E-print Network

    Craparo, Emily M.

    This paper describes new algorithms for throughput optimization in a mobile backbone network. This hierarchical communication framework combines mobile backbone nodes, which have superior mobility and communication capability, ...

  4. Electronic specific heat of DNA: Effects of backbones and disorder

    NASA Astrophysics Data System (ADS)

    Kundu, Sourav; Karmakar, S. N.

    2015-07-01

    In the present work we report the results of our investigation of the electronic specific heat (ESH) of DNA molecule modeled within the tight-binding framework. We take four different DNA sequences ranging from periodic, quasi-periodic to random and studied both ESH and also the density of states to supplement our ESH results. The role of the backbone structure and the effects of environment on ESH is discussed. We observe that irrespective of the sequences there is a universal response of the ESH spectra for a given disorder. The nature of response of specific heat for backbone disorder is totally opposite in low and high temperature regimes.

  5. Solution behavior of graft copolymers of poly(methyl methacrylate) backbone and poly(propylene oxide-b-ethylene oxide) branches: effect of structure and composition

    Microsoft Academic Search

    Elizabete F. Lucas; Clara Marize F. Oliveira

    1995-01-01

    The effect of structure and composition of poly(methyl methacrylate) (PMMA) main chain and poly(propylene oxide-b-ethylene oxide) (PPO-b-PEO) graft chain on solution behavior was evaluated. Separated samples of homopolymers were also analysed to provide comparisons. The solutions were prepared by dissolving the sample in selective mixtures of tetrahydrofuran (THF) and hexane. The polymer solutions were submitted to viscometric measurements as function

  6. Backbone construction in selfish wireless networks

    Microsoft Academic Search

    Seungjoon Lee; Dave Levin; Vijay Gopalakrishnan; Bobby Bhattacharjee

    2007-01-01

    We present a protocol to construct routing backbones in wireless networks composed of selfish participants. Backbones are inherently cooperative, so constructing them in selfish environments is particularly difficult; participants want a backbone to exist (soothers relay their packets) but do not want to join the backbone (so they do not have to relay packets for others). We model the wireless

  7. Pseudodihedrals: simplified protein backbone representation with knowledge-based energy.

    PubMed Central

    DeWitte, R. S.; Shakhnovich, E. I.

    1994-01-01

    Pairwise contact energies do not explicitly take protein secondary structure into account, and so provide an incomplete description of conformational energy. In order to construct a Hamiltonian that specifically relates to protein backbone conformations, a simplified backbone angle is used. The pseudodihedral angle (the torsion angle between planes defined by 4 consecutive alpha-carbon atoms) provides a simplified backbone representation and continues to manifest information about secondary-structure elements: the pseudo-Ramachandran plot contains helical and sheetlike regions. The distribution of pseudodihedral angles is highly sensitive to the identity of the central pair of amino acids. Therefore, a sequence-dependent, knowledge-based potential energy was found according to a quasichemical approximation. These functions form complementary additions to the contact potentials currently in use. This pseudodihedral potential greatly enhances the ability to design sequences that are specific to a given conformation and also improves the ability to discriminate a native conformation from many other conformations. PMID:7833816

  8. Estimating local backbone structural deviation in homology models.

    PubMed

    Cardozo, T; Batalov, S; Abagyan, R

    2000-01-01

    After the atomic coordinates themselves, the most important data in a homology model are the spatial reliability estimates associated with each of the atoms (atom annotation). Recent blind homology modeling predictions have demonstrated that principally correct sequence-structure alignments are achievable to sequence identities as low as 25% [Martin, A.C., MacArthur, M.W., Thornton, J.M., 1997. Assessment of comparative modeling in CASP2. Proteins Suppl(1), 14-28]. The locations and extent of spatial deviations in the backbone between correctly aligned homologous protein structures remained very poorly estimated however, and these errors were the cause of errant loop predictions [Abagyan, R., Batalov, S., Cardozo, T., Totrov, M., Webber, J., Zhou, Y., 1997. Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search. Proteins Suppl(1), 29-37]. In order to derive accurate measures for local backbone deviations, we made a systematic study of static local backbone deviations between homologous pairs of protein structures. We found that 'through space' proximity to gaps and chain termini, local three-dimensional 'density', three-dimensional environment conservation, and B-factor of the template contribute to local deviations in the backbone in addition to local sequence identity. Based on these finding, we have identified the meaningful ranges of values within which each of these parameters correlates with static local backbone deviation and produced a combined scoring function to greatly improve the estimation of local backbone deviations. The optimized function has more than twice the accuracy of local sequence identity or B-factor alone and was validated in a recent blind structure prediction experiment. This method may be used to evaluate the utility of a preliminary homology model for a particular biological investigation (e.g. drug design) or to provide an improved starting point for molecular mechanics loop prediction methods. PMID:10642877

  9. Nucleosome positioning based on the sequence word composition.

    PubMed

    Yi, Xian-Fu; He, Zhi-Song; Chou, Kuo-Chen; Kong, Xiang-Yin

    2012-01-01

    The DNA of all eukaryotic organisms is packaged into nucleosomes (a basic repeating unit of chromatin). A nucleosome consists of histone octamer wrapped by core DNA and linker histone H1 associated with linker DNA. It has profound effects on all DNA-dependent processes by affecting sequence accessibility. Understanding the factors that influence nucleosome positioning has great help to the study of genomic control mechanism. Among many determinants, the inherent DNA sequence has been suggested to have a dominant role in nucleosome positioning in vivo. Here, we used the method of minimum redundancy maximum relevance (mRMR) feature selection and the nearest neighbor algorithm (NNA) combined with the incremental feature selection (IFS) method to identify the most important sequence features that either favor or inhibit nucleosome positioning. We analyzed the words of 53,021 nucleosome DNA sequences and 50,299 linker DNA sequences of Saccharomyces cerevisiae. 32 important features were abstracted from 5,460 features, and the overall prediction accuracy through jackknife cross-validation test was 76.5%. Our results support that sequence-dependent DNA flexibility plays an important role in positioning nucleosome core particles and that genome sequence facilitates the rapid nucleosome reassembly instead of nucleosome depletion. Besides, our results suggest that there exist some additional features playing a considerable role in discriminating nucleosome forming and inhibiting sequences. These results confirmed that the underlying DNA sequence plays a major role in nucleosome positioning. PMID:21919856

  10. High-Fidelity Adiabatic Passage by Composite Sequences of Chirped Pulses

    NASA Astrophysics Data System (ADS)

    Torosov, Boyan T.; Guérin, Stéphane; Vitanov, Nikolay V.

    2011-06-01

    We present a method for optimization of the technique of adiabatic passage between two quantum states by composite sequences of frequency-chirped pulses with specific relative phases: composite adiabatic passage (CAP). By choosing the composite phases appropriately the nonadiabatic losses can be canceled to any desired order with sufficiently long sequences, regardless of the nonadiabatic coupling. The values of the composite phases are universal for they do not depend on the pulse shapes and the chirp. The accuracy of the CAP technique and its robustness against parameter variations make CAP suitable for high-fidelity quantum information processing.

  11. A design backbone for the biomedical engineering curriculum

    Microsoft Academic Search

    W. J. Tompkins; D. Beebe; J. A. Gimm; M. Nicosia; N. Ramanujam; P. Thompson; M. E. Tyler; J. G. Webster

    2002-01-01

    In this paper, we summarize our experiences as advisors supervising biomedical engineering design projects in the design backbone of our curriculum, the six-semester design course sequence required for all biomedical engineering majors at the University of Wisconsin-Madison.

  12. Recapitulation of Protein Family Divergence using Flexible Backbone Protein Design

    E-print Network

    Baker, David

    the backbone for a fixed amino acid sequence using atomic-resolution structure prediction. We find for assigning homologous relationships between proteins, and mature instances of these techniques, such as PSI-BLAST the success of this approach, a subsequent step is to use more detailed, atomic-resolution methods

  13. Efficient Scene Change Detection in MPEG Compressed Video Using Composite Block Averaged Luminance Image Sequence

    Microsoft Academic Search

    Wing-San Chau; O. C. Au; Tak-Song Chong; Tai-Wai Chan; Chi-Shun Cheung

    2005-01-01

    In video indexing and segmentation, scene change detection is an essential step. However, the problems of inaccuracy and high complexity for existing scene change detection methods are still unsolved. This work presents several advance methods using the partially decoded information from MPEG compressed video. The DC composite image sequence is proposed for scene change detection. DC sequence is widely used

  14. Diverse nucleotide compositions and sequence fluctuation in Rubisco protein genes

    NASA Astrophysics Data System (ADS)

    Holden, Todd; Dehipawala, S.; Cheung, E.; Bienaime, R.; Ye, J.; Tremberger, G., Jr.; Schneider, P.; Lieberman, D.; Cheung, T.

    2011-10-01

    The Rubisco protein-enzyme is arguably the most abundance protein on Earth. The biology dogma of transcription and translation necessitates the study of the Rubisco genes and Rubisco-like genes in various species. Stronger correlation of fractal dimension of the atomic number fluctuation along a DNA sequence with Shannon entropy has been observed in the studied Rubisco-like gene sequences, suggesting a more diverse evolutionary pressure and constraints in the Rubisco sequences. The strategy of using metal for structural stabilization appears to be an ancient mechanism, with data from the porphobilinogen deaminase gene in Capsaspora owczarzaki and Monosiga brevicollis. Using the chi-square distance probability, our analysis supports the conjecture that the more ancient Rubisco-like sequence in Microcystis aeruginosa would have experienced very different evolutionary pressure and bio-chemical constraint as compared to Bordetella bronchiseptica, the two microbes occupying either end of the correlation graph. Our exploratory study would indicate that high fractal dimension Rubisco sequence would support high carbon dioxide rate via the Michaelis- Menten coefficient; with implication for the control of the whooping cough pathogen Bordetella bronchiseptica, a microbe containing a high fractal dimension Rubisco-like sequence (2.07). Using the internal comparison of chi-square distance probability for 16S rRNA (~ E-22) versus radiation repair Rec-A gene (~ E-05) in high GC content Deinococcus radiodurans, our analysis supports the conjecture that high GC content microbes containing Rubisco-like sequence are likely to include an extra-terrestrial origin, relative to Deinococcus radiodurans. Similar photosynthesis process that could utilize host star radiation would not compete with radiation resistant process from the biology dogma perspective in environments such as Mars and exoplanets.

  15. Effects of laminate sequencing on thermoforming of thermoplastic matrix composites

    Microsoft Academic Search

    M. Sadighi; E. Rabizadeh; F. Kermansaravi

    2008-01-01

    Continuous fiber-reinforced thermoplastic composites are promising materials for light-weight structural components. Their medium to high processing and temperature-dependent properties, and the complex deformation mechanisms that occur within the composite sheet during the forming, are main problems in the practical production of parts. Thermoforming is an effective fabrication method due to the reversible solid–liquid phase transformation of thermoplastic materials. Deep drawing

  16. Backbone construction in selfish wireless networks

    Microsoft Academic Search

    Seungjoon Lee; Dave Levin; Vijay Gopalakrishnan; Bobby Bhattacharjee

    2007-01-01

    We present a protocol to construct routing backbones in wireless networks composed of selsh participants. Back- bones are inherently cooperative, so constructing them in selsh environments is particularly dicult; participants want a backbone to exist (so others relay their packets) but do not want to join the backbone (so they do not have to relay packets for others). We model

  17. Nucleic acid compositions with scissile linkage useful for detecting nucleic acid sequences

    SciTech Connect

    Duck, P.; Bender, R.; Crosby, W.; Robertson, J.G.

    1989-10-24

    This patent describes a composition. It comprises the structure: S-L(NA{sub 1}-S-NA{sub 2}){sub n}M. NA{sub 1} and NA{sub 2} are nucleic acid sequences; -S- is a scissile linkage which is capable of being cleaved or disrupted without cleaving or disrupting the nuclei acid sequences of NA{sub 1} or NA{sub 2} or of a target nuclei acid sequence capable of hybridizing to the NA{sub 1} and NA{sub 2} sequences, or to the NA{sub 1} and NA{sub 2} sequences and the scissile linkage of the composition, wherein if the scissile linkage is a nuclei acid sequence it is RNA when both NA{sub 1} and NA{sub 2} are DNA sequences, or the scissile linkage is DNA when both NA{sub 1} and NA{sub 2} are RNA sequences; and n is an integer from 1 to 4. The solid lines represent chemical bonds; X is a solid support; L is a chemical entity which links NA{sub 1} to the solid support; and M is a marker.

  18. Simple Sequence Repeats in Escherichia coli: Abundance, Distribution, Composition, and Polymorphism

    Microsoft Academic Search

    Riva Gur-Arie; Cyril J. Cohen; Yuval Eitan; Leora Shelef; Eric M. Hallerman

    Computer-based genome-wide screening of the DNA sequence of Escherichia coli strain K12 revealed tens of thousands of tandem simple sequence repeat (SSR) tracts, with motifs ranging from 1 to 6 nucleotides. SSRs were well distributed throughout the genome. Mononucleotide SSRs were over-represented in noncoding regions and under-represented in open reading frames (ORFs). Nucleotide composition of mono- and dinucleotide SSRs, both

  19. Enzymes/non-enzymes classification model complexity based on composition, sequence, 3D and topological indices.

    PubMed

    Munteanu, Cristian Robert; González-Díaz, Humberto; Magalhães, Alexandre L

    2008-09-21

    The huge amount of new proteins that need a fast enzymatic activity characterization creates demands of protein QSAR theoretical models. The protein parameters that can be used for an enzyme/non-enzyme classification includes the simpler indices such as composition, sequence and connectivity, also called topological indices (TIs) and the computationally expensive 3D descriptors. A comparison of the 3D versus lower dimension indices has not been reported with respect to the power of discrimination of proteins according to enzyme action. A set of 966 proteins (enzymes and non-enzymes) whose structural characteristics are provided by PDB/DSSP files was analyzed with Python/Biopython scripts, STATISTICA and Weka. The list of indices includes, but it is not restricted to pure composition indices (residue fractions), DSSP secondary structure protein composition and 3D indices (surface and access). We also used mixed indices such as composition-sequence indices (Chou's pseudo-amino acid compositions or coupling numbers), 3D-composition (surface fractions) and DSSP secondary structure amino acid composition/propensities (obtained with our Prot-2S Web tool). In addition, we extend and test for the first time several classic TIs for the Randic's protein sequence Star graphs using our Sequence to Star Graph (S2SG) Python application. All the indices were processed with general discriminant analysis models (GDA), neural networks (NN) and machine learning (ML) methods and the results are presented versus complexity, average of Shannon's information entropy (Sh) and data/method type. This study compares for the first time all these classes of indices to assess the ratios between model accuracy and indices/model complexity in enzyme/non-enzyme discrimination. The use of different methods and complexity of data shows that one cannot establish a direct relation between the complexity and the accuracy of the model. PMID:18606172

  20. Effects of stacking sequence on the impact resistance in composite laminates — Part 1: parametric study

    Microsoft Academic Search

    Edgar Fuoss; Paul V. Straznicky; Cheung Poon

    1998-01-01

    A study was undertaken to determine the effects of key stacking sequence parameters on the impact damage resistance in composite laminates. A finite element model using linear, quasi-static analysis was developed to analyse the internal stress state in the laminate and predict delamination damage. The model was found capable of predicting the relative damage trends with respect to changes in

  1. Protein location prediction using atomic composition and global features of the amino acid sequence

    SciTech Connect

    Cherian, Betsy Sheena, E-mail: betsy.skb@gmail.com [Centre for Bioinformatics, University of Kerala, Kariyavattom Campus, Thiruvananthapuram, Kerala (India); Nair, Achuthsankar S. [Centre for Bioinformatics, University of Kerala, Kariyavattom Campus, Thiruvananthapuram, Kerala (India)] [Centre for Bioinformatics, University of Kerala, Kariyavattom Campus, Thiruvananthapuram, Kerala (India)

    2010-01-22

    Subcellular location of protein is constructive information in determining its function, screening for drug candidates, vaccine design, annotation of gene products and in selecting relevant proteins for further studies. Computational prediction of subcellular localization deals with predicting the location of a protein from its amino acid sequence. For a computational localization prediction method to be more accurate, it should exploit all possible relevant biological features that contribute to the subcellular localization. In this work, we extracted the biological features from the full length protein sequence to incorporate more biological information. A new biological feature, distribution of atomic composition is effectively used with, multiple physiochemical properties, amino acid composition, three part amino acid composition, and sequence similarity for predicting the subcellular location of the protein. Support Vector Machines are designed for four modules and prediction is made by a weighted voting system. Our system makes prediction with an accuracy of 100, 82.47, 88.81 for self-consistency test, jackknife test and independent data test respectively. Our results provide evidence that the prediction based on the biological features derived from the full length amino acid sequence gives better accuracy than those derived from N-terminal alone. Considering the features as a distribution within the entire sequence will bring out underlying property distribution to a greater detail to enhance the prediction accuracy.

  2. Optimum stacking sequence design of composite sandwich panel using genetic algorithms

    NASA Astrophysics Data System (ADS)

    Bir, Amarpreet Singh

    Composite sandwich structures recently gained preference for various structural components over conventional metals and simple composite laminates in the aerospace industries. For most widely used composite sandwich structures, the optimization problems only requires the determination of the best stacking sequence and the number of laminae with different fiber orientations. Genetic algorithm optimization technique based on Darwin's theory of survival of the fittest and evolution is most suitable for solving such optimization problems. The present research work focuses on the stacking sequence optimization of composite sandwich panels with laminated face-sheets for both critical buckling load maximization and thickness minimization problems, subjected to bi-axial compressive loading. In the previous studies, only balanced and even-numbered simple composite laminate panels have been investigated ignoring the effects of bending-twisting coupling terms. The current work broadens the application of genetic algorithms to more complex composite sandwich panels with balanced, unbalanced, even and odd-numbered face-sheet laminates including the effects of bending-twisting coupling terms.

  3. The Bitcoin Backbone Protocol: Analysis and Applications

    E-print Network

    The Bitcoin Backbone Protocol: Analysis and Applications Juan A. Garay Yahoo Labs garay.leonardos@gmail.com November 16, 2014 Abstract Bitcoin is the first and most popular decentralized cryptocurrency to date. In this work, we extract and analyze the core of the Bitcoin protocol, which we term the Bitcoin backbone

  4. Utilisation of cod backbone by biochemical fractionation

    Microsoft Academic Search

    Asbjørn Gildberg; Jan A Arnesen; Mats Carlehög

    2002-01-01

    The backbone fraction obtained from industrial processing of Atlantic cod (Gadus morhua) yields about 15% of the whole fish weight. Due to a high content of muscle and bone proteins, it is a valuable raw material for further processing. In the present work minced backbones were subjected to gentle hydrolysis by proteinases to solubilize muscle proteins before the pure bone

  5. Polyolefin backbone substitution in binders for low temperature powder injection moulding feedstocks.

    PubMed

    Hausnerova, Berenika; Kuritka, Ivo; Bleyan, Davit

    2014-01-01

    This paper reports the substitution of polyolefin backbone binder components with low melting temperature carnauba wax for powder injection moulding applications. The effect of various binder compositions of Al?O? feedstock on thermal degradation parameters is investigated by thermogravimetric analysis. Within the experimental framework 29 original feedstock compositions were prepared and the superiority of carnauba wax over the polyethylene binder backbone was demonstrated in compositions containing polyethylene glycol as the initial opening agent and governing the proper mechanism of the degradation process. Moreover, the replacement of synthetic polymer by the natural wax contributes to an increase of environmental sustainability of modern industrial technologies. PMID:24583880

  6. Composite Sequences for Triple-dot Qubits that Compensate for Miscalibration and Hyperfine Gradients

    NASA Astrophysics Data System (ADS)

    Ladd, Thaddeus

    2014-03-01

    Exchange-only qubits defined in triple quantum dots form a promising means for all-electrical semiconductor quantum control, but they suffer from both charge noise and random magnetic field gradients. Low-frequency noise sources can be compensated using composite sequences, but the development of such sequences is constrained by the fact that exchange energies are always positive and the control axes are non-orthogonal. Here, we present the results of both analytical approaches and computational searches for composite pulse sequences, which compensate for simultaneous low-frequency miscalibration (due to fixed random electric fields) and hyperfine effects (due to nuclear magnetic fields) in a single triple-dot qubit. We also present compensation sequences for multi-qubit gates. These results can substantially improve the working fidelity of quantum operations in semiconductor quantum dot devices. Sponsored by United States Department of Defense. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressly or implied, of the United States Department of Defense or the U.S. Government.

  7. Conformational Entropy of the RNA Phosphate Backbone and Its Contribution to the Folding Free Energy

    PubMed Central

    Mak, Chi H.; Matossian, Tyler; Chung, Wen-Yeuan

    2014-01-01

    While major contributors to the free energy of RNA tertiary structures such as basepairing, base-stacking, and charge and counterion interactions have been studied extensively, little is known about the intrinsic free energy of the backbone. To assess the magnitude of the entropic strains along the phosphate backbone and their impact on the folding free energy, we have formulated a mathematical treatment for computing the volume of the main-chain torsion-angle conformation space between every pair of nucleobases along any sequence to compute the corresponding backbone entropy. To validate this method, we have compared the computed conformational entropies against a statistical free energy analysis of structures in the crystallographic database from several-thousand backbone conformations between nearest-neighbor nucleobases as well as against extensive computer simulations. Using this calculation, we analyzed the backbone entropy of several ribozymes and riboswitches and found that their entropic strains are highly localized along their sequences. The total entropic penalty due to steric congestions in the backbone for the native fold can be as high as 2.4 cal/K/mol per nucleotide for these medium and large RNAs, producing a contribution to the overall free energy of up to 0.72 kcal/mol per nucleotide. For these RNAs, we found that low-entropy high-strain residues are predominantly located at loops with tight turns and at tertiary interaction platforms with unusual structural motifs. PMID:24703311

  8. External Tank - The Structure Backbone

    NASA Technical Reports Server (NTRS)

    Welzyn, Kenneth; Pilet, Jeffrey C.; Diecidue-Conners, Dawn; Worden, Michelle; Guillot, Michelle

    2011-01-01

    The External Tank forms the structural backbone of the Space Shuttle in the launch configuration. Because the tank flies to orbital velocity with the Space Shuttle Orbiter, minimization of weight is mandatory, to maximize payload performance. Choice of lightweight materials both for structure and thermal conditioning was necessary. The tank is large, and unique manufacturing facilities, tooling, handling, and transportation operations were required. Weld processes and tooling evolved with the design as it matured through several block changes, to reduce weight. Non Destructive Evaluation methods were used to assure integrity of welds and thermal protection system materials. The aluminum-lithium alloy was used near the end of the program and weld processes and weld repair techniques had to be refined. Development and implementation of friction stir welding was a substantial technology development incorporated during the Program. Automated thermal protection system application processes were developed for the majority of the tank surface. Material obsolescence was an issue throughout the 40 year program. The final configuration and tank weight enabled international space station assembly in a high inclination orbit allowing international cooperation with the Russian Federal Space Agency. Numerous process controls were implemented to assure product quality, and innovative proof testing was accomplished prior to delivery. Process controls were implemented to assure cleanliness in the production environment, to control contaminants, and to preclude corrosion. Each tank was accepted via rigorous inspections, including non-destructive evaluation techniques, proof testing, and all systems testing. In the post STS-107 era, the project focused on ascent debris risk reduction. This was accomplished via stringent process controls, post flight assessment using substantially improved imagery, and selective redesigns. These efforts were supported with a number of test programs to simulate combined environments. Processing improvements included development and use of low spray guns for foam application, additional human factors considerations for production, use of high fidelity mockups during hardware processing with video review, improved tank access, extensive use of non destructive evaluation, and producibility enhancements. Design improvements included redesigned bipod fittings, a bellows heater, a feedline camera active during ascent flight, removal of the protuberance airload ramps, redesigned ice frost ramps, and titanium brackets replaced aluminum brackets on the liquid oxygen feedline. Post flight assessment improved due to significant addition of imagery assets, greatly improving situational awareness. The debris risk was reduced by two orders of magnitude. During this time a major natural disaster was overcome when Katrina damaged the manufacturing facility. Numerous lessons from these efforts are documented within the paper.

  9. Simple sequence repeats and compositional bias in the bipartite Ralstonia solanacearum GMI1000 genome

    PubMed Central

    Coenye, Tom; Vandamme, Peter

    2003-01-01

    Background Ralstonia solanacearum is an important plant pathogen. The genome of R. solananearum GMI1000 is organised into two replicons (a 3.7-Mb chromosome and a 2.1-Mb megaplasmid) and this bipartite genome structure is characteristic for most R. solanacearum strains. To determine whether the megaplasmid was acquired via recent horizontal gene transfer or is part of an ancestral single chromosome, we compared the abundance, distribution and compositon of simple sequence repeats (SSRs) between both replicons and also compared the respective compositional biases. Results Our data show that both replicons are very similar in respect to distribution and composition of SSRs and presence of compositional biases. Minor variations in SSR and compositional biases observed may be attributable to minor differences in gene expression and regulation of gene expression or can be attributed to the small sample numbers observed. Conclusions The observed similarities indicate that both replicons have shared a similar evolutionary history and thus suggest that the megaplasmid was not recently acquired from other organisms by lateral gene transfer but is a part of an ancestral R. solanacearum chromosome. PMID:12697060

  10. Sequencer

    NSDL National Science Digital Library

    2010-01-01

    In this activity, you will learn about number patterns in sequences and recursions. You will have the opportunity to choose a starting number, a multiplier, and an add-on. When the graph is made, the numbers in the sequence are displayed on a graph, and they are also listed below the graph.

  11. Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence.

    PubMed

    Schimelman, Jacob B; Dryden, Daniel M; Poudel, Lokendra; Krawiec, Katherine E; Ma, Yingfang; Podgornik, Rudolf; Parsegian, V Adrian; Denoyer, Linda K; Ching, Wai-Yim; Steinmetz, Nicole F; French, Roger H

    2015-02-14

    The role of base pair composition and stacking sequence in the optical properties and electronic transitions of DNA is of fundamental interest. We present and compare the optical properties of DNA oligonucleotides (AT)10, (AT)5(GC)5, and (AT-GC)5 using both ab initio methods and UV-vis molar absorbance measurements. Our data indicate a strong dependence of both the position and intensity of UV absorbance features on oligonucleotide composition and stacking sequence. The partial densities of states for each oligonucleotide indicate that the valence band edge arises from a feature associated with the PO4(3-) complex anion, and the conduction band edge arises from anti-bonding states in DNA base pairs. The results show a strong correspondence between the ab initio and experimentally determined optical properties. These results highlight the benefit of full spectral analysis of DNA, as opposed to reductive methods that consider only the 260 nm absorbance (A260) or simple purity ratios, such as A260/A230 or A260/A280, and suggest that the slope of the absorption edge onset may provide a useful metric for the degree of base pair stacking in DNA. These insights may prove useful for applications in biology, bioelectronics, and mesoscale self-assembly. PMID:25584920

  12. Backbone chemical shift assignments of mouse HOXA13 DNA binding domain bound to duplex DNA.

    PubMed

    Zhang, Yonghong; Thornburg, Chelsea K; Stadler, H Scott; Ames, James B

    2010-04-01

    The homeobox gene (Hoxa13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of many important proteins during embryonic morphogenesis. We report complete backbone NMR chemical shift assignments of mouse Hoxa13 DNA binding domain bound to an 11-residue DNA duplex (BMRB no. 16577). PMID:20232265

  13. Backbone chemical shift assignments of mouse HOXA13 DNA binding domain bound to duplex DNA

    Microsoft Academic Search

    Yonghong Zhang; Chelsea K. Thornburg; H. Scott Stadler; James B. Ames

    2010-01-01

    The homeobox gene (Hoxa13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression\\u000a of many important proteins during embryonic morphogenesis. We report complete backbone NMR chemical shift assignments of mouse\\u000a Hoxa13 DNA binding domain bound to an 11-residue DNA duplex (BMRB no. 16577).

  14. Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition

    PubMed Central

    Ulpinnis, Chris; Scholz, Uwe; Altmann, Thomas

    2015-01-01

    A major goal of maize genomic research is to identify sequence polymorphisms responsible for phenotypic variation in traits of economic importance. Large-scale detection of sequence variation is critical for linking genes, or genomic regions, to phenotypes. However, due to its size and complexity, it remains expensive to generate whole genome sequences of sufficient coverage for divergent maize lines, even with access to next generation sequencing (NGS) technology. Because methods involving reduction of genome complexity, such as genotyping-by-sequencing (GBS), assess only a limited fraction of sequence variation, targeted sequencing of selected genomic loci offers an attractive alternative. We therefore designed a sequence capture assay to target 29 Mb genomic regions and surveyed a total of 4,648 genes possibly affecting biomass production in 21 diverse inbred maize lines (7 flints, 14 dents). Captured and enriched genomic DNA was sequenced using the 454 NGS platform to 19.6-fold average depth coverage, and a broad evaluation of read alignment and variant calling methods was performed to select optimal procedures for variant discovery. Sequence alignment with the B73 reference and de novo assembly identified 383,145 putative single nucleotide polymorphisms (SNPs), of which 42,685 were non-synonymous alterations and 7,139 caused frameshifts. Presence/absence variation (PAV) of genes was also detected. We found that substantial sequence variation exists among genomic regions targeted in this study, which was particularly evident within coding regions. This diversification has the potential to broaden functional diversity and generate phenotypic variation that may lead to new adaptations and the modification of important agronomic traits. Further, annotated SNPs identified here will serve as useful genetic tools and as candidates in searches for phenotype-altering DNA variation. In summary, we demonstrated that sequencing of captured DNA is a powerful approach for variant discovery in maize genes. PMID:26151830

  15. Pyrrolidinyl PNA with ?/?-Dipeptide Backbone: From Development to Applications.

    PubMed

    Vilaivan, Tirayut

    2015-06-16

    The specific pairing between two complementary nucleobases (A·T, C·G) according to the Watson-Crick rules is by no means unique to natural nucleic acids. During the past few decades a number of nucleic acid analogues or mimics have been developed, and peptide nucleic acid (PNA) is one of the most intriguing examples. In addition to forming hybrids with natural DNA/RNA as well as itself with high affinity and specificity, the uncharged peptide-like backbone of PNA confers several unique properties not observed in other classes of nucleic acid analogues. PNA is therefore suited to applications currently performed by conventional oligonucleotides/analogues and others potentially beyond this. In addition, PNA is also interesting in its own right as a new class of oligonucleotide mimics. Unlimited opportunities exist to modify the PNA structure, stimulating the search for new systems with improved properties or additional functionality not present in the original PNA, driving future research and applications of these in nanotechnology and beyond. Although many structural variations of PNA exist, significant improvements to date have been limited to a few constrained derivatives of the privileged N-2-aminoethylglycine PNA scaffold. In this Account, we summarize our contributions in this field: the development of a new family of conformationally constrained pyrrolidinyl PNA having a nonchimeric ?/?-dipeptide backbone derived from nucleobase-modified proline and cyclic ?-amino acids. The conformational constraints dictated by the pyrrolidine ring and the ?-amino acid are essential requirements determining the binding efficiency, as the structure and stereochemistry of the PNA backbone significantly affect its ability to interact with DNA, RNA, and in self-pairing. The modular nature of the dipeptide backbone simplifies the synthesis and allows for rapid structural optimization. Pyrrolidinyl PNA having a (2'R,4'R)-proline/(1S,2S)-2-aminocyclopentanecarboxylic backbone (acpcPNA) binds to DNA with outstanding affinity and sequence specificity. It also binds to RNA in a highly sequence-specific fashion, albeit with lower affinity than to DNA. Additional characteristics include exclusive antiparallel/parallel selectivity and a low tendency for self-hybridization. Modification of the nucleobase or backbone allowing site-specific incorporation of labels and other functions to acpcPNA via click and other conjugation chemistries is possible, generating functional PNAs that are suitable for various applications. DNA sensing and biological applications of acpcPNA have been demonstrated, but these are still in their infancy and the full potential of pyrrolidinyl PNA is yet to be realized. With properties competitive with, and in some aspects superior to, the best PNA technology available to date, pyrrolidinyl PNA offers great promise as a platform system for future elaboration for the fabrication of new functional materials, nanodevices, and next-generation analytical tools. PMID:26022340

  16. Sparse Reliable Graph Backbones Shiri Chechik

    E-print Network

    ) ) times that of G. Moreover, for any pair of vertices s, t in G, the (s, t)-reliability of the backbone, with a trade-off spectrum Supported in part by Israel Science Foundation (grant 1372/09) and by the Israel

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

    NASA Astrophysics Data System (ADS)

    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.

  18. Comparison of base composition analysis and Sanger sequencing of mitochondrial DNA for four U.S. population groups.

    PubMed

    Kiesler, Kevin M; Coble, Michael D; Hall, Thomas A; Vallone, Peter M

    2014-01-01

    A set of 711 samples from four U.S. population groups was analyzed using a novel mass spectrometry based method for mitochondrial DNA (mtDNA) base composition profiling. Comparison of the mass spectrometry results with Sanger sequencing derived data yielded a concordance rate of 99.97%. Length heteroplasmy was identified in 46% of samples and point heteroplasmy was observed in 6.6% of samples in the combined mass spectral and Sanger data set. Using discrimination capacity as a metric, Sanger sequencing of the full control region had the highest discriminatory power, followed by the mass spectrometry base composition method, which was more discriminating than Sanger sequencing of just the hypervariable regions. This trend is in agreement with the number of nucleotides covered by each of the three assays. PMID:24315613

  19. Mapping Fusarium wilt race 1 resistance genes in cotton by inheritance, QTL and sequencing composition.

    PubMed

    Ulloa, Mauricio; Wang, Congli; Hutmacher, Robert B; Wright, Steven D; Davis, R Michael; Saski, Christopher A; Roberts, Philip A

    2011-07-01

    Knowledge of the inheritance of disease resistance and genomic regions housing resistance (R) genes is essential to prevent expanding pathogen threats such as Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans] in cotton (Gossypium spp.). We conducted a comprehensive study combining conventional inheritance, genetic and quantitative trait loci (QTL) mapping, QTL marker-sequence composition, and genome sequencing to examine the distribution, structure and organization of disease R genes to race 1 of FOV in the cotton genome. Molecular markers were applied to F(2) and recombinant inbred line (RIL) interspecific mapping populations from the crosses Pima-S7 (G. barbadense L.) × 'Acala NemX' (G. hirsutum L.) and Upland TM-1 (G. hirsutum) × Pima 3-79 (G. barbadense), respectively. Three greenhouse tests and one field test were used to obtain sequential estimates of severity index (DSI) of leaves, and vascular stem and root staining (VRS). A single resistance gene model was observed for the F(2) population based on inheritance of phenotypes. However, additional inheritance analyses and QTL mapping indicated gene interactions and inheritance from nine cotton chromosomes, with major QTLs detected on five chromosomes [Fov1-C06, Fov1-C08, (Fov1-C11 ( 1 ) and Fov1-C11 ( 2)) , Fov1-C16 and Fov1-C19 loci], explaining 8-31% of the DSI or VRS variation. The Fov1-C16 QTL locus identified in the F(2) and in the RIL populations had a significant role in conferring FOV race 1 resistance in different cotton backgrounds. Identified molecular markers may have important potential for breeding effective FOV race 1 resistance into elite cultivars by marker-assisted selection. Reconciliation between genetic and physical mapping of gene annotations from marker-DNA and new DNA sequences of BAC clones tagged with the resistance-associated QTLs revealed defenses genes induced upon pathogen infection and gene regions rich in disease-response elements, respectively. These offer candidate gene targets for Fusarium wilt resistance response in cotton and other host plants. PMID:21533837

  20. Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles.

    PubMed

    Davey, James A; Chica, Roberto A

    2014-05-01

    Multistate computational protein design (MSD) with backbone ensembles approximating conformational flexibility can predict higher quality sequences than single-state design with a single fixed backbone. However, it is currently unclear what characteristics of backbone ensembles are required for the accurate prediction of protein sequence stability. In this study, we aimed to improve the accuracy of protein stability predictions made with MSD by using a variety of backbone ensembles to recapitulate the experimentally measured stability of 85 Streptococcal protein G domain ?1 sequences. Ensembles tested here include an NMR ensemble as well as those generated by molecular dynamics (MD) simulations, by Backrub motions, and by PertMin, a new method that we developed involving the perturbation of atomic coordinates followed by energy minimization. MSD with the PertMin ensembles resulted in the most accurate predictions by providing the highest number of stable sequences in the top 25, and by correctly binning sequences as stable or unstable with the highest success rate (?90%) and the lowest number of false positives. The performance of PertMin ensembles is due to the fact that their members closely resemble the input crystal structure and have low potential energy. Conversely, the NMR ensemble as well as those generated by MD simulations at 500 or 1000 K reduced prediction accuracy due to their low structural similarity to the crystal structure. The ensembles tested herein thus represent on- or off-target models of the native protein fold and could be used in future studies to design for desired properties other than stability. PMID:24174277

  1. Linear discrete diffraction and transverse localization of light in two-dimensional backbone lattices.

    PubMed

    Qi, Yiling; Zhang, Guoquan

    2010-09-13

    We study the linear discrete diffraction characteristics of light in two-dimensional backbone lattices. It is found that, as the refractive index modulation depth of the backbone lattice increases, high-order band gaps become open and broad in sequence, and the allowed band curves of the Floquet-Bloch modes become flat gradually. As a result, the diffraction pattern at the exit face converges gradually for both the on-site and off-site excitation cases. Particularly, when the refractive index modulation depth of the backbone lattice is high enough, for example, on the order of 0.01 for a square lattice, the light wave propagating in the backbone lattice will be localized in transverse dimension for both the on-site and off-site excitation cases. This is because only the first several allowed bands with nearly flat band curves are excited in the lattice, and the transverse expansion velocities of the Floquet-Bloch modes in these flat allowed bands approach to zero. Such a linear transverse localization of light may have potential applications in navigating light propagation dynamics and optical signal processing. PMID:20940908

  2. RNA-Redesign: a web server for fixed-backbone 3D design of RNA.

    PubMed

    Yesselman, Joseph D; Das, Rhiju

    2015-07-01

    RNA is rising in importance as a design medium for interrogating fundamental biology and for developing therapeutic and bioengineering applications. While there are several online servers for design of RNA secondary structure, there are no tools available for the rational design of 3D RNA structure. Here we present RNA-Redesign (http://rnaredesign.stanford.edu), an online 3D design tool for RNA. This resource utilizes fixed-backbone design to optimize the sequence identity and nucleobase conformations of an RNA to match a desired backbone, analogous to fundamental tools that underlie rational protein engineering. The resulting sequences suggest thermostabilizing mutations that can be experimentally verified. Further, sequence preferences that differ between natural and computationally designed sequences can suggest whether natural sequences possess functional constraints besides folding stability, such as cofactor binding or conformational switching. Finally, for biochemical studies, the designed sequences can suggest experimental tests of 3D models, including concomitant mutation of base triples. In addition to the designs generated, detailed graphical analysis is presented through an integrated and user-friendly environment. PMID:25964298

  3. RNA-Redesign: a web server for fixed-backbone 3D design of RNA

    PubMed Central

    Yesselman, Joseph D.; Das, Rhiju

    2015-01-01

    RNA is rising in importance as a design medium for interrogating fundamental biology and for developing therapeutic and bioengineering applications. While there are several online servers for design of RNA secondary structure, there are no tools available for the rational design of 3D RNA structure. Here we present RNA-Redesign (http://rnaredesign.stanford.edu), an online 3D design tool for RNA. This resource utilizes fixed-backbone design to optimize the sequence identity and nucleobase conformations of an RNA to match a desired backbone, analogous to fundamental tools that underlie rational protein engineering. The resulting sequences suggest thermostabilizing mutations that can be experimentally verified. Further, sequence preferences that differ between natural and computationally designed sequences can suggest whether natural sequences possess functional constraints besides folding stability, such as cofactor binding or conformational switching. Finally, for biochemical studies, the designed sequences can suggest experimental tests of 3D models, including concomitant mutation of base triples. In addition to the designs generated, detailed graphical analysis is presented through an integrated and user-friendly environment. PMID:25964298

  4. RosettaDesign-Plastic: designing a moving target using backbone and rotamer ensembles. Christian D. Schenkelberg1, Derek J. Pitman1, Alisa Neeman2, Yao-ming Huang3, Christopher

    E-print Network

    Bystroff, Chris

    RosettaDesign-Plastic: designing a moving target using backbone and rotamer ensembles. Christian D computational design, we have implemented a design scheme termed "plastic" design which incorporates elements of these existing backbone flexibility models. Plastic design involves designing a protein primary sequence

  5. Sofosbuvir as backbone of interferon free treatments.

    PubMed

    Bourlière, Marc; Oules, Valèrie; Ansaldi, Christelle; Adhoute, Xavier; Castellani, Paul

    2014-12-15

    Sofosbuvir is the first-in-class NS5B nucleotide analogues to be launched for hepatitis C virus (HCV) treatment. Its viral potency, pangenotypic activity and high barrier to resistance make it the ideal candidate to become a backbone for several IFN-free regimens. Recent data demonstrated that sofosbuvir either with ribavirin alone or in combination with other direct-acting antivirals (DAAs) as daclatasvir, ledipasvir or simeprevir are able to cure HCV in at least 90% or over of patients. Treatment experienced genotype 3 population may remain the most difficult to treat population, but ongoing DAA combination studies will help to fill this gap. Safety profile of sofosbuvir or combination with other DAAs is good. Resistance to sofosbuvir did not appear as a significant issue. The rationale for using this class of drug and the available clinical data are reviewed. PMID:25453869

  6. Deploying Diffserv in Backbone Networks for Tight SLA Control

    Microsoft Academic Search

    Clarence Filsfils; John Evans

    2005-01-01

    The differentiated services architecture (Diffserv) enables service providers to offer tighter, more comprehensive service-level agreements (SLAs) for IP service performance. One way it does this is by letting designers engineer IP backbone networks to assure that SLA parameters are met on a per-class basis. This review covers best practices for designing, validating, deploying, and operating Diffserv in the network backbone.

  7. Palynological composition of a Lower Cretaceous South American tropical sequence: Climatic implications and diversity comparisons with other latitudes.

    USGS Publications Warehouse

    Mejia-Velasquez, Paula J.; Dilcher, David L.; Jaramillo, Carlos A.; Fortini, Lucas B.; Manchester, Steven R.

    2012-01-01

    Premise of the study: Reconstruction of floristic patterns during the early diversification of angiosperms is impeded by the scarce fossil record, especially in tropical latitudes. Here we collected quantitative palynological data from a stratigraphic sequence in tropical South America to provide floristic and climatic insights into such tropical environments during the Early Cretaceous. Methods: We reconstructed the floristic composition of an Aptian-Albian tropical sequence from central Colombia using quantitative palynology (rarefied species richness and abundance) and used it to infer its predominant climatic conditions. Additionally, we compared our results with available quantitative data from three other sequences encompassing 70 floristic assemblages to determine latitudinal diversity patterns. Key results: Abundance of humidity indicators was higher than that of aridity indicators (61% vs. 10%). Additionally, we found an angiosperm latitudinal diversity gradient (LDG) for the Aptian, but not for the Albian, and an inverted LDG of the overall diversity for the Albian. Angiosperm species turnover during the Albian, however, was higher in humid tropics. Conclusions: There were humid climates in northwestern South America during the Aptian-Albian interval contrary to the widespread aridity expected for the tropical belt. The Albian inverted overall LDG is produced by a faster increase in per-sample angiosperm and pteridophyte diversity in temperate latitudes. However, humid tropical sequences had higher rates of floristic turnover suggesting a higher degree of morphological variation than in temperate regions.

  8. Three-Dimensional Solutions for Contact Area in Laminated Composite Pinned Joints with Symmetric and Non-Symmetric Stacking Sequences

    NASA Astrophysics Data System (ADS)

    Javadi, H.; Rajabi, I.; Yavari, V.; Kadivar, M. H.

    The aim of this study is computing and evaluating the behavior of the laminated composite plate at the contact area in single lap, mechanically fastened joints. The analyses involve three dimensional finite element models performed by ABAQUS 6.4-PR11 code to evaluate the stress distribution in contact surface, separation angle, the magnitude and location of maximum radial stress. Results are determined for composite laminates with different layer configurations and attempts are made to validate the models with previous works. For cross ply and angle ply configurations only symmetric stacking sequences are used while for quasi-isotropic laminate both symmetric and non-symmetric models are generated. In cross-ply laminate symmetric separation about bearing plane could be found while in quasi-isotropic and angle-ply laminates non-symmetric separation occurs. Also, the separation angle is less than 90° in symmetric laminates and greater than 90° in some plies of non-symmetric laminates.

  9. Estimating the composition of species in metagenomes by clustering of next-generation read sequences.

    PubMed

    Seok, Ho-Sik; Hong, Woonyoung; Kim, Jaebum

    2014-10-01

    Faster and cheaper sequencing technologies together with the ability to sequence uncultured microbes collected from any environment present us an opportunity to distill meaningful information from the millions of new genomic sequences from environmental samples, called metagenome. Contrary to conventional cultured microbes, however, the metagenomic data is extremely heterogeneous and noisy. Therefore the separation of the sets of sequenced genomic fragments that belong to different microbes is essential for successful assembly of microbial genomes. In this paper, we present a novel clustering method for a given metagenomic dataset. The metagenomic dataset has some distinguished features because (i) it is possible that similar sequence patterns may exist in different species and (ii) each species has different number of individuals in the given metagenomic dataset. Our method overcomes these obstacles by using the Gaussian mixture model and analysis of mixture profiles, and taking advantage of genomic signatures extracted from the metagenomic dataset. Unlike conventional clustering methods where clusters are discovered through global similarities of data instances, our method builds clusters by combining the data instances sharing local similarities captured by mixture analysis. By considering shared mixture components, our method is able to create clusters of genomic sequences although they are globally distinct each other. We applied our method to an artificial metagenomic dataset comprised of simulated 47 million reads from 25 real microbial genomes, and analyzed the resulting clusters in terms of the number of clusters, the number of participating species and dominant species in each cluster. Even though our approach cannot address all challenges in the field of metagenome sequence clustering, we believe that out method can contribute to take a step forward to achieve the goals. PMID:25072168

  10. Backbones of evolutionary history test biodiversity theory for microbes.

    PubMed

    O'Dwyer, James P; Kembel, Steven W; Sharpton, Thomas J

    2015-07-01

    Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities. PMID:26106159

  11. Backbones of evolutionary history test biodiversity theory for microbes

    PubMed Central

    O’Dwyer, James P.; Kembel, Steven W.; Sharpton, Thomas J.

    2015-01-01

    Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities. PMID:26106159

  12. Apollo 17 petrology and experimental determination of differentiation sequences in model moon compositions

    NASA Technical Reports Server (NTRS)

    Hodges, F. N.; Kushiro, I.

    1974-01-01

    Experimental studies of model moon compositions are discussed, taking into account questions related to the differentiation of the outer layer of the moon. Phase relations for a series of proposed lunar compositions have been determined and a petrographic and electron microprobe study was conducted on four Apollo 17 samples. Two of the samples consist of high-titanium mare basalts, one includes crushed anorthosite and gabbro, and another contains blue-gray breccia.

  13. The Backbone of the Climate Networks

    NASA Astrophysics Data System (ADS)

    Zou, Y.; Donges, J. F.; Marwan, N.; Kurths, J.

    2009-12-01

    We propose a method to reconstruct and analyze a complex network from data generated by a spatio-temporal dynamical system, relying on the nonlinear mutual information of time series analysis and betweenness centrality of complex network theory. We show, that this approach reveals a rich internal structure in complex climate networks constructed from reanalysis and model surface air temperature data. Our novel method uncovers peculiar wave-like structures of high energy flow, that we relate to global surface ocean currents. This points to a major role of the oceanic surface circulation in coupling and stabilizing the global temperature field in the long term mean (140 years for the model run and 60 years for reanalysis data). We find that these results cannot be obtained using classical linear methods of multivariate data analysis. Furthermore, we introduce significance tests to quantify the robustness of measured network properties to uncertainties. References: [1] J.F. Donges, Y. Zou, N. Marwan, and J. Kurths. Complex networks in climate dynamics -- -- Comparing linear and nonlinear network construction methods. European Physical Journal -- Special Topics, 174, 157-179, 2009. [2] J.F. Donges, Y. Zou, N. Marwan, and J. Kurths. Backbone of the climate network. Europhysics Letters, in press, 2009.

  14. Extracting the information backbone in online system.

    PubMed

    Zhang, Qian-Ming; Zeng, An; Shang, Ming-Sheng

    2013-01-01

    Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity) of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such "less can be more" feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency. PMID:23690946

  15. Manipulating the backbone structure of semiconducting polymers

    NASA Astrophysics Data System (ADS)

    Luscombe, Christine

    2015-03-01

    Pi-Conjugated polymers are being used in the fabrication of a wide variety of organic electronic devices such as organic field-effect transistors (OFETs), organic photovoltaic (OPV) devices, and organic light-emitting diodes (OLEDs). The advances made in organic electronics have been driven by the syntheses of pi-conjugated polymers with increasingly complex structures but have heavily relied on an Edisonian approach. Despite these advances, there are many contradictory reports in the literature about our understanding of the performance of ?-conjugated polymers in many applications. Our group has been studying and developing techniques to grow semiconducting polymers using a living polymerization method. This has allowed us to synthesize polymer architectures that we haven't been able to access till now including polythiophene brushes, star-shaped P3HT, as well as hyperbranched P3HT. It also allows us to accurately control the molecular weights of P3HT and produce materials with a narrow molecular weight distribution. In this presentation, our work towards creating brush polymers will be presented where a series of fully conjugated graft copolymers containing poly(3-hexylthiophene) (P3HT) side chains and a p-type carbazole-diketopyrrolopyrrole donor-acceptor backbone were synthesized via a graft through Suzuki polymerization.

  16. Extracting the Information Backbone in Online System

    PubMed Central

    Zhang, Qian-Ming; Zeng, An; Shang, Ming-Sheng

    2013-01-01

    Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity) of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such “less can be more” feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency. PMID:23690946

  17. Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol.

    PubMed

    Milani, Christian; Lugli, Gabriele A; Turroni, Francesca; Mancabelli, Leonardo; Duranti, Sabrina; Viappiani, Alice; Mangifesta, Marta; Segata, Nicola; van Sinderen, Douwe; Ventura, Marco

    2014-11-01

    The precise appraisal of the composition of the human gut microbiota still represents a challenging task. The advent of next generation sequencing approaches has opened new ways to dissect the microbial biodiversity of this ecosystem through the use of 16S rRNA gene-based microbiota analysis approaches. However, the detailed representation of specific groups or members of the human gut microbiota, for example Bifidobacteria, may be skewed by the PCR primers employed in the amplification step of the 16S rRNA gene-based microbial profiling pipeline and by the limited resolution of the 16S rRNA gene variable regions. Here, we define the internal transcribed spacer (ITS) sequences of all currently known Bifidobacterium taxa, providing a Bifidobacterium-specific primer pair that targets a hypervariable region within the ITS suitable for precise taxonomic identification of all 48 so far recognized members of the Bifidobacterium genus. In addition, we present an optimized protocol for ITS-based profiling utilizing qiime software, allowing accurate and subspecies-specific compositional reconstruction of the bifidobacterial community in the human gut. PMID:25117972

  18. Impact of HIV-1 Backbone on Neutralization Sensitivity: Neutralization Profiles of Heterologous Envelope Glycoproteins Expressed in Native Subtype C and CRF01_AE Backbone

    PubMed Central

    Sanders-Buell, Eric; Wesberry, Maggie; Towle, Teresa; Pillis, Devin M.; Molnar, Sebastian; McLinden, Robert; Edmonds, Tara; Hirsch, Ivan; O’Connell, Robert; McCutchan, Francine E.; Montefiori, David C.; Ochsenbauer, Christina; Kappes, John C.; Kim, Jerome H.; Polonis, Victoria R.; Tovanabutra, Sodsai

    2013-01-01

    Standardized assays to assess vaccine and antiviral drug efficacy are critical for the development of protective HIV-1 vaccines and drugs. These immune assays will be advanced by the development of standardized viral stocks, such as HIV-1 infectious molecular clones (IMC), that i) express a reporter gene, ii) are representative of globally diverse subtypes and iii) are engineered to easily exchange envelope (env) genes for expression of sequences of interest. Thus far, a subtype B IMC backbone expressing Renilla luciferase (LucR), and into which the ectodomain of heterologous env coding sequences can be expressed has been successfully developed but as execution of HIV-1 vaccine efficacy trials shifts increasingly to non-subtype B epidemics (Southern African and Southeast Asia), non-subtype B HIV-1 reagents are needed to support vaccine development. Here we describe two IMCs derived from subtypes C and CRF01_AE HIV-1 primary isolates expressing LucR (IMC.LucR) that were engineered to express heterologous gp160 Envs. 18 constructs expressing various subtypes C and CRF01_AE Envs, mostly acute, in subtype-matched and –unmatched HIV backbones were tested for functionality and neutralization sensitivity. Our results suggest a possible effect of non-env HIV-1 genes on the interaction of Env and neutralizing antibodies and highlight the need to generate a library of IMCs representative of the HIV-1 subtype spectrum to be used as standardized neutralization assay reagents for assessing HIV-1 vaccine efficacy. PMID:24312165

  19. A Business Process Testing Sequence Generation Approach Based on Test Cases Composition

    Microsoft Academic Search

    Lizhi Cai

    2011-01-01

    This paper proposes a business process testing scenario generation based on test cases composition. Just like path oriented testing technique in structure testing area, this testing method focuses on finding the logical error in the process implementation according to the formal business process presentation. The test cases against a node of process designed by the techniques such as boundary value

  20. Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

    PubMed Central

    Chiapello, H; Bourgait, I; Sourivong, F; Heuclin, G; Gendrault-Jacquemard, A; Petit, M-A; El Karoui, M

    2005-01-01

    Background Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. Results Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. Conclusion The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: . PMID:16011797

  1. Fragmentation characteristics of deprotonated N-linked glycopeptides: influences of amino acid composition and sequence.

    PubMed

    Nishikaze, Takashi; Kawabata, Shin-ichirou; Tanaka, Koichi

    2014-06-01

    Glycopeptide structural analysis using tandem mass spectrometry is becoming a common approach for elucidating site-specific N-glycosylation. The analysis is generally performed in positive-ion mode. Therefore, fragmentation of protonated glycopeptides has been extensively investigated; however, few studies are available on deprotonated glycopeptides, despite the usefulness of negative-ion mode analysis in detecting glycopeptide signals. Here, large sets of glycopeptides derived from well-characterized glycoproteins were investigated to understand the fragmentation behavior of deprotonated N-linked glycopeptides under low-energy collision-induced dissociation (CID) conditions. The fragment ion species were found to be significantly variable depending on their amino acid sequence and could be classified into three types: (i) glycan fragment ions, (ii) glycan-lost fragment ions and their secondary cleavage products, and (iii) fragment ions with intact glycan moiety. The CID spectra of glycopeptides having a short peptide sequence were dominated by type (i) glycan fragments (e.g., (2,4)AR, (2,4)AR-1, D, and E ions). These fragments define detailed structural features of the glycan moiety such as branching. For glycopeptides with medium or long peptide sequences, the major fragments were type (ii) ions (e.g., [peptide + (0,2)X0-H](-) and [peptide-NH3-H](-)). The appearance of type (iii) ions strongly depended on the peptide sequence, and especially on the presence of Asp, Asn, and Glu. When a glycosylated Asn is located on the C-terminus, an interesting fragment having an Asn residue with intact glycan moiety, [glycan + Asn-36](-), was abundantly formed. Observed fragments are reasonably explained by a combination of existing fragmentation rules suggested for N-glycans and peptides. PMID:24664808

  2. A composite map of expressed sequences and phenotypic traits of the sunflower (Helianthus annuus L.) genome

    Microsoft Academic Search

    L. Gentzbittel; E. Mestries; S. Mouzeyar; F. Mazeyrat; S. Badaoui; F. Vear; D. Tourvieille de Labrouhe; P. Nicolas

    1999-01-01

    A map of the sunflower genome, based on expressed sequences and consisting of 273 loci, was constructed. The map incorporates\\u000a data from seven F2 populations, for a total of 1115 individuals. Two hundred and fourty five loci corresponding to 170 anonymous cDNA markers\\u000a and four loci for morphological markers were mapped. We also mapped 18 loci corresponding to previously described

  3. Integer Programming Approaches to Access and Backbone IP Network Planning

    Microsoft Academic Search

    Andreas Bley; Thorsten Koch

    In this article we study the problem of designing a nation-wide communication network. Such networks usually consist of an\\u000a access layer, a backbone layer, and maybe several intermediate layers. The nodes of each layer must be connected to those\\u000a of the next layer in a tree-like fashion. The backbone layer must satisfy survivability and IP-routing constraints.\\u000a \\u000a Given the node locations,

  4. Large-scale graph mining using backbone refinement classes

    Microsoft Academic Search

    Andreas Maunz; Christoph Helma; Stefan Kramer

    2009-01-01

    We present a new approach to large-scale graph mining based on so-called backbone refinement classes. The method efficiently mines tree-shaped subgraph descriptors under min- imum frequency and significance constraints, using classes of fragments to reduce feature set size and running times. The classes are defined in terms of fragments sharing a com- mon backbone. The method is able to optimize

  5. Design issues of optical IP routers for Internet backbone applications

    Microsoft Academic Search

    Franco Callegati; A. C. Cankaya; Yijun Xiong; Marc Vandenhoute

    1999-01-01

    The rapid increase of Internet traffic is pushing the deployment of WDM technology in the next-generation high-speed Internet backbone. Routers in the backbone could still be the potential bottleneck. In this article we consider some design issues of high-throughput optical routers which combine the advantages of WDM with the new optical switching technology. We first introduce a proposed Internet architecture

  6. Sequence-based analysis of the microbial composition of water kefir from multiple sources.

    PubMed

    Marsh, Alan J; O'Sullivan, Orla; Hill, Colin; Ross, R Paul; Cotter, Paul D

    2013-11-01

    Water kefir is a water-sucrose-based beverage, fermented by a symbiosis of bacteria and yeast to produce a final product that is lightly carbonated, acidic and that has a low alcohol percentage. The microorganisms present in water kefir are introduced via water kefir grains, which consist of a polysaccharide matrix in which the microorganisms are embedded. We aimed to provide a comprehensive sequencing-based analysis of the bacterial population of water kefir beverages and grains, while providing an initial insight into the corresponding fungal population. To facilitate this objective, four water kefirs were sourced from the UK, Canada and the United States. Culture-independent, high-throughput, sequencing-based analyses revealed that the bacterial fraction of each water kefir and grain was dominated by Zymomonas, an ethanol-producing bacterium, which has not previously been detected at such a scale. The other genera detected were representatives of the lactic acid bacteria and acetic acid bacteria. Our analysis of the fungal component established that it was comprised of the genera Dekkera, Hanseniaspora, Saccharomyces, Zygosaccharomyces, Torulaspora and Lachancea. This information will assist in the ultimate identification of the microorganisms responsible for the potentially health-promoting attributes of these beverages. PMID:24004255

  7. Radical-driven peptide backbone dissociation tandem mass spectrometry.

    PubMed

    Oh, Han Bin; Moon, Bongjin

    2015-01-01

    In recent years, a number of novel tandem mass spectrometry approaches utilizing radical-driven peptide gas-phase fragmentation chemistry have been developed. These approaches show a peptide fragmentation pattern quite different from that of collision-induced dissociation (CID). The peptide fragmentation features of these approaches share some in common with electron capture dissociation (ECD) or electron transfer dissociation (ETD) without the use of sophisticated equipment such as a Fourier-transform mass spectrometer. For example, Siu and coworkers showed that CID of transition metal (ligand)-peptide ternary complexes led to the formation of peptide radical ions through dissociative electron transfer (Chu et al., 2000. J Phys Chem B 104:3393-3397). The subsequent collisional activation of the generated radical ions resulted in a number of characteristic product ions, including a, c, x, z-type fragments and notable side-chain losses. Another example is the free radical initiated peptide sequencing (FRIPS) approach, in which Porter et al. and Beauchamp et al. independently introduced a free radical initiator to the primary amine group of the lysine side chain or N-terminus of peptides (Masterson et al., 2004. J Am Chem Soc 126:720-721; Hodyss et al., 2005 J Am Chem Soc 127: 12436-12437). Photodetachment of gaseous multiply charged peptide anions (Joly et al., 2008. J Am Chem Soc 130:13832-13833) and UV photodissociation of photolabile radical precursors including a C-I bond (Ly & Julian, 2008. J Am Chem Soc 130:351-358; Ly & Julian, 2009. J Am Soc Mass Spectrom 20:1148-1158) also provide another route to generate radical ions. In this review, we provide a brief summary of recent results obtained through the radical-driven peptide backbone dissociation tandem mass spectrometry approach. PMID:24863492

  8. 'Genome order index' should not be used for defining compositional constraints in nucleotide sequences.

    PubMed

    Elhaik, Eran; Graur, Dan; Josi?, Kresimir

    2008-04-01

    A "genome order index," defined as S=a(2)+c(2)+t(2)+g(2), where a, c, t, and g are the nucleotide frequencies of A, C, T, and G, respectively, was used to suggest that there exist genome-specific constraints on nucleotide composition. We show that the "evidence" for constraint, S<1/3, is in fact a mathematical property that is always true regardless of data. Moreover, we show that S is strictly equivalent to and derivable from the Shannon H-function and has no advantage over it. PMID:18243804

  9. Kerogen and biomarker compositions of uranium-rich coaly shales from Miocene sequence at Kanamaru, Japan

    NASA Astrophysics Data System (ADS)

    Yamamoto, M.; Watanabe, Y.

    2005-12-01

    We obtained a continuous 40 m-long core from the Miocene sedimentary sequence and basement Cretaceous granite at Kanamaru, northeast Japan. The Miocene sequence intercalates with a uranium-rich coaly shale seam (U = 25-100 ppm; Th = 23-42 ppm). We have analyzed the kerogen macerals and biomarkers in the core to characterize the organic matter in the uranium-rich seam. Visual kerogen analysis indicated that the relative abundance of coaly and woody kerogens in total kerogen is generally high in the samples that contain high amount of uranium. The coaly and woody kerogens consist about 80 percent of total kerogen, and the rest 20 percent are herbaceous and amorphous kerogens in uranium-rich coaly shales. TMAH-pyrolysis-GC/MS analysis showed that the organic matter in pyrolysates comprises mainly alkyl-aromatic hydrocarbons (alkyl-benzenes, alkyl-indenes, alkyl-naphthalenes, etc.) and n-alkanes. Acyclic isoprenoid alkanes (mainly pristane), n-alkenes, n-fatty acids and acyclic isoprenoid acids were detected as minor components. Most of these compounds are characteristic of the type-III kerogen that derived from terrestrial higher plants. Thermal alteration index (TAI) of Pinus pollen was about 2.6, which indicates that the thermal maturation of the coaly shale reached the stage of early catagenesis. This maturity was also suggested by high abundance of diagenetically generated isomers of hopanes in TMAH pyrolysates. A good correspondence that uranium-rich samples are always rich in type-III organic matter suggests that the type-III organic matter was able to concentrate uranium by the absorption and/or reduction of uranium during deposition and/or early diagenesis.

  10. Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing.

    PubMed

    Ma, Qiao; Qu, Yuanyuan; Shen, Wenli; Zhang, Zhaojing; Wang, Jingwei; Liu, Ziyan; Li, Duanxing; Li, Huijie; Zhou, Jiti

    2015-03-01

    In this study, Illumina high-throughput sequencing was used to reveal the community structures of nine coking wastewater treatment plants (CWWTPs) in China for the first time. The sludge systems exhibited a similar community composition at each taxonomic level. Compared to previous studies, some of the core genera in municipal wastewater treatment plants such as Zoogloea, Prosthecobacter and Gp6 were detected as minor species. Thiobacillus (20.83%), Comamonas (6.58%), Thauera (4.02%), Azoarcus (7.78%) and Rhodoplanes (1.42%) were the dominant genera shared by at least six CWWTPs. The percentages of autotrophic ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were unexpectedly low, which were verified by both real-time PCR and fluorescence in situ hybridization analyses. Hierarchical clustering and canonical correspondence analysis indicated that operation mode, flow rate and temperature might be the key factors in community formation. This study provides new insights into our understanding of microbial community compositions and structures of CWWTPs. PMID:25569032

  11. A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences.

    PubMed

    Tsay, Jyh-Jong; Su, Shih-Chieh; Yu, Chin-Sheng

    2015-01-01

    Protein structure prediction (PSP) is concerned with the prediction of protein tertiary structure from primary structure and is a challenging calculation problem. After decades of research effort, numerous solutions have been proposed for optimisation methods based on energy models. However, further investigation and improvement is still needed to increase the accuracy and similarity of structures. This study presents a novel backbone angle preference factor, which is one of the factors inducing protein folding. The proposed multiobjective optimisation approach simultaneously considers energy models and backbone angle preferences to solve the ab initio PSP. To prove the effectiveness of the multiobjective optimisation approach based on the energy models and backbone angle preferences, 75 amino acid sequences with lengths ranging from 22 to 88 amino acids were selected from the CB513 data set to be the benchmarks. The data sets were highly dissimilar, therefore indicating that they are meaningful. The experimental results showed that the root-mean-square deviation (RMSD) of the multiobjective optimization approach based on energy model and backbone angle preferences was superior to those of typical energy models, indicating that the proposed approach can facilitate the ab initio PSP. PMID:26151847

  12. Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples.

    PubMed

    Marsh, Alan J; O'Sullivan, Orla; Hill, Colin; Ross, R Paul; Cotter, Paul D

    2014-04-01

    Kombucha is a sweetened tea beverage that, as a consequence of fermentation, contains ethanol, carbon dioxide, a high concentration of acid (gluconic, acetic and lactic) as well as a number of other metabolites and is thought to contain a number of health-promoting components. The sucrose-tea solution is fermented by a symbiosis of bacteria and yeast embedded within a cellulosic pellicle, which forms a floating mat in the tea, and generates a new layer with each successful fermentation. The specific identity of the microbial populations present has been the focus of attention but, to date, the majority of studies have relied on culture-based analyses. To gain a more comprehensive insight into the kombucha microbiota we have carried out the first culture-independent, high-throughput sequencing analysis of the bacterial and fungal populations of 5 distinct pellicles as well as the resultant fermented kombucha at two time points. Following the analysis it was established that the major bacterial genus present was Gluconacetobacter, present at >85% in most samples, with only trace populations of Acetobacter detected (<2%). A prominent Lactobacillus population was also identified (up to 30%), with a number of sub-dominant genera, not previously associated with kombucha, also being revealed. The yeast populations were found to be dominated by Zygosaccharomyces at >95% in the fermented beverage, with a greater fungal diversity present in the cellulosic pellicle, including numerous species not identified in kombucha previously. Ultimately, this study represents the most accurate description of the microbiology of kombucha to date. PMID:24290641

  13. The composition of coding joints formed in V(D)J recombination is strongly affected by the nucleotide sequence of the coding ends and their relationship to the recombination signal sequences.

    PubMed Central

    Ezekiel, U R; Sun, T; Bozek, G; Storb, U

    1997-01-01

    V(D)J recombination proceeds in two stages. Precise cleavage at the border of the conserved recombination signal sequences (RSSs) and the coding ends results in flush double-stranded signal ends and coding ends terminating in hairpins. In the second stage, the signal and coding ends are processed into signal and coding joints. Coding ends containing certain nucleotide homopolymers affect the efficiency of V(D)J recombination. In this study, we have tested the effect of small changes in coding-end nucleotide composition on the frequency of coding- and signal joint formation. Furthermore, we have determined the sequences of coding joints resulting from recombination of coding ends with different compositions. We found that the presence of two T nucleotides 5' of both RSSs, but not a single T, reduces the frequency of signal joint formation, i.e., interferes with the cleavage stage of V(D)J recombination. However, coding-joint processing is sensitive even to a single T. Both the sequence of the coding ends and the particular RSS (12-mer or 23-mer) with which the coding end is associated affect the final composition of the coding joints. Thus, the presence of P nucleotides, the conservation of one undeleted coding end, the formation of joints without any deletions, and the template-dependent insertion of nucleotides are strongly influenced by the coding-end nucleotide composition and/or RSS association. The implications of these results with respect to the processing of coding ends are discussed. PMID:9199354

  14. PS1-10jh: The disruption of a main-sequence star of near-solar composition

    SciTech Connect

    Guillochon, James; Manukian, Haik; Ramirez-Ruiz, Enrico [Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064 (United States)

    2014-03-01

    When a star comes within a critical distance to a supermassive black hole (SMBH), immense tidal forces disrupt the star, resulting in a stream of debris that falls back onto the SMBH and powers a luminous flare. In this paper, we perform hydrodynamical simulations of the disruption of a main-sequence star by an SMBH to characterize the evolution of the debris stream after a tidal disruption. We demonstrate that this debris stream is confined by self-gravity in the two directions perpendicular to the original direction of the star's travel and as a consequence has a negligible surface area and makes almost no contribution to either the continuum or line emission. We therefore propose that any observed emission lines are not the result of photoionization in this unbound debris, but are produced in the region above and below the forming elliptical accretion disk, analogous to the broad-line region (BLR) in steadily accreting active galactic nuclei. As each line within a BLR is observationally linked to a particular location in the accretion disk, we suggest that the absence of a line indicates that the accretion disk does not yet extend to the distance required to produce that line. This model can be used to understand the spectral properties of the tidal disruption event PS1-10jh, for which He II lines are observed, but the Balmer series and He I are not. Using a maximum likelihood analysis, we show that the disruption of a main-sequence star of near-solar composition can reproduce this event.

  15. Congestion Avoid Movement Aware Routing Protocol in Interplanetary Backbone Networks

    NASA Astrophysics Data System (ADS)

    Sun, Haoliang; Hu, Xiaohui; Liu, Lixiang

    The existing routing protocols for the interplanetary backbone network did not consider future link connection and link congestion. A novel routing protocol named CAMARP for the interplanetary backbone network is proposed in this letter. We use wait delay to consider future link connection and make the best next hop selection. A load balancing mechanism is used to avoid congestion. The proposed method leads to a better and more efficient distribution of traffic, and also leads to lower packet drop rates and higher throughput. CAMARP demonstrates good performance in the experiment.

  16. Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment.

    PubMed Central

    Liwo, A.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Scheraga, H. A.

    1993-01-01

    An algorithm is proposed for the conversion of a virtual-bond polypeptide chain (connected C alpha atoms) to an all-atom backbone, based on determining the most extensive hydrogen-bond network between the peptide groups of the backbone, while maintaining all of the backbone atoms in energetically feasible conformations. Hydrogen bonding is represented by aligning the peptide-group dipoles. These peptide groups are not contiguous in the amino acid sequence. The first dipoles to be aligned are those that are both sufficiently close in space to be arranged in approximately linear arrays termed dipole paths. The criteria used in the construction of dipole paths are: to assure good alignment of the greatest possible number of dipoles that are close in space; to optimize the electrostatic interactions between the dipoles that belong to different paths close in space; and to avoid locally unfavorable amino acid residue conformations. The equations for dipole alignment are solved separately for each path, and then the remaining single dipoles are aligned optimally with the electrostatic field from the dipoles that belong to the dipole-path network. A least-squares minimizer is used to keep the geometry of the alpha-carbon trace of the resulting backbone close to that of the input virtual-bond chain. This procedure is sufficient to convert the virtual-bond chain to a real chain; in applications to real systems, however, the final structure is obtained by minimizing the total ECEPP/2 (empirical conformational energy program for peptides) energy of the system, starting from the geometry resulting from the solution of the alignment equations. When applied to model alpha-helical and beta-sheet structures, the algorithm, followed by the ECEPP/2 energy minimization, resulted in an energy and backbone geometry characteristic of these alpha-helical and beta-sheet structures. Application to the alpha-carbon trace of the backbone of the crystallographic 5PTI structure of bovine pancreatic trypsin inhibitor, followed by ECEPP/2 energy minimization with C alpha-distance constraints, led to a structure with almost as low energy and root mean square deviation as the ECEPP/2 geometry analog of 5PTI, the best agreement between the crystal and reconstructed backbone being observed for the residues involved in the dipole-path network. PMID:7504550

  17. A Consistent Phylogenetic Backbone for the Fungi

    PubMed Central

    Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

    2012-01-01

    The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

  18. A unique signal distorts the perception of species richness and composition in high-throughput sequencing surveys of microbial communities: a case study of fungi in indoor dust.

    PubMed

    Adams, Rachel I; Amend, Anthony S; Taylor, John W; Bruns, Thomas D

    2013-11-01

    Sequence-based surveys of microorganisms in varied environments have found extremely diverse assemblages. A standard practice in current high-throughput sequence (HTS) approaches in microbial ecology is to sequence the composition of many environmental samples at once by pooling amplicon libraries at a common concentration before processing on one run of a sequencing platform. Biomass of the target taxa, however, is not typically determined prior to HTS, and here, we show that when abundances of the samples differ to a large degree, this standard practice can lead to a perceived bias in community richness and composition. Fungal signal in settled dust of five university teaching laboratory classrooms, one of which was used for a mycology course, was surveyed. The fungal richness and composition in the dust of the nonmycology classrooms were remarkably similar to each other, while the mycology classroom was dominated by abundantly sporulating specimen fungi, particularly puffballs, and appeared to have a lower overall richness based on rarefaction curves and richness estimators. The fungal biomass was three to five times higher in the mycology classroom than the other classrooms, indicating that fungi added to the mycology classroom swamped the background fungi present in indoor air. Thus, the high abundance of a few taxa can skew the perception of richness and composition when samples are sequenced to an even depth. Next, we used in silico manipulations of the observed data to confirm that a unique signature can be identified with HTS approaches when the source is abundant, whether or not the taxon identity is distinct. Lastly, aerobiology of indoor fungi is discussed. PMID:23880792

  19. Novel variants of AbaR resistance islands with a common backbone in Acinetobacter baumannii isolates of European clone II.

    PubMed

    Seputiene, Vaida; Povilonis, Justas; Suziedeliene, Edita

    2012-04-01

    In this study, the genetic organization of three novel genomic antibiotic resistance islands (AbaRs) in Acinetobacter baumannii isolates belonging to group of European clone II (EC II) comM integrated sequences of 18-, 21-, and 23-kb resistance islands were determined. These resistance islands carry the backbone of AbaR-type transposon structures, which are composed of the transposition module coding for potential transposition proteins and other genes coding for the intact universal stress protein (uspA), sulfate permease (sul), and proteins of unknown function. The antibiotic resistance genes strA, strB, tetB, and tetR and insertion sequence CR2 element were found to be inserted into the AbaR transposons. GenBank homology searches indicated that they are closely related to the AbaR sequences found integrated in comM in strains of EC II (A. baumannii strains 1656-2 and TCDC-AB0715) and AbaR4 integrated in another location of A. baumannii AB0057 (EC I). All of the AbaRs showed structural similarity to the previously described AbaR4 island and share a 12,008-bp backbone. AbaRs contain Tn1213, Tn2006, and the multiple fragments which could be derived from transposons Tn3, Tn10, Tn21, Tn1000, Tn5393, and Tn6020, the insertion sequences IS26, ISAba1, ISAba14, and ISCR2, and the class 1 integron. Moreover, chromosomal DNA was inserted into distinct regions of the AbaR backbone. Sequence analysis suggested that the AbaR-type transposons have evolved through insertions, deletions, and homologous recombination. AbaR islands, sharing the core structure similar to AbaR4, appeared to be distributed in isolates of EC I and EC II via integration into distinct genomic sites, i.e., pho and comM, respectively. PMID:22290980

  20. LARC-IA: A flexible backbone polyimide

    NASA Technical Reports Server (NTRS)

    Progar, Donald J.; Stclair, Terry L.

    1990-01-01

    A new linear, aromatic, thermoplastic polyimide, prepared from oxydiphthalic anhydride (ODPA) and 3,4'-oxydianiline (ODA) in diglyme and identified as LARC-IA, was synthesized and evaluated. The monomers are relatively inexpensive and physiologically safe. Molecular weight was controlled by use of a monofunctional anhydride, phthalic anhydride (PA), in order to promote controlled flow and wetting properties. The polymer is considered a safe alternative to commercially available LARC-TPI which is prepared with an expensive diamine of uncertain carcinogenicity. The evaluation was based primarily on the polymer's adhesive properties as determined by thermal and water boil exposure of lap shear specimens. Strengths were determined at room temperature, 177, 204 and 232 C before and after exposure to determine the adhesive system's durability to adverse environments over a period of time. Other properties (FWT, G(1c), film and composite properties) were examined which were determined to be typical of a high temperature polyimide. Results of the study show a favorable comparison to LARC-TPI, a commercially available polyimide.

  1. Analysis of Failures Characteristics in the UNINETT IP Backbone Network

    E-print Network

    Nørvåg, Kjetil

    Analysis of Failures Characteristics in the UNINETT IP Backbone Network Andr´es J. Gonz-known distributions. We observe that the Weibull assumption that is traditionally used to model link failures that interval availability analysis has on SLAs under unprotected and shared protected connections, assuming

  2. Increasing protein production by directed vector backbone evolution

    PubMed Central

    2013-01-01

    Recombinant protein production in prokaryotic and eukaryotic organisms was a key enabling technology for the rapid development of industrial and molecular biotechnology. However, despite all progress the improvement of protein production is an ongoing challenge and of high importance for cost-effective enzyme production. With the epMEGAWHOP mutagenesis protocol for vector backbone optimization we report a novel directed evolution based approach to increase protein production levels by randomly introducing mutations in the vector backbone. In the current study we validate the epMEGAWHOP mutagenesis protocol for three different expression systems. The latter demonstrated the general applicability of the epMEGAWHOP method. Cellulase and lipase production was doubled in one round of directed evolution by random mutagenesis of pET28a(+) and pET22b(+) vector backbones. Protease production using the vector pHY300PLK was increased ~4-times with an average of ~1.25 mutations per kb vector backbone. The epMEGAWHOP does not require any rational understanding of the expression machinery and can generally be applied to enzymes, expression vectors and related hosts. epMEGAWHOP is therefore from our point of view a robust, rapid and straight forward alternative for increasing protein production in general and for biotechnological applications. PMID:23890095

  3. Interconnection of long-reach PON and backbone networks

    Microsoft Academic Search

    Piero Castoldi; Francesco Paolucci; Alessio Giorgetti; Martin Maier

    2009-01-01

    This paper proposes an evolution of the STARGATE long-reach PON architecture to allow the optical interconnection of multiple STARGATEs by means of a GMPLS-based backbone network. The architecture of the optical bypass gateway is proposed and the distributed signalling for establishing inter-STARGATE connection requests is detailed. The optical bypassing capacity of the proposed architecture is evaluated through simulations.

  4. Backbone-based roadmaps for robot navigation in sensor networks

    Microsoft Academic Search

    Zhenwang Yao; Kamal Gupta

    2008-01-01

    In this paper, we propose a distributed path planning method for robot navigation amidst a wireless sensor network. Our method uses communication backbone as a roadmap. In building and maintaining the roadmap, it takes path safety and network longevity into account, and therefore the roadmap adapts to dynamic dangers and evolves over time to increase network longevity. To find a

  5. Cooperative UAV-Based Communications Backbone for Sensor Networks

    SciTech Connect

    Roberts, R S

    2001-10-07

    The objective of this project is to investigate the use of unmanned air vehicles (UAVs) as mobile, adaptive communications backbones for ground-based sensor networks. In this type of network, the UAVs provide communication connectivity to sensors that cannot communicate with each other because of terrain, distance, or other geographical constraints. In these situations, UAVs provide a vertical communication path for the sensors, thereby mitigating geographic obstacles often imposed on networks. With the proper use of UAVs, connectivity to a widely disbursed sensor network in rugged terrain is readily achieved. Our investigation has focused on networks where multiple cooperating UAVs are used to form a network backbone. The advantage of using multiple UAVs to form the network backbone is parallelization of sensor connectivity. Many widely spaced or isolated sensors can be connected to the network at once using this approach. In these networks, the UAVs logically partition the sensor network into sub-networks (subnets), with one UAV assigned per subnet. Partitioning the network into subnets allows the UAVs to service sensors in parallel thereby decreasing the sensor-to-network connectivity. A UAV services sensors in its subnet by flying a route (path) through the subnet, uplinking data collected by the sensors, and forwarding the data to a ground station. An additional advantage of using multiple UAVs in the network is that they provide redundancy in the communications backbone, so that the failure of a single UAV does not necessarily imply the loss of the network.

  6. TREND Big Picture on Energy-Efficient Backbone Networks

    E-print Network

    Wichmann, Felix

    or Peering Points (PPs) and includes transport equipment, optical transmission and data centers. We considerTREND Big Picture on Energy-Efficient Backbone Networks Esther Le Rouzic, Raluca-Maria Indre Orange network of excellence TREND focusing on core and metro networks including data centers. Potential savings

  7. IP Backbone Design for Multimedia Distribution: Architecture and Performance

    Microsoft Academic Search

    Robert D. Doverspike; Guangzhi Li; Konstantinos Oikonomou; K. K. Ramakrishnan; Dongmei Wang

    2007-01-01

    Multimedia distribution, especially broadcast TV distribution over an IP network requires high bandwidth combined with tight latency and loss constraints, even under failure conditions. Due to the high bandwidth requirements of broadcast TV distribution, use of IP-based multicast to distribute TV content is needed for efficient use of capacity. The protection and restoration mechanisms currently adopted in IP backbones use

  8. Large-scale Measurement and Modeling of Backbone Internet Trac

    E-print Network

    Roughan, Matthew

    the implicit definition of smoothness used by the human eye. In fact traffic can be both Long­Range Dependent,joelg@research.att.com ABSTRACT There is a brewing controversy in the traffic modeling community concerning how to model backbone traffic. The fun­ damental work on self­similarity in data traffic appears to be contradicted by recent

  9. Backbone Additivity in the Transfer Model of Protein Solvation

    SciTech Connect

    Hu, Char Y.; Kokubo, Hironori; Lynch, Gillian C.; Bolen, D Wayne; Pettitt, Bernard M.

    2010-05-01

    The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (?Gtr) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and ?Gtr values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of –54 cal/mol/Mcompares quite favorably with –43 cal/mol/M determined experimentally.

  10. Ultradeep 16S rRNA Sequencing Analysis of Geographically Similar but Diverse Unexplored Marine Samples Reveal Varied Bacterial Community Composition

    PubMed Central

    Karutha Pandian, Shunmugiah

    2013-01-01

    Background Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. Methods and Principal Findings In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62–71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples. Conclusion This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater) and the host associated marine samples (Seaweed and Seagrass) at higher depths from uncharacterised coastal region of Palk Bay, India using next generation sequencing technology. PMID:24167548

  11. Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

    PubMed Central

    Zhu, Wei; Ouyang, Shu; Iovene, Marina; O'Brien, Kimberly; Vuong, Hue; Jiang, Jiming; Buell, C Robin

    2008-01-01

    Background The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum) which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses. Results In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC) clone library (87 Mb) and sequencing of 22 potato BAC clones (2.9 Mb). The GC content of potato is very similar to Solanum lycopersicon (tomato) and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed. Conclusion Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that this conservation can be leveraged in genomic applications including cross-species annotation and genome sequencing initiatives. While tomato and potato share genic features, they differ in their repetitive sequence content and composition suggesting that repetitive sequences may have a more significant role in shaping speciation than previously reported. PMID:18554403

  12. Photodegradation of human growth hormone: a novel backbone cleavage between Glu-88 and Pro-89.

    PubMed

    Steinmann, Daniel; Ji, J Andrea; Wang, Y John; Schöneich, Christian

    2013-07-01

    The exposure of protein pharmaceuticals to light can cause loss of potency, oxidation, structural changes and aggregation. To elucidate the chemical pathways of photodegradation, we irradiated human growth hormone (hGH) at ? = 254 nm, ? ? 265-340 nm, and ? ? 295-340 nm (using the spectral cutoff of borosilicate glass) and analyzed the products by mass spectrometry. By means of LC-MS/MS analysis, we observed an unusual peptide backbone cleavage between Glu-88 and Pro-89. The crystal structure of hGH indicates that these residues are in proximity to Trp-86, which likely mediates this backbone cleavage. The two cleavage fragments observed by MS/MS analysis indicate the loss of CO from the amide bond and replacement of the Glu-C(? O)Pro bond with a Glu-H bond, accompanied by double bond formation on proline. The reaction is oxygen-independent and likely involves hydrogen transfer to the C? of Glu-88. To probe the influence of the protein fold, we irradiated hGH in its unfolded state, in 1:1 (v/v) acetonitrile/water, and also the isolated tryptic peptide Ile-78-Arg-90, which contains the Glu-88-Pro-89 sequence. In both cases, the cleavage between Glu-88 and Pro-89 was largely suppressed, while other cleavage pathways became dominant, notably between Gln-84 and Ser-85, as well as Ser-85 and Trp-86. PMID:23721578

  13. Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources

    PubMed Central

    Marsh, Alan J.; O’Sullivan, Orla; Hill, Colin; Ross, R. Paul; Cotter, Paul D.

    2013-01-01

    Kefir is a fermented milk-based beverage to which a number of health-promoting properties have been attributed. The microbes responsible for the fermentation of milk to produce kefir consist of a complex association of bacteria and yeasts, bound within a polysaccharide matrix, known as the kefir grain. The consistency of this microbial population, and that present in the resultant beverage, has been the subject of a number of previous, almost exclusively culture-based, studies which have indicated differences depending on geographical location and culture conditions. However, culture-based identification studies are limited by virtue of only detecting species with the ability to grow on the specific medium used and thus culture-independent, molecular-based techniques offer the potential for a more comprehensive analysis of such communities. Here we describe a detailed investigation of the microbial population, both bacterial and fungal, of kefir, using high-throughput sequencing to analyse 25 kefir milks and associated grains sourced from 8 geographically distinct regions. This is the first occasion that this technology has been employed to investigate the fungal component of these populations or to reveal the microbial composition of such an extensive number of kefir grains or milks. As a result several genera and species not previously identified in kefir were revealed. Our analysis shows that the bacterial populations in kefir are dominated by 2 phyla, the Firmicutes and the Proteobacteria. It was also established that the fungal populations of kefir were dominated by the genera Kazachstania, Kluyveromyces and Naumovozyma, but that a variable sub-dominant population also exists. PMID:23894461

  14. Strong liquid-crystalline polymeric compositions

    DOEpatents

    Dowell, F.

    1993-12-07

    Strong liquid-crystalline polymeric (LCP) compositions of matter are described. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment. 27 figures.

  15. Composition.

    ERIC Educational Resources Information Center

    Nemanich, Donald, Ed.

    1974-01-01

    The articles in this special issue of the "Illinois English Bulletin" concern the state of composition instruction at the secondary and college levels. The titles and authors are "Monologues or Dialogues? A Plea for Literacy" by Dr. Alfred J. Lindsey, "Teaching Composition: Curiouser and Curiouser" by Denny Brandon, and "Teaching Writing to High…

  16. Snake-Like Units Using Flexible Backbones and Actuation Redundancy for Enhanced Miniaturization

    E-print Network

    Simaan, Nabil

    Snake-Like Units Using Flexible Backbones and Actuation Redundancy for Enhanced Miniaturization-backbone snake-like unit with actuation redundancy and push-pull actuation. The design of this snake-like unit kinematic and virtual work model is used to perform this comparison between a multi-backbone snake like unit

  17. Paleoproterozoic sequences and magmatic complexes of the Losevo suture zone of the Voronezh crystalline massif: Geological position, material composition, geochemistry, and paleogeodynamics

    NASA Astrophysics Data System (ADS)

    Terentiev, R. A.

    2014-03-01

    In order to resolve the contradictions associated with uncertainty in the identification of the material composition, subdivision, and conditions of formation of the Paleoproterozoic intrusive, metavolcanogenic, and metasedimentary sequences of the Losevo suture zone of the Voronezh crystalline massif, this work presents geological, petrographic, petrochemical, and geochemical features of these sequences. The stratigraphic and magmatic scheme of the central part of the Losevo suture zone is clarified. In particular, the Paleoproterozoic Losevo Series is divided into two sequences: Strelitsa (marginal sea) and Podgornoe (island arc). A new hypabyssal Novo-Voronezh metagabbro-diabase complex, comagmatic to metatholeiites of the Podgornoe sequence, is distinguished. The isotope age of the Strelitsa sequence is assumed to be 2172 ± 17 Ma on the basis of the results of age dating of zircon cores from the Usman plagiogranites, intruding this sequence. The upper age boundary of the Strelitsa sequence corresponds to the age of premetamorphic gabbro of the Rozhdestvenskoe complex, comagmatic to metavolcanites (2120 ± 11-2158 ± 43 Ma). The age of the Usman plagiogranite complex is clarified. On the basis of geological-structural and petrographic-mineralogical analyses of metavolcanogenic rocks, lithological analysis of metasedimentary formations, and new geochemical data obtained from metavolcanites and metamorphosed deposits, the pattern of paleogeodynamic evolution of the Losevo suture zone in the first half of the Paleoproterozoic is proposed. The next stages are distinguished: (1) intrusion of tholeiites of transition T-MORB type in spreading zones and deposition of terrigenous strata in the marginal sea basins; (2) intrusion of Nb-depleted tholeiites and plagiorhyolites, the geochemical characteristics indicating their formation in the subduction setting; (3) intrusion of gabbroids of the Rozhdestvenskoe complex; (4) formation of an island arc synchronously with stage 2, tholeiitic and calc-alkaline (Podgornoe sequence) volcanism; (5) intrusions of gabbro-diabases, subsynchronous to volcanism, of the Novovoronezh complex and diorite-granitoides, crystallization of granitoides of the Usman complex; (6) a break in sedimentation and formation of molasses of the Voronezh (Somovo) Formation.

  18. Selective backbone labelling of ILV methyl labelled proteins.

    PubMed

    Sibille, Nathalie; Hanoulle, Xavier; Bonachera, Fanny; Verdegem, Dries; Landrieu, Isabelle; Wieruszeski, Jean-Michel; Lippens, Guy

    2009-04-01

    Adding the 13C labelled 2-keto-isovalerate and 2-oxobutanoate precursors to a minimal medium composed of 12C labelled glucose instead of the commonly used (2D, 13C) glucose leads not only to the 13C labelling of (I, L, V) methyls but also to the selective 13C labelling of the backbone C(alpha) and CO carbons of the Ile and Val residues. As a result, the backbone (1H, 15N) correlations of the Ile and Val residues and their next neighbours in the (i + 1) position can be selectively identified in HN(CA) and HN(CO) planes. The availability of a selective HSQC spectrum corresponding to the sole amide resonances of the Ile and Val residues allows connecting them to their corresponding methyls by the intra-residue NOE effect, and should therefore be applicable to larger systems. PMID:19288066

  19. Packet-level traffic measurements from the Sprint IP backbone

    Microsoft Academic Search

    Chuck Fraleigh; Sue Moon; Bryan Lyles; Chase Cotton; Mujahid Khan; Deb Moll; Rob Rockell; Ted Seely; S. C. Diot

    2003-01-01

    Network traffic measurements provide essential data for networking research and network management. In this article we describe a passive monitoring system designed to capture GPS synchronized packet-level traffic measurements on OC-3, OC-12, and OC-48 links. Our system is deployed in four POP in the Sprint IP backbone. Measurement data is stored on a 10 Tbyte storage area network and analyzed

  20. On construction of the virtual backbone in wireless mesh networks

    Microsoft Academic Search

    Deepesh Man Shrestha; Young Bae Ko

    2006-01-01

    This paper deals with the selection of backbone nodes among end-user nodes in the wireless mesh networks. Although current IEEE 802.11 standards does not allow direct client-client or wireless AP-AP communication in the infrastructure mode, new concepts on mesh networks is arising in which all types of wireless links (i.e. AP-AP, client-client and client-AP) can be formed. This leads to

  1. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

    PubMed

    Heffernan, Rhys; Paliwal, Kuldip; Lyons, James; Dehzangi, Abdollah; Sharma, Alok; Wang, Jihua; Sattar, Abdul; Yang, Yuedong; Zhou, Yaoqi

    2015-01-01

    Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independently. In a previous study, we found that an iterative use of predicted secondary structure and backbone torsion angles can further improve secondary structure and torsion angle prediction. In this study, we expand the iterative features to include solvent accessible surface area and backbone angles and dihedrals based on C? atoms. By using a deep learning neural network in three iterations, we achieved 82% accuracy for secondary structure prediction, 0.76 for the correlation coefficient between predicted and actual solvent accessible surface area, 19° and 30° for mean absolute errors of backbone ? and ? angles, respectively, and 8° and 32° for mean absolute errors of C?-based ? and ? angles, respectively, for an independent test dataset of 1199 proteins. The accuracy of the method is slightly lower for 72 CASP 11 targets but much higher than those of model structures from current state-of-the-art techniques. This suggests the potentially beneficial use of these predicted properties for model assessment and ranking. PMID:26098304

  2. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning

    PubMed Central

    Heffernan, Rhys; Paliwal, Kuldip; Lyons, James; Dehzangi, Abdollah; Sharma, Alok; Wang, Jihua; Sattar, Abdul; Yang, Yuedong; Zhou, Yaoqi

    2015-01-01

    Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independently. In a previous study, we found that an iterative use of predicted secondary structure and backbone torsion angles can further improve secondary structure and torsion angle prediction. In this study, we expand the iterative features to include solvent accessible surface area and backbone angles and dihedrals based on C? atoms. By using a deep learning neural network in three iterations, we achieved 82% accuracy for secondary structure prediction, 0.76 for the correlation coefficient between predicted and actual solvent accessible surface area, 19° and 30° for mean absolute errors of backbone ? and ? angles, respectively, and 8° and 32° for mean absolute errors of C?-based ? and ? angles, respectively, for an independent test dataset of 1199 proteins. The accuracy of the method is slightly lower for 72 CASP 11 targets but much higher than those of model structures from current state-of-the-art techniques. This suggests the potentially beneficial use of these predicted properties for model assessment and ranking. PMID:26098304

  3. Bacterial Community Composition in Central European Running Waters Examined by Temperature Gradient Gel Electrophoresis and Sequence Analysis of 16S rRNA Genes? †

    PubMed Central

    Beier, Sara; Witzel, Karl-Paul; Marxsen, Jürgen

    2008-01-01

    The bacterial community composition in small streams and a river in central Germany was examined by temperature gradient gel electrophoresis (TGGE) with PCR products of 16S rRNA gene fragments and sequence analysis. Complex TGGE band patterns suggested high levels of diversity of bacterial species in all habitats of these environments. Cluster analyses demonstrated distinct differences among the communities in stream and spring water, sandy sediments, biofilms on stones, degrading leaves, and soil. The differences between stream water and sediment were more significant than those between sites within the same habitat along the stretch from the stream source to the mouth. TGGE data from an entire stream course suggest that, in the upper reach of the stream, a special suspended bacterial community is already established and changes only slightly downstream. The bacterial communities in water and sediment in an acidic headwater with a pH below 5 were highly similar to each other but deviated distinctly from the communities at the other sites. As ascertained by nucleotide sequence analysis, stream water communities were dominated by Betaproteobacteria (one-third of the total bacteria), whereas sediment communities were composed mainly of Betaproteobacteria and members of the Fibrobacteres/Acidobacteria group (each accounting for about 25% of bacteria). Sequences obtained from bacteria from water samples indicated the presence of typical cosmopolitan freshwater organisms. TGGE bands shared between stream and soil samples, as well as sequences found in bacteria from stream samples that were related to those of soil bacteria, demonstrated the occurrence of some species in both stream and soil habitats. Changes in bacterial community composition were correlated with geographic distance along a stream, but in comparisons of different streams and rivers, community composition was correlated only with environmental conditions. PMID:18024682

  4. Animal Protection and Structural Studies of a Consensus Sequence Vaccine Targeting the Receptor Binding Domain of the Type IV Pilus of Pseudomonas aeruginosa

    SciTech Connect

    Kao, Daniel J.; Churchill, Mair E.A.; Irvin, Randall T.; Hodges, Robert S. (Alberta); (Colorado)

    2008-09-23

    One of the main obstacles in the development of a vaccine against Pseudomonas aeruginosa is the requirement that it is protective against a wide range of virulent strains. We have developed a synthetic-peptide consensus-sequence vaccine (Cs1) that targets the host receptor-binding domain (RBD) of the type IV pilus of P. aeruginosa. Here, we show that this vaccine provides increased protection against challenge by the four piliated strains that we have examined (PAK, PAO, KB7 and P1) in the A.BY/SnJ mouse model of acute P. aeruginosa infection. To further characterize the consensus sequence, we engineered Cs1 into the PAK monomeric pilin protein and determined the crystal structure of the chimeric Cs1 pilin to 1.35 {angstrom} resolution. The substitutions (T130K and E135P) used to create Cs1 do not disrupt the conserved backbone conformation of the pilin RBD. In fact, based on the Cs1 pilin structure, we hypothesize that the E135P substitution bolsters the conserved backbone conformation and may partially explain the immunological activity of Cs1. Structural analysis of Cs1, PAK and K122-4 pilins reveal substitutions of non-conserved residues in the RBD are compensated for by complementary changes in the rest of the pilin monomer. Thus, the interactions between the RBD and the rest of the pilin can either be mediated by polar interactions of a hydrogen bond network in some strains or by hydrophobic interactions in others. Both configurations maintain a conserved backbone conformation of the RBD. Thus, the backbone conformation is critical in our consensus-sequence vaccine design and that cross-reactivity of the antibody response may be modulated by the composition of exposed side-chains on the surface of the RBD. This structure will guide our future vaccine design by focusing our investigation on the four variable residue positions that are exposed on the RBD surface.

  5. Origin of the Temporal-compositional Variations in Monogenetic Vent Eruptions: Insights from the Crystal Cargo in the Papoose Canyon Sequence, Big Pine Volcanic Field, CA

    NASA Astrophysics Data System (ADS)

    Gao, R.; Ramirez, G.; Lassiter, J. C.

    2014-12-01

    Systematic temporal-compositional variations observed in many monogenetic vent eruption sequences (e.g. decreasing incompatible element concentrations, variation in major element and isotopic compositions) may reflect varying extents of crustal contamination (c.f., [1]), or melting and mixing of small-scale mantle heterogeneities (c.f., [2]). During eruption of the Papoose Canyon (PC) monogenetic vent incompatible trace element concentrations decreased a factor of 2, 87Sr/86Sr decreased (from ~0.7063 to 0.7055), and 143Nd/144Nd increased (from ~0.51246 to 0.51258) (c.f., [2]). Blondes et al. (2008) argued that the relatively primitive melt MgO content and apparent presence of mantle xenoliths in the sequence indicate limited melt storage and crustal contamination prior to eruption, and proposed melting and mixing of two distinct mantle components to explain the variations. However, PC olivine phenocryst compositions (Fo# ~76-89) span a wide range, extending to evolved (low-Fo) compositions, and the vast majority of phenocrysts are more evolved than olivines in equilibrium with the host scoria (Mg# ~87-89). In addition, olivine and clinopyroxene from xenoliths within the early sequence have Mg# (73-87) similar to the phenocrysts, and lower than typical mantle peridotites. Sr-Nd isotopic compositions of the xenoliths are similar to the early PC lavas, but less enriched than the host melts. Therefore, the xenoliths are most likely cognate xenoliths derived from fractionated PC magmas. Finally, both phenocryst and xenolith olivines have ?18O (~5.5 to 5.7 ‰) higher than most mantle peridotites (~5.2 ±0.2 ‰), and clinopyroxene trace element abundances indicate derivation from melts with trace element abundances higher than the most enriched PC lavas. In conjunction, these features suggest that the phenocrysts and xenoliths derive from early PC melts that ponded and fractionated and assimilated continental crust, possibly in crustal sills. These melts were drained and mixed with more primitive melts as the eruption began, and the temporal-compositional trends in part reflect decreasing contaminated sill component over time. These results indicate that even "primitive" melts may contain a significant signature of crustal contamination. [1] Erlund et al., 2010. [2] Blondes et al., 2008.

  6. Composite-180° pulse-based symmetry sequences to recouple proton chemical shift anisotropy tensors under ultrafast MAS solid-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Pandey, Manoj Kumar; Malon, Michal; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

    2015-01-01

    There is considerable interest in the measurement of proton (1H) chemical shift anisotropy (CSA) tensors to obtain deeper insights into H-bonding interactions which find numerous applications in chemical and biological systems. However, the presence of strong 1H/1H dipolar interaction makes it difficult to determine small size 1H CSAs from the homogeneously broadened NMR spectra. Previously reported pulse sequences for 1H CSA recoupling are prone to the effects of radio frequency field (B1) inhomogeneity. In the present work we have carried out a systematic study using both numerical and experimental approaches to evaluate ?-encoded radio frequency (RF) pulse sequences based on R-symmetries that recouple 1H CSA in the indirect dimension of a 2D 1H/1H anisotropic/isotropic chemical shift correlation experiment under ultrafast magic angle spinning (MAS) frequencies. The spectral resolution and sensitivity can be significantly improved in both frequency dimensions of the 2D 1H/1H correlation spectrum without decoupling 1H/1H dipolar couplings but by using ultrafast MAS rates up to 70 kHz. We successfully demonstrate that with a reasonable RF field requirement (<200 kHz) a set of symmetry-based recoupling sequences, with a series of phase-alternating 270°0-90°180 composite-180° pulses, are more robust in combating B1 inhomogeneity effects. In addition, our results show that the new pulse sequences render remarkable 1H CSA recoupling efficiency and undistorted CSA lineshapes. Experimental results on citric acid and malonic acid comparing the efficiencies of these newly developed pulse sequences with that of previously reported CSA recoupling pulse sequences are also reported under ultrafast MAS conditions.

  7. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure.

    PubMed

    Rubin, Benjamin E R; Sanders, Jon G; Hampton-Marcell, Jarrad; Owens, Sarah M; Gilbert, Jack A; Moreau, Corrie S

    2014-12-01

    The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied. PMID:25257543

  8. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure

    PubMed Central

    Rubin, Benjamin E R; Sanders, Jon G; Hampton-Marcell, Jarrad; Owens, Sarah M; Gilbert, Jack A; Moreau, Corrie S

    2014-01-01

    The recent development of methods applying next-generation sequencing to microbial community characterization has led to the proliferation of these studies in a wide variety of sample types. Yet, variation in the physical properties of environmental samples demands that optimal DNA extraction techniques be explored for each new environment. The microbiota associated with many species of insects offer an extraction challenge as they are frequently surrounded by an armored exoskeleton, inhibiting disruption of the tissues within. In this study, we examine the efficacy of several commonly used protocols for extracting bacterial DNA from ants. While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. These results indicate that the concentration necessary for dependable sequencing is around 10,000 copies of target DNA per microliter. Exoskeletal pulverization and tissue digestion increased the reliability of extractions, suggesting that these steps should be included in any study of insect-associated microorganisms that relies on obtaining microbial DNA from intact body segments. Although laboratory and analysis techniques should be standardized across diverse sample types as much as possible, minimal modifications such as these will increase the number of environments in which bacterial communities can be successfully studied. PMID:25257543

  9. Quantitative 2D and 3D Gamma-HCP experiments for the determination of the angles alpha and zeta in the phosphodiester backbone of oligonucleotides.

    PubMed

    Nozinovic, Senada; Richter, Christian; Rinnenthal, Jörg; Fürtig, Boris; Duchardt-Ferner, Elke; Weigand, Julia E; Schwalbe, Harald

    2010-08-01

    The quantitative Gamma-(HCP) experiment, a novel heteronuclear NMR pulse sequence for the determination of the RNA backbone angles alpha(O3'(i-1)-P(i)-O5'(i)-C5'(i)) and zeta(C3'(i)-O3'(i)-P(i+1)-O5'(i+1)) in (13)C-labeled RNA, is introduced. The experiment relies on the interaction between the CH bond vector dipole and the (31)P chemical shift anisotropy (CSA), which affects the relaxation of the (13)C,(31)P double- and zero-quantum coherence and thus the intensity of the detectable magnetization. With the new pulse sequence, five different cross-correlated relaxation rates along the phosphodiester backbone can be measured in a quantitative manner, allowing projection-angle and torsion-angle restraints for the two backbone angles alpha and zeta to be extracted. Two versions of the pulse sequence optimized for the CH and CH(2) groups are introduced and demonstrated for a 14-mer cUUCGg tetraloop RNA model system and for a 27-mer RNA with a previously unknown structure. The restraints were incorporated into the calculation of a very high resolution structure of the RNA model system (Nozinovic, S.; et al. Nucleic Acids Res. 2010, 38, 683). Comparison with the X-ray structure of the cUUCGg tetraloop confirmed the high quality of the data, suggesting that the method can significantly improve the quality of RNA structure determination. PMID:20614918

  10. Unique Backbone-Water Interaction Detected in Sphingomyelin Bilayers with 1H/31P and 1H/13C HETCOR MAS NMR Spectroscopy

    PubMed Central

    Holland, Gregory P.; Alam, Todd M.

    2008-01-01

    Two-dimensional 1H/31P dipolar heteronuclear correlation (HETCOR) magic-angle spinning nuclear magnetic resonance (NMR) is used to investigate the correlation of the lipid headgroup with various intra- and intermolecular proton environments. Cross-polarization NMR techniques involving 31P have not been previously pursued to a great extent in lipid bilayers due to the long 1H-31P distances and high degree of headgroup mobility that averages the dipolar coupling in the liquid crystalline phase. The results presented herein show that this approach is very promising and yields information not readily available with other experimental methods. Of particular interest is the detection of a unique lipid backbone-water intermolecular interaction in egg sphingomyelin (SM) that is not observed in lipids with glycerol backbones like phosphatidylcholines. This backbone-water interaction in SM is probed when a mixing period allowing magnetization exchange between different 1H environments via the nuclear Overhauser effect (NOE) is included in the NMR pulse sequence. The molecular information provided by these 1H/31P dipolar HETCOR experiments with NOE mixing differ from those previously obtained by conventional NOE spectroscopy and heteronuclear NOE spectroscopy NMR experiments. In addition, two-dimensional 1H/13C INEPT HETCOR experiments with NOE mixing support the 1H/31P dipolar HETCOR results and confirm the presence of a H2O environment that has nonvanishing dipolar interactions with the SM backbone. PMID:18390621

  11. Relaxation of backbone bond geometry improves protein energy landscape modeling.

    PubMed

    Conway, Patrick; Tyka, Michael D; DiMaio, Frank; Konerding, David E; Baker, David

    2014-01-01

    A key issue in macromolecular structure modeling is the granularity of the molecular representation. A fine-grained representation can approximate the actual structure more accurately, but may require many more degrees of freedom than a coarse-grained representation and hence make conformational search more challenging. We investigate this tradeoff between the accuracy and the size of protein conformational search space for two frequently used representations: one with fixed bond angles and lengths and one that has full flexibility. We performed large-scale explorations of the energy landscapes of 82 protein domains under each model, and find that the introduction of bond angle flexibility significantly increases the average energy gap between native and non-native structures. We also find that incorporating bonded geometry flexibility improves low resolution X-ray crystallographic refinement. These results suggest that backbone bond angle relaxation makes an important contribution to native structure energetics, that current energy functions are sufficiently accurate to capture the energetic gain associated with subtle deformations from chain ideality, and more speculatively, that backbone geometry distortions occur late in protein folding to optimize packing in the native state. PMID:24265211

  12. Water proton spin saturation affects measured protein backbone 15 N spin relaxation rates

    NASA Astrophysics Data System (ADS)

    Chen, Kang; Tjandra, Nico

    2011-12-01

    Protein backbone 15N NMR spin relaxation rates are useful in characterizing the protein dynamics and structures. To observe the protein nuclear-spin resonances a pulse sequence has to include a water suppression scheme. There are two commonly employed methods, saturating or dephasing the water spins with pulse field gradients and keeping them unperturbed with flip-back pulses. Here different water suppression methods were incorporated into pulse sequences to measure 15N longitudinal T1 and transversal rotating-frame T1? spin relaxation. Unexpectedly the 15N T1 relaxation time constants varied significantly with the choice of water suppression method. For a 25-kDa Escherichiacoli. glutamine binding protein (GlnBP) the T1 values acquired with the pulse sequence containing a water dephasing gradient are on average 20% longer than the ones obtained using a pulse sequence containing the water flip-back pulse. In contrast the two T1? data sets are correlated without an apparent offset. The average T1 difference was reduced to 12% when the experimental recycle delay was doubled, while the average T1 values from the flip-back measurements were nearly unchanged. Analysis of spectral signal to noise ratios ( s/ n) showed the apparent slower 15N relaxation obtained with the water dephasing experiment originated from the differences in 1H N recovery for each relaxation time point. This in turn offset signal reduction from 15N relaxation decay. The artifact becomes noticeable when the measured 15N relaxation time constant is comparable to recycle delay, e.g., the 15N T1 of medium to large proteins. The 15N relaxation rates measured with either water suppression schemes yield reasonable fits to the structure. However, data from the saturated scheme results in significantly lower Model-Free order parameters (< S2> = 0.81) than the non-saturated ones (< S2> = 0.88), indicating such order parameters may be previously underestimated.

  13. Water proton spin saturation affects measured protein backbone 15N spin relaxation rates

    PubMed Central

    Chen, Kang; Tjandra, Nico

    2011-01-01

    Protein backbone 15N NMR spin relaxation rates are useful in characterizing the protein dynamics and structures. To observe the protein nuclear-spin resonances a pulse sequence has to include a water suppression scheme. There are two commonly employed methods, saturating or dephasing the water spins with pulse field gradients and keeping them unperturbed with flip-back pulses. Here different water suppression methods were incorporated into pulse sequences to measure 15N longitudinal T1 and transversal rotating-frame T1? spin relaxation. Unexpectedly the 15N T1 relaxation time constants varied significantly with the choice of water suppression method. For a 25-kDa Escherichia coli. glutamine binding protein (GlnBP) the T1 values acquired with the pulse sequence containing a water dephasing gradient are on average 20% longer than the ones obtained using a pulse sequence containing the water flip-back pulse. In contrast the two T1? data sets are correlated without an apparent offset. The average T1 difference was reduced to 12% when the experimental recycle delay was doubled, while the average T1 values from the flip-back measurements were nearly unchanged. Analysis of spectral signal to noise ratios (s/n) showed the apparent slower 15N relaxation obtained with the water dephasing experiment originated from the differences in 1HN recovery for each relaxation time point. This in turn offset signal reduction from 15N relaxation decay. The artifact becomes noticeable when the measured 15N relaxation time constant is comparable to recycle delay, e.g., the 15N T1 of medium to large proteins. The 15N relaxation rates measured with either water suppression schemes yield reasonable fits to the structure. However, data from the saturated scheme results in significantly lower Model-Free order parameters (?S2? = 0.81) than the non-saturated ones (?S2? = 0.88), indicating such order parameters may be previously underestimated. PMID:22015249

  14. Variation in seed fatty acid composition and sequence divergence in the FAD2 gene coding region between wild and cultivated sesame.

    PubMed

    Chen, Zhenbang; Tonnis, Brandon; Morris, Brad; Wang, Richard B; Zhang, Amy L; Pinnow, David; Wang, Ming Li

    2014-12-01

    Sesame germplasm harbors genetic diversity which can be useful for sesame improvement in breeding programs. Seven accessions with different levels of oleic acid were selected from the entire USDA sesame germplasm collection (1232 accessions) and planted for morphological observation and re-examination of fatty acid composition. The coding region of the FAD2 gene for fatty acid desaturase (FAD) in these accessions was also sequenced. Cultivated sesame accessions flowered and matured earlier than the wild species. The cultivated sesame seeds contained a significantly higher percentage of oleic acid (40.4%) than the seeds of the wild species (26.1%). Nucleotide polymorphisms were identified in the FAD2 gene coding region between wild and cultivated species. Some nucleotide polymorphisms led to amino acid changes, one of which was located in the enzyme active site and may contribute to the altered fatty acid composition. Based on the morphology observation, chemical analysis, and sequence analysis, it was determined that two accessions were misnamed and need to be reclassified. The results obtained from this study are useful for sesame improvement in molecular breeding programs. PMID:25386691

  15. Bacterial Pathogens and Community Composition in Advanced Sewage Treatment Systems Revealed by Metagenomics Analysis Based on High-Throughput Sequencing

    PubMed Central

    Lu, Xin; Zhang, Xu-Xiang; Wang, Zhu; Huang, Kailong; Wang, Yuan; Liang, Weigang; Tan, Yunfei; Liu, Bo; Tang, Junying

    2015-01-01

    This study used 454 pyrosequencing, Illumina high-throughput sequencing and metagenomic analysis to investigate bacterial pathogens and their potential virulence in a sewage treatment plant (STP) applying both conventional and advanced treatment processes. Pyrosequencing and Illumina sequencing consistently demonstrated that Arcobacter genus occupied over 43.42% of total abundance of potential pathogens in the STP. At species level, potential pathogens Arcobacter butzleri, Aeromonas hydrophila and Klebsiella pneumonia dominated in raw sewage, which was also confirmed by quantitative real time PCR. Illumina sequencing also revealed prevalence of various types of pathogenicity islands and virulence proteins in the STP. Most of the potential pathogens and virulence factors were eliminated in the STP, and the removal efficiency mainly depended on oxidation ditch. Compared with sand filtration, magnetic resin seemed to have higher removals in most of the potential pathogens and virulence factors. However, presence of the residual A. butzleri in the final effluent still deserves more concerns. The findings indicate that sewage acts as an important source of environmental pathogens, but STPs can effectively control their spread in the environment. Joint use of the high-throughput sequencing technologies is considered a reliable method for deep and comprehensive overview of environmental bacterial virulence. PMID:25938416

  16. Sequence-Based Analysis of Structural Organization and Composition of the Cultivated Sunflower (Helianthus annuus L.) Genome.

    PubMed

    Gill, Navdeep; Buti, Matteo; Kane, Nolan; Bellec, Arnaud; Helmstetter, Nicolas; Berges, Hélène; Rieseberg, Loren H

    2014-01-01

    Sunflower is an important oilseed crop, as well as a model system for evolutionary studies, but its 3.6 gigabase genome has proven difficult to assemble, in part because of the high repeat content of its genome. Here we report on the sequencing, assembly, and analyses of 96 randomly chosen BACs from sunflower to provide additional information on the repeat content of the sunflower genome, assess how repetitive elements in the sunflower genome are organized relative to genes, and compare the genomic distribution of these repeats to that found in other food crops and model species. We also examine the expression of transposable element-related transcripts in EST databases for sunflower to determine the representation of repeats in the transcriptome and to measure their transcriptional activity. Our data confirm previous reports in suggesting that the sunflower genome is >78% repetitive. Sunflower repeats share very little similarity to other plant repeats such as those of Arabidopsis, rice, maize and wheat; overall 28% of repeats are "novel" to sunflower. The repetitive sequences appear to be randomly distributed within the sequenced BACs. Assuming the 96 BACs are representative of the genome as a whole, then approximately 5.2% of the sunflower genome comprises non TE-related genic sequence, with an average gene density of 18kbp/gene. Expression levels of these transposable elements indicate tissue specificity and differential expression in vegetative and reproductive tissues, suggesting that expressed TEs might contribute to sunflower development. The assembled BACs will also be useful for assessing the quality of several different draft assemblies of the sunflower genome and for annotating the reference sequence. PMID:24833511

  17. Composites

    NASA Astrophysics Data System (ADS)

    Chmielewski, M.; Nosewicz, S.; Pietrzak, K.; Rojek, J.; Strojny-N?dza, A.; Mackiewicz, S.; Dutkiewicz, J.

    2014-11-01

    It is commonly known that the properties of sintered materials are strongly related to technological conditions of the densification process. This paper shows the sintering behavior of a NiAl-Al2O3 composite, and its individual components sintered separately. Each kind of material was processed via the powder metallurgy route (hot pressing). The progress of sintering at different stages of the process was tested. Changes in the microstructure were examined using scanning and transmission electron microscopy. Metal-ceramics interface was clean and no additional phases were detected. Correlation between the microstructure, density, and mechanical properties of the sintered materials was analyzed. The values of elastic constants of NiAl/Al2O3 were close to intermetallic ones due to the volume content of the NiAl phase particularly at low densities, where small alumina particles had no impact on the composite's stiffness. The influence of the external pressure of 30 MPa seemed crucial for obtaining satisfactory stiffness for three kinds of the studied materials which were characterized by a high dense microstructure with a low number of isolated spherical pores.

  18. Laccase-assisted grafting of poly(3-hydroxybutyrate) onto the bacterial cellulose as backbone polymer: development and characterisation.

    PubMed

    Iqbal, Hafiz M N; Kyazze, Godfrey; Tron, Thierry; Keshavarz, Tajalli

    2014-11-26

    Bacterial cellulose (BC) exhibits high purity, mechanical strength and an ultra-fine fibrous 3-D network structure with bio-compatible and bio-degradable characteristics, while P(3 HB) are a bio-degradable matrix material derived from natural resources. Herein, we report a mild and eco-friendly fabrication of indigenously isolated P(3 HB) based novel composites consisting of BC (a straight-chain polysaccharide) as a backbone polymer and laccase was used as a grafting tool. The resulting composites were characterised by Fourier-transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), X-ray diffraction (XRD), differential scanning calorimetry (DSC), dynamic mechanical analyser (DMA) and water contact angle analyser (WCA). The FTIR spectra of the pure P(3 HB) and P(3 HB) containing graft composites [P(3 HB)-g-BC] showed their strong characteristic bands at 3358 cm(-1), 1721 cm(-1) and 1651 cm(-1), respectively. A homogenous dispersion of P(3 HB) in the backbone polymer of BC was achieved as evident by the SEM micrographs. XRD pattern for P(3 HB) showed distinct peaks at 2? values that represent the crystalline nature of P(3 HB). While, in comparison with those of neat P(3 HB), the degree of crystallinity for P(3 HB)-g-BC decreased and this reduction is mainly because of the new cross-linking of P(3 HB) within the backbone polymer that changes the morphology and destroys the crystallites. Laccase-assisted graft composite prepared from P(3 HB) and BC was fairly flexible and strong, judged by the tensile strength (64.5 MPa), elongations at break (15.7%), and Young's modulus (0.98 GPa) because inherently high strength of BC allowed the mechanical properties of P(3 HB) to improve in the P(3 HB)-g-BC composite. The hydrophilic property of the P(3 HB)-g-BC was much better than that of the individual counterparts which is also a desired characteristic to enhance the biocompatibility of the materials for proper cell adhesion and proliferation. PMID:25256467

  19. Evolution of Robust Network Topologies: Emergence of Central Backbones

    NASA Astrophysics Data System (ADS)

    Peixoto, Tiago P.; Bornholdt, Stefan

    2012-09-01

    We model the robustness against random failure or an intentional attack of networks with an arbitrary large-scale structure. We construct a block-based model which incorporates—in a general fashion—both connectivity and interdependence links, as well as arbitrary degree distributions and block correlations. By optimizing the percolation properties of this general class of networks, we identify a simple core-periphery structure as the topology most robust against random failure. In such networks, a distinct and small “core” of nodes with higher degree is responsible for most of the connectivity, functioning as a central “backbone” of the system. This centralized topology remains the optimal structure when other constraints are imposed, such as a given fraction of interdependence links and fixed degree distributions. This distinguishes simple centralized topologies as the most likely to emerge, when robustness against failure is the dominant evolutionary force.

  20. Selectivity in ROS-induced peptide backbone bond cleavage.

    PubMed

    Stringfellow, Hannah M; Jones, Michael R; Green, Mandy C; Wilson, Angela K; Francisco, Joseph S

    2014-12-01

    Post-translational mechanisms of protein oxidation as a result of reactive oxygen species (ROS) can occur under physiological conditions to yield selective side-chain and backbone modifications including abstractions, donations, additions, substitutions, and fragmentation. In order to characterize the selectivity of radical-mediated fragmentation, quantum mechanical investigations using ab initio and density functional methods were employed to evaluate site, conformation, and pathway trends of small trialanine peptides resembling a ?-strand and a ?-turn. Comparisons of reaction enthalpies show that the diamide pathway is more energetically favorable than the ?-amidation pathway and that both pathways are site and conformationally selective. These findings readily contribute to the understanding of oxidative stress in biochemical processes. PMID:25369550

  1. Sequence analysis of styrenic copolymers by tandem mass spectrometry.

    PubMed

    Yol, Aleer M; Janoski, Jonathan; Quirk, Roderic P; Wesdemiotis, Chrys

    2014-10-01

    Styrene and smaller molar amounts of either m-dimethylsilylstyrene (m-DMSS) or p-dimethylsilylstyrene (p-DMSS) were copolymerized under living anionic polymerization conditions, and the compositions, architectures, and sequences of the resulting copolymers were characterized by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and tandem mass spectrometry (MS(2)). MS analysis revealed that linear copolymer chains containing phenyl-Si(CH3)2H pendants were the major product for both DMSS comonomers. In addition, two-armed architectures with phenyl-Si(CH3)2-benzyl branches were detected as minor products. The comonomer sequence in the linear chains was established by MS(2) experiments on lithiated oligomers, based on the DMSS content of fragments generated by backbone C-C bond scissions and with the help of reference MS(2) spectra obtained from a polystyrene homopolymer and polystyrene end-capped with a p-DMSS block. The MS(2) data provided conclusive evidence that copolymerization of styrene/DMSS mixtures leads to chains with a rather random distribution of the silylated comonomer when m-DMSS is used, but to chains with tapered block structures, with the silylated units near the initiator, when p-DMSS is used. Hence, MS(2) fragmentation patterns permit not only differentiation of the sequences generated in the synthesis, but also the determination of specific comonomer locations along the polymer chain. PMID:25181590

  2. RNA Structure and Function 485 RNA backbone rotamers finding your way in

    E-print Network

    Richardson, David

    . Introduction Detailed structural analysis has always been much more difficult for nucleic acid backbone than for nucleic acid bases: the backbone has a high number of degrees of freedom, frequently underdetermined that library, and developing tools and applications for it in structure determination and analysis

  3. Experimental Study of Internet Stability and Wide-Area Backbone Failures

    E-print Network

    Krishnamurthy, Arvind

    Experimental Study of Internet Stability and Wide-Area Backbone Failures Craig Labovitz and Abha an experimental study of Internet stability and the origins of failure in Internet protocol backbones. The stability of end-to-end Internet paths is depen- dent both on the underlying telecommunication switching

  4. Distributed Mobile Disk Cover A Building Block for Mobile Backbone Networks

    E-print Network

    Zussman, Gil

    1 Distributed Mobile Disk Cover ­ A Building Block for Mobile Backbone Networks Anand Srinivas, Gil. with at least one MBN, and (ii) the network formed by the MBNs is connected. We assume a disk connectivity model of Mobile Backbone Networks has been recently studied by a few different approaches. An important subproblem

  5. UW / MADISON CS TR-1451 1 Modeling Congestion in Backbone Routers

    E-print Network

    Liblit, Ben

    UW / MADISON CS TR-1451 1 Modeling Congestion in Backbone Routers Jim Gast and Paul Barford,pb}@cs.wisc.edu UW-Madison CS Technical Report 1451 Abstract Traffic engineering models based on end-to-end loss probabilities and delays do not scale well to fast backbone links. In this paper, we investigate the nature

  6. Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity

    E-print Network

    Heller, Eric

    Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity Simon of alternative nucleotides would support the assembly of nucleic acid polymers containing nonheritable backbone of heterogeneous nucleic acid molecules could evolve reproducible function. For such evolution to be possible

  7. Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope

    E-print Network

    Baker, David

    Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope Edited by I. Wilson Keywords: protein grafting; flexible backbone design; epitope scaffold; immunogen epitopes onto heterologous proteins to design novel "epitope-scaffold" antigens. However, side

  8. Supporting Internet Protocol TV (IPTV) in Backbone Networks: Design of Robust Routing Strategies

    E-print Network

    Fisher, Kathleen

    Supporting Internet Protocol TV (IPTV) in Backbone Networks: Design of Robust Routing Strategies Paper ID: 261 (13 pages) Abstract In this paper, we consider the problem of providing IPTV services by designing routing strategies to handle catastrophic failures in a backbone network. In a typi- cal IPTV

  9. Investigations into Sequence and Conformational Dependence of Backbone Entropy, Inter-basin

    E-print Network

    Berry, R. Stephen

    . Stephen Berry1,3 Karl F. Freed1,3 * and Tobin R. Sosnick2,4 * 1 Department of Chemistry, The University pep- tide unit to be in one Ramachandran basin or another and the inter-basin hopping rates directly

  10. Evaluation of composition and individual variability of rumen microbiota in yaks by 16S rRNA high-throughput sequencing technology.

    PubMed

    Guo, Wei; Li, Ying; Wang, Lizhi; Wang, Jiwen; Xu, Qin; Yan, Tianhai; Xue, Bai

    2015-08-01

    The Yak (Bos grunniens) is a unique species of ruminant animals that is important to agriculture of the Tibetan plateau, and has a complex intestinal microbial community. The objective of the present study was to characterize the composition and individual variability of microbiota in the rumen of yaks using 16S rRNA gene high-throughput sequencing technique. Rumen samples used in the present study were obtained from grazing adult male yaks (n = 6) in a commercial farm in Ganzi Autonomous Prefecture of Sichuan Province, China. Universal prokaryote primers were used to target the V4-V5 hypervariable region of 16S rRNA gene. A total of 7200 operational taxonomic units (OTUs) were obtained after sequence filtering and chimera removal. Within these OTUs, 0.56% belonged to Archaea (40 OTUs), 7.19% to unassigned species (518 OTUs), and the remaining OTUs (6642) in all samples were of bacterial origin. When examining the community structure of bacteria, we identified 23 phyla within 159 families after taxonomic summarization. Bacteroidetes and Firmicutes were the predominant phyla accounting for 39.68% (SD = 0.05) and 45.90% (SD = 0.06), respectively. Moreover, 3764 OTUs were identified as shared OTUs (i.e. represented in all yaks) and belonged to 35 genera, exhibiting highly variable abundance across individual samples. Phylogenetic placement of these genera across individual samples was examined. In addition, we evaluated the distance among the 6 rumen samples by adding taxon phylogeny using UniFrac, representing 24.1% of average distance. In summary, the current study reveals a shared rumen microbiome and phylogenetic lineage and presents novel information on composition and individual variability of the bacterial community in the rumen of yaks. PMID:25911445

  11. Evaluation of Diverse ?/? Backbone Patterns for Functional ?-Helix Mimicry: Analogues of the Bim BH3 Domain

    PubMed Central

    Boersma, Melissa D.; Haase, Holly S.; Peterson-Kaufman, Kimberly J.; Lee, Erinna F.; Clarke, Oliver B.; Colman, Peter M.; Smith, Brian J.; Horne, W. Seth; Fairlie, W. Douglas; Gellman, Samuel H.

    2012-01-01

    Peptidic oligomers that contain both ?- and ?-amino acid residues, in regular patterns throughout the backbone, are emerging as structural mimics of ?-helix-forming conventional peptides (composed exclusively of ?-amino acid residues). Here we describe a comprehensive evaluation of diverse ?/?-peptide homologues of the Bim BH3 domain in terms of their ability to bind to the BH3-recognition sites on two partner proteins, Bcl-xL and Mcl-1. These proteins are members of the anti-apoptotic Bcl-2 family, and both bind tightly to the Bim BH3 domain itself. All ?/?-peptide homologues retain the side chain sequence of the Bim BH3 domain, but each homologue contains periodic ?-residue ? ?3-residue substitutions. Previous work has shown that the ??????? pattern, which aligns the ?3-residues in a 'stripe' along one side of the helix, can support functional ?-helix mimicry, and the results reported here support this conclusion. The present study provides the first evaluation of functional mimicry by ??? and ???? patterns, which cause the ?3-residues to spiral around the helix periphery. We find that the ???? pattern can support effective mimicry of the Bim BH3 domain, as manifested by the crystal structure of an ?/?-peptide bound to Bcl-xL, affinity for a variety of Bcl-2 family proteins, and induction of apoptotic signaling in mouse embryonic fibroblast extracts. The best ???? homologue shows substantial protection from proteolytic degradation relative to the Bim BH3 ?-peptide. PMID:22040025

  12. Flexible backbone sampling methods to model and design protein alternative conformations.

    PubMed

    Ollikainen, Noah; Smith, Colin A; Fraser, James S; Kortemme, Tanja

    2013-01-01

    Sampling alternative conformations is key to understanding how proteins work and engineering them for new functions. However, accurately characterizing and modeling protein conformational ensembles remain experimentally and computationally challenging. These challenges must be met before protein conformational heterogeneity can be exploited in protein engineering and design. Here, as a stepping stone, we describe methods to detect alternative conformations in proteins and strategies to model these near-native conformational changes based on backrub-type Monte Carlo moves in Rosetta. We illustrate how Rosetta simulations that apply backrub moves improve modeling of point mutant side-chain conformations, native side-chain conformational heterogeneity, functional conformational changes, tolerated sequence space, protein interaction specificity, and amino acid covariation across protein-protein interfaces. We include relevant Rosetta command lines and RosettaScripts to encourage the application of these types of simulations to other systems. Our work highlights that critical scoring and sampling improvements will be necessary to approximate conformational landscapes. Challenges for the future development of these methods include modeling conformational changes that propagate away from designed mutation sites and modulating backbone flexibility to predictively design functionally important conformational heterogeneity. PMID:23422426

  13. iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

    PubMed Central

    Lin, Hao; Deng, En-Ze; Ding, Hui; Chen, Wei; Chou, Kuo-Chen

    2014-01-01

    The ?54 promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the ?54 promoters. Here, a predictor called ‘iPro54-PseKNC’ was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called ‘pseudo k-tuple nucleotide composition’, which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the ?54 promoters. PMID:25361964

  14. iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition.

    PubMed

    Lin, Hao; Deng, En-Ze; Ding, Hui; Chen, Wei; Chou, Kuo-Chen

    2014-12-01

    The ?(54) promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the ?(54) promoters. Here, a predictor called 'iPro54-PseKNC' was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called 'pseudo k-tuple nucleotide composition', which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the ?(54) promoters. PMID:25361964

  15. Quantitative analysis of PMLA nanoconjugate components after backbone cleavage.

    PubMed

    Ding, Hui; Patil, Rameshwar; Portilla-Arias, Jose; Black, Keith L; Ljubimova, Julia Y; Holler, Eggehard

    2015-01-01

    Multifunctional polymer nanoconjugates containing multiple components show great promise in cancer therapy, but in most cases complete analysis of each component is difficult. Polymalic acid (PMLA) based nanoconjugates have demonstrated successful brain and breast cancer treatment. They consist of multiple components including targeting antibodies, Morpholino antisense oligonucleotides (AONs), and endosome escape moieties. The component analysis of PMLA nanoconjugates is extremely difficult using conventional spectrometry and HPLC method. Taking advantage of the nature of polyester of PMLA, which can be cleaved by ammonium hydroxide, we describe a method to analyze the content of antibody and AON within nanoconjugates simultaneously using SEC-HPLC by selectively cleaving the PMLA backbone. The selected cleavage conditions only degrade PMLA without affecting the integrity and biological activity of the antibody. Although the amount of antibody could also be determined using the bicinchoninic acid (BCA) method, our selective cleavage method gives more reliable results and is more powerful. Our approach provides a new direction for the component analysis of polymer nanoconjugates and nanoparticles. PMID:25894227

  16. Bond distances in polypeptide backbones depend on the local conformation.

    PubMed

    Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

    2015-06-01

    By combining quantum-mechanical analysis of small model peptides and statistical surveys of high-resolution protein structures, a systematic conformational dependence of bond lengths in polypeptide backbones has been unveiled which involves both the peptide bond (C-O and C-N) and those bonds centred on the C(?) atom. All of these bond lengths indeed display a systematic variability in the ? angle according to both calculations and surveys of protein structures. The overall agreement between the computed and the statistical data suggests that these trends are essentially driven by local effects. The dependence of C(?) distances on ? is governed by interactions between the ? system of the C(?) moiety and the C-O ? system of the peptide bond. Maximum and minimum values for each bond distance are found for conformations with the specific bond perpendicular and parallel to the adjacent CONH peptide plane, respectively. On the other hand, the variability of the C-O and C-N distances is related to the strength of the interactions between the lone pair of the N atom and the C-O ?* system, which is modulated by the ? angle. The C-O and C-N distances are related but their trends are not strictly connected to peptide-bond planarity, although a correlation amongst all of these parameters is expected on the basis of the classical resonance model. PMID:26057667

  17. Quantitative Analysis of PMLA Nanoconjugate Components after Backbone Cleavage

    PubMed Central

    Ding, Hui; Patil, Rameshwar; Portilla-Arias, Jose; Black, Keith L.; Ljubimova, Julia Y.; Holler, Eggehard

    2015-01-01

    Multifunctional polymer nanoconjugates containing multiple components show great promise in cancer therapy, but in most cases complete analysis of each component is difficult. Polymalic acid (PMLA) based nanoconjugates have demonstrated successful brain and breast cancer treatment. They consist of multiple components including targeting antibodies, Morpholino antisense oligonucleotides (AONs), and endosome escape moieties. The component analysis of PMLA nanoconjugates is extremely difficult using conventional spectrometry and HPLC method. Taking advantage of the nature of polyester of PMLA, which can be cleaved by ammonium hydroxide, we describe a method to analyze the content of antibody and AON within nanoconjugates simultaneously using SEC-HPLC by selectively cleaving the PMLA backbone. The selected cleavage conditions only degrade PMLA without affecting the integrity and biological activity of the antibody. Although the amount of antibody could also be determined using the bicinchoninic acid (BCA) method, our selective cleavage method gives more reliable results and is more powerful. Our approach provides a new direction for the component analysis of polymer nanoconjugates and nanoparticles. PMID:25894227

  18. Data Acquisition Backbone Core DABC release v1.0

    NASA Astrophysics Data System (ADS)

    Adamczewski-Musch, J.; Essel, H. G.; Kurz, N.; Linev, S.

    2010-04-01

    The Data Acquisition Backbone Core (DABC) is a general purpose software framework designed for the implementation of a wide-range of data acquisition systems - from various small detector test beds to high performance systems. DABC consists of a compact data-flow kernel and a number of plug-ins for various functional components like data inputs, device drivers, user functional modules and applications. DABC provides configurable components for implementing event building over fast networks like InfiniBand or Gigabit Ethernet. A generic Java GUI provides the dynamic control and visualization of control parameters and commands, provided by DIM servers. A first set of application plug-ins has been implemented to use DABC as event builder for the front-end components of the GSI standard DAQ system MBS (Multi Branch System). Another application covers the connection to DAQ readout chains from detector front-end boards (N-XYTER) linked to read-out controller boards (ROC) over UDP into DABC for event building, archiving and data serving. This was applied for data taking in the September 2008 test beamtime for the CBM experiment at GSI. DABC version 1.0 is released and available from the website.

  19. Backbones and borders from shortest-path trees

    NASA Astrophysics Data System (ADS)

    Grady, Daniel; Thiemann, Christian; Brockmann, Dirk

    2011-03-01

    One of the most important tasks in complex network research is to distinguish between vertices and edges that are topologically essential and those that are not. To this end, a variety of vertex and edge centrality measures have been introduced, ranging from measuring local properties (degree, strength) to quantities that depend on the global structure of the graph (betweenness). Here we introduce a novel technique based on the family of shortest-path trees, which is applicable to strongly heterogeneous networks. This approach can identify significant edges in the network, distinct from conventional edge betweenness, and these edges make up a network backbone relevant to dynamical processes that evolve on such networks. We will show that important network structures can be extracted by investigating the similarity and differences of shortest-path trees and show that tree dissimilarity in combination with hierarchical clustering can identify communities in heterogeneous networks more successfully than ordinary reciprocal-weight distance measures. We demonstrate the success of this technique on complex multi-scale mobility networks.

  20. MCBT: Multi-Hop Cluster Based Stable Backbone Trees for Data Collection and Dissemination in WSNs.

    PubMed

    Shin, Inyoung; Kim, Moonseong; Mutka, Matt W; Choo, Hyunseung; Lee, Tae-Jin

    2009-01-01

    We propose a stable backbone tree construction algorithm using multi-hop clusters for wireless sensor networks (WSNs). The hierarchical cluster structure has advantages in data fusion and aggregation. Energy consumption can be decreased by managing nodes with cluster heads. Backbone nodes, which are responsible for performing and managing multi-hop communication, can reduce the communication overhead such as control traffic and minimize the number of active nodes. Previous backbone construction algorithms, such as Hierarchical Cluster-based Data Dissemination (HCDD) and Multicluster, Mobile, Multimedia radio network (MMM), consume energy quickly. They are designed without regard to appropriate factors such as residual energy and degree (the number of connections or edges to other nodes) of a node for WSNs. Thus, the network is quickly disconnected or has to reconstruct a backbone. We propose a distributed algorithm to create a stable backbone by selecting the nodes with higher energy or degree as the cluster heads. This increases the overall network lifetime. Moreover, the proposed method balances energy consumption by distributing the traffic load among nodes around the cluster head. In the simulation, the proposed scheme outperforms previous clustering schemes in terms of the average and the standard deviation of residual energy or degree of backbone nodes, the average residual energy of backbone nodes after disseminating the sensed data, and the network lifetime. PMID:22454570

  1. Molecular dynamics simulations of single-component bottle-brush polymers with flexible backbones under poor solvent conditions

    E-print Network

    Theodorakis, Panagiotis E.

    Molecular dynamics simulations of single-component bottle-brush polymers with flexible backbones.1088/0953-8984/25/28/285105 Molecular dynamics simulations of single-component bottle-brush polymers with flexible backbones under poor/285105 Abstract Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor

  2. J. Chem. Soc., Perkin Trans. 1, 1997 1501 Building units for N-backbone cyclic peptides. Part 4.1

    E-print Network

    Kasher, Roni

    J. Chem. Soc., Perkin Trans. 1, 1997 1501 Building units for N-backbone cyclic peptides. Part 4 for the synthesis of backbone-cyclic peptides. They are orthogonally protected at the -amino position for their incorporation into peptides by solid phase peptide synthesis. Introduction Backbone-Cyclization is a method

  3. Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

    SciTech Connect

    Azoitei, Mihai L.; Correia, Bruno E.; Ban, Yih-En Andrew; Carrico, Chris; Kalyuzhniy, Oleksandr; Chen, Lei; Schroeter, Alexandria; Huang, Po-Ssu; McLellan, Jason S.; Kwong, Peter D.; Baker, David; Strong, Roland K.; Schief, William R. (UWASH); (FHCRC); (NIAID)

    2012-02-07

    The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.

  4. Genotyping by RAD sequencing enables mapping of fatty acid composition traits in perennial ryegrass (Lolium perenne (L.)).

    PubMed

    Hegarty, Matthew; Yadav, Rattan; Lee, Michael; Armstead, Ian; Sanderson, Ruth; Scollan, Nigel; Powell, Wayne; Skøt, Leif

    2013-06-01

    Perennial ryegrass (Lolium perenne L.) is the most important forage crop in temperate livestock agriculture. Its nutritional quality has significant impact on the quality of meat and milk for human consumption. Evidence suggests that higher energy content in forage can assist in reducing greenhouse gas emissions from ruminants. Increasing the fatty acid content (especially ?-linolenic acid, an omega-3 fatty acid) may thus contribute to better forage, but little is known about the genetic basis of variation for this trait. To this end, quantitative trait loci (QTLs) were identified associated with major fatty acid content in perennial ryegrass using a population derived from a cross between the heterozygous and outbreeding high-sugar grass variety AberMagic and an older variety, Aurora. A genetic map with 434 restriction-associated DNA (RAD) and SSR markers was generated. Significant QTLs for the content of palmitic (C16:0) on linkage groups (LGs) 2 and 7; stearic (C18:0) on LGs 3, 4 and 7; linoleic (C18:2n-6) on LGs 2 and 5; and ?-linolenic acids (C18:3n-3) on LG 1 were identified. Two candidate genes (a lipase and a beta-ketoacyl CoA synthase), both associated with C16:0, and separately with C18:2n-6 and C18:0 contents, were identified. The physical positions of these genes in rice and their genetic positions in perennial ryegrass were consistent with established syntenic relationships between these two species. Validation of these associations is required, but the utility of RAD markers for rapid generation of genetic maps and QTL analysis has been demonstrated for fatty acid composition in a global forage crop. PMID:23331642

  5. Acute Effects of TiO2 Nanomaterials on the Viability and Taxonomic Composition of Aquatic Bacterial Communities Assessed via High-Throughput Screening and Next Generation Sequencing

    PubMed Central

    Binh, Chu Thi Thanh; Tong, Tiezheng; Gaillard, Jean-François; Gray, Kimberly A.; Kelly, John J.

    2014-01-01

    The nanotechnology industry is growing rapidly, leading to concerns about the potential ecological consequences of the release of engineered nanomaterials (ENMs) to the environment. One challenge of assessing the ecological risks of ENMs is the incredible diversity of ENMs currently available and the rapid pace at which new ENMs are being developed. High-throughput screening (HTS) is a popular approach to assessing ENM cytotoxicity that offers the opportunity to rapidly test in parallel a wide range of ENMs at multiple concentrations. However, current HTS approaches generally test one cell type at a time, which limits their ability to predict responses of complex microbial communities. In this study toxicity screening via a HTS platform was used in combination with next generation sequencing (NGS) to assess responses of bacterial communities from two aquatic habitats, Lake Michigan (LM) and the Chicago River (CR), to short-term exposure in their native waters to several commercial TiO2 nanomaterials under simulated solar irradiation. Results demonstrate that bacterial communities from LM and CR differed in their sensitivity to nano-TiO2, with the community from CR being more resistant. NGS analysis revealed that the composition of the bacterial communities from LM and CR were significantly altered by exposure to nano-TiO2, including decreases in overall bacterial diversity, decreases in the relative abundance of Actinomycetales, Sphingobacteriales, Limnohabitans, and Flavobacterium, and a significant increase in Limnobacter. These results suggest that the release of nano-TiO2 to the environment has the potential to alter the composition of aquatic bacterial communities, which could have implications for the stability and function of aquatic ecosystems. The novel combination of HTS and NGS described in this study represents a major advance over current methods for assessing ENM ecotoxicity because the relative toxicities of multiple ENMs to thousands of naturally occurring bacterial species can be assessed simultaneously under environmentally relevant conditions. PMID:25162615

  6. Monitoramento de Trafego de Backbones Baseado em Sistemas Gerenciadores de Streams de Dados

    E-print Network

    Hara, Carmem Satie

    on the Borealis SPE and obtains backbone traffic information based on a stream of Netflow data. Several Borealis tempo real. Foi implementada uma ferramenta baseada no SGSD Borealis e o pro- tocolo Netflow

  7. Peptide backbone effect on hydration free energies of amino acid side chains.

    PubMed

    Hajari, Timir; van der Vegt, Nico F A

    2014-11-20

    We have studied the hydrophobicity of amino acid side chains by computing conditional solvation free energies that account for effects of the peptide backbone on the side chains' solvent environment. The free energies reported herein correspond to a gas-liquid transfer process, which mimics solvation of the side chain under the condition that the backbone has been solvated already, and have been obtained on the basis of free energy calculations with empirical force field models. We find that the peptide backbone strongly impacts the solvation of nonpolar side chains, while its effect on the polar side chains is less pronounced. The results indicate that, in the presence of the short peptide backbone, nonpolar amino acid side chains are less hydrophobic than what is expected based on small molecule (analogue) solvation data. PMID:25338222

  8. RNA tetraloop folding reveals tension between backbone restraints and molecular interactions.

    PubMed

    Mohan, Srividya; Hsiao, Chiaolong; Bowman, Jessica C; Wartell, Roger; Williams, Loren Dean

    2010-09-15

    In RNA, A-form helices are commonly terminated by tetraloops or 3' dangling ends. Aside from helices themselves, these helix-breaking motifs appear to be among the most frequent and repetitive structural elements of large folded RNAs. We show here that within a frequent type of tetraloop, cGNRAg (G is guanine, N is any base, R is purine, A is adenine), a tension exists between the backbone torsional energy of the loop and the energy contributed by molecular interactions (stacking and pairing). A model in which favorable bond rotamers are opposed by favorable stacking and pairing interactions is consistent with our observation that release of torsional restraints upon conversion of one or more loop riboses to more flexible trimethylene phosphate(s) contributes favorably to the enthalpy of folding. This effect presumably results from improved stacking and hydrogen-bonding interactions upon release of torsional restraints. The most obvious possibility for improving molecular interactions is a repositioning of A, which is proximal to the unfavorable torsion angles in native cGNRAg tetraloops, and which is unstacked on the 3' side and unpaired (it forms a single hydrogen bond with the opposing G). This tension between favorable bond rotamers and favorable molecular interactions may be representative of a general evolutionary strategy to prevent achievement of deep and irreversible thermodynamic wells in folded RNAs. Finally, we observe a simple stacking substructure with conserved geometry and sequence that forms a scaffold for both tetraloops and 3' dangling ends. It seems that simple substructures can build RNA motifs, which combine to establish the fundamental architecture of RNA. PMID:20726568

  9. Methods and Compositions for Amplification and Detection of microRNAs (miRNAs) and Noncoding RNAs (ncRNAs) Using the Signature Sequence Amplification Method (SSAM)

    PubMed Central

    Ginsberg, Stephen D.; Che, Shaoli

    2015-01-01

    The signature sequence amplification method (SSAM) described herein is an approach for amplifying noncoding RNA (ncRNA), microRNA (miRNA), and small polynucleotide sequences. A key point of the SSAM technology is the generation of signature sequences. The signature sequences include target sequences (miRNA, ncRNA, and/or any small polynucleotide sequence) flanked by two DNA fragments. Target sequences can be amplified through DNA synthesis, RNA synthesis, or the combination of DNA and RNA synthesis. The amplification of signature sequences provides an efficient and reproducible mechanism to determine the presence or absence of the target miRNAs/ncRNAs, to analyze the quantities of the miRNAs in biological samples, and for miRNA/ncRNA profiling. PMID:25564022

  10. Lactobacillus rhamnosus accelerates zebrafish backbone calcification and gonadal differentiation through effects on the GnRH and IGF systems.

    PubMed

    Avella, Matteo A; Place, Allen; Du, Shao-Jun; Williams, Ernest; Silvi, Stefania; Zohar, Yonathan; Carnevali, Oliana

    2012-01-01

    Endogenous microbiota play essential roles in the host's immune system, physiology, reproduction and nutrient metabolism. We hypothesized that a continuous administration of an exogenous probiotic might also influence the host's development. Thus, we treated zebrafish from birth to sexual maturation (2-months treatment) with Lactobacillus rhamnosus, a probiotic species intended for human use. We monitored for the presence of L. rhamnosus during the entire treatment. Zebrafish at 6 days post fertilization (dpf) exhibited elevated gene expression levels for Insulin-like growth factors -I and -II, Peroxisome proliferator activated receptors -? and -?, VDR-? and RAR-? when compared to untreated-10 days old zebrafish. Using a gonadotropin-releasing hormone 3 GFP transgenic zebrafish (GnRH3-GFP), higher GnRH3 expression was found at 6, 8 and 10 dpf upon L. rhamnosus treatment. The same larvae exhibited earlier backbone calcification and gonad maturation. Noteworthy in the gonad development was the presence of first testes differentiation at 3 weeks post fertilization in the treated zebrafish population -which normally occurs at 8 weeks- and a dramatic sex ratio modulation (93% females, 7% males in control vs. 55% females, 45% males in the treated group). We infer that administration of L. rhamnosus stimulated the IGF system, leading to a faster backbone calcification. Moreover we hypothesize a role for administration of L. rhamnosus on GnRH3 modulation during early larval development, which in turn affects gonadal development and sex differentiation. These findings suggest a significant role of the microbiota composition on the host organism development profile and open new perspectives in the study of probiotics usage and application. PMID:23029107

  11. Subgraph “Backbone” Analysis of Dynamic Brain Networks during Consciousness and Anesthesia

    PubMed Central

    Shin, Jeongkyu; Mashour, George A.; Ku, Seungwoo; Kim, Seunghwan; Lee, Uncheol

    2013-01-01

    General anesthesia significantly alters brain network connectivity. Graph-theoretical analysis has been used extensively to study static brain networks but may be limited in the study of rapidly changing brain connectivity during induction of or recovery from general anesthesia. Here we introduce a novel method to study the temporal evolution of network modules in the brain. We recorded multichannel electroencephalograms (EEG) from 18 surgical patients who underwent general anesthesia with either propofol (n?=?9) or sevoflurane (n?=?9). Time series data were used to reconstruct networks; each electroencephalographic channel was defined as a node and correlated activity between the channels was defined as a link. We analyzed the frequency of subgraphs in the network with a defined number of links; subgraphs with a high probability of occurrence were deemed network “backbones.” We analyzed the behavior of network backbones across consciousness, anesthetic induction, anesthetic maintenance, and two points of recovery. Constitutive, variable and state-specific backbones were identified across anesthetic state transitions. Brain networks derived from neurophysiologic data can be deconstructed into network backbones that change rapidly across states of consciousness. This technique enabled a granular description of network evolution over time. The concept of network backbones may facilitate graph-theoretical analysis of dynamically changing networks. PMID:23967131

  12. Structural characterization of the pectic polysaccharide rhamnogalacturonan II: evidence for the backbone location of the aceric acid-containing oligoglycosyl side chain.

    PubMed

    Vidal, S; Doco, T; Williams, P; Pellerin, P; York, W S; O'Neill, M A; Glushka, J; Darvill, A G; Albersheim, P

    2000-06-30

    Monomeric rhamnogalacturonan II (mRG-II) was isolated from red wine and the reducing-end galacturonic acid of the backbone converted to L-galactonic acid by treatment with NaBH4. The resulting product (mRG-II'ol) was treated with a cell-free extract from Penicillium daleae, a fungus that has been shown to produce RG-II-fragmenting glycanases. The enzymatically generated products were fractionated by size-exclusion and anion-exchange chromatographies and the quantitatively major oligosaccharide fraction isolated. This fraction contained structurally related oligosaccharides that differed only in the presence or absence of a single Kdo residue. The Kdo residue was removed by acid hydrolysis and the resulting oligosaccharide then characterized by 1- and 2D 1H NMR spectroscopy, ESMS, and by glycosyl-residue and glycosyl-linkage composition analyses. The results of these analyses provide evidence for the presence of at least two structurally related oligosaccharides in the ratio approximately 6:1. The backbone of these oligosaccharides is composed of five (1-->4)-linked alpha-D-GalpA residues and a (1-->3)-linked L-galactonate. The (1-->4)-linked GalpA residue adjacent to the terminal non-reducing GalpA residue of the backbone is substituted at O-2 with an apiosyl-containing side chain. Beta3-L-Araf-(1-->5)-beta-D-DhapA is likely to be linked to O-3 of the GalpA residue at the non-reducing end of the backbone in the quantitatively major oligosaccharide and to O-3 of a (1-->4)-linked GalpA residue in the backbone of the minor oligosaccharide. Furthermore, the results of our studies have shown that the enzymically generated aceryl acid-containing oligosaccharide contains an alpha-linked aceryl acid residue and a beta-linked galactosyl residue. Thus, the anomeric linkages of these residues in RG-II should be revised. PMID:10890275

  13. RASP: rapid and robust backbone chemical shift assignments from protein structure.

    PubMed

    MacRaild, Christopher A; Norton, Raymond S

    2014-03-01

    Chemical shift prediction has an unappreciated power to guide backbone resonance assignment in cases where protein structure is known. Here we describe Resonance Assignment by chemical Shift Prediction (RASP), a method that exploits this power to derive protein backbone resonance assignments from chemical shift predictions. Robust assignments can be obtained from a minimal set of only the most sensitive triple-resonance experiments, even for spectroscopically challenging proteins. Over a test set of 154 proteins RASP assigns 88 % of residues with an accuracy of 99.7 %, using only information available from HNCO and HNCA spectra. Applied to experimental data from a challenging 34 kDa protein, RASP assigns 90 % of manually assigned residues using only 40 % of the experimental data required for the manual assignment. RASP has the potential to significantly accelerate the backbone assignment process for a wide range of proteins for which structural information is available, including those for which conventional assignment strategies are not feasible. PMID:24445369

  14. External tank composite lightning protection selection

    Microsoft Academic Search

    D. A. Brickner; A. W. Anderson Jr.

    1985-01-01

    The External Tank is the structural backbone of the Space Transportation System. Alike conventional aircraft, the metallic skin of the ET provides a conductive path for lightning, electromagnetic energy, and electrostatic discharges. Non-metallic composite structures may require a conductive surface coating to meet the lightning protection requirement established by NASA-JSC. An engineering trade study of various types of lightning protection

  15. Anion-conducting polymer, composition, and membrane

    DOEpatents

    Pivovar, Bryan S. (Los Alamos, NM); Thorn, David L. (Los Alamos, NM)

    2011-11-22

    Anion-conducing polymers and membranes with enhanced stability to aqueous alkali include a polymer backbone with attached sulfonium, phosphazenium, phosphazene, and guanidinium residues. Compositions also with enhanced stability to aqueous alkali include a support embedded with sulfonium, phosphazenium, and guanidinium salts.

  16. Anion-Conducting Polymer, Composition, and Membrane

    DOEpatents

    Pivovar, Bryan S. (Los Alamos, NM); Thorn, David L. (Los Alamos, NM)

    2008-10-21

    Anion-conducing polymers and membranes with enhanced stability to aqueous alkali include a polymer backbone with attached sulfonium, phosphazenium, phosphazene, and guanidinium residues. Compositions also with enhanced stability to aqueous alkali include a support embedded with sulfonium, phosphazenium, and guanidinium salts.

  17. Anion-conducting polymer, composition, and membrane

    DOEpatents

    Pivovar, Bryan S. (Los Alamos, NM); Thorn, David L. (Los Alamos, NM)

    2010-12-07

    Anion-conducing polymers and membranes with enhanced stability to aqueous alkali include a polymer backbone with attached sulfonium, phosphazenium, phosphazene, and guanidinium residues. Compositions also with enhanced stability to aqueous alkali include a support embedded with sulfonium, phosphazenium, and guanidinium salts.

  18. Anion-conducting polymer, composition, and membrane

    DOEpatents

    Pivovar, Bryan S. (Los Alamos, NM); Thorn, David L. (Los Alamos, NM)

    2009-09-01

    Anion-conducing polymers and membranes with enhanced stability to aqueous alkali include a polymer backbone with attached sulfonium, phosphazenium, phosphazene, and guanidinium residues. Compositions also with enhanced stability to aqueous alkali include a support embedded with sulfonium, phosphazenium, and guanidinium salts.

  19. Influence of backbone conformational rigidity in temperature-sensitive amphiphilic supramolecular assemblies.

    PubMed

    Raghupathi, Krishna R; Sridhar, Uma; Byrne, Kevin; Raghupathi, Kishore; Thayumanavan, S

    2015-04-29

    Molecular design features that endow amphiphilic supramolecular assemblies with a unique temperature-sensitive transition have been investigated. We find that conformational rigidity in the backbone is an important feature for eliciting this feature. We also find that intramolecular hydrogen-bonding can induce such rigidity in amphiphile backbone. Guest encapsulation stability of these assemblies was found to be significantly altered within a narrow temperature window, which correlates with the temperature-sensitive size transition of the molecular assembly. Molecular design principles demonstrated here could have broad implications in developing future temperature-responsive systems. PMID:25893806

  20. Transcriptome Sequencing and Expression Analysis of Terpenoid Biosynthesis Genes in Litsea cubeba

    PubMed Central

    Han, Xiao-Jiao; Wang, Yang-Dong; Chen, Yi-Cun; Lin, Li-Yuan; Wu, Qing-Ke

    2013-01-01

    Background Aromatic essential oils extracted from fresh fruits of Litsea cubeba (Lour.) Pers., have diverse medical and economic values. The dominant components in these essential oils are monoterpenes and sesquiterpenes. Understanding the molecular mechanisms of terpenoid biosynthesis is essential for improving the yield and quality of terpenes. However, the 40 available L. cubeba nucleotide sequences in the public databases are insufficient for studying the molecular mechanisms. Thus, high-throughput transcriptome sequencing of L. cubeba is necessary to generate large quantities of transcript sequences for the purpose of gene discovery, especially terpenoid biosynthesis related genes. Results Using Illumina paired-end sequencing, approximately 23.5 million high-quality reads were generated. De novo assembly yielded 68,648 unigenes with an average length of 834 bp. A total of 38,439 (56%) unigenes were annotated for their functions, and 35,732 and 25,806 unigenes could be aligned to the GO and COG database, respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 16,130 unigenes were assigned to 297 KEGG pathways, and 61 unigenes, which contained the mevalonate and 2-C-methyl-D-erythritol 4-phosphate pathways, could be related to terpenoid backbone biosynthesis. Of the 12,963 unigenes, 285 were annotated to the terpenoid pathways using the PlantCyc database. Additionally, 14 terpene synthase genes were identified from the transcriptome. The expression patterns of the 16 genes related to terpenoid biosynthesis were analyzed by RT-qPCR to explore their putative functions. Conclusion RNA sequencing was effective in identifying a large quantity of sequence information. To our knowledge, this study is the first exploration of the L. cubeba transcriptome, and the substantial amount of transcripts obtained will accelerate the understanding of the molecular mechanisms of essential oils biosynthesis. The results may help improve future genetic and genomics studies on the molecular mechanisms behind the chemical composition of essential oils in L. cubeba fruits. PMID:24130803

  1. A backbone based protein model with explicit solvent

    NASA Astrophysics Data System (ADS)

    Sharma, Sumit; Buldyrev, Sergey; Rossky, Peter J.; Stanley, H. Eugene; Debenedetti, Pablo G.; Angell, C. Austen; Kumar, Sanat K.

    2011-03-01

    The computational expense of folding atomistically detailed protein models is prohibitive. Hence minimalist models of proteins are a popular choice. The minimalist models developed so far have excluded water, and treated the hydrophobic effect as an effective attraction between hydrophobic monomers. This simplified treatment does not capture the temperature-dependent variations in entropy and enthalpy of water molecules. Proteins have a predominantly water-screened hydrophobic core and water-exposed polar groups. This structural feature should alter the dynamics of proteins and surrounding water from that of a hydrophobic homopolymer in water. To include these features in a minimalist model, we designed heteropolymers of polar and hydrophobic monomers in explicit water-like medium. The polar monomers and water molecules were modeled with the Jagla potential, which has been shown to reproduce many water-like thermodynamic properties, and the hydrophobic monomers as hard spheres. We discuss a methodology for optimizing the sequence of these heteropolymers and how the hydrophobic collapse of these heteropolymers differs from that of a random heteropolymer.

  2. Purification and characterization of an antioxidant peptide obtained from tuna backbone protein by enzymatic hydrolysis

    Microsoft Academic Search

    Jae-Young Je; Zhong-Ji Qian; Hee-Guk Byun; Se-Kwon Kim

    2007-01-01

    To utilize fish processing waste, tuna backbone protein was hydrolyzed using different proteases (alcalase, ?-chymotrypsin, neutrase, papain, pepsin and trypsin) for production of antioxidant peptide. Antioxidant activities of hydrolysates were evaluated using lipid peroxidation inhibition assay and direct free radical scavenging activity by using electron spin resonance (ESR) spectrometer. Among hydrolysates, peptic hydrolysate exhibited the highest antioxidant activity compared to

  3. Mixed-Backbone Oligonucleotides as Second Generation Antisense Oligonucleotides: In vitro and in vivo Studies

    Microsoft Academic Search

    Sudhir Agrawal; Zhiwei Jiang; Qiuyan Zhao; Denise Shaw; Qiuyin Cai; Allysen Roskey; Lakshmi Channavajjala; Carl Saxinger; Ruiwen Zhang

    1997-01-01

    Antisense oligonucleotides are being evaluated in clinical trials as novel therapeutic agents. To further improve the properties of antisense oligonucleotides, we have designed mixed-backbone oligonucleotides (MBOs) that contain phosphorothioate segments at the 3' and 5' ends and have a modified oligodeoxynucleotide or oligoribonucleotide segment located in the central portion of the oligonucleotide. Some of these MBOs indicate improved properties compared

  4. Communication A `just-in-time' HN(CA)CO experiment for the backbone

    E-print Network

    Richardson, David

    Communication A `just-in-time' HN(CA)CO experiment for the backbone assignment of large proteins,4] have vast- ly expanded our capability to study large proteins and protein complexes, with near complete with increasing protein size and at higher magnetic field. Different approaches have been used to improve the sen

  5. Determination of the Backbone Structure of Nucleic Acids and Nucleic Acid Oligomers by Laser Raman Scattering

    Microsoft Academic Search

    Stephen C. Erfurth; Ernest J. Kiser; Warner L. Peticolas

    1972-01-01

    Raman spectra of fibers of DNA that have been prepared in the A, B, and C forms are presented and compared with Raman spectra of DNA and RNA in dilute solution. It is shown that the phosphate vibrations in the region 750-850 cm-1 are very sensitive to the specific conformation of the phosphate group in the backbone chain and are

  6. Switched optical backbone for cost-effective scalable core IP networks

    Microsoft Academic Search

    Sudipta Sengupta; Vijay Kumar; Debanjan Saha

    2003-01-01

    With the advent of WDM technology, IP backbone carriers are now connecting core routers directly over point-to-point WDM links (IP over WDM). The advances and standardization in optical control plane technologies like GMPLS have substantially increased the intelligence of the optical layer and shown promise toward making dynamic provisioning and restoration of optical layer circuits a basic capability to be

  7. Analysis of Measured Single-Hop Delay from an Operational Backbone Network

    E-print Network

    Moon, Sue B.

    Analysis of Measured Single-Hop Delay from an Operational Backbone Network Konstantina Papagiannaki a Weibull distribu- tion with the scale parameter, ¼ , and the shape parameter, ¼ to ¼ . The measured. ¯ The amount of data for in-depth analysis easily reaches hundreds of gigabytes. Data from input and output

  8. Analysis of Measured SingleHop Delay from an Operational Backbone Network

    E-print Network

    Tobagi, Fouad

    Analysis of Measured Single­Hop Delay from an Operational Backbone Network Konstantina Papagiannaki a Weibull distribu­ tion with the scale parameter, a = 0:5, and the shape parameter, b = 0:58 to 0 to another interface of the same router. #15; The amount of data for in­depth analysis easily reaches

  9. Link Estimation and Routing in Sensor Network Backbones: Beacon-based or Data-driven?

    E-print Network

    Zhang, Hongwei

    sensor network traffic trace and an 802.11b testbed of 195 Stargates, we experimentally compare experiment ExScal [6], where 203 Stargates and 985 XSM motes were deployed in an area of 1260 meters by 288 meters. Each Stargate is equipped with a 802.11b radio, and the 203 Stargates form the backbone network

  10. ExScal Backbone Network Architecture Anish Arora Prasun Sinha Emre Ertin Vinayak Naik Hongwei Zhang

    E-print Network

    Sinha, Prasun

    powered nodes was laid over the sensor network. We adopted the Stargate platform for the backbone tier-network had one mote as its head. XSS Hardware and Network: XSS stands for eXtreme Scaling Stargate. A stargate is a linux-based single board computer. It has a 400 MHz processor, 64 MB SDRAM, 32 MB flash

  11. A Markov Chain Model for Local Path Protection in Mobile Optical Backbone Networks

    E-print Network

    Shayman, Mark A.

    optical point-to-point links. We assume that the backbone nodes are mobile and with unpredictable-hop way. The QoS demanding applications are vulnerable to mobility imposed link failures in such networks is achieved. I. INTRODUCTION A mobile ad hoc network (MANET) is composed of a group of mobile nodes without

  12. TRACKING ELEPHANT FLOWS IN INTERNET BACKBONE TRAFFIC WITH AN FPGA-BASED CACHE

    E-print Network

    Haddadi, Hamed

    TRACKING ELEPHANT FLOWS IN INTERNET BACKBONE TRAFFIC WITH AN FPGA-BASED CACHE Martin Zadnik an FPGA-friendly approach to track- ing elephant flows in network traffic. Our approach, Single Step elephant flows: con- servatively promoting potential elephants and evicting low- rate flows in LRU manner

  13. Sparsely sampled high-resolution 4-D experiments for efficient backbone resonance assignment of disordered proteins

    Microsoft Academic Search

    Jie Wen; Jihui Wu; Pei Zhou

    2011-01-01

    Intrinsically disordered proteins (IDPs) play important roles in many critical cellular processes. Due to their limited chemical shift dispersion, IDPs often require four pairs of resonance connectivities (H?, C?, C? and CO) for establishing sequential backbone assignment. Because most conventional 4-D triple-resonance experiments share an overlapping C? evolution period, combining existing 4-D experiments does not offer an optimal solution for

  14. Computer simulation of bottle brush polymers with flexible backbone: Good solvent versus Theta solvent conditions

    E-print Network

    Panagiotis E. Theodorakis; Hsiao-Ping Hsu; Wolfgang Paul; Kurt Binder

    2011-11-02

    By Molecular Dynamics simulation of a coarse-grained bead-spring type model for a cylindrical molecular brush with a backbone chain of $N_b$ effective monomers to which with grafting density $\\sigma$ side chains with $N$ effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side chain lengths are in the range $5 \\le N \\le 40$, backbone chain lengths are in the range $50 \\le N_b \\le 200$, and we perform a comparison to results for the bond fluctuation model on the simple cubic lattice (for which much longer chains are accessible, $N_b \\le 1027$, and which corresponds to an athermal, very good, solvent). We obtain linear dimensions of side chains and the backbone chain and discuss their $N$-dependence in terms of power laws and the associated effective exponents. We show that even at the Theta point the side chains are considerably stretched, their linear dimension depending on the solvent quality only weakly. Effective persistence lengths are extracted both from the orientational correlations and from the backbone end-to-end distance; it is shown that different measures of the persistence length (which would all agree for Gaussian chains) are not mutually consistent with each other, and depend distinctly both on $N_b$ and the solvent quality. A brief discussion of pertinent experiments is given.

  15. Differentiated Services for Wireless Mesh Backbone Hai Jiang, Weihua Zhuang, Xuemin (Sherman) Shen

    E-print Network

    Zhuang, Weihua

    wireless access. Differentiated services (DiffServ) over the wireless mesh backbone is proposed, and the wireless DiffServ provisioning techniques are investigated in the avenues of QoS routing and MAC mechanisms. Index Terms -- Wireless mesh, quality-of-service (QoS), differentiated services (DiffServ), rout- ing

  16. Photophysics of Backbone Fluorescent DNA Modifications: Reducing Uncertainties in FRET Suman Ranjit,,

    E-print Network

    Thorpe, Michael

    Photophysics of Backbone Fluorescent DNA Modifications: Reducing Uncertainties in FRET Suman Ranjit of uncertainty commonly encountered in Fo¨rster resonance energy transfer (FRET) measurements. We show. Unusually large FRET efficiencies for donor-acceptor pairs separated by 102 Å (three helical turns) were

  17. Carbohydrate Phosphinites as Practical Ligands in Asymmetric Catalysis: Electronic Effects and Dependence of Backbone

    E-print Network

    RajanBabu, T. V. "Babu"

    Using Natural Sugars as Ligand Precursors T. V. RajanBabu,* Timothy A. Ayers, Gary A. Halliday, Kimberly K. You, and Joseph C. Calabrese Department of Chemistry, The Ohio State University, 100 W. 18th diphosphinites on a given sugar backbone. When readily available D-glucopyranosides are used as the starting

  18. Simulation Study of Chiral Two-Dimensional Ultraviolet Spectroscopy of the Protein Backbone

    E-print Network

    Mukamel, Shaul

    of proteins derives from the variety of stable and flexible three-dimensional geometrical structures.1 structure using optical methods. Two-dimensional (2D) resonance laser spectroscopy in the infraredSimulation Study of Chiral Two-Dimensional Ultraviolet Spectroscopy of the Protein Backbone Darius

  19. Hidden Markov Models That Use Predicted Local Structure for Fold Recognition: Alphabets of Backbone Geometry

    E-print Network

    Karplus, Kevin

    Hidden Markov Models That Use Predicted Local Structure for Fold Recognition: Alphabets of Backbone-recognition methods.1­5 In this article, we evaluate the results of enriching hidden Markov models (HMMs), built using- dicted local structure, a generalization of secondary structure, into two-track profile hidden Markov mod

  20. Importance of the Peptide Backbone Description in Modeling the Selectivity Filter in Potassium Channels

    Microsoft Academic Search

    Turgut Bastug; Serdar Kuyucak

    2009-01-01

    A dihedral energy correction (CMAP) term has been recently included in the CHARMM force field to obtain a more accurate description of the peptide backbone. Its importance in improving dynamical properties of proteins and preserving their stability in long molecular-dynamics simulations has been established for several globular proteins. Here we investigate its role in maintaining the structure and function of

  1. Simulation and evaluation of FTP and TCP\\/IP on FDDI backbone network

    Microsoft Academic Search

    Milica Barjaktarovic; Kamal Jabbour

    1991-01-01

    Presents an evaluation of the TCP\\/IP (Transmission Control Protocol\\/Internet Protocol) under various traffic conditions by simulating file transfer between two Ethernet stations connected via an FDDI (Fiber Distributed Data Interface) backbone. The model is built using a simulation language called Research Queueing Package. The results presented indicate that TCP works slower for smaller files, partly because of the chosen parameter

  2. Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments

    PubMed Central

    Hotchko, Matthew; Anand, Ganesh S.; Komives, Elizabeth A.; Ten Eyck, Lynn F.

    2006-01-01

    A Fourier deconvolution method has been developed to explicitly determine the amount of backbone amide deuterium incorporated into protein regions or segments by hydrogen/deuterium (H/D) exchange with high-resolution mass spectrometry. Determination and analysis of the level and number of backbone amide exchanging in solution provide more information about the solvent accessibility of the protein than do previous centroid methods, which only calculate the average deuterons exchanged. After exchange, a protein is digested into peptides as a way of determining the exchange within a local area of the protein. The mass of a peptide upon deuteration is a sum of the natural isotope abundance, fast exchanging side-chain hydrogens (present in MALDI-TOF H/2H data) and backbone amide exchange. Removal of the components of the isotopic distribution due to the natural isotope abundances and the fast exchanging side-chains allows for a precise quantification of the levels of backbone amide exchange, as is shown by an example from protein kinase A. The deconvoluted results are affected by overlapping peptides or inconsistent mass envelopes, and evaluation procedures for these cases are discussed. Finally, a method for determining the back exchange corrected populations is presented, and its effect on the data is discussed under various circumstances. PMID:16501228

  3. Interconnection of FDDI-II Networks Through an ATM Backbone -An Analysis

    E-print Network

    Jayasumana, Anura P.

    will eventually lead to ATM networks being used as the backbone. ATM provides essentially a connection oriented- less and isochronous service is connection oriented[5]. Therefore, the gateway between FDDI-I1 and ATM Engineering Colorado State University Ft-Collins, CO 80523 connection oriented traffic for the ATM networki

  4. Backbone Ordering in Amphiphile Monolayers Jeremy Schofield and Stuart A. Rice,

    E-print Network

    Schofield, Jeremy

    Backbone Ordering in Amphiphile Monolayers Jeremy Schofield and Stuart A. Rice, Department. An alternative to the Landau theory of the phase transitions in amphiphile monolayers, namely density functional­chain amphiphile monolayers, correctly predicting the direction, magnitude and the dependence on surface area per

  5. NMR Structure Determination for Larger Proteins Using Backbone-Only Data

    E-print Network

    Baker, David

    assignments (6,7), can be obtained from HN-HN NOESY, residual dipolar coupling (RDC) (8), and other (9;major bottleneck that currently prevents routine application of NMR to larger (> 15 kDa) systems(14 information from backbone (HN, N, C, C, C') NMR data by taking advantage of the conformational sampling

  6. Cost and Reliability Considerations in Designing the Next-Generation IP over WDM Backbone Networks

    E-print Network

    Fisher, Kathleen

    Cost and Reliability Considerations in Designing the Next-Generation IP over WDM Backbone Networks-Lincoln, Lincoln, NE, USA AT&T Labs - Research, New Jersey, USA Email: byrav@cse.unl.edu,{kkrama,sinha}@research networks. To address the reliability challenges due to failures and planned outages, ISPs typically use two

  7. Abstract--Human operation of continuum "continuous-backbone" manipulators remains difficult, because of both the

    E-print Network

    Abstract--Human operation of continuum "continuous- backbone" manipulators remains difficult are fielded in unstructured real-world situations, the importance of a well-designed human interface becomes apparent. For example, most instances of user error observed during robotic operations at the World Trade

  8. Phase behaviour of two-component bottle-brush polymers with flexible backbones under poor solvent conditions

    E-print Network

    Nikolaos G. Fytas; Panagiotis E. Theodorakis

    2014-04-16

    The phase behaviour of two-component bottle-brush polymers with fully flexible backbones under poor solvent conditions is studied via molecular-dynamics simulations, using a coarse-grained bead-spring model and side chains of up to $N=40$ effective monomers. We consider a symmetric model where side chains of type A and B are grafted alternately onto a flexible backbone. The aim of this study to explore the phase behaviour of two-component bottle-brushes depending on parameters, such as as the grafting density $\\sigma$, the backbone length $N_b$, the side-chain length $N$, and the temperature $T$. Based on a cluster analysis, we identify for our range of parameters the regimes of fully phase separated systems, i.e., A-type side chains form one cluster and B-type chains another, while the interface that separates these two clusters contains the backbone monomers. We find that pearl-necklace or Janus-like structures, which normally occur for bottle-brush polymers with rigid backbones under poor solvent conditions, are fully attributed to the backbone rigidity, and, therefore, such structures are unlikely in the case of bottle brushes with fully flexible backbones. Also, a comparative discussion with earlier work on the phase behaviour of single-component bottle-brush polymers with flexible backbones is performed.

  9. Phase behaviour of two-component bottle-brush polymers with flexible backbones under poor solvent conditions

    NASA Astrophysics Data System (ADS)

    Fytas, Nikolaos G.; Theodorakis, Panagiotis E.

    2014-03-01

    The phase behaviour of two-component bottle-brush polymers with fully flexible backbones under poor solvent conditions is studied via molecular-dynamics simulations, using a coarse-grained bead-spring model and side chains of up to N = 40 effective monomers. We consider a symmetric model where side chains of type A and B are grafted alternately onto a flexible backbone. The aim of this study is to explore the phase behaviour of two-component bottle-brushes depending on parameters, such as as the grafting density \\sigma , the backbone length {{N}_{b}}, the side-chain length N, and the temperature T. Based on a cluster analysis, we identify for our range of parameters the regimes of fully phase separated systems, i.e., A-type side chains form one cluster and B-type chains another, while the interface that separates these two clusters contains the backbone monomers. We find that pearl-necklace or Janus-like structures, which normally occur for bottle-brush polymers with rigid backbones under poor solvent conditions, are fully attributed to the backbone rigidity, and, therefore, such structures are unlikely in the case of bottle brushes with fully flexible backbones. Also, a comparative discussion with earlier work on the phase behaviour of single-component bottle-brush polymers with flexible backbones is performed.

  10. Green Network Planning Model for Optical Backbones Jose Gutierrez, Tahir Riaz, Michael Jensen, Jens M. Pedersen and Ole B. Madsen

    E-print Network

    Paris-Sud XI, Université de

    to define the relations between optical backbone network planning and generic Green House Gases emissionsGreen Network Planning Model for Optical Backbones Jose Gutierrez, Tahir Riaz, Michael Jensen, Jens demands of the transmission systems. This power usage might have a significant negative effect

  11. Biosynthesis of novel carotenoid families based on unnatural carbon backbones: A model for diversification of natural product pathways

    E-print Network

    Arnold, Frances H.

    Biosynthesis of novel carotenoid families based on unnatural carbon backbones: A model Available online 30 January 2006 Abstract We show that the C40 carotenoid desaturase CrtI from Pantoea ananatis (Erwinia uredovora) is capable of desaturating unnaturally long C45 and C50 carotenoid backbones

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

    SciTech Connect

    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}.

  13. Remote Enantioselection Transmitted by an Achiral Peptide Nucleic Acid Backbone

    NASA Technical Reports Server (NTRS)

    Kozlov, Igor A.; Orgel, Leslie E.; Nielsen, Peter E.

    2000-01-01

    short homochiral segment of DNA into a PNA helix could have guaranteed that the next short segment of DNA to be incorporated would have the same handedness as the first. Once two segments of the same handedness were present, the probability that a third segment would have the same handedness would increase, and so on. Evolution could then slowly dilute out the PNA part. This scenario would ultimately allow the formation of a chiral oligonucleotide by processes that are largely resistant to enantiomeric crossinhibition. It is important to note that the ligation of homochiral dinucleotides on a nucleic acid template would probably be at least as enantiospecific as the reaction that we have studied. The disadvantage of using chiral monomers as components of a replicating system arises from the difficulty of generating a first long homochiral template from a racemic mixture of monomers, although results of experiments designed to overcome this difficulty by employing homochiral tetramers have been reported.l l The probability of obtaining a homochiral n-mer from achiral substrates is approximately 1P-I if the nontemplate-directed extension of the primer is not enantioselective. Hence, it would be very hard to get started with a homochiral 40-mer, for example. No such difficulty exists in a scenario that originates with an achiral genetic material and in which the incorporation of very few chiral monomers in this achiral background gradually progresses towards homochirality. It seems possible that some PNA sequences could act as catalysts, analogous to ribozymes, even though PNA lacks clear metal binding sites. Although such catalysts could not be enantioselective, the incorporation of as few as two chiral nucleotides could then impose chiral specificity on the system. Furthermore, such patch chimeras could help to bridge the gap in catalytic potential between PNA and RNA, while guaranteeing enantioselectivity.

  14. Inferring the Evolutionary History of IncP-1 Plasmids Despite Incongruence among Backbone Gene Trees

    PubMed Central

    Sen, Diya; Brown, Celeste J.; Top, Eva M.; Sullivan, Jack

    2013-01-01

    Plasmids of the incompatibility group IncP-1 can transfer and replicate in many genera of the Proteobacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental remediation. Although it is well understood that the accessory genes are transferred horizontally between plasmids, recent studies have also provided examples of recombination in the backbone genes of IncP-1 plasmids. As a consequence, phylogeny estimation based on backbone genes is expected to produce conflicting gene tree topologies. The main goal of this study was therefore to infer the evolutionary history of IncP-1 plasmids in the presence of both vertical and horizontal gene transfer. This was achieved by quantifying the incongruence among gene trees and attributing it to known causes such as 1) phylogenetic uncertainty, 2) coalescent stochasticity, and 3) horizontal inheritance. Topologies of gene trees exhibited more incongruence than could be attributed to phylogenetic uncertainty alone. Species-tree estimation using a Bayesian framework that takes coalescent stochasticity into account was well supported, but it differed slightly from the maximum-likelihood tree estimated by concatenation of backbone genes. After removal of the gene that demonstrated a signal of intergroup recombination, the concatenated tree was congruent with the species-tree estimate, which itself was robust to inclusion/exclusion of the recombinant gene. Thus, in spite of horizontal gene exchange both within and among IncP-1 subgroups, the backbone genome of these IncP-1 plasmids retains a detectable vertical evolutionary history. PMID:22936717

  15. Estimation of accuracy in determining protein backbone conformations from NOE data and empirical ?, ? probability distributions

    NASA Astrophysics Data System (ADS)

    Sherman, S. A.; Johnson, Michael E.

    Comprehensive computational experiments were carried out to examine systematically the potential for deriving protein backbone conformations using NOE data in conjunction with the probability distribution function of known backbone conformations of amino acid residues in proteins. It is shown that, in combination with the backbone conformational probability distribution, the measurement of NOE distances with moderate precision, consistent with the precision of modem NMR methods, is adequate to produce good local conformations of the protein backbone. The apparent need for much higher precision is not a fundamental property of the problem; it arose in previous treatments only from the mathematical statement of the problem and the approaches used. To demonstrate the improved precision resulting from combined use of NOE data and the ?, ? probability distribution, a computer program, FISINOE, was developed, and control calculations with both simulated and experimental NOE data for bovine pancreatic trypsin inhibitor were performed. An ensemble of conformations obtained from the X-ray Protein Data Bank was used to obtain an approximate probability distribution for existing conformations of amino acid residues in proteins. A comprehensive statistical analysis of the results clearly shows that the set of sequential d connectivities (data on the presence or absence of sequential NOE cross peaks related to nearest-neighbor residues), combined with prior information about existing conformations, is sufficient to obtain a satisfactorily determined local conformation of the protein backbone in most cases; in some cases it would be helpful to use, as additional information, the cross-peak intensity between the NH and C ?H intraresidual protons. Comparative studies indicate that the stability and accuracy in estimating the ? and ? angles by the FISINOE program exceed those of other traditional approaches. The principal advantages of the FISINOE method are discussed, and the extension of this method for the determination of protein three-dimensional structures is outlined.

  16. Peptide backbone fragmentation initiated by side-chain loss at cysteine residue in matrix-assisted laser desorption/ionization in-source decay mass spectrometry.

    PubMed

    Asakawa, Daiki; Smargiasso, Nicolas; Quinton, Loïc; De Pauw, Edwin

    2013-03-01

    Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) is initiated by hydrogen transfer from matrix molecules to the carbonyl oxygen of peptide backbone with subsequent radical-induced cleavage leading to c'/z• fragments pair. MALDI-ISD is a very powerful method to obtain long sequence tags from proteins or to do de novo sequencing of peptides. Besides classical fragmentation, MALDI-ISD also shows specific fragments for which the mechanism of formation enlightened the MALDI-ISD process. In this study, the MALDI-ISD mechanism is reviewed, and a specific mechanism is studied in details: the N-terminal side of Cys residue (Xxx-Cys) is described to promote the generation of c' and w fragments in MALDI-ISD. Our data suggest that for sequences containing Xxx-Cys motifs, the N-C? bond cleavage occurs following the hydrogen attachment to the thiol group of Cys side-chain. The c•/w fragments pair is formed by side-chain loss of the Cys residue with subsequent radical-induced cleavage at the N-C? bond located at the left side (N-terminal direction) of the Cys residue. This fragmentation pathway preferentially occurs at free Cys residue and is suppressed when the cysteines are involved in disulfide bonds. Hydrogen attachment to alkylated Cys residues using iodoacetamide gives free Cys residue by the loss of •CH2CONH2 radical. The presence of alkylated Cys residue also suppress the formation of c•/w fragments pair via the (C?)-centered radical, whereas w fragment is still observed as intense signal. In this case, the z• fragment formed by hydrogen attachment of carbonyl oxygen followed side-chain loss at alkylated Cys leads to a w fragment. Hydrogen attachment on peptide backbone and side-chain of Cys residue occurs therefore competitively during MALDI-ISD process. PMID:23494792

  17. Folding a protein by discretizing its backbone torsional dynamics

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel

    1999-05-01

    The aim of this work is to provide a coarse codification of local conformational constraints associated with each folding motif of a peptide chain in order to obtain a rough solution to the protein folding problem. This is accomplished by implementing a discretized version of the soft-mode dynamics on a personal computer (PC). Our algorithm mimics a parallel process as it evaluates concurrent folding possibilities by pattern recognition. It may be implemented in a PC as a sequence of perturbation-translation-renormalization (p-t-r) cycles performed on a matrix of local topological constraints (LTM). This requires suitable representational tools and a periodic quenching of the dynamics required for renormalization. We introduce a description of the peptide chain based on a local discrete variable the values of which label the basins of attraction of the Ramachandran map for each residue. Thus, the local variable indicates the basin in which the torsional coordinates of each residue lie at a given time. In addition, a coding of local topological constraints associated with each secondary and tertiary structural motif is introduced. Our treatment enables us to adopt a computation time step of 81 ps, a value far larger than hydrodynamic drag time scales. Folding pathways are resolved as transitions between patterns of locally encoded structural signals that change within the 10 ?s-100 ms time scale range. These coarse folding pathways are generated by the periodic search for structural patterns in the time-evolving LTM. Each pattern is recorded as a contact matrix, an operation subject to a renormalization feedback loop. The validity of our approach is tested vis-a-vis experimentally-probed folding pathways eventually generating tertiary interactions in proteins which recover their active structure under in vitro renaturation conditions. As an illustration, we focus on determining significant folding intermediates and late kinetic bottlenecks that occur within the first 10 ms of the bovine pancreatic trypsin inhibitor renaturation process. The probed cooperativity and nucleation effects, as well as diffusion-collision stabilization of secondary structure are shown to result from the persistence of relatively stable patterns through successive (p-t-r) cycles, thus acting as seeding patterns for further growth or hierarchical development.

  18. Facile backbone (1H, 15N, 13Ca, and 13C') assignment of 13C/15N-labeled proteins using orthogonal projection planes of HNN and HN(C)N experiments and its automation.

    PubMed

    Kumar, Dinesh; Borkar, Aditi; Hosur, Ramakrishna V

    2012-05-01

    Recently, we introduced an efficient high-throughput protocol for backbone assignment of small folded proteins based on two-dimensional (2D) projections of HN(C)N suite of experiments and its automation [Borkar et al., J. Biomol. NMR 2011, 50(3), 285-297]. This strategy provides complete sequence-specific assignment of backbone ((1)H, (15)N, (13)C(?), and (13)C') resonances in less than a day; thus, it has great implications for high-throughput structural proteomics. However, in cases when such small folded protein exhibits substantial amide (1)H shift degeneracy (typically seen in alpha-helical proteins), the strategy may fail or lead to ambiguities. Another limitation is with respect to the identification of checkpoints from the variants of 2D-hncNH spectrum. For example, a protein with many GG, GA, AA, SS, TS, TT, and TS types of dipeptide stretches along its sequence, thus the identification of NH cross-peak corresponding to second G, A, S, or T becomes difficult. In this backdrop, we present here two improvements to enhance the utility of the proposed high-throughput AUTOmatic Backbone Assignment protocol: (i) use of 2D-hNnH spectrum and its variants that display additional (1)H-(15)N correlations and thus help to resolve ambiguities arising because of amide (1)H shift degeneracy and (ii) optimization of the ?(CN) delay in the 2D-hncNH experiment that, when properly adjusted, is observed to help remove ambiguities in the identification of the checkpoints. These improvements have also been incorporated in the automation program AUTOmatic Backbone Assignment. Finally, the performance of the strategy and the automation has been demonstrated using the chicken SH3 domain protein. PMID:22508472

  19. Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data.

    PubMed

    Perczel, András; Jákli, Imre; McAllister, Michael A; Csizmadia, Imre G

    2003-06-01

    Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly. PMID:12794897

  20. Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus

    PubMed Central

    Nuccitelli, Annalisa; Rinaudo, C. Daniela; Brogioni, Barbara; Cozzi, Roberta; Ferrer-Navarro, Mario; Yero, Daniel; Telford, John L.; Grandi, Guido; Daura, Xavier; Zacharias, Martin; Maione, Domenico

    2013-01-01

    The pilus 2a backbone protein (BP-2a) is one of the most structurally and functionally characterized components of a potential vaccine formulation against Group B Streptococcus. It is characterized by six main immunologically distinct allelic variants, each inducing variant-specific protection. To investigate the molecular determinants driving the variant immunogenic specificity of BP-2a, in terms of single residue contributions, we generated six monoclonal antibodies against a specific protein variant based on their capability to recognize the polymerized pili structure on the bacterial surface. Three mAbs were also able to induce complement-dependent opsonophagocytosis killing of live GBS and target the same linear epitope present in the structurally defined and immunodominant domain D3 of the protein. Molecular docking between the modelled scFv antibody sequences and the BP-2a crystal structure revealed the potential role at the binding interface of some non-conserved antigen residues. Mutagenesis analysis confirmed the necessity of a perfect balance between charges, size and polarity at the binding interface to obtain specific binding of mAbs to the protein antigen for a neutralizing response. PMID:23825940

  1. Structural Conservation, Variability, and Immunogenicity of the T6 Backbone Pilin of Serotype M6 Streptococcus pyogenes

    PubMed Central

    Moreland, Nicole J.; Loh, Jacelyn M.; Bell, Anita; Atatoa Carr, Polly; Proft, Thomas; Baker, Edward N.

    2014-01-01

    Group A streptococcus (GAS; Streptococcus pyogenes) is a Gram-positive human pathogen that causes a broad range of diseases ranging from acute pharyngitis to the poststreptococcal sequelae of acute rheumatic fever. GAS pili are highly diverse, long protein polymers that extend from the cell surface. They have multiple roles in infection and are promising candidates for vaccine development. This study describes the structure of the T6 backbone pilin (BP; Lancefield T-antigen) from the important M6 serotype. The structure reveals a modular arrangement of three tandem immunoglobulin-like domains, two with internal isopeptide bonds. The T6 pilin lysine, essential for polymerization, is located in a novel VAKS motif that is structurally homologous to the canonical YPKN pilin lysine in other three- and four-domain Gram-positive pilins. The T6 structure also highlights a conserved pilin core whose surface is decorated with highly variable loops and extensions. Comparison to other Gram-positive BPs shows that many of the largest variable extensions are found in conserved locations. Studies with sera from patients diagnosed with GAS-associated acute rheumatic fever showed that each of the three T6 domains, and the largest of the variable extensions (V8), are targeted by IgG during infection in vivo. Although the GAS BP show large variations in size and sequence, the modular nature of the pilus proteins revealed by the T6 structure may aid the future design of a pilus-based vaccine. PMID:24778112

  2. Gas-phase models of ? turns: Effect of side-chain/backbone interactions investigated by IR/UV spectroscopy and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Chin, Wutharath; Piuzzi, François; Dognon, Jean-Pierre; Dimicoli, Iliana; Mons, Michel

    2005-08-01

    The conformations of laser-desorbed jet-cooled short peptide chains Ac -Phe-Xxx-NH2 (Xxx =Gly, Ala, Val, and Pro) have been investigated by IR/UV double resonance spectroscopy and density-functional-theory (DFT) quantum chemistry calculations. Singly ?-folded backbone conformations (?L-?) are systematically observed as the most stable conformers, showing that in these two-residue peptide chains, the local conformational preference of each residue is retained (?L for Phe and ? turn for Xxx). Besides, ? turns are also spontaneously formed but appear as minor conformers. The theoretical analysis suggests negligible inter-residue interactions of the main conformers, which enables us to consider these species as good models of ? turns. In the case of valine, two similar types of ? turns, differing by the strength of their hydrogen bond, have been found both experimentally and theoretically. This observation provides evidence for a strong flexibility of the peptide chain, whose minimum-energy structures are controlled by side-chain/backbone interactions. The qualitative conformational difference between the present species and the reversed sequence Ac -Xxx-Phe-NH2 is also discussed.

  3. The Composition of Coding Joints Formed in V(D)J Recombination Is Strongly Affected by the Nucleotide Sequence of the Coding Ends and Their Relationship to the Recombination Signal Sequences

    Microsoft Academic Search

    UTHAYASHANKER R. EZEKIEL; TIANHE SUN; GRAZYNA BOZEK; URSULA STORB

    1997-01-01

    V(D)J recombination proceeds in two stages. Precise cleavage at the border of the conserved recombination signal sequences (RSSs) and the coding ends results in flush double-stranded signal ends and coding ends terminating in hairpins. In the second stage, the signal and coding ends are processed into signal and coding joints. Coding ends containing certain nucleotide homopolymers affect the efficiency of

  4. The Manufacturing Process for the NASA Composite Crew Module Demonstration Structure

    NASA Technical Reports Server (NTRS)

    Pelham, Larry; Higgins, John E.

    2008-01-01

    This paper will describe the approaches and methods selected in fabrication of a carbon composite demonstration structure for the Composite Crew Module (CCM) Program. The program is managed by the NASA Safety and Engineering Center with participants from ten NASA Centers and AFRL. Multiple aerospace contractors are participating in the design development, tooling and fabrication effort as well. The goal of the program is to develop an agency wide design team for composite habitable spacecraft. The specific goals for this development project are: a).To gain hands on experience in design, building and testing a composite crew module. b) To validate key assumptions by resolving composite spacecraft design details through fabrication and testing of hardware. This abstract is based on Preliminary Design data..The final design will continue to evolve through the fall of 2007 with fabrication mostly completed by conference date. From a structures perspective, the.CCM can be viewed as a pressure module with variable pressure time histories and a series of both impact and quasi-static, high intensity point, line, and area distributed loads. The portion of the overall space vehicle being designed and. fabricated by the CCM team is just the pressure module and primary loading points. The heaviest point loads are applied and distributed to the pressure module at.an aluminum Service Module/Alternate Launch Abort System (SM/ALAS) fittings and at Main and Drogue Chute fittings. Significant line loads with metal to metal impact is applied at.the Lids ring. These major external point and line loads as well as pressure impact loads (blast and water landing) are applied to the lobed floor though the reentry shield and crushable materials. The pressure module is divided into upper and lower. shells that mate together with a bonded belly band splice joint to create the completed structural assembly. The benefits of a split CCM far outweigh the risks of a joint. These benefits include lower tooling cost and less manufacturing risk. Assembly of the top and bottom halves of the pressure shell will allow access to the interior of the shell throughout remaining fabrication sequence and can also potentially permit extensive installation of equipment and .crew facilities prior to final assembly of the two shell halves. A Pi pre-form is a woven carbon composite material which is provided in pre-impregnated form and frozen for long term storage. The cross-section shape allows the top of the pi to be bonded to a flat or curved surface with a second flat plate composite section bonded between two upstanding legs of the Pi. One of the regions relying on the merits of the Pi pre-form is the backbone. All connections among plates of the backbone structure, including the upper flanges, and to the lobe base of the pressure shell are currently joined by Pi pre-forms. The intersection of backbone composite plates is formed by application of two Pi pre-forms, top flanges and lobed surfaces are bonded with one Pi pre-form. The process of applying the pre-impregnated pi-preform will be demonstrated to include important steps like surface preparation, forming, application of pressure dams, vacuum bagging for consolidation, and curing techniques. Chopped carbon fiber tooling was selected over other traditional metallic and carbon fiber tooling. The requirement of schedule and cost economy for a moderate reuse cure tool warranted composite tooling options. Composite tooling schedule duration of 18 weeks compared favorably against other metallic tooling including invar tooling. Composite tooling also shows significant cost savings over low CTE metallic options. The composite tooling options were divided into two groups and the final decision was based on the cost, schedule, tolerance, temperature, and reuse requirements.

  5. Characterization of binding-induced changes in dynamics suggests a model for sequence-nonspecific binding of ssDNA by replication protein A

    PubMed Central

    Bhattacharya, Shibani; Botuyan, Maria-Victoria; Hsu, Fred; Shan, Xi; Arunkumar, A.I.; Arrowsmith, Cheryl H.; Edwards, Aled M.; Chazin, Walter J.

    2002-01-01

    Single-stranded-DNA-binding proteins (SSBs) are required for numerous genetic processes ranging from DNA synthesis to the repair of DNA damage, each of which requires binding with high affinity to ssDNA of variable base composition. To gain insight into the mechanism of sequence-nonspecific binding of ssDNA, NMR chemical shift and 15N relaxation experiments were performed on an isolated ssDNA-binding domain (RPA70A) from the human SSB replication protein A. The backbone 13C, 15N, and 1H resonances of RPA70A were assigned for the free protein and the d-CTTCA complex. The binding-induced changes in backbone chemical shifts were used to map out the ssDNA-binding site. Comparison to results obtained for the complex with d-C5 showed that the basic mode of binding is independent of the ssDNA sequence, but that there are differences in the binding surfaces. Amide nitrogen relaxation rates (R1 and R2) and 1H–15N NOE values were measured for RPA70A in the absence and presence of d-CTTCA. Analysis of the data using the Model-Free formalism and spectral density mapping approaches showed that the structural changes in the binding site are accompanied by some significant changes in flexibility of the primary DNA-binding loops on multiple timescales. On the basis of these results and comparisons to related proteins, we propose that the mechanism of sequence-nonspecific binding of ssDNA involves dynamic remodeling of the binding surface. PMID:12237454

  6. Influence of Backbone Fluorination in Regioregular Poly(3-alkyl-4-fluoro)thiophenes.

    PubMed

    Fei, Zhuping; Boufflet, Pierre; Wood, Sebastian; Wade, Jessica; Moriarty, John; Gann, Eliot; Ratcliff, Erin L; McNeill, Christopher R; Sirringhaus, Henning; Kim, Ji-Seon; Heeney, Martin

    2015-06-01

    We report two strategies toward the synthesis of 3-alkyl-4-fluorothiophenes containing straight (hexyl and octyl) and branched (2-ethylhexyl) alkyl groups. We demonstrate that treatment of the dibrominated monomer with 1 equiv of alkyl Grignard reagent leads to the formation of a single regioisomer as a result of the pronounced directing effect of the fluorine group. Polymerization of the resulting species affords highly regioregular poly(3-alkyl-4-fluoro)thiophenes. Comparison of their properties to those of the analogous non-fluorinated polymers shows that backbone fluorination leads to an increase in the polymer ionization potential without a significant change in optical band gap. Fluorination also results in an enhanced tendency to aggregate in solution, which is ascribed to a more co-planar backbone on the basis of Raman and DFT calculations. Average charge carrier mobilities in field-effect transistors are found to increase by up to a factor of 5 for the fluorinated polymers. PMID:25994804

  7. The molecular structure of spider dragline silk: Folding and orientation of the protein backbone

    PubMed Central

    van Beek, J. D.; Hess, S.; Vollrath, F.; Meier, B. H.

    2002-01-01

    The design principles of spider dragline silk, nature's high-performance fiber, are still largely unknown, in particular for the noncrystalline glycine-rich domains, which form the bulk of the material. Here we apply two-dimensional solid-state NMR to determine the distribution of the backbone torsion angles (?,?) as well as the orientation of the polypeptide backbone toward the fiber at both the glycine and alanine residues. Instead of an “amorphous matrix,” suggested earlier for the glycine-rich domains, these new data indicate that all domains in dragline silk have a preferred secondary structure and are strongly oriented, with the chains predominantly parallel to the fiber. As proposed previously, the alanine residues are predominantly found in a ? sheet conformation. The glycine residues are partly incorporated into the ? sheets and otherwise form helical structures with an approximate 3-fold symmetry. PMID:12149440

  8. Simulation study of chiral two dimensional ultraviolet (2DUV) spectroscopy of the protein backbone

    PubMed Central

    Abramavicius, Darius; Jiang, Jun; Bulheller, Benjamin M.; Hirst, Jonathan D.; Mukamel, Shaul

    2010-01-01

    Amide n –?* and ?-?* excitations around 200 nm are prominent spectroscopic signatures of the protein backbone, which are routinely used in ultraviolet (UV) circular dichroism for structure characterization. Recently developed ultrafast laser sources may be used to extend these studies to two dimensions (2D). We apply a new algorithm for modelling protein electronic transitions to simulate two-dimensional ultraviolet (2DUV) photon echo signals in this regime and to identify signatures of protein backbone secondary (and tertiary) structure. Simulated signals for a set of globular and fibrillar proteins and their specific regions reveal characteristic patterns of helical and sheet secondary structures. We investigate how these patterns vary and converge with the size of the structural motif. Specific chiral polarization configurations of the UV pulses are found to be sensitive to aspects of the protein structure. This information significantly augments that available from linear circular dichroism. PMID:20481498

  9. On the reliability of backbone-assisted end-to-end transmissions in WSNs

    Microsoft Academic Search

    Ali Tufail; Syed Ali Khayam; Amna Ali; Waleed Akram Baig; Fatima Muhammad Anwar; Ki-Hyung Kim; Seung-Wha Yoo

    2009-01-01

    Many anticipated deployment scenarios, in particular military, healthcare, and disaster-recovery applications, of Wireless Sensor Networks (WSNs) require reliable source to sink communication. Since transmission range of sensors is quite limited, to achieve higher end-to-end transmission reliability, WSNs generally employ intermediate backbone links (wired or wireless) that can deliver packets at larger distances. In this paper, we evaluate the reliability of

  10. Supramolecular Organization of the Repetitive Backbone Unit of the Streptococcus pneumoniae Pilus

    Microsoft Academic Search

    Glen Spraggon; Eric Koesema; Maria Scarselli; Enrico Malito; Massimiliano Biagini; Nathalie Norais; Carla Emolo; Michèle Anne Barocchi; Fabiola Giusti; Markus Hilleringmann; Rino Rappuoli; Scott Lesley; Antonello Covacci; Vega Masignani; Ilaria Ferlenghi; Georg Häcker

    2010-01-01

    Streptococcus pneumoniae, like many other Gram-positive bacteria, assembles long filamentous pili on their surface through which they adhere to host cells. Pneumococcal pili are formed by a backbone, consisting of the repetition of the major component RrgB, and two accessory proteins (RrgA and RrgC). Here we reconstruct by transmission electron microscopy and single particle image reconstruction method the three dimensional

  11. Backbone and side chain NMR assignments for the ribosome assembly factor Nop6 from Saccharomyces cerevisiae.

    PubMed

    Wurm, Jan Philip; Lioutikov, Anatoli; Kötter, Peter; Entian, Karl-Dieter; Wöhnert, Jens

    2014-10-01

    The Saccharomyces cerevisiae Nop6 protein is involved in the maturation of the small ribosomal subunit. It contains a central RNA binding domain and a predicted C-terminal coiled-coil domain. Here we report the almost complete (>90%) (1)H,(13)C,(15)N backbone and side chain NMR assignment of a 15 kDa Nop6 construct comprising the RNA binding and coiled-coil domains. PMID:23921755

  12. Rerouting for handover in mobile networks with connection-oriented backbones: an experimental testbed

    Microsoft Academic Search

    Andreas Festag; T. Assimakopulos; Lars Westerhoff; Adam Wolisz

    2000-01-01

    The rerouting of connections for handover in a broadband mobile cellular network is investigated. We address networks with a connection-oriented backbone, which supports quality-of-service (QoS). Moreover it is assumed an IP-style multicast on top of the connection-oriented network. We advocate to utilize the IP-style multicast in order to reroute connections for handover. Three rerouting schemes are proposed, which are based

  13. Tritium containing polymers having a polymer backbone substantially void of tritium

    DOEpatents

    Jensen, George A. (Richland, WA); Nelson, David A. (Richland, WA); Molton, Peter M. (Richland, WA)

    1992-01-01

    A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium.

  14. Tritium containing polymers having a polymer backbone substantially void of tritium

    DOEpatents

    Jensen, G.A.; Nelson, D.A.; Molton, P.M.

    1992-03-31

    A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium. 2 figs.

  15. Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature

    Microsoft Academic Search

    Haukur Gudnason; Martin Dufva; D. D. Bang; Anders Wolff

    2007-01-01

    The importance of real-time polymerase chain reaction (PCR) has increased steadily in clinical applications over the last decade. Many applica- tions utilize SYBR Green I dye to follow the accumulation of amplicons in real time. SYBR Green I has, however, a number of limitations that include the inhibition of PCR, preferential binding to GC-rich sequences and effects on melting curve

  16. Biosensors for DNA sequence detection

    NASA Technical Reports Server (NTRS)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  17. On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent

    PubMed Central

    Riml, Christian; Glasner, Heidelinde; Rodgers, M. T.; Micura, Ronald; Breuker, Kathrin

    2015-01-01

    Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in ‘top-down’ strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively charged RNA. We found that CAD of RNA is a stepwise reaction that is facilitated by, but does not require, the presence of positive charge. Preferred backbone cleavage next to adenosine and guanosine in CAD of (M+nH)n+ and (M?nH)n? ions, respectively, is based on hydrogen bonding between nucleobase and phosphodiester moieties. Moreover, CAD of RNA involves an intermediate that is sufficiently stable to survive extension of the RNA structure and intramolecular proton redistribution according to simple Coulombic repulsion prior to backbone cleavage into c and y ions from phosphodiester bond cleavage. PMID:25904631

  18. Computer simulation of bottle brush polymers with flexible backbone: Good solvent versus Theta solvent conditions

    E-print Network

    Theodorakis, Panagiotis E; Paul, Wolfgang; Binder, Kurt; 10.1063/1.3656072

    2011-01-01

    By Molecular Dynamics simulation of a coarse-grained bead-spring type model for a cylindrical molecular brush with a backbone chain of $N_b$ effective monomers to which with grafting density $\\sigma$ side chains with $N$ effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side chain lengths are in the range $5 \\le N \\le 40$, backbone chain lengths are in the range $50 \\le N_b \\le 200$, and we perform a comparison to results for the bond fluctuation model on the simple cubic lattice (for which much longer chains are accessible, $N_b \\le 1027$, and which corresponds to an athermal, very good, solvent). We obtain linear dimensions of side chains and the backbone chain and discuss their $N$-dependence in terms of power laws and the associated effective exponents. We show that even at the Theta point the side chains are considerably stretched, their linear dimension depending on the solvent quality only weakly. Effective persistence lengths are extracted ...

  19. Backbone and Side-Chain Contributions in Protein Denaturation by Urea

    PubMed Central

    Canchi, Deepak R.; García, Angel E.

    2011-01-01

    Urea is a commonly used protein denaturant, and it is of great interest to determine its interaction with various protein groups to elucidate the molecular basis of its effect on protein stability. Using the Trp-cage miniprotein as a model system, we report what we believe to be the first computation of changes in the preferential interaction coefficient of the protein upon urea denaturation from molecular-dynamics simulations and examine the contributions from the backbone and the side-chain groups. The preferential interaction is obtained from reversible folding/unfolding replica exchange molecular-dynamics simulations of Trp-cage in presence of urea, over a wide range of urea concentration. The increase in preferential interaction upon unfolding is dominated by the side-chain contribution, rather than the backbone. Similar trends are observed in simulations using two different force fields, Amber94 and Amber99sb, for the protein. The magnitudes of the side-chain and backbone contributions differ in the two force fields, despite containing identical protein-solvent interaction terms. The differences arise from the unfolded ensembles sampled, with Amber99sb favoring conformations with larger surface area and lower helical content. These results emphasize the importance of the side-chain interactions with urea in protein denaturation, and highlight the dependence of the computed driving forces on the unfolded ensemble sampled. PMID:21402035

  20. Repeat Sequence Proteins as Matrices for Nanocomposites

    SciTech Connect

    Drummy, L.; Koerner, H; Phillips, D; McAuliffe, J; Kumar, M; Farmer, B; Vaia, R; Naik, R

    2009-01-01

    Recombinant protein-inorganic nanocomposites comprised of exfoliated Na+ montmorillonite (MMT) in a recombinant protein matrix based on silk-like and elastin-like amino acid motifs (silk elastin-like protein (SELP)) were formed via a solution blending process. Charged residues along the protein backbone are shown to dominate long-range interactions, whereas the SELP repeat sequence leads to local protein/MMT compatibility. Up to a 50% increase in room temperature modulus and a comparable decrease in high temperature coefficient of thermal expansion occur for cast films containing 2-10 wt.% MMT.

  1. Sequencing Puzzle

    NSDL National Science Digital Library

    The sequencing puzzle is designed to teach high school students, and perhaps even middle school, and the general public about the basics of genome sequencing. The sequencing of the tomato genome is used as the basis for this activity. It is an interactive puzzle. In addition to the puzzle, the site also contains background information on tomatoes, DNA, and various molecular terms.

  2. Cycle Sequencing

    NSDL National Science Digital Library

    This animation from Cold Spring Harbor Laboratory's Dolan DNA Learning Center presents the cycle sequencing. The animation contains instructions on how to sequence a piece of DNA beginning with the raw materials needed, and details on the process: "Fluorescent dyes are added to the reactions, and a laser within an automated DNA sequencing machine is used to analyze the DNA fragments produced."

  3. Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.

    PubMed

    Svozil, Daniel; Sponer, Judit E; Marchan, Ivan; Pérez, Alberto; Cheatham, Thomas E; Forti, F; Luque, F Javier; Orozco, Modesto; Sponer, Jirí

    2008-07-10

    The anionic sugar-phosphate backbone of nucleic acids substantially contributes to their structural flexibility. To model nucleic acid structure and dynamics correctly, the potentially sampled substates of the sugar-phosphate backbone must be properly described. However, because of the complexity of the electronic distribution in the nucleic acid backbone, its representation by classical force fields is very challenging. In this work, the three-dimensional potential energy surfaces with two independent variables corresponding to rotations around the alpha and gamma backbone torsions are studied by means of high-level ab initio methods (B3LYP/6-31+G*, MP2/6-31+G*, and MP2 complete basis set limit levels). The ability of the AMBER ff99 [Wang, J. M.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074] and parmbsc0 [Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E.; Laughten, C. A.; Orozco, M. Biophys. J. 2007, 92, 3817-3829] force fields to describe the various alpha/gamma conformations of the DNA backbone accurately is assessed by comparing the results with those of ab initio quantum chemical calculations. Two model systems differing in structural complexity were used to describe the alpha/gamma energetics. The simpler one, SPM, consisting of a sugar and methyl group linked through a phosphodiester bond was used to determine higher-order correlation effects covered by the CCSD(T) method. The second, more complex model system, SPSOM, includes two deoxyribose residues (without the bases) connected via a phosphodiester bond. It has been shown by means of a natural bond orbital analysis that the SPSOM model provides a more realistic representation of the hyperconjugation network along the C5'-O5'-P-O3'-C3' linkage. However, we have also shown that quantum mechanical investigations of this model system are nontrivial because of the complexity of the SPSOM conformational space. A comparison of the ab initio data with the ff99 potential energy surface clearly reveals an incorrect ff99 force-field description in the regions where the gamma torsion is in the trans conformation. An explanation is proposed for why the alpha/gamma flips are eliminated so successfully when the parmbsc0 force-field modification is used. PMID:18558755

  4. ViTAMin: A Virtual Backbone Tree Algorithm for Minimal energy consumption in wireless sensor network routing

    Microsoft Academic Search

    Jaekwang Kim; Jee-Hyong Lee

    2012-01-01

    In wireless sensor networks (WSNs), routing algorithms are one of the important research topics because low energy consumption is strongly needed. In comparison with single hop and cluster routing scheme, virtual backbone tree schemes have recently attracted considerable attention in WSN routing algorithms as they offer energy-efficient transmission based on multi-hop routing approaches. The Energy-aware Virtual Backbone Tree (EVBT) is

  5. Global transcriptional regulator KorC coordinates expression of three backbone modules of the broad-host-range RA3 plasmid from IncU incompatibility group.

    PubMed

    Ludwiczak, M; Dolowy, P; Markowska, A; Szarlak, J; Kulinska, A; Jagura-Burdzy, G

    2013-07-01

    The broad-host-range conjugative RA3 plasmid from IncU incompatibility group has been isolated from the fish pathogen Aeromonas hydrophila. DNA sequencing has revealed a mosaic modular structure of RA3 with the stabilization module showing some similarity to IncP-1 genes and the conjugative transfer module highly similar to that from PromA plasmids. The integrity of the mosaic plasmid genome seems to be specified by its regulatory network. In this paper the transcriptional regulator KorC was analyzed. KorCRA3 (98 amino acids) is encoded in the stabilization region and represses four strong promoters by binding to a conserved palindrome sequence, designated OC on the basis of homology to the KorC operator sequences in IncP-1 plasmids. Two of the KorCRA3-regulated promoters precede the first two cistrons in the stabilization module, one fires towards replication module, remaining one controls a tricistronic operon, whose products are involved in the conjugative transfer process. Despite the similarity between the binding sites in IncU and IncP-1 plasmids, no cross-reactivity between their KorC proteins has been detected. KorC emerges as a global regulator of RA3, coordinating all its backbone functions: replication, stable maintenance and conjugative transfer. PMID:23583562

  6. Hydrogels Containing Peptide or Aminosugar Sequences Implanted into the Rat Brain: Influence on Cellular Migration and Axonal Growth

    Microsoft Academic Search

    Giles W. Plant; Stèphane Woerly; Alan R. Harvey

    1997-01-01

    Biocompatible polymer matrices for implantation into lesion sites in the brain were synthesized by incorporating peptide or aminosugar sequences intoN-(2-hydroxypropyl)methacrylamide (HPMA) hydrogels. RGD peptide sequences were chemically linked to the hydrogel backbone via a glycylglycine spacer; aminosugars were glucosamine (NHGlc) orN-acetylglucosamine residues. Unmodified or sequence containing HPMA hydrogels were implanted into the lesioned optic tract or cerebral cortex of juvenile

  7. TaALMT1 promoter sequence compositions, acid tolerance, and Al tolerance in wheat cultivars and landraces from Sichuan in China.

    PubMed

    Han, C; Dai, S F; Liu, D C; Pu, Z J; Wei, Y M; Zheng, Y L; Wen, D J; Zhao, L; Yan, Z H

    2013-01-01

    Previous genetic studies on wheat from various sources have indicated that aluminum (Al) tolerance may have originated independently in USA, Brazil, and China. Here, TaALMT1 promoter sequences of 92 landraces and cultivars from Sichuan, China, were sequenced. Five promoter types (I', II, III, IV, and V) were observed in 39 cultivars, and only three promoter types (I, II, and III) were observed in 53 landraces. Among the wheat collections worldwide, only the Chinese Spring (CS) landrace native to Sichuan, China, carried the TaALMT1 promoter type III. Besides CS, two other Sichuan-bred landraces and six cultivars with TaALMT1 promoter type III were identified in this study. In the phylogenetic tree constructed based on the TaALMT1 promoter sequences, type III formed a separate branch, which was supported by a high bootstrap value. It is likely that TaALMT1 promoter type III originated from Sichuan-bred wheat landraces of China. In addition, the landraces with promoter type I showed the lowest Al tolerance among all landraces and cultivars. Furthermore, the cultivars with promoter type IV showed better Al tolerance than landraces with promoter type II. A comparison of acid tolerance and Al tolerance between cultivars and landraces showed that the landraces had better acid tolerance than the cultivars, whereas the cultivars showed better Al tolerance than the landraces. Moreover, significant difference in Al tolerance was also observed between the cultivars raised by the National Ministry of Agriculture and by Sichuan Province. Among the landraces from different regions, those from the East showed better acid tolerance and Al tolerance than those from the South and West of Sichuan. Additional Al-tolerant and acid-tolerant wheat lines were also identified. PMID:24301929

  8. DNA Sequencing

    NSDL National Science Digital Library

    Teachers' Domain presents this interactive, adapted from the Dolan DNA Learning Center, with reading material and animations to help students learn the basics of DNA sequencing. The lesson is divided two parts: Sanger Sequencing and Cycle Sequencing. The processes for both techniques are covered and animations help students visualize the material presented. On the site, visitors will also find a supplemental background essay, discussion questions, and standards alignment from Teachers' Domain.

  9. A PDDA/poly(2,6-pyridinedicarboxylic acid)-CNTs composite film DNA electrochemical sensor and its application for the detection of specific sequences related to PAT gene and NOS gene.

    PubMed

    Yang, Tao; Zhang, Wei; Du, Meng; Jiao, Kui

    2008-05-30

    2,6-Pyridinedicarboxylic acid (PDC) was electropolymerized on the glassy carbon electrode (GCE) surface combined with carboxylic group-functionalized single-walled carbon nanotubes (SWNTs) by cyclic voltammetry (CV) to form PDC-SWNTs composite film, which was rich in negatively charged carboxylic group. Then, poly(diallyldimethyl ammonium chloride) (PDDA), a linear cationic polyelectrolyte, was electrostatically adsorbed on the PDC-SWNTs/GCE surface. DNA probes with negatively charged phosphate group at the 5' end were immobilized on the PDDA/PDC-SWNTs/GCE due to the strong electrostatic attraction between PDDA and phosphate group of DNA. It has been found that modification of the electrode with PDC-SWNTs film has enhanced the effective electrode surface area and electron-transfer ability, in addition to providing negatively charged groups for the electrostatic assembly of cationic polyelectrolyte. PDDA plays a key role in the attachment of DNA probes to the PDC-SWNTs composite film and acts as a bridge to connect DNA with PDC-SWNTs film. The cathodic peak current of methylene blue (MB), an electroactive label, decreased obviously after the hybridization of DNA probe (ssDNA) with the complementary DNA (cDNA). This peak current change was used to monitor the recognition of the specific sequences related to PAT gene in the transgenic corn and the polymerase chain reaction (PCR) amplification of NOS gene from the sample of transgenic soybean with satisfactory results. Under optimal conditions, the dynamic detection range of the sensor to PAT gene target sequence was from 1.0x10(-11) to 1.0x10(-6) mol/L with the detection limit of 2.6x10(-12) mol/L. PMID:18585173

  10. Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing

    Microsoft Academic Search

    Pradeep S. Pallan; Paolo Lubini; Martin Bolli; Martin Egli

    2007-01-01

    The crystal structure of the duplex formed by oligo(2',3'-dideoxy-b-D-glucopyranosyl)nucleotides (homo-DNA) revealed strongly inclined backbone and base-pair axes (Egli,M., Pallan,P.S., Pattanayek,R., Wilds,C.J., Lubini,P., Minasov,G., Dobler,M., Leumann,C.J. and Eschenmoser,A. (2006) Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J. Am. Chem. Soc., 128, 10847-10856). This inclination is easily perceived because homo- DNA exhibits only a

  11. Effect of Steric Constraint at the ?-Backbone Position on the Conformations and Hybridization Properties of PNAs

    PubMed Central

    Crawford, Matthew J.; Rapireddy, Srinivas; Bahal, Raman; Sacui, Iulia; Ly, Danith H.

    2011-01-01

    Conformationally preorganized peptide nucleic acids (PNAs) have been synthesized through backbone modifications at the ?-position, where R = alanine, valine, isoleucine, and phenylalanine side chains. The effects of these side-chains on the conformations and hybridization properties of PNAs were determined using a combination of CD and UV-Vis spectroscopic techniques. Our results show that the ?-position can accommodate varying degrees of sterically hindered side-chains, reaffirming the bimodal function of PNAs as the true hybrids of “peptides” and “nucleic acids.” PMID:21776375

  12. Observational Study on HIV-Infected Subjects Failing HAART Receiving Tenofovir Plus Didanosine as NRTI Backbone

    Microsoft Academic Search

    M. Bongiovanni; N. Gianotti; E. Chiesa; P. Nasta; P. Cicconi; A. Capetti; A. di Biagio; A. Matti; V. Tirelli; P. Marconi; A. de Luca; C. Mussini; F. Gatti; M. Zaccarelli; C. Abeli; C. Torti; A. Antinori; A. Castagna; A. d'Arminio Monforte

    2007-01-01

    We evaluated the efficacy of tenofovir (TDF) – and didanosine (ddI)-containing backbones in HIV-infected experienced subjects.\\u000a We included in the study 245 subjects who started a TDF\\/ddI-containing HAART with HIV-RNA > 3 log10 cp\\/ml and an available genotypic resistance test at baseline. At baseline, median CD4 counts and HIV-RNA were 278 cell\\/mmc\\u000a and 4.32 log10 cp\\/ml, respectively. Seventy-four subjects (30.2%)

  13. Sequence Bracelets

    NSDL National Science Digital Library

    Wellcome Trust Sanger Institute

    2012-06-26

    In this craft-based activity, learners make DNA sequence bracelets that carry the code of an organism such as a human, trout, chimpanzee or butterfly. This activity reinforces the principle of complementary base pairs as learners are given one strand of the sequence and they have to match up the other strand correctly.

  14. DNA binding to proteolytically activated TLR9 is sequence-independent and enhanced by DNA curvature

    PubMed Central

    Li, Yue; Berke, Ian C; Modis, Yorgo

    2012-01-01

    Toll-like receptor 9 (TLR9) recognizes microbial DNA in endolysosomal compartments. The ectodomain of TLR9 must be proteolytically cleaved by endosomal proteases to produce the active receptor capable of inducing an innate immune signal. We show that the cleaved TLR9 ectodomain is a monomer in solution and that DNA ligands with phosphodiester backbones induce TLR9 dimerization in a sequence-independent manner. Ligands with phosphorothioate (PS) backbones induce the formation of large TLR9–DNA aggregates, possibly due to the propensity of PS ligands to self-associate. DNA curvature-inducing proteins including high-mobility group box 1 and histones H2A and H2B significantly enhance TLR9 binding, suggesting that TLR9 preferentially recognizes curved DNA backbones. Our work sheds light on the molecular mechanism of TLR9 activation by endogenous protein–nucleic acid complexes, which are associated with autoimmune diseases including systemic lupus erythematosus. PMID:22258621

  15. Jumping sequences

    E-print Network

    Butler, Steve; Zang, Nan

    2008-01-01

    An integer sequence a(n) is called a jump sequence if a(1)=1 and 1=2. Such a sequence has the property that a^k(n)=a(a(...(a(n))...)) goes to 1 in finitely many steps and we call the pattern (n,a(n),a^2(n),...,a^k(n)=1) a jumping pattern from n down to 1. In this paper we look at jumping sequences which are weight minimizing with respect to various weight functions (where a weight w(i,j) is given to each jump from j down to i). Our main result is to show that if w(i,j)=(i+j)/i^2 then the cost minimizing jump sequence has the property that the number m satisfies m=a^q(p) for arbitrary q and some p (depending on q) if and only if m is a Pell number.

  16. Oligomerization and aggregation of bovine pancreatic ribonuclease A: backbone hydration probed by infrared band-shift.

    PubMed

    Zhang, Jun; Yan, Yong-Bin

    2008-01-01

    Protein hydration plays a crucial role in almost all aspects of biomolecular processes. In this research, we studied the hydration/dehydration-induced infrared amide I band-shift by using poly-L-lysine and bovine pancreas ribonuclease A as model polypeptides. It was found that a 1-4 cm(-1) shift could be clearly distinguished for all regular secondary structures during protein thermal unfolding. This shift was proven to be due to backbone hydration but not from experimental error, temperature effect or possible incomplete hydrogen/deuterium exchange of the samples. Moreover, we also found that protein aggregation was closely associated with the backbone hydration/dehydration status of proteins. In conditions favoring aggregation, a significant shift to a higher wavenumber of the band from the intermolecular beta-sheet structures in aggregates was observed. The present study suggested that the changes of the amounts of regular secondary structures could be monitored by the intensity changes, while the changes of the hydration status could be monitored by the shift of the infrared bands. PMID:18782058

  17. Generation of Transgenic Drosophila Expressing shRNAs in the miR-1 Backbone

    PubMed Central

    Chang, Kenneth; Marran, Krista; Valentine, Amy; Hannon, Gregory J.

    2015-01-01

    In Drosophila, long-term effects of RNA interference (RNAi) must be achieved by integrating into the genome a template from which an RNAi trigger is transcribed by cellular RNA polymerases, generally RNA polymerase II or III. With encoded triggers, not only can essentially permanent silencing be achieved, but control can also be exerted over the level of trigger expression, with a resulting variation in the degree to which the target is silenced. Knockdown can also be controlled in a temporal and cell-type-dependent fashion through the use of well-established transgenic methodologies and well-tested promoters. The forms of encoded triggers vary. Long double-stranded RNAs can be expressed as extended inverted repeats. The nearest equivalent of a small interfering RNA is an artificial microRNA (miRNA) or short hairpin RNA (shRNA), where a natural miRNA backbone (also called a scaffold) is remodeled to produce a different small RNA or a small inverted repeat (<30 nucleotides) is simply expressed. This protocol describes creation of transgenic Drosophila carrying shRNA inserts in a remodeled endogenous miRNA backbone. The protocol applies to the use of miRNA-based shRNAs, but most of the vectors, principles of experimental design, and methods are also applicable to long inverted repeat transgenes. PMID:24786506

  18. Backbone Model of an Aquareovirus Virion by Cryo-Electron Microscopy and Bioinformatics

    PubMed Central

    Cheng, Lingpeng; Zhu, Jiang; Hui, Wong Hoi; Zhang, Xiaokang; Honig, Barry; Fang, Qin; Zhou, Z. Hong

    2010-01-01

    Grass carp reovirus (GCRV) is a member of the aquareovirus genus in the Reoviridae family and has a capsid with two shells—a transcription-competent core surrounded by a coat. We report a near-atomic-resolution reconstruction of the GCRV virion by cryo-electron microscopy and single-particle reconstruction. A backbone model of the GCRV virion, including seven conformers of the five capsid proteins making up the 1500 molecules in both the core and the coat, was derived using cryo-electron microscopy density-map-constrained homology modeling and refinement. Our structure clearly showed that the amino-terminal segment of core protein VP3B forms an ~120-Å-long ?-helix-rich extension bridging across the icosahedral 2-fold-symmetry-related molecular interface. The presence of this unique structure across this interface and the lack of an external cementing molecule at this location in GCRV suggest a stabilizing role of this extended amino-terminal density. Moreover, part of this amino-terminal extension becomes invisible in the reconstruction of transcription-competent core particles, suggesting its involvement in endogenous viral RNA transcription. Our structure of the VP1 turret represents its open state, and comparison with its related structures at the closed state suggests hinge-like domain movements associated with the mRNA-capping machinery. Overall, this first backbone model of an aquareovirus virion provides a wealth of structural information for understanding the structural basis of GCRV assembly and transcription. PMID:20036256

  19. Efficient delivery of RNAi prodrugs containing reversible charge-neutralizing phosphotriester backbone modifications.

    PubMed

    Meade, Bryan R; Gogoi, Khirud; Hamil, Alexander S; Palm-Apergi, Caroline; van den Berg, Arjen; Hagopian, Jonathan C; Springer, Aaron D; Eguchi, Akiko; Kacsinta, Apollo D; Dowdy, Connor F; Presente, Asaf; Lönn, Peter; Kaulich, Manuel; Yoshioka, Naohisa; Gros, Edwige; Cui, Xian-Shu; Dowdy, Steven F

    2014-12-01

    RNA interference (RNAi) has great potential to treat human disease. However, in vivo delivery of short interfering RNAs (siRNAs), which are negatively charged double-stranded RNA macromolecules, remains a major hurdle. Current siRNA delivery has begun to move away from large lipid and synthetic nanoparticles to more defined molecular conjugates. Here we address this issue by synthesis of short interfering ribonucleic neutrals (siRNNs) whose phosphate backbone contains neutral phosphotriester groups, allowing for delivery into cells. Once inside cells, siRNNs are converted by cytoplasmic thioesterases into native, charged phosphodiester-backbone siRNAs, which induce robust RNAi responses. siRNNs have favorable drug-like properties, including high synthetic yields, serum stability and absence of innate immune responses. Unlike siRNAs, siRNNs avidly bind serum albumin to positively influence pharmacokinetic properties. Systemic delivery of siRNNs conjugated to a hepatocyte-specific targeting domain induced extended dose-dependent in vivo RNAi responses in mice. We believe that siRNNs represent a technology that will open new avenues for development of RNAi therapeutics. PMID:25402614

  20. Antibacterial Studies of Cationic Polymers with Alternating, Random and Uniform Backbones

    PubMed Central

    Song, Airong; Walker, Stephen G.; Parker, Kathlyn A.; Sampson, Nicole S.

    2011-01-01

    Antibacterial polymers have potential as pharmaceuticals and as coatings for implantation devices. The design of these materials will be optimized when we have a complete understanding of the structural features that impart activity toward target organisms and those that are benign with respect to the mammalian host. In this work, four series of polymers in which cationic and hydrophobic groups were distributed along the backbone were tested against six different bacterial species (both Gram positive and Gram negative) and for host cytotoxicities (red blood cell lysis). The most effective of the polymers studied are regularly spaced, featuring a 6–8 carbon stretch along the backbone between side chains that present positively charged groups. They cause potassium efflux, disorder the bacterial cytoplasmic membrane, and disrupt the membrane potential. These polymers, available from alternating ring opening metathesis polymerization (AROMP), offer proof of principle for the importance of regular spacing in antibacterial polymers and for the synthesis of additional functional materials based on regularly spaced scaffolds. PMID:21370918

  1. Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

    DOE PAGESBeta

    Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; Karplus, P. Andrew

    2014-09-01

    Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common usage today have been designed based on the assumption that each type of bond or angle has a single ideal value independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and as a first step toward using such information to build more accurate models, ultra-high resolution protein crystal structures have been used to derive a conformation-dependent library (CDL)more »of restraints for the protein backbone (Berkholz et al. 2009. Structure. 17, 1316). Here, we report the introduction of this CDL into the Phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the conformation dependent library yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In Phenix usage of the CDL can be selected by simply specifying the cdl=True option. This successful implementation paves the way for further aspects of the context-dependence of ideal geometry to be characterized and applied to improve experimental and predictive modelling accuracy.« less

  2. Di-Isocyanate Crosslinked Aerogels with 1, 6-Bis (Trimethoxysilyl) Hexane Incorporated in Silica Backbone

    NASA Technical Reports Server (NTRS)

    Vivod, Stephanie L.; Meador, Mary Ann B.; Nguyen, Baochau N.; Quade, Derek; Randall, Jason; Perry, Renee

    2008-01-01

    Silica aerogels are desirable materials for many applications that take advantage of their light weight and low thermal conductivity. Addition of a conformal polymer coating which bonds with the amine decorated surface of the silica network improves the strength of the aerogels by as much as 200 times. Even with vast improvement in strength they still tend to undergo brittle failure due to the rigid silica backbone. We hope to increase the flexibility and elastic recovery of the silica based aerogel by altering the silica back-bone by incorporation of more flexible hexane links. To this end, we investigated the use of 1,6-bis(trimethoxysilyl)hexane (BTMSH), a polysilsesquioxane precursor3, as an additional co-reactant to prepare silica gels which were subsequently cross-linked with di-isocyanate. Previously, this approach of adding flexibility by BTMSH incorporation was demonstrated with styrene cross-linked aerogels. In our study, we varied silane concentration, mol % of silicon from BTMSH and di-isocyanate concentration by weight percent to attempt to optimize both the flexibility and the strength of the aerogels.

  3. Supramolecular Organization of the Repetitive Backbone Unit of the Streptococcus pneumoniae Pilus

    PubMed Central

    Spraggon, Glen; Koesema, Eric; Scarselli, Maria; Malito, Enrico; Biagini, Massimiliano; Norais, Nathalie; Emolo, Carla; Barocchi, Michèle Anne; Giusti, Fabiola; Hilleringmann, Markus; Rappuoli, Rino; Lesley, Scott; Covacci, Antonello; Masignani, Vega; Ferlenghi, Ilaria

    2010-01-01

    Streptococcus pneumoniae, like many other Gram-positive bacteria, assembles long filamentous pili on their surface through which they adhere to host cells. Pneumococcal pili are formed by a backbone, consisting of the repetition of the major component RrgB, and two accessory proteins (RrgA and RrgC). Here we reconstruct by transmission electron microscopy and single particle image reconstruction method the three dimensional arrangement of two neighbouring RrgB molecules, which represent the minimal repetitive structural domain of the native pilus. The crystal structure of the D2-D4 domains of RrgB was solved at 1.6 Å resolution. Rigid-body fitting of the X-ray coordinates into the electron density map enabled us to define the arrangement of the backbone subunits into the S. pneumoniae native pilus. The quantitative fitting provide evidence that the pneumococcal pilus consists uniquely of RrgB monomers assembled in a head-to-tail organization. The presence of short intra-subunit linker regions connecting neighbouring domains provides the molecular basis for the intrinsic pilus flexibility. PMID:20559564

  4. Phosphorylation-induced changes in backbone dynamics of the dematin headpiece C-terminal domain

    PubMed Central

    Vugmeyster, Liliya; McKnight, C. James

    2009-01-01

    Dematin is an actin-binding protein abundant in red blood cells and other tissues. It contains a villin-type `headpiece' F-actin-binding domain at its extreme C-terminus. The isolated dematin headpiece domain (DHP) undergoes a significant conformational change upon phosphorylation. The mutation of Ser74 to Glu closely mimics the phosphorylation of DHP. We investigated motions in the backbone of DHP and its mutant DHPS74E using several complementary NMR relaxation techniques: laboratory frame 15N NMR relaxation, which is sensitive primarily to the ps–ns time scale, cross-correlated chemical shift modulation NMR relaxation detecting correlated ?s–ms time scale motions of neighboring 13C? and 15N nuclei, and cross-correlated relaxation of two 15N–1H dipole–dipole interactions detecting slow motions of backbone NH vectors in successive amino acid residues. The results indicate a reduction in mobility upon the mutation in several regions of the protein. The additional salt bridge formed in DHPS74E that links the N- and C-terminal subdomains is likely to be responsible for these changes. PMID:19030997

  5. Backbone and benzoyl mustard carrying moiety modifies DNA interactions of distamycin analogues.

    PubMed Central

    Ciucci, A; Manzini, S; Lombardi, P; Arcamone, F

    1996-01-01

    Alkylating distamycin derivative FCE-24517 (l) is the prototype of a novel class of alkylating agents. In the present study we have investigated the effect of further chemical modifications introduced in the alkylating distamycin-derived molecule with the aim of improving their ability to bind DNA. The new compound, MEN 10710 (II), has a four pyrrolecarboxamide backbone linked at its N-terminus and through a butanamido residue to a 4-[bis(chloroethyl)amino]phenyl moiety. We have demonstrated that the presence of the flexible trimethylene chain confers to the novel distamycin derivative a peculiar mode of interaction with DNA as compared with I or melphalan. In fact, interstrand cross-links are detected in DNA samples treated even with low concentrations of II (being 200-fold more efficient than melphalan) but not with I. Similar results were obtained with a related compound of II containing a three pyrrole ring backbone. Compound II induces a conformational change in the DNA structure as deduced from the inhibition of T4 DNA ligase activity. In alkylation experiments, unlike melphalan, both I and II induce DNA breaks at bases closely located to AT-rich tracts, however II was more potent than I in producing greater amount of covalent adducts. These data suggest that the new compound shows a different and peculiar mechanism of interaction with DNA. PMID:8628655

  6. Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

    DOE PAGESBeta

    Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.; Karplus, P. Andrew

    2014-09-01

    Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common usage today have been designed based on the assumption that each type of bond or angle has a single ideal value independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and as a first step toward using such information to build more accurate models, ultra-high resolution protein crystal structures have been used to derive a conformation-dependent library (CDL) of restraints for the protein backbone (Berkholz et al. 2009. Structure. 17, 1316). Here, we report the introduction of this CDL into the Phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the conformation dependent library yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In Phenix usage of the CDL can be selected by simply specifying the cdl=True option. This successful implementation paves the way for further aspects of the context-dependence of ideal geometry to be characterized and applied to improve experimental and predictive modelling accuracy.

  7. Combination cytotoxicity of backbone degradable HPMA copolymer gemcitabine and platinum conjugates toward human ovarian carcinoma cells

    PubMed Central

    Duangjai, Acharaporn; Luo, Kui; Zhou, Yan; Yang, Jiyuan; Kope?ek, Jind?ich

    2014-01-01

    Multiblock, backbone degradable HPMA copolymer-drug conjugates containing gemcitabine and DACH platinum (mP-GEM and mP-DACH Pt), respectively were synthesized by reversible addition fragmentation (RAFT) polymerization and subsequent chain extension by click chemistry. Using combination index analysis, the cytotoxicities of the two multiblock conjugates, as single agents and in combination, were evaluated in vitro in A2780 human ovarian cancer cells, with free drugs as controls. The greatest synergistic cytotoxic effect was observed when A2780 cells were sequentially exposed to mP-GEM for 24 h and mP-DACH Pt for 48 h. In addition, mechanistic studies support the rationale of the synergy between mP-GEM and mP-DACH Pt: mP-GEM pretreatment was able to enhance the platinum-DNA adduct accumulation and inhibit cell proliferation to a higher extent than single mPDACH Pt treatment. These observations are useful for the development of combination macromolecular therapeutics for ovarian cancer based on the second-generation backbone degradable HPMA copolymers. PMID:24316339

  8. Highly stable alkaline polymer electrolyte based on a poly(ether ether ketone) backbone.

    PubMed

    Han, Juanjuan; Peng, Hanqing; Pan, Jing; Wei, Ling; Li, Guangwei; Chen, Chen; Xiao, Li; Lu, Juntao; Zhuang, Lin

    2013-12-26

    Alkaline polymer electrolyte fuel cells (APEFCs) promise the use of nonprecious metal catalysts and thus have attracted much research attention in the recent decade. Among the challenges of developing practical APEFC technology, the chemical stability of alkaline polymer electrolytes (APEs) seems to be rather difficult. Research found that, upon attachment of a cationic functional group, an originally stable polymer backbone, such as polysulfone (PSF), would degrade in an alkaline environment. In the present work, we try to employ poly(ether ether ketone) (PEEK), a very inert engineering plastic, as the backbone of APEs. The PEEK is functionalized with both a sulfonic acid (SA) group and a quaternary ammonia (QA) group, with the latter as the majority amount. Ionic cross-linking between SA and QA has rendered the thus-obtained membrane (xQAPEEK) with high mechanical strength and low swelling degree. More importantly, the xQAPEEK membrane exhibits outstanding stability in a 1 mol/L KOH solution at 80 °C for a test period of 30 days: the total weight loss of xQAPEEK is only 6 wt %, in comparison to a large degradation of quaternary ammonia PSF (more than 40 wt %) under the same conditions. Our findings not only have demonstrated an effective approach to preparing PEEK-based APE but also cast a new light on the development of highly stable APEs for fuel-cell application. PMID:24229363

  9. Wavelength division multiplexed add/drop ring technology in corporate backbone networks

    NASA Astrophysics Data System (ADS)

    Bona, Gian-Luca; Denzel, Wolfgang; Offrein, Bert J.; Germann, Roland; Salemink, Huub W.; Horst, Folkert

    1998-12-01

    The Corporate Optical Backbone Network (COBNET) project is a joint research project within the ACTS program of the European Commission. The COBNET consortium is considering the use of advanced optical networking technologies for the backbones of future corporate networks. In particular, multichannel add/drop ring networks based on wavelength division multiplexing (WDM) as well as on optical space- division multiplexing technologies are being pursued. An overview is given of the system concept, the device technology, and the demonstration network that was developed within COBNET. The WDM ring option and specifically the related add/drop devices are focused on in more detail. These devices are fabricated in a newly developed high- refractive-index contrast planar silica-on-silicon technology by using silicon-oxynitride as the core waveguide material. Compact add/drop components based on the resonant coupler concept are realized. The filter characteristic can be tailored and tuned by thermo-optic heaters, which enables the selection of any given wavelength out of a series of wavelengths from the WDM ring using the same device.

  10. BEST-HNN and 2D-(HN)NH experiments for rapid backbone assignment in proteins.

    PubMed

    Kumar, Dinesh; Paul, Subhradip; Hosur, Ramakrishna V

    2010-05-01

    HNN has proven to be an extremely valuable experiment for rapid and unambiguous backbone (H(N), (15)N) assignment in ((13)C, (15)N) labeled proteins. However, low sensitivity of the experiment is often a limiting factor, especially when the transverse relaxation times (T(2)) are short. We show here that BEST modification Schanda et al. (2006) [2] increases the sensitivity per unit time by more than a factor of 2.0 and thus substantially increases the speed of data collection; good 3D data can be collected in 8-10h. Next, we present a simple method for amino-acid type identification based on simple 2D versions of the HNN experiment, labeled here as 2D-(HN)NH. Each of these experiments which produce anchor points for Gly, Ala, Ser/Thr residues, can be recorded in less than an hour. These enable rapid data acquisition, rapid analysis, and consequently rapid assignment of backbone (H(N), (15)N) resonances. The 2D-(HN)NH experiment does not involve aliphatic/aromatic protons and hence can be applied to deuterated protein samples as well, which is an additional advantage. The experiments have been demonstrated with human ubiquitin (76 aa) and acetic-acid denatured HIV-1 protease (99 aa), as representatives of folded and unfolded protein systems, respectively. PMID:20236846

  11. BEST-HNN and 2D-(HN) NH experiments for rapid backbone assignment in proteins

    NASA Astrophysics Data System (ADS)

    Kumar, Dinesh; Paul, Subhradip; Hosur, Ramakrishna V.

    2010-05-01

    HNN has proven to be an extremely valuable experiment for rapid and unambiguous backbone (H N, 15N) assignment in ( 13C, 15N) labeled proteins. However, low sensitivity of the experiment is often a limiting factor, especially when the transverse relaxation times ( T2) are short. We show here that BEST modification Schanda et al. (2006) [2] increases the sensitivity per unit time by more than a factor of 2.0 and thus substantially increases the speed of data collection; good 3D data can be collected in 8-10 h. Next, we present a simple method for amino-acid type identification based on simple 2D versions of the HNN experiment, labeled here as 2D-(HN) NH. Each of these experiments which produce anchor points for Gly, Ala, Ser/Thr residues, can be recorded in less than an hour. These enable rapid data acquisition, rapid analysis, and consequently rapid assignment of backbone (H N, 15N) resonances. The 2D-(HN) NH experiment does not involve aliphatic/aromatic protons and hence can be applied to deuterated protein samples as well, which is an additional advantage. The experiments have been demonstrated with human ubiquitin (76 aa) and acetic-acid denatured HIV-1 protease (99 aa), as representatives of folded and unfolded protein systems, respectively.

  12. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

    PubMed

    Wilburn, Damien B; Bowen, Kathleen E; Doty, Kari A; Arumugam, Sengodagounder; Lane, Andrew N; Feldhoff, Pamela W; Feldhoff, Richard C

    2014-01-01

    In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique adaptation may establish new paradigms for how receptor:ligand pairs co-evolve, in particular with respect to sexual conflict. PMID:24849290

  13. Structural Insights into the Evolution of a Sexy Protein: Novel Topology and Restricted Backbone Flexibility in a Hypervariable Pheromone from the Red-Legged Salamander, Plethodon shermani

    PubMed Central

    Wilburn, Damien B.; Bowen, Kathleen E.; Doty, Kari A.; Arumugam, Sengodagounder; Lane, Andrew N.; Feldhoff, Pamela W.; Feldhoff, Richard C.

    2014-01-01

    In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions – such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake “three-finger” topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique adaptation may establish new paradigms for how receptor:ligand pairs co-evolve, in particular with respect to sexual conflict. PMID:24849290

  14. Helium-abundance and other composition effects on the properties of stellar surface convection in solar-like main-sequence stars

    SciTech Connect

    Tanner, Joel D.; Basu, Sarbani; Demarque, Pierre [Department of Astronomy, Yale University, P.O. Box 208101, New Haven, CT 06520-8101 (United States)

    2013-12-01

    We investigate the effect of helium abundance and ?-element enhancement on the properties of convection in envelopes of solar-like main-sequence stars using a grid of three-dimensional radiation hydrodynamic simulations. Helium abundance increases the mean molecular weight of the gas and alters opacity by displacing hydrogen. Since the scale of the effect of helium may depend on the metallicity, the grid consists of simulations with three helium abundances (Y = 0.1, 0.2, 0.3), each with two metallicities (Z = 0.001, 0.020). We find that changing the helium mass fraction generally affects structure and convective dynamics in a way opposite to that of metallicity. Furthermore, the effect is considerably smaller than that of metallicity. The signature of helium differs from that of metallicity in the manner in which the photospheric velocity distribution is affected. We also find that helium abundance and surface gravity behave largely in similar ways, but differ in the way they affect the mean molecular weight. A simple model for spectral line formation suggests that the bisectors and absolute Doppler shifts of spectral lines depend on the helium abundance. We look at the effect of ?-element enhancement and find that it has a considerably smaller effect on the convective dynamics in the superadiabatic layer compared to that of helium abundance.

  15. sequence quality values Sanger sequencing

    E-print Network

    Borenstein, Elhanan

    phred sequence quality values #12;Sanger sequencing · DNA is fragmented · Cloned to a plasmid concept of phred quality values #12;Phred Qualities )(log10 10 pq -= · p=error probability for the base · if p=0.01 (1% chance of error), then q=20 · Phred quality values are rounded to the nearest integer #12

  16. Recurrence Sequences

    NSDL National Science Digital Library

    Everest, Graham.

    A book on recurrence sequences, an advanced topic in number theory, can be downloaded from this site. It deals mainly with linear recurrence sequences, and provides extensive theory, methods, and equations. While the material is quite complex, it has applications for various disciplines. The authors state, "these sequences appear almost everywhere in mathematics and computer science." The book is in draft form, and will be featured in the Surveys and Monographs series of the American Mathematical Society sometime in 2003. Until then, however, the book can be accessed here for the purpose of correcting any errors.

  17. Thermoplastic copolyimides and composites therefrom

    NASA Technical Reports Server (NTRS)

    Harris, Frank (Inventor); Gabori, Patricia A. (Inventor)

    1994-01-01

    Copolyimide compositions and methods for their preparation which are melt-processible at relative low pressures, i.e. less than 1000 psi, and are suited for laminating and molding, are described. The invention additionally encompasses copolyimide precursors, reinforced polyimide composites and laminates made from said polyimides where the composite is reinforced by fibrous materials. This is achieved by reacting at least one aromatic dianhydride where each anhydride group is located on an aromatic ring with the carbonyl units in an ortho orientation relative to one another, with at least one diamine which is capable of a transmidization reaction upon incorporation into the polyimide backbone, and with at least one other diamine which is not capable of undergoing such reaction, the diamine which is capable of undergoing the transimidization reaction being present in an amount of from about 1-50 mole percent in relation to the diamine that is not susceptable to transimidization.

  18. Electron Transfer Dissociation Reveals Changes in the Cleavage Frequencies of Backbone Bonds Distant to Amide-to-Ester Substitutions in Polypeptides

    NASA Astrophysics Data System (ADS)

    Hansen, Thomas A.; Jung, Hye R.; Kjeldsen, Frank

    2011-11-01

    Interrogation of electron transfer dissociation (ETD) mass spectra of peptide amide-to-ester backbone bond substituted analogues (depsipeptides) reveals substantial differences in the entire backbone cleavage frequencies. It is suggested that the point permutation of backbone bonds leads to changes in the predominant ion structures by removal/weakening of specific hydrogen bonding. ETD responds to these changes by redistributing the cleavage frequencies of the peptide backbone bonds. In comparison, no distinction between depsi-/peptide was observed using collision-activated dissociation, which is consistent with a general unfolding and elimination of structural information of these ions. These results should encourage further exploration of depsipeptides for gas-phase structural characterization.

  19. Solution structure and backbone dynamics of human epidermal-type fatty acid-binding protein (E-FABP).

    PubMed Central

    Gutiérrez-González, Luis H; Ludwig, Christian; Hohoff, Carsten; Rademacher, Martin; Hanhoff, Thorsten; Rüterjans, Heinz; Spener, Friedrich; Lücke, Christian

    2002-01-01

    Human epidermal-type fatty acid-binding protein (E-FABP) belongs to a family of intracellular 14-15 kDa lipid-binding proteins, whose functions have been associated with fatty acid signalling, cell growth, regulation and differentiation. As a contribution to understanding the structure-function relationship, we report in the present study features of its solution structure and backbone dynamics determined by NMR spectroscopy. Applying multi-dimensional high-resolution NMR techniques on unlabelled and 15N-enriched recombinant human E-FABP, the 1H and 15N resonance assignments were completed. On the basis of 2008 distance restraints, the three-dimensional solution structure of human E-FABP was subsequently obtained (backbone atom root-mean-square deviation of 0.92+/-0.11 A; where 1 A=0.1 nm), consisting mainly of 10 anti-parallel beta-strands that form a beta-barrel structure. 15N relaxation experiments (T1, T2 and heteronuclear nuclear Overhauser effects) at 500, 600 and 800 MHz provided information on the internal dynamics of the protein backbone. Nearly all non-terminal backbone amide groups showed order parameters S(2)>0.8, with an average value of 0.88+/-0.04, suggesting a uniformly low backbone mobility in the nanosecond-to-picosecond time range. Moreover, hydrogen/deuterium exchange experiments indicated a direct correlation between the stability of the hydrogen-bonding network in the beta-sheet structure and the conformational exchange in the millisecond-to-microsecond time range. The features of E-FABP backbone dynamics elaborated in the present study differ markedly from those of the phylogenetically closely related heart-type FABP and the more distantly related ileal lipid-binding protein, implying a strong interdependence with the overall protein stability and possibly also with the ligand-binding affinity for members of the lipid-binding protein family. PMID:12049637

  20. An effective approach for alleviating cation-induced backbone degradation in aromatic ether-based alkaline polymer electrolytes.

    PubMed

    Han, Juanjuan; Liu, Qiong; Li, Xueqi; Pan, Jing; Wei, Ling; Wu, Ying; Peng, Hanqing; Wang, Ying; Li, Guangwei; Chen, Chen; Xiao, Li; Lu, Juntao; Zhuang, Lin

    2015-02-01

    Aromatic ether-based alkaline polymer electrolytes (APEs) are one of the most popular types of APEs being used in fuel cells. However, recent studies have demonstrated that upon being grafted by proximal cations some polar groups in the backbone of such APEs can be attacked by OH(-), leading to backbone degradation in an alkaline environment. To resolve this issue, we performed a systematic study on six APEs. We first replaced the polysulfone (PS) backbone with polyphenylsulfone (PPSU) and polyphenylether (PPO), whose molecular structures contain fewer polar groups. Although improved stability was seen after this change, cation-induced degradation was still obvious. Thus, our second move was to replace the ordinary quaternary ammonia (QA) cation, which had been closely attached to the polymer backbone, with a pendant-type QA (pQA), which was linked to the backbone through a long side chain. After a stability test in a 1 mol/L KOH solution at 80 °C for 30 days, all pQA-type APEs (pQAPS, pQAPPSU, and pQAPPO) exhibited as low as 8 wt % weight loss, which is close to the level of the bare backbone (5 wt %) and remarkably lower than those of the QA-type APEs (QAPS, QAPPSU, and QAPPO), whose weight losses under the same conditions were >30%. The pQA-type APEs also possessed clear microphase segregation morphology, which led to ionic conductivities that were higher, and water uptakes and degrees of membrane swelling that were lower, than those of the QA-type APEs. These observations unambiguously indicate that designing pendant-type cations is an effective approach to increasing the chemical stability of aromatic ether-based APEs. PMID:25594224

  1. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

    E-print Network

    2011-01-01

    plants have large and complex genomes with an abundance of repeated sequences.plants have large and complex genomes with a great abundance of repeated sequences.Sequence composition, organization, and evolution of the core Triticeae genome. Plant

  2. EMSCOPE - Electromagnetic Component of EarthScope Backbone and Transportable Array Experiments 2006-2008

    NASA Astrophysics Data System (ADS)

    Egbert, G.; Evans, R.; Ingate, S.; Livelybrooks, D.; Mickus, K.; Park, S.; Schultz, A.; Unsworth, M.; Wannamaker, P.

    2007-12-01

    USArray (http://www.iris.edu/USArray) in conjunction with EMSOC (Electromagnetic Studies of the Continents) (http://emsoc.ucr.edu/emsoc) is installing magnetotelluric (MT) stations as part of Earthscope. The MT component of Earthscope consists of permanent (Backbone) and transportable long period stations to record naturally occurring, time varying electric and magnetic fields to produce a regional lithospheric/asthensospheric electrical conductivity map of the United States. The recent arrival of 28 long period MT instruments allows for the final installation of the Backbone stations throughout the US and yearly transportable array studies. The Backbone MT survey consists of 7 stations spaced throughout the continental US with preliminary installation at Soap Creek, Oregon; Parkfield, California; Braden, Missouri and Socorro, New Mexico.Siting and permitting are underway or completed at stations in eastern Montana, northern Wisconsin and Virginia. These stations will be recording for at least five years to determine electrical conductivities at depths that extend into the mantle transition zone. The first transportable array experiment was performed in the summer and fall of 2006 in central and eastern Oregon (Oregon Pilot Project) using equipment loaned from EMSOC. Thirty-one long period MT stations were recorded with 14 to 21 day occupations. Preliminary 3D inverse models indicate several lithospheric electrical conductivity anomalies including a linear zone marked by low-high conductivity transition along the Klamath-Blue Mountain Lineament associated with a linear trend of gravity minima. High electrical conductivity values occur in the upper crust under the accreted terrains in the Blue Mountains region. The second transportable array experiment was performed in the summer and fall of 2007 and completes coverage of the Oregon, Washington, and western Idaho, targeting the Cascadia subduction zone, Precambrian boundaries, and sub-basalt lithologies. The 2008 transportable MT experiment will focus on the Snake River Plain and the Yellowstone Hot Spot. The disposition of future USArray magnetotelluric geotransects will be the subject of an upcoming NSF-supported planning workshop. Time series are available now from the IRIS data center (www.iris.edu/data), and magnetotelluric transfer functions will soon be available.

  3. Backbone and side chain dynamics of uncomplexed human adipocyte and muscle fatty acid-binding proteins.

    PubMed

    Constantine, K L; Friedrichs, M S; Wittekind, M; Jamil, H; Chu, C H; Parker, R A; Goldfarb, V; Mueller, L; Farmer, B T

    1998-06-01

    Adipocyte lipid-binding protein (A-LBP) and muscle fatty acid-binding protein (M-FABP) are members of a family of small ( approximately 15 kDa) cytosolic proteins that are involved in the metabolism of fatty acids and other lipid-soluble molecules. Although highly homologous (65%) and structurally very similar, A-LBP and M-FABP display distinct ligand binding characteristics. Since ligand binding may be influenced by intrinsic protein dynamical properties, we have characterized the backbone and side chain dynamics of uncomplexed (apo) human A-LBP and M-FABP. Backbone dynamics were characterized by measurements of 15N T1 and T2 values and ¿1H¿-15N NOEs. These data were analyzed using model-free spectral density functions and reduced spectral density mapping. The dynamics of methyl-containing side chains were charaterized by measurements of 2H T1 and T1rho relaxation times of 13C1H22H groups. The 2H relaxation data were analyzed using the model-free approach. For A-LBP, 15N relaxation data were obtained for 111 residues and 2H relaxation data were obtained for 42 methyl groups. For M-FABP, 15N relaxation data were obtained for 111 residues and 2H relaxation data were obtained for 53 methyl groups. The intrinsic flexibilities of these two proteins are compared, with particular emphasis placed on binding pocket residues. There are a number of distinct dynamical differences among corresponding residues between the two proteins. In particular, many residues display greater backbone picosecond to nanosecond and/or microsecond to millisecond time scale mobility in A-LBP relative to M-FABP, including F57, K58, and most residues in alpha-helix 2 (residues 28-35). Variations in the dynamics of this region may play a role in ligand selectivity. The side chains lining the fatty acid binding pocket display a wide range of motional restriction in both proteins. Side chains showing distinct dynamical differences between the two proteins include those of residues 20, 29, and 51. This information provides a necessary benchmark for determining dynamical changes induced by ligand binding and may ultimately lead to an enhanced understanding of ligand affinity and selectivity among fatty acid-binding proteins. PMID:9609689

  4. Verifying liveness properties of multifunction composite protocols

    Microsoft Academic Search

    Jun-cheol Park

    2003-01-01

    In protocol composition techniques, component protocols are combined in various ways to obtain a complex protocol whose execution sequences consist of interleaved execution sequences of the component protocols. In this paper, we investigate the problem of verifying liveness properties of the composite protocol from the known properties of its components. We first characterize a class of composite protocols that encompasses

  5. Monolignol ferulate transferase introduces chemically labile linkages into the lignin backbone.

    PubMed

    Wilkerson, C G; Mansfield, S D; Lu, F; Withers, S; Park, J-Y; Karlen, S D; Gonzales-Vigil, E; Padmakshan, D; Unda, F; Rencoret, J; Ralph, J

    2014-04-01

    Redesigning lignin, the aromatic polymer fortifying plant cell walls, to be more amenable to chemical depolymerization can lower the energy required for industrial processing. We have engineered poplar trees to introduce ester linkages into the lignin polymer backbone by augmenting the monomer pool with monolignol ferulate conjugates. Herein, we describe the isolation of a transferase gene capable of forming these conjugates and its xylem-specific introduction into poplar. Enzyme kinetics, in planta expression, lignin structural analysis, and improved cell wall digestibility after mild alkaline pretreatment demonstrate that these trees produce the monolignol ferulate conjugates, export them to the wall, and use them during lignification. Tailoring plants to use such conjugates during cell wall biosynthesis is a promising way to produce plants that are designed for deconstruction. PMID:24700858

  6. Extensive Air Showers: from the muonic smoking guns to the hadronic backbone

    E-print Network

    L. Cazon

    2013-01-15

    Extensive Air Showers are complex macroscopic objects initiated by single ultra-high energy particles. They are the result of millions of high energy reactions in the atmosphere and can be described as the superposition of hadronic and electromagnetic cascades. The hadronic cascade is the air shower backbone, and it is mainly made of pions. Decays of neutral pions initiate electromagnetic cascades, while the decays of charged pions produce muons which leave the hadronic core and travel many kilometers almost unaffected. Muons are smoking guns of the hadronic cascade: the energy, transverse momentum, spatial distribution and depth of production are key to reconstruct the history of the air shower. In this work, we overview the phenomenology of muons on the air shower and its relation to the hadronic cascade. We briefly review the experimental efforts to analyze muons within air showers and discuss possible paths to use this information.

  7. Synthesis and backbone conformations of cyclic hexapeptides cyclo-(Xxx-Pro-D-Gln)2.

    PubMed

    Kopple, K D; Parameswaran, K N

    1983-03-01

    The solution syntheses of cyclo-(Xxx-Pro-D-Gln)2, where Xxx = Gly, Ala, Leu, Phe and Val are described. Several routes were examined, the most successful involving the intermediate Z-Xxx-Pro-D-Gln-O-tBu and proceeding to cyclization of H-Xxx-Pro-D-Gln-Xxx-Pro-D-Gln-OH using diphenylphosphoryl azide. The N--H regions of the proton magnetic resonance spectra of aqueous solutions of these peptides were examined, and in the Xxx = Leu and Val peptides an unsymmetrical backbone, presumably with one cis Xxx-Pro peptide bond, was found to be important. Previous reports of cyclo-(Xxx-Pro-D-Yyy)2 peptides have shown only C2-symmetric forms. PMID:6853028

  8. Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants

    PubMed Central

    2014-01-01

    Background Chaining is a major problem in constructing gene families. Results We define a new kind of cluster on graphs with strong and weak edges: soft cliques with backbones (SCWiB). This differs from other definitions in how it controls the "chaining effect", by ensuring clusters satisfy a tolerant edge density criterion that takes into account cluster size. We implement algorithms for decomposing a graph of similarities into SCWiBs. We compare examples of output from SCWiB and the Markov Cluster Algorithm (MCL), and also compare some curated Arabidopsis thaliana gene families with the results of automatic clustering. We apply our method to 44 published angiosperm genomes with annotation, and discover that Amborella trichopoda is distinct from all the others in having substantially and systematically smaller proportions of moderate- and large-size gene families. Conclusions We offer several possible evolutionary explanations for this result. PMID:25572777

  9. The optimization issues in an agile all-photonic backbone network

    NASA Astrophysics Data System (ADS)

    Zhang, Yiming; Yang, Oliver W.; Zhai, Yihua

    2005-02-01

    The Agile All-photonic Backbone Network (AAPN) architecture has been proposed by the telecommunication industry as a potential candidate for the ultra high speed Next Generation Optical Network (NGON) architecture. AAPN network structure is composed of adaptive optical core switches and edge routers in an overlaid star physical topology. In this paper, we examine various optimization issues for AAPN architectures. The optimization procedure is based on a Lagrangean relaxation and subgradient method. Based on the optimization methodology provided in the previous research, we propose a modified algorithm to optimize AAPN networks, with respect to the assumptions used in AAPN. The results for different network configurations are studied and the influence of network resources is also studied. Our algorithm is shown to be very computational effective on the AAPN networks, and the bounds generated are mostly within 1% of the final objective value.

  10. Facile backbone structure determination of human membrane proteins by NMR spectroscopy

    PubMed Central

    Klammt, Christian; Maslennikov, Innokentiy; Bayrhuber, Monika; Eichmann, Cédric; Vajpai, Navratna; Chiu, Ellis Jeremy Chua; Blain, Katherine Y; Esquivies, Luis; Kwon, June Hyun Jung; Balana, Bartosz; Pieper, Ursula; Sali, Andrej; Slesinger, Paul A; Kwiatkowski, Witek; Riek, Roland; Choe, Senyon

    2013-01-01

    Although nearly half of today’s major pharmaceutical drugs target human integral membrane proteins (hIMPs), only 30 hIMP structures are currently available in the Protein Data Bank, largely owing to inefficiencies in protein production. Here we describe a strategy for the rapid structure determination of hIMPs, using solution NMR spectroscopy with systematically labeled proteins produced via cell-free expression. We report new backbone structures of six hIMPs, solved in only 18 months from 15 initial targets. Application of our protocols to an additional 135 hIMPs with molecular weight <30 kDa yielded 38 hIMPs suitable for structural characterization by solution NMR spectroscopy without additional optimization. PMID:22609626

  11. Side chain and backbone contributions of Phe508 to CFTR folding

    SciTech Connect

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  12. Efficient use of pseudo-noise sequences in synchronous direct-sequence spread-spectrum multiple-access communication systems

    Microsoft Academic Search

    Chi-Kin Chan; Wong-Hing Lam

    1994-01-01

    In this paper, four different spreading schemes have been employed in a synchronous direct-sequence spread-spectrum multiple-access systems (S-DS\\/SSMA) over a Gaussian channel. These include different sets of pseudo-noise (PN) sequences, composite sequences, bit-scrambling on PN sequences and PN sequences as error-correction coding. The bit-error-rate (BER) performance of these schemes showed that the orthogonal sets of sequences is optimal for S-DS\\/SSMA

  13. An avian live attenuated master backbone for potential use in epidemic and pandemic influenza vaccines.

    PubMed

    Hickman, Danielle; Hossain, Md Jaber; Song, Haichen; Araya, Yonas; Solórzano, Alicia; Perez, Daniel R

    2008-11-01

    The unprecedented emergence in Asia of multiple avian influenza virus (AIV) subtypes with a broad host range poses a major challenge in the design of vaccination strategies that are both effective and available in a timely manner. The present study focused on the protective effects of a genetically modified AIV as a source for the preparation of vaccines for epidemic and pandemic influenza. It has previously been demonstrated that a live attenuated AIV based on the internal backbone of influenza A/Guinea fowl/Hong Kong/WF10/99 (H9N2), called WF10att, is effective at protecting poultry species against low- and high-pathogenicity influenza strains. More importantly, this live attenuated virus provided effective protection when administered in ovo. In order to characterize the WF10att backbone further for use in epidemic and pandemic influenza vaccines, this study evaluated its protective effects in mice. Intranasal inoculation of modified attenuated viruses in mice provided adequate protective immunity against homologous lethal challenges with both the wild-type influenza A/WSN/33 (H1N1) and A/Vietnam/1203/04 (H5N1) viruses. Adequate heterotypic immunity was also observed in mice vaccinated with modified attenuated viruses carrying H7N2 surface proteins. The results presented in this report suggest that the internal genes of a genetically modified AIV confer similar protection in a mouse model and thus could be used as a master donor strain for the generation of live attenuated vaccines for epidemic and pandemic influenza. PMID:18931063

  14. 40-Gbps optical backbone network deep packet inspection based on FPGA

    NASA Astrophysics Data System (ADS)

    Zuo, Yuan; Huang, Zhiping; Su, Shaojing

    2014-11-01

    In the era of information, the big data, which contains huge information, brings about some problems, such as high speed transmission, storage and real-time analysis and process. As the important media for data transmission, the Internet is the significant part for big data processing research. With the large-scale usage of the Internet, the data streaming of network is increasing rapidly. The speed level in the main fiber optic communication of the present has reached 40Gbps, even 100Gbps, therefore data on the optical backbone network shows some features of massive data. Generally, data services are provided via IP packets on the optical backbone network, which is constituted with SDH (Synchronous Digital Hierarchy). Hence this method that IP packets are directly mapped into SDH payload is named POS (Packet over SDH) technology. Aiming at the problems of real time process of high speed massive data, this paper designs a process system platform based on ATCA for 40Gbps POS signal data stream recognition and packet content capture, which employs the FPGA as the CPU. This platform offers pre-processing of clustering algorithms, service traffic identification and data mining for the following big data storage and analysis with high efficiency. Also, the operational procedure is proposed in this paper. Four channels of 10Gbps POS signal decomposed by the analysis module, which chooses FPGA as the kernel, are inputted to the flow classification module and the pattern matching component based on TCAM. Based on the properties of the length of payload and net flows, buffer management is added to the platform to keep the key flow information. According to data stream analysis, DPI (deep packet inspection) and flow balance distribute, the signal is transmitted to the backend machine through the giga Ethernet ports on back board. Practice shows that the proposed platform is superior to the traditional applications based on ASIC and NP.

  15. Building (1 - ?) Dominating Sets Partition as Backbones in Wireless Sensor Networks Using Distributed Graph Coloring

    NASA Astrophysics Data System (ADS)

    Mahjoub, Dhia; Matula, David W.

    We recently proposed in [19,20] to use sequential graph coloring as a systematic algorithmic method to build (1 - ?) dominating sets partition in Wireless Sensor Networks (WSN) modeled as Random Geometric Graphs (RGG). The resulting partition of the network into dominating and almost dominating sets can be used as a series of rotating backbones in a WSN to prolong the network lifetime for the benefit of various applications. Graph coloring algorithms in RGGs offer proven constant approximation guarantees on the chromatic number. In this paper, we demonstrate that by combining a local vertex ordering with the greedy color selection strategy, we can in practice, minimize the number of colors used to color an RGG within a very narrow window of the chromatic number and concurrently also obtain a domatic partition size within a competitive factor of the domatic number. We also show that the minimal number of colors results in the first (? + 1) color classes being provably dense enough to form independent sets that are (1 - ?) dominating. The resulting first (? + 1) independent sets, where ? is the minimum degree of the graph, are shown to cover typically over 99% of the nodes (e.g. ?< 0.01), with at least 20% being fully dominating. These independent sets are subsequently made connected through virtual links using localized proximity rules to constitute planar connected backbones. The novelty of this paper is that we extend our recent work in [20] into the distributed setting and present an extensive experimental evaluation of known distributed coloring algorithms to answer the (1 - ?) dominating sets partition problem. These algorithms are both topology and geometry-based and yield O(1) times the chromatic number. They are also shown to be inherently localized with running times in O(?) where ? is the maximum degree of the graph.

  16. Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins

    E-print Network

    Shaw, David E.

    Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD folding, molecular recognition, and catalysis.4 Values of S2 obtained from protein molecular dynamics (MD

  17. A Dexterous System for Laryngeal Surgery Multi-Backbone Bending Snake-like Slaves for Teleoperated Dexterous Surgical Tool Manipulation

    E-print Network

    Simaan, Nabil

    ]), serial-link robots with passive joints [3], and mini-parallel robots (e.g., [4], [5]). Further examples early experiment with a prototype of the snake-like unit. Keywords- NiTi, multy backbone robot, snake robots, surgical assistant, master-slave mode. I. INTRODUCTION This paper reports our work to develop

  18. Pearl-necklace structures of molecular brushes with rigid backbone under poor solvent conditions: A simulation study

    E-print Network

    Theodorakis, Panagiotis E.

    Pearl-necklace structures of molecular brushes with rigid backbone under poor solvent conditions structure of "pearl-necklace" type is formed. The "pearls," however, have a strongly nonspherical ellipsoidal shape, due to the fact that several side chains cluster together in one pearl, qualitatively

  19. Numerical modeling and Hardware-in-the-Loop simulation of undersea networks, ocean observatories and offshore communications backbones

    Microsoft Academic Search

    Andrew M. Clark; Donna M. Kocak; Ken Martindale; Adrian Woodroffe

    2009-01-01

    This paper discusses the importance of taking a systems engineering approach when designing undersea networks, ocean observatories and offshore communications backbones. A design that utilizes modular components and systems, and places diligence in modeling and testing communications, power and data bandwidth requirements is essential for sustained operation and economic feasibility. An example is the modular seafloor communications network described -

  20. On the consequences of side chain flexibility and backbone conformation on hydration and proton dissociation in perfluorosulfonic acid membranes

    E-print Network

    Elliott, James

    dissociation in perfluorosulfonic acid membranes Stephen J. Paddison*a and James A. Elliottb Received 14th in the backbone on hydration and proton transfer in the short-side-chain (SSC) perfluorosulfonic acid fuel cell of the terminal sulfonic acids with the water. These electronic structure calculations show that the fragments

  1. IEEE/ACM TRANSACTIONS ON NETWORKING, VOL. 18, NO. 5, OCTOBER 2010 1599 Optical Packet Buffers for Backbone Internet Routers

    E-print Network

    Ganjali, Yashar

    for Backbone Internet Routers Neda Beheshti, Graduate Student Member, IEEE, Emily Burmeister, Member, IEEE McKeown, Fellow, IEEE Abstract--If optical routers are to become reality, we will need several new buffers for routers is daunting: Today's electronic routers often hold millions of packets, which is well

  2. Two-dimensional NMR spectroscopy reveals cation-triggered backbone degradation in polysulfone-based anion exchange membranes.

    PubMed

    Arges, Christopher G; Ramani, Vijay

    2013-02-12

    Anion exchange membranes (AEMs) find widespread applications as an electrolyte and/or electrode binder in fuel cells, electrodialysis stacks, flow and metal-air batteries, and electrolyzers. AEMs exhibit poor stability in alkaline media; their degradation is induced by the hydroxide ion, a potent nucleophile. We have used 2D NMR techniques to investigate polymer backbone stability (as opposed to cation stability) of the AEM in alkaline media. We report the mechanism behind a peculiar, often-observed phenomenon, wherein a demonstrably stable polysulfone backbone degrades rapidly in alkaline solutions upon derivatization with alkaline stable fixed cation groups. Using COSY and heteronuclear multiple quantum correlation spectroscopy (2D NMR), we unequivocally demonstrate that the added cation group triggers degradation of the polymer backbone in alkaline via quaternary carbon hydrolysis and ether hydrolysis, leading to rapid failure. This finding challenges the existing perception that having a stable cation moiety is sufficient to yield a stable AEM and emphasizes the importance of the often ignored issue of backbone stability. PMID:23335629

  3. Application of REDOR subtraction for filtered MAS observation of labeled backbone carbons of membrane-bound fusion peptides

    E-print Network

    Weliky, David

    Application of REDOR subtraction for filtered MAS observation of labeled backbone carbons December 2001; revised 5 August 2002 Abstract Clean MAS observation of 13 C-labeled carbons in membrane-echo double-resonance spectroscopy (REDOR) is one of the most widely used magic angle spinning (MAS) NMR

  4. Empirical Study of a National-Scale Distributed Intrusion Detection System: Backbone-Level Filtering of HTML Responses in China

    Microsoft Academic Search

    Jong Chun Park; Jedidiah R. Crandall

    2010-01-01

    We present results from measurements of the filtering of HTTP HTML responses in China, which is based on string matching and TCP reset injection by backbone-level routers. This system, intended mainly for Internet censorship, is a national-scale filter based on intrusion detection system (IDS) technologies. Our results indicate that the Chinese censors discontinued this HTML response filtering for the majority

  5. Exploring the correlation between the sequence composition of the nucleotide binding G5 loop of the FeoB GTPase domain (NFeoB) and intrinsic rate of GDP release

    PubMed Central

    Guilfoyle, Amy P.; Deshpande, Chandrika N.; Schenk, Gerhard; Maher, Megan J.; Jormakka, Mika

    2014-01-01

    GDP release from GTPases is usually extremely slow and is in general assisted by external factors, such as association with guanine exchange factors or membrane-embedded GPCRs (G protein-coupled receptors), which accelerate the release of GDP by several orders of magnitude. Intrinsic factors can also play a significant role; a single amino acid substitution in one of the guanine nucleotide recognition motifs, G5, results in a drastically altered GDP release rate, indicating that the sequence composition of this motif plays an important role in spontaneous GDP release. In the present study, we used the GTPase domain from EcNFeoB (Escherichia coli FeoB) as a model and applied biochemical and structural approaches to evaluate the role of all the individual residues in the G5 loop. Our study confirms that several of the residues in the G5 motif have an important role in the intrinsic affinity and release of GDP. In particular, a T151A mutant (third residue of the G5 loop) leads to a reduced nucleotide affinity and provokes a drastically accelerated dissociation of GDP. PMID:25374115

  6. Composition of the summer photosynthetic pico and nanoplankton communities in the Beaufort Sea assessed by T-RFLP and sequences of the 18S rRNA gene from flow cytometry sorted samples

    PubMed Central

    Balzano, Sergio; Marie, Dominique; Gourvil, Priscillia; Vaulot, Daniel

    2012-01-01

    The composition of photosynthetic pico and nanoeukaryotes was investigated in the North East Pacific and the Arctic Ocean with special emphasis on the Beaufort Sea during the MALINA cruise in summer 2009. Photosynthetic populations were sorted using flow cytometry based on their size and pigment fluorescence. Diversity of the sorted photosynthetic eukaryotes was determined using terminal-restriction fragment length polymorphism analysis and cloning/sequencing of the 18S ribosomal RNA gene. Picoplankton was dominated by Mamiellophyceae, a class of small green algae previously included in the prasinophytes: in the North East Pacific, the contribution of an Arctic Micromonas ecotype increased steadily northward becoming the only taxon occurring at most stations throughout the Beaufort Sea. In contrast, nanoplankton was more diverse: North Pacific stations were dominated by Pseudo-nitzschia sp. whereas those in the Beaufort Sea were dominated by two distinct Chaetoceros species as well as by Chrysophyceae, Pelagophyceae and Chrysochromulina spp.. This study confirms the importance of Arctic Micromonas within picoplankton throughout the Beaufort Sea and demonstrates that the photosynthetic picoeukaryote community in the Arctic is much less diverse than at lower latitudes. Moreover, in contrast to what occurs in warmer waters, most of the key pico- and nanoplankton species found in the Beaufort Sea could be successfully established in culture. PMID:22278671

  7. Sequencing Time

    NSDL National Science Digital Library

    2007-12-12

    In this activity, students gain an understanding of relative and numerical time by placing events in sequence and assigning relative times to the events. This will familarize them with the methods used by scientists to develop the geologic time scale. This activity contains objectives, materials, procedure, and extensions.

  8. Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities

    NASA Astrophysics Data System (ADS)

    Lu, Bing-Sui; Naji, Ali; Podgornik, Rudolf

    2015-06-01

    We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each polymer has a quenched-in polarizability sequence which reflects, for example, the polynucleotide sequence of a double-stranded DNA molecule, we study the van der Waals interaction energy between a pair of such polymers with rod-like structure for the cases where their respective polarizability sequences are (i) distinct and (ii) identical, with both zero and non-zero correlation length of the polarizability correlator along the polymer backbones in the latter case. For identical polymers, we find a novel r-5 scaling behavior of the van der Waals interaction energy for small inter-polymer separation r, in contradistinction to the r-4 scaling behavior of distinct polymers, with furthermore a pronounced angular dependence favoring attraction between sufficiently aligned identical polymers. Such behavior can assist the molecular recognition between polymers.

  9. Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities.

    PubMed

    Lu, Bing-Sui; Naji, Ali; Podgornik, Rudolf

    2015-06-01

    We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each polymer has a quenched-in polarizability sequence which reflects, for example, the polynucleotide sequence of a double-stranded DNA molecule, we study the van der Waals interaction energy between a pair of such polymers with rod-like structure for the cases where their respective polarizability sequences are (i) distinct and (ii) identical, with both zero and non-zero correlation length of the polarizability correlator along the polymer backbones in the latter case. For identical polymers, we find a novel r(-5) scaling behavior of the van der Waals interaction energy for small inter-polymer separation r, in contradistinction to the r(-4) scaling behavior of distinct polymers, with furthermore a pronounced angular dependence favoring attraction between sufficiently aligned identical polymers. Such behavior can assist the molecular recognition between polymers. PMID:26049521

  10. Solution studies of staphylococcal nuclease H124L. 1. Backbone sup 1 H and sup 15 N resonances and secondary structure of the unligated enzyme as identified by three-dimensional NMR spectroscopy

    SciTech Connect

    Wang, Jinfeng; Mooberry, E.S.; Walkenhorst, W.F.; Markley, J.L. (Univ. of Wisconsin, Madison (United States))

    1992-01-28

    The backbone {sup 1}H and {sup 15}N resonances of unligated staphylococcal nuclease H124L (recombinant protein produced in Escherichia coli whose sequence is identical to the nuclease produced by the V8 strain of Staphylococcus aureus) have been assigned by three-dimensional (3D) {sup 1}H-{sup 15}N NOESY-HMQC NMR spectroscopy at 14.1 tesla. The protein sample used in this study was labeled uniformly with {sup 15}N to a level greater than 95% by growing the E. coli host on a medium containing (99% {sup 15}N)ammonium sulfate as the sole nitrogen source. The assignments include 82% of the backbone {sup 1}H{sup N} and {sup 1}H{sup {alpha}} resonances as well as the {sup 15}N resonances of non-proline residues. Secondary structural elements ({alpha}-helices, {beta}-sheets, reverse turns, and loops) were determined by analysis of patterns of NOE connectivities present in the 3D spectrum.

  11. Nucleotide sequence of pOLA52: a conjugative IncX1 plasmid from Escherichia coli which enables biofilm formation and multidrug efflux.

    PubMed

    Norman, Anders; Hansen, Lars Hestbjerg; She, Qunxin; Sørensen, Søren Johannes

    2008-07-01

    The large conjugative multidrug resistance (MDR) plasmid pOLA52 was sequenced and annotated. The plasmid encodes two phenotypes normally associated with the chromosomes of opportunistic pathogens, namely MDR via a resistance-nodulation-division (RND)-type efflux-pump (oqxAB), and the formation of type 3 fimbriae (mrkABCDF). The plasmid was found to be 51,602 bp long with 68 putative genes. About half of the plasmid constituted a conserved IncX1-type backbone with predicted regions for conjugation, replication and partitioning, as well as a toxin/antitoxin (TA) plasmid addiction system. The plasmid was also classified as IncX1 with incompatibility testing. The conjugal transfer and plasmid maintenance regions of pOLA52 therefore seem to represent IncX1 orthologues of the well-characterized IncX2 plasmid R6K. Sequence homology searches in GenBank also suggested a considerably higher prevalence of IncX1 group plasmids than IncX2. The 21 kb 'genetic load' region of pOLA52 was shown to consist of a mosaic, among other things a fragmented Tn3 transposon encoding ampicillin resistance. Most notably the oqxAB and mrkABCDF cassettes were contained within two composite transposons (Tn6010 and Tn6011) that seemed to originate from Klebsiella pneumoniae, thus demonstrating the capability of IncX1 plasmids of facilitating lateral transfer of gene cassettes between different Enterobacteriaceae. PMID:18440636

  12. A Proof Technique for Liveness Properties of Multifunction Composite Protocols

    Microsoft Academic Search

    Jun-Cheol Park; R. E. Miller

    1998-01-01

    In protocol composition techniques, component protocols are combined in various ways to obtain a complex protocol whose execution sequences consist of interleaved execution sequences of the component protocols. We investigate the problem of verifying liveness properties of the composite protocol from the known properties of its components. We first characterize a class of composition techniques that encompasses almost all composition

  13. MSLICE Sequencing

    NASA Technical Reports Server (NTRS)

    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.

  14. Complete DNA sequence of yeast chromosome XI

    Microsoft Academic Search

    B. Dujon; D. Alexandraki; B. André; W. Ansorge; V. Baladron; J. P. G. Ballesta; A. Banrevi; P. A. Bolle; M. Bolotin-Fukuhara; P. Bossier; G. Bou; J. Boyer; M. J. Buitrago; G. Cherét; L. Colleaux; B. Dalgnan-Fornier; F. Del Rey; C. Dion; H. Domdey; A. Düsterhöft; S. Düsterhus; K.-D. Entian; H. Erfle; P. F. Esteban; H. Feldmann; L. Fernandes; G. M. Fobo; C. Fritz; H. Fukuhara; C. Gabel; L. Gaillon; J. M. Carcia-Cantalejo; J. J. Garcia-Ramirez; M. E. Gent; M. Ghazvini; A. Goffeau; A. Gonzaléz; D. Grothues; P. Guerreiro; J. Hegemann; N. Hewitt; F. Hilger; C. P. Hollenberg; O. Horaitis; K. J. Indge; A. Jacquier; C. M. James; J. C. Jauniaux; A. Jimenez; H. Keuchel; L. Kirchrath; K. Kleine; P. Kötter; P. Legrain; S. Liebl; E. J. Louis; A. Maia E Silva; C. Marck; A.-L. Monnier; D. Möstl; S. Müller; B. Obermaier; S. G. Oliver; C. Pallier; S. Pascolo; F. Pfeiffer; P. Philippsen; R. J. Planta; F. M. Pohl; T. M. Pohl; R. Pöhlmann; D. Portetelle; B. Purnelle; V. Puzos; M. Ramezani Rad; S. W. Rasmussen; M. Remacha; J. L. Revuelta; G.-F. Richard; M. Rieger; C. Rodrigues-Pousada; M. Rose; T. Rupp; M. A. Santos; C. Schwager; C. Sensen; J. Skala; H. Soares; F. Sor; J. Stegemann; H. Tettelin; A. Thierry; M. Tzermia; L. A. Urrestarazu; L. van Dyck; J. C. van Vliet-Reedijk; M. Valens; M. Vandenbo; C. Vilela; S. Vissers; D. von Wettstein; H. Voss; S. Wiemann; G. Xu; J. Zimmermann; M. Haasemann; I. Becker; H. W. Mewes

    1994-01-01

    The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined. In addition to a compact arrangement of potential protein coding sequences, the 666,448-base-pair sequence has revealed general chromosome patterns; in particular, alternating regional variations in average base composition correlate with variations in local gene density along the chromosome. Significant discrepancies with the previously published genetic map

  15. Insertion Sequences

    PubMed Central

    Mahillon, Jacques; Chandler, Michael

    1998-01-01

    Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

  16. Paucity of moderately repetitive sequences

    SciTech Connect

    Schmid, C.W.

    1991-01-01

    We examined clones of renatured repetitive human DNA to find novel repetitive DNAs. After eliminating known repeats, the remaining clones were subjected to sequence analysis. These clones also corresponded to known repeats, but with greater sequence diversity. This indicates that either these libraries were depleted of short interspersed repeats in construction, or these repeats are much less prevalent in the human genome than is indicated by data from {und Xenopus} or sea urchin studies. We directly investigated the sequence composition of human DNA through traditional renaturation techniques with the goal of estimating the limits of abundance of repetitive sequence classes in human DNA. Our results sharply limit the maximum possible abundance to 1--2% of the human genome. Our estimate, minus the known repeats in this fraction, leaves about 1% (3 {times} 10{sup 7} nucleotides) of the human genome for novel repetitive elements. 2 refs. (MHB)

  17. Backbone and side-chain cleavages in electron detachment dissociation (EDD).

    PubMed

    Anusiewicz, Iwona; Jasionowski, Marek; Skurski, Piotr; Simons, Jack

    2005-12-15

    Ab-initio electronic structure methods are used to explore potential energy profiles pertinent to the fragmentations of gas-phase radicals thought to be formed in the new negative-ion mode EDD mass spectroscopic studies of peptides. Barriers to fragmentation as well as the associated overall energy differences are computed for the observed Calpha-C backbone bond cleavage as well as for side-chain loss for a variety of side chains (valine, arginine, glutamic acid, and tyrosine). It is found that Calpha-C bond cleavage is favored over side-chain loss, although loss of a tyrosine side chain may compete with Calpha-C cleavage because the tyrosine radical formed can delocalize its unpaired electron over its aromatic ring. In addition, it is found that fragmentation of the nitrogen-centered radicals formed in EDD results in cleavage to produce so-called a*/x fragments rather than a/x* fragments both because producing the former involves a significantly smaller barrier and is nearly thermoneutral, while cleavage to yield a/x* is significantly endothermic. PMID:16331920

  18. Mechanics and chemistry: single molecule bond rupture forces correlate with molecular backbone structure.

    PubMed

    Frei, Michael; Aradhya, Sriharsha V; Koentopp, Max; Hybertsen, Mark S; Venkataraman, L

    2011-04-13

    We simultaneously measure conductance and force across nanoscale junctions. A new, two-dimensional histogram technique is introduced to statistically extract bond rupture forces from a large data set of individual junction elongation traces. For the case of Au point contacts, we find a rupture force of 1.4 ± 0.2 nN, which is in good agreement with previous measurements. We then study systematic trends for single gold metal-molecule-metal junctions for a series of molecules terminated with amine and pyridine linkers. For all molecules studied, single molecule junctions rupture at the Au-N bond. Selective binding of the linker group allows us to correlate the N-Au bond-rupture force to the molecular backbone. We find that the rupture force ranges from 0.8 nN for 4,4' bipyridine to 0.5 nN in 1,4 diaminobenzene. These experimental results are in excellent quantitative agreement with density functional theory based adiabatic molecular junction elongation and rupture calculations. PMID:21366230

  19. Backbone Trace of Partitivirus Capsid Protein from Electron Cryomicroscopy and Homology Modeling

    PubMed Central

    Tang, Jinghua; Pan, Junhua; Havens, Wendy M.; Ochoa, Wendy F.; Guu, Tom S.Y.; Ghabrial, Said A.; Nibert, Max L.; Tao, Yizhi Jane; Baker, Timothy S.

    2010-01-01

    Abstract Most dsRNA viruses have a genome-enclosing capsid that comprises 120 copies of a single coat protein (CP). These 120 CP subunits are arranged as asymmetrical dimers that surround the icosahedral fivefold axes, forming pentamers of dimers that are thought to be assembly intermediates. This scheme is violated, however, in recent structures of two dsRNA viruses, a fungal virus from family Partitiviridae and a rabbit virus from family Picobirnaviridae, both of which have 120 CP subunits organized as dimers of quasisymmetrical dimers. In this study, we report the CP backbone trace of a second fungal partitivirus, determined in this case by electron cryomicroscopy and homology modeling. This virus also exhibits quasisymmetrical CP dimers that are connected by prominent surface arches and stabilized by domain swapping between the two CP subunits. The CP fold is dominated by ?-helices, although ?-strands mediate several important contacts. A dimer-of-dimers assembly intermediate is again implicated. The disordered N-terminal tail of each CP subunit protrudes into the particle interior and likely interacts with the genome during packaging and/or transcription. These results broaden our understanding of conserved and variable aspects of partitivirus structure and reflect the growing use of electron cryomicroscopy for atomic modeling of protein folds. PMID:20643089

  20. Toward High Performance n-Type Thermoelectric Materials by Rational Modification of BDPPV Backbones.

    PubMed

    Shi, Ke; Zhang, Fengjiao; Di, Chong-An; Yan, Tian-Wei; Zou, Ye; Zhou, Xu; Zhu, Daoben; Wang, Jie-Yu; Pei, Jian

    2015-06-10

    Three n-type polymers BDPPV, ClBDPPV, and FBDPPV which exhibit outstanding electrical conductivities when mixed with an n-type dopant, N-DMBI ((4-(1,3-dimethyl-2,3-dihydro-1H-benzoimidazol-2-yl)phenyl)dimethylamine), in solution. High electron mobility and an efficient doping process endow FBDPPV with the highest electrical conductivities of 14 S cm(-1) and power factors up to 28 ?W m(-1) K(-2), which is the highest thermoelectric (TE) power factor that has been reported for solution processable n-type conjugated polymers. Our investigations reveal that introduction of halogen atoms to the polymer backbones has a dramatic influence on not only the electron mobilities but also the doping levels, both of which are critical to the electrical conductivities. This work suggests the significance of rational modification of polymer structures and opens the gate for applying the rapidly developed organic semiconductors with high carrier mobilities to thermoelectric field. PMID:25997085

  1. Noise assisted excitation energy transfer in a linear model of a selectivity filter backbone strand

    NASA Astrophysics Data System (ADS)

    Bassereh, Hassan; Salari, Vahid; Shahbazi, Farhad

    2015-07-01

    In this paper, we investigate the effect of noise and disorder on the efficiency of excitation energy transfer (EET) in a N=5 sites linear chain with ‘static’ dipole–dipole couplings. In fact, here, the disordered chain is a toy model for one strand of the selectivity filter backbone in ion channels. It has recently been discussed that the presence of quantum coherence in the selectivity filter is possible and can play a role in mediating ion-conduction and ion-selectivity in the selectivity filter. The question is ‘how a quantum coherence can be effective in such structures while the environment of the channel is dephasing (i.e. noisy)?’ Basically, we expect that the presence of the noise should have a destructive effect in the quantum transport. In fact, we show that such expectation is valid for ordered chains. However, our results indicate that introducing the dephasing in the disordered chains leads to the weakening of the localization effects, arising from the multiple back-scatterings due to the randomness, and then increases the efficiency of quantum energy transfer. Thus, the presence of noise is crucial for the enhancement of EET efficiency in disordered chains. We also show that the contribution of both classical and quantum mechanical effects are required to improve the speed of energy transfer along the chain. Our analysis may help for better understanding of fast and efficient functioning of the selectivity filters in ion channels.

  2. An enhanced backbone-assisted reliable framework for wireless sensor networks.

    PubMed

    Tufail, Ali; Khayam, Syed Ali; Raza, Muhammad Taqi; Ali, Amna; Kim, Ki-Hyung

    2010-01-01

    An extremely reliable source to sink communication is required for most of the contemporary WSN applications especially pertaining to military, healthcare and disaster-recovery. However, due to their intrinsic energy, bandwidth and computational constraints, Wireless Sensor Networks (WSNs) encounter several challenges in reliable source to sink communication. In this paper, we present a novel reliable topology that uses reliable hotlines between sensor gateways to boost the reliability of end-to-end transmissions. This reliable and efficient routing alternative reduces the number of average hops from source to the sink. We prove, with the help of analytical evaluation, that communication using hotlines is considerably more reliable than traditional WSN routing. We use reliability theory to analyze the cost and benefit of adding gateway nodes to a backbone-assisted WSN. However, in hotline assisted routing some scenarios where source and the sink are just a couple of hops away might bring more latency, therefore, we present a Signature Based Routing (SBR) scheme. SBR enables the gateways to make intelligent routing decisions, based upon the derived signature, hence providing lesser end-to-end delay between source to the sink communication. Finally, we evaluate our proposed hotline based topology with the help of a simulation tool and show that the proposed topology provides manifold increase in end-to-end reliability. PMID:22294890

  3. Design and Synthesis of Efficient Fluorescent Dyes for Incorporation into DNA Backbone and Biomolecule Detection

    PubMed Central

    Wang, Wei; Li, Alexander D. Q.

    2008-01-01

    We report here the design and synthesis of a series of ?-conjugated fluorescent dyes with D-A-D (D: donor; A: Acceptor), D-?-D, A-?-A, and D-?-A for applications as the signaling motif in biological-synthetic hybrid foldamers for DNA detection. Horner-Wadsworth-Emmons (HWE) reaction and Knoevenagel condensation were demonstrated as the optimum ways for construction of long ?-conjugated systems. Such rod-like chromophores have distinct advantages, as their fluorescence properties are not quenched by the presence of DNA. To be incorporated into the backbone of DNA, the chromophores need to be reasonably soluble in organic solvent for solid-phase synthesis, and therefore a strategy of using flexible tetra(ethylene glycol) (TEG) linkers at either end of these rod-like dyes were developed. The presence of TEG facilitates the protection of the chain-growing hydroxyl group with DMTrCl (dimethoxy trityl chloride) as well as the activation of the coupling step with phosphoramidite chemistry on an automated DNA synthesizer. To form fluorescence resonance energy transfer (FRET) pairs, six synthetic chromophores with blue to red fluorescence have been developed and those with orthogonal fluorescent emission were chosen for incorporation into DNA-chromophore hybrid foldamers. PMID:17508711

  4. Noise assisted excitation energy transfer in a linear model of a selectivity filter backbone strand.

    PubMed

    Bassereh, Hassan; Salari, Vahid; Shahbazi, Farhad

    2015-07-15

    In this paper, we investigate the effect of noise and disorder on the efficiency of excitation energy transfer (EET) in a [Formula: see text] sites linear chain with 'static' dipole-dipole couplings. In fact, here, the disordered chain is a toy model for one strand of the selectivity filter backbone in ion channels. It has recently been discussed that the presence of quantum coherence in the selectivity filter is possible and can play a role in mediating ion-conduction and ion-selectivity in the selectivity filter. The question is 'how a quantum coherence can be effective in such structures while the environment of the channel is dephasing (i.e. noisy)?' Basically, we expect that the presence of the noise should have a destructive effect in the quantum transport. In fact, we show that such expectation is valid for ordered chains. However, our results indicate that introducing the dephasing in the disordered chains leads to the weakening of the localization effects, arising from the multiple back-scatterings due to the randomness, and then increases the efficiency of quantum energy transfer. Thus, the presence of noise is crucial for the enhancement of EET efficiency in disordered chains. We also show that the contribution of both classical and quantum mechanical effects are required to improve the speed of energy transfer along the chain. Our analysis may help for better understanding of fast and efficient functioning of the selectivity filters in ion channels. PMID:26061758

  5. Quantitative residue-specific protein backbone torsion angle dynamics from concerted measurement of 3J couplings

    PubMed Central

    Lee, Jung Ho; Li, Fang; Grishaev, Alexander; Bax, Ad

    2015-01-01

    Three-bond 3JC?C? and 3JHNH? couplings in peptides and proteins both are functions of the intervening backbone torsion angle ?. In well ordered regions, 3JHNH? is tightly correlated with 3JC?C?, but the presence of large ? angle fluctuations differentially affects the two types of couplings. Assuming the ? angles to follow a Gaussian distribution, the width of this distribution can be extracted from 3JC?C? and 3JHNH?, as demonstrated for the folded proteins ubiquitin and GB3. In intrinsically disordered proteins, slow transverse relaxation permits measurement of 3JC?C? and 3JHNH couplings at very high precision, and impact of factors other than the intervening torsion angle on 3J will be minimal, making these couplings exceptionally valuable structural reporters. Analysis of ?-synuclein yields rather homogeneous widths of 69±6° for the ? angle distributions, and 3JC?C? values that agree well with those of a recent maximum entropy analysis of chemical shifts, J couplings, and 1H-1H NOEs. Data are consistent with a modest (? 30%) population of the polyproline II region. PMID:25590347

  6. Ionization Cross Sections and Dissociation Channels of the DNA Sugar-Phosphate Backbone by Electron Collisions

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher; Huo, Winifred M.; Fletcher, Graham D.

    2004-01-01

    It has been suggested that the genotoxic effects of ionizing radiation in living cells are not caused by the highly energetic incident radiation, but rather are induced by less energetic secondary species generated, the most abundant of which are free electrons.' The secondary electrons will further react to cause DNA damage via indirect and direct mechanisms. Detailed knowledge of these mechanisms is ultimately important for the development of global models of cellular radiation damage. We are studying one possible mechanism for the formation cf DNA strand breaks involving dissociative ionization of the DNA sugar-phosphate backbone induced by secondary electron co!lisions. We will present ionization cross sections at electron collision energies between threshold and 10 KeV using the improved binary encounter dipole (iBED) formulation' Preliminary results of the possible dissociative ionization pathways will be presented. It is speculated that radical fragments produced from the dissociative ionization can further react, providing a possible mechanism for double strand breaks and base damage.

  7. Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution.

    PubMed

    Bond, Jason E; Garrison, Nicole L; Hamilton, Chris A; Godwin, Rebecca L; Hedin, Marshal; Agnarsson, Ingi

    2014-08-01

    Spiders represent an ancient predatory lineage known for their extraordinary biomaterials, including venoms and silks. These adaptations make spiders key arthropod predators in most terrestrial ecosystems. Despite ecological, biomedical, and biomaterial importance, relationships among major spider lineages remain unresolved or poorly supported. Current working hypotheses for a spider "backbone" phylogeny are largely based on morphological evidence, as most molecular markers currently employed are generally inadequate for resolving deeper-level relationships. We present here a phylogenomic analysis of spiders including taxa representing all major spider lineages. Our robust phylogenetic hypothesis recovers some fundamental and uncontroversial spider clades, but rejects the prevailing paradigm of a monophyletic Orbiculariae, the most diverse lineage, containing orb-weaving spiders. Based on our results, the orb web either evolved much earlier than previously hypothesized and is ancestral for a majority of spiders or else it has multiple independent origins, as hypothesized by precladistic authors. Cribellate deinopoid orb weavers that use mechanically adhesive silk are more closely related to a diverse clade of mostly webless spiders than to the araneoid orb-weaving spiders that use adhesive droplet silks. The fundamental shift in our understanding of spider phylogeny proposed here has broad implications for interpreting the evolution of spiders, their remarkable biomaterials, and a key extended phenotype--the spider web. PMID:25042592

  8. Antimicrobial activity of chitosan derivatives containing N-quaternized moieties in its backbone: a review.

    PubMed

    Martins, Alessandro F; Facchi, Suelen P; Follmann, Heveline D M; Pereira, Antonio G B; Rubira, Adley F; Muniz, Edvani C

    2014-01-01

    Chitosan, which is derived from a deacetylation reaction of chitin, has attractive antimicrobial activity. However, chitosan applications as a biocide are only effective in acidic medium due to its low solubility in neutral and basic conditions. Also, the positive charges carried by the protonated amine groups of chitosan (in acidic conditions) that are the driving force for its solubilization are also associated with its antimicrobial activity. Therefore, chemical modifications of chitosan are required to enhance its solubility and broaden the spectrum of its applications, including as biocide. Quaternization on the nitrogen atom of chitosan is the most used route to render water-soluble chitosan-derivatives, especially at physiological pH conditions. Recent reports in the literature demonstrate that such chitosan-derivatives present excellent antimicrobial activity due to permanent positive charge on nitrogen atoms side-bonded to the polymer backbone. This review presents some relevant work regarding the use of quaternized chitosan-derivatives obtained by different synthetic paths in applications as antimicrobial agents. PMID:25402643

  9. Antimicrobial Activity of Chitosan Derivatives Containing N-Quaternized Moieties in Its Backbone: A Review

    PubMed Central

    Martins, Alessandro F.; Facchi, Suelen P.; Follmann, Heveline D. M.; Pereira, Antonio G. B.; Rubira, Adley F.; Muniz, Edvani C.

    2014-01-01

    Chitosan, which is derived from a deacetylation reaction of chitin, has attractive antimicrobial activity. However, chitosan applications as a biocide are only effective in acidic medium due to its low solubility in neutral and basic conditions. Also, the positive charges carried by the protonated amine groups of chitosan (in acidic conditions) that are the driving force for its solubilization are also associated with its antimicrobial activity. Therefore, chemical modifications of chitosan are required to enhance its solubility and broaden the spectrum of its applications, including as biocide. Quaternization on the nitrogen atom of chitosan is the most used route to render water-soluble chitosan-derivatives, especially at physiological pH conditions. Recent reports in the literature demonstrate that such chitosan-derivatives present excellent antimicrobial activity due to permanent positive charge on nitrogen atoms side-bonded to the polymer backbone. This review presents some relevant work regarding the use of quaternized chitosan-derivatives obtained by different synthetic paths in applications as antimicrobial agents. PMID:25402643

  10. Participation of bacteriorhodopsin active-site lysine backbone in vibrations associated with retinal photochemistry.

    PubMed Central

    Gat, Y; Grossjean, M; Pinevsky, I; Takei, H; Rothman, Z; Sigrist, H; Lewis, A; Sheves, M

    1992-01-01

    Bacteriorhodopsin (bR) has been biosynthetically prepared with lysine deuterated at its alpha carbon (C alpha--H). The labeled membranes containing bR were investigated by difference Fourier transform infrared (FTIR) spectroscopy. It has been derived from K/bR and M/bR difference spectra (K and M are photocycle intermediates) that several bands previously assigned to the retinal chromophore are coupled to the C alpha--H. The vibrational modes that exhibit this coupling are principally associated with C15--H and N--H vibrations. [C alpha--2H]Lysine-labeled bR was fragmented enzymatically, and bR structures were regenerated with the C alpha--2H label either on lysine-216 and -172 or on the remaining five lysine residues of the protein. FTIR studies of the regenerated bR system, together with methylation of all lysines except the active-site lysine, reveal that the changes observed due to backbone labeling arise from the active-site lysine. The intensity of the C15--H out-of-plane wag is interpreted as a possible indication of a twist around the C15 = N bond. PMID:1549607

  11. Mechanics and Chemistry: Sinle Molecule Bond Rupture Forces Correlate with Molecular Backbone Structure

    SciTech Connect

    Frei, M.; Hybertsen, M.; Aradhya, S.V.; Koentopp, M.; Venkataraman, L.

    2011-03-02

    We simultaneously measure conductance and force across nanoscale junctions. A new, two-dimensional histogram technique is introduced to statistically extract bond rupture forces from a large data set of individual junction elongation traces. For the case of Au point contacts, we find a rupture force of 1.4 {+-} 0.2 nN, which is in good agreement with previous measurements. We then study systematic trends for single gold metal-molecule-metal junctions for a series of molecules terminated with amine and pyridine linkers. For all molecules studied, single molecule junctions rupture at the Au-N bond. Selective binding of the linker group allows us to correlate the N-Au bond-rupture force to the molecular backbone. We find that the rupture force ranges from 0.8 nN for 4,4' bipyridine to 0.5 nN in 1,4 diaminobenzene. These experimental results are in excellent quantitative agreement with density functional theory based adiabatic molecular junction elongation and rupture calculations.

  12. Scalability issues in corporate optical backbone wavelength division multiplexing add/drop ring networks

    NASA Astrophysics Data System (ADS)

    Stavdas, A.; Bona, G. L.; Denzel, W.

    2000-10-01

    The corporate optical backbone network (COBNET) joint research project is aiming at the next generation of high-performance corporate networks based on wavelength division multiplexing (WDM) add/drop rings. Scalability considerations are of primary importance for these networks. Based on the measured spectral performance for WDM tunable add-after-drop filters fabricated in planar waveguide technology, the operational parameters of the ring network have been optimized using the bit error rates at the corresponding receivers as merit functions. With the current performance of the add-after-drop filters, a ring with three add/drop nodes, each dropping and adding a single wavelength, can be constructed. If these filters are used, a COBNET-like network will be power limited. The projected loss performance of the filters indicates that a network with five add/drop nodes is feasible. With the addition of an optical amplifier at the mid-point of the network that exactly compensates the losses in the first half of the network, the feasibility of an eight-node ring has been demonstrated.

  13. Backbone resonance assignment and order tensor estimation using residual dipolar couplings

    PubMed Central

    Shealy, Paul; Liu, Yizhou; Simin, Mikhail

    2014-01-01

    An NMR investigation of proteins with known X-ray structures is of interest in a number of endeavors. Performing these studies through nuclear magnetic resonance (NMR) requires the costly step of resonance assignment. The prevalent assignment strategy does not make use of existing structural information and requires uniform isotope labeling. Here we present a rapid and cost-effective method of assigning NMR data to an existing structure—either an X-ray or computationally modeled structure. The presented method, Exhaustively Permuted Assignment of RDCs (EPAR), utilizes unassigned residual dipolar coupling (RDC) data that can easily be obtained by NMR spectroscopy. The algorithm uses only the backbone N–H RDCs from multiple alignment media along with the amino acid type of the RDCs. It is inspired by previous work from Zweckstetter and provides several extensions. We present results on 13 synthetic and experimental datasets from 8 different structures, including two homodimers. Using just two alignment media, EPAR achieves an average assignment accuracy greater than 80%. With three media, the average accuracy is higher than 94%. The algorithm also outputs a prediction of the assignment accuracy, which has a correlation of 0.77 to the true accuracy. This prediction score can be used to establish the needed confidence in assignment accuracy. PMID:21667298

  14. Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Bathany, Katell; Owens, Neil W.; Guichard, Gilles; Schmitter, Jean-Marie

    2013-03-01

    This study is focused on sequence analysis of peptidomimetic helical oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. After the evaluation of MS/MS spectra obtained for model compounds with either MALDI or ESI sources, we found that the MALDI-TOF-TOF instrument gave more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N'H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b, and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.

  15. Sequence Matching of Images

    Microsoft Academic Search

    Nasser Yazdani; Z. Meral Özsoyoglu

    1996-01-01

    We propose an inter-sequence matching method for exact and similarity matching of image sequences. Our method transforms the image sequence matching problem into matching sequences of real numbers. The method does not require sequences to be of the same length. It uses a modified version of the longest common sequence (LCS) method for actually matching two sequences. We also propose

  16. Photoinduced bending behavior of cross-linked azobenzene liquid-crystalline polymer films with a poly(oxyethylene) backbone.

    PubMed

    Lv, Jiu-an; Wang, Weiru; Xu, Jixiang; Ikeda, Tomiki; Yu, Yanlei

    2014-07-01

    Cross-linked azobenzene liquid-crystalline polymer films with a poly(oxyethylene) backbone are synthesized by photoinitiated cationic copolymerization. Azobenzene moieties in the film surface toward the light source are simultaneously photoaligned during photopolymerization with unpolarized 436 nm light and thus form a splayed alignment in the whole film. The prepared films show reversible photoinduced bending behavior with opposite bending directions when different surfaces of one film face to ultraviolet light irradiation. PMID:24771514

  17. A QoS guaranteed Mobile IP communication scheme with scalability in terms of resource management in backbone network

    Microsoft Academic Search

    Toshihiko KATO; Wei Liu; Seiji Ueno; Shuichi ITOH

    2003-01-01

    Resulting from the spread of the Mobile Internet, mobile communication with QoS guarantees will be required in order to realize mobile video interactions. So far, there are some studies which focused on QoS guaranteed Mobile IP communication, but they require backbone routers to maintain per flow QoS information for all individual mobile nodes. These approaches suffer from a lack of

  18. Assessing side-chain perturbations of the protein backbone: a knowledge-based classification of residue Ramachandran space.

    PubMed

    Dahl, David B; Bohannan, Zach; Mo, Qianxing; Vannucci, Marina; Tsai, Jerry

    2008-05-01

    Grouping the 20 residues is a classic strategy to discover ordered patterns and insights about the fundamental nature of proteins, their structure, and how they fold. Usually, this categorization is based on the biophysical and/or structural properties of a residue's side-chain group. We extend this approach to understand the effects of side chains on backbone conformation and to perform a knowledge-based classification of amino acids by comparing their backbone phi, psi distributions in different types of secondary structure. At this finer, more specific resolution, torsion angle data are often sparse and discontinuous (especially for nonhelical classes) even though a comprehensive set of protein structures is used. To ensure the precision of Ramachandran plot comparisons, we applied a rigorous Bayesian density estimation method that produces continuous estimates of the backbone phi, psi distributions. Based on this statistical modeling, a robust hierarchical clustering was performed using a divergence score to measure the similarity between plots. There were seven general groups based on the clusters from the complete Ramachandran data: nonpolar/beta-branched (Ile and Val), AsX (Asn and Asp), long (Met, Gln, Arg, Glu, Lys, and Leu), aromatic (Phe, Tyr, His, and Cys), small (Ala and Ser), bulky (Thr and Trp), and, lastly, the singletons of Gly and Pro. At the level of secondary structure (helix, sheet, turn, and coil), these groups remain somewhat consistent, although there are a few significant variations. Besides the expected uniqueness of the Gly and Pro distributions, the nonpolar/beta-branched and AsX clusters were very consistent across all types of secondary structure. Effectively, this consistency across the secondary structure classes implies that side-chain steric effects strongly influence a residue's backbone torsion angle conformation. These results help to explain the plasticity of amino acid substitutions on protein structure and should help in protein design and structure evaluation. PMID:18377931

  19. Molecular dynamics simulations of single-component bottle-brush polymers with a flexible backbone under poor solvent conditions

    E-print Network

    Nikolaos G. Fytas; Panagiotis E. Theodorakis

    2013-06-04

    Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40 effective monomers. By variation of the solvent quality and the grafting density $\\sigma$ with which side chains are grafted onto the flexible backbone, we study for backbone lengths of up to $N_b=100$ the crossover from the brush/coil regime to the dense collapsed state. At lower temperatures, where collapsed chains with a constant monomer density are observed, the choice of the above parameters does not play any role and it is the total number of monomers that defines the dimensions of the chains. Furthermore, bottle-brush polymers with longer side chains possess higher spherical symmetry compared to chains with lower side-chain lengths in contrast to what one may intuitively expect, as the stretching of the side chains is less important than the increase of their length. At higher temperatures, always below the Theta ($\\Theta$) temperature, coil-like configurations, similar to a single polymer chain, or brush-like configurations, similar to a homogeneous cylindrical bottle-brush polymer with a rigid backbone, are observed, depending on the choice of the particular parameters $N$ and $\\sigma$. In the crossover regime between the collapsed state (globule) and the coil/brush regime the acylindricity increases, whereas for temperatures outside of this range, bottle-brush polymers maintain a highly cylindrical symmetry in all configurational states.

  20. Orbital dynamics of three-dimensional bars I. The backbone of three-dimensional bars. A fiducial case

    E-print Network

    Skokos, Charalampos "Haris"

    A B S T R AC T In this series of papers we investigate the orbital structure of three-dimensional (3D show that, in a 3D bar, the backbone of the orbital structure is not just the x1 family, as in two-dimensional support 3D bar-like structures along the minor axis of the main bar. Banana-like orbits around the stable

  1. Direct Formation of the C5?-Radical in the Sugar-Phosphate Backbone of DNA by High Energy Radiation

    PubMed Central

    Adhikary, Amitava; Becker, David; Palmer, Brian J.; Heizer, Alicia N.; Sevilla, Michael D.

    2012-01-01

    Neutral sugar radicals formed in DNA sugar-phosphate backbone are well-established as precursors of biologically important damage such as DNA-strand scission and crosslinking. In this work, we present electron spin resonance (ESR) evidence showing that the sugar radical at C5? (C5?•) is one of the most abundant (ca. 30%) sugar radicals formed by ?- and Ar ion-beam irradiated hydrated DNA samples. Taking dimethyl phosphate as a model of sugar-phosphate backbone, ESR and theoretical (DFT) studies of ?-irradiated dimethyl phosphate were carried out. CH3OP(O2?)OCH2• is formed via deprotonation from the methyl group of directly ionized dimethyl phosphate at 77 K. Formation of CH3OP(O2?)OCH2• is independent of dimethyl phosphate concentration (neat or in aqueous solution) or pH. ESR spectra of C5?• found in DNA and of CH3OP(O2?)OCH2• do not show an observable ?-phosphorous hyperfine coupling (HFC). Further, C5?• found in DNA does not show a significant C4?-H ?–proton HFC. Applying the DFT/B3LYP/6-31G(d) method, a study of conformational dependence of the phosphorous HFC in CH3OP(O2?)OCH2• shows that in its minimum energy conformation, CH3OP(O2?)OCH2• has a negligible ?-phosphorous HFC. Based on these results, formation of radiation-induced C5?• is proposed to occur via a very rapid deprotonation from the directly ionized sugar-phosphate backbone and rate of this deprotonation must be faster than that of energetically downhill transfer of the unpaired spin (hole) from ionized sugar-phosphate backbone to the DNA bases. Moreover, C5?• in irradiated DNA is found to be in a conformation that does not exhibit ? proton or ? phosphorous HFCs. PMID:22553971

  2. NMR structure determination of the Escherichia coli DnaJ molecular chaperone: secondary structure and backbone fold of the N-terminal region (residues 2-108) containing the highly conserved J domain.

    PubMed Central

    Szyperski, T; Pellecchia, M; Wall, D; Georgopoulos, C; Wüthrich, K

    1994-01-01

    DnaJ from Escherichia coli is a 376-amino acid protein that functions in conjunction with DnaK and GrpE as a chaperone machine. The N-terminal fragment of residues 2-108, DnaJ-(2-108), retains many of the activities of the full-length protein and contains a structural motif, the J domain of residues 2-72, which is highly conserved in a superfamily of proteins. In this paper, NMR spectroscopy was used to determine the secondary structure and the three-dimensional polypeptide backbone fold of DnaJ-(2-108). By using 13C/15N doubly labeled DnaJ-(2-108), nearly complete sequence-specific assignments were obtained for 1H, 15N, 13C alpha, and 13C beta, and about 40% of the peripheral aliphatic carbon resonances were also assigned. Four alpha-helices in polypeptide segments of residues 6-11, 18-31, 41-55, and 61-68 in the J domain were identified by sequential and medium-range nuclear Overhauser effects. For the J domain, the three-dimensional structure was calculated with the program DIANA from an input of 536 nuclear Overhauser effect upper-distance constraints and 52 spin-spin coupling constants. The polypeptide backbone fold is characterized by the formation of an antiparallel bundle of two long helices, residues 18-31 and 41-55, which is stabilized by a hydrophobic core of side chains that are highly conserved in homologous J domain sequences. The Gly/Phe-rich region from residues 77 to 108 is flexibly disordered in solution. Images PMID:7972061

  3. Direct measurement of the correlated dynamics of the protein-backbone and proximal waters of hydration in mechanically strained elastin

    E-print Network

    Cheng Sun; Odingo Mitchell; Jiaxin Huang; Gregory S. Boutis

    2011-04-05

    We report on the direct measurement of the correlation times of the protein backbone carbons and proximal waters of hydration in mechanically strained elastin by nuclear magnetic resonance methods. The experimental data indicate a decrease in the correlation times of the carbonyl carbons as the strain on the biopolymer is increased. These observations are in good agreement with short 4ns molecular dynamics simulations of (VPGVG)3, a well studied mimetic peptide of elastin. The experimental results also indicate a reduction in the correlation time of proximal waters of hydration with increasing strain applied to the elastomer. A simple model is suggested that correlates the increase in the motion of proximal waters of hydration to the increase in frequency of libration of the protein backbone that develops with increasing strain. Together, the reduction in the protein entropy accompanied with the increase in entropy of the proximal waters of hydration with increasing strain, support the notion that the source of elasticity is driven by an entropic mechanism arising from the change in entropy of the protein backbone.

  4. Backbone Dynamics of Alamethicin Bound to Lipid Membranes: Spin-Echo Electron Paramagnetic Resonance of TOAC-Spin Labels

    PubMed Central

    Bartucci, Rosa; Guzzi, Rita; De Zotti, Marta; Toniolo, Claudio; Sportelli, Luigi; Marsh, Derek

    2008-01-01

    Alamethicin F50/5 is a hydrophobic peptide that is devoid of charged residues and that induces voltage-dependent ion channels in lipid membranes. The peptide backbone is likely to be involved in the ion conduction pathway. Electron spin-echo spectroscopy of alamethicin F50/5 analogs in which a selected Aib residue (at position n = 1, 8, or 16) is replaced by the TOAC amino-acid spin label was used to study torsional dynamics of the peptide backbone in association with phosphatidylcholine bilayer membranes. Rapid librational motions of limited angular amplitude were observed at each of the three TOAC sites by recording echo-detected spectra as a function of echo delay time, 2?. Simulation of the time-resolved spectra, combined with conventional EPR measurements of the librational amplitude, shows that torsional fluctuations of the peptide backbone take place on the subnanosecond to nanosecond timescale, with little temperature dependence. Associated fluctuations in polar fields from the peptide could facilitate ion permeation. PMID:18096632

  5. Electron-impact total ionization cross sections of DNA sugar-phosphate backbone and an additivity principle

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.; Dateo, Christopher E.

    2005-01-01

    The improved binary-encounter dipole (iBED) model [W.M. Huo, Phys. Rev. A64, 042719-1 (2001)l is used to study the total ionization cross sections of the DNA sugar-phosphate backbone by electron impact. Calculations using neutral fragments found that the total ionization cross sections of C3' - and C5', -deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3' - and C5" -deoxyribose-phospate cross sections, differing by less than 10%. The result implies that certain properties of the-DNA, like the total singly ionization cross section, are localized properties and a building-up or additivity principle may apply. This allows us to obtain accurate properties of larger molecular systems built up from the results of smaller subsystem fragments. Calculations are underway using a negatively charged sugar-phosphate backbone with a metal counter-ion.

  6. A model of orientational ordering in phosphatidylcholine bilayers based on conformational analysis of the glycerol backbone region.

    PubMed Central

    Strenk, L M; Westerman, P W; Doane, J W

    1985-01-01

    Molecular and conformational ordering in aqueous multilamellar suspensions of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) have been examined by deuterium nuclear magnetic resonance (2H NMR) in the liquid crystalline (L alpha) phase. Motionally averaged quadrupolar splittings vQ from six sites in the vicinity of the glycerol backbone have been analyzed by a molecular frame and order matrix approach in which the usual assumption of a freely-rotating molecule is not invoked. By assuming a relatively rigid glycerol backbone region, the six vQ values are found to be consistent with a conformation of the glycerol backbone that is almost identical to that of one of the two structures in crystalline DMPC dihydrate (Pearson, R. H., and I. Pascher, 1979, Nature (Lond.) 281: 499-501). The orientation of the most-ordered axis of the DMPC molecule is found to be tilted at an angle of 27 +/- 2 degrees with respect to the long axis of the sn-1 chain in its extended all trans conformation. The ordering of the most ordered molecular axis with respect to the bilayer normal is expressed by an order parameter of Szz approximately equal to 0.6 +/- 0.1, consistent with values in analogous thermotropic liquid crystals. PMID:4074836

  7. Composite Nonwovens

    Microsoft Academic Search

    Dipayan Das; Arun Kumar Pradhan; R. Chattopadhyay; S. N. Singh

    2012-01-01

    The term ‘composite nonwovens’ refers to a category of materials different from ‘nonwoven composites’, which consist of a resinous matrix reinforced by an embedded nonwoven fabric. Many scientists would like to rename ‘composite nonwovens’ as ‘soft nonwoven composites’ and ‘nonwoven composites’ as ‘hard nonwoven composites’. Composite nonwovens are created by a modern and innovative industry employing nonwoven technologies to bring

  8. Fluoride anion binding by cyclic boronic esters: influence of backbone chelate on receptor integrity.

    PubMed

    Bresner, Christopher; Day, Joanna K; Coombs, Natalie D; Fallis, Ian A; Aldridge, Simon; Coles, Simon J; Hursthouse, Michael B

    2006-08-14

    A systematic investigation of fluoride anion binding properties as a function of chelate backbone has been carried out for ferrocene functionalised boronic esters of the types FcB(OR)2 and fc[B(OR)2]2 [Fc = ferrocenyl = (eta5-C5H5)Fe(eta5-C5H4); fc = ferrocendiyl = Fe(eta5-C5H4)2]. Cyclic boronic esters containing a saturated five- or six-membered chelate ring are readily synthesized from ferrocene, and selectively bind fluoride via Lewis acid/base chemistry in chloroform solution. The resulting complexes are characterized by relatively weak fluoride binding (e.g.K = 35.8 +/- 9.8 M(-1) for FcBO2C2H2Ph2-S,S), and by cathodic shifts in the ferrocene oxidation potential that form the basis for electrochemical or colorimetric fluoride detection. The fluoride selectivity of these systems is attributed to relatively weak Lewis acidity, resulting in weak F- binding, and essentially no binding of potentially competitive anions. By contrast, more elaborate Lewis acid frameworks based on calix[4]arene (calixH4), such as (FcB)2calix or fcB2calix, do not survive intact exposure to standard fluoride sources (e.g. [nBu4N]F.xH2O solutions in chloroform or acetonitrile). Instead B-O bond cleavage occurs yielding the parent calixarene; the differences between alkoxo- and aryloxo-functionalised derivatives can be rationalised, at least in part, by consideration of the differences in electron donating capabilities of RO- (R = alkyl, aryl). PMID:16865177

  9. Phosphorus chemical shifts in a nucleic acid backbone from combined molecular dynamics and density functional calculations.

    PubMed

    P?ececht?lová, Jana; Novák, Petr; Munzarová, Markéta L; Kaupp, Martin; Sklená?, Vladimír

    2010-12-01

    A comprehensive quantum chemical analysis of the influence of backbone torsion angles on (31)P chemical shifts in DNAs has been carried out. An extensive DFT study employed snapshots obtained from the molecular dynamics simulation of [d(CGCGAATTCGCG)]2 to construct geometries of a hydrated dimethyl phosphate, which was used as a model for the phosphodiester linkage. Our calculations provided differences of 2.1 ± 0.3 and 1.6 ± 0.3 ppm between the B(I) and B(II) chemical shifts in two B-DNA residues of interest, which is in a very good agreement with the difference of 1.6 ppm inferred from experimental data. A more negative (31)P chemical shift for a residue in pure BI conformation compared to residues in mixed B(I)/B(II) conformation states is provided by DFT, in agreement with the NMR experiment. Statistical analysis of the MD/DFT data revealed a large dispersion of chemical shifts in both B(I) and B(II) regions of DNA structures. ?P ranges within 3.5 ± 0.8 ppm in the B(I) region and within 4.5 ± 1.5 ppm in the B(II) region. While the (31)P chemical shift becomes more negative with increasing ? in B(I)-DNA, it has the opposite trend in B(II)-DNA when both ? and ? increase simultaneously. The (31)P chemical shift is dominated by the torsion angles ? and ?, while an implicit treatment of ? and ? is sufficient. The presence of an explicit solvent leads to a damping and a 2-3 ppm upfield shift of the torsion angle dependences. PMID:21073198

  10. Holoprosencephaly sequence.

    PubMed

    Colet?, Elena; Siminel, Mirela; Gheonea, Mihaela

    2011-01-01

    Holoprosencephaly (HPE) sequence is a rare spectrum of cerebral and facial malformations resulting from incomplete division of the embryonic forebrain into distinct lateral cerebral hemisphere. Three ranges of increasing severity are described: lobar, semi-lobar and alobar HPE. A subtype of HPE called middle inter-hemispheric variant (MIHF) has been also reported. The etiology is heterogeneous: teratogens, chromosomal abnormalities and single gene mutations can be involved. Holoprosencephaly results in early morbidity and mortality with a reduced survival beyond neonatal period. The disorder is estimated to occur in 1/16,000 live births. This case report presents a male new born diagnosed with holoprosencephaly, accompanied by median cleft palate, absent nasal bones and chromosomal abnormalities. PMID:21655669

  11. Inferring phylogenies of evolving sequences without multiple sequence alignment

    PubMed Central

    Chan, Cheong Xin; Bernard, Guillaume; Poirion, Olivier; Hogan, James M.; Ragan, Mark A.

    2014-01-01

    Alignment-free methods, in which shared properties of sub-sequences (e.g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference. However, the scalability and robustness of these methods to key evolutionary processes remain to be investigated. Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. We find that compared to a multiple sequence alignment approach, D2 methods are more robust against among-site rate heterogeneity, compositional biases, genetic rearrangements and insertions/deletions, but are more sensitive to recent sequence divergence and sequence truncation. Across diverse empirical datasets, the alignment-free methods perform well for sequences sharing low divergence, at greater computation speed. Our findings provide strong evidence for the scalability and the potential use of alignment-free methods in large-scale phylogenomics. PMID:25266120

  12. Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans

    Microsoft Academic Search

    Kaifu Chen; Lei Wang; Meng Yang; Jiucheng Liu; Chengqi Xin; Songnian Hu; Jun Yu

    2010-01-01

    Our recent investigation in the protist Trichomonas vaginalis suggested a DNA sequence periodicity with a unit length of 120.9 nt, which represents a sequence signature for nucleosome positioning. We now extended our observation in higher eukaryotes and identified a similar periodicity of 175 nt in length in Caenorhabditis elegans. In the process of defining the sequence compositional characteristics, we found

  13. Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences

    PubMed Central

    Sevy, Alexander M.; Jacobs, Tim M.; Crowe, James E.; Meiler, Jens

    2015-01-01

    Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a ‘single state’ design (SSD) paradigm. Multi-specificity design (MSD), on the other hand, involves considering the stability of multiple protein states simultaneously. We have developed a novel MSD algorithm, which we refer to as REstrained CONvergence in multi-specificity design (RECON). The algorithm allows each state to adopt its own sequence throughout the design process rather than enforcing a single sequence on all states. Convergence to a single sequence is encouraged through an incrementally increasing convergence restraint for corresponding positions. Compared to MSD algorithms that enforce (constrain) an identical sequence on all states the energy landscape is simplified, which accelerates the search drastically. As a result, RECON can readily be used in simulations with a flexible protein backbone. We have benchmarked RECON on two design tasks. First, we designed antibodies derived from a common germline gene against their diverse targets to assess recovery of the germline, polyspecific sequence. Second, we design “promiscuous”, polyspecific proteins against all binding partners and measure recovery of the native sequence. We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes. PMID:26147100

  14. Self-assembled peptide amphiphile nanofibers and peg composite hydrogels as tunable ECM mimetic microenvironment.

    PubMed

    Goktas, Melis; Cinar, Goksu; Orujalipoor, Ilghar; Ide, Semra; Tekinay, Ayse B; Guler, Mustafa O

    2015-04-13

    Natural extracellular matrix (ECM) consists of complex signals interacting with each other to organize cellular behavior and responses. This sophisticated microenvironment can be mimicked by advanced materials presenting essential biochemical and physical properties in a synergistic manner. In this work, we developed a facile fabrication method for a novel nanofibrous self-assembled peptide amphiphile (PA) and poly(ethylene glycol) (PEG) composite hydrogel system with independently tunable biochemical, mechanical, and physical cues without any chemical modification of polymer backbone or additional polymer processing techniques to create synthetic ECM analogues. This approach allows noninteracting modification of multiple niche properties (e.g., bioactive ligands, stiffness, porosity), since no covalent conjugation method was used to modify PEG monomers for incorporation of bioactivity and porosity. Combining the self-assembled PA nanofibers with a chemically cross-linked polymer network simply by facile mixing followed by photopolymerization resulted in the formation of porous bioactive hydrogel systems. The resulting porous network can be functionalized with desired bioactive signaling epitopes by simply altering the amino acid sequence of the self-assembling PA molecule. In addition, the mechanical properties of the composite system can be precisely controlled by changing the PEG concentration. Therefore, nanofibrous self-assembled PA/PEG composite hydrogels reported in this work can provide new opportunities as versatile synthetic mimics of ECM with independently tunable biological and mechanical properties for tissue engineering and regenerative medicine applications. In addition, such systems could provide useful tools for investigation of how complex niche cues influence cellular behavior and tissue formation both in two-dimensional and three-dimensional platforms. PMID:25751623

  15. Preserving sequence annotations across reference sequences

    PubMed Central

    2014-01-01

    Background Matching and comparing sequence annotations of different reference sequences is vital to genomics research, yet many annotation formats do not specify the reference sequence types or versions used. This makes the integration of annotations from different sources difficult and error prone. Results As part of our effort to create linked data for interoperable sequence annotations, we present an RDF data model for sequence annotation using the ontological framework established by the OBO Foundry ontologies and the Basic Formal Ontology (BFO). We defined reference sequences as the common domain of integration for sequence annotations, and identified three semantic relationships between sequence annotations. In doing so, we created the Reference Sequence Annotation to compensate for gaps in the SO and in its mapping to BFO, particularly for annotations that refer to versions of consensus reference sequences. Moreover, we present three integration models for sequence annotations using different reference assemblies. Conclusions We demonstrated a working example of a sequence annotation instance, and how this instance can be linked to other annotations on different reference sequences. Sequence annotations in this format are semantically rich and can be integrated easily with different assemblies. We also identify other challenges of modeling reference sequences with the BFO. PMID:25093075

  16. ?ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.

    PubMed

    Pasi, Marco; Maddocks, John H; Beveridge, David; Bishop, Thomas C; Case, David A; Cheatham, Thomas; Dans, Pablo D; Jayaram, B; Lankas, Filip; Laughton, Charles; Mitchell, Jonathan; Osman, Roman; Orozco, Modesto; Pérez, Alberto; Petkevi?i?t?, Daiva; Spackova, Nada; Sponer, Jiri; Zakrzewska, Krystyna; Lavery, Richard

    2014-10-29

    We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequence effects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters. PMID:25260586

  17. ?ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

    PubMed Central

    Pasi, Marco; Maddocks, John H.; Beveridge, David; Bishop, Thomas C.; Case, David A.; Cheatham, Thomas; Dans, Pablo D.; Jayaram, B.; Lankas, Filip; Laughton, Charles; Mitchell, Jonathan; Osman, Roman; Orozco, Modesto; Pérez, Alberto; Petkevi?i?t?, Daiva; Spackova, Nada; Sponer, Jiri; Zakrzewska, Krystyna; Lavery, Richard

    2014-01-01

    We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequence effects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters. PMID:25260586

  18. A NOTE ON THE COMPOSITION PRODUCT OF SYMMETRIC MICHAEL CHING

    E-print Network

    Ching, Michael

    sequences, it has enough structure, namely that of a `normal oplax' monoidal product, to be able to defineA NOTE ON THE COMPOSITION PRODUCT OF SYMMETRIC SEQUENCES MICHAEL CHING Abstract. We consider the composition product of symmetric sequences in the case where the underlying symmetric monoidal structure does

  19. Development of novel bifunctional chelating agents containing rigid cyclic hydrocarbon backbones

    SciTech Connect

    Sweet, M.P.; Joshi, V.; Mease, R.C. [Brookhaven National Laboratory, Upton, NY (United States)] [and others

    1995-05-01

    We are developing a new class of ligands in which the metal-binding polyaminocarboxylate groups are incorporated onto rigid cyclic hydrocarbon backbones. These ligands, with increased preorganization, should produce radiometal-bioconjugates with higher in-vivo stability. The synthesis of the first in this series of ligands (2,3-diaminobicyclo[2.2.2] octanetetraacetic acid, BODTA) began with a Diels-Alder reaction of 1,3-diacetylimidazolin-2-one and 1,3-cyclohexadiene. Base hydrolysis, alkylation with ethyl iodoacetate, hydrolysis of the esters, and catalytic hydrogenation gave BODTA. For conjugation to MAbs, an average of one COOH group of unsaturated BODTA was converted into an NHS ester using 0.8 equivalent of DCC. The second ligand under development is the decadentate tethered bis-cyclohexyl-EDTA (bis-CDTA) in which 2 cyclohexyl rings are tied together with an ethylene tether. Acylation of monotrityl-1,2-diaminocyclohexane with the di-NHS ester of oxalic acid, reduction of the amide moieties, and removal of the trityl groups followed by cyanomethylation has afforded a hexanitrile whose hydrolysis will produce tethered bis-CDTA. An anti-CEA F(ab{prime}){sub 2} MAb was conjugated with an average of 0.6 BODTA per MAb molecule, labeled with Co-57, and purified by size-exclusion HPLC. Stability of this radioconjugate in mouse serum at 48 h was somewhat better (2% loss) than that of the conventional DTPA-dianhydride (DTPA-DA) conjugate (8% loss). In human tumor-xenografted nude mice (LS-174T cells), tumor (T), blood (B), liver (L), and kidney (K) uptakes (% ID/g) at 24h were: TODTA, 21.6, 4.4, 4.8, 6.0; DTPA-DA, 13.6, 2.5, 5.0, 2.9. The tumor to normal tissue ratios at 48 h for BODTA and DTPA-DA respectively were: T/B, 18.0, 13.9; T/L 4.9, 2.3; T/K, 5.4, 3.9. These preliminary results show promise for using the basic BODTA structure to produce improved bioconjugates with small radiometal ions.

  20. Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design

    PubMed Central

    Varela, Rocco; Ó Conchúir, Shane; Kortemme, Tanja

    2012-01-01

    Predicting which mutations proteins tolerate while maintaining their structure and function has important applications for modeling fundamental properties of proteins and their evolution; it also drives progress in protein design. Here we develop a computational model to predict the tolerated sequence space of HIV-1 protease reachable by single mutations. We assess the model by comparison to the observed variability in more than 50,000 HIV-1 protease sequences, one of the most comprehensive datasets on tolerated sequence space. We then extend the model to a second protein, reverse transcriptase. The model integrates multiple structural and functional constraints acting on a protein and uses ensembles of protein conformations. We find the model correctly captures a considerable fraction of protease and reverse-transcriptase mutational tolerance and shows comparable accuracy using either experimentally determined or computationally generated structural ensembles. Predictions of tolerated sequence space afforded by the model provide insights into stability-function tradeoffs in the emergence of resistance mutations and into strengths and limitations of the computational model. PMID:22927804

  1. UV-driven switching of chain orientation and liquid crystal alignment in nanoscale thin films of a novel polyimide bearing stilbene moieties in the backbone.

    PubMed

    Hahm, Suk Gyu; Lee, Seung Woo; Lee, Taek Joon; Cho, Seon Ah; Chae, Boknam; Jung, Young Mee; Kim, Seung Bin; Ree, Moonhor

    2008-04-24

    A novel photosensitive polyimide, poly(4,4'-stilbenylene 4,4'-oxidiphthalimide) (ODPA-Stilbene PSPI) was newly synthesized. The most surprising feature of this PSPI is that the PSPI films irradiated with linear polarized ultraviolet light (LPUVL) can favorably induce a unidirectional alignment of liquid crystals (LCs) in contact with the film surface and further switch the director of the unidirectionally aligned LCs from a perpendicular direction to a parallel direction with respect to the polarization direction of LPUVL by simply controlling the exposure dose in the irradiation process. These LPUVL-irradiated films were found to provide high anchoring energy to LCs, always giving very stable, homogeneous cells with unidirectionally aligned LCs regardless of the LC alignment directions. In the films, the PSPI polymer chains were found to undergo favorably unidirectional orientation via a specific orientation sequence of the polymer chain segments led by the directionally selective trans-cis photoisomerization of the stilbene chromophore units in the backbone induced by LPUVL exposure. Such unidirectionally oriented polymer chains of the films induce alignment of the LCs along the orientation direction of the polymer chains via favorable anisotropic molecular interactions between the oriented polymer chain segments and the LC molecules. In addition, the PSPI has an excellent film formation processibility; good quality PSPI thin films with a smooth surface are easily produced by simple spin-coating of the soluble poly(amic acid) precursor and subsequent thermal imidization process. In summary, this new PSPI is the promising LC alignment layer candidate with rubbing-free processing for the production of advanced LC display devices, including LC display televisions with large display areas. PMID:18386867

  2. Intramolecular hydrogen atom migration along the backbone of cationic and neutral radical tripeptides and subsequent radical-induced dissociations.

    PubMed

    Zhao, Junfang; Song, Tao; Xu, Minjie; Quan, Quan; Siu, K W Michael; Hopkinson, Alan C; Chu, Ivan K

    2012-06-28

    Dissociation of peptide radical ions involves competition between charge-induced and radical-induced reactions that can be preceded by isomerization. The isomeric radical cations of the peptide methyl ester [G?GR-OMe](+) and [GG?R-OMe](+) provide very similar collision-induced dissociation (CID) spectra, suggesting that isomerization occurs prior to fragmentation. They undergo characteristic radical-induced bond cleavage of the peptide N-terminal amide bond resulting in the y2(+) ion, and of the arginine side-chain's C?-C? bond giving protonated allylguanidine {[CH2[double bond, length as m-dash]CHCH2NHC(NH2)2](+), m/z 100}. The absence of a y2(+) fragment ion in the CID of the radical cationic tripeptide [ACH3G?R](+) and of an m/z 100 ion in the spectrum of [G?ACH3R](+) (where ACH3 is an ?-aminoisobutyric acid residue, which cannot form an ?-carbon-centered radical through hydrogen atom transfer) establishes the importance of hydrogen atom migration along the peptide backbone prior to specific radical-induced fragmentations. Herein we use density functional theory (DFT) at the B3LYP/6-31++G(d,p) level to evaluate the barriers for interconversion between the ?-carbon-centered radicals and for dissociation. The radical cations [G?GR](+) and [GG?R](+) have their radicals located on the ?-carbon atoms of the peptide backbone and their charge densities largely sequestered on the guanidine groups of the side-chain of arginine residues. This is in contrast to the isomeric radical cations of [GGG]?(+), in which the charge resides necessarily on the peptide backbone. The lower charge densities on the backbones of [G?GR](+) and [GG?R](+) result in greater structural flexibility, decreasing the barrier for interconversion between these ?-carbon-centered radicals to 36.2 kcal mol(-1) (cf. 44.7 kcal mol(-1) for [GGG]?(+)). The total absence of charge, assessed by examining intramolecular hydrogen atom transfers among the three ?-carbon centers of the isomeric neutral ?-carbon-centered triglycine radicals [GGG-H]?, leads to an additional but slight reduction in enthalpy, to approximately 34 kcal mol(-1). PMID:22614151

  3. CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures.

    PubMed

    Blanchet, Christophe; Pasi, Marco; Zakrzewska, Krystyna; Lavery, Richard

    2011-07-01

    Curves+, a revised version of the Curves software for analyzing the conformation of nucleic acid structures, is now available as a web server. This version, which can be freely accessed at http://gbio-pbil.ibcp.fr/cgi/Curves_plus/, allows the user to upload a nucleic acid structure file, choose the nucleotides to be analyzed and after optionally setting a number of input variables, view the numerical and graphic results online or download files containing a set of helical, backbone and groove parameters that fully describe the structure. PDB format files are also provided for offline visualization of the helical axis and groove geometry. PMID:21558323

  4. CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

    PubMed Central

    Blanchet, Christophe; Pasi, Marco; Zakrzewska, Krystyna; Lavery, Richard

    2011-01-01

    Curves+, a revised version of the Curves software for analyzing the conformation of nucleic acid structures, is now available as a web server. This version, which can be freely accessed at http://gbio-pbil.ibcp.fr/cgi/Curves_plus/, allows the user to upload a nucleic acid structure file, choose the nucleotides to be analyzed and after optionally setting a number of input variables, view the numerical and graphic results online or download files containing a set of helical, backbone and groove parameters that fully describe the structure. PDB format files are also provided for offline visualization of the helical axis and groove geometry. PMID:21558323

  5. Backbone and side-chain 1H, 15N, and 13C resonance assignments of Norwalk virus protease

    PubMed Central

    Takahashi, Daisuke; Kim, Yunjeong; Chang, Kyeong-Ok; Anbanandam, Asokan

    2015-01-01

    Norovirus protease cleaves the virus-encoded polyprotein into six mature nonstructural proteins, presenting itself as an essential enzyme for the viral replication as well as an attractive target for the antiviral drug development. A deeper understanding of the structural mechanism of the protease-substrates/inhibitors interactions by means of solution NMR methods would facilitate a rational design of the virus protease inhibitor. We here report the backbone and side-chain resonance assignment of the protease from Norwalk virus, which is the prototype strain of norovirus. The assignment data has been deposited in the BMRB database under the accession number 17523. PMID:21647610

  6. Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea

    PubMed Central

    Goldsmith, Dawn B.; Parsons, Rachel J.; Beyene, Damitu; Salamon, Peter

    2015-01-01

    Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS) site in the summer (September) and winter (March) of three years. Viral phoH sequences reveal differences in the viral communities throughout a depth profile and between seasons in the same year. Variation was also detected between the same seasons in subsequent years, though these differences were not as great as the summer/winter distinctions. Over 3,600 phoH operational taxonomic units (OTUs; 97% sequence identity) were identified. Despite high richness, most phoH sequences belong to a few large, common OTUs whereas the majority of the OTUs are small and rare. While many OTUs make sporadic appearances at just a few times or depths, a small number of OTUs dominate the community throughout the seasons, depths, and years. PMID:26157645

  7. Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field

    PubMed Central

    2015-01-01

    Continuing our effort to introduce d-amino-acid residues in the united residue (UNRES) force field developed in our laboratory, in this work the C? ··· C? ··· C? backbone-virtual-bond-valence-angle (?) potentials for systems containing d-amino-acid residues have been developed. The potentials were determined by integrating the combined energy surfaces of all possible triplets of terminally blocked glycine, alanine, and proline obtained with ab initio molecular quantum mechanics at the MP2/6-31G(d,p) level to calculate the corresponding potentials of mean force (PMFs). Subsequently, analytical expressions were fitted to the PMFs to give the virtual-bond-valence potentials to be used in UNRES. Alanine represented all types of amino-acid residues except glycine and proline. The blocking groups were either the N-acetyl and N?,N?-dimethyl or N-acetyl and pyrrolidyl group, depending on whether the residue next in sequence was an alanine-type or a proline residue. A total of 126 potentials (63 symmetry-unrelated potentials for each set of terminally blocking groups) were determined. Together with the torsional, double-torsional, and side-chain-rotamer potentials for polypeptide chains containing d-amino-acid residues determined in our earlier work (Sieradzan et al. J. Chem. Theory Comput., 2012, 8, 4746), the new virtual-bond-angle (?) potentials now constitute the complete set of physics-based potentials with which to run coarse-grained simulations of systems containing d-amino-acid residues. The ability of the extended UNRES force field to reproduce thermodynamics of polypeptide systems with d-amino-acid residues was tested by comparing the experimentally measured and the calculated free energies of helix formation of model KLALKLALxxLKLALKLA peptides, where x denotes any d- or l- amino-acid residue. The obtained results demonstrate that the UNRES force field with the new potentials reproduce the changes of free energies of helix formation upon d-substitution but overestimate the free energies of helix formation. To test the ability of UNRES with the new potentials to reproduce the structures of polypeptides with d-amino-acid residues, an ab initio replica-exchange folding simulation of thurincin H from Bacillus thuringiensis, which has d-amino-acid residues in the sequence, was carried out. UNRES was able to locate the native ?-helical hairpin structure as the dominant structure even though no native sulfide–carbon bonds were present in the simulation. PMID:24839411

  8. Complete Sequences of Six IncA/C Plasmids of Multidrug-Resistant Salmonella enterica subsp. enterica Serotype Newport.

    PubMed

    Cao, Guojie; Allard, Marc W; Hoffmann, Maria; Monday, Steven R; Muruvanda, Tim; Luo, Yan; Payne, Justin; Rump, Lydia; Meng, Kevin; Zhao, Shaohua; McDermott, Patrick F; Brown, Eric W; Meng, Jianghong

    2015-01-01

    Multidrug-resistant (MDR) Salmonella enterica subsp. enterica serotype Newport has been a long-standing public health concern in the United States. We present the complete sequences of six IncA/C plasmids from animal-derived MDR S. Newport ranging from 80.1 to 158.5 kb. They shared a genetic backbone with S. Newport IncA/C plasmids pSN254 and pAM04528. PMID:25720681

  9. Complete Sequences of Six IncA/C Plasmids of Multidrug-Resistant Salmonella enterica subsp. enterica Serotype Newport

    PubMed Central

    Cao, Guojie; Allard, Marc W.; Hoffmann, Maria; Monday, Steven R.; Muruvanda, Tim; Luo, Yan; Payne, Justin; Rump, Lydia; Meng, Kevin; Zhao, Shaohua; McDermott, Patrick F.; Brown, Eric W.

    2015-01-01

    Multidrug-resistant (MDR) Salmonella enterica subsp. enterica serotype Newport has been a long-standing public health concern in the United States. We present the complete sequences of six IncA/C plasmids from animal-derived MDR S. Newport ranging from 80.1 to 158.5 kb. They shared a genetic backbone with S. Newport IncA/C plasmids pSN254 and pAM04528. PMID:25720681

  10. The Line Sequence Diagram

    Microsoft Academic Search

    Calvin R. Srock

    1966-01-01

    This paper describes the symbols and techniques used to construct and apply a line sequence diagram. A line sequence diagram, as the name implies, describes the sequence of operations for an electrical control circuit.

  11. Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid

    PubMed Central

    Babbitt, Gregory A.; Alawad, Mohammed A.; Schulze, Katharina V.; Hudson, André O.

    2014-01-01

    While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (?GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an ‘accessory’ during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context. PMID:25200075

  12. Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: 2H NMR studies on perdeuterated C-phycocyanin.

    PubMed

    Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

    2014-03-01

    Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high. PMID:24730877

  13. Effect of distribution of stickers along backbone on temperature-dependent structural properties in associative polymer solutions

    E-print Network

    X. -G. Han; X. -F. Zhang; Y. -H. Ma

    2012-10-05

    Effect of distribution of stickers along the backbone on structural properties in associating polymer solutions is studied using self-consistent field lattice model. Only two inhomogeneous morphologies, i.e., microfluctuation homogenous (MFH) and micelle morphologies, are observed. If the system is cooled, the solvent content within the aggregates decreases. When the spacing of stickers along the backbone is increased the temperature-dependent range of aggregation in MFH morphology and half-width of specific heat peak for homogenous solutions-MFH transition increase, and the symmetry of the peak decreases. However, with increasing spacing of stickers, the above three corresponding quantities related to micelles behave differently. It is demonstrated that the broad nature of the observed transitions can be ascribed to the structural changes which accompany the replacement of solvents in aggregates by polymer, which is consistent with the experimental conclusion. It is found that different effect of spacing of stickers on the two transitions can be interpreted in terms of intrachain and interchain associations.

  14. Resolution of deep nodes yields an improved backbone phylogeny and a new basal lineage to study early evolution of Asteraceae.

    PubMed

    Panero, Jose L; Freire, Susana E; Ariza Espinar, Luis; Crozier, Bonnie S; Barboza, Gloria E; Cantero, Juan J

    2014-11-01

    A backbone phylogeny that fully resolves all subfamily and deeper nodes of Asteraceae was constructed using 14 chloroplast DNA loci. The recently named genus Famatinanthus was found to be sister to the Mutisioideae-Asteroideae clade that represents more than 99% of Asteraceae and was found to have the two chloroplast inversions present in all Asteraceae except the nine genera of Barnadesioideae. A monotypic subfamily Famatinanthoideae and tribe Famatinantheae are named herein as new. Relationships among the basal lineages of the family were resolved with strong support in the Bayesian analysis as (Barnadesioideae (Famatinanthoideae (Mutisioideae (Stifftioideae (Wunderlichioideae-Asteroideae))))). Ancestral state reconstruction of ten morphological characters at the root node of the Asteraceae showed that the ancestral sunflower would have had a woody habit, alternate leaves, solitary capitulescences, epaleate receptacles, smooth styles, smooth to microechinate pollen surface sculpturing, white to yellow corollas, and insect-mediated pollination. Herbaceous habit, echinate pollen surface, pubescent styles, and cymose capitulescences were reconstructed for backbone nodes of the phylogeny corresponding to clades that evolved shortly after Asteraceae dispersed out of South America. No support was found for discoid capitula, multiseriate involucres or bird pollination as the ancestral character condition for any node. Using this more resolved phylogenetic tree, the recently described Raiguenrayun cura+Mutisiapollis telleriae fossil should be associated to a more derived node than previously suggested when time calibrating phylogenies of Asteraceae. PMID:25083940

  15. Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin

    NASA Astrophysics Data System (ADS)

    Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

    2014-03-01

    Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

  16. Dynamic behavior of an intrinsically unstructured linker domain is conserved in the face of negligible amino acid sequence conservation.

    PubMed

    Daughdrill, Gary W; Narayanaswami, Pranesh; Gilmore, Sara H; Belczyk, Agniezka; Brown, Celeste J

    2007-09-01

    Proteins or regions of proteins that do not form compact globular structures are classified as intrinsically unstructured proteins (IUPs). IUPs are common in nature and have essential molecular functions, but even a limited understanding of the evolution of their dynamic behavior is lacking. The primary objective of this work was to test the evolutionary conservation of dynamic behavior for a particular class of IUPs that form intrinsically unstructured linker domains (IULD) that tether flanking folded domains. This objective was accomplished by measuring the backbone flexibility of several IULD homologues using nuclear magnetic resonance (NMR) spectroscopy. The backbone flexibility of five IULDs, representing three kingdoms, was measured and analyzed. Two IULDs from animals, one IULD from fungi, and two IULDs from plants showed similar levels of backbone flexibility that were consistent with the absence of a compact globular structure. In contrast, the amino acid sequences of the IULDs from these three taxa showed no significant similarity. To investigate how the dynamic behavior of the IULDs could be conserved in the absence of detectable sequence conservation, evolutionary rate studies were performed on a set of nine mammalian IULDs. The results of this analysis showed that many sites in the IULD are evolving neutrally, suggesting that dynamic behavior can be maintained in the absence of natural selection. This work represents the first experimental test of the evolutionary conservation of dynamic behavior and demonstrates that amino acid sequence conservation is not required for the conservation of dynamic behavior and presumably molecular function. PMID:17721672

  17. Use of NOESY for estimation of coupling constants in the DNA backbone

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, N.; Majumdar, A.; Hosur, R. V.

    1992-12-01

    We demonstrate here the use of the two-dimensional NOESY technique for measurement of the most elusive coupling constants, J(H4'-H5'), J(H4'-H5?), J(H3'-H4') and J(H3'-P) in long DNA segments. The band selective BURP family of pulses has been used in the NOESY pulse sequence for achieving high resolution in the spectra and the coupling constants have been estimated by simulating cross-sections through H1'-H4' and H8-H3' cross-peaks in two illustrative cases.

  18. Solvable Sequence Evolution Models and Genomic Correlations

    NASA Astrophysics Data System (ADS)

    Messer, Philipp W.; Arndt, Peter F.; Lässig, Michael

    2005-04-01

    We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions, and insertion of random segments. These processes are found to generate long-range correlations in the composition of letters as long as the sequence length is growing; i.e., the combined rates of duplications and insertions are higher than the deletion rate. For constant sequence length, on the other hand, all initial correlations decay exponentially. These results are obtained analytically and by simulations. They are compared with the long-range correlations observed in genomic DNA, and the implications for genome evolution are discussed.

  19. Sequence control in polymer chemistry through the Passerini three-component reaction.

    PubMed

    Solleder, Susanne C; Meier, Michael A R

    2014-01-13

    A new strategy to achieve sequence control in polymer chemistry based on the iterative application of the versatile Passerini three-component reaction (P-3CR) in combination with efficient thiol-ene addition reactions is introduced. First, stearic acid was used as a starting substrate to build up a sequence-defined tetramer with a molecular weight of 1.6 kDa. Using an acid-functionalized PEG allowed for an easier isolation of the sequence-defined macromolecules by simple precipitation and led to a sequence-defined pentamer in a block-copolymer architecture. Importantly, this new strategy completely avoids protecting group chemistry. By following this strategy, a different side chain can be introduced to the polymer/oligomer backbone in a simple way and at a defined position within the macromolecule. PMID:24307280

  20. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

    PubMed Central

    Delaneau, Olivier; Marchini, Jonathan

    2014-01-01

    A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low coverage sequencing data that can take advantage of SNP microarray genotypes on the same samples. Firstly the SNP array data are phased in order to build a backbone (or ’scaffold’) of haplotypes across each chromosome. We then phase the sequence data ‘onto’ this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and biallelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low frequency variants. PMID:25653097

  1. Discovery of Recurrent Sequence Motifs in Saccharomyces cerevisiae Cell Wall Proteins

    E-print Network

    Epstein, Susan L.

    searches for local sequence similarities by sequence alignments. Nonetheless, our new, composition- based results of this paper are the discovery of such motifs for yeast cell wall proteins in the fungus

  2. Qualifying high-throughput immune repertoire sequencing.

    PubMed

    Niklas, Norbert; Pröll, Johannes; Weinberger, Johannes; Zopf, Agnes; Wiesinger, Karin; Krismer, Konstantin; Bettelheim, Peter; Gabriel, Christian

    2014-01-01

    Diversity of B and T cell receptors, achieved by gene recombination and somatic hypermutation, allows the immune system for recognition and targeted reaction against various threats. Next-generation sequencing for assessment of a cell's gene composition and variation makes deep analysis of one individual's immune spectrum feasible. An easy to apply but detailed analysis and visualization strategy is necessary to process all sequences generated. We performed sequencing utilizing the 454 system for CLL and control samples, utilized the IMGT database and applied the presented analysis tools. With the applied protocol, malignant clones are found and characterized, mutational status compared to germline identity is elaborated in detail showing that the CLL mutation status is not as monoclonal as generally thought. On the other hand, this strategy is not solely applicable to the 454 sequencing system but can easily be transferred to any other next-generation sequencing platform. PMID:24607567

  3. Marburg Virus VP35 Can Both Fully Coat the Backbone and Cap the Ends of dsRNA for Interferon Antagonism

    PubMed Central

    Bale, Shridhar; Halfmann, Peter; Zandonatti, Michelle A.; Kunert, John; Kroon, Gerard J. A.; Kawaoka, Yoshihiro; MacRae, Ian J.; Wilson, Ian A.; Saphire, Erica Ollmann

    2012-01-01

    Filoviruses, including Marburg virus (MARV) and Ebola virus (EBOV), cause fatal hemorrhagic fever in humans and non-human primates. All filoviruses encode a unique multi-functional protein termed VP35. The C-terminal double-stranded (ds)RNA-binding domain (RBD) of VP35 has been implicated in interferon antagonism and immune evasion. Crystal structures of the VP35 RBD from two ebolaviruses have previously demonstrated that the viral protein caps the ends of dsRNA. However, it is not yet understood how the expanses of dsRNA backbone, between the ends, are masked from immune surveillance during filovirus infection. Here, we report the crystal structure of MARV VP35 RBD bound to dsRNA. In the crystal structure, molecules of dsRNA stack end-to-end to form a pseudo-continuous oligonucleotide. This oligonucleotide is continuously and completely coated along its sugar-phosphate backbone by the MARV VP35 RBD. Analysis of dsRNA binding by dot-blot and isothermal titration calorimetry reveals that multiple copies of MARV VP35 RBD can indeed bind the dsRNA sugar-phosphate backbone in a cooperative manner in solution. Further, MARV VP35 RBD can also cap the ends of the dsRNA in solution, although this arrangement was not captured in crystals. Together, these studies suggest that MARV VP35 can both coat the backbone and cap the ends, and that for MARV, coating of the dsRNA backbone may be an essential mechanism by which dsRNA is masked from backbone-sensing immune surveillance molecules. PMID:23028316

  4. Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution.

    PubMed

    Desai, Bijoy J; Goto, Yuki; Cembran, Alessandro; Fedorov, Alexander A; Almo, Steven C; Gao, Jiali; Suga, Hiroaki; Gerlt, John A

    2014-10-21

    Hydrogen bonds between backbone amide groups of enzymes and their substrates are often observed, but their importance in substrate binding and/or catalysis is not easy to investigate experimentally. We describe the generation and kinetic characterization of a backbone amide to ester substitution in the orotidine 5'-monophosphate (OMP) decarboxylase from Methanobacter thermoautotrophicum (MtOMPDC) to determine the importance of a backbone amide-substrate hydrogen bond. The MtOMPDC-catalyzed reaction is characterized by a rate enhancement (?10(17)) that is among the largest for enzyme-catalyzed reactions. The reaction proceeds through a vinyl anion intermediate that may be stabilized by hydrogen bonding interaction between the backbone amide of a conserved active site serine residue (Ser-127) and oxygen (O4) of the pyrimidine moiety and/or electrostatic interactions with the conserved general acidic lysine (Lys-72). In vitro translation in conjunction with amber suppression using an orthogonal amber tRNA charged with L-glycerate ((HO)S) was used to generate the ester backbone substitution (S127(HO)S). With 5-fluoro OMP (FOMP) as substrate, the amide to ester substitution increased the value of Km by ?1.5-fold and decreased the value of kcat by ?50-fold. We conclude that (i) the hydrogen bond between the backbone amide of Ser-127 and O4 of the pyrimidine moiety contributes a modest factor (?10(2)) to the 10(17) rate enhancement and (ii) the stabilization of the anionic intermediate is accomplished by electrostatic interactions, including its proximity of Lys-72. These conclusions are in good agreement with predictions obtained from hybrid quantum mechanical/molecular mechanical calculations. PMID:25275007

  5. Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs

    PubMed Central

    2014-01-01

    Background We introduce Sequence Bundles--a novel data visualisation method for representing multiple sequence alignments (MSAs). We identify and address key limitations of the existing bioinformatics data visualisation methods (i.e. the Sequence Logo) by enabling Sequence Bundles to give salient visual expression to sequence motifs and other data features, which would otherwise remain hidden. Methods For the development of Sequence Bundles we employed research-led information design methodologies. Sequences are encoded as uninterrupted, semi-opaque lines plotted on a 2-dimensional reconfigurable grid. Each line represents a single sequence. The thickness and opacity of the stack at each residue in each position indicates the level of conservation and the lines' curved paths expose patterns in correlation and functionality. Several MSAs can be visualised in a composite image. The Sequence Bundles method is designed to favour a tangible, continuous and intuitive display of information. Results We have developed a software demonstration application for generating a Sequence Bundles visualisation of MSAs provided for the BioVis 2013 redesign contest. A subsequent exploration of the visualised line patterns allowed for the discovery of a number of interesting features in the dataset. Reported features include the extreme conservation of sequences displaying a specific residue and bifurcations of the consensus sequence. Conclusions Sequence Bundles is a novel method for visualisation of MSAs and the discovery of sequence motifs. It can aid in generating new insight and hypothesis making. Sequence Bundles is well disposed for future implementation as an interactive visual analytics software, which can complement existing visualisation tools. PMID:25237395

  6. Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3

    PubMed Central

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    2011-01-01

    One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA have backbone RMSD 0.8 – 1.5 Å from the reference structures determined by traditional NMR approaches. PMID:21706248

  7. Antimicrobial Treatment and Containment Measures for an Extremely Drug-Resistant Klebsiella pneumoniae ST101 Isolate Carrying pKPN101-IT, a Novel Fully Sequenced blaKPC-2 Plasmid

    PubMed Central

    Frasson, Ilaria; Lavezzo, Enrico; Franchin, Elisa; Toppo, Stefano; Barzon, Luisa; Cavallaro, Antonietta; Palù, Giorgio

    2012-01-01

    An extremely drug-resistant Klebsiella pneumoniae isolate, sequence type ST101, was isolated from a patient in Italy. We describe antibiotic treatment, measures to clear and contain the infection, and a complete sequence analysis of a novel large plasmid, pKPN101-IT, harboring the blaKPC-2 gene and arising from the threatening recombination of different worldwide-distributed backbones. PMID:22972824

  8. Antimicrobial treatment and containment measures for an extremely drug-resistant Klebsiella pneumoniae ST101 isolate carrying pKPN101-IT, a novel fully sequenced bla(KPC-2) plasmid.

    PubMed

    Frasson, Ilaria; Lavezzo, Enrico; Franchin, Elisa; Toppo, Stefano; Barzon, Luisa; Cavallaro, Antonietta; Richter, Sara N; Palù, Giorgio

    2012-11-01

    An extremely drug-resistant Klebsiella pneumoniae isolate, sequence type ST101, was isolated from a patient in Italy. We describe antibiotic treatment, measures to clear and contain the infection, and a complete sequence analysis of a novel large plasmid, pKPN101-IT, harboring the bla(KPC-2) gene and arising from the threatening recombination of different worldwide-distributed backbones. PMID:22972824

  9. Oligonucleotide labeling methods. 3. Direct labeling of oligonucleotides employing a novel, non-nucleosidic, 2-aminobutyl-1,3-propanediol backbone.

    PubMed Central

    Nelson, P S; Kent, M; Muthini, S

    1992-01-01

    Novel CE-phosphoramidite (7a-e) and CPG (8a, c, d, e) reagents have been prepared from a unique 2-aminobutyl-1,3-propanediol backbone. The reagents have been used to directly label oligonucleotides with fluorescein, acridine, and biotin via automated DNA synthesis. The versatile 2-aminobutyl-1,3-propanediol backbone allows for labeling at any position (5', internal, and 3') during solid phase oligonucleotide synthesis. Multiple labels can be achieved by repetitive coupling cycles. Furthermore, the 3-carbon atom internucleotide phosphate distance is retained when inserted internally. Using this method, individual oligonucleotides possessing two and three different reporter molecules have been prepared. PMID:1475185

  10. MRO Sequence Checking Tool

    NASA Technical Reports Server (NTRS)

    Fisher, Forest; Gladden, Roy; Khanampornpan, Teerapat

    2008-01-01

    The MRO Sequence Checking Tool program, mro_check, automates significant portions of the MRO (Mars Reconnaissance Orbiter) sequence checking procedure. Though MRO has similar checks to the ODY s (Mars Odyssey) Mega Check tool, the checks needed for MRO are unique to the MRO spacecraft. The MRO sequence checking tool automates the majority of the sequence validation procedure and check lists that are used to validate the sequences generated by MRO MPST (mission planning and sequencing team). The tool performs more than 50 different checks on the sequence. The automation varies from summarizing data about the sequence needed for visual verification of the sequence, to performing automated checks on the sequence and providing a report for each step. To allow for the addition of new checks as needed, this tool is built in a modular fashion.

  11. Chemical synthesis of a polypeptide backbone derived from the primary sequence of the cancer protein NY-ESO-1 enabled by kinetically controlled ligation and pseudoprolines.

    PubMed

    Harris, Paul W R; Brimble, Margaret A

    2015-03-01

    The cancer protein NY-ESO-1 has been shown to be one of the most promising vaccine candidates although little is known about its cellular function. Using a chemical protein strategy, the 180 amino acid polypeptide, tagged with an arginine solubilizing tail, was assembled in a convergent manner from four unprotected peptide ?-thioester peptide building blocks and one cysteinyl polypeptide, which were in turn prepared by Boc and Fmoc solid phase peptide synthesis (SPPS) respectively. To facilitate the assembly by ligation chemistries, non-native cysteines were introduced as chemical handles into the polypeptide fragments; pseudoproline dipeptides and microwave assisted Fmoc SPPS were crucial techniques to prepare the challenging hydrophobic C-terminal fragment. Three sequential kinetically controlled ligations, which exploited the reactivity between peptide arylthioesters and peptide alkylthioesters, were then used in order to assemble the more tractable N-terminal region of NY-ESO-1. The ensuing 147 residue polypeptide thioester then underwent successful final native chemical ligation with the very hydrophobic C-terminal polypeptide bearing an N-terminal cysteine affording the 186 residue polypeptide as an advanced intermediate en route to the native NY-ESO-1 protein. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 116-127, 2015. PMID:25656702

  12. Ignimbrite sequence on Gran Canaria

    Microsoft Academic Search

    H. U. Schmincke

    1969-01-01

    The Miocene sequence of felsic extrusive rocks of about 1000 m total thickness on Gran Canaria is divided into three units:\\u000a \\u000a \\u000a a) \\u000a \\u000a A lower unit of trachytic rhyolites (lavas, composite flows, ignimbrites) characterized by a phenocryst assemblage of anorthoclase\\u000a (Or15–20, wt%), clinopyroxene, hypersthene (amphibole substituted for both in ignimbrites), and Fe\\/Ti-oxides. The commonest groundmass\\u000a minerals are anorthoclase and alkali-amphibole, with

  13. Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins

    NASA Astrophysics Data System (ADS)

    Chevelkov, Veniamin; Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam

    2014-05-01

    Proton-detected solid-state NMR was applied to a highly deuterated insoluble, non-crystalline biological assembly, the Salmonella typhimurium type iii secretion system (T3SS) needle. Spectra of very high resolution and sensitivity were obtained at a low protonation level of 10-20% at exchangeable amide positions. We developed efficient experimental protocols for resonance assignment tailored for this system and the employed experimental conditions. Using exclusively dipolar-based interspin magnetization transfers, we recorded two sets of 3D spectra allowing for an almost complete backbone resonance assignment of the needle subunit PrgI. The additional information provided by the well-resolved proton dimension revealed the presence of two sets of resonances in the N-terminal helix of PrgI, while in previous studies employing 13C detection only a single set of resonances was observed.

  14. Backbone and stereospecific (13)C methyl Ile (?1), Leu and Val side-chain chemical shift assignments of Crc.

    PubMed

    Sharma, Rakhi; Sahu, Bhubanananda; Ray, Malay K; Deshmukh, Mandar V

    2015-04-01

    Carbon catabolite repression (CCR) allows bacteria to selectively assimilate a preferred compound among a mixture of several potential carbon sources, thus boosting growth and economizing the cost of adaptability to variable nutrients in the environment. The RNA-binding catabolite repression control (Crc) protein acts as a global post-transcriptional regulator of CCR in Pseudomonas species. Crc triggers repression by inhibiting the expression of genes involved in transport and catabolism of non-preferred substrates, thus indirectly favoring assimilation of preferred one. We report here a nearly complete backbone and stereospecific (13)C methyl side-chain chemical shift assignments of Ile (?1), Leu and Val of Crc (~ 31 kDa) from Pseudomonas syringae Lz4W. PMID:24496608

  15. ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization

    NASA Astrophysics Data System (ADS)

    Fingerhut, Benjamin P.; Oesterling, Sven; Haiser, Karin; Heil, Korbinian; Glas, Andreas; Schreier, Wolfgang J.; Zinth, Wolfgang; Carell, Thomas; de Vivie-Riedle, Regina

    2012-05-01

    Non-adiabatic on-the-fly molecular dynamics (NA-O-MD) simulations require the electronic wavefunction, energy gradients, and derivative coupling vectors in every timestep. Thus, they are commonly restricted to the excited state dynamics of molecules with up to ?20 atoms. We discuss an approximation that combines the ONIOM(QM:QM) method with NA-O-MD simulations to allow calculations for larger molecules. As a proof of principle we present the excited state dynamics of a (6-4)-lesion containing dinucleotide (63 atoms), and especially the importance to include the confinement effects of the DNA backbone. The method is able to include electron correlation on a high level of theory and offers an attractive alternative to QM:MM approaches for moderate sized systems with unknown force fields.

  16. ¹H, ¹?N and ¹³C backbone chemical shift assignment of the titin A67-A68 domain tandem.

    PubMed

    Czajlik, András; Thompson, Gary S; Khan, Ghulam N; Kalverda, Arnout P; Homans, Steve W; Trinick, John

    2012-04-01

    Single molecules of the giant protein titin extend across half of the muscle sarcomere, from the Z-line to the M-line, and have roles in muscle assembly and elasticity. In the A-band titin is attached to thick filaments and here the domain arrangement occurs in regular patterns of eleven called the large super-repeat. The large super-repeat itself occurs eleven times and forms nearly half the titin molecule. Interactions of the large super-repeats with myosin are consistent with a role in thick filament assembly. Here we report backbone assignments of the titin A67-A68 domain tandem (Fn-Ig) from the third super-repeat (A65-A75) completed using triple resonance NMR experiments. PMID:21779926

  17. Backbone and side-chain NMR assignments for the C-terminal domain of mammalian Vps28.

    PubMed

    Peterson, Tabitha A; Yu, Liping; Piper, Robert C

    2015-04-01

    Vps28 is one of four cytosolic proteins comprising the endosomal sorting complex required for transport I (ESCRT-I). ESCRT-I is involved in sorting ubiquitinated proteins to multivesicular bodies as well as in mediating budding of retroviruses. Here, we report the backbone and side-chain assignments of the mammalian C-terminal domain of Vps28 (mVps28(CTD)), which is involved in interactions with other ESCRT components. We also compare the predicted secondary structures of mVps28(CTD) with those of the published X-ray crystal structures of Saccharomyces cerevisiae and Xenopus laevis Vps28(CTD). These NMR resonance assignments will facilitate chemical shift mapping and structural determination of mammalian Vps28 interactions with other components of the endosomal sorting machinery that sorts ubiquitinated proteins for lysosomal degradation. PMID:24366722

  18. High Accuracy of Karplus Equations for Relating Three-Bond J Couplings to Protein Backbone Torsion Angles

    PubMed Central

    Li, Fang; Lee, Jung Ho; Grishaev, Alexander; Ying, Jinfa; Bax, Ad

    2015-01-01

    3JC?C? and 3JHNH? couplings are related to the intervening backbone torsion angle ? by standard Karplus equations. Although these couplings are known to be affected by parameters other than ?, including H-bonding, valence angles and residue type, experimental results and quantum calculations indicate that the impact of these latter parameters is typically very small. The solution NMR structure of protein GB3, newly refined by using extensive sets of residual dipolar couplings (RDCs), yields 50–60% better Karplus equation agreement between ? angles and experimental 3JC?C? and 3JHNH? values than does the high resolution X-ray structure. In intrinsically disordered proteins, 3JC?C? and 3JHNH? couplings can be measured at even higher accuracy, and the impact of factors other than the intervening torsion angle on 3J will be smaller than in folded proteins, making these couplings exceptionally valuable reporters on the ensemble of ? angles sampled by each residue. PMID:25511552

  19. Backbone cyclised peptides from plants show molluscicidal activity against the rice pest Pomacea canaliculata (golden apple snail).

    PubMed

    Plan, Manuel Rey R; Saska, Ivana; Cagauan, Arsenia G; Craik, David J

    2008-07-01

    Golden apple snails ( Pomacea canaliculata) are serious pests of rice in South East Asia. Cyclotides are backbone cyclized peptides produced by plants from Rubiaceae and Violaceae. In this study, we investigated the molluscicidal activity of cyclotides against golden apple snails. Crude cyclotide extracts from both Oldenlandia affinis and Viola odorata plants showed molluscicidal activity comparable to the synthetic molluscicide metaldehyde. Individual cyclotides from each extract demonstrated a range of molluscicidal activities. The cyclotides cycloviolacin O1, kalata B1, and kalata B2 were more toxic to golden apple snails than metaldehyde, while kalata B7 and kalata B8 did not cause significant mortality. The toxicity of the cyclotide kalata B2 on a nontarget species, the Nile tilapia ( Oreochromis niloticus), was three times lower than the common piscicide rotenone. Our findings suggest that the existing diversity of cyclotides in plants could be used to develop natural molluscicides. PMID:18557620

  20. The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog

    SciTech Connect

    Cuneo, Matthew J.; Tian, Yaji; Allert, Malin; Hellinga, Homme W. (Duke)

    2008-10-27

    We report the X-ray crystal structure of a Thermoanaerobacter tengcongensis ribose binding protein (tteRBP) determined to 1.9 {angstrom} resolution. We find that tteRBP is significantly more stable ({sup app}T{sub m} value {approx} 102 C) than the mesophilic Escherichia coli ribose binding protein (ecRBP) ({sup app}T{sub m} value {approx} 56 C). The tteRBP has essentially the identical backbone conformation (0.41 {angstrom} RMSD of 235/271 C{sub {alpha}} positions and 0.65 {angstrom} RMSD of 270/271 C{sub {alpha}} positions) as ecRBP. Classification of the amino acid substitutions as a function of structure therefore allows the identification of amino acids which potentially contribute to the observed thermal stability of tteRBP in the absence of large structural heterogeneities.

  1. A Hausdorff-based NOE assignment algorithm using protein backbone determined from residual dipolar couplings and rotamer patterns.

    PubMed

    Zeng, Jianyang; Tripathy, Chittaranjan; Zhou, Pei; Donald, Bruce R

    2008-01-01

    High-throughput structure determination based on solution Nuclear Magnetic Resonance (NMR) spectroscopy plays an important role in structural genomics. One of the main bottlenecks in NMR structure determination is the interpretation of NMR data to obtain a sufficient number of accurate distance restraints by assigning nuclear Overhauser effect (NOE) spectral peaks to pairs of protons. The difficulty in automated NOE assignment mainly lies in the ambiguities arising both from the resonance degeneracy of chemical shifts and from the uncertainty due to experimental errors in NOE peak positions. In this paper we present a novel NOE assignment algorithm, called HAusdorff-based NOE Assignment (HANA), that starts with a high-resolution protein backbone computed using only two residual dipolar couplings (RDCs) per residue, employs a Hausdorff-based pattern matching technique to deduce similarity between experimental and back-computed NOE spectra for each rotamer from a statistically diverse library, and drives the selection of optimal position-specific rotamers for filtering ambiguous NOE assignments. Our algorithm runs in time O(tn3 + tn log t), where t is the maximum number of rotamers per residue and n is the size of the protein. Application of our algorithm on biological NMR data for three proteins, namely, human ubiquitin, the zinc finger domain of the human DNA Y-polymerase Eta (pol eta) and the human Set2-Rpb1 interacting domain (hSRI) demonstrates that our algorithm overcomes spectral noise to achieve more than 90% assignment accuracy. Additionally, the final structures calculated using our automated NOE assignments have backbone RMSD < 1.7 A and all-heavy-atom RMSD < 2.5 A from reference structures that were determined either by X-ray crystallography or traditional NMR approaches. These results show that our NOE assignment algorithm can be successfully applied to protein NMR spectra to obtain high-quality structures. PMID:19642278

  2. Direct measurements of protein backbone 15N spin relaxation rates from peak line-width using a fully-relaxed Accordion 3D HNCO experiment

    NASA Astrophysics Data System (ADS)

    Chen, Kang; Tjandra, Nico

    2009-03-01

    Protein backbone 15N spin relaxation rates measured by solution NMR provide useful dynamic information with a site-specific resolution. The conventional method is to record a series of 2D 1H- 15N HSQC spectra with varied relaxation delays, and derive relaxation rate from the following curve fitting on the resonance intensities. Proteins with poorly resolved spectra often require several 3D HNCO spectra to be collected on a 15N/ 13C double labeled protein sample. In order to reduce the relaxation dimension Carr et al . (P.A. Carr, D.A. Fearing, A.G. Palmer, 3D accordion spectroscopy for measuring N-15 and (CO)-Carbon-13 relaxation rates in poorly resolved NMR spectra, J. Magn. Reson. 132 (1998) 25-33) employed an Accordion type HNCO pulse sequence to obtain 15N or 13C T1 relaxation rates by numerical fitting of the relaxation interfered free induction decay (FID) data. To avoid intensive analysis of the time domain data, we propose a modified protocol to measure 15N T1 and T2 relaxation rates from easily obtained line-widths in an Accordion HNCO spectrum. Both T1 and T2 relaxation could be simultaneously convoluted into the constant-time evolution periods of 13C' and 15N, respectively. The relaxation delay was allowed to reach at least 3 × T1 or 3 × T2 so that the signal was substantially decayed by the end of the FID, and the resulting peak full-width at half height (FWHH) could be directly used to calculate relaxation rate. When applied to the 76-residue Ubiquitin and the 226-residue glutamine-binding protein (GlnBP), this method yielded T1 and T2 values deviating on average by 4-6% and 5-7%, respectively, from the measurements based on the conventional 2D method. In comparison, the conventional methods possessed intrinsic error ranges of 2-4% for T1 and 3-6% for T2. In addition to comparable accuracy, the fully-relaxed Accordion HNCO method presented here allowed measurements of relaxation rates for resonances unresolved in 2D spectra, thus providing a more complete dynamic picture of the protein.

  3. Bonobos extract meaning from call sequences.

    PubMed

    Clay, Zanna; Zuberbühler, Klaus

    2011-01-01

    Studies on language-trained bonobos have revealed their remarkable abilities in representational and communication tasks. Surprisingly, however, corresponding research into their natural communication has largely been neglected. We address this issue with a first playback study on the natural vocal behaviour of bonobos. Bonobos produce five acoustically distinct call types when finding food, which they regularly mix together into longer call sequences. We found that individual call types were relatively poor indicators of food quality, while context specificity was much greater at the call sequence level. We therefore investigated whether receivers could extract meaning about the quality of food encountered by the caller by integrating across different call sequences. We first trained four captive individuals to find two types of foods, kiwi (preferred) and apples (less preferred) at two different locations. We then conducted naturalistic playback experiments during which we broadcasted sequences of four calls, originally produced by a familiar individual responding to either kiwi or apples. All sequences contained the same number of calls but varied in the composition of call types. Following playbacks, we found that subjects devoted significantly more search effort to the field indicated by the call sequence. Rather than attending to individual calls, bonobos attended to the entire sequences to make inferences about the food encountered by a caller. These results provide the first empirical evidence that bonobos are able to extract information about external events by attending to vocal sequences of other individuals and highlight the importance of call combinations in their natural communication system. PMID:21556149

  4. Bonobos Extract Meaning from Call Sequences

    PubMed Central

    Clay, Zanna; Zuberbühler, Klaus

    2011-01-01

    Studies on language-trained bonobos have revealed their remarkable abilities in representational and communication tasks. Surprisingly, however, corresponding research into their natural communication has largely been neglected. We address this issue with a first playback study on the natural vocal behaviour of bonobos. Bonobos produce five acoustically distinct call types when finding food, which they regularly mix together into longer call sequences. We found that individual call types were relatively poor indicators of food quality, while context specificity was much greater at the call sequence level. We therefore investigated whether receivers could extract meaning about the quality of food encountered by the caller by integrating across different call sequences. We first trained four captive individuals to find two types of foods, kiwi (preferred) and apples (less preferred) at two different locations. We then conducted naturalistic playback experiments during which we broadcasted sequences of four calls, originally produced by a familiar individual responding to either kiwi or apples. All sequences contained the same number of calls but varied in the composition of call types. Following playbacks, we found that subjects devoted significantly more search effort to the field indicated by the call sequence. Rather than attending to individual calls, bonobos attended to the entire sequences to make inferences about the food encountered by a caller. These results provide the first empirical evidence that bonobos are able to extract information about external events by attending to vocal sequences of other individuals and highlight the importance of call combinations in their natural communication system. PMID:21556149

  5. Eight Hateful Sequences

    E-print Network

    Sloane, N J A

    2008-01-01

    In his July 1974 Scientific American column, Martin Gardner mentioned the Handbook of Integer Sequences, which then contained 2372 sequences. Today the On-Line Encyclopedia of Integer Sequences (the OEIS) contains 140000 sequences. This paper discusses eight of them, suggested by the theme of the Eighth Gathering For Gardner: they are all infinite, and all 'ateful in one way or another. Each one is connected with an unsolved problem. The sequences are related to: hateful numbers, Angelini's 1995 puzzle, the persistence of a number, Alekseyev's 123 sequence, the curling number conjecture, Quet's prime-generating recurrence, the traveling salesman's problem, and the Riemann Hypothesis.

  6. The fungal cell wall: Modern concepts of its composition and biological function

    Microsoft Academic Search

    E. P. Feofilova

    2010-01-01

    This review deals with the cell wall (CW), a poorly known surface structure of the cell of mycelial fungi. Data are presented\\u000a concerning (i) isolation techniques and purity control methods securing the absence of the cytoplasm content in the CW fraction\\u000a and (ii) the chemical composition of the CW. The structural (backbone) and intrastructural components of the CW, such as

  7. Progress in compensating pulse sequences for quantum computation

    E-print Network

    J. True Merrill; Kenneth R. Brown

    2012-03-28

    The control of qubit states is often impeded by systematic control errors. Compensating pulse sequences have emerged as a resource efficient method for quantum error reduction. In this review, we discuss compensating composite pulse methods, and introduce a unifying control-theoretic framework using a dynamic interaction picture. This admits a novel geometric picture where sequences are interpreted as vector paths on the dynamical Lie algebra. Sequences for single-qubit and multi-qubit operations are described with this method.

  8. Human colonic biota studied by ribosomal DNA sequence analysis

    Microsoft Academic Search

    KENNETH H. WILSON; R. B. Blitchington

    1996-01-01

    Human colonic biota is a complex microbial ecosystem that serves as a host defense. Unlike most microbial ecosystems, its composition has been studied extensively by relatively efficient culture methods. We have compared an established culture-based method with direct amplification and partial sequencing of cloned 16S rRNAgenesfromahumanfecalspecimen.NinecyclesofPCRwerealsocomparedwith35cycles.Coloniesand clonedampliconswereclassifiedbycomparingtheirribosomalDNA(rDNA;DNAcodingforrRNA)sequences with rDNA sequences of known phylogeny. Quantitative culture recovered 58% of the microscopic

  9. 1H, 13C, 15N backbone and side-chain resonance assignments of the Bright/ARID domain from the human histone demethylase JARID1B.

    PubMed

    Yao, Wenming; Peng, Yu; Chen, Qun; Lin, Donghai

    2009-06-01

    We report backbone and side-chain resonance assignments of the Bright/ARID domain from the human JARID1B protein. These assignments provide a basis for the detailed structural investigation of the interaction between DNA and ARID domains. PMID:19636953

  10. Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

    Microsoft Academic Search

    Alexander D. MacKerell Jr.; Michael Feig; Charles L. Brooks III

    2004-01-01

    Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure- function relationships at an atomic level, and are central in current efforts to solve the protein folding problem. The results from studies applying these tools are, however, dependent on the quality of the force fields used. In particular, accurate treatment of the peptide backbone

  11. Automated DNA Sequencing System

    SciTech Connect

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  12. Amino acid sequence and posttranslational modifications of human factor VII sub a from plasma and transfected baby hamster kidney cells

    SciTech Connect

    Thim, L.; Bjoern, S.; Christensen, M.; Nicolaisen, E.M.; Lund-Hansen, T.; Pedersen, A.H.; Hedner, U. (Novo Research Institute, Bagsvaerd (Denmark))

    1988-10-04

    Blood coagulation factor VII is a vitamin K dependent glycoprotein which in its activated form, factor VII{sub a}, participates in the coagulation process by activating factor X and/or factor IX in the presence of Ca{sup 2+} and tissue factor. Three types of potential posttranslational modifications exist in the human factor VII{sub a} molecule, namely, 10 {gamma}-carboxylated, N-terminally located glutamic acid residues, 1 {beta}-hydroxylated aspartic acid residue, and 2 N-glycosylated asparagine residues. In the present study, the amino acid sequence and posttranslational modifications of recombinant factor VII{sub a} as purified from the culture medium of a transfected baby hamster kidney cell line have been compared to human plasma factor VII{sub a}. By use of HPLC, amino acid analysis, peptide mapping, and automated Edman degradation, the protein backbone of recombinant factor VII{sub a} was found to be identical with human factor VII{sub a}. Asparagine residues 145 and 322 were found to be fully N-glycosylated in human plasma factor VII{sub a}. In the recombinant factor VII{sub a}, asparagine residue 322 was fully glycosylated whereas asparagine residue 145 was only partially (approximately 66%) glycosylated. Besides minor differences in the sialic acid and fucose contents, the overall carbohydrate compositions were nearly identical in recombinant factor VII{sub a} and human plasma factor VII{sub a}. These results show that factor VII{sub a} as produced in the transfected baby hamster kidney cells is very similar to human plasma factor VII{sub a} and that this cell line thus might represent an alternative source for human factor VII{sub a}.

  13. Methods for making nucleotide probes for sequencing and synthesis

    SciTech Connect

    Church, George M; Zhang, Kun; Chou, Joseph

    2014-07-08

    Compositions and methods for making a plurality of probes for analyzing a plurality of nucleic acid samples are provided. Compositions and methods for analyzing a plurality of nucleic acid samples to obtain sequence information in each nucleic acid sample are also provided.

  14. DIMACS Technical Report 956 Relation between Protein Structure, Sequence

    E-print Network

    and Composition of Amino Acids by Eddy N. Mayoraz 1 RUTCOR--Rutgers University's Center for Operations Research, P. Classification of proteins based on sequence homology and based on amino acid composition were compared residue identity they have a similar fold. This threshold of 50% is usually used as a ``safe definition

  15. Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences

    E-print Network

    Stadler, Peter F.

    Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences Roman R. Stocsits 1 , Ivo L sequence data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared use of the amino acid sequence when aligning coding nucleic acid sequences. In many cases, however

  16. Assignment of congested NMR spectra: Carbonyl backbone enrichment via the Entner Doudoroff pathway

    NASA Astrophysics Data System (ADS)

    Goldbourt, Amir; Day, Loren A.; McDermott, Ann E.

    2007-12-01

    In NMR spectra of complex proteins, sparse isotope enrichment can be important, in that the removal of many 13C- 13C homonuclear J-couplings can narrow the lines and thereby facilitate the process of spectral assignment and structure elucidation. We present a simple scheme for selective yet extensive isotopic enrichment applicable for production of proteins in organisms utilizing the Entner-Doudoroff (ED) metabolic pathway. An enrichment scheme so derived is demonstrated in the context of a magic-angle spinning solid-state NMR (MAS SSNMR) study of Pf1 bacteriophage, the host of which is Pseudomonas aeruginosa, strain K (PAK), an organism that uses the ED pathway for glucose catabolism. The intact and infectious Pf1 phage in this study was produced by infected PAK cells grown on a minimal medium containing 1- 13C D-glucose ( 13C in position 1) as the sole carbon source, as well as 15NH 4Cl as the only nitrogen source. The 37 MDa Pf1 phage consists of about 93% major coat protein, 1% minor coat proteins, and 6% single-stranded, circular DNA. As a consequence of this composition and the enrichment scheme, the resonances in the MAS SSNMR spectra of the Pf1 sample were almost exclusively due to carbonyl carbons in the major coat protein. Moreover, 3D heteronuclear NCOCX correlation experiments also show that the amino acids leucine, serine, glycine, and tyrosine were not isotopically enriched in their carbonyl positions (although most other amino acids were), which is as expected based upon considerations of the ED metabolic pathway. 3D NCOCX NMR data and 2D 15N- 15N data provided strong verification of many previous assignments of 15N amide and 13C carbonyl shifts in this highly congested spectrum; both the semi-selective enrichment patterns and the narrowed linewidths allowed for greater certainty in the assignments as compared with use of uniformly enriched samples alone.

  17. Multispectral labeling of antibodies with polyfluorophores on a DNA backbone and application in cellular imaging

    PubMed Central

    Guo, Jia; Wang, Shenliang; Dai, Nan; Teo, Yin Nah; Kool, Eric T.

    2011-01-01

    Most current approaches to multiantigen fluorescent imaging require overlaying of multiple images taken with separate filter sets as a result of differing dye excitation requirements. This requirement for false-color composite imaging prevents the user from visualizing multiple species in real time and disallows imaging of rapidly moving specimens. To address this limitation, here we investigate the use of oligodeoxyfluoroside (ODF) fluorophores as labels for antibodies. ODFs are short DNA-like oligomers with fluorophores replacing the DNA bases and can be assembled in many colors with excitation at a single wavelength. A DNA synthesizer was used to construct several short ODFs carrying a terminal alkyne group and having emission maxima of 410–670 nm. We developed a new approach to antibody conjugation, using Huisgen–Sharpless cycloaddition, which was used to react the alkynes on ODFs with azide groups added to secondary antibodies. Multiple ODF-tagged secondary antibodies were then used to mark primary antibodies. The set of antibodies was tested for spectral characteristics in labeling tubulin in HeLa cells and revealed a wide spectrum of colors, ranging from violet-blue to red with excitation through a single filter (340–380 nm). Selected sets of the differently labeled secondary antibodies were then used to simultaneously mark four antigens in fixed cells, using a single image and filter set. We also imaged different surface tumor markers on two live cell lines. Experiments showed that all colors could be visualized simultaneously by eye under the microscope, yielding multicolor images of multiple cellular antigens in real time. PMID:21321224

  18. Sequence information signal processor

    DOEpatents

    Peterson, John C. (Alta Loma, CA); Chow, Edward T. (San Dimas, CA); Waterman, Michael S. (Culver City, CA); Hunkapillar, Timothy J. (Pasadena, CA)

    1999-01-01

    An electronic circuit is used to compare two sequences, such as genetic sequences, to determine which alignment of the sequences produces the greatest similarity. The circuit includes a linear array of series-connected processors, each of which stores a single element from one of the sequences and compares that element with each successive element in the other sequence. For each comparison, the processor generates a scoring parameter that indicates which segment ending at those two elements produces the greatest degree of similarity between the sequences. The processor uses the scoring parameter to generate a similar scoring parameter for a comparison between the stored element and the next successive element from the other sequence. The processor also delivers the scoring parameter to the next processor in the array for use in generating a similar scoring parameter for another pair of elements. The electronic circuit determines which processor and alignment of the sequences produce the scoring parameter with the highest value.

  19. Sequencing General Chemistry

    NSDL National Science Digital Library

    B.J. Yoblinski

    2003-03-01

    The material in the authors' general chemistry curriculum has been rearranged into a sequence thought to be more logical to students than the traditional sequence. This fresh approach does not radically change course content but rather produces a systemat

  20. Cellulases and coding sequences

    DOEpatents

    Li, Xin-Liang (Athens, GA); Ljungdahl, Lars G. (Athens, GA); Chen, Huizhong (Lawrenceville, GA)

    2001-02-20

    The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

  1. Roles of repetitive sequences

    SciTech Connect

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  2. The LHC Sequencer

    E-print Network

    Alemany-Fernandez, Reyes; Gorbonosov, Roman; Khasbulatov, Denis; Lamont, Mike; Le Roux, Pascal; Roderick, Chris

    2011-01-01

    The Large Hadron Collider (LHC) at CERN is a highly complex system made of many different sub-systems whose operation implies the execution of many tasks with stringent constraints on the order and duration of the execution. To be able to operate such a system in the most efficient and reliable way, the operators in the CERN control room use a high level control system: the LHC Sequencer. The LHC Sequencer system is composed of several components, including an Oracle database where operational sequences are configured, a core server that orchestrates the execution of the sequences, and two graphical user interfaces: one for sequence edition, and another for sequence execution. This paper describes the architecture of the LHC Sequencer system, and how the sequences are prepared and used for LHC operation.

  3. Contamination of sequence databases with adaptor sequences

    SciTech Connect

    Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D. [National Institute of Mental Health, Bethesda, MD (United States)

    1997-02-01

    Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable of transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.

  4. Complete nucleotide sequence of two multidrug-resistant IncR plasmids from Klebsiella pneumoniae.

    PubMed

    Compain, Fabrice; Frangeul, Lionel; Drieux, Laurence; Verdet, Charlotte; Brisse, Sylvain; Arlet, Guillaume; Decré, Dominique

    2014-07-01

    We report here the complete nucleotide sequence of two IncR replicons encoding multidrug resistance determinants, including ?-lactam (blaDHA-1, blaSHV-12), aminoglycoside (aphA1, strA, strB), and fluoroquinolone (qnrB4, aac6'-1b-cr) resistance genes. The plasmids have backbones that are similar to each other, including the replication and stability systems, and contain a wide variety of transposable elements carrying known antibiotic resistance genes. This study confirms the increasing clinical importance of IncR replicons as resistance gene carriers. PMID:24752259

  5. Complete Nucleotide Sequence of Two Multidrug-Resistant IncR Plasmids from Klebsiella pneumoniae

    PubMed Central

    Compain, Fabrice; Frangeul, Lionel; Drieux, Laurence; Verdet, Charlotte; Brisse, Sylvain; Arlet, Guillaume

    2014-01-01

    We report here the complete nucleotide sequence of two IncR replicons encoding multidrug resistance determinants, including ?-lactam (blaDHA-1, blaSHV-12), aminoglycoside (aphA1, strA, strB), and fluoroquinolone (qnrB4, aac6?-1b-cr) resistance genes. The plasmids have backbones that are similar to each other, including the replication and stability systems, and contain a wide variety of transposable elements carrying known antibiotic resistance genes. This study confirms the increasing clinical importance of IncR replicons as resistance gene carriers. PMID:24752259

  6. Complete Nucleotide Sequence of a Conjugative Plasmid Carrying blaPER-1.

    PubMed

    Li, Ruichao; Wong, Marcus Ho Yin; Zhou, Yuanjie; Chan, Edward Wai-Chi; Chen, Sheng

    2015-06-01

    The nucleotide sequence of a self-transmissible plasmid pVPH1 harboring blaPER-1 from Vibrio parahaemolyticus was determined. pVPH1 was 183,730 bp in size and shared a backbone similar to pAQU1 and pAQU2, differing mainly in an ?40-kb multidrug resistance (MDR) region. A complex class 1 integron was identified together with ISCR1 and blaPER-1 (ISCR1-blaPER-1-gst-abct-qacE?1-sul1), which was shown to form a circular intermediate playing an important role in the dissemination of blaPER-1. PMID:25779581

  7. Recycle of random sequences

    E-print Network

    Nobuyasu Ito; Macoto Kikuchi; Yutaka Okabe

    1993-02-07

    The correlation between a random sequence and its transformed sequences is studied. In the case of a permutation operation or, in other word, the shuffling operation, it is shown that the correlation can be so small that the sequences can be regarded as independent random sequences. The applications to the Monte Carlo simulations are also given. This method is especially useful in the Ising Monte Carlo simulation.

  8. Spooky Sequences- Square Numbers

    NSDL National Science Digital Library

    Mark Cogan

    2002-01-01

    This interactive Flash game helps students recognize and generate the sequence of square numbers, and also to discover the pattern of differences between them. The applet displays a sequence of six consecutive square numbers with one number missing. The player provides the missing number to "send the ghosts back to the haunted house." Each game consists of five sequences to complete.

  9. Career Academy Course Sequences.

    ERIC Educational Resources Information Center

    Markham, Thom; Lenz, Robert

    This career academy course sequence guide is designed to give teachers a quick overview of the course sequences of well-known career academy and career pathway programs from across the country. The guide presents a variety of sample course sequences for the following academy themes: (1) arts and communication; (2) business and finance; (3)…

  10. Watermarking Using Decimal Sequences

    Microsoft Academic Search

    Navneet Mandhani; Subhash Kak

    2005-01-01

    This paper introduces the use of decimal sequences in a code division multiple access (CDMA) based watermarking system to hide information for authentication in black and white images. Matlab version 6.5 was used to implement the algorithms discussed in this paper. The advantage of using d-sequences over PN sequences is that one can choose from a variety of prime numbers

  11. Watermarking Using Decimal Sequences

    Microsoft Academic Search

    Navneet Mandhani; Subhash Kak

    2006-01-01

    This paper introduces the use of decimal sequences in a code division multiple access (CDMA) based watermarking system to hide information for authentication in black and white images. Matlab version 6.5 was used to implement the algorithms discussed in this paper. The advantage of using d-sequences over PN sequences is that one can choose from a variety of prime numbers

  12. Composite stimulated Raman adiabatic passage

    NASA Astrophysics Data System (ADS)

    Torosov, Boyan T.; Vitanov, Nikolay V.

    2013-04-01

    We introduce a high-fidelity technique for coherent control of three-state quantum systems, which combines two popular control tools—stimulated Raman adiabatic passage (STIRAP) and composite pulses. By using composite sequences of pairs of partly delayed pulses with appropriate phases, the nonadiabatic transitions, which prevent STIRAP from reaching unit fidelity, can be canceled to an arbitrary order by destructive interference, and therefore, the technique can be made arbitrarily accurate. The composite phases are given by simple analytic formulas, and they are universal for they do not depend on the specific pulse shapes, the pulse delay, and the pulse areas.

  13. Asphaltic compositions

    SciTech Connect

    Wright, W.E.; Zaweski, E.F.

    1987-02-24

    This patent describes an asphaltic composition of enhanced utility for vehicular pavement which composition comprises a road paving grade of asphalt in admixture with at least one alkylene dithiocarbamate. The composition is characterized by having a reduced increase in absolute viscosity to original absolute viscosity after thin film aging as measured by ASTM Test D 1754 at 140/sup 0/F.

  14. Computational methods in sequence and structure prediction

    NASA Astrophysics Data System (ADS)

    Lang, Caiyi

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

  15. Composites of vinyl polystyrylpyridine/bismaleimide-aliphatic ether copolymers

    NASA Technical Reports Server (NTRS)

    Heimbuch, Alvin H.; Rosser, Robert W.; Hsu, Ming-Ta S.

    1989-01-01

    An aliphatic ether bismaleimide was prepared and coreacted with a polyvinylstyrylpyridine (VPSP) oligomer. Studies showed that a controlled ratio of aliphatic to aromatic units in the polymer backbone improved both processibility and interlaminar shear properties for the carbon-fiber composite system. This modified resin was readily soluble in tetrahydrofuran, allowing for better fiber impregnation and thus enhancing adhesive properties and reproducibility. DSC studies have shown a lower cure temperature for the copolymer than for the neat aliphatic bismaleimide, and a glass transition temperature of 260 C, which is more than adequate for most applications. Limited measurements indicated an improvement in toughness (impact resistance).

  16. One short cysteine-rich sequence pattern - two different disulfide-bonded structures - a molecular dynamics simulation study.

    PubMed

    Dames, Sonja A

    2015-06-01

    The nematocyst walls of Hydra are formed by proteins containing small cysteine-rich domains (CRDs) of ~25 amino acids. The first CRD of nematocyst outer all antigen (NW1) and the C-terminal CRD of minicollagen-1 (Mcol1C) contain six cysteines at identical sequence positions, however adopt different disulfide bonded structures. NW1 shows the disulfide connectivities C2-C14/C6-C19/C10-C18 and Mcol1C C2-C18/C6-C14/C10-C19. To analyze if both show structural preferences in the open, non-disulfide bonded form, which explain the formation of either disulfide connectivity pattern, molecular dynamics (MD) simulations at different temperatures were performed. NW1 maintained in the 100-ns MD simulations at 283?K a rather compact fold that is stabilized by specific hydrogen bonds. The Mcol1C structure fluctuated overall more, however stayed most of the time also rather compact. The analysis of the backbone ?/? angles indicated different turn propensities for NW1 and Mcol1C, which mostly can be explained based on published data about the influence of different amino acid side chains on the local backbone conformation. Whereas a folded precursor mechanism may be considered for NW1, Mcol1C may fold according to the quasi-stochastic folding model involving disulfide bond reshuffling and conformational changes, locking the native disulfide conformations. The study further demonstrates the power of MD simulations to detect local structural preferences in rather dynamic systems such as the open, non-disulfide bonded forms of NW1 and Mcol1C, which complement published information from NMR backbone residual dipolar couplings. Because the backbone structural preferences encoded by the amino acid sequence embedding the cysteines influence which disulfide connectivities are formed, the data are generally interesting for a better understanding of oxidative folding and the design of disulfide stabilized therapeutics. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd. PMID:25781269

  17. The Fibonacci Sequence & Robots

    NSDL National Science Digital Library

    2014-09-18

    Using the LEGO® NXT robotics kit, students construct and program robots to illustrate and explore the Fibonacci sequence. Within teams, students are assigned roles: group leader, chassis builder, arm builder, chief programmer, and Fibonacci verifier. By designing a robot that moves based on the Fibonacci sequence of numbers, they can better visualize how quickly the numbers in the sequence grow. To program the robot to move according to these numbers, students break down the sequence into simple algebraic equations so that the computer can understand the Fibonacci sequence.

  18. Simultaneously high stiffness and damping in nanoengineered microtruss composites.

    PubMed

    Meaud, Julien; Sain, Trisha; Yeom, Bongjun; Park, Sei Jin; Shoultz, Anna Brieland; Hulbert, Gregory; Ma, Zheng-Dong; Kotov, Nicholas A; Hart, A John; Arruda, Ellen M; Waas, Anthony M

    2014-04-22

    Materials combining high stiffness and mechanical energy dissipation are needed in automotive, aviation, construction, and other technologies where structural elements are exposed to dynamic loads. In this paper we demonstrate that a judicious combination of carbon nanotube engineered trusses held in a dissipative polymer can lead to a composite material that simultaneously exhibits both high stiffness and damping. Indeed, the combination of stiffness and damping that is reported is quite high in any single monolithic material. Carbon nanotube (CNT) microstructures grown in a novel 3D truss topology form the backbone of these nanocomposites. The CNT trusses are coated by ceramics and by a nanostructured polymer film assembled using the layer-by-layer technique. The crevices of the trusses are then filled with soft polyurethane. Each constituent of the composite is accurately modeled, and these models are used to guide the manufacturing process, in particular the choice of the backbone topology and the optimization of the mechanical properties of the constituent materials. The resulting composite exhibits much higher stiffness (80 times) and similar damping (specific damping capacity of 0.8) compared to the polymer. Our work is a step forward in implementing the concept of materials by design across multiple length scales. PMID:24620996

  19. Identifying features in biological sequences: Sixth workshop report

    SciTech Connect

    Burks, C. [Los Alamos National Lab., NM (United States); Myers, E. [Univ. of Arizona (United States); Pearson, W.R. [Univ. of Virginia (United States)

    1995-12-31

    This report covers the sixth of an annual series of workshops held at the Aspen Center for Physics concentrating particularly on the identification of features in DNA sequence, and more broadly on related topics in computational molecular biology. The workshop series originally focused primarily on discussion of current needs and future strategies for identifying and predicting the presence of complex functional units on sequenced, but otherwise uncharacterized, genomic DNA. We addressed the need for computationally-based, automatic tools for synthesizing available data about individual consensus sequences and local compositional patterns into the composite objects (e.g., genes) that are -- as composite entities -- the true object of interest when scanning DNA sequences. The workshop was structured to promote sustained informal contact and exchange of expertise between molecular biologists, computer scientists, and mathematicians.

  20. Deoxyribonucleic Acid Base Sequence Relatedness among Members of the Yeast Genus Kluyveromyces

    Microsoft Academic Search

    GAYLE B. FUSON; HEATHER L. PRESLEY; HERMAN J. PHAFF

    1987-01-01

    Deoxyribonucleic acid (DNA) base composition and DNA base sequence relatedness comparisons were used for species delineation in the genus Kluyveromyces. Base composition values separated the members of the genus into three groups. The groups were further subdivided by comparing base sequences by using DNAIDNA renaturation experiments. Two DNA homology groups were identified. The first group included Kluyveromyces marxianus, Kluyveromyces fragilis,

  1. Dynamic fracture of advanced fiber composites

    NASA Technical Reports Server (NTRS)

    Williams, J. H., Jr.

    1977-01-01

    Efforts to investigate some of the theoretical bases for the dynamic fracture of graphite fiber reinforced composites are described. In particular, the initiation of unstable fracture in unidirectional cracked composites, dynamic crack propagation as modeled by orthotropic double cantilever beams, and interlaminar stresses for laminates having arbitrary stacking sequences are summarized.

  2. Natural melanin composites by layer-by-layer assembly

    NASA Astrophysics Data System (ADS)

    Eom, Taesik; Shim, Bong Sub

    2015-04-01

    Melanin is an electrically conductive and biocompatible material, because their conjugated backbone structures provide conducting pathways from human skin, eyes, brain, and beyond. So there is a potential of using as materials for the neural interfaces and the implantable devices. Extracted from Sepia officinalis ink, our natural melanin was uniformly dispersed in mostly polar solvents such as water and alcohols. Then, the dispersed melanin was further fabricated to nano-thin layered composites by the layer-by-layer (LBL) assembly technique. Combined with polyvinyl alcohol (PVA), the melanin nanoparticles behave as an LBL counterpart to from finely tuned nanostructured films. The LBL process can adjust the smart performances of the composites by varying the layering conditions and sandwich thickness. We further demonstrated the melanin loading degree of stacked layers, combination nanostructures, electrical properties, and biocompatibility of the resulting composites by UV-vis spectrophotometer, scanning electron microscope (SEM), multimeter, and in-vitro cell test of PC12, respectively.

  3. Additive-assisted control over phase-separated nanostructures by manipulating alkylthienyl position at donor backbone for solution-processed, non-fullerene, all-small-molecule solar cells.

    PubMed

    Huang, Jianhua; Wang, Xue; Zhang, Xin; Niu, Zhixiao; Lu, Zhenhuan; Jiang, Bo; Sun, Yuxi; Zhan, Chuanlang; Yao, Jiannian

    2014-03-26

    A non-fullerene, all-small-molecule solar cell (NF-SMSC) device uses the blend of a small molecule donor and a small molecule acceptor as the active layer. Aggregation ability is a key factor for this type of solar cell. Herein, we used the alkylthienyl unit to tune the aggregation ability of the diketopyrrolopyrrole (DPP)-based small molecule donors. Replacing two alkoxyl units in BDT-O-DPP with two alkylthienyl units yields BDT-T-DPP, and further introducing another two alkylthienyl units into the backbone produces BDT-T-2T-DPP. With the introduction of alkylthienyl, the backbone becomes twisted. As a result, the ??-stacking strength, aggregation ability, and crystallite size all obey the sequence of BDT-O-DPP > BDT-T-DPP > BDT-T-2T-DPP. When selected a reported perylene diimide dimer of bis-PDI-T-EG as acceptor, the best NF-SMSC device exhibits a power conversion efficiency of 1.34, 2.01, and 1.62%, respectively, for the BDT-O-DPP, BDT-T-DPP, and BDT-T-2T-DPP based system. The BDT-T-DPP/bis-PDI-T-EG system yields the best efficiency of 2.01% among the three combinations. This is due to the moderate aggregation ability of BDT-T-DPP yields moderate phase size of 30-50 nm, whereas the strong aggregation ability of BDT-O-DPP gives a bigger size of 50-80 nm, and the weak aggregation ability of BDT-T-2T-DPP produces a smaller size of 10-30 nm. The BDT-T-DPP/bis-PDI-T-EG combination exhibits balanced hole/electron mobility of 0.022/0.016 cm(2)/(V s), whereas the BDT-O-DPP/bis-PDI-T-EG and the BDT-T-2T-DPP/bis-PDI-T-EG blend show a hole/electron mobility of 0.0011/0.0057 cm(2)/(V s) and 0.0016/0.11 cm(2)/(V s), respectively. PMID:24559327

  4. Dipeptide Sequence Determination: Analyzing Phenylthiohydantoin Amino Acids by HPLC

    NASA Astrophysics Data System (ADS)

    Barton, Janice S.; Tang, Chung-Fei; Reed, Steven S.

    2000-02-01

    Amino acid composition and sequence determination, important techniques for characterizing peptides and proteins, are essential for predicting conformation and studying sequence alignment. This experiment presents improved, fundamental methods of sequence analysis for an upper-division biochemistry laboratory. Working in pairs, students use the Edman reagent to prepare phenylthiohydantoin derivatives of amino acids for determination of the sequence of an unknown dipeptide. With a single HPLC technique, students identify both the N-terminal amino acid and the composition of the dipeptide. This method yields good precision of retention times and allows use of a broad range of amino acids as components of the dipeptide. Students learn fundamental principles and techniques of sequence analysis and HPLC.

  5. A Network Flow Approach to Predict Protein Targets and Flavonoid Backbones to Treat Respiratory Syncytial Virus Infection

    PubMed Central

    Poloni, Joice de Faria; Saraiva Macedo Timmers, Luis Fernando; Bonatto, Diego; Condessa Pitrez, Paulo Márcio; Tetelbom Stein, Renato

    2015-01-01

    Background. Respiratory syncytial virus (RSV) infection is the major cause of respiratory disease in lower respiratory tract in infants and young children. Attempts to develop effective vaccines or pharmacological treatments to inhibit RSV infection without undesired effects on human health have been unsuccessful. However, RSV infection has been reported to be affected by flavonoids. The mechanisms underlying viral inhibition induced by these compounds are largely unknown, making the development of new drugs difficult. Methods. To understand the mechanisms induced by flavonoids to inhibit RSV infection, a systems pharmacology-based study was performed using microarray data from primary culture of human bronchial cells infected by RSV, together with compound-proteomic interaction data available for Homo sapiens. Results. After an initial evaluation of 26 flavonoids, 5 compounds (resveratrol, quercetin, myricetin, apigenin, and tricetin) were identified through topological analysis of a major chemical-protein (CP) and protein-protein interacting (PPI) network. In a nonclustered form, these flavonoids regulate directly the activity of two protein bottlenecks involved in inflammation and apoptosis. Conclusions. Our findings may potentially help uncovering mechanisms of action of early RSV infection and provide chemical backbones and their protein targets in the difficult quest to develop new effective drugs. PMID:25879022

  6. Inter-domain orientation and motions in VAT-N explored by residual dipolar couplings and 15N backbone relaxation.

    PubMed

    Deshmukh, Mandar V; John, Michael; Coles, Murray; Peters, Jürgen; Baumeister, Wolfgang; Kessler, Horst

    2006-07-01

    The N-terminal domain of VAT (Valosine-containing protein-like ATPase of Thermoplasma acidophilum), VAT-N (20.5 kDa), is considered to be the primary substrate-recognition site of the complex. The solution structure of VAT-N derived in our laboratory using conventionally obtained NMR restraints shows the existence of two equally sized sub-domains, VAT-Nn and VAT-Nc, together forming a kidney-shaped overall structure. The putative substrate-binding site of VAT-N involves free loops and a highly charged groove located on the surface of the protein. Alternatively, the opening of the cleft between the domains to accommodate substrate has been proposed to be part of the functional mechanism. We have used the residual dipolar couplings (RDCs) obtained in a bicelle medium to refine the structure of VAT-N. The long-range information available from RDCs both defines the sub-domain orientation and probes possible inter-domain motions. In addition, 15N backbone relaxation data were obtained and analysed within the model-free framework. Together, the data provides a refined structure with improved local geometry, but with the overall kidney shape intact. Further, the protein is rigid overall, with no evidence of inter-domain motions. PMID:16826545

  7. DYNAFOLD: A DYNAMIC PROGRAMMING APPROACH TO PROTEIN BACKBONE STRUCTURE DETERMINATION FROM MINIMAL SETS OF RESIDUAL DIPOLAR COUPLINGS

    PubMed Central

    MUKHOPADHYAY, RISHI; IRAUSQUIN, STEPHANIE; SCHMIDT, CHRISTOPHER; VALAFAR, HOMAYOUN

    2014-01-01

    Residual Dipolar Couplings (RDCs) are a source of NMR data that can provide a powerful set of constraints on the orientation of inter-nuclear vectors, and are quickly becoming a larger part of the experimental toolset for molecular biologists. However, few reliable protocols exist for the determination of protein backbone structures from small sets of RDCs. DynaFold is a new dynamic programming algorithm designed specifically for this task, using minimal sets of RDCs collected in multiple alignment media. DynaFold was first tested utilizing synthetic data generated for the N-H, C?-H?, and C-N vectors of 1BRF, 1F53, 110M and 3LAY proteins, with up to ±1 Hz error in 3 alignment media, and was able to produce structures with less than 1.9Å of the original structures. DynaFold was then tested using experimental data, obtained from the Biological Magnetic Resonance Bank, for proteins PDBID:1P7E and PDBID:1D3Z using RDC data from two alignment media. This exercise yielded structures within 1.0Å of their respective published structures in segments with high data density, and less than 1.9Å over the entire protein. The same sets of RDC data were also used in comparisons with traditional methods for analysis of RDCs, which failed to match the accuracy of DynaFold's approach to structure determination. PMID:24467760

  8. Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding.

    PubMed

    Du, Qi-Shi; Chen, Dong; Xie, Neng-Zhong; Huang, Ri-Bo; Chou, Kuo-Chen

    2015-09-01

    Although not being classified as the most fundamental protein structural elements like ?-helices and ?-strands, the loop segment may play considerable roles for protein stability, flexibility, and dynamic activity. Meanwhile, the protein loop is also quite elusive; i.e. its interactions with the other parts of protein as well as its own shape-maintaining forces have still remained as a puzzle or at least not quite clear yet. Here, we report a molecular force, the so-called polar hydrogen-? interaction (Hp-?), which may play an important role in supporting the backbones of protein loops. By conducting the potential energy surface scanning calculations on the quasi ?-plane of peptide bond unit, we have observed the following intriguing phenomena: (1) when the polar hydrogen atom of a peptide unit is perpendicularly pointing to the ?-plane of other peptide bond units, a remarkable Hp-? interaction occurs; (2) the interaction is distance and orientation dependent, acting in a broad space, and belonging to the 'point-to-plane' one. The molecular force reported here may provide useful interaction concepts and insights into better understanding the loop's unique stability and flexibility feature, as well as the driving force of the protein global folding. PMID:25375237

  9. Synthesis and in vitro antioxidant functions of protein hydrolysate from backbones of Rastrelliger kanagurta by proteolytic enzymes

    PubMed Central

    Sheriff, Sheik Abdulazeez; Sundaram, Balasubramanian; Ramamoorthy, Baranitharan; Ponnusamy, Ponmurugan

    2013-01-01

    Every year, a huge quantity of fishery wastes and by-products are generated by fish processing industries. These wastes are either underutilized to produce low market value products or dumped leading to environmental issues. Complete utilization of fishery wastes for recovering value added products would be beneficial to the society and individual. The fish protein hydrolysates and derived peptides of fishery resources are widely used as nutritional supplements, functional ingredients, and flavor enhancers in food, beverage and pharmaceutical industries. Antioxidants from fishery resources have attracted the attention of researchers as they are cheaper in cost, easy to derive, and do not have side effects. Thus the present investigation was designed to produce protein hydrolysate by pepsin and papain digestion from the backbones of Rastrelliger kanagurta (Indian mackerel) and evaluate its antioxidant properties through various in vitro assays. The results reveal that both hydrolysates are potent antioxidants, capable of scavenging 46% and 36% of DPPH (1,1-diphenyl-2 picrylhydrazyl) and 58.5% and 37.54% of superoxide radicals respectively. The hydrolysates exhibit significant (p < 0.05) reducing power and lipid peroxidation inhibition. Among the two hydrolysates produced, pepsin derived fraction is superior than papain derived fraction in terms of yield, DH (Degree of hydrolysis), and antioxidant activity. PMID:24596496

  10. Backbone and ILV methyl resonance assignments of E. coli thymidylate synthase bound to cofactor and a nucleotide analogue

    PubMed Central

    Sapienza, Paul J.; Lee, Andrew L.

    2013-01-01

    Thymidylate synthase (TSase) is a 62 kDa homodimeric enzyme required for de novo synthesis of thymidine monophosphate (dTMP) in most organisms. This makes the enzyme an excellent target for anticancer and microbial antibiotic drugs. In addition, TSase has been shown to exhibit negative cooperativity and half-the-sites reactivity. For these collective reasons, TSase is widely studied, and much is known about its kinetics and structure as it progresses through a multi-step catalytic cycle. Recently, nuclear magnetic resonance (NMR) spin relaxation has been instrumental in demonstrating the critical role of dynamics in enzyme function in small model systems. These studies raise questions about how dynamics affect function in larger enzymes with more complex reaction coordinates. TSase is an ideal candidate given its size, oligomeric state, cooperativity, and status as a drug target. Here, as a pre-requisite to spin relaxation studies, we present the backbone and ILV methyl resonance assignments of TSase from Escherichia coli bound to a substrate analogue and cofactor. PMID:23653343

  11. Backbone nuclear relaxation characteristics and calorimetric investigation of the human Grb7-SH2/erbB2 peptide complex

    PubMed Central

    Ivancic, Monika; Spuches, Anne M.; Guth, Ethan C.; Daugherty, Margaret A.; Wilcox, Dean E.; Lyons, Barbara A.

    2005-01-01

    Grb7 is a member of the Grb7 family of proteins, which also includes Grb10 and Grb14. All three proteins have been found to be overexpressed in certain cancers and cancer cell lines. In particular, Grb7 (along with the receptor tyrosine kinase erbB2) is overexpressed in 20%–30% of breast cancers. Grb7 binds to erbB2 and may be involved in cell signaling pathways that promote the formation of metastases and inflammatory responses. In a prior study, we reported the solution structure of the Grb7-SH2/erbB2 peptide complex. In this study, T1, T2, and steady-state NOE measurements were performed on the Grb7-SH2 domain, and the backbone relaxation behavior of the domain is discussed with respect to the potential function of an insert region present in all three members of this protein family. Isothermal titration calorimetry (ITC) studies were completed measuring the thermodynamic parameters of the binding of a 10-residue phosphorylated peptide representative of erbB2 to the SH2 domain. These measurements are compared to calorimetric studies performed on other SH2 domain/phosphorylated peptide complexes available in the literature. PMID:15930003

  12. Quantifying sequence and structural features of protein–RNA interactions

    PubMed Central

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

    2014-01-01

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

  13. Sequence-structure relationships in DNA oligomers: a computational approach.

    PubMed

    Packer, M J; Hunter, C A

    2001-08-01

    A collective-variable model for DNA structure is used to predict the conformation of a set of 30 octamer, decamer, and dodecamer oligomers for which high-resolution crystal structures are available. The model combines an all-atom base pair representation with an empirical backbone, emphasizing the role of base stacking in fixing sequence-dependent structure. We are able to reproduce trends in roll and twist to within 5 degrees across a large database of both A- and B-DNA oligomers. A genetic algorithm approach is used to search for global minimum structures and this is augmented by a grid search to identify local minimums. We find that the number of local minimums is highly sequence dependent, with certain sequences having a set of minimums that span the entire range between canonical A- and B-DNA conformations. Although the global minimum does not always agree with the crystal structure, for 24 of the 30 oligomers, we find low-energy local minimums that match the experimental step parameters. Discrepancies throw some light on the role of crystal packing in determining the solid-state conformation of double-helical DNA. PMID:11472171

  14. Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences

    E-print Network

    Stadler, Peter F.

    Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences Roman R. Stocsits1 , Ivo L data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared use of the amino acid sequence when aligning coding nucleic acid sequences. In many cases, however

  15. Genomic Sequence Analysis Using Gap Sequences and Pattern Filtering

    Microsoft Academic Search

    Shih-chieh Su; Chia H. Yeh; C.-C. Jay Kuo

    2003-01-01

    A new pattern filtering technique is developed to ana- lyze the genomic sequence in this research based on gap sequences, in which the distance of the same symbol is re- corded consecutively as a sequence of integers. Sequence alignment and similarity testing can be performed on a family of gap sequences over selected patterns. The gap sequence offers a new

  16. An investigation into hybrid carbon\\/glass fiber reinforced epoxy composite automotive drive shaft

    Microsoft Academic Search

    M. A. Badie; E. Mahdi; A. M. S. Hamouda

    2011-01-01

    This paper examines the effect of fiber orientation angles and stacking sequence on the torsional stiffness, natural frequency, buckling strength, fatigue life and failure modes of composite tubes. Finite element analysis (FEA) has been used to predict the fatigue life of composite drive shaft (CDS) using linear dynamic analysis for different stacking sequence. Experimental program on scaled woven fabric composite

  17. ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets

    Microsoft Academic Search

    Guan Ning Lin; Zhipeng Cai; Guohui Lin; Sounak Chakraborty; Dong Xu

    2009-01-01

    BACKGROUND: With the increasing availability of whole genome sequences, it is becoming more and more important to use complete genome sequences for inferring species phylogenies. We developed a new tool ComPhy, 'Composite Distance Phylogeny', based on a composite distance matrix calculated from the comparison of complete gene sets between genome pairs to produce a prokaryotic phylogeny. RESULTS: The composite distance

  18. Altered Amino Acid Sequence Affects Amyloid Formation In A?(25-35) 

    E-print Network

    Chateau, Morgan

    2007-09-17

    papers have shown, the peptide loses the ability to form amyloid fibrils when the sequence of amino acids is changed (2). For this experiment, four different A?(25-35) sequences were tested, each having the same composition but a different sequence. FPLC...

  19. The KH domain of the branchpoint sequence binding protein determines specificity for the pre-mRNA branchpoint sequence.

    PubMed Central

    Berglund, J A; Fleming, M L; Rosbash, M

    1998-01-01

    The yeast and mammalian branchpoint sequence binding proteins (BBP and mBBP/SF1) contain both KH domain and Zn knuckle RNA-binding motifs. The single KH domain of these proteins is sufficient for specific recognition of the pre-mRNA branchpoint sequence (BPS). However, an interaction is only apparent if one or more accessory modules are present to increase binding affinity. The Zn knuckles of BBP/mBBP can be replaced by an RNA-binding peptide derived from the HIV-1 nucleocapsid protein or by an arginine-serine (RS)7 peptide, without loss of specificity. Only the seven-nucleotide branchpoint sequence and two nucleotides to either side are necessary for RNA binding to the chimeric proteins. Therefore, we propose that all three of these accessory RNA-binding modules bind the phosphate backbone, whereas the KH domain interacts specifically with the bases of the BPS. Proteins and protein complexes with multiple RNA-binding motifs are frequent, suggesting that an intimate collaboration between two or more motifs will be a general theme in RNA-protein interactions. PMID:9701290

  20. Comparison of metagenomic samples using sequence signatures

    PubMed Central

    2012-01-01

    Background Sequence signatures, as defined by the frequencies of k-tuples (or k-mers, k-grams), have been used extensively to compare genomic sequences of individual organisms, to identify cis-regulatory modules, and to study the evolution of regulatory sequences. Recently many next-generation sequencing (NGS) read data sets of metagenomic samples from a variety of different environments have been generated. The assembly of these reads can be difficult and analysis methods based on mapping reads to genes or pathways are also restricted by the availability and completeness of existing databases. Sequence-signature-based methods, however, do not need the complete genomes or existing databases and thus, can potentially be very useful for the comparison of metagenomic samples using NGS read data. Still, the applications of sequence signature methods for the comparison of metagenomic samples have not been well studied. Results We studied several dissimilarity measures, including d2, d2* and d2S recently developed from our group, a measure (hereinafter noted as Hao) used in CVTree developed from Hao’s group (Qi et al., 2004), measures based on relative di-, tri-, and tetra-nucleotide frequencies as in Willner et al. (2009), as well as standard lp measures between the frequency vectors, for the comparison of metagenomic samples using sequence signatures. We compared their performance using a series of extensive simulations and three real next-generation sequencing (NGS) metagenomic datasets: 39 fecal samples from 33 mammalian host species, 56 marine samples across the world, and 13 fecal samples from human individuals. Results showed that the dissimilarity measure d2S can achieve superior performance when comparing metagenomic samples by clustering them into different groups as well as recovering environmental gradients affecting microbial samples. New insights into the environmental factors affecting microbial compositions in metagenomic samples are obtained through the analyses. Our results show that sequence signatures of the mammalian gut are closely associated with diet and gut physiology of the mammals, and that sequence signatures of marine communities are closely related to location and temperature. Conclusions Sequence signatures can successfully reveal major group and gradient relationships among metagenomic samples from NGS reads without alignment to reference databases. The d2S dissimilarity measure is a good choice in all application scenarios. The optimal choice of tuple size depends on sequencing depth, but it is quite robust within a range of choices for moderate sequencing depths. PMID:23268604

  1. Composite Materials

    NASA Technical Reports Server (NTRS)

    1985-01-01

    Composites are lighter and stronger than metals. Aramid fibers like Kevlar and Nomex were developed by DuPont Corporation and can be combined in a honeycomb structure which can give an airplane a light, tough structure. Composites can be molded into many aerodynamic shapes eliminating rivets and fasteners. Langley Research Center has tested composites for both aerospace and non-aerospace applications. They are also used in boat hulls, military shelters, etc.

  2. The Linus Sequence

    Microsoft Academic Search

    Paul Balister; Steve Kalikow; Amites Sarkar

    2010-01-01

    Define the Linus sequence Ln for n ? 1 as a 0-1 sequence with L1 = 0, and Ln chosen so as to minimize the length of the longest repeated block Ln?2r+1 ...Ln?r = Ln?r+1 ...Ln. Define the Sally sequence Sn as the length r of the longest repeated block that was avoided by the choice of Ln. We prove

  3. Sulfur-infiltrated graphene-backboned mesoporous carbon nanosheets with a conductive polymer coating for long-life lithium-sulfur batteries

    NASA Astrophysics Data System (ADS)

    Dong, Yanfeng; Liu, Shaohong; Wang, Zhiyu; Liu, Yang; Zhao, Zongbin; Qiu, Jieshan

    2015-04-01

    Sandwich-type, two-dimensional hybrid nanosheets were fabricated by the infiltration of nanosized sulfur into graphene-backboned mesoporous carbon with a PPy nanocoating. They exhibit a high reversible capacity for as long as 400 cycles with an ultra slow decay rate of 0.05% per cycle at the high rate of 1-3 C due to the efficient immobilization of polysulfides.Sandwich-type, two-dimensional hybrid nanosheets were fabricated by the infiltration of nanosized sulfur into graphene-backboned mesoporous carbon with a PPy nanocoating. They exhibit a high reversible capacity for as long as 400 cycles with an ultra slow decay rate of 0.05% per cycle at the high rate of 1-3 C due to the efficient immobilization of polysulfides. Electronic supplementary information (ESI) available: Experimental details, BET, SEM, XPS and more electrochemical data. See DOI: 10.1039/c5nr01015b

  4. New theories for smectic and nematic liquid-crystal polymers: Backbone LCPs (liquid crystalline polymers) and their mixtures and side-chain LCPs

    SciTech Connect

    Dowell, F.

    1987-01-01

    A summary of predictions and explanations from statistical-physics theories for both backbone and side-chain liquid crystalline polymers (LCPs) and for mixtures with backbone LCPs are presented. Trends in the thermodynamic and molecular ordering properties have been calculated as a function of pressure, density, temperature, and molecule chemical structures (including degree of polymerization and the following properties of the chemical structures of the repeat units: lengths and shapes, intra-chain rotation energies, dipole moments, site-site polarizabilities and Lennard-Jones potentials, etc.) in nematic and multiple smectic-A LC phases and in the isotropic liquid phase. The theoretical results are found to be in good agreement with existing experimental data. These theories can also be applied to combined LCPs. Since these theories have no ad hoc or arbitrarily adjustable parameters, these theories can be used to design new LCPs and new solvents as well as to predict and explain properties. 27 refs., 4 tabs.

  5. Energetic composites

    DOEpatents

    Danen, Wayne C. (Los Alamos, NM); Martin, Joe A. (Espanola, NM)

    1993-01-01

    A method for providing chemical energy and energetic compositions of matter consisting of thin layers of substances which will exothermically react with one another. The layers of reactive substances are separated by thin layers of a buffer material which prevents the reactions from taking place until the desired time. The reactions are triggered by an external agent, such as mechanical stress or an electric spark. The compositions are known as metastable interstitial composites (MICs). This class of compositions includes materials which have not previously been capable of use as energetic materials. The speed and products of the reactions can be varied to suit the application.

  6. Computer assisted multiplex sequencing

    SciTech Connect

    Church, G.M.

    1992-08-01

    The objectives of this project are automation and optimization of multiplex sequencing. This year we have integrated direct transfer electrophoresis, automated multiplex hybridizations and automated film reading and applied this toward sequencing of three contiguous E. coli cosmids. Primers for the directed dideoxy sequence walking and sequence confirmation steps were synthesized with a 15 base tag complimentary to an alkaline phosphatase conjugate. A higher throughput synthesis device is well along in testing as are new automated hybridization devices. We have developed software for automatically annotating ORFs and databases of precise termini of proteis and RNA.

  7. Effect of Hydroxyl Concentration on Chemical Sensitivity of Polyvinyl Alcohol/Carbon-Black Composite Chemiresistors

    SciTech Connect

    Hughes, Robert C.; Patel, Sanjay V.; Yelton, W. Graham

    1999-05-19

    The sensitivity and selectivity of polyvinyl alcohol (PVA) / carbon black composite films have been found to vary depending upon the hydroxylation percentage ("-OH") of the polymer. These chemiresistors made from PVA films whose polymer backbone is 88% hydroxylated (PVA88) have a high sensitivity to water, while chemiresistors made from PVA75 have a higher sensitivity to methanol. The minor differences in polymer composition result in films with different Hildebrand volubility parameters. The relative responses of several different PVA-based chemiresistors to solvents with different volubility parameters are presented. In addition, polyvinyl acetate (PVAC) films with PVA88 are used in an array to distinguish the responses to methanol-water mixtures.

  8. Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies

    Microsoft Academic Search

    Donald Hamelberg; Loren Dean Williams; W. David Wilson

    2002-01-01

    Alternative models have been presented to provide explanations for the sequence-dependent variation of the DNA minor groove width. In a structural model groove narrowing in A-tracts results from direct, short-range interactions among DNA bases. In an electrostatic model, the narrow minor groove of A-tracts is proposed to respond to sequence- dependent localization of water and cations. Molecular dynamics simulations on

  9. Fluorescent signatures for variable DNA sequences.

    PubMed

    Rice, John E; Reis, Arthur H; Rice, Lisa M; Carver-Brown, Rachel K; Wangh, Lawrence J

    2012-11-01

    Life abounds with genetic variations writ in sequences that are often only a few hundred nucleotides long. Rapid detection of these variations for identification of genetic diseases, pathogens and organisms has become the mainstay of molecular science and medicine. This report describes a new, highly informative closed-tube polymerase chain reaction (PCR) strategy for analysis of both known and unknown sequence variations. It combines efficient quantitative amplification of single-stranded DNA targets through LATE-PCR with sets of Lights-On/Lights-Off probes that hybridize to their target sequences over a broad temperature range. Contiguous pairs of Lights-On/Lights-Off probes of the same fluorescent color are used to scan hundreds of nucleotides for the presence of mutations. Sets of probes in different colors can be combined in the same tube to analyze even longer single-stranded targets. Each set of hybridized Lights-On/Lights-Off probes generates a composite fluorescent contour, which is mathematically converted to a sequence-specific fluorescent signature. The versatility and broad utility of this new technology is illustrated in this report by characterization of variant sequences in three different DNA targets: the rpoB gene of Mycobacterium tuberculosis, a sequence in the mitochondrial cytochrome C oxidase subunit 1 gene of nematodes and the V3 hypervariable region of the bacterial 16?s ribosomal RNA gene. We anticipate widespread use of these technologies for diagnostics, species identification and basic research. PMID:22879378

  10. Characteristics of composited AVHRR data and problems in their classification

    Microsoft Academic Search

    A. Moody; A. H. Strahler

    1994-01-01

    Unsupervised classification procedures were applied to a temporal sequence of fifteen bi-weekly composited NDVI images produced from AVHRR LAC data. Individual examination of the input images appeared to show substantial contamination due to clouds which persist through the compositing period. These apparent cloud features dominated the results of the clustering procedures. The composites also include large numbers of far off-nadir

  11. Antitumor Activity and Pharmacokinetics of a Mixed-Backbone Antisense Oligonucleotide Targeted to the RIalpha Subunit of Protein Kinase A after Oral Administration

    Microsoft Academic Search

    Hui Wang; Qiuyin Cai; Xiaofei Zeng; Dong Yu; Sudhir Agrawal; Ruiwen Zhang

    1999-01-01

    Overexpression of the RIalpha subunit of cAMP-dependent protein kinase (PKA) has been demonstrated in various human cancers. PKA has been suggested as a potential target for cancer therapy. The goal of the present study was to evaluate an anti-PKA antisense oligonucleotide (mixed-backbone oligonucleotide) as a therapeutic approach to human cancer treatment. The identified oligonucleotide inhibited the growth of cell lines

  12. Probing nucleotide-binding effects on backbone dynamics and folding of the nucleotide-binding domain of the sarcoplasmic/endoplasmic-reticulum Ca2+-ATPase.

    PubMed Central

    Abu-Abed, Mona; Millet, Oscar; MacLennan, David H; Ikura, Mitsuhiko

    2004-01-01

    In muscle cells, SERCA (sarcoplasmic/endoplasmic-reticulum Ca2+-ATPase) plays a key role in restoring cytoplasmic Ca2+ levels to resting concentrations after transient surges caused by excitation-coupling cycles. The mechanism by which Ca2+ is translocated to the lumen of the ER (endoplasmic reticulum) involves major conformational rearrangements among the three cytoplasmic domains: actuator (A), nucleotide-binding (N) and phosphorylation (P) domains; and within the transmembrane Ca2+-binding domain of SERCA. CD, fluorescence spectroscopy and NMR spectroscopy were used in the present study to probe the conformation and stability of the isolated N domain of SERCA (SERCA-N), in the presence and absence of AMP-PNP (adenosine 5'-[beta,gamma-imido]triphosphate). CD and tryptophan fluorescence spectroscopy results established that the effects of nucleotide binding were not readily manifested on the global fold and structural stability of SERCA-N. 15N-backbone-relaxation experiments revealed site-specific changes in backbone dynamics that converge on the central beta-sheet domain. Nucleotide binding produced diverse effects on dynamics, with enhanced mobility observed for Ile369, Cys420, Arg467, Asp568, Phe593 and Gly598, whereas rigidifying effects were found for Ser383, Leu419, Thr484 and Thr532. These results demonstrate that the overall fold and backbone motional properties of SERCA-N remained essentially the same in the presence of AMP-PNP, yet revealing evidence for internal counter-balancing effects on backbone dynamics upon binding the nucleotide, which propagate through the central beta-sheet. PMID:14987197

  13. Cloned cDNA of A/swine/Iowa/15/1930 internal genes as a candidate backbone for reverse genetics vaccine against influenza A viruses

    PubMed Central

    Lekcharoensuk, Porntippa; Wiriyarat, Witthawat; Petcharat, Nuntawan; Lekcharoensuk, Chalermpol; Auewarakul, Prasert; Richt, Juergen A

    2012-01-01

    Reverse genetics viruses for influenza vaccine production usually utilize the internal genes of the egg-adapted A/Puerto Rico/8/34 (PR8) strain. This egg-adapted strain provides high production yield in embryonated eggs but does not necessarily give the best yield in mammalian cell culture. In order to generate a reverse genetics viral backbone that is well-adapted to high growth in mammalian cell culture, a swine influenza isolate (A/swine/Iowa/15/30 (H1N1) (rg1930) that was shown to give high yield in Madin-Darby Canine Kidney (MDCK) cells was used as the internal gene donor for reverse genetics plasmids. In this report, the internal genes from rg1930 were used for construction of reverse genetics viruses carrying a cleavage site-modified hemagglutinin (HA) gene and neuraminidase (NA) gene from a highly pathogenic H5N1 virus. The resulting virus (rg1930H5N1) was low pathogenic in vivo. Inactivated rg1930H5N1 vaccine completely protected chickens from morbidity and mortality after challenge with highly pathogenic H5N1. Protective immunity was obtained when chickens were immunized with an inactivated vaccine consisting of at least 29 HA units of the rg1930H5N1 virus. In comparison to the PR8-based reverse genetics viruses carrying the same HA and NA genes from an H5N1 virus, rg1930 based viruses yielded higher viral titers in MDCK and Vero cells. In addition, the reverse genetics derived H3N2 and H5N2 viruses with the rg1930 backbone replicated in MDCK cells better than the cognate viruses with the rgPR8 backbone. It is concluded that this newly established reverse genetics backbone system could serve as a candidate for a master donor strain for development of inactivated influenza vaccines in cell-based systems. PMID:22230579

  14. N-Heterocyclic carbene-phosphino-picolines as precursors of anionic 'pincer' ligands with dearomatised pyridine backbones; transmetallation from potassium to chromium.

    PubMed

    Simler, Thomas; Danopoulos, Andreas A; Braunstein, Pierre

    2015-06-18

    Deprotonation of the ?-picolinyl-CH2 in the hybrid ligands R2P-NCNHC (-N = substituted 2-picoline, R = Cy, t-Bu; CNHC = N-heterocyclic carbene) () with KN(SiMe3)2 in ether gave [KL(ether)]2 featuring a dearomatised picoline backbone. Assisted by 18-crown-6, K(+) dissociation afforded the Z- and E-isomers of [L](-). Transmetallation of L from KL led to [CrCl(L)]. PMID:26050938

  15. Inter-Ring and Hexyl Chain Torsional Potentials in Poly (3-HEXYLTHIOPHENE) Oligomers: Scaling with the Length of the Conjugted Polymer Backbone

    NASA Astrophysics Data System (ADS)

    Bhatta, Ram S.; Perry, David S.; Yimer, Yeneneh; Tsige, Mesfin

    2011-06-01

    Density functional theory calculations are presented for the equilibrium structures and torsional potentials for isolated Poly (3-Hexylthiophene) (P3HT) oligomers up to 12 monomer units (up to 302 atoms). Calculations were performed at B3LYP/6-31++G(d,p) treating both the backbone of thiophene rings and the hexyl chains explicitly. One-dimensional inter-ring torsional potentials were calculated by rotating backbone around the central inter-ring bond and hexyl torsional potentials were calculated rotating n-hexyl group adjacent to the central inter-ring bond for each oligomer. The torsional and electronic properties change significantly for oligomers with 2 to 8 units but reach asymptotic values for a 10 unit P3HT chain, thereby suggesting the 10 unit long oligomer as a molecular model for the extended polymer. For P3HT oligomers having 10 or more units, all the rings and the hexyl groups are approximately coplanar except for one hexyl group at head end. The principal interaction that promotes the coplanarity of the hexyl groups is the attraction of the proximal methylene hydrogens to the sulfur on the adjacent thiophene ring. The cis conformation of the backbone is about 2kT higher than the trans minimum at room temperature. The gauche conformation of the hexyl group is within about half kT of the planar minimum. Therefore conformational polymorphisms of both types will likely be significant in the heterogeneous environment of photovoltaic devices.

  16. In Sup35p filaments (the [PSI+] prion), the globular C-terminal domains are widely offset from the amyloid fibril backbone

    SciTech Connect

    Baxa, U.; Wall, J.; Keller, P. W.; Cheng, N.; Steven, A. C.

    2011-01-01

    In yeast cells infected with the [PSI+] prion, Sup35p forms aggregates and its activity in translation termination is downregulated. Transfection experiments have shown that Sup35p filaments assembled in vitro are infectious, suggesting that they reproduce or closely resemble the prion. We have used several EM techniques to study the molecular architecture of filaments, seeking clues as to the mechanism of downregulation. Sup35p has an N-terminal 'prion' domain; a highly charged middle (M-)domain; and a C-terminal domain with the translation termination activity. By negative staining, cryo-EM and scanning transmission EM (STEM), filaments of full-length Sup35p show a thin backbone fibril surrounded by a diffuse 65-nm-wide cloud of globular C-domains. In diameter ({approx}8 nm) and appearance, the backbones resemble amyloid fibrils of N-domains alone. STEM mass-per-unit-length data yield -1 subunit per 0.47 nm for N-fibrils, NM-filaments and Sup35p filaments, further supporting the fibril backbone model. The 30 nm radial span of decorating C-domains indicates that the M-domains assume highly extended conformations, offering an explanation for the residual Sup35p activity in infected cells, whereby the C-domains remain free enough to interact with ribosomes.

  17. Linear Sequence-to-Sequence Alignment

    Microsoft Academic Search

    Rodrigo L. Carceroni; Flávio L. C. Pádua; Geraldo A. M. R. Santos; Kiriakos N. Kutulakos

    2004-01-01

    In this paper, we consider the problem of estimating the spatiotemporal alignment between N unsynchronized video sequences of the same dynamic 3D scene, captured from distinct viewpoints. Unlike most existing methods, which work for N = 2 and rely on a computationally intensive search in the space of temporal alignments, we present a novel approach that reduces the problem for

  18. The preparation, characterization and evaluation of regenerated cellulose/collagen composite hydrogel films.

    PubMed

    Cheng, Yongmei; Lu, Jinting; Liu, Shilin; Zhao, Peng; Lu, Guozhong; Chen, Jinghua

    2014-07-17

    Porous structured regenerated cellulose films were oxidized by periodate oxidation to obtain 2,3-dialdehyde cellulose (DARC) films, which were then reacted with collagen to obtain DARC/Col composite films. The subsequent FT-IR spectra indicated that collagen was immobilized on the DARC matrix via the Schiff base reaction between NH2 in collagen and CHO in DARC backbone. Scanning electron microscopy revealed that DARC/Col exhibited a refined 3D network structure and its porosity and pore size decreased with increasing of collagen concentration. The composite films demonstrated a good equilibrium-swelling ratio, air permeability and water retention properties. The composite films also showed excellent mechanical properties, which was vital for practical application. Finally, the cytotoxicity of the composite film was evaluated using NIH3T3 mice fibroblast cells, the results revealed that DARC/Col composite films have good biocompatibility for use as scaffold material in tissue engineering. PMID:24702918

  19. In Silico Conformational Analysis of the Short-Sequence Hypomurocin A Peptides

    PubMed Central

    Násztor, Zoltán; Horváth, János

    2015-01-01

    In this theoretical study, a conformational analysis was performed on short-sequence hypomurocin A peptides, in order to identify their characteristic structural properties. For each hypomurocin A molecule, not only the backbone conformations, but also the side-chain conformations were examined. The results indicated that certain tetrapeptide units could be characterized by types I and III ?-turn structures, and considering the helical conformations, it could be concluded that the hypomurocin A peptides showed a preference for the 310-helical structure over the ?-helical structure. Beside the backbone conformations, the side-chain conformations were investigated, and the preferred rotamer states of the side-chains of amino acids were determined. Furthermore, the occurrence of i ? i + 3 and i ? i + 4 intramolecular H-bonds was studied, which could play a role in the structural stabilization of ?-turns and helical conformations. On the whole, our theoretical study supplied a comprehensive characterization of the three-dimensional structure of short-sequence hypomurocin A peptides. PMID:25699083

  20. Solution structure and backbone dynamics of recombinant Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy.

    PubMed

    Liu, J; Prakash, O; Cai, M; Gong, Y; Huang, Y; Wen, L; Wen, J J; Huang, J K; Krishnamoorthi, R

    1996-02-01

    The solution structure of recombinant Cucurbita maxima trypsin inhibitor-V (rCMTI-V), whose N-terminal is unacetylated and carries an extra glycine residue, was determined by means of two-dimensional (2D) homo and 3D hetero NMR experiments in combination with a distance geometry and simulated annealing algorithm. A total of 927 interproton distances and 123 torsion angle constraints were utilized to generate 18 structures. The root mean squared deviation (RMSD) of the mean structure is 0.53 A for main-chain atoms and 0.95 A for all the non-hydrogen atoms of residues 3-40 and 49-67. The average structure of rCMTI-V is found to be almost the same as that of the native protein [Cai, M., Gong, Y., Kao, J.-L., & Krishnamoorthi, R. (1995) Biochemistry 34, 5201-5211]. The backbone dynamics of uniformly 15N-labeled rCMTI-V were characterized by 2D 1H-15N NMR methods. 15N spin-lattice and spin-spin relaxation rate constants (R1 and R2, respectively) and [1H]-15N steady-state heteronuclear Overhauser effect enhancements were measured for the peptide NH units and, using the model-free formalism [Lipari, G., & Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559, 4559-4570], the following parameters were determined: overall tumbling correlation time for the protein molecule (tau m), generalized order parameters for the individual N-H vectors (S2), effective correlation times for their internal motions (tau e), and terms to account for motions on a slower time scale (second) due to chemical exchange and/or conformational averaging (R(ex)). Most of the backbone NH groups of rCMTI-V are found to be highly constrained ((S2) = 0.83) with the exception of those in the binding loop (residues 41-48, (S2) = 0.71) and the N-terminal region ((S2) = 0.73). Main-chain atoms in these regions show large RMSD values in the average NMR structure. Residues involved in turns also appear to have more mobility ((S2) = 0.80). Dynamical properties of rCMTI-V were compared with those of two other inhibitors of the potato I family--eglin c [Peng, J. W., & Wagner, G. (1992) Biochemistry 31, 8571-8586] and barley chymotrypsin inhibitor 2 [CI-2; Shaw, G. L., Davis, B., Keeler, J., & Fersht, A. R. (1995) Biochemistry 34, 2225-2233]. The Cys3-Cys48 linkage found only in rCMTI-V appears to somewhat reduce the N-terminal flexibility; likewise, the C-terminal of rCMTI-V, being part of a beta-sheet, appears to be more rigid. PMID:8634282

  1. Complete nucleotide sequence of the first KPC-2- and SHV-12-encoding IncX plasmid, pKpS90, from Klebsiella pneumoniae.

    PubMed

    Kassis-Chikhani, Najiby; Frangeul, Lionel; Drieux, Laurence; Sengelin, Christian; Jarlier, Vincent; Brisse, Sylvain; Arlet, Guillaume; Decré, Dominique

    2013-01-01

    We report the complete nucleotide sequence of the pKpS90 plasmid, carrying the bla(KPC-2) and bla(SHV-12) genes. This plasmid was isolated from a sequence type 258 (ST258) Klebsiella pneumoniae strain responsible for an outbreak in a French university hospital in 2009. pKpS90 is a 53,286-bp plasmid that belongs to the IncX incompatibility group. pKpS90 consists of a backbone from IncX plasmids, in which the KPC-2-encoding Tn4401 transposon and a bla(SHV-12)-encoding region have been inserted. PMID:23089759

  2. Blue Stragglers After the Main Sequence

    E-print Network

    Alison Sills; Amanda Karakas; John Lattanzio

    2008-11-18

    We study the post-main sequence evolution of products of collisions between main sequence stars (blue stragglers), with particular interest paid to the horizontal branch and asymptotic giant branch phases. We found that the blue straggler progeny populate the colour-magnitude diagram slightly blueward of the red giant branch and between 0.2 and 1 magnitudes brighter than the horizontal branch. We also found that the lifetimes of collision products on the horizontal branch is consistent with the numbers of so-called "evolved blue straggler stars" (E-BSS) identified by various authors in a number of globular clusters, and is almost independent of mass or initial composition profile. The observed ratio of the number of E-BSS to blue stragglers points to a main sequence lifetime for blue stragglers of approximately 1-2 Gyr on average.

  3. Backbone ¹HN, ¹³C, and ¹?N resonance assignments of the tandem RNA-binding domains of human DGCR8.

    PubMed

    Roth, Braden M; Hennig, Mirko

    2013-10-01

    Double-stranded RNA binding domain (dsRBD) containing proteins are critical components of the microRNA (miRNA) pathway, with key roles in small RNA biogenesis, modification, and regulation. DiGeorge Critical Region 8 (DGCR8) is a 773 amino acid, dsRBD-containing protein that was originally identified in humans as a protein encoded in the region of chromosome 22 that is deleted in patients with DiGeorge syndrome. Now, it is realized that DGCR8 complements the nuclear RNase III Drosha to initiate miRNA biogenesis by promoting efficient recognition and cleavage of primary miRNAs (pri-miRNA). A pair of C-terminal tandem dsRBDs separated by a flexible linker are required for pri-miRNA substrate binding and recognition. The crystal structure of the DGCR8 core region comprising residues 493-720 revealed that each dsRBD adopts the canonical ????? fold. However, several residues located in important flexible regions including the ?1-?2-loop implicated in canonical dsRNA recognition are absent in the crystal structure and no RNA-bound structure of DGCR8 has been reported. Here we report the (1)H(N), (13)C, and (15)N backbone resonance assignments of the 24 kDa, 214 amino acid human DGCR8(core) (residues 493-706) by heteronuclear NMR spectroscopy. Our assignments lay the foundation for a detailed solution state characterization of the dynamical and RNA-binding properties of this protein in solution. PMID:22752847

  4. Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase.

    PubMed

    Choi, Yong-Geun; Park, Chin-Ju; Kim, Hee-Eun; Seo, Yeo-Jin; Lee, Ae-Ree; Choi, Seo-Ree; Lee, Shim Sung; Lee, Joon-Hwa

    2015-02-01

    Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one ?-helix, three 3(10)-helices, and two ?-strands. Sialic acids play important roles in a variety of biological functions, such as development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins. PMID:25575834

  5. A Semisynthetic Strategy Leads to Alteration of the Backbone Amidate Ligand in the NiSOD Active Site.

    PubMed

    Campeciño, Julius O; Dudycz, Lech W; Tumelty, David; Berg, Volker; Cabelli, Diane E; Maroney, Michael J

    2015-07-22

    Computational investigations have implicated the amidate ligand in nickel superoxide dismutase (NiSOD) in stabilizing Ni-centered redox catalysis and in preventing cysteine thiolate ligand oxidation. To test these predictions, we have used an experimental approach utilizing a semisynthetic scheme that employs native chemical ligation of a pentapeptide (HCDLP) to recombinant S. coelicolor NiSOD lacking these N-terminal residues, N?5-NiSOD. Wild-type enzyme produced in this manner exhibits the characteristic spectral properties of recombinant WT-NiSOD and is as catalytically active. The semisynthetic scheme was also employed to construct a variant where the amidate ligand was converted to a secondary amine, H1*-NiSOD, a novel strategy that retains a backbone N-donor atom. The H1*-NiSOD variant was found to have only ?1% of the catalytic activity of the recombinant wild-type enzyme, and had altered spectroscopic properties. X-ray absorption spectroscopy reveals a four-coordinate planar site with N2S2-donor ligands, consistent with electronic absorption spectroscopic results indicating that the Ni center in H1*-NiSOD is mostly reduced in the as-isolated sample, as opposed to 50:50 Ni(II)/Ni(III) mixture that is typical for the recombinant wild-type enzyme. The EPR spectrum of as-isolated H1*-NiSOD accounts for ?11% of the Ni in the sample and is similar to WT-NiSOD, but more axial, with gz < gx,y. (14)N-hyperfine is observed on gz, confirming the addition of the apical histidine ligand in the Ni(III) complex. The altered electronic properties and implications for redox catalysis are discussed in light of predictions based on synthetic and computational models. PMID:26135142

  6. Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

    PubMed Central

    2012-01-01

    Background Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule's introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening. Results We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better. Conclusions Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. PMID:22536902

  7. Characterization of the Burkholderia mallei tonB Mutant and Its Potential as a Backbone Strain for Vaccine Development

    PubMed Central

    Mott, Tiffany M.; Vijayakumar, Sudhamathi; Sbrana, Elena; Endsley, Janice J.; Torres, Alfredo G.

    2015-01-01

    Background In this study, a Burkholderia mallei tonB mutant (TMM001) deficient in iron acquisition was constructed, characterized, and evaluated for its protective properties in acute inhalational infection models of murine glanders and melioidosis. Methodology/Principal Findings Compared to the wild-type, TMM001 exhibits slower growth kinetics, siderophore hyper-secretion and the inability to utilize heme-containing proteins as iron sources. A series of animal challenge studies showed an inverse correlation between the percentage of survival in BALB/c mice and iron-dependent TMM001 growth. Upon evaluation of TMM001 as a potential protective strain against infection, we found 100% survival following B. mallei CSM001 challenge of mice previously receiving 1.5 x 104 CFU of TMM001. At 21 days post-immunization, TMM001-treated animals showed significantly higher levels of B. mallei-specific IgG1, IgG2a and IgM when compared to PBS-treated controls. At 48 h post-challenge, PBS-treated controls exhibited higher levels of serum inflammatory cytokines and more severe pathological damage to target organs compared to animals receiving TMM001. In a cross-protection study of acute inhalational melioidosis with B. pseudomallei, TMM001-treated mice were significantly protected. While wild type was cleared in all B. mallei challenge studies, mice failed to clear TMM001. Conclusions/Significance Although further work is needed to prevent chronic infection by TMM001 while maintaining immunogenicity, our attenuated strain demonstrates great potential as a backbone strain for future vaccine development against both glanders and melioidosis. PMID:26114445

  8. Nano-structured composite cathodes for intermediate temperature solid oxide fuel cells via an infiltration/impregnation technique

    SciTech Connect

    Jiang, Zhiyi; Xia, Changrong; Chen, Fanglin

    2010-04-01

    Solid oxide fuel cells (SOFCs) are high temperature energy conversion devices working efficiently and environmental friendly. SOFC requires a functional cathode with high electrocatalytic activity for the electrochemical reduction of oxygen. The electrode is often fabricated at high temperature to achieve good bonding between the electrode and electrolyte. The high temperature not only limits material choice but also results in coarse particles with low electrocatalytic activity. Nano-structured electrodes fabricated at low temperature by an infiltration/impregnation technique have shown many advantages including superior activity and wider range of material choices. The impregnation technique involves depositing nanoparticle catalysts into a pre-sintered electrode backbone. Two basic types of nano-structures are developed since the electrode is usually a composite consists of an electrolyte and an electrocatalyst. One is infiltrating electronically conducting nano-catalyst into a single phase ionic conducting backbone, while the other is infiltrating ionically conducting nanoparticles into a single phase electronically conducting backbone. In addition, nanoparticles of the electrocatalyst, electrolyte and other oxides have also been infiltrated into mixed conducting backbones. These nano-structured cathodes are reviewed here regarding the preparation methods, their electrochemical performance, and stability upon thermal cycling.

  9. Composite material

    Microsoft Academic Search

    Stacy A. Hutchens; Jonathan Woodward; Barbara R. Evans; Hugh M. ONeill

    2012-01-01

    A composite biocompatible hydrogel material includes a porous polymer matrix, the polymer matrix including a plurality of pores and providing a Young's modulus of at least 10 GPa. A calcium comprising salt is disposed in at least some of the pores. The porous polymer matrix can comprise cellulose, including bacterial cellulose. The composite can be used as a bone graft

  10. Electrode compositions

    DOEpatents

    Block, J.; Fan, X.

    1998-10-27

    An electrode composition is described for use as an electrode in a non-aqueous battery system. The electrode composition contains an electrically active powder in a solid polymer and, as a dispersant, a C{sub 8}-C{sub 15} alkyl capped oligomer of a hexanoic acid that is electrochemically inert at 2.5--4.5 volts.

  11. Triggered message sequence charts

    Microsoft Academic Search

    Bikram Sengupta; Rance Cleaveland

    2002-01-01

    We propose an extension to Message Sequence Charts called Triggered Message Sequence Charts (TMSCs) that are intended to capture system specifications involving nondeterminism in the form of conditional scenarios. The visual syntax of TMSCs closely resembles that of MSCs; the semantics allows us to translate a TMSC specification into a framework that supports a notion of refinement based on Denicola's

  12. Triggered Message Sequence Charts

    Microsoft Academic Search

    Bikram Sengupta; Rance Cleaveland

    2006-01-01

    This paper introduces triggered message sequence charts (TMSCs), a graphical, mathematically well-founded framework for capturing scenario-based system requirements of distributed systems. Like message sequence charts (MSCs), TMSCs are graphical depictions of scenarios, or exchanges of messages between processes in a distributed system. Unlike MSCs, however, TMSCs are equipped with a notion of trigger that permits requirements to be made conditional,

  13. 1 -Sequence Polydispersed, wrong

    E-print Network

    Lebendiker, Mario

    3 -Expression conditions and 4 - Small-scale production Mono- dispersed 2-Cloning 3 2 1 3 2 1 Soluble 6 - Scale-up 5 4 6 #12;Sequence: a) Gene ID from a known database (PubMed tools, etc.) b) Domain removal f) Full translated region, DNA and AA sequences Cloning a) Vector name either commercial or from

  14. M&m Sequences

    ERIC Educational Resources Information Center

    Schultz, Harris S.; Shiflett, Ray C.

    2005-01-01

    Consider a sequence recursively formed as follows: Start with three real numbers, and then when k are known, let the (k +1)st be such that the mean of all k +1 equals the median of the first k. The authors conjecture that every such sequence eventually becomes stable. This article presents results related to their conjecture.

  15. Porcine Genomic Sequencing Initiative

    Microsoft Academic Search

    Gary Rohrer; Jonathan E. Beever; Max F. Rothschild; Lawrence Schook; Richard Gibbs; George Weinstock; W. Gregory

    A. Specific biological rationales for the utility of the porcine sequence information Rationale and Objectives. Completion of the human genome sequence provides the starting point for understanding the genetic complexity of humans and how genetic variation contributes to diverse phenotypes and disease. It is clear that model organisms have played an invaluable role in the synthesis of this understanding. It

  16. Twin mitochondrial sequence analysis

    PubMed Central

    Bouhlal, Yosr; Martinez, Selena; Gong, Henry; Dumas, Kevin; Shieh, Joseph T C

    2013-01-01

    When applying genome-wide sequencing technologies to disease investigation, it is increasingly important to resolve sequence variation in regions of the genome that may have homologous sequences. The human mitochondrial genome challenges interpretation given the potential for heteroplasmy, somatic variation, and homologous nuclear mitochondrial sequences (numts). Identical twins share the same mitochondrial DNA (mtDNA) from early life, but whether the mitochondrial sequence remains similar is unclear. We compared an adult monozygotic twin pair using high-throughput sequencing and evaluated variants with primer extension and mitochondrial preenrichment. Thirty-seven variants were shared between the twin individuals, and the variants were verified on the original genomic DNA. These studies support highly identical genetic sequence in this case. Certain low-level variant calls were of high quality and homology to the mtDNA, and they were further evaluated. When we assessed calls in preenriched mtDNA templates, we found that these may represent numts, which can be differentiated from mtDNA variation. We conclude that twin identity extends to mtDNA, and it is critical to differentiate between numts and mtDNA in genome sequencing, particularly as significant heteroplasmy could influence genome interpretation. Further studies on mtDNA and numts will aid in understanding how variation occurs and persists. PMID:24040623

  17. Microbial genome sequencing

    Microsoft Academic Search

    Claire M. Fraser; Jonathan A. Eisen; Steven L. Salzberg

    2000-01-01

    Complete genome sequences of 30 microbial species have been determined during the past five years, and work in progress indicates that the complete sequences of more than 100 further microbial species will be available in the next two to four years. These results have revealed a tremendous amount of information on the physiology and evolution of microbial species, and should

  18. CREST – Classification Resources for Environmental Sequence Tags

    PubMed Central

    Lanzén, Anders; Jørgensen, Steffen L.; Huson, Daniel H.; Gorfer, Markus; Grindhaug, Svenn Helge; Jonassen, Inge; Øvreås, Lise; Urich, Tim

    2012-01-01

    Sequencing of taxonomic or phylogenetic markers is becoming a fast and efficient method for studying environmental microbial communities. This has resulted in a steadily growing collection of marker sequences, most notably of the small-subunit (SSU) ribosomal RNA gene, and an increased understanding of microbial phylogeny, diversity and community composition patterns. However, to utilize these large datasets together with new sequencing technologies, a reliable and flexible system for taxonomic classification is critical. We developed CREST (Classification Resources for Environmental Sequence Tags), a set of resources and tools for generating and utilizing custom taxonomies and reference datasets for classification of environmental sequences. CREST uses an alignment-based classification method with the lowest common ancestor algorithm. It also uses explicit rank similarity criteria to reduce false positives and identify novel taxa. We implemented this method in a web server, a command line tool and the graphical user interfaced program MEGAN. Further, we provide the SSU rRNA reference database and taxonomy SilvaMod, derived from the publicly available SILVA SSURef, for classification of sequences from bacteria, archaea and eukaryotes. Using cross-validation and environmental datasets, we compared the performance of CREST and SilvaMod to the RDP Classifier. We also utilized Greengenes as a reference database, both with CREST and the RDP Classifier. These analyses indicate that CREST performs better than alignment-free methods with higher recall rate (sensitivity) as well as precision, and with the ability to accurately identify most sequences from novel taxa. Classification using SilvaMod performed better than with Greengenes, particularly when applied to environmental sequences. CREST is freely available under a GNU General Public License (v3) from http://apps.cbu.uib.no/crest and http://lcaclassifier.googlecode.com. PMID:23145153

  19. Sequence History Update Tool

    NASA Technical Reports Server (NTRS)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  20. Numerical Characterization of DNA Sequence Based on Dinucleotides

    PubMed Central

    Qi, Xingqin; Fuller, Edgar; Wu, Qin; Zhang, Cun-Quan

    2012-01-01

    Sequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented by a curve in high-dimension Euclidean space) have been used popularly for a long time. In this contribution we will introduce a new nongraphical and nonalignment approach based on the frequencies of the dinucleotide XY in DNA sequences. The most important feature of this method is that it not only identifies adjacent XY pairs but also nonadjacent XY ones where X and Y are separated by some number of nucleotides. This methodology preserves information in DNA sequence that is ignored by other methods. We test our method on the coding regions of exon-1 of ?–globin for 11 species, and the utility of this new method is demonstrated. PMID:22619571