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Sample records for additional secondary structure

  1. Combinatorics of saturated secondary structures of RNA.

    PubMed

    Clote, P

    2006-11-01

    Following Zuker (1986), a saturated secondary structure for a given RNA sequence is a secondary structure such that no base pair can be added without violating the definition of secondary structure, e.g., without introducing a pseudoknot. In the Nussinov-Jacobson energy model (Nussinov and Jacobson, 1980), where the energy of a secondary structure is -1 times the number of base pairs, saturated secondary structures are local minima in the energy landscape, hence form kinetic traps during the folding process. Here we present recurrence relations and closed form asymptotic limits for combinatorial problems related to the number of saturated secondary structures. In addition, Python source code to compute the number of saturated secondary structures having k base pairs can be found at the web servers link of bioinformatics.bc.edu/clotelab/. PMID:17147486

  2. Secondary Structure Switch

    ERIC Educational Resources Information Center

    King, Angela G.

    2006-01-01

    Neurogenerative diseases like Alzheimer's disease and Parkinson's disease involve a transformation between two peptide and protein structures of alpha-helices and beta-sheets, where the peptide backbone can also participate in metal ion binding in addition to histidine residues. However, the complete absence of change in conformation of Coiled…

  3. Conserved Secondary Structures in Aspergillus

    PubMed Central

    McGuire, Abigail Manson; Galagan, James E.

    2008-01-01

    Background Recent evidence suggests that the number and variety of functional RNAs (ncRNAs as well as cis-acting RNA elements within mRNAs ) is much higher than previously thought; thus, the ability to computationally predict and analyze RNAs has taken on new importance. We have computationally studied the secondary structures in an alignment of six Aspergillus genomes. Little is known about the RNAs present in this set of fungi, and this diverse set of genomes has an optimal level of sequence conservation for observing the correlated evolution of base-pairs seen in RNAs. Methodology/Principal Findings We report the results of a whole-genome search for evolutionarily conserved secondary structures, as well as the results of clustering these predicted secondary structures by structural similarity. We find a total of 7450 predicted secondary structures, including a new predicted ∼60 bp long hairpin motif found primarily inside introns. We find no evidence for microRNAs. Different types of genomic regions are over-represented in different classes of predicted secondary structures. Exons contain the longest motifs (primarily long, branched hairpins), 5′ UTRs primarily contain groupings of short hairpins located near the start codon, and 3′ UTRs contain very little secondary structure compared to other regions. There is a large concentration of short hairpins just inside the boundaries of exons. The density of predicted intronic RNAs increases with the length of introns, and the density of predicted secondary structures within mRNA coding regions increases with the number of introns in a gene. Conclusions/Sigificance There are many conserved, high-confidence RNAs of unknown function in these Aspergillus genomes, as well as interesting spatial distributions of predicted secondary structures. This study increases our knowledge of secondary structure in these aspergillus organisms. PMID:18665251

  4. Combinatorics of locally optimal RNA secondary structures.

    PubMed

    Fusy, Eric; Clote, Peter

    2014-01-01

    It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366∙n-3/2∙2.618034n. Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy model. In the Nussinov energy model, where each base pair contributes -1 towards the energy of the structure, locally optimal structures are exactly the saturated structures, for which we have previously shown that asymptotically, there are 1.07427∙n-3/2∙2.35467n many saturated structures for a sequence of length n. In this paper, we consider the base stacking energy model, a mild variant of the Nussinov model, where each stacked base pair contributes -1 toward the energy of the structure. Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended. Such structures were first considered by Evers and Giegerich, who described a dynamic programming algorithm to enumerate all locally optimal structures. In this paper, we apply methods from enumerative combinatorics to compute the asymptotic number of such structures. Additionally, we consider analogous combinatorial problems for secondary structures with annotated single-stranded, stacking nucleotides (dangles). PMID:23263300

  5. Interaction between Polymeric Additives and Secondary Fluids in Capillary Suspensions.

    PubMed

    Bitsch, Boris; Braunschweig, Björn; Willenbacher, Norbert

    2016-02-16

    Capillary suspensions are ternary systems including a solid and two liquid phases representing a novel formulation platform for pastes with unique processing and end-use properties. Here we have investigated aqueous suspensions of non-Brownian graphite particles including different polymers commonly used as thickening agents or binders in paste formulations. We have studied the interaction between these additives and organic solvents in order to elucidate its effect on the characteristic formation of a particle network structure in corresponding ternary capillary suspension systems. Organic solvents with different polarity have been employed, and in the presence of nonadsorbing poly(ethylene oxide), all of them, whether they preferentially wet the graphite surface or not, induce the formation of a network structure within the suspension as indicated by a strong change in rheological properties. However, when the adsorbing polymers carboxymethylcellulose and poly(vinylpyrrolidone) are included, the drastic change in rheological behavior occurs only when polar organic solvents are used as secondary liquids. Obviously, these solvents can form pendular bridges, finally resulting in a sample-spanning particle network. Vibrational sum frequency spectroscopy provides evidence that these polar liquids remove the adsorbed polymer from the graphite particles. In contrast, nonpolar and nonwetting solvents do not force polymer desorption. In these cases, the formation of a percolating network structure within the suspensions is presumably prevented by the strong steric repulsion among graphite particles, not allowing for the formation of particle clusters encapsulating the secondary liquid. Accordingly, polymeric additives and secondary fluids have to be carefully selected in capillary suspension formulations, then offering a new pathway to customize paste formulations. The polymer may serve to adjust an appropriate viscosity level, and the capillary bridging induces the

  6. Secondary structure formation in peptide amphiphile micelles

    NASA Astrophysics Data System (ADS)

    Tirrell, Matthew

    2012-02-01

    Peptide amphiphiles (PAs) are capable of self-assembly into micelles for use in the targeted delivery of peptide therapeutics and diagnostics. PA micelles exhibit a structural resemblance to proteins by having folded bioactive peptides displayed on the exterior of a hydrophobic core. We have studied two factors that influence PA secondary structure in micellar assemblies: the length of the peptide headgroup and amino acids closest to the micelle core. Peptide length was systematically varied using a heptad repeat PA. For all PAs the addition of a C12 tail induced micellization and secondary structure. PAs with 9 amino acids formed beta-sheet interactions upon aggregation, whereas the 23 and 30 residue peptides were displayed in an apha-helical conformation. The 16 amino acid PA experienced a structural transition from helix to sheet, indicating that kinetics play a role in secondary structure formation. A p53 peptide was conjugated to a C16 tail via various linkers to study the effect of linker chemistry on PA headgroup conformation. With no linker the p53 headgroup was predominantly alpha helix and a four alanine linker drastically changed the structure of the peptide headgroup to beta-sheet, highlighting the importance of hydrogen boding potential near the micelle core.

  7. Maximum expected accuracy structural neighbors of an RNA secondary structure

    PubMed Central

    2012-01-01

    Background Since RNA molecules regulate genes and control alternative splicing by allostery, it is important to develop algorithms to predict RNA conformational switches. Some tools, such as paRNAss, RNAshapes and RNAbor, can be used to predict potential conformational switches; nevertheless, no existent tool can detect general (i.e., not family specific) entire riboswitches (both aptamer and expression platform) with accuracy. Thus, the development of additional algorithms to detect conformational switches seems important, especially since the difference in free energy between the two metastable secondary structures may be as large as 15-20 kcal/mol. It has recently emerged that RNA secondary structure can be more accurately predicted by computing the maximum expected accuracy (MEA) structure, rather than the minimum free energy (MFE) structure. Results Given an arbitrary RNA secondary structure S0 for an RNA nucleotide sequence a = a1,..., an, we say that another secondary structure S of a is a k-neighbor of S0, if the base pair distance between S0 and S is k. In this paper, we prove that the Boltzmann probability of all k-neighbors of the minimum free energy structure S0 can be approximated with accuracy ε and confidence 1 - p, simultaneously for all 0 ≤ k < K, by a relative frequency count over N sampled structures, provided that N>N(ε,p,K)=Φ-1p2K24ε2, where Φ(z) is the cumulative distribution function (CDF) for the standard normal distribution. We go on to describe the algorithm RNAborMEA, which for an arbitrary initial structure S0 and for all values 0 ≤ k < K, computes the secondary structure MEA(k), having maximum expected accuracy over all k-neighbors of S0. Computation time is O(n3 · K2), and memory requirements are O(n2 · K). We analyze a sample TPP riboswitch, and apply our algorithm to the class of purine riboswitches. Conclusions The approximation of RNAbor by sampling, with rigorous bound on accuracy, together with the computation of

  8. Enumeration of Secondary Structure Element Bundles

    SciTech Connect

    Brown, William Michael; Faulon, Jean-Loup

    2004-10-26

    A deterministic algorithm for enumeration of transmembrane protein folds is implemented. Using a set of sparse pairwise atomic distance constraints (such as those obtained from chemical cross-linking, FRET, or dipolar EPR experiments), the algorithm performs an exhaustive search of secondary structure element packing conformations distributed throughout the entire conformational space. The end result is a set of distinct protein conformations which can be scored and refined as part of a process designed for computational elucidation of transmembrane protein structures. Algorithm Overview: The ESSEB algorithm works by dividing the conforrnational space of each secondary structure element (SSE) into a set of cells. For each cell there is a representative conformation and for each atom in the SSE for which a distance restraint is available, there is an associated internal error, The internal error for a distance restraint is the maximum distance that the atom, when positioned in any conformation within a cell, can be from the atom in the representative conformation. The algorithm works recursively by positioning one representative conformation of an SSE. AdI distance restraints are checked with a tolerance that includes both the experimental and internal error. If all restraints are satisfied, every representative conformation of the next SSE is checked, otherwise, the program moves on to the next representative conformation of the current SSE. In addition to the distance restraints, other constraints on protein conformation can be enforced. These include the distance of closest approach between SSE axes, a restraint which prevents the crossover of loops connecting adjacent SSEs, and a restriction on the minimum and maximum distances between axis end-points. Any protein conformation satisfying all of the restraints is enumerated for later scoring and possible refinement. Additionally, in order to make run-times feasible, a divide-and-conquer approach is used in which

  9. Pairwise amino acid secondary structural propensities

    NASA Astrophysics Data System (ADS)

    Chemmama, Ilan E.; Chapagain, Prem P.; Gerstman, Bernard S.

    2015-04-01

    We investigate the propensities for amino acids to form a specific secondary structure when they are paired with other amino acids. Our investigations use molecular dynamics (MD) computer simulations, and we compare the results to those from the Protein Data Bank (PDB). Proper comparison requires weighting of the MD results in a manner consistent with the relative frequency of appearance in the PDB of each possible pair of amino acids. We find that the propensity for an amino acid to assume a secondary structure varies dramatically depending on the amino acid that is before or after it in the primary sequence. This cooperative effect means that when selecting amino acids to facilitate the formation of a secondary structure in peptide engineering experiments, the adjacent amino acids must be considered. We also examine the preference for a secondary structure in bacterial proteins and compare the results to those of human proteins.

  10. Current perspectives on RNA secondary structure probing.

    PubMed

    Kenyon, Julia; Prestwood, Liam; Lever, Andrew

    2014-08-01

    The range of roles played by structured RNAs in biological systems is vast. At the same time as we are learning more about the importance of RNA structure, recent advances in reagents, methods and technology mean that RNA secondary structural probing has become faster and more accurate. As a result, the capabilities of laboratories that already perform this type of structural analysis have increased greatly, and it has also become more widely accessible. The present review summarizes established and recently developed techniques. The information we can derive from secondary structural analysis is assessed, together with the areas in which we are likely to see exciting developments in the near future. PMID:25110033

  11. Enumeration of Secondary Structure Element Bundles

    2004-10-26

    A deterministic algorithm for enumeration of transmembrane protein folds is implemented. Using a set of sparse pairwise atomic distance constraints (such as those obtained from chemical cross-linking, FRET, or dipolar EPR experiments), the algorithm performs an exhaustive search of secondary structure element packing conformations distributed throughout the entire conformational space. The end result is a set of distinct protein conformations which can be scored and refined as part of a process designed for computational elucidationmore » of transmembrane protein structures. Algorithm Overview: The ESSEB algorithm works by dividing the conforrnational space of each secondary structure element (SSE) into a set of cells. For each cell there is a representative conformation and for each atom in the SSE for which a distance restraint is available, there is an associated internal error, The internal error for a distance restraint is the maximum distance that the atom, when positioned in any conformation within a cell, can be from the atom in the representative conformation. The algorithm works recursively by positioning one representative conformation of an SSE. AdI distance restraints are checked with a tolerance that includes both the experimental and internal error. If all restraints are satisfied, every representative conformation of the next SSE is checked, otherwise, the program moves on to the next representative conformation of the current SSE. In addition to the distance restraints, other constraints on protein conformation can be enforced. These include the distance of closest approach between SSE axes, a restraint which prevents the crossover of loops connecting adjacent SSEs, and a restriction on the minimum and maximum distances between axis end-points. Any protein conformation satisfying all of the restraints is enumerated for later scoring and possible refinement. Additionally, in order to make run-times feasible, a divide-and-conquer approach is used

  12. Secondary structures in long compact polymers

    NASA Astrophysics Data System (ADS)

    Oberdorf, Richard; Ferguson, Allison; Jacobsen, Jesper L.; Kondev, Jané

    2006-11-01

    Compact polymers are self-avoiding random walks that visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform numerical calculations is generating a sufficiently large number of randomly sampled configurations. We present a Monte Carlo algorithm that uniformly samples compact polymer configurations in an efficient manner, allowing investigations of chains much longer than previously studied. Chain configurations generated by the algorithm are used to compute statistics of secondary structures in compact polymers. We determine the fraction of monomers participating in secondary structures, and show that it is self-averaging in the long-chain limit and strictly less than 1. Comparison with results for lattice models of open polymer chains shows that compact chains are significantly more likely to form secondary structure.

  13. Secondary structures in long compact polymers.

    PubMed

    Oberdorf, Richard; Ferguson, Allison; Jacobsen, Jesper L; Kondev, Jané

    2006-11-01

    Compact polymers are self-avoiding random walks that visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform numerical calculations is generating a sufficiently large number of randomly sampled configurations. We present a Monte Carlo algorithm that uniformly samples compact polymer configurations in an efficient manner, allowing investigations of chains much longer than previously studied. Chain configurations generated by the algorithm are used to compute statistics of secondary structures in compact polymers. We determine the fraction of monomers participating in secondary structures, and show that it is self-averaging in the long-chain limit and strictly less than 1. Comparison with results for lattice models of open polymer chains shows that compact chains are significantly more likely to form secondary structure. PMID:17279930

  14. PEGylated nanoparticles: protein corona and secondary structure

    NASA Astrophysics Data System (ADS)

    Runa, Sabiha; Hill, Alexandra; Cochran, Victoria L.; Payne, Christine K.

    2014-09-01

    Nanoparticles have important biological and biomedical applications ranging from drug and gene delivery to biosensing. In the presence of extracellular proteins, a "corona" of proteins adsorbs on the surface of the nanoparticles, altering their interaction with cells, including immune cells. Nanoparticles are often functionalized with polyethylene glycol (PEG) to reduce this non-specific adsorption of proteins. To understand the change in protein corona that occurs following PEGylation, we first quantified the adsorption of blood serum proteins on bare and PEGylated gold nanoparticles using gel electrophoresis. We find a threefold decrease in the amount of protein adsorbed on PEGylated gold nanoparticles compared to the bare gold nanoparticles, showing that PEG reduces, but does not prevent, corona formation. To determine if the secondary structure of corona proteins was altered upon adsorption onto the bare and PEGylated gold nanoparticles, we use CD spectroscopy to characterize the secondary structure of bovine serum albumin following incubation with the nanoparticles. Our results show no significant change in protein secondary structure following incubation with bare or PEGylated nanoparticles. Further examination of the secondary structure of bovine serum albumin, α2-macroglobulin, and transferrin in the presence of free PEG showed similar results. These findings provide important insights for the use of PEGylated gold nanoparticles under physiological conditions.

  15. Chemoselective synthesis of ketones and ketimines by addition of organometallic reagents to secondary amides

    NASA Astrophysics Data System (ADS)

    Bechara, William S.; Pelletier, Guillaume; Charette, André B.

    2012-03-01

    The development of efficient and selective transformations is crucial in synthetic chemistry as it opens new possibilities in the total synthesis of complex molecules. Applying such reactions to the synthesis of ketones is of great importance, as this motif serves as a synthetic handle for the elaboration of numerous organic functionalities. In this context, we report a general and chemoselective method based on an activation/addition sequence on secondary amides allowing the controlled isolation of structurally diverse ketones and ketimines. The generation of a highly electrophilic imidoyl triflate intermediate was found to be pivotal in the observed exceptional functional group tolerance, allowing the facile addition of readily available Grignard and diorganozinc reagents to amides, and avoiding commonly observed over-addition or reduction side reactions. The methodology has been applied to the formal synthesis of analogues of the antineoplastic agent Bexarotene and to the rapid and efficient synthesis of unsymmetrical diketones in a one-pot procedure.

  16. Mechanical tuning of elastomers via peptide secondary structure

    NASA Astrophysics Data System (ADS)

    Wanasekara, Nandula; Johnson, J. Casey; Korley, Lashanda T. J.

    2014-03-01

    Nature utilizes an array of design tools for engineering materials with multiple functions and tunable mechanical properties. The precise control of hierarchical structure, self-assembly, and secondary structure is essential to achieve the desired properties in bio-inspired materials design. We have developed a series of peptidic-poyurea hybrids to determine the effects of peptide secondary structure and hydrogen bonding arrangement on morphology, thermal and mechanical properties. These materials were fabricated by incorporating peptide segments containing either poly(β-benzyl-L-aspartate) or poly(ɛ-carbobenzyloxy-L-lysine) into non-chain extended polyureas to form either β-sheets or α-helix conformations based on peptide length. Infrared analysis proved the retention of peptide secondary structure when incorporated into peptidic-polyureas. The polymers containing β-sheet forming peptide blocks exhibited higher modulus and toughness due to intermolecular H-bonding. Additionally, higher peptide weight fractions lead to higher plateau moduli due to a transition of continuous domain morphology from a soft segment continuous to a fibrous and interconnected stiffer peptide domain. All the polymers exhibited microphase separated morphology with nanofibrous or ribbon-like structures. It is observed that fiber aspect ratio and percolation were influenced by the peptide secondary structure and the weight fraction.

  17. RNA secondary structure prediction using soft computing.

    PubMed

    Ray, Shubhra Sankar; Pal, Sankar K

    2013-01-01

    Prediction of RNA structure is invaluable in creating new drugs and understanding genetic diseases. Several deterministic algorithms and soft computing-based techniques have been developed for more than a decade to determine the structure from a known RNA sequence. Soft computing gained importance with the need to get approximate solutions for RNA sequences by considering the issues related with kinetic effects, cotranscriptional folding, and estimation of certain energy parameters. A brief description of some of the soft computing-based techniques, developed for RNA secondary structure prediction, is presented along with their relevance. The basic concepts of RNA and its different structural elements like helix, bulge, hairpin loop, internal loop, and multiloop are described. These are followed by different methodologies, employing genetic algorithms, artificial neural networks, and fuzzy logic. The role of various metaheuristics, like simulated annealing, particle swarm optimization, ant colony optimization, and tabu search is also discussed. A relative comparison among different techniques, in predicting 12 known RNA secondary structures, is presented, as an example. Future challenging issues are then mentioned. PMID:23702539

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

    NASA Astrophysics Data System (ADS)

    Bundschuh, Ralf

    2003-03-01

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

  19. JPred4: a protein secondary structure prediction server.

    PubMed

    Drozdetskiy, Alexey; Cole, Christian; Procter, James; Barton, Geoffrey J

    2015-07-01

    JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials. PMID:25883141

  20. JPred4: a protein secondary structure prediction server

    PubMed Central

    Drozdetskiy, Alexey; Cole, Christian; Procter, James; Barton, Geoffrey J.

    2015-01-01

    JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials. PMID:25883141

  1. Secondary flow structures in large rivers

    NASA Astrophysics Data System (ADS)

    Chauvet, H.; Devauchelle, O.; Metivier, F.; Limare, A.; Lajeunesse, E.

    2012-04-01

    Measuring the velocity field in large rivers remains a challenge, even with recent measurement techniques such as Acoustic Doppler Current Profiler (ADCP). Indeed, due to the diverging angle between its ultrasonic beams, an ADCP cannot detect small-scale flow structures. However, when the measurements are limited to a single location for a sufficient period of time, averaging can reveal large, stationary flow structures. Here we present velocity measurements in a straight reach of the Seine river in Paris, France, where the cross-section is close to rectangular. The transverse modulation of the streamwise velocity indicates secondary flow cells, which seem to occupy the entire width of the river. This observation is reminiscent of the longitudinal vortices observed in laboratory experiments (e.g. Blanckaert et al., Advances in Water Resources, 2010, 33, 1062-1074). Although the physical origin of these secondary structures remains unclear, their measured velocity is sufficient to significantly impact the distribution of streamwise momentum. We propose a model for the transverse profile of the depth-averaged velocity based on a crude representation of the longitudinal vortices, with a single free parameter. Preliminary results are in good agreement with field measurements. This model also provides an estimate for the bank shear stress, which controls bank erosion.

  2. The Development of Students' Use of Additive and Proportional Methods along Primary and Secondary School

    ERIC Educational Resources Information Center

    Fernandez, Ceneida; Llinares, Salvador; Van Dooren, Wim; De Bock, Dirk; Verschaffel, Lieven

    2012-01-01

    This study investigates the development of proportional and additive methods along primary and secondary school. In particular, it simultaneously investigates the use of additive methods in proportional word problems and the use of proportional methods in additive word problems. We have also studied the role played by integer and non-integer…

  3. Computing folding pathways between RNA secondary structures.

    PubMed

    Dotu, Ivan; Lorenz, William A; Van Hentenryck, Pascal; Clote, Peter

    2010-03-01

    Given an RNA sequence and two designated secondary structures A, B, we describe a new algorithm that computes a nearly optimal folding pathway from A to B. The algorithm, RNAtabupath, employs a tabu semi-greedy heuristic, known to be an effective search strategy in combinatorial optimization. Folding pathways, sometimes called routes or trajectories, are computed by RNAtabupath in a fraction of the time required by the barriers program of Vienna RNA Package. We benchmark RNAtabupath with other algorithms to compute low energy folding pathways between experimentally known structures of several conformational switches. The RNApathfinder web server, source code for algorithms to compute and analyze pathways and supplementary data are available at http://bioinformatics.bc.edu/clotelab/RNApathfinder. PMID:20044352

  4. A folding algorithm for extended RNA secondary structures

    PubMed Central

    zu Siederdissen, Christian Höner; Bernhart, Stephan H.; Stadler, Peter F.; Hofacker, Ivo L.

    2011-01-01

    Motivation: RNA secondary structure contains many non-canonical base pairs of different pair families. Successful prediction of these structural features leads to improved secondary structures with applications in tertiary structure prediction and simultaneous folding and alignment. Results: We present a theoretical model capturing both RNA pair families and extended secondary structure motifs with shared nucleotides using 2-diagrams. We accompany this model with a number of programs for parameter optimization and structure prediction. Availability: All sources (optimization routines, RNA folding, RNA evaluation, extended secondary structure visualization) are published under the GPLv3 and available at www.tbi.univie.ac.at/software/rnawolf/. Contact: choener@tbi.univie.ac.at PMID:21685061

  5. RNA-SSPT: RNA Secondary Structure Prediction Tools.

    PubMed

    Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

    2013-01-01

    The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes. PMID:24250115

  6. PCI-SS: MISO dynamic nonlinear protein secondary structure prediction

    PubMed Central

    Green, James R; Korenberg, Michael J; Aboul-Magd, Mohammed O

    2009-01-01

    Background Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to determining the one dimensional secondary structure of proteins (distinguishing α-helices, β-strands, and non-regular structures) from primary sequence data which makes use of Parallel Cascade Identification (PCI), a powerful technique from the field of nonlinear system identification. Results Using PSI-BLAST divergent evolutionary profiles as input data, dynamic nonlinear systems are built through a black-box approach to model the process of protein folding. Genetic algorithms (GAs) are applied in order to optimize the architectural parameters of the PCI models. The three-state prediction problem is broken down into a combination of three binary sub-problems and protein structure classifiers are built using 2 layers of PCI classifiers. Careful construction of the optimization, training, and test datasets ensures that no homology exists between any training and testing data. A detailed comparison between PCI and 9 contemporary methods is provided over a set of 125 new protein chains guaranteed to be dissimilar to all training data. Unlike other secondary structure prediction methods, here a web service is developed to provide both human- and machine-readable interfaces to PCI-based protein secondary structure prediction. This server, called PCI-SS, is available at . In addition to a dynamic PHP-generated web interface for humans, a Simple Object Access Protocol (SOAP) interface is added to permit invocation of the PCI-SS service remotely. This machine-readable interface facilitates incorporation of PCI-SS into multi-faceted systems biology analysis pipelines requiring protein secondary structure information, and greatly simplifies high-throughput analyses. XML is used to represent the input protein sequence data and also to encode the resulting

  7. Notch Transmembrane Domain: Secondary Structure and Topology

    PubMed Central

    2016-01-01

    The Notch signaling pathway is critical in development, neuronal maintenance, and hematopoiesis. An obligate step in the activation of this pathway is cleavage of its transmembrane (TM) domain by γ-secretase. While the soluble domains have been extensively studied, little has been done to characterize its TM and flanking juxtamembrane (JM) segments. Here, we present the results of nuclear magnetic resonance (NMR) studies of the human Notch1 TM/JM domain. The TM domain is largely α-helical. While the flanking JM segments do not adopt regular secondary structure, they interact with the membrane surface, suggesting membrane interactions may play a role in modulating its cleavage by γ-secretase and subsequent NOTCH signaling function. PMID:26023825

  8. Structural changes in gluten protein structure after addition of emulsifier. A Raman spectroscopy study

    NASA Astrophysics Data System (ADS)

    Ferrer, Evelina G.; Gómez, Analía V.; Añón, María C.; Puppo, María C.

    2011-06-01

    Food protein product, gluten protein, was chemically modified by varying levels of sodium stearoyl lactylate (SSL); and the extent of modifications (secondary and tertiary structures) of this protein was analyzed by using Raman spectroscopy. Analysis of the Amide I band showed an increase in its intensity mainly after the addition of the 0.25% of SSL to wheat flour to produced modified gluten protein, pointing the formation of a more ordered structure. Side chain vibrations also confirmed the observed changes.

  9. Prediction of protein folding rates from simplified secondary structure alphabet.

    PubMed

    Huang, Jitao T; Wang, Titi; Huang, Shanran R; Li, Xin

    2015-10-21

    Protein folding is a very complicated and highly cooperative dynamic process. However, the folding kinetics is likely to depend more on a few key structural features. Here we find that secondary structures can determine folding rates of only large, multi-state folding proteins and fails to predict those for small, two-state proteins. The importance of secondary structures for protein folding is ordered as: extended β strand > α helix > bend > turn > undefined secondary structure>310 helix > isolated β strand > π helix. Only the first three secondary structures, extended β strand, α helix and bend, can achieve a good correlation with folding rates. This suggests that the rate-limiting step of protein folding would depend upon the formation of regular secondary structures and the buckling of chain. The reduced secondary structure alphabet provides a simplified description for the machine learning applications in protein design. PMID:26247139

  10. Distinct circular dichroism spectroscopic signatures of polyproline II and unordered secondary structures: Applications in secondary structure analyses

    PubMed Central

    Lopes, Jose L S; Miles, Andrew J; Whitmore, Lee; Wallace, B A

    2014-01-01

    Circular dichroism (CD) spectroscopy is a valuable method for defining canonical secondary structure contents of proteins based on empirically-defined spectroscopic signatures derived from proteins with known three-dimensional structures. Many proteins identified as being “Intrinsically Disordered Proteins” have a significant amount of their structure that is neither sheet, helix, nor turn; this type of structure is often classified by CD as “other”, “random coil”, “unordered”, or “disordered”. However the “other” category can also include polyproline II (PPII)-type structures, whose spectral properties have not been well-distinguished from those of unordered structures. In this study, synchrotron radiation circular dichroism spectroscopy was used to investigate the spectral properties of collagen and polyproline, which both contain PPII-type structures. Their native spectra were compared as representatives of PPII structures. In addition, their spectra before and after treatment with various conditions to produce unfolded or denatured structures were also compared, with the aim of defining the differences between CD spectra of PPII and disordered structures. We conclude that the spectral features of collagen are more appropriate than those of polyproline for use as the representative spectrum for PPII structures present in typical amino acid-containing proteins, and that the single most characteristic spectroscopic feature distinguishing a PPII structure from a disordered structure is the presence of a positive peak around 220nm in the former but not in the latter. These spectra are now available for inclusion in new reference data sets used for CD analyses of the secondary structures of soluble proteins. PMID:25262612

  11. Structure Property Studies for Additively Manufactured Parts

    SciTech Connect

    Milenski, Helen M; Schmalzer, Andrew Michael; Kelly, Daniel

    2015-08-17

    Since the invention of modern Additive Manufacturing (AM) processes engineers and designers have worked hard to capitalize on the unique building capabilities that AM allows. By being able to customize the interior fill of parts it is now possible to design components with a controlled density and customized internal structure. The creation of new polymers and polymer composites allow for even greater control over the mechanical properties of AM parts. One of the key reasons to explore AM, is to bring about a new paradigm in part design, where materials can be strategically optimized in a way that conventional subtractive methods cannot achieve. The two processes investigated in my research were the Fused Deposition Modeling (FDM) process and the Direct Ink Write (DIW) process. The objectives of the research were to determine the impact of in-fill density and morphology on the mechanical properties of FDM parts, and to determine if DIW printed samples could be produced where the filament diameter was varied while the overall density remained constant.

  12. Study of coal structure using secondary ion mass spectrometry

    SciTech Connect

    Tingey, G.L.; Lytle, J.M.; Baer, D.R.; Thomas, M.T.

    1980-12-01

    Secondary-ion Mass Spectrometry (SIMS) is examined as a tool for studying the chemical structure of coal. SIMS has potential for analysis of coal because of the following characteristics: sensitivity to chemical structure; high sensitivity to all masses; application to solids; excellent depth resolution; and reasonable spatial resolution. SIMS spectra of solid coals show differences with respect to coal rank, the spectra of high rank coal being similar to that of graphite, and the spectra of low rank coal being similar to that of wood. Some functional group analysis is also possible using SIMS. Low rank coals show a larger peak at 15 amu indicating more methyl groups than found in the higher rank coals. Fragments with two and three carbon atoms have also been examined; much larger fragments are undoubtedly present but were not evaluated in this study. Examination of these groups, which are expected to contain valuable information on coal structure, is planned for future work. It has been observed that mineral atoms present in the coal have large secondary ion yields which complicate the interpretation of the spectra. Studies on mineral-free coals and model compounds are therefore recommended to facilitate determination of organic coal structure. In addition, mass spectrometry with much greater mass resolution will aid in distinguishing between various ion species.

  13. Neural network definitions of highly predictable protein secondary structure classes

    SciTech Connect

    Lapedes, A. |; Steeg, E.; Farber, R.

    1994-02-01

    We use two co-evolving neural networks to determine new classes of protein secondary structure which are significantly more predictable from local amino sequence than the conventional secondary structure classification. Accurate prediction of the conventional secondary structure classes: alpha helix, beta strand, and coil, from primary sequence has long been an important problem in computational molecular biology. Neural networks have been a popular method to attempt to predict these conventional secondary structure classes. Accuracy has been disappointingly low. The algorithm presented here uses neural networks to similtaneously examine both sequence and structure data, and to evolve new classes of secondary structure that can be predicted from sequence with significantly higher accuracy than the conventional classes. These new classes have both similarities to, and differences with the conventional alpha helix, beta strand and coil.

  14. Laser Additive Manufacturing of Gas Permeable Structures

    NASA Astrophysics Data System (ADS)

    Klahn, C.; Bechmann, F.; Hofmann, S.; Dinkel, M.; Emmelmann, C.

    Laser additive manufacturing offers a variety of new design possibilities. In mold making laser additive manufactured inserts with conformal cooling channels are already state of the art. Pneumatic ejectors for injection molds are a new application for laser additive manufacturing. The pneumatic ejectors require a durable gas permeable material. This material is produced by placing the scan vectors for the laser additive manufacturing process in a defined pattern. Trials with different plastics proofed the function and reliability of the pneumatic ejector concept in the injection molding cycle.

  15. A novel approach to represent and compare RNA secondary structures

    PubMed Central

    Mattei, Eugenio; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2014-01-01

    Structural information is crucial in ribonucleic acid (RNA) analysis and functional annotation; nevertheless, how to include such structural data is still a debated problem. Dot-bracket notation is the most common and simple representation for RNA secondary structures but its simplicity leads also to ambiguity requiring further processing steps to dissolve. Here we present BEAR (Brand nEw Alphabet for RNA), a new context-aware structural encoding represented by a string of characters. Each character in BEAR encodes for a specific secondary structure element (loop, stem, bulge and internal loop) with specific length. Furthermore, exploiting this informative and yet simple encoding in multiple alignments of related RNAs, we captured how much structural variation is tolerated in RNA families and convert it into transition rates among secondary structure elements. This allowed us to compute a substitution matrix for secondary structure elements called MBR (Matrix of BEAR-encoded RNA secondary structures), of which we tested the ability in aligning RNA secondary structures. We propose BEAR and the MBR as powerful resources for the RNA secondary structure analysis, comparison and classification, motif finding and phylogeny. PMID:24753415

  16. Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structure.

    PubMed

    Saraswathi, S; Fernández-Martínez, J L; Koliński, A; Jernigan, R L; Kloczkowski, A

    2013-10-01

    Exponential growth in the number of available protein sequences is unmatched by the slower growth in the number of structures. As a result, the development of efficient and fast protein secondary structure prediction methods is essential for the broad comprehension of protein structures. Computational methods that can efficiently determine secondary structure can in turn facilitate protein tertiary structure prediction, since most methods rely initially on secondary structure predictions. Recently, we have developed a fast learning optimized prediction methodology (FLOPRED) for predicting protein secondary structure (Saraswathi et al. in JMM 18:4275, 2012). Data are generated by using knowledge-based potentials combined with structure information from the CATH database. A neural network-based extreme learning machine (ELM) and advanced particle swarm optimization (PSO) are used with this data to obtain better and faster convergence to more accurate secondary structure predicted results. A five-fold cross-validated testing accuracy of 83.8 % and a segment overlap (SOV) score of 78.3 % are obtained in this study. Secondary structure predictions and their accuracy are usually presented for three secondary structure elements: α-helix, β-strand and coil but rarely have the results been analyzed with respect to their constituent amino acids. In this paper, we use the results obtained with FLOPRED to provide detailed behaviors for different amino acid types in the secondary structure prediction. We investigate the influence of the composition, physico-chemical properties and position specific occurrence preferences of amino acids within secondary structure elements. In addition, we identify the correlation between these properties and prediction accuracy. The present detailed results suggest several important ways that secondary structure predictions can be improved in the future that might lead to improved protein design and engineering. PMID:23907551

  17. Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases

    PubMed Central

    Sharma, Sudha

    2011-01-01

    In addition to the canonical B-form structure first described by Watson and Crick, DNA can adopt a number of alternative structures. These non-B-form DNA secondary structures form spontaneously on tracts of repeat sequences that are abundant in genomes. In addition, structured forms of DNA with intrastrand pairing may arise on single-stranded DNA produced transiently during various cellular processes. Such secondary structures have a range of biological functions but also induce genetic instability. Increasing evidence suggests that genomic instabilities induced by non-B DNA secondary structures result in predisposition to diseases. Secondary DNA structures also represent a new class of molecular targets for DNA-interactive compounds that might be useful for targeting telomeres and transcriptional control. The equilibrium between the duplex DNA and formation of multistranded non-B-form structures is partly dependent upon the helicases that unwind (resolve) these alternate DNA structures. With special focus on tetraplex, triplex, and cruciform, this paper summarizes the incidence of non-B DNA structures and their association with genomic instability and emphasizes the roles of RecQ-like DNA helicases in genome maintenance by resolution of DNA secondary structures. In future, RecQ helicases are anticipated to be additional molecular targets for cancer chemotherapeutics. PMID:21977309

  18. Rhodium-catalyzed anti-Markovnikov addition of secondary amines to arylacetylenes at room temperature.

    PubMed

    Sakai, Kazunori; Kochi, Takuya; Kakiuchi, Fumitoshi

    2011-08-01

    An efficient method for synthesis of E-enamines by the anti-Markovnikov addition of secondary amines to terminal alkynes is described. The reaction of a variety of aryl- and heteroarylacetylenes proceeded at room temperature using a combination of a 8-quinolinolato rhodium complex and P(p-MeOC(6)H(4))(3) as a catalyst. The products were obtained as enamines by simple bulb-to-bulb distillation. PMID:21699251

  19. Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy

    PubMed Central

    Garmann, Rees F.; Gopal, Ajaykumar; Athavale, Shreyas S.; Knobler, Charles M.; Gelbart, William M.; Harvey, Stephen C.

    2015-01-01

    The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures. PMID:25752599

  20. Protein secondary structure classification revisited: processing DSSP information with PSSC.

    PubMed

    Zacharias, Jan; Knapp, Ernst-Walter

    2014-07-28

    A first step toward three-dimensional protein structure description is the characterization of secondary structure. The most widely used program for secondary structure assignment remains DSSP, introduced in 1983, with currently more than 400 citations per year. DSSP output is in a one-letter representation, where much of the information on DSSP's internal description is lost. Recently it became evident that DSSP overlooks most π-helical structures, which are more prevalent and important than anticipated before. We introduce an alternative concept, representing the internal structure characterization of DSSP as an eight-character string that is human-interpretable and easy to parse by software. We demonstrate how our protein secondary structure characterization (PSSC) code allows for inspection of complicated structural features. It recognizes ten times more π-helical residues than does the standard DSSP. The plausibility of introduced changes in interpreting DSSP information is demonstrated by better clustering of secondary structures in (φ, ψ) dihedral angle space. With a sliding sequence window (SSW), helical assignments with PSSC remain invariant compared with an assignment based on the complete structure. In contrast, assignment with DSSP can be changed by residues in the neighborhood that are in fact not interacting with the residue under consideration. We demonstrate how one can easily define new secondary structure classification schemes with PSSC and perform the classifications. Our approach works without changing the DSSP source code and allows for more detailed protein characterization. PMID:24866861

  1. Unified approach to partition functions of RNA secondary structures.

    PubMed

    Bundschuh, Ralf

    2014-11-01

    RNA secondary structure formation is a field of considerable biological interest as well as a model system for understanding generic properties of heteropolymer folding. This system is particularly attractive because the partition function and thus all thermodynamic properties of RNA secondary structure ensembles can be calculated numerically in polynomial time for arbitrary sequences and homopolymer models admit analytical solutions. Such solutions for many different aspects of the combinatorics of RNA secondary structure formation share the property that the final solution depends on differences of statistical weights rather than on the weights alone. Here, we present a unified approach to a large class of problems in the field of RNA secondary structure formation. We prove a generic theorem for the calculation of RNA folding partition functions. Then, we show that this approach can be applied to the study of the molten-native transition, denaturation of RNA molecules, as well as to studies of the glass phase of random RNA sequences. PMID:24177391

  2. Combinatorics of RNA Secondary Structures with Base Triples.

    PubMed

    Müller, Robert; Nebel, Markus E

    2015-07-01

    The structure of RNA has been the subject of intense research over the last decades due to its importance for the correct functioning of RNA molecules in biological processes. Hence, a large number of models for RNA folding and corresponding algorithms for structure prediction have been developed. However, previous models often only consider base pairs, although every base is capable of up to three edge-to-edge interactions with other bases. Recently, Höner zu Siederdissen et al. presented an extended model of RNA secondary structure, including base triples together with a folding algorithm-the first thermodynamics-based algorithm that allows the prediction of secondary structures with base triples. In this article, we investigate the search space processed by this new algorithm, that is, the combinatorics of extended RNA secondary structures with base triples. We present generalized definitions for structural motifs like hairpins, stems, bulges, or interior loops occurring in structures with base triples. Furthermore, we prove precise asymptotic results for the number of different structures (size of search space) and expectations for various parameters associated with structural motifs (typical shape of folding). Our analysis shows that the asymptotic number of secondary structures of size n increases exponentially to [Formula: see text] compared to the classic model by Stein and Waterman for which [Formula: see text] structures exist. A comparison with the classic model reveals large deviations in the expected structural appearance, too. The inclusion of base triples constitutes a significant refinement of the combinatorial model of RNA secondary structure, which, by our findings, is quantitatively characterized. Our results are of special theoretical interest, because a closer look at the numbers involved suggests that extended RNA secondary structures constitute a new combinatorial class not bijective with any other combinatorial objects studied so far. PMID

  3. BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms.

    PubMed

    Allali, Julien; Saule, Cédric; Chauve, Cédric; d'Aubenton-Carafa, Yves; Denise, Alain; Drevet, Christine; Ferraro, Pascal; Gautheret, Daniel; Herrbach, Claire; Leclerc, Fabrice; de Monte, Antoine; Ouangraoua, Aida; Sagot, Marie-France; Termier, Michel; Thermes, Claude; Touzet, Hélène

    2012-01-01

    The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for annotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available for comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc annotated sequences, and multilevel trees) and computational principles (edit distance, alignment). We describe here the website BRASERO that offers tools for evaluating such software tools on real and synthetic datasets. PMID:22675348

  4. Predicting RNA secondary structures from sequence and probing data.

    PubMed

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

    2016-07-01

    RNA secondary structures have proven essential for understanding the regulatory functions performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success is in part due to the availability of efficient computational methods for predicting RNA secondary structures. Recent advances focus on dealing with the inherent uncertainty of prediction by considering the ensemble of possible structures rather than the single most stable one. Moreover, the advent of high-throughput structural probing has spurred the development of computational methods that incorporate such experimental data as auxiliary information. PMID:27064083

  5. Principles for Predicting RNA Secondary Structure Design Difficulty.

    PubMed

    Anderson-Lee, Jeff; Fisker, Eli; Kosaraju, Vineet; Wu, Michelle; Kong, Justin; Lee, Jeehyung; Lee, Minjae; Zada, Mathew; Treuille, Adrien; Das, Rhiju

    2016-02-27

    Designing RNAs that form specific secondary structures is enabling better understanding and control of living systems through RNA-guided silencing, genome editing and protein organization. Little is known, however, about which RNA secondary structures might be tractable for downstream sequence design, increasing the time and expense of design efforts due to inefficient secondary structure choices. Here, we present insights into specific structural features that increase the difficulty of finding sequences that fold into a target RNA secondary structure, summarizing the design efforts of tens of thousands of human participants and three automated algorithms (RNAInverse, INFO-RNA and RNA-SSD) in the Eterna massive open laboratory. Subsequent tests through three independent RNA design algorithms (NUPACK, DSS-Opt and MODENA) confirmed the hypothesized importance of several features in determining design difficulty, including sequence length, mean stem length, symmetry and specific difficult-to-design motifs such as zigzags. Based on these results, we have compiled an Eterna100 benchmark of 100 secondary structure design challenges that span a large range in design difficulty to help test future efforts. Our in silico results suggest new routes for improving computational RNA design methods and for extending these insights to assess "designability" of single RNA structures, as well as of switches for in vitro and in vivo applications. PMID:26902426

  6. Secondary Structure and Secondary Structure Dynamics of DNA Hairpins Complexed with HIV-1 NC Protein

    PubMed Central

    Cosa, Gonzalo; Harbron, Elizabeth J.; Zeng, Yining; Liu, Hsiao-Wei; O'Connor, Donald B.; Eta-Hosokawa, Chie; Musier-Forsyth, Karin; Barbara, Paul F.

    2004-01-01

    Reverse transcription of the HIV-1 RNA genome involves several complex nucleic acid rearrangement steps that are catalyzed by the HIV-1 nucleocapsid protein (NC), including for example, the annealing of the transactivation response (TAR) region of the viral RNA to the complementary region (TAR DNA) in minus-strand strong-stop DNA. We report herein single-molecule fluorescence resonance energy transfer measurements on single immobilized TAR DNA hairpins and hairpin mutants complexed with NC (i.e., TAR DNA/NC). Using this approach we have explored the conformational distribution and dynamics of the hairpins in the presence and absence of NC protein. The data demonstrate that NC shifts the equilibrium secondary structure of TAR DNA hairpins from a fully “closed” conformation to essentially one specific “partially open” conformation. In this specific conformation, the two terminal stems are “open” or unwound and the other stems are closed. This partially open conformation is arguably a key TAR DNA intermediate in the NC-induced annealing mechanism of TAR DNA. PMID:15454467

  7. 1. Building #3, original structure and first addition, north side, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Building #3, original structure and first addition, north side, looking south. Photo shows (from left) the original 1911 structure, the 1939 infill addition, and the 1934 structure. - S. W. Shattuck Chemical Company, Incorporated, Building No. 3, 1805 South Bannock Street, Denver, Denver County, CO

  8. 46 CFR 72.01-25 - Additional structural requirements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 3 2010-10-01 2010-10-01 false Additional structural requirements. 72.01-25 Section 72.01-25 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PASSENGER VESSELS CONSTRUCTION AND ARRANGEMENT Hull Structure § 72.01-25 Additional structural requirements. (a) Vessels required by part 171 of this chapter to have...

  9. The 5'-3' distance of RNA secondary structures.

    PubMed

    Han, Hillary S W; Reidys, Christian M

    2012-07-01

    Recently, Yoffe and colleagues observed that the average distances between 5'-3' ends of RNA molecules are very small and largely independent of sequence length. This observation is based on numerical computations as well as theoretical arguments maximizing certain entropy functionals. In this article, we compute the exact distribution of 5'-3' distances of RNA secondary structures for any finite n. Furthermore, we compute the limit distribution and show that for n = 30 the exact distribution and the limit distribution are very close. Our results show that the distances of random RNA secondary structures are distinctively lower than those of minimum free energy structures of random RNA sequences. PMID:22731624

  10. A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments.

    PubMed

    Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

    2016-01-01

    The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure-function relationship. PMID:26978354

  11. SRP-RNA sequence alignment and secondary structure.

    PubMed Central

    Larsen, N; Zwieb, C

    1991-01-01

    The secondary structures of the RNAs from the signal recognition particle, termed SRP-RNA, were derived buy comparative analyses of an alignment of 39 sequences. The models are minimal in that only base pairs are included for which there is comparative evidence. The structures represent refinements of earlier versions and include a new short helix. PMID:1707519

  12. Enhanced performance of a submerged membrane bioreactor with powdered activated carbon addition for municipal secondary effluent treatment.

    PubMed

    Lin, Hongjun; Wang, Fangyuan; Ding, Linxian; Hong, Huachang; Chen, Jianrong; Lu, Xiaofeng

    2011-09-15

    The aim of this study was to investigate the feasibility of PAC-MBR process treating municipal secondary effluent. Two laboratory-scale submerged MBRs (SMBR) with and without PAC addition were continuously operated in parallel for secondary effluent treatment. Approximately 63%TOC, 95% NH(4)(+)-N and 98% turbidity in secondary effluent were removed by the PAC-MBR process. Most organics in the secondary effluent were found to be low molecular weight (MW) substances, which could be retained in the reactor and then removed to some extent by using PAC-MBR process. Parallel experiments showed that the addition of PAC significantly increased organic removal and responsible for the largest fraction of organic removal. Membrane fouling analysis showed the enhanced membrane performance in terms of sustainable operational time and filtration resistances by PAC addition. Based on these results, the PAC-MBR process was considered as an attractive option for the reduction of pollutants in secondary effluent. PMID:21794980

  13. A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments

    PubMed Central

    Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

    2016-01-01

    The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure–function relationship. PMID:26978354

  14. Secondary structure adventures with Carl Woese.

    PubMed

    Noller, Harry F

    2014-01-01

    Not long after my arrival at UCSC as an assistant professor, I came across Carl Woese's paper "Molecular Mechanics of Translation: A Reciprocating Ratchet Mechanism." (1) In the days before the crystal structure of tRNA was known, Fuller and Hodgson (2) had proposed two alternative conformations for its anticodon loop; one was stacked on the 3' side (as later found in the crystal structure) and the other on the 5' side. In an ingenious and elegant model, Woese proposed that the conformation of the loop flips between Fuller and Hodgson's 5'- and 3'-stacked forms during protein synthesis, changing the local direction of the mRNA such that the identities of the tRNA binding sites alternated between binding aminoacyl-tRNA and peptidyl-tRNA. The model predicted that there are no A and P sites, only two binding sites whose identities changed following translation of each codon, and that there would be no translocation of tRNAs in the usual sense--only binding and release. I met Carl in person the following year when he presented a seminar on his ratchet model in Santa Cruz. He was chatting in my colleague Ralph Hinegardner's office in what Carl termed a "Little Jack Horner appointment" (the visitor sits and listens to his host describing "What a good boy am I"). He was of compact stature, and bore a striking resemblance to Oskar Werner in Truffaut's film "Jules and Jim." He projected the impression of a New-Age guru--a shiny black amulet suspended over the front of his black turtleneck sweater and a crown of prematurely white hair. Ralph asked me to explain to Carl what we were doing with ribosomes. I quickly summarized our early experiments that were pointing to a functional role for 16S rRNA. Carl regarded me silently, with a penetrating stare. He then turned to Ralph and said, in an ominous low voice, "I'm going to have some more tanks made as soon as I get back." Carl's beautiful model was, unfortunately, wrong--it was simpler and more elegant than the complex

  15. Secondary structure adventures with Carl Woese

    PubMed Central

    Noller, Harry F

    2014-01-01

    Not long after my arrival at UCSC as an assistant professor, I came across Carl Woese's paper “Molecular Mechanics of Translation: A Reciprocating Ratchet Mechanism.”1 In the days before the crystal structure of tRNA was known, Fuller and Hodgson2 had proposed two alternative conformations for its anticodon loop; one was stacked on the 3′ side (as later found in the crystal structure) and the other on the 5′ side. In an ingenious and elegant model, Woese proposed that the conformation of the loop flips between Fuller and Hodgson's 5′- and 3′-stacked forms during protein synthesis, changing the local direction of the mRNA such that the identities of the tRNA binding sites alternated between binding aminoacyl-tRNA and peptidyl-tRNA. The model predicted that there are no A and P sites, only two binding sites whose identities changed following translation of each codon, and that there would be no translocation of tRNAs in the usual sense—only binding and release. I met Carl in person the following year when he presented a seminar on his ratchet model in Santa Cruz. He was chatting in my colleague Ralph Hinegardner's office in what Carl termed a “Little Jack Horner appointment” (the visitor sits and listens to his host describing “What a good boy am I”). He was of compact stature, and bore a striking resemblance to Oskar Werner in Truffaut's film “Jules and Jim.” He projected the impression of a New-Age guru—a shiny black amulet suspended over the front of his black turtleneck sweater and a crown of prematurely white hair. Ralph asked me to explain to Carl what we were doing with ribosomes. I quickly summarized our early experiments that were pointing to a functional role for 16S rRNA. Carl regarded me silently, with a penetrating stare. He then turned to Ralph and said, in an ominous low voice, “I'm going to have some more tanks made as soon as I get back.” Carl's beautiful model was, unfortunately, wrong—it was simpler and more

  16. Quantifying variances in comparative RNA secondary structure prediction

    PubMed Central

    2013-01-01

    Background With the advancement of next-generation sequencing and transcriptomics technologies, regulatory effects involving RNA, in particular RNA structural changes are being detected. These results often rely on RNA secondary structure predictions. However, current approaches to RNA secondary structure modelling produce predictions with a high variance in predictive accuracy, and we have little quantifiable knowledge about the reasons for these variances. Results In this paper we explore a number of factors which can contribute to poor RNA secondary structure prediction quality. We establish a quantified relationship between alignment quality and loss of accuracy. Furthermore, we define two new measures to quantify uncertainty in alignment-based structure predictions. One of the measures improves on the “reliability score” reported by PPfold, and considers alignment uncertainty as well as base-pair probabilities. The other measure considers the information entropy for SCFGs over a space of input alignments. Conclusions Our predictive accuracy improves on the PPfold reliability score. We can successfully characterize many of the underlying reasons for and variances in poor prediction. However, there is still variability unaccounted for, which we therefore suggest comes from the RNA secondary structure predictive model itself. PMID:23634662

  17. Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function.

    PubMed

    Del Campo, Cristian; Bartholomäus, Alexander; Fedyunin, Ivan; Ignatova, Zoya

    2015-10-01

    Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation. PMID:26495981

  18. Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function

    PubMed Central

    Fedyunin, Ivan; Ignatova, Zoya

    2015-01-01

    Messenger RNA acts as an informational molecule between DNA and translating ribosomes. Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity. Although individual examples show that specific structural features of mRNA regulate translation and transcript stability, their role and function throughout the bacterial transcriptome remains unknown. Combining three sequencing approaches to provide a high resolution view of global mRNA secondary structure, translation efficiency and mRNA abundance, we unraveled structural features in E. coli mRNA with implications in translation and mRNA degradation. A poorly structured site upstream of the coding sequence serves as an additional unspecific binding site of the ribosomes and the degree of its secondary structure propensity negatively correlates with gene expression. Secondary structures within coding sequences are highly dynamic and influence translation only within a very small subset of positions. A secondary structure upstream of the stop codon is enriched in genes terminated by UAA codon with likely implications in translation termination. The global analysis further substantiates a common recognition signature of RNase E to initiate endonucleolytic cleavage. This work determines for the first time the E. coli RNA structurome, highlighting the contribution of mRNA secondary structure as a direct effector of a variety of processes, including translation and mRNA degradation. PMID:26495981

  19. A novel fold recognition method using composite predicted secondary structures.

    PubMed

    An, Yuling; Friesner, Richard A

    2002-08-01

    In this work, we introduce a new method for fold recognition using composite secondary structures assembled from different secondary structure prediction servers for a given target sequence. An automatic, complete, and robust way of finding all possible combinations of predicted secondary structure segments (SSS) for the target sequence and clustering them into a few flexible clusters, each containing patterns with the same number of SSS, is developed. This program then takes two steps in choosing plausible homologues: (i) a SSS-based alignment excludes impossible templates whose SSS patterns are very different from any of those of the target; (ii) a residue-based alignment selects good structural templates based on sequence similarity and secondary structure similarity between the target and only those templates left in the first stage. The secondary structure of each residue in the target is selected from one of the predictions to find the best match with the template. Truncation is applied to a target where different predictions vary. In most cases, a target is also divided into N-terminal and C-terminal fragments, each of which is used as a separate subsequence. Our program was tested on the fold recognition targets from CASP3 with known PDB codes and some available targets from CASP4. The results are compared with a structural homologue list for each target produced by the CE program (Shindyalov and Bourne, Protein Eng 1998;11:739-747). The program successfully locates homologues with high Z-score and low root-mean-score deviation within the top 30-50 predictions in the overwhelming majority of cases. PMID:12112702

  20. Small Molecule Ligands for Bulged RNA Secondary Structures

    PubMed Central

    Meyer, S. Todd; Hergenrother, Paul J.

    2016-01-01

    A class of wedge-shaped small molecules has been designed, synthesized, and shown to bind bulged RNA secondary structures. These minimally cationic ligands exhibit good affinity and selectivity for certain RNA bulges as demonstrated in a fluorescent intercalator displacement assay. PMID:19678613

  1. Alternate rRNA secondary structures as regulators of translation.

    PubMed

    Feng, Shu; Li, Heng; Zhao, Jing; Pervushin, Konstantin; Lowenhaupt, Ky; Schwartz, Thomas U; Dröge, Peter

    2011-02-01

    Structural dynamics of large molecular assemblies are intricately linked to function. For ribosomes, macromolecular changes occur especially during mRNA translation and involve participation of ribosomal RNA. Without suitable probes specific to RNA secondary structure, however, elucidation of more subtle dynamic ribosome structure-function relationships, especially in vivo, remains challenging. Here we report that the Z-DNA- and Z-RNA-binding domain Zα, derived from the human RNA editing enzyme ADAR1-L, binds with high stability to specific rRNA segments of Escherichia coli and human ribosomes. Zα impaired in Z-RNA recognition does not associate with ribosomes. Notably, Zα(ADAR1)-ribosome interaction blocks translation in vitro and in vivo, with substantial physiological consequences. Our study shows that ribosomes can be targeted by a protein that specifically recognizes an alternate rRNA secondary structure, and suggests a new mechanism of translational regulation on the ribosome. PMID:21217697

  2. Refinement by shifting secondary structure elements improves sequence alignments.

    PubMed

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V

    2015-03-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  3. Refinement by shifting secondary structure elements improves sequence alignments

    PubMed Central

    Tong, Jing; Pei, Jimin; Otwinowski, Zbyszek; Grishin, Nick V.

    2015-01-01

    Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa. PMID:25546158

  4. Protein structure prediction: assembly of secondary structure elements by basin-hopping.

    PubMed

    Hoffmann, Falk; Vancea, Ioan; Kamat, Sanjay G; Strodel, Birgit

    2014-10-20

    The prediction of protein tertiary structure from primary structure remains a challenging task. One possible approach to this problem is the application of basin-hopping global optimization combined with an all-atom force field. In this work, the efficiency of basin-hopping is improved by introducing an approach that derives tertiary structures from the secondary structure assignments of individual residues. This approach is termed secondary-to-tertiary basin-hopping and benchmarked for three miniproteins: trpzip, trp-cage and ER-10. For each of the three miniproteins, the secondary-to-tertiary basin-hopping approach successfully and reliably predicts their three-dimensional structure. When it is applied to larger proteins, correctly folded structures are obtained. It can be concluded that the assembly of secondary structure elements using basin-hopping is a promising tool for de novo protein structure prediction. PMID:25056272

  5. Computation of statistical secondary structure of nucleic acids.

    PubMed Central

    Yamamoto, K; Kitamura, Y; Yoshikura, H

    1984-01-01

    This paper presents a computer analysis of statistical secondary structure of nucleic acids. For a given single stranded nucleic acid, we generated "structure map" which included all the annealing structures in the sequence. The map was transformed into "energy map" by rough approximation; here, the energy level of every pairing structure consisting of more than 2 successive nucleic acid pairs was calculated. By using the "energy map", the probability of occurrence of each annealed structure was computed, i.e., the structure was computed statistically. The basis of computation was the 8-queen problem in the chess game. The validity of our computer programme was checked by computing tRNA structure which has been well established. Successful application of this programme to small nuclear RNAs of various origins is demonstrated. PMID:6198622

  6. Biobased extreme pressure additives: Structure-property considerations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Extreme pressure additives are widely used in lubricant formulations for engine oils, hydraulic fluids, gear oils, metalworking fluids, and many others. Extreme pressure additives contain selected elements such as sulfur, phosphorus, and halogens in their structures. These elements, under extreme tr...

  7. Improving protein secondary structure prediction using a multi-modal BP method.

    PubMed

    Qu, Wu; Sui, Haifeng; Yang, Bingru; Qian, Wenbin

    2011-10-01

    Methods for predicting protein secondary structures provide information that is useful both in ab initio structure prediction and as additional restraints for fold recognition algorithms. Secondary structure predictions may also be used to guide the design of site directed mutagenesis studies, and to locate potential functionally important residues. In this article, we propose a multi-modal back propagation neural network (MMBP) method for predicting protein secondary structures. Using a Knowledge Discovery Theory based on Inner Cognitive Mechanism (KDTICM) method, we have constructed a compound pyramid model (CPM), which is composed of three layers of intelligent interface that integrate multi-modal back propagation neural network (MMBP), mixed-modal SVM (MMS), modified Knowledge Discovery in Databases (KDD(⁎)) process and so on. The CPM method is both an integrated web server and a standalone application that exploits recent advancements in knowledge discovery and machine learning to perform very accurate protein secondary structure predictions. Using a non-redundant test dataset of 256 proteins from RCASP256, the CPM method achieves an average Q(3) score of 86.13% (SOV99=84.66%). Extensive testing indicates that this is significantly better than any other method currently available. Assessments using RS126 and CB513 datasets indicate that the CPM method can achieve average Q(3) score approaching 83.99% (SOV99=80.25%) and 85.58% (SOV99=81.15%). By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called CPM, which performs these secondary structure predictions, is accessible at http://kdd.ustb.edu.cn/protein_Web/. PMID:21880310

  8. Additive Manufacturing of Metal Cellular Structures: Design and Fabrication

    NASA Astrophysics Data System (ADS)

    Yang, Li; Harrysson, Ola; Cormier, Denis; West, Harvey; Gong, Haijun; Stucker, Brent

    2015-03-01

    With the rapid development of additive manufacturing (AM), high-quality fabrication of lightweight design-efficient structures no longer poses an insurmountable challenge. On the other hand, much of the current research and development with AM technologies still focuses on material and process development. With the design for additive manufacturing in mind, this article explores the design issue for lightweight cellular structures that could be efficiently realized via AM processes. A unit-cell-based modeling approach that combines experimentation and limited-scale simulation was demonstrated, and it was suggested that this approach could potentially lead to computationally efficient design optimizations with the lightweight structures in future applications.

  9. Secondary Fast Magnetoacoustic Waves Trapped in Randomly Structured Plasmas

    NASA Astrophysics Data System (ADS)

    Yuan, Ding; Li, Bo; Walsh, Robert W.

    2016-09-01

    Fast magnetoacoustic waves are an important tool for inferring parameters of the solar atmosphere. We numerically simulate the propagation of fast wave pulses in randomly structured plasmas that mimic the highly inhomogeneous solar corona. A network of secondary waves is formed by a series of partial reflections and transmissions. These secondary waves exhibit quasi-periodicities in both time and space. Since the temporal and spatial periods are related simply through the speed of the fast wave, we quantify the properties of secondary waves by examining the dependence of the average temporal period (\\bar{p}) on the initial pulse width (w 0) and studying the density contrast ({δ }ρ ) and correlation length (L c ) that characterize the randomness of the equilibrium density profiles. For small-amplitude pulses, {δ }ρ does not alter \\bar{p} significantly. Large-amplitude pulses, on the other hand, enhance the density contrast when {δ }ρ is small but have a smoothing effect when {δ }ρ is sufficiently large. We found that \\bar{p} scales linearly with L c and that the scaling factor is larger for a narrower pulse. However, in terms of the absolute values of \\bar{p}, broader pulses generate secondary waves with longer periods, and this effect is stronger in random plasmas with shorter correlation lengths. Secondary waves carry the signatures of both the leading wave pulse and the background plasma. Our study may find applications in magnetohydrodynamic seismology by exploiting the secondary waves detected in the dimming regions after coronal mass ejections or extreme ultraviolet waves.

  10. Secondary Pollutants from Ozone Reaction with Ventilation Filters and Degradation of Filter Media Additives

    SciTech Connect

    Destaillats, Hugo; Chen, Wenhao; Apte, Michael; Li, Nuan; Spears, Michael; Almosni, Jérémie; Brunner, Gregory; Zhang, Jianshun; Fisk, William J.

    2011-05-01

    Prior research suggests that chemical processes taking place on the surface of particle filters employed in buildings may lead to the formation of harmful secondary byproducts. We investigated ozone reactions with fiberglass, polyester, cotton/polyester and polyolefin filter media, as well as hydrolysis of filter media additives. Studies were carried out on unused media, and on filters that were installed for 3 months in buildings at two different locations in the San Francisco Bay Area. Specimens from each filter media were exposed to {approx}150 ppbv ozone in a flow tube under a constant flow of dry or humidified air (50percent RH). Ozone breakthrough was recorded for each sample over periods of {approx}1000 min; the ozone uptake rate was calculated for an initial transient period and for steady-state conditions. While ozone uptake was observed in all cases, we did not observe significant differences in the uptake rate and capacity for the various types of filter media tested. Most experiments were performed at an airflow rate of 1.3 L/min (face velocity = 0.013 m/s), and a few tests were also run at higher rates (8 to 10 L/min). Formaldehyde and acetaldehyde, two oxidation byproducts, were quantified downstream of each sample. Those aldehydes (m/z 31 and 45) and other volatile byproducts (m/z 57, 59, 61 and 101) were also detected in real-time using Proton-Transfer Reaction - Mass Spectrometry (PTR-MS). Low-ppbv byproduct emissions were consistently higher under humidified air than under dry conditions, and were higher when the filters were loaded with particles, as compared with unused filters. No significant differences were observed when ozone reacted over various types of filter media. Fiberglass filters heavily coated with impaction oil (tackifier) showed higher formaldehyde emissions than other samples. Those emissions were particularly high in the case of used filters, and were observed even in the absence of ozone, suggesting that hydrolysis of additives

  11. Coating concrete secondary containment structures exposed to agrichemicals

    SciTech Connect

    Broder, M.F.; Nguyen, D.T.

    1995-06-01

    Concrete has traditionally been the material of choice for building secondary containment structures because it is relatively inexpensive and has structural properties which make it ideal for supporting the loads of vehicles and large tanks. However, concrete`s chemical properties make it susceptible to corrosion by some common fertilizers. Though fairly impervious to water movement, concrete is easily penetrated by vapors and solvents. It is also prone to cracking. For these reasons, the Environmental Protection Agency (EPA) believes that concrete alone may not provide an effective barrier to pesticide movement and has proposed that concrete in pesticide secondary containment structures be sealed or coated to reduce its permeability. Some state secondary containment regulations require that concrete exposed to fertilizers and pesticides be sealed or protected with a coating. Lacking guidelines, some retailers have used penetrating sealants to satisfy the law, even though these products provide little protection from chemical attack nor do they prevent pesticide egress. Other retailers who have applied thick film coatings which were properly selected have had disastrous results because the application was poorly done. Consequently, much skepticism exists regarding the performance and benefit of protective coatings.

  12. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  13. Derivation of the Secondary Structure of the ITS-1 Transcript in Volvocales and its Taxonomic Correlations.

    PubMed

    Coleman, A W; Maria Preparata, R; Mehrotra, B; Mai, J C

    1998-05-01

    Knowledge of secondary structure, formed by the gene spacer regions of the primary transcript of nuclear rDNA cistrons, is lacking for most phyla of eukaryotes. We have sequenced the first internal transcribed spacer region (ITS-1) of multiple representatives of the Volvocales, and from comparisons of these, derived a secondary structure common to the entire group. The secondary structure model is supported by numerous compensating base pair changes located within the paired regions of the stem-loops. Within the morphological species, such as those of Astrephomene and Gonium, the three basal nucleotide pairs of helices are highly conserved in primary sequence, and the single stranded region rich in CCAA is identical in sequence, even when isolates come from all continents of the earth. In other Volvocacean species known to include many pairs of mating types, this same level of conservation is found to correlate with the mating subgroups of the species. Thus a comparable degree of sequence similarity appears to characterize all isolates of a "biological" species; this is valid for taxonomic species only where the biological and taxonomic species levels coincide. In addition, the ITS-1 contains information useful for population analyses, and spacer secondary structure may have additional phylogenetic utility at the level of class or subclass when that information becomes available for other protistan groups. PMID:23196163

  14. Friction Stir Additive Manufacturing: Route to High Structural Performance

    NASA Astrophysics Data System (ADS)

    Palanivel, S.; Sidhar, H.; Mishra, R. S.

    2015-03-01

    Aerospace and automotive industries provide the next big opportunities for additive manufacturing. Currently, the additive industry is confronted with four major challenges that have been identified in this article. These challenges need to be addressed for the additive technologies to march into new frontiers and create additional markets. Specific potential success in the transportation sectors is dependent on the ability to manufacture complicated structures with high performance. Most of the techniques used for metal-based additive manufacturing are fusion based because of their ability to fulfill the computer-aided design to component vision. Although these techniques aid in fabrication of complex shapes, achieving high structural performance is a key problem due to the liquid-solid phase transformation. In this article, friction stir additive manufacturing (FSAM) is shown as a potential solid-state process for attaining high-performance lightweight alloys for simpler geometrical applications. To illustrate FSAM as a high-performance route, manufactured builds of Mg-4Y-3Nd and AA5083 are shown as examples. In the Mg-based alloy, an average hardness of 120 HV was achieved in the built structure and was significantly higher than that of the base material (97 HV). Similarly for the Al-based alloy, compared with the base hardness of 88 HV, the average built hardness was 104 HV. A potential application of FSAM is illustrated by taking an example of a simple stiffener assembly.

  15. Secondary Impacts on Structures on the Lunar Surface

    NASA Technical Reports Server (NTRS)

    Christiansen, Eric; Walker, James D.; Grosch, Donald J.

    2010-01-01

    The Altair Lunar Lander is being designed for the planned return to the Moon by 2020. Since it is hoped that lander components will be re-used by later missions, studies are underway to examine the exposure threat to the lander sitting on the Lunar surface for extended periods. These threats involve both direct strikes of meteoroids on the vehicle as well as strikes from Lunar regolith and rock thrown by nearby meteorite strikes. Currently, the lander design is comprised of up to 10 different types of pressure vessels. These vessels included the manned habitation module, fuel, cryogenic fuel and gas storage containers, and instrument bays. These pressure vessels have various wall designs, including various aluminum alloys, honeycomb, and carbon-fiber composite materials. For some of the vessels, shielding is being considered. This program involved the test and analysis of six pressure vessel designs, one of which included a Whipple bumper shield. In addition to the pressure vessel walls, all the pressure vessels are wrapped in multi-layer insulation (MLI). Two variants were tested without the MLI to better understand the role of the MLI in the impact performance. The tests of performed were to examine the secondary impacts on these structures as they rested on the Lunar surface. If a hypervelocity meteor were to strike the surface nearby, it would throw regolith and rock debris into the structure at a much lower velocity. Also, when the manned module departs for the return to Earth, its rocket engines throw up debris that can impact the remaining lander components and cause damage. Glass spheres were used as a stimulant for the regolith material. Impact tests were performed with a gas gun to find the V50 of various sized spheres striking the pressure vessels. The impacts were then modeled and a fast-running approximate model for the V50 data was developed. This model was for performing risk analysis to assist in the vessel design and in the identification of ideal

  16. Secondary electron emission from surfaces with small structure

    NASA Astrophysics Data System (ADS)

    Dzhanoev, A. R.; Spahn, F.; Yaroshenko, V.; Lühr, H.; Schmidt, J.

    2015-09-01

    It is found that for objects possessing small surface structures with differing radii of curvature the secondary electron emission (SEE) yield may be significantly higher than for objects with smooth surfaces of the same material. The effect is highly pronounced for surface structures of nanometer scale, often providing a more than 100 % increase of the SEE yield. The results also show that the SEE yield from surfaces with structure does not show a universal dependence on the energy of the primary, incident electrons as it is found for flat surfaces in experiments. We derive conditions for the applicability of the conventional formulation of SEE using the simplifying assumption of universal dependence. Our analysis provides a basis for studying low-energy electron emission from nanometer structured surfaces under a penetrating electron beam important in many technological applications.

  17. A protein structural classes prediction method based on predicted secondary structure and PSI-BLAST profile.

    PubMed

    Ding, Shuyan; Li, Yan; Shi, Zhuoxing; Yan, Shoujiang

    2014-02-01

    Knowledge of protein secondary structural classes plays an important role in understanding protein folding patterns. In this paper, 25 features based on position-specific scoring matrices are selected to reflect evolutionary information. In combination with other 11 rational features based on predicted protein secondary structure sequences proposed by the previous researchers, a 36-dimensional representation feature vector is presented to predict protein secondary structural classes for low-similarity sequences. ASTRALtraining dataset is used to train and design our method, other three low-similarity datasets ASTRALtest, 25PDB and 1189 are used to test the proposed method. Comparisons with other methods show that our method is effective to predict protein secondary structural classes. Stand alone version of the proposed method (PSSS-PSSM) is written in MATLAB language and it can be downloaded from http://letsgob.com/bioinfo_PSSS_PSSM/. PMID:24067326

  18. Detection of Secondary and Supersecondary Structures of Proteins from Cryo-Electron Microscopy

    PubMed Central

    Bajaj, Chandrajit; Goswami, Samrat; Zhang, Qin

    2012-01-01

    Recent advances in three-dimensional electron microscopy (3D EM) have enabled the quantitative visualization of the structural building blocks of proteins at improved resolutions. We provide algorithms to detect the secondary structures (α-helices and β-sheets) from proteins for which the volumetric maps are reconstructed at 6–10Å resolution. Additionally, we show that when the resolution is coarser than 10Å, some of the super-secondary structures can be detected from 3D EM maps. For both these algorithms, we employ tools from computational geometry and differential topology, specifically the computation of stable/unstable manifolds of certain critical points of the distance function induced by the molecular surface. Our results connect mathematically well-defined constructions with bio-chemically induced structures observed in proteins. PMID:22186625

  19. Data-directed RNA secondary structure prediction using probabilistic modeling.

    PubMed

    Deng, Fei; Ledda, Mirko; Vaziri, Sana; Aviran, Sharon

    2016-08-01

    Structure dictates the function of many RNAs, but secondary RNA structure analysis is either labor intensive and costly or relies on computational predictions that are often inaccurate. These limitations are alleviated by integration of structure probing data into prediction algorithms. However, existing algorithms are optimized for a specific type of probing data. Recently, new chemistries combined with advances in sequencing have facilitated structure probing at unprecedented scale and sensitivity. These novel technologies and anticipated wealth of data highlight a need for algorithms that readily accommodate more complex and diverse input sources. We implemented and investigated a recently outlined probabilistic framework for RNA secondary structure prediction and extended it to accommodate further refinement of structural information. This framework utilizes direct likelihood-based calculations of pseudo-energy terms per considered structural context and can readily accommodate diverse data types and complex data dependencies. We use real data in conjunction with simulations to evaluate performances of several implementations and to show that proper integration of structural contexts can lead to improvements. Our tests also reveal discrepancies between real data and simulations, which we show can be alleviated by refined modeling. We then propose statistical preprocessing approaches to standardize data interpretation and integration into such a generic framework. We further systematically quantify the information content of data subsets, demonstrating that high reactivities are major drivers of SHAPE-directed predictions and that better understanding of less informative reactivities is key to further improvements. Finally, we provide evidence for the adaptive capability of our framework using mock probe simulations. PMID:27251549

  20. HOTAIR forms an intricate and modular secondary structure

    PubMed Central

    Somarowthu, Srinivas; Legiewicz, Michal; Chillón, Isabel; Marcia, Marco; Liu, Fei; Pyle, Anna Marie

    2015-01-01

    SUMMARY Long non-coding RNAs (lncRNAs) have recently emerged as key players in fundamental cellular processes and diseases, but their functions are poorly understood. HOTAIR is a 2,148-nucleotide-long lncRNA molecule involved in physiological epidermal development and in pathogenic cancer progression, where it has been demonstrated to repress tumor and metastasis suppressor genes. To gain insights into the molecular mechanisms of HOTAIR, we purified it in a stable and homogenous form in vitro and we determined its functional secondary structure through chemical probing and phylogenetic analysis. The HOTAIR structure reveals a degree of structural organization comparable to well-folded RNAs, like the group II intron, rRNA or lncRNA steroid receptor activator. It is composed of four independently-folding modules, two of which correspond to predicted protein-binding domains. Secondary structure elements that surround protein-binding motifs are evolutionarily conserved. Our work serves as a guide for “navigating” through the lncRNA HOTAIR and ultimately for understanding its function. PMID:25866246

  1. Metallic sulfide additives for positive electrode material within a secondary electrochemical cell

    DOEpatents

    Walsh, William J.; McPheeters, Charles C.; Yao, Neng-ping; Koura, Kobuyuki

    1976-01-01

    An improved active material for use within the positive electrode of a secondary electrochemical cell includes a mixture of iron disulfide and a sulfide of a polyvalent metal. Various metal sulfides, particularly sulfides of cobalt, nickel, copper, cerium and manganese, are added in minor weight proportion in respect to iron disulfide for improving the electrode performance and reducing current collector requirements.

  2. RNA secondary structures of the bacteriophage phi6 packaging regions.

    PubMed Central

    Pirttimaa, M J; Bamford, D H

    2000-01-01

    Bacteriophage phi6 genome consists of three segments of double-stranded RNA. During maturation, single-stranded copies of these segments are packaged into preformed polymerase complex particles. Only phi6 RNA is packaged, and each particle contains only one copy of each segment. An in vitro packaging and replication assay has been developed for phi6, and the packaging signals (pac sites) have been mapped to the 5' ends of the RNA segments. In this study, we propose secondary structure models for the pac sites of phi6 single-stranded RNA segments. Our models accommodate data from structure-specific chemical modifications, free energy minimizations, and phylogenetic comparisons. Previously reported pac site deletion studies are also discussed. Each pac site possesses a unique architecture, that, however, contains common structural elements. PMID:10864045

  3. [Conserved motifs in the primary and secondary ITS1 structures in bryophytes].

    PubMed

    Milyutina, I A; Ignatov, M S

    2015-01-01

    A study of the ITS1 nucleotide sequences of 1000 moss species of 62 families, 11 liverwort species from five orders, and one hornwort Anthoceros agrestis identified five highly conserved motifs (CM1-CM5), which are presumably involved in pre-rRNA processing. Although the ITS1 sequences substantially differ in length and the extent of divergence, the conserved motifs are found in all of them. ITS1 secondary structures were constructed for 76 mosses, and main regularities at conserved motif positioning were observed. The positions of processing sites in the ITS1 secondary structure of the yeast Saccharomyces cerevisiae were found to be similar to the positions of the conserved motifs in the ITS1 secondary structures of mosses and liverworts. In addition, a potential hairpin formation in the putative secondary structure of a pre-rRNA fragment was considered for the region between ITS1 CM4-CM5 and a highly conserved region between hairpins 49 and 50 (H49 and H50) of the 18S rRNA. PMID:26107892

  4. Protein secondary structure prediction using logic-based machine learning.

    PubMed

    Muggleton, S; King, R D; Sternberg, M J

    1992-10-01

    Many attempts have been made to solve the problem of predicting protein secondary structure from the primary sequence but the best performance results are still disappointing. In this paper, the use of a machine learning algorithm which allows relational descriptions is shown to lead to improved performance. The Inductive Logic Programming computer program, Golem, was applied to learning secondary structure prediction rules for alpha/alpha domain type proteins. The input to the program consisted of 12 non-homologous proteins (1612 residues) of known structure, together with a background knowledge describing the chemical and physical properties of the residues. Golem learned a small set of rules that predict which residues are part of the alpha-helices--based on their positional relationships and chemical and physical properties. The rules were tested on four independent non-homologous proteins (416 residues) giving an accuracy of 81% (+/- 2%). This is an improvement, on identical data, over the previously reported result of 73% by King and Sternberg (1990, J. Mol. Biol., 216, 441-457) using the machine learning program PROMIS, and of 72% using the standard Garnier-Osguthorpe-Robson method. The best previously reported result in the literature for the alpha/alpha domain type is 76%, achieved using a neural net approach. Machine learning also has the advantage over neural network and statistical methods in producing more understandable results. PMID:1480619

  5. Secondary Structure of Rat and Human Amylin across Force Fields

    PubMed Central

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi-cheng; de Pablo, Juan J.

    2015-01-01

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable

  6. Secondary structure of rat and human amylin across force fields

    DOE PAGESBeta

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi -cheng; de Pablo, Juan J.; Paci, Emanuele

    2015-07-29

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin wasmore » determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states

  7. Secondary structure of rat and human amylin across force fields

    SciTech Connect

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi -cheng; de Pablo, Juan J.; Paci, Emanuele

    2015-07-29

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable

  8. Secondary Structure of Rat and Human Amylin across Force Fields.

    PubMed

    Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi-Cheng; de Pablo, Juan J

    2015-01-01

    The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable

  9. Isolation, Structure Elucidation, Biosynthesis, and Synthesis of Antalid, a Secondary Metabolite from Polyangium species.

    PubMed

    Tautz, Thomas; Hoffmann, Judith; Hoffmann, Thomas; Steinmetz, Heinrich; Washausen, Peter; Kunze, Brigitte; Huch, Volker; Kitsche, Andreas; Reichenbach, Hans; Höfle, Gerhard; Müller, Rolf; Kalesse, Markus

    2016-06-01

    The isolation, structure elucidation, and synthesis of antalid (1), a novel secondary metabolite from Polyangium sp., is described herein. The structure elucidation of 1 was performed with the aid of mass spectrometry, high field NMR experiments, and crystal structure analysis. The absolute configuration of antalid was confirmed through the Mosher ester method and ultimately by total synthesis. In addition, the biosynthetic origin of this hybrid PKS-NRPS natural product was unraveled by the in silico analysis of its biosynthetic gene cluster. PMID:27220069

  10. RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

    ERIC Educational Resources Information Center

    Ellington, Roni; Wachira, James; Nkwanta, Asamoah

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses…

  11. The design of impact absorbing structures for additive manufacture

    NASA Astrophysics Data System (ADS)

    Brennan-Craddock, J.; Brackett, D.; Wildman, R.; Hague, R.

    2012-08-01

    Additive manufacturing (AM) is increasingly becoming a viable manufacturing process due to dramatic advantages that it facilitates in the area of design complexity. This paper investigates the potential of additively manufactured lattice structures for the application of tailored impact absorption specifically for conformal body protection. It explores lattice cell types based on foam microstructures and assesses their suitability for impact absorption. The effect of varying the cell strut edge design is also investigated. The implications of scaling these cells up for AM are discussed as well as the design issues regarding the handling of geometric complexity and the requirement for body conformity. The suitability of AM materials for this application is also discussed.

  12. The role of G-quadruplex/i-motif secondary structures as cis-acting regulatory elements

    PubMed Central

    Kendrick, Samantha; Hurley, Laurence H.

    2011-01-01

    The nature of DNA has captivated scientists for more than fifty years. The discovery of the double-helix model of DNA by Watson and Crick in 1953 not only established the primary structure of DNA, but also provided the mechanism behind DNA function. Since then, researchers have continued to further the understanding of DNA structure and its pivotal role in transcription. The demonstration of DNA secondary structure formation has allowed for the proposal that the dynamics of DNA itself can function to modulate transcription. This review presents evidence that DNA can exist in a dynamic equilibrium between duplex and secondary conformations. In addition, data demonstrating that intracellular proteins as well as small molecules can shift this equilibrium in either direction to alter gene transcription will be discussed, with a focus on the modulation of proto-oncogene expression. PMID:21796223

  13. RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

    PubMed Central

    Antczak, Maciej; Zok, Tomasz; Popenda, Mariusz; Lukasiak, Piotr; Adamiak, Ryszard W.; Blazewicz, Jacek; Szachniuk, Marta

    2014-01-01

    In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee—a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/. PMID:24771339

  14. Test of circular dichroism (CD) methods for crambin and CD-assisted secondary structure prediction of its homologous toxins.

    PubMed

    Teeter, M M; Whitlow, M

    1988-01-01

    Methods that analyze protein circular dichroism (CD) spectra for fractions of secondary structure are evaluated for the plant protein crambin, which has a known high-resolution crystal structure. In addition, a two-step secondary structure prediction scheme is presented and used for the toxins homologous to crambin, shown by others to have secondary structures similar to crambin. The test of CD spectral analysis methods with the protein crambin employed two computer programs and several CD basis sets. Crambin's crystal structure, known to 0.945A resolution (Hendrickson, W.A., Teeter, M.M. Nature 290:107-113, 1981), allows accurate evaluation of results. Analysis with the protein spectra basis sets (Provencher, S.W., Glöckner, J. Biochemistry 20:33-37, 1981) as modified (Manavalan, P., Johnson, W.C., Jr. Anal. Biochem. 167:76-85, 1987) agreed most closely with crambin's crystal structure. This method was then applied to the CD spectra of the membrane-active toxins homologous to crambin (alpha 1- and beta-purothionin, phoratoxin A and B, and viscotoxin A3 and B). The new program SEQ (pronounced "seek") was developed to assign the secondary structure along the protein chain in a hierarchical fashion and applied to the plant toxins. The method constrained the secondary structure fractions to those from CD analysis and combined standard statistical methods with amphipathic helix location. Both CD-arrived secondary structure percentages and sequence assignment indicate that the viscotoxins are structurally most similar to crambin. Purothionin's secondary structure was predicted to be fundamentally similar to crambin's with a difference at the start of the first helix. This assignment agreed with Raman and NMR analyses of purothionin and lends validity to the method presented here. Differences from the NMR in the CD secondary structure fraction analysis for phoratoxin suggest interference in the CD from tryptophan residues. PMID:3253736

  15. A grid-enabled protein secondary structure predictor.

    PubMed

    Mirto, Maria; Cafaro, Massimo; Fiore, Sandro Luigi; Tartarini, Daniele; Aloisio, Giovanni

    2007-06-01

    We present an integrated Grid system for the prediction of protein secondary structures, based on the frequent automatic update of proteins in the training set. The predictor model is based on a feed-forward multilayer perceptron (MLP) neural network which is trained with the back-propagation algorithm; the design reuses existing legacy software and exploits novel grid components. The predictor takes into account the evolutionary information found in multiple sequence alignment (MSA); the information is obtained running an optimized parallel version of the PSI-BLAST tool, based on the MPI Master-Worker paradigm. The training set contains proteins of known structure. Using Grid technologies and efficient mechanisms for running the tools and extracting the data, the time needed to train the neural network is dramatically reduced, whereas the results are comparable to a set of well-known predictor tools. PMID:17695746

  16. Peptoid nanosheets exhibit a new secondary-structure motif

    NASA Astrophysics Data System (ADS)

    Mannige, Ranjan V.; Haxton, Thomas K.; Proulx, Caroline; Robertson, Ellen J.; Battigelli, Alessia; Butterfoss, Glenn L.; Zuckermann, Ronald N.; Whitelam, Stephen

    2015-10-01

    A promising route to the synthesis of protein-mimetic materials that are capable of complex functions, such as molecular recognition and catalysis, is provided by sequence-defined peptoid polymers--structural relatives of biologically occurring polypeptides. Peptoids, which are relatively non-toxic and resistant to degradation, can fold into defined structures through a combination of sequence-dependent interactions. However, the range of possible structures that are accessible to peptoids and other biological mimetics is unknown, and our ability to design protein-like architectures from these polymer classes is limited. Here we use molecular-dynamics simulations, together with scattering and microscopy data, to determine the atomic-resolution structure of the recently discovered peptoid nanosheet, an ordered supramolecular assembly that extends macroscopically in only two dimensions. Our simulations show that nanosheets are structurally and dynamically heterogeneous, can be formed only from peptoids of certain lengths, and are potentially porous to water and ions. Moreover, their formation is enabled by the peptoids' adoption of a secondary structure that is not seen in the natural world. This structure, a zigzag pattern that we call a Σ(`sigma')-strand, results from the ability of adjacent backbone monomers to adopt opposed rotational states, thereby allowing the backbone to remain linear and untwisted. Linear backbones tiled in a brick-like way form an extended two-dimensional nanostructure, the Σ-sheet. The binary rotational-state motif of the Σ-strand is not seen in regular protein structures, which are usually built from one type of rotational state. We also show that the concept of building regular structures from multiple rotational states can be generalized beyond the peptoid nanosheet system.

  17. RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data.

    PubMed

    Wu, Yang; Qu, Rihao; Huang, Yiming; Shi, Binbin; Liu, Mengrong; Li, Yang; Lu, Zhi John

    2016-07-01

    Several high-throughput technologies have been developed to probe RNA base pairs and loops at the transcriptome level in multiple species. However, to obtain the final RNA secondary structure, extensive effort and considerable expertise is required to statistically process the probing data and combine them with free energy models. Therefore, we developed an RNA secondary structure prediction server that is enhanced by experimental data (RNAex). RNAex is a web interface that enables non-specialists to easily access cutting-edge structure-probing data and predict RNA secondary structures enhanced by in vivo and in vitro data. RNAex annotates the RNA editing, RNA modification and SNP sites on the predicted structures. It provides four structure-folding methods, restrained MaxExpect, SeqFold, RNAstructure (Fold) and RNAfold that can be selected by the user. The performance of these four folding methods has been verified by previous publications on known structures. We re-mapped the raw sequencing data of the probing experiments to the whole genome for each species. RNAex thus enables users to predict secondary structures for both known and novel RNA transcripts in human, mouse, yeast and Arabidopsis The RNAex web server is available at http://RNAex.ncrnalab.org/. PMID:27137891

  18. RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data

    PubMed Central

    Wu, Yang; Qu, Rihao; Huang, Yiming; Shi, Binbin; Liu, Mengrong; Li, Yang; Lu, Zhi John

    2016-01-01

    Several high-throughput technologies have been developed to probe RNA base pairs and loops at the transcriptome level in multiple species. However, to obtain the final RNA secondary structure, extensive effort and considerable expertise is required to statistically process the probing data and combine them with free energy models. Therefore, we developed an RNA secondary structure prediction server that is enhanced by experimental data (RNAex). RNAex is a web interface that enables non-specialists to easily access cutting-edge structure-probing data and predict RNA secondary structures enhanced by in vivo and in vitro data. RNAex annotates the RNA editing, RNA modification and SNP sites on the predicted structures. It provides four structure-folding methods, restrained MaxExpect, SeqFold, RNAstructure (Fold) and RNAfold that can be selected by the user. The performance of these four folding methods has been verified by previous publications on known structures. We re-mapped the raw sequencing data of the probing experiments to the whole genome for each species. RNAex thus enables users to predict secondary structures for both known and novel RNA transcripts in human, mouse, yeast and Arabidopsis. The RNAex web server is available at http://RNAex.ncrnalab.org/. PMID:27137891

  19. The secondary structure of guide RNA molecules from Trypanosoma brucei.

    PubMed Central

    Schmid, B; Riley, G R; Stuart, K; Göringer, H U

    1995-01-01

    RNA editing in kinetoplastid organisms is a mitochondrial RNA processing phenomenon that is characterized by the insertion and deletion of uridine nucleotides into incomplete mRNAs. Key molecules in the process are guide RNAs which direct the editing reaction by virtue of their primary sequences in an RNA-RNA interaction with the pre-edited mRNAs. To understand the molecular details of this reaction, especially potential RNA folding and unfolding processes as well as assembly phenomena with mitochondrial proteins, we analyzed the secondary structure of four different guide RNAs from Trypanosoma brucei at physiological conditions. By using structure-sensitive chemical and enzymatic probes in combination with spectroscopic techniques we found that the four molecules despite their different primary sequences, fold into similar structures consisting of two imperfect hairpin loops of low thermodynamic stability. The molecules melt in two-state monomolecular transitions with Tms between 33 and 39 degrees C and transition enthalpies of -32 to -38 kcal/mol. Both terminal ends of the RNAs are single-stranded with the 3' ends possibly adopting a single-stranded, helical conformation. Thus, it appears that the gRNA structures are fine tuned to minimize stability for an optimal annealing reaction to the pre-mRNAs while at the same time maximizing higher order structural features to permit the assembly with other mitochondrial components into the editing machinery. Images PMID:7667084

  20. Secondary Structure Transition and Critical Stress for a Model of Spider Silk Assembly.

    PubMed

    Giesa, Tristan; Perry, Carole C; Buehler, Markus J

    2016-02-01

    Spiders spin their silk from an aqueous solution to a solid fiber in ambient conditions. However, to date, the assembly mechanism in the spider silk gland has not been satisfactorily explained. In this paper, we use molecular dynamics simulations to model Nephila clavipes MaSp1 dragline silk formation under shear flow and determine the secondary structure transitions leading to the experimentally observed fiber structures. While no experiments are performed on the silk fiber itself, insights from this polypeptide model can be transferred to the fiber scale. The novelty of this study lies in the calculation of the shear stress (300-700 MPa) required for fiber formation and identification of the amino acid residues involved in the transition. This is the first time that the shear stress has been quantified in connection with a secondary structure transition. By study of molecules containing varying numbers of contiguous MaSp1 repeats, we determine that the smallest molecule size giving rise to a "silk-like" structure contains six polyalanine repeats. Through a probability analysis of the secondary structure, we identify specific amino acids that transition from α-helix to β-sheet. In addition to portions of the polyalanine section, these amino acids include glycine, leucine, and glutamine. The stability of β-sheet structures appears to arise from a close proximity in space of helices in the initial spidroin state. Our results are in agreement with the forces exerted by spiders in the silking process and the experimentally determined global secondary structure of spidroin and pulled MaSp1 silk. Our study emphasizes the role of shear in the assembly process of silk and can guide the design of microfluidic devices that attempt to mimic the natural spinning process and predict molecular requirements for the next generation of silk-based functional materials. PMID:26669270

  1. Bioinspired Cellular Structures: Additive Manufacturing and Mechanical Properties

    NASA Astrophysics Data System (ADS)

    Stampfl, J.; Pettermann, H. E.; Liska, R.

    Biological materials (e.g., wood, trabecular bone, marine skeletons) rely heavily on the use of cellular architecture, which provides several advantages. (1) The resulting structures can bear the variety of "real life" load spectra using a minimum of a given bulk material, featuring engineering lightweight design principles. (2) The inside of the structures is accessible to body fluids which deliver the required nutrients. (3) Furthermore, cellular architectures can grow organically by adding or removing individual struts or by changing the shape of the constituting elements. All these facts make the use of cellular architectures a reasonable choice for nature. Using additive manufacturing technologies (AMT), it is now possible to fabricate such structures for applications in engineering and biomedicine. In this chapter, we present methods that allow the 3D computational analysis of the mechanical properties of cellular structures with open porosity. Various different cellular architectures including disorder are studied. In order to quantify the influence of architecture, the apparent density is always kept constant. Furthermore, it is shown that how new advanced photopolymers can be used to tailor the mechanical and functional properties of the fabricated structures.

  2. Fretting Wear Properties of TiCN-Ni Cermets: Influence of Load and Secondary Carbide Addition

    NASA Astrophysics Data System (ADS)

    Manoj Kumar, B. V.; Basu, Bikramjit

    2008-03-01

    The increasing demand for TiCN-based cermets in tribological applications necessitates a thorough understanding of the influence of experimental as well as material parameters on the friction and wear properties. In optimizing microstructure and properties, secondary carbides are added to baseline TiCN-Ni cermet. The present work aims at evaluating the fretting wear behavior of Ti(CN)-Ni cermets containing various secondary carbides, such as WC, NbC, TaC, and HfC, against steel at different loading (2, 6, and 10 N) conditions. The evolution of tangential frictional force for the investigated cermets was analyzed in terms of fretting logs and fretting loops. The topographical characterization of worn surfaces was performed, using laser surface profilometry and a scanning electron microscope (SEM) equipped with energy-dispersive spectroscopy (EDS) capability. The steady-state coefficient of friction (COF) was minimum (0.33) for a TiCN-20Ni cermet/steel tribocouple, while a maximum COF (0.47) was recorded for TiCN-20Ni-10HfC cermet/steel at a 2-N load. The wear rate of the cermets varied in the range of 1.7 × 10-6 to 3.5 × 10-6 mm3/Nm. The TiCN-20Ni-10HfC cermet exhibited poor wear resistance among investigated cermets. The dominant wear mechanisms were found as abrasion and tribolayer formation. The dominance of abrasion is explained in terms of cumulative energy dissipation.

  3. Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme

    PubMed Central

    Mustoe, Anthony M.; Al-Hashimi, Hashim M.; Brooks, Charles L.

    2016-01-01

    A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use coarse-grained molecular dynamics simulations to explore how secondary structure shapes the tertiary free-energy landscape of the Azoarcus ribozyme. We show that steric and connectivity constraints posed by secondary structure strongly limit the accessible conformational space of the ribozyme, and that these so-called topological constraints in turn pose strong free-energy penalties on forming different tertiary contacts. Notably, native A-minor and base-triple interactions form with low conformational free energy, while non-native tetraloop/tetraloop–receptor interactions are penalized by high conformational free energies. Topological constraints also give rise to strong cooperativity between distal tertiary interactions, quantitatively matching prior experimental measurements. The specificity of the folding landscape is further enhanced as tertiary contacts place additional constraints on the conformational space, progressively funneling the molecule to the native state. These results indicate that secondary structure assists the ribozyme in navigating the otherwise rugged tertiary folding landscape, and further emphasize topological constraints as a key force in RNA folding. PMID:26481360

  4. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.

    PubMed

    Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

    2016-01-01

    Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility. PMID:26752681

  5. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

    PubMed Central

    Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

    2016-01-01

    Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility. PMID:26752681

  6. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

    NASA Astrophysics Data System (ADS)

    Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo

    2016-01-01

    Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which has not been improved in the past decade. Here we present DeepCNF (Deep Convolutional Neural Fields) for protein SS prediction. DeepCNF is a Deep Learning extension of Conditional Neural Fields (CNF), which is an integration of Conditional Random Fields (CRF) and shallow neural networks. DeepCNF can model not only complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent SS labels, so it is much more powerful than CNF. Experimental results show that DeepCNF can obtain ~84% Q3 accuracy, ~85% SOV score, and ~72% Q8 accuracy, respectively, on the CASP and CAMEO test proteins, greatly outperforming currently popular predictors. As a general framework, DeepCNF can be used to predict other protein structure properties such as contact number, disorder regions, and solvent accessibility.

  7. An RNA secondary structure prediction method based on minimum and suboptimal free energy structures.

    PubMed

    Fu, Haoyue; Yang, Lianping; Zhang, Xiangde

    2015-09-01

    The function of an RNA-molecule is mainly determined by its tertiary structures. And its secondary structure is an important determinant of its tertiary structure. The comparative methods usually give better results than the single-sequence methods. Based on minimum and suboptimal free energy structures, the paper presents a novel method for predicting conserved secondary structure of a group of related RNAs. In the method, the information from the known RNA structures is used as training data in a SVM (Support Vector Machine) classifier. Our method has been tested on the benchmark dataset given by Puton et al. The results show that the average sensitivity of our method is higher than that of other comparative methods such as CentroidAlifold, MXScrana, RNAalifold, and TurboFold. PMID:26100179

  8. Additional developments regarding manifest dream structure and function.

    PubMed

    Wolowitz, H

    1998-06-01

    Detailed observation of manifest dream sequences indicated self-advocating occurrences facilitating the dreamer's self interests, opposed by self-adversarial interferences. Further examination of manifest dream syntactical structure additionally suggested a recurrent, four-step, algorithm for personal problem-solving within an interpersonal matrix consisting of the following cycle: (1) an opening scene setting the stage, (2) for the emergence of a self-concern, (3) which evokes a strategy to deal with dreamer's self-concern, (4) that eventuates in a consequence of the strategy. These steps repeat until the dream ends. Observing these manifest dream structural features, attributable to broadening past theorizing with "bottom-up" approaches, clarifies the dream's problem-solving process by providing an empirical, observable framework for dream interpretation and by contributing to their consensual validation. PMID:9656284

  9. Structural order in additive processed bulk heterojunction organic solar cells

    NASA Astrophysics Data System (ADS)

    Rogers, James Thomas

    Considerable academic and industrial efforts have been dedicated to resolving scientific and technological issues associated with the fabrication of efficient plastic solar cells via solution deposition techniques. The most successful strategy used to generate solution processable devices implements a two component donor-acceptor type system composed of a (p-type) narrow bandgap conjugated polymer donor blended with a (n-type) fullerene acceptor. Due to the limited exciton diffusion lengths (~10 nm) inherent to these materials, efficient photoinduced charge generation requires heterojunction formation (i.e. donor/acceptor interfaces) in close proximity to the region of exciton generation. Maximal charge extraction therefore requires that donor and acceptor components form nanoscale phase separated percolating pathways to their respective electrodes. Devices exhibiting these structural characteristics are termed bulk heterojunction devices (BHJ). Although the BHJ architecture highlights the basic characteristics of functional donor-acceptor type organic solar cells, device optimization requires internal order within each phase and proper organization relative to the substrate in order to maximize charge transport efficiencies and minimize charge carrier recombination losses. The economic viability of BHJ solar cells hinges upon the minimization of processing costs; thus, commercially relevant processing techniques should generate optimal structural characteristics during film formation, eliminating the need for additional post deposition processing steps. Empirical optimization has shown that solution deposition using high boiling point additives (e.g. octanedithiol (ODT)) provides a simple and widely used fabrication method for maximizing the power conversion efficiencies of BHJ solar cells. This work will show using x-ray scattering that a small percentage of ODT (~2%) in chlorobenzene induces the nucleation of polymeric crystallites within 2 min of deposition

  10. Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch

    PubMed Central

    Xue, Yi; Gracia, Brant; Herschlag, Daniel; Russell, Rick; Al-Hashimi, Hashim M.

    2016-01-01

    Intermediates play important roles in RNA folding but can be difficult to characterize when short-lived or not significantly populated. By combining 15N relaxation dispersion NMR with chemical probing, we visualized a fast (kex=k1+k−1≈423 s−1) secondary structural switch directed towards a low-populated (∼3%) partially folded intermediate in tertiary folding of the P5abc subdomain of the ‘Tetrahymena' group I intron ribozyme. The secondary structure switch changes the base-pairing register across the P5c hairpin, creating a native-like structure, and occurs at rates of more than two orders of magnitude faster than tertiary folding. The switch occurs robustly in the absence of tertiary interactions, Mg2+ or even when the hairpin is excised from the three-way junction. Fast, highly modular secondary structural switches may be quite common during RNA tertiary folding where they may help smoothen the folding landscape by allowing folding to proceed efficiently via additional pathways. PMID:27292179

  11. Protein secondary structural types are differentially coded on messenger RNA.

    PubMed Central

    Thanaraj, T. A.; Argos, P.

    1996-01-01

    Tricodon regions on messenger RNAs corresponding to a set of proteins from Escherichia coli were scrutinized for their translation speed. The fractional frequency values of the individual codons as they occur in mRNAs of highly expressed genes from Escherichia coli were taken as an indicative measure of the translation speed. The tricodons were classified by the sum of the frequency values of the constituent codons. Examination of the conformation of the encoded amino acid residues in the corresponding protein tertiary structures revealed a correlation between codon usage in mRNA and topological features of the encoded proteins. Alpha helices on proteins tend to be preferentially coded by translationally fast mRNA regions while the slow segments often code for beta strands and coil regions. Fast regions correspondingly avoid coding for beta strands and coil regions while the slow regions similarly move away from encoding alpha helices. Structural and mechanistic aspects of the ribosome peptide channel support the relevance of sequence fragment translation and subsequent conformation. A discussion is presented relating the observation to the reported kinetic data on the formation and stabilization of protein secondary structural types during protein folding. The observed absence of such strong positive selection for codons in non-highly expressed genes is compatible with existing theories that mutation pressure may well dominate codon selection in non-highly expressed genes. PMID:8897597

  12. 77 FR 71695 - Secondary Direct Food Additives Permitted in Food for Human Consumption; Sodium...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-04

    ...The Food and Drug Administration (FDA) is amending the food additive regulations to provide for the safe use of sodium dodecylbenzenesulfonate (CAS No. 25155-30-0) as an antimicrobial agent for use in wash water for fruits and vegetables without the requirement of a potable water rinse. This action is in response to a petition filed by Ecolab,...

  13. Electrical inhibition of lens epithelial cell proliferation: an additional factor in secondary cataract?

    PubMed Central

    Wang, Entong; Reid, Brian; Lois, Noemi; Forrester, John V.; McCaig, Colin D.; Zhao, Min

    2005-01-01

    Cataract is the most common cause of blindness but is at least curable by surgery. Unfortunately, many patients gradually develop the complication of posterior capsule opacification (PCO) or secondary cataract. This arises from stimulated cell growth within the lens capsule and can greatly impair vision. It is not fully understood why residual lens epithelial cell growth occurs after surgery. We propose and show that cataract surgery might remove an important inhibitory factor for lens cell growth, namely electric fields. The lens generates a unique pattern of electric currents constantly flowing out from the equator and entering the anterior and posterior poles. We show here that cutting and removing part of the anterior capsule as in cataract surgery significantly decreases the equatorial outward electric currents. Application of electric fields in culture inhibits proliferation of human lens epithelial cells. This inhibitory effect is likely to be mediated through a cell cycle control mechanism that decreases entry of cells into S phase from G1 phase by decreasing the G1-specific cell cycle protein cyclin E and increasing the cyclin-Cdk complex inhibitor p27kip1. Capsulorrhexis in vivo, which reduced endogenous lens electric fields, significantly increased LEC growth. This, together with our previous findings that electric fields have significant effects on the direction of lens cell migration, points to a controlling mechanism for the aberrant cell growth in posterior capsule opacification. A novel approach to control growth of lens epithelial cells using electric fields combined with other controlling mechanisms may be more effective in the prevention and treatment of this common complication of cataract surgery. PMID:15764648

  14. Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide

    NASA Astrophysics Data System (ADS)

    Birdsall, A. W.; Miner, C. R.; Mael, L. E.; Elrod, M. J.

    2014-08-01

    Recently, methacrylic acid epoxide (MAE) has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA): 2-methylglyceric acid (2-MG) and a set of oligomers, nitric acid esters and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR) spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG), and acids (including MAE and 2-MG) in their reactions with MAE were found to be of a similar magnitude, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water); this finding is consistent with previous environmental chamber investigations of the relative humidity-dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.

  15. Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide

    NASA Astrophysics Data System (ADS)

    Birdsall, A. W.; Miner, C. R.; Mael, L. E.; Elrod, M. J.

    2014-12-01

    Recently, methacrylic acid epoxide (MAE) has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA): 2-methylglyceric acid (2-MG) and a set of oligomers, nitric acid esters, and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied with experimental methods. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR) spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG), and acids (including MAE and 2-MG) in their reactions with MAE were found to be of similar magnitudes, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water); this finding is consistent with previous environmental chamber investigations of the relative humidity dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.

  16. On the structure and dynamics of secondary n-alkyl cations

    NASA Astrophysics Data System (ADS)

    East, Allan L. L.; Bučko, Tomáš; Hafner, Jürgen

    2009-09-01

    A variety of computational studies was undertaken to examine and establish the relative importance of open versus closed structures for unbranched secondary n-alkyl cations. First, the PW91 level of density functional theory was used to optimize over 20 minimum-energy structures of sec-pentyl, sec-hexyl, and sec-heptyl ions, demonstrating that closed structures are more stable than open ones on the potential energy surface (PES). Second, PW91 was used with a theoretical Andersen thermostat to perform a molecular dynamics simulation (150 ps) of C9H19+ at a typical catalytic temperature of 800 K, demonstrating that the structure preference is inverted on the free-energy surface. Third, both quantum (rigid-rotor/harmonic oscillator) and classical partition functions were used to demonstrate that the simulated structure-opening at catalytic temperatures is due to the floppiness of the open forms, which improves its free energy by both lowering its zero-point vibrational energy and increasing its molecular entropy. The particular conformer of the preferred open form (at 800 K) is dependent on length of alkyl ion, with pentyl ions preferring syn/anti structures but longer ions preferring open-clinal ones. These results, plus an additional set of PES optimized structures from an alternative level of theory (MP2/6-31G(d,p)), are used to discuss the likely nature of secondary n-alkyl ions.

  17. PSRna: Prediction of small RNA secondary structures based on reverse complementary folding method.

    PubMed

    Li, Jin; Xu, Chengzhen; Wang, Lei; Liang, Hong; Feng, Weixing; Cai, Zhongxi; Wang, Ying; Cong, Wang; Liu, Yunlong

    2016-08-01

    Prediction of RNA secondary structures is an important problem in computational biology and bioinformatics, since RNA secondary structures are fundamental for functional analysis of RNA molecules. However, small RNA secondary structures are scarce and few algorithms have been specifically designed for predicting the secondary structures of small RNAs. Here we propose an algorithm named "PSRna" for predicting small-RNA secondary structures using reverse complementary folding and characteristic hairpin loops of small RNAs. Unlike traditional algorithms that usually generate multi-branch loops and 5[Formula: see text] end self-folding, PSRna first estimated the maximum number of base pairs of RNA secondary structures based on the dynamic programming algorithm and a path matrix is constructed at the same time. Second, the backtracking paths are extracted from the path matrix based on backtracking algorithm, and each backtracking path represents a secondary structure. To improve accuracy, the predicted RNA secondary structures are filtered based on their free energy, where only the secondary structure with the minimum free energy was identified as the candidate secondary structure. Our experiments on real data show that the proposed algorithm is superior to two popular methods, RNAfold and RNAstructure, in terms of sensitivity, specificity and Matthews correlation coefficient (MCC). PMID:27045556

  18. Tuning structure and mobility of solvation shells surrounding tracer additives

    SciTech Connect

    Carmer, James; Jain, Avni; Bollinger, Jonathan A.; Truskett, Thomas M.; Swol, Frank van

    2015-03-28

    Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are rationally modified to affect corresponding solvation structure. For tracers in a dense hard-sphere fluid, we compare two types of tracer-solvent interactions: (1) a hard-sphere-like interaction, and (2) a soft repulsion extending beyond the hard core designed via statistical mechanical theory to enhance tracer mobility at infinite dilution by suppressing coordination-shell structure [Carmer et al., Soft Matter 8, 4083–4089 (2012)]. For the latter case, we show that the mobility of surrounding solvent particles is also increased by addition of the soft repulsive interaction, which helps to rationalize the mechanism underlying the tracer’s enhanced diffusivity. However, if multiple tracer surfaces are in closer proximity (as at higher tracer concentrations), similar interactions that disrupt local solvation structure instead suppress the position-dependent solvent dynamics.

  19. Tuning structure and mobility of solvation shells surrounding tracer additives.

    PubMed

    Carmer, James; Jain, Avni; Bollinger, Jonathan A; van Swol, Frank; Truskett, Thomas M

    2015-03-28

    Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are rationally modified to affect corresponding solvation structure. For tracers in a dense hard-sphere fluid, we compare two types of tracer-solvent interactions: (1) a hard-sphere-like interaction, and (2) a soft repulsion extending beyond the hard core designed via statistical mechanical theory to enhance tracer mobility at infinite dilution by suppressing coordination-shell structure [Carmer et al., Soft Matter 8, 4083-4089 (2012)]. For the latter case, we show that the mobility of surrounding solvent particles is also increased by addition of the soft repulsive interaction, which helps to rationalize the mechanism underlying the tracer's enhanced diffusivity. However, if multiple tracer surfaces are in closer proximity (as at higher tracer concentrations), similar interactions that disrupt local solvation structure instead suppress the position-dependent solvent dynamics. PMID:25833590

  20. Additives Induced Structural Transformation of ABC Triblock Copolymer Particles.

    PubMed

    Xu, Jiangping; Yang, Yi; Wang, Ke; Li, Jingyi; Zhou, Huamin; Xie, Xiaolin; Zhu, Jintao

    2015-10-13

    Here we report the structural control of polystyrene-b-polyisoprene-b-poly(2-vinylpyridine) (PS-b-PI-b-P2VP) asymmetric ABC triblock copolymer particles under 3D confinement by tuning the interactions among blocks. The additives, including 3-n-pentadecylphenol, homopolystyrene, and solvents, which can modulate the interactions among polymer blocks, play significant roles in the particle morphology. Moreover, the structured particles can be disassembled into isolated micellar aggregates with novel morphologies or mesoporous particles with tunable pore shape. Interestingly, the formed pupa-like PS-b-PI-b-P2VP particles display interesting dynamic stretch-retraction behavior when the solvent property is changed after partial cross-linking of the P2VP block. We further prove that such dynamic behavior is closely related to the density of cross-linking. The strategies presented here are believed to be promising routes to rationally design and fabricate block copolymer particles with desirable shape and internal structure. PMID:26388457

  1. Expected distance between terminal nucleotides of RNA secondary structures.

    PubMed

    Clote, Peter; Ponty, Yann; Steyaert, Jean-Marc

    2012-09-01

    In "The ends of a large RNA molecule are necessarily close", Yoffe et al. (Nucleic Acids Res 39(1):292-299, 2011) used the programs RNAfold [resp. RNAsubopt] from Vienna RNA Package to calculate the distance between 5' and 3' ends of the minimum free energy secondary structure [resp. thermal equilibrium structures] of viral and random RNA sequences. Here, the 5'-3' distance is defined to be the length of the shortest path from 5' node to 3' node in the undirected graph, whose edge set consists of edges {i, i + 1} corresponding to covalent backbone bonds and of edges {i, j} corresponding to canonical base pairs. From repeated simulations and using a heuristic theoretical argument, Yoffe et al. conclude that the 5'-3' distance is less than a fixed constant, independent of RNA sequence length. In this paper, we provide a rigorous, mathematical framework to study the expected distance from 5' to 3' ends of an RNA sequence. We present recurrence relations that precisely define the expected distance from 5' to 3' ends of an RNA sequence, both for the Turner nearest neighbor energy model, as well as for a simple homopolymer model first defined by Stein and Waterman. We implement dynamic programming algorithms to compute (rather than approximate by repeated application of Vienna RNA Package) the expected distance between 5' and 3' ends of a given RNA sequence, with respect to the Turner energy model. Using methods of analytical combinatorics, that depend on complex analysis, we prove that the asymptotic expected 5'-3' distance of length n homopolymers is approximately equal to the constant 5.47211, while the asymptotic distance is 6.771096 if hairpins have a minimum of 3 unpaired bases and the probability that any two positions can form a base pair is 1/4. Finally, we analyze the 5'-3' distance for secondary structures from the STRAND database, and conclude that the 5'-3' distance is correlated with RNA sequence length. PMID:21984358

  2. RNAsoft: a suite of RNA secondary structure prediction and design software tools

    PubMed Central

    Andronescu, Mirela; Aguirre-Hernández, Rosalía; Condon, Anne; Hoos, Holger H.

    2003-01-01

    DNA and RNA strands are employed in novel ways in the construction of nanostructures, as molecular tags in libraries of polymers and in therapeutics. New software tools for prediction and design of molecular structure will be needed in these applications. The RNAsoft suite of programs provides tools for predicting the secondary structure of a pair of DNA or RNA molecules, testing that combinatorial tag sets of DNA and RNA molecules have no unwanted secondary structure and designing RNA strands that fold to a given input secondary structure. The tools are based on standard thermodynamic models of RNA secondary structure formation. RNAsoft can be found online at http://www.RNAsoft.ca. PMID:12824338

  3. Changes in secondary structure of gluten proteins due to emulsifiers

    NASA Astrophysics Data System (ADS)

    Gómez, Analía V.; Ferrer, Evelina G.; Añón, María C.; Puppo, María C.

    2013-02-01

    Changes in the secondary structure of gluten proteins due to emulsifiers were analyzed by Raman Spectroscopy. The protein folding induced by 0.25% SSL (Sodium Stearoyl Lactylate) (GS0.25, Gluten + 0.25% SSL) included an increase in α-helix conformation and a decrease in β-sheet, turns and random coil. The same behavior, although in a less degree, was observed for 0.5% gluten-DATEM (Diacetyl Tartaric Acid Esters of Monoglycerides) system. The low burial of Tryptophan residues to a more hydrophobic environment and the low percentage area of the C-H stretching band for GS0.25 (Gluten + 0.25% SSL), could be related to the increased in α-helix conformation. This behavior was also confirmed by changes in stretching vibrational modes of disulfide bridges (S-S) and the low exposure of Tyrosine residues. High levels of SSL (0.5% and 1.0%) and DATEM (1.0%) led to more disordered protein structures, with different gluten networks. SSL (1.0%) formed a more disordered and opened gluten matrix than DATEM, the last one being laminar and homogeneous.

  4. Control of cerium oxidation state through metal complex secondary structures

    SciTech Connect

    Levin, Jessica R.; Dorfner, Walter L.; Carroll, Patrick J.; Schelter, Eric J.

    2015-08-11

    A series of alkali metal cerium diphenylhydrazido complexes, Mx(py)y[Ce(PhNNPh)4], M = Li, Na, and K, x = 4 (Li and Na) or 5 (K), and y = 4 (Li), 8 (Na), or 7 (K), were synthesized to probe how a secondary coordination sphere would modulate electronic structures at a cerium cation. The resulting electronic structures of the heterobimetallic cerium diphenylhydrazido complexes were found to be strongly dependent on the identity of the alkali metal cations. When M = Li+ or Na+, the cerium(III) starting material was oxidized with concomitant reduction of 1,2-diphenylhydrazine to aniline. Reduction of 1,2-diphenylhydrazine was not observed when M = K+, and the complex remained in the cerium(III) oxidation state. Oxidation of the cerium(III) diphenylhydrazido complex to the Ce(IV) diphenylhydrazido one was achieved through a simple cation exchange reaction of the alkali metals. As a result, UV-Vis spectroscopy, FTIR spectroscopy, electrochemistry, magnetic susceptibility, and DFT studies were used to probe the oxidation state and the electronic changes that occurred at the metal centre.

  5. Control of cerium oxidation state through metal complex secondary structures

    DOE PAGESBeta

    Levin, Jessica R.; Dorfner, Walter L.; Carroll, Patrick J.; Schelter, Eric J.

    2015-08-11

    A series of alkali metal cerium diphenylhydrazido complexes, Mx(py)y[Ce(PhNNPh)4], M = Li, Na, and K, x = 4 (Li and Na) or 5 (K), and y = 4 (Li), 8 (Na), or 7 (K), were synthesized to probe how a secondary coordination sphere would modulate electronic structures at a cerium cation. The resulting electronic structures of the heterobimetallic cerium diphenylhydrazido complexes were found to be strongly dependent on the identity of the alkali metal cations. When M = Li+ or Na+, the cerium(III) starting material was oxidized with concomitant reduction of 1,2-diphenylhydrazine to aniline. Reduction of 1,2-diphenylhydrazine was not observedmore » when M = K+, and the complex remained in the cerium(III) oxidation state. Oxidation of the cerium(III) diphenylhydrazido complex to the Ce(IV) diphenylhydrazido one was achieved through a simple cation exchange reaction of the alkali metals. As a result, UV-Vis spectroscopy, FTIR spectroscopy, electrochemistry, magnetic susceptibility, and DFT studies were used to probe the oxidation state and the electronic changes that occurred at the metal centre.« less

  6. Faxing Structures to the Moon: Freeform Additive Construction System (FACS)

    NASA Technical Reports Server (NTRS)

    Howe, A. Scott; Wilcox, Brian; McQuin, Christopher; Townsend, Julie; Rieber, Richard; Barmatz, Martin; Leichty, John

    2013-01-01

    Using the highly articulated All-Terrain Hex-Limbed Extra-Terrestrial Explorer (ATHLETE) robotic mobility system as a precision positioning tool, a variety of print head technologies can be used to 3D print large-scale in-situ structures on planetary surfaces such as the moon or Mars. In effect, in the same way CAD models can be printed in a 3D printer, large-scale structures such as walls, vaults, domes, berms, paving, trench walls, and other insitu derived elements can be FAXed to the planetary surface and built in advance of the arrival of crews, supplementing equipment and materials brought from earth. This paper discusses the ATHLETE system as a mobility / positioning platform, and presents several options for large-scale additive print head technologies, including tunable microwave "sinterator" approaches and in-situ concrete deposition. The paper also discusses potential applications, such as sintered-in-place habitat shells, radiation shielding, road paving, modular bricks, and prefabricated construction components.

  7. Boundary Layer Dynamical Structure During Secondary Eyewall Formation

    NASA Astrophysics Data System (ADS)

    Abarca, S. F.; Montgomery, M. T.; McWilliams, J. C.

    2014-12-01

    Secondary eyewall formation (SEF) is widely recognized as an important research problem in the dynamics of mature tropical cyclones. It has been shown that the development of the wind maxima in SEF occurs within the boundary layer and that it follows a chain of events initiated by a substantial radial expansion of the tangential wind field. In this context, there is not yet a consensus on the phenomenon's essential physics. It has been proposed that the boundary-layer dynamics of a maturing hurricane vortex is an important controlling element in SEF. However, recent literature also argues that hurricane boundary layers and the related coupling with the interior flow can be described through an Ekman-like balance and that shock-like structures are relevant in the swirling boundary layer of the inner core of mature storms. We analyze the radial and vertical structure of the specific forces and accelerations in in the boundary layer in a mature hurricane that includes a canonical eyewall replacement cycle. The case occurred in a mesoscale, convection-permitting numerical simulation of a tropical cyclone, integrated from an initial weak mesoscale vortex in an idealized quiescent environment. The simulation has been studied extensively in the literature. We find that momentum advection is almost everywhere important (some of it is associated with asymmetric eddies). We discuss the implication of our findings on the proposed importance of Ekman-like balance dynamics during SEF. Finally, our analysis does not support the recently proposed idea that the radial advection of radial momentum, and shock-like structures, are closely related to the supergradient wind phenomena observed during SEF.

  8. Sheath structure in plasma with two species of positive ions and secondary electrons

    NASA Astrophysics Data System (ADS)

    Xiao-Yun, Zhao; Nong, Xiang; Jing, Ou; De-Hui, Li; Bin-Bin, Lin

    2016-02-01

    The properties of a collisionless plasma sheath are investigated by using a fluid model in which two species of positive ions and secondary electrons are taken into account. It is shown that the positive ion speeds at the sheath edge increase with secondary electron emission (SEE) coefficient, and the sheath structure is affected by the interplay between the two species of positive ions and secondary electrons. The critical SEE coefficients and the sheath widths depend strongly on the positive ion charge number, mass and concentration in the cases with and without SEE. In addition, ion kinetic energy flux to the wall and the impact of positive ion species on secondary electron density at the sheath edge are also discussed. Project supported by the National Natural Science Foundation of China (Grant Nos. 11475220 and 11405208), the Program of Fusion Reactor Physics and Digital Tokamak with the CAS “One-Three-Five” Strategic Planning, the National ITER Program of China (Grant No. 2015GB101003), and the Higher Education Natural Science Research Project of Anhui Province, China (Grant No. 2015KJ009).

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

    PubMed Central

    Lees, Jonathan G; Janes, Robert W

    2008-01-01

    Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained. PMID:18197968

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

    PubMed Central

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

    2007-01-01

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

  11. Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

    PubMed

    Washietl, Stefan; Bernhart, Stephan H; Kellis, Manolis

    2014-01-01

    Many biologically important RNA structures are conserved in evolution leading to characteristic mutational patterns. RNAalifold is a widely used program to predict consensus secondary structures in multiple alignments by combining evolutionary information with traditional energy-based RNA folding algorithms. Here we describe the theory and applications of the RNAalifold algorithm. Consensus secondary structure prediction not only leads to significantly more accurate structure models, but it also allows to study structural conservation of functional RNAs. PMID:24639158

  12. Rtools: a web server for various secondary structural analyses on single RNA sequences.

    PubMed

    Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

    2016-07-01

    The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. PMID:27131356

  13. The effects of various alcohols on the secondary structural integrity of melittin, TH-10Aox, and Tc1 by molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Zhao, Jian-Hua; Liu, Hsuan-Liang

    2006-03-01

    In this study, molecular dynamics simulations were conducted to investigate the effects of various alcohols on the structural integrity of three peptides: melittin with 2 α-helices, TH-10Aox with 3 β-strands, and Tc1 with 1 α-helix and 2 β-strands. The results reveal that the secondary structural integrity of these peptides increased with decreasing dielectric constant of the solvent, indicating that there is a positive correlation between the number of carbon atoms in alcohols and the stability of the secondary structures. In addition, TFE enhanced the secondary structural stability of these peptides to a greater extent than the other alcohols.

  14. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

    PubMed

    Hafsa, Noor E; Arndt, David; Wishart, David S

    2015-07-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

  15. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE.

    PubMed

    Flynn, Ryan A; Zhang, Qiangfeng Cliff; Spitale, Robert C; Lee, Byron; Mumbach, Maxwell R; Chang, Howard Y

    2016-02-01

    icSHAPE (in vivo click selective 2-hydroxyl acylation and profiling experiment) captures RNA secondary structure at a transcriptome-wide level by measuring nucleotide flexibility at base resolution. Living cells are treated with the icSHAPE chemical NAI-N3 followed by selective chemical enrichment of NAI-N3-modified RNA, which provides an improved signal-to-noise ratio compared with similar methods leveraging deep sequencing. Purified RNA is then reverse-transcribed to produce cDNA, with SHAPE-modified bases leading to truncated cDNA. After deep sequencing of cDNA, computational analysis yields flexibility scores for every base across the starting RNA population. The entire experimental procedure can be completed in ∼5 d, and the sequencing and bioinformatics data analysis take an additional 4-5 d with no extensive computational skills required. Comparing in vivo and in vitro icSHAPE measurements can reveal in vivo RNA-binding protein imprints or facilitate the dissection of RNA post-transcriptional modifications. icSHAPE reactivities can additionally be used to constrain and improve RNA secondary structure prediction models. PMID:26766114

  16. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

    PubMed Central

    Flynn, Ryan A; Zhang, Qiangfeng Cliff; Spitale, Robert C; Lee, Byron; Mumbach, Maxwell R; Chang, Howard Y

    2016-01-01

    icSHAPE (in vivo click selective 2-hydroxyl acylation and profiling experiment) captures RNA secondary structure at a transcriptome-wide level by measuring nucleotide flexibility at base resolution. Living cells are treated with the icSHAPE chemical NAI-N3 followed by selective chemical enrichment of NAI-N3–modified RNA, which provides an improved signal-to-noise ratio compared with similar methods leveraging deep sequencing. Purified RNA is then reverse-transcribed to produce cDNA, with SHAPE-modified bases leading to truncated cDNA. After deep sequencing of cDNA, computational analysis yields flexibility scores for every base across the starting RNA population. The entire experimental procedure can be completed in ~5 d, and the sequencing and bioinformatics data analysis take an additional 4–5 d with no extensive computational skills required. Comparing in vivo and in vitro icSHAPE measurements can reveal in vivo RNA-binding protein imprints or facilitate the dissection of RNA post-transcriptional modifications. icSHAPE reactivities can additionally be used to constrain and improve RNA secondary structure prediction models. PMID:26766114

  17. Effective stiffness and formation of secondary structures in a protein-like model.

    PubMed

    Škrbić, Tatjana; Hoang, Trinh X; Giacometti, Achille

    2016-08-28

    We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is formed by tethered beads where non-consecutive backbone beads attract each other via a square-well potential representing the tendency of the chain to fold. In addition, smaller hard spheres are attached to each non-terminal backbone bead along the direction normal to the chain to mimic the steric hindrance of side chains in real proteins. The two models, however, differ in the way bending rigidity is enforced. In the first model, partial overlap between consecutive beads is allowed. This reduces the possible bending angle between consecutive bonds thus producing an effective entropic stiffness that competes with a short-range attraction, and leads to the formation of secondary structures characteristic of proteins. We discuss the low-temperature phase diagram as a function of increasing interpenetration and find a transition from a planar, beta-like structure, to helical shape. In the second model, an energetic stiffness is explicitly introduced by imposing an infinitely large energy penalty for bending above a critical angle between consecutive bonds, and no penalty below it. The low-temperature phase of this model does not show any sign of protein-like secondary structures. At intermediate temperatures, however, where the chain is still in the coil conformation but stiffness is significant, we find the two models to predict a quite similar dependence of the persistence length as a function of the stiffness. This behaviour is rationalized in terms of a simple geometrical mapping between the two models. Finally, we discuss the effect of shrinking side chains to zero and find the above mapping to still hold true. PMID:27586943

  18. Secondary structure of proteins analyzed ex vivo in vascular wall in diabetic animals using FT-IR spectroscopy.

    PubMed

    Majzner, Katarzyna; Wrobel, Tomasz P; Fedorowicz, Andrzej; Chlopicki, Stefan; Baranska, Malgorzata

    2013-11-12

    In recent years many methods for ex vivo tissue analysis or diagnosis of diseases have been applied, including infrared absorption spectroscopy. Fourier-transform infrared (FT-IR) absorption microspectroscopy allows the simultaneous monitoring of the content of various chemical compounds in tissues with both high selectivity and resolution. Imaging of tissue samples in very short time can be performed using a spectrometer equipped with a Focal Plane Array (FPA) detector. Additionally, a detection of minor components or subtle changes associated with the functional status of a tissue sample is possible when advanced methods of data analysis, such as chemometric techniques, are applied. Monitoring of secondary structures of proteins has already proved to be useful in the analysis of animal tissues in disease states. The aim of this work was to build a mathematical model based on FT-IR measurements for the prediction of alterations in the content of secondary structures of proteins analyzed by FT-IR in the vascular wall of diabetic animals. For that purpose a spectral database of proteins of known crystallography and secondary structures was assembled. Thirty-seven proteins were measured by means of two FT-IR techniques: transflection and Attenuated Total Reflectance (ATR). The obtained model was tested on cross-sections of rat tail, for which the content of proteins and their secondary structures was well characterized. Then, the model was applied for the detection of possible alterations in the secondary structures of proteins in the vascular wall of diabetic rats and mice. The obtained results suggest a prominent increase in E- and S-structures and a decrease in the content of H-structures in the vascular wall from diabetic mice and rats. FT-IR-based studies of secondary structures of proteins may be a novel approach to study complex processes ongoing in the vascular wall. The obtained results are satisfactory; however, the existing limitations of the method are

  19. Evaluation of the information content of RNA structure mapping data for secondary structure prediction.

    PubMed

    Quarrier, Scott; Martin, Joshua S; Davis-Neulander, Lauren; Beauregard, Arthur; Laederach, Alain

    2010-06-01

    Structure mapping experiments (using probes such as dimethyl sulfate [DMS], kethoxal, and T1 and V1 RNases) are used to determine the secondary structures of RNA molecules. The process is iterative, combining the results of several probes with constrained minimum free-energy calculations to produce a model of the structure. We aim to evaluate whether particular probes provide more structural information, and specifically, how noise in the data affects the predictions. Our approach involves generating "decoy" RNA structures (using the sFold Boltzmann sampling procedure) and evaluating whether we are able to identify the correct structure from this ensemble of structures. We show that with perfect information, we are always able to identify the optimal structure for five RNAs of known structure. We then collected orthogonal structure mapping data (DMS and RNase T1 digest) under several solution conditions using our high-throughput capillary automated footprinting analysis (CAFA) technique on two group I introns of known structure. Analysis of these data reveals the error rates in the data under optimal (low salt) and suboptimal solution conditions (high MgCl(2)). We show that despite these errors, our computational approach is less sensitive to experimental noise than traditional constraint-based structure prediction algorithms. Finally, we propose a novel approach for visualizing the interaction of chemical and enzymatic mapping data with RNA structure. We project the data onto the first two dimensions of a multidimensional scaling of the sFold-generated decoy structures. We are able to directly visualize the structural information content of structure mapping data and reconcile multiple data sets. PMID:20413617

  20. A MYLK variant regulates asthmatic inflammation via alterations in mRNA secondary structure.

    PubMed

    Wang, Ting; Zhou, Tong; Saadat, Laleh; Garcia, Joe G N

    2015-06-01

    Myosin light-chain kinase (MYLK) is a gene known to be significantly associated with severe asthma in African Americans. Here we further examine the molecular function of a single-nucleotide polymorphism (SNP), located in the non-muscle myosin light-chain kinase isoform (nmMLCK), in asthma susceptibility and pathobiology. We identified nmMLCK variant (reference SNP: rs9840993, NM_053025: 721C>T, c.439C>T) with a distinct mRNA secondary structure from the other variants. The nmMLCK variant (721C) secondary structure exhibits increased stability with an elongated half-life in the human endothelial cell, and greater efficiency in protein translation initiation owing to an increased accessibility to translation start site. Finally, nmMLCK expression of 721C- and 721T-containing MYLK transgenes were compared in nmMLCK(-/-) mice and confirmed deleterious effects of nmMLCK expression on asthmatic indices and implicated the augmented influence of MYLK 721C>T (c.439C>T) SNP on asthma severity. The confirmation of the novel mechanism of the regulation of asthmatic inflammation by a MYLK advances knowledge of the genetic basis for asthma disparities, and further suggests the potential of nmMLCK as a therapeutic target. Our study suggests that in addition to altering protein structure and function, non-synonymous SNPs may also lead to phenotypic disparity by altering protein expression. PMID:25271083

  1. A novel predictor for protein structural class based on integrated information of the secondary structure sequence.

    PubMed

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

    2014-08-01

    The structural class has become one of the most important features for characterizing the overall folding type of a protein and played important roles in many aspects of protein research. At present, it is still a challenging problem to accurately predict protein structural class for low-similarity sequences. In this study, an 18-dimensional integrated feature vector is proposed by fusing the information about content and position of the predicted secondary structure elements. The consistently high accuracies of jackknife and 10-fold cross-validation tests on different low-similarity benchmark datasets show that the proposed method is reliable and stable. Comparison of our results with other methods demonstrates that our method is an effective computational tool for protein structural class prediction, especially for low-similarity sequences. PMID:24859536

  2. A survey of machine learning methods for secondary and supersecondary protein structure prediction.

    PubMed

    Ho, Hui Kian; Zhang, Lei; Ramamohanarao, Kotagiri; Martin, Shawn

    2013-01-01

    In this chapter we provide a survey of protein secondary and supersecondary structure prediction using methods from machine learning. Our focus is on machine learning methods applicable to β-hairpin and β-sheet prediction, but we also discuss methods for more general supersecondary structure prediction. We provide background on the secondary and supersecondary structures that we discuss, the features used to describe them, and the basic theory behind the machine learning methods used. We survey the machine learning methods available for secondary and supersecondary structure prediction and compare them where possible. PMID:22987348

  3. Situational Interest: Its Multifaceted Structure in the Secondary Mathematics Classroom.

    ERIC Educational Resources Information Center

    Mitchell, Mathew

    Classroom boredom in the secondary mathematics classroom is a problem that can be addressed from knowledge of the intrinsic motivational variable of "interestingness." The lack of a theoretical model of interest is an obstacle in research that investigates this variable. This paper describes the three stages in the development of a model of…

  4. Ambient modal identification of a primary-secondary structure by Fast Bayesian FFT method

    NASA Astrophysics Data System (ADS)

    Au, Siu-Kui; Zhang, Feng-Liang

    2012-04-01

    The Mong Man Wai Building is a seven-storied reinforced concrete structure situated on the campus of the City University of Hong Kong. On its roof a two-storied steel frame has been recently constructed to host a new wind tunnel laboratory. The roof frame and the main building form a primary-secondary structure. The dynamic characteristics of the resulting system are of interest from a structural dynamics point of view. This paper presents work on modal identification of the structure using ambient vibration measurement. An array of tri-axial acceleration data has been obtained using a number of setups to cover all locations of interest with a limited number of sensors. Modal identification is performed using a recently developed Fast Bayesian FFT method. In addition to the most probable modal properties, their posterior uncertainties can also be assessed using the method. The posterior uncertainty of mode shape is assessed by the expected value of the Modal Assurance Criteria (MAC) of the most probable mode shape with a random mode shape consistent with the posterior distribution. The mode shapes of the overall structural system are obtained by assembling those from individual setups using a recently developed least-square method. The identification results reveal a number of interesting features about the structural system and provide important information defining the baseline modal properties of the building. Practical interpretation of the statistics of modal parameters calculated from frequentist and Bayesian context is also discussed.

  5. The Globular State of the Single-Stranded RNA: Effect of the Secondary Structure Rearrangements

    PubMed Central

    Grigoryan, Zareh A.; Karapetian, Armen T.

    2015-01-01

    The mutual influence of the slow rearrangements of secondary structure and fast collapse of the long single-stranded RNA (ssRNA) in approximation of coarse-grained model is studied with analytic calculations. It is assumed that the characteristic time of the secondary structure rearrangement is much longer than that for the formation of the tertiary structure. A nonequilibrium phase transition of the 2nd order has been observed. PMID:26345143

  6. Quantifying the energetic interplay of RNA tertiary and secondary structure interactions.

    PubMed Central

    Silverman, S K; Zheng, M; Wu, M; Tinoco, I; Cech, T R

    1999-01-01

    To understand the RNA-folding problem, we must know the extent to which RNA structure formation is hierarchical (tertiary folding of preformed secondary structure). Recently, nuclear magnetic resonance (NMR) spectroscopy was used to show that Mg2+-dependent tertiary interactions force secondary structure rearrangement in the 56-nt tP5abc RNA, a truncated subdomain of the Tetrahymena group I intron. Here we combine mutagenesis with folding computations, nondenaturing gel electrophoresis, high-resolution NMR spectroscopy, and chemical-modification experiments to probe further the energetic interplay of tertiary and secondary interactions in tP5abc. Point mutations predicted to destabilize the secondary structure of folded tP5abc greatly disrupt its Mg2+-dependent folding, as monitored by nondenaturing gels. Imino proton assignments and sequential NOE walks of the two-dimensional NMR spectrum of one of the tP5abc mutants confirm the predicted secondary structure, which does not change in the presence of Mg2+. In contrast to these data on tP5abc, the same point mutations in the context of the P4-P6 domain (of which P5abc is a subdomain) shift the Mg2+ dependence of P4-P6 folding only moderately, and dimethyl sulfate (DMS) modification experiments demonstrate that Mg2+ does cause secondary structure rearrangement of the P4-P6 mutants' P5abc subdomains. Our data provide experimental support for two simple conclusions: (1) Even single point mutations at bases involved only in secondary structure can be enough to tip the balance between RNA tertiary and secondary interactions. (2) Domain context must be considered in evaluating the relative importance of tertiary and secondary contributions. This tertiary/secondary interplay is likely relevant to the folding of many large RNA and to bimolecular snRNA-snRNA and snRNA-intron RNA interactions. PMID:10606276

  7. The mitochondrial respiratory chain of the secondary green alga Euglena gracilis shares many additional subunits with parasitic Trypanosomatidae.

    PubMed

    Perez, Emilie; Lapaille, Marie; Degand, Hervé; Cilibrasi, Laura; Villavicencio-Queijeiro, Alexa; Morsomme, Pierre; González-Halphen, Diego; Field, Mark C; Remacle, Claire; Baurain, Denis; Cardol, Pierre

    2014-11-01

    The mitochondrion is an essential organelle for the production of cellular ATP in most eukaryotic cells. It is extensively studied, including in parasitic organisms such as trypanosomes, as a potential therapeutic target. Recently, numerous additional subunits of the respiratory-chain complexes have been described in Trypanosoma brucei and Trypanosoma cruzi. Since these subunits had apparently no counterparts in other organisms, they were interpreted as potentially associated with the parasitic trypanosome lifestyle. Here we used two complementary approaches to characterise the subunit composition of respiratory complexes in Euglena gracilis, a non-parasitic secondary green alga related to trypanosomes. First, we developed a phylogenetic pipeline aimed at mining sequence databases for identifying homologues to known respiratory-complex subunits with high confidence. Second, we used MS/MS proteomics after two-dimensional separation of the respiratory complexes by Blue Native- and SDS-PAGE both to confirm in silico predictions and to identify further additional subunits. Altogether, we identified 41 subunits that are restricted to E. gracilis, T. brucei and T. cruzi, along with 48 classical subunits described in other eukaryotes (i.e. plants, mammals and fungi). This moreover demonstrates that at least half of the subunits recently reported in T. brucei and T. cruzi are actually not specific to Trypanosomatidae, but extend at least to other Euglenozoa, and that their origin and function are thus not specifically associated with the parasitic lifestyle. Furthermore, preliminary biochemical analyses suggest that some of these additional subunits underlie the peculiarities of the respiratory chain observed in Euglenozoa. PMID:24561571

  8. Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model.

    PubMed

    Waldispühl, J; Clote, P

    2007-03-01

    An RNA secondary structure is saturated if no base pairs can be added without violating the definition of secondary structure. Here we describe a new algorithm, RNAsat, which for a given RNA sequence a, an integral temperature 0 secondary structures of a which have exactly k base pairs, R is the universal gas constant and E(S) denotes the free energy with respect to the Turner nearest neighbor energy model. By dynamic programming, we compute Z(k)(T)simultaneously for all values of k in time O(n(5)) and space O(n(3)).Additionally, RNAsat computes the partition function Q(k)(T)(a) = SigmaSepsilonS(k)(a) exp(-E(S)/RT), where the sum is over all secondary structures of a which have k base pairs; the latter computation is performed simultaneously for all values of k in O(n(4)) time and O(n(3)) space. Lastly, using the partition function Z(k)(T) [resp. Q(k)(T)] with stochastic backtracking, RNAsat rigorously samples the collection of saturated secondary structures [resp. secondary structures] having k base pairs; for Q(k)(T) this provides a parametrized form of Sfold sampling (Ding and Lawrence, 2003). Using RNAsat, (i) we compute the ensemble free energy for saturated secondary structures having k base pairs, (ii) show cooperativity of the Turner model, (iii) demonstrate a temperature-dependent phase transition, (iv) illustrate the predictive advantage of RNAsat for precursor microRNA cel-mir-72 of C. elegans and for the pseudoknot PKB 00152 of Pseudobase (van Batenburg et al., 2001), (v) illustrate the RNA shapes (Giegerich et al., 2004) of sampled secondary structures [resp. saturated structures] having exactly k base pairs. A web server for RNAsat is under construction at bioinformatics.bc.edu/clotelab/RNAsat/. PMID:17456015

  9. A Tool Preference Choice Method for RNA Secondary Structure Prediction by SVM with Statistical Tests

    PubMed Central

    Hor, Chiou-Yi; Yang, Chang-Biau; Chang, Chia-Hung; Tseng, Chiou-Ting; Chen, Hung-Hsin

    2013-01-01

    The Prediction of RNA secondary structures has drawn much attention from both biologists and computer scientists. Many useful tools have been developed for this purpose. These tools have their individual strengths and weaknesses. As a result, based on support vector machines (SVM), we propose a tool choice method which integrates three prediction tools: pknotsRG, RNAStructure, and NUPACK. Our method first extracts features from the target RNA sequence, and adopts two information-theoretic feature selection methods for feature ranking. We propose a method to combine feature selection and classifier fusion in an incremental manner. Our test data set contains 720 RNA sequences, where 225 pseudoknotted RNA sequences are obtained from PseudoBase, and 495 nested RNA sequences are obtained from RNA SSTRAND. The method serves as a preprocessing way in analyzing RNA sequences before the RNA secondary structure prediction tools are employed. In addition, the performance of various configurations is subject to statistical tests to examine their significance. The best base-pair accuracy achieved is 75.5%, which is obtained by the proposed incremental method, and is significantly higher than 68.8%, which is associated with the best predictor, pknotsRG. PMID:23641141

  10. Influence of microenvironment and liposomal formulation on secondary structure and bilayer interaction of lysozyme.

    PubMed

    Witoonsaridsilp, Wasu; Panyarachun, Busaba; Sarisuta, Narong; Müller-Goymann, Christel C

    2010-02-01

    The conformation of peptide and protein drugs in various microenvironments and the interaction with drug carriers such as liposomes are of considerable interest. In this study the influence of microenvironments such as pH, salt concentration, and surface charge on the secondary structure of a model protein, lysozyme, either in solution or entrapped in liposomes with various molar ratios of phosphatidylcholine (PC):cholesterol (Chol) was investigated. It was found that entrapment efficiency was more pronounced in negatively charged liposomes than in non-charged liposomes, which was independent of Chol content and pH of hydration medium. The occurrence of aggregation, decrease in zeta potential, and alteration of 31P NMR chemical shift of negatively charged lysozyme liposomes compared to blank liposomes suggested that the electrostatic interaction plays a major role in protein-lipid binding. Addition of sodium chloride could impair the neutralizing ability of positively charged lysozyme on negatively charged membrane via chloride counterion binding. Neither lysozyme in various buffer solutions with sodium chloride nor that entrapped in liposomes showed any significant change in their secondary structures. However, significant decrease in alpha-helical content of lysozyme in non-charged liposomes at higher pH and salt concentrations was discovered. PMID:19880295

  11. Prediction of RNA secondary structures: from theory to models and real molecules

    NASA Astrophysics Data System (ADS)

    Schuster, Peter

    2006-05-01

    empirical parameters can be determined and by principal deficiencies, for example by the lack of energy contributions resulting from tertiary interactions. In addition, native structures may be determined by folding kinetics rather than by thermodynamics. We address the first problem by considering base pair probabilities or base pairing entropies, which are derived from the partition function of conformations. A high base pair probability corresponding to a low pairing entropy is taken as an indicator of a high reliability of prediction. Pseudoknots are discussed as an example of a tertiary interaction that is highly important for RNA function. Moreover, pseudoknot formation is readily incorporated into structure prediction algorithms. Some examples of experimental data on RNA secondary structures that are readily explained using the landscape concept are presented. They deal with (i) properties of RNA molecules with random sequences, (ii) RNA molecules from restricted alphabets, (iii) existence of neutral networks, (iv) shape space covering, (v) riboswitches and (vi) evolution of non-coding RNAs as an example of evolution restricted to neutral networks.

  12. Mechanical properties of amyloid-like fibrils defined by secondary structures

    NASA Astrophysics Data System (ADS)

    Bortolini, C.; Jones, N. C.; Hoffmann, S. V.; Wang, C.; Besenbacher, F.; Dong, M.

    2015-04-01

    are extensively studied - among these parameters, the secondary structures and the pH have been revealed to be crucial, since a variation in pH changes the fibril morphology and net chirality during protein aggregation. It is important to quantify the mechanical properties of these fibrils in order to help the design of effective strategies for treating diseases related to the presence of amyloid fibrils. In this work, we show that by changing pH the mechanical properties of amyloid-like fibrils vary as well. In particular, we reveal that these mechanical properties are strongly related to the content of secondary structures. We analysed and estimated the Young's modulus (E) by comparing the persistence length (Lp) - measured from the observation of TEM images by using statistical mechanics arguments - with the mechanical information provided by peak force quantitative nanomechanical property mapping (PF-QNM). The secondary structure content and the chirality are investigated by means of synchrotron radiation circular dichroism (SR-CD). Results arising from this study could be fruitfully used as a protocol to investigate other medical or engineering relevant peptide fibrils. Electronic supplementary information (ESI) available: A molecular model for the peptide studied and the charge chart associated to it. In addition, an AFM image of pH 4 fibrils is presented. See DOI: 10.1039/c4nr05109b

  13. The Structure of Secondary School Teacher Job Satisfaction and Its Relationship with Attrition and Work Enthusiasm

    ERIC Educational Resources Information Center

    Weiqi, Chen

    2007-01-01

    This study used the results of a questionnaire survey of 230 secondary school teachers to analyze the factors constituting job satisfaction and its effects on teacher attrition and work enthusiasm. The results show that (a) the structure of secondary school teacher job satisfaction is made up of ten components and is consistent with the model put…

  14. Testing Mediation Using Multiple Regression and Structural Equation Modeling Analyses in Secondary Data

    ERIC Educational Resources Information Center

    Li, Spencer D.

    2011-01-01

    Mediation analysis in child and adolescent development research is possible using large secondary data sets. This article provides an overview of two statistical methods commonly used to test mediated effects in secondary analysis: multiple regression and structural equation modeling (SEM). Two empirical studies are presented to illustrate the…

  15. Determination of Secondary School Students' Cognitive Structure, and Misconception in Ecological Concepts through Word Association Test

    ERIC Educational Resources Information Center

    Yücel, Elif Özata; Özkan, Mulis

    2015-01-01

    In this study, we determined cognitive structures and misconceptions about basic ecological concepts by using "word association" tests on secondary school students, age between 12-14 years. Eighty-nine students participated in this study. Before WAT was generated, basic ecological concepts that take place in the secondary science…

  16. Characterization and comparative study of coal combustion residues from a primary and additional flue gas secondary desulfurization process

    SciTech Connect

    Gomes, S.; Francois, M.; Evrard, O.; Pellissier, C.

    1998-11-01

    An extensive characterization and comparative study was done on two flue gas desulfurization (FGD) residues derived from the same coal. LR residues (originated from Loire/Rhone in the south of Lyon, France) are obtained after a primary desulfurization process (SO{sub 2} is trapped by reaction with CaO at a temperature of about 1100 C), and LM residues (originating from La Maxe, near Metz in the east of France) are obtained after an additional secondary desulfurization process (SO{sub 2} is removed further by reaction with Ca(OH){sub 2} at a temperature of about 120 C). Various and complementary investigation methods were used to determine their chemical, physical, and mineralogical properties: x-ray fluorescence and diffraction, scanning electron microscopy, differential scanning calorimetry, thermogravimetry analysis, granulometric distribution, pycnometric density, BET specific surface area and pH, conductivity measurements, and chemical analysis of their insoluble fraction. The FGD residues contain basically two main components: a silico-aluminous fly ash part and calcic FGD phases. In the LR residues the two components can be considered as independent, whereas they are linked in the LM residues because chemical reactions have occurred, leading to the formation of silico-calcic gel CSH, hydrated aluminate AFm, and AFt phases.

  17. Conductivity and structure of bilinear organic addition compounds

    PubMed Central

    Phillips, J. C.

    1976-01-01

    The relationship between crystal structures and metallic conductivities of linear organic materials such as tetrathiafulvalene-tetracyanoquinodimethane is explained in terms of strong lateral elastic interactions between chains. A microdomain model is presented in which at high temperatures there are, in general, two coexisting phases on each stacked molecular chain. The ordering of (in general, four) phases on two interacting chains leads to a variety of phase transitions at low temperatures. By examining temperature-dependent electrical conductivities and magnetic susceptibilities one can establish the character of each such transition. PMID:16592359

  18. Putative secondary structures of unusually long strepsipteran SSU rRNAs and its phylogenetic implications.

    PubMed

    Choe, C P; Hwang, U W; Kim, W

    1999-04-30

    We constructed the putative secondary structures of the small subunit rRNAs (SSU rRNA) from three strepsipteran insects. The primary sequences of the strepsipteran SSU rRNAs are unusually long due to unique and long insertions. In spite of these insertions, the basic shapes of their secondary structures are well maintained as shown in those of other eukaryotes, because these insertions appear mainly in the variable regions. The secondary structures for the V1, V3, V5, V8, and V9 regions are well conserved, even though the primary structures of V1, V5, and V8 regions are quite variable. However, the predicted secondary structures for the V2, V4, and V7 regions are quite different from those of other insects. In the V4 and V7 regions, helices specific to the Strepsiptera exist. These helices have not been reported in other organisms so far. Similarly, four eukaryotic specific helices (E8-1, E10-2, E23-4 and E45-1) not reported in insects exist in the V2, V4, and V8 regions. These helices are formed by the inserted sequences. The secondary structures of the expanded segments of the strepsipteran SSU rRNA were applied to infer the phylogenetic position of Strepsiptera, one of the most enigmatic problems in insect phylogeny. Only the secondary structure of the V7 region showed the weak Strepsiptera/Diptera sister-group relationship. PMID:10340475

  19. RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology

    PubMed Central

    Taufer, Michela; Leung, Ming-Ying; Solorio, Thamar; Licon, Abel; Mireles, David; Araiza, Roberto; Johnson, Kyle L.

    2009-01-01

    As ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation, their secondary structures have been the focus of many recent studies. Despite the computing power of supercomputers, computationally predicting secondary structures with thermodynamic methods is still not feasible when the RNA molecules have long nucleotide sequences and include complex motifs such as pseudoknots. This paper presents RNAVLab (RNA Virtual Laboratory), a virtual laboratory for studying RNA secondary structures including pseudoknots that allows scientists to address this challenge. Two important case studies show the versatility and functionalities of RNAVLab. The first study quantifies its capability to rebuild longer secondary structures from motifs found in systematically sampled nucleotide segments. The extensive sampling and predictions are made feasible in a short turnaround time because of the grid technology used. The second study shows how RNAVLab allows scientists to study the viral RNA genome replication mechanisms used by members of the virus family Nodaviridae. PMID:19885376

  20. A secondary copulatory structure in a female insect: a clasp for a nuptial meal?

    NASA Astrophysics Data System (ADS)

    Gwynne, Darryl T.

    2002-03-01

    Secondary copulatory structures are well-known in male dragonflies and spiders. Here I report a secondary copulatory organ in female ground weta, Hemiandrus pallitarsis (Ensifera, Orthoptera - crickets and allies). The organ, located on the underside of the abdomen, appears to secure the male's genitalia during the transfer of a spermatophylax nuptial meal to this location, an area quite separate from the female's primary copulatory structures, where the sperm ampulla is attached.

  1. Sheath structure transition controlled by secondary electron emission

    NASA Astrophysics Data System (ADS)

    Schweigert, I. V.; Langendorf, S. J.; Walker, M. L. R.; Keidar, M.

    2015-04-01

    In particle-in-cell Monte Carlo collision (PIC MCC) simulations and in an experiment we study sheath formation over an emissive floating Al2O3 plate in a direct current discharge plasma at argon gas pressure 10-4 Torr. The discharge glow is maintained by the beam electrons emitted from a negatively biased hot cathode. We observe three types of sheaths near the floating emissive plate and the transition between them is driven by changing the negative bias. The Debye sheath appears at lower voltages, when secondary electron emission is negligible. With increasing applied voltage, secondary electron emission switches on and a first transition to a new sheath type, beam electron emission (BEE), takes place. For the first time we find this specific regime of sheath operation near the floating emissive surface. In this regime, the potential drop over the plate sheath is about four times larger than the temperature of plasma electrons. The virtual cathode appears near the emissive plate and its modification helps to maintain the BEE regime within some voltage range. Further increase of the applied voltage U initiates the second smooth transition to the plasma electron emission sheath regime and the ratio Δφs/Te tends to unity with increasing U. The oscillatory behavior of the emissive sheath is analyzed in PIC MCC simulations. A plasmoid of slow electrons is formed near the plate and transported to the bulk plasma periodically with a frequency of about 25 kHz.

  2. Internal Transcribed Spacer 1 Secondary Structure Analysis Reveals a Common Core throughout the Anaerobic Fungi (Neocallimastigomycota)

    PubMed Central

    Koetschan, Christian; Kittelmann, Sandra; Lu, Jingli; Al-Halbouni, Djamila; Jarvis, Graeme N.; Müller, Tobias; Wolf, Matthias; Janssen, Peter H.

    2014-01-01

    The internal transcribed spacer (ITS) is a popular barcode marker for fungi and in particular the ITS1 has been widely used for the anaerobic fungi (phylum Neocallimastigomycota). A good number of validated reference sequences of isolates as well as a large number of environmental sequences are available in public databases. Its highly variable nature predisposes the ITS1 for low level phylogenetics; however, it complicates the establishment of reproducible alignments and the reconstruction of stable phylogenetic trees at higher taxonomic levels (genus and above). Here, we overcame these problems by proposing a common core secondary structure of the ITS1 of the anaerobic fungi employing a Hidden Markov Model-based ITS1 sequence annotation and a helix-wise folding approach. We integrated the additional structural information into phylogenetic analyses and present for the first time an automated sequence-structure-based taxonomy of the ITS1 of the anaerobic fungi. The methodology developed is transferable to the ITS1 of other fungal groups, and the robust taxonomy will facilitate and improve high-throughput anaerobic fungal community structure analysis of samples from various environments. PMID:24663345

  3. A cell-compatible PEO-PPO-PEO (Pluronic®)-based hydrogel stabilized through secondary structures.

    PubMed

    Peng, Sydney; Lin, Ji-Yu; Cheng, Ming-Huei; Wu, Chih-Wei; Chu, I-Ming

    2016-12-01

    Pluronic F-127 (PF127) is a thermosensitive polymer that has been widely recognized as a potential candidate for various bio-applications. However, in hydrogel form, its rapid disintegration and inhospitality toward cells have significantly limited its usage. As a means to increase the integrity and cell compatibility of a PF127 hydrogel, we propose the introduction of stabilizing secondary structures to the gel network by the addition of secondary structure-forming oligo-alanine and oligo-phenylalanine. Results indicate that increasing the oligo(peptides) attached to PF127 led to a significant decrease in the gelation concentration and temperature. A selected oligo(peptide)-modified PF127 was capable of forming a stable hydrogel network at 5% and suffered only 20% weight loss after 7days of incubation in media. Scanning electron microscopy (SEM) revealed comparably more interconnected morphology in modified hydrogels which may be attributed to the presence of secondary structures, as verified by circular dichroism (CD) and Fourier-transformed infrared (FT-IR) spectroscopy. Nuclear magnetic resonance (NMR) provided insights into the extensive interactions at the micelle core, which is the key to altered gelation behavior. Furthermore, modified hydrogels maintained structural integrity within culturing media and supported the proliferation of encapsulated chondrocytes. In addition, in vivo residence time was extended to well beyond 2weeks after oligo(peptide) modification, thereby broadening the application scope of the PF127 hydrogel to encompass long-term drug delivery and cell culturing. PMID:27612731

  4. RNACluster: An integrated tool for RNA secondary structure comparison and clustering.

    PubMed

    Liu, Qi; Olman, V; Liu, Huiqing; Ye, Xiuzi; Qiu, Shilun; Xu, Ying

    2008-07-15

    RNA structure comparison is a fundamental problem in structural biology, structural chemistry, and bioinformatics. It can be used for analysis of RNA energy landscapes, conformational switches, and facilitating RNA structure prediction. The purpose of our integrated tool RNACluster is twofold: to provide a platform for computing and comparison of different distances between RNA secondary structures, and to perform cluster identification to derive useful information of RNA structure ensembles, using a minimum spanning tree (MST) based clustering algorithm. RNACluster employs a cluster identification approach based on a MST representation of the RNA ensemble data and currently supports six distance measures between RNA secondary structures. RNACluster provides a user-friendly graphical interface to allow a user to compare different structural distances, analyze the structure ensembles, and visualize predicted structural clusters. PMID:18271070

  5. The role of a metastable RNA secondary structure in hepatitis delta virus genotype III RNA editing

    PubMed Central

    Linnstaedt, Sarah D.; Kasprzak, Wojciech K.; Shapiro, Bruce A.; Casey, John L.

    2006-01-01

    RNA editing plays a critical role in the life cycle of hepatitis delta virus (HDV). The host editing enzyme ADAR1 recognizes specific RNA secondary structure features around the amber/W site in the HDV antigenome and deaminates the amber/W adenosine. A previous report suggested that a branched secondary structure is necessary for editing in HDV genotype III. This branched structure, which is distinct from the characteristic unbranched rod structure required for HDV replication, was only partially characterized, and knowledge concerning its formation and stability was limited. Here, we examine the secondary structures, conformational dynamics, and amber/W site editing of HDV genotype III RNA using a miniaturized HDV genotype III RNA in vitro. Computational analysis of this RNA using the MPGAfold algorithm indicated that the RNA has a tendency to form both metastable and stable unbranched secondary structures. Moreover, native polyacrylamide gel electrophoresis demonstrated that this RNA forms both branched and unbranched rod structures when transcribed in vitro. As predicted, the branched structure is a metastable structure that converts readily to the unbranched rod structure. Only branched RNA was edited at the amber/W site by ADAR1 in vitro. The structural heterogeneity of HDV genotype III RNA is significant because not only are both conformations of the RNA functionally important for viral replication, but the ratio of the two forms could modulate editing by determining the amount of substrate RNA available for modification. PMID:16790843

  6. An image processing approach to computing distances between RNA secondary structures dot plots

    PubMed Central

    Ivry, Tor; Michal, Shahar; Avihoo, Assaf; Sapiro, Guillermo; Barash, Danny

    2009-01-01

    Background Computing the distance between two RNA secondary structures can contribute in understanding the functional relationship between them. When used repeatedly, such a procedure may lead to finding a query RNA structure of interest in a database of structures. Several methods are available for computing distances between RNAs represented as strings or graphs, but none utilize the RNA representation with dot plots. Since dot plots are essentially digital images, there is a clear motivation to devise an algorithm for computing the distance between dot plots based on image processing methods. Results We have developed a new metric dubbed 'DoPloCompare', which compares two RNA structures. The method is based on comparing dot plot diagrams that represent the secondary structures. When analyzing two diagrams and motivated by image processing, the distance is based on a combination of histogram correlations and a geometrical distance measure. We introduce, describe, and illustrate the procedure by two applications that utilize this metric on RNA sequences. The first application is the RNA design problem, where the goal is to find the nucleotide sequence for a given secondary structure. Examples where our proposed distance measure outperforms others are given. The second application locates peculiar point mutations that induce significant structural alternations relative to the wild type predicted secondary structure. The approach reported in the past to solve this problem was tested on several RNA sequences with known secondary structures to affirm their prediction, as well as on a data set of ribosomal pieces. These pieces were computationally cut from a ribosome for which an experimentally derived secondary structure is available, and on each piece the prediction conveys similarity to the experimental result. Our newly proposed distance measure shows benefit in this problem as well when compared to standard methods used for assessing the distance similarity

  7. Structural evolution of gold nanorods during controlled secondary growth.

    PubMed

    Keul, Heidrun A; Möller, Martin; Bockstaller, Michael R

    2007-09-25

    Single-crystalline gold nanorods synthesized by the Ag(I)-mediated seeded-growth method (see: El-Sayed, M. A.; Nikoobakht, B. Chem. Mater. 2003, 15, 1957) were used as seeds for the preferential overgrowth of gold on particular crystallographic facets by systematic variation of the conditions during overgrowth. The results support previous reports about the relevance of the cationic surfactant cetyltrimethylammonium bromide (CTAB) and Ag(I) in stabilizing anisotropic particle shapes and demonstrate that the regulation of the amount of ascorbic acid facilitates the preferential overgrowth of {111} crystal facets to form Xi-type particle shapes. Interestingly, secondary overgrowth is found to inevitably result in a loss of particle shape anisotropy. A mechanism based on surface reconstruction is proposed to rationalize the "shape-reversal" that is generally observed in the nanorod growth process, that is, the initial increase and subsequent decrease of particle anisotropy with increasing reaction time. High-resolution electron microscopy analysis of gold nanorods reveals clear evidence for (1 x 2) missing row surface reconstruction of high energetic {110} facets that form during the initial phase during particle growth. PMID:17713936

  8. GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops

    PubMed Central

    2012-01-01

    Background Accurate and efficient RNA secondary structure prediction remains an important open problem in computational molecular biology. Historically, advances in computing technology have enabled faster and more accurate RNA secondary structure predictions. Previous parallelized prediction programs achieved significant improvements in runtime, but their implementations were not portable from niche high-performance computers or easily accessible to most RNA researchers. With the increasing prevalence of multi-core desktop machines, a new parallel prediction program is needed to take full advantage of today’s computing technology. Findings We present here the first implementation of RNA secondary structure prediction by thermodynamic optimization for modern multi-core computers. We show that GTfold predicts secondary structure in less time than UNAfold and RNAfold, without sacrificing accuracy, on machines with four or more cores. Conclusions GTfold supports advances in RNA structural biology by reducing the timescales for secondary structure prediction. The difference will be particularly valuable to researchers working with lengthy RNA sequences, such as RNA viral genomes. PMID:22747589

  9. Aspects of the secondary and tertiary structure of DNA.

    PubMed

    Dougherty, G

    1983-11-21

    DNA is the primary genetic material of most organisms. A wide variety of naturally occurring duplex DNA's are known to exist as covalently closed circles. This covalent continuity introduces a topological constraint, and consequently these molecules possess aspects of tertiary and even higher-order structure. Virtually every physical, chemical and biological property of DNA - its transcription, hydrodynamic behaviour, energetics, enzymology and so on - are related to these structural features. We describe the parameters describing the topology and conformation of covalently-closed, duplex DNA's (form I DNA's), the conservation relationship between them and its implications. PMID:6316054

  10. Argumentation in Secondary School Students' Structured and Unstructured Chat Discussions

    ERIC Educational Resources Information Center

    Salminen, Timo; Marttunen, Miika; Laurinen, Leena

    2012-01-01

    Joint construction of new knowledge demands that persons can express their statements in a convincing way and explore other people's arguments constructively. For this reason, more knowledge on different means to support collaborative argumentation is needed. This study clarifies whether structured interaction supports students' critical and…

  11. Charge‐Induced Unzipping of Isolated Proteins to a Defined Secondary Structure

    PubMed Central

    González Flórez, Ana Isabel; Mucha, Eike; Ahn, Doo‐Sik; Gewinner, Sandy; Schöllkopf, Wieland; Pagel, Kevin

    2016-01-01

    Abstract Here we present a combined experimental and theoretical study on the secondary structure of isolated proteins as a function of charge state. In infrared spectra of the proteins ubiquitin and cytochrome c, amide I (C=O stretch) and amide II (N–H bend) bands can be found at positions that are typical for condensed‐phase proteins. For high charge states a new band appears, substantially red‐shifted from the amide II band observed at lower charge states. The observations are interpreted in terms of Coulomb‐driven transitions in secondary structures from mostly helical to extended C5‐type hydrogen‐bonded structures. Support for this interpretation comes from simple energy considerations as well as from quantum chemical calculations on model peptides. This transition in secondary structure is most likely universal for isolated proteins that occur in mass spectrometric experiments. PMID:26847383

  12. A parallel strategy for predicting the secondary structure of polycistronic microRNAs.

    PubMed

    Han, Dianwei; Tang, Guiliang; Zhang, Jun

    2013-01-01

    The biogenesis of a functional microRNA is largely dependent on the secondary structure of the microRNA precursor (pre-miRNA). Recently, it has been shown that microRNAs are present in the genome as the form of polycistronic transcriptional units in plants and animals. It will be important to design efficient computational methods to predict such structures for microRNA discovery and its applications in gene silencing. In this paper, we propose a parallel algorithm based on the master-slave architecture to predict the secondary structure from an input sequence. We conducted some experiments to verify the effectiveness of our parallel algorithm. The experimental results show that our algorithm is able to produce the optimal secondary structure of polycistronic microRNAs. PMID:23467060

  13. Charge-Induced Unzipping of Isolated Proteins to a Defined Secondary Structure.

    PubMed

    González Flórez, Ana Isabel; Mucha, Eike; Ahn, Doo-Sik; Gewinner, Sandy; Schöllkopf, Wieland; Pagel, Kevin; von Helden, Gert

    2016-03-01

    Here we present a combined experimental and theoretical study on the secondary structure of isolated proteins as a function of charge state. In infrared spectra of the proteins ubiquitin and cytochrome c, amide I (C=O stretch) and amide II (N-H bend) bands can be found at positions that are typical for condensed-phase proteins. For high charge states a new band appears, substantially red-shifted from the amide II band observed at lower charge states. The observations are interpreted in terms of Coulomb-driven transitions in secondary structures from mostly helical to extended C5 -type hydrogen-bonded structures. Support for this interpretation comes from simple energy considerations as well as from quantum chemical calculations on model peptides. This transition in secondary structure is most likely universal for isolated proteins that occur in mass spectrometric experiments. PMID:26847383

  14. Macromolecular ab initio phasing enforcing secondary and tertiary structure

    PubMed Central

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

    Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors’ approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a ‘still-life’, but some are correct enough for density modification and main-chain tracing to reveal the protein’s true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases. PMID:25610631

  15. RNA Secondary Structure Prediction by Using Discrete Mathematics: An Interdisciplinary Research Experience for Undergraduate Students

    PubMed Central

    Ellington, Roni; Wachira, James

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems. PMID:20810968

  16. RNA secondary structure prediction by using discrete mathematics: an interdisciplinary research experience for undergraduate students.

    PubMed

    Ellington, Roni; Wachira, James; Nkwanta, Asamoah

    2010-01-01

    The focus of this Research Experience for Undergraduates (REU) project was on RNA secondary structure prediction by using a lattice walk approach. The lattice walk approach is a combinatorial and computational biology method used to enumerate possible secondary structures and predict RNA secondary structure from RNA sequences. The method uses discrete mathematical techniques and identifies specified base pairs as parameters. The goal of the REU was to introduce upper-level undergraduate students to the principles and challenges of interdisciplinary research in molecular biology and discrete mathematics. At the beginning of the project, students from the biology and mathematics departments of a mid-sized university received instruction on the role of secondary structure in the function of eukaryotic RNAs and RNA viruses, RNA related to combinatorics, and the National Center for Biotechnology Information resources. The student research projects focused on RNA secondary structure prediction on a regulatory region of the yellow fever virus RNA genome and on an untranslated region of an mRNA of a gene associated with the neurological disorder epilepsy. At the end of the project, the REU students gave poster and oral presentations, and they submitted written final project reports to the program director. The outcome of the REU was that the students gained transferable knowledge and skills in bioinformatics and an awareness of the applications of discrete mathematics to biological research problems. PMID:20810968

  17. A Multi-faceted Secondary Structure Mimic Based On Piperidine-piperidinones

    PubMed Central

    Xin, Dongyue; Perez, Lisa M.; Ioerger, Thomas R.

    2014-01-01

    Minimalist secondary structure mimics are typically made to resemble one interface in a protein-protein interaction (PPI), and thus perturb it. We recently proposed suitable chemotypes can be matched with interface regions directly, without regard for secondary structures. This communication describes a modular synthesis of a new chemotype 1, simulation of its solution-state conformational ensemble, and correlation of that with ideal secondary structures and real interface regions in PPIs. Scaffold 1 presents amino acid side-chains that are quite separated from each other, in orientations that closely resemble ideal sheet or helical structures, similar non-ideal structures at PPI interfaces, and regions of other PPI interfaces where the mimic conformation does not resemble any secondary structure. Sixty-eight different PPIs where conformations of 1 matched well were identified. A new method is also presented to determine the relevance of a minimalist mimic crystal structure to its solution conformations. Thus DLD-1faf crystallized in a conformation that is estimated to be 0.91 kcal•mol−1 above the minimum energy solution state. PMID:24591004

  18. Structuring Free-text Microbiology Culture Reports For Secondary Use

    PubMed Central

    Yim, Wen-wai; Evans, Heather L.; Yetisgen, Meliha

    2015-01-01

    Microbiology lab culture reports are a frequently used diagnostic tool for clinical providers. However, their incorporation into clinical surveillance applications and evidence-based medicine can be severely hindered by the free-text nature of these reports. In this work, we (1) created a microbiology culture template to structure free-text microbiology reports, (2) generated an annotated microbiology report corpus, and (3) built a microbiology information extraction system. Specifically, we combined rule-based, hybrid, and statistical techniques to extract microbiology entities and fill templates for structuring data. System performances were favorable, with entity f1-score 0.889 and relation f1-score 0.795. We plan to incorporate these extractions as features for our ongoing ventilator-associated pneumonia surveillance project, though this tool can be used as an upstream process in other applications. Our newly created corpus includes 1442 unique gram stain and culture microbiology reports generated from a cohort of 715 patients at the University of Washington Medical Facilities. PMID:26306288

  19. Secondary flow structure from stent-induced perturbations in a bent pipe model for curved arteries

    NASA Astrophysics Data System (ADS)

    Shu, Fangjun; Glenn, Autumn; Bulusu, Kartik; Plesniak, Michael W.

    2010-11-01

    Secondary flow structures were investigated in a 180-degree circular bend under physiological (pulsatile) flow conditions with a stent model installed upstream of the bend. Upstream Reynolds number ranged from 200 to 1400 and the cardiac cycle period was scaled to match the physiological Womersley number, Wo=4.2. Experimental data were acquired using 2-D PIV at various cross-sectional planes along the bend. Similar to the results in absence of the stent model, symmetric counter-rotating vortex pairs were observed to develop during the cardiac cycle. In addition, transient unstable flow was initiated at the deceleration phase of the systolic peak (t/T=0.21). This complex flow is mainly attributable to perturbations induced by the stent model. It is characterized by breakdown of Dean- and Lyne-type vortices into various multiple-scale vortices. The phase-averaged flow fields were analyzed using the proper orthogonal decomposition (POD) method to gain further insight regarding the structural features of the flow.

  20. Structural class prediction of protein using novel feature extraction method from chaos game representation of predicted secondary structure.

    PubMed

    Zhang, Lichao; Kong, Liang; Han, Xiaodong; Lv, Jinfeng

    2016-07-01

    Protein structural class prediction plays an important role in protein structure and function analysis, drug design and many other biological applications. Extracting good representation from protein sequence is fundamental for this prediction task. In recent years, although several secondary structure based feature extraction strategies have been specially proposed for low-similarity protein sequences, the prediction accuracy still remains limited. To explore the potential of secondary structure information, this study proposed a novel feature extraction method from the chaos game representation of predicted secondary structure to mainly capture sequence order information and secondary structure segments distribution information in a given protein sequence. Several kinds of prediction accuracies obtained by the jackknife test are reported on three widely used low-similarity benchmark datasets (25PDB, 1189 and 640). Compared with the state-of-the-art prediction methods, the proposed method achieves the highest overall accuracies on all the three datasets. The experimental results confirm that the proposed feature extraction method is effective for accurate prediction of protein structural class. Moreover, it is anticipated that the proposed method could be extended to other graphical representations of protein sequence and be helpful in future research. PMID:27084358

  1. Secondary structure determination for alpha-neurotoxin from Dendroaspis polylepis polylepis based on sequence-specific 1H-nuclear-magnetic-resonance assignments.

    PubMed

    Labhardt, A M; Hunziker-Kwik, E H; Wüthrich, K

    1988-11-01

    Sequence-specific assignments are presented for the polypeptide backbone protons and a majority of the amino-acid-side-chain protons of alpha-neurotoxin from Dendroaspis polylepis polylepis, and individual amide proton-exchange rates with the solvent are reported. The secondary structure and the hydrogen-bonding patterns in the regular secondary structure elements are deduced from nuclear Overhauser effects and the sequence locations of the slowly exchanging amide protons. The molecule includes a three-stranded antiparallel beta-sheet, and there are indications that two additional short chain segments are arranged in an antiparallel beta-sheet. These structural elements are similar, but not identical, to either the secondary structure reported for erabutoxin b in single crystals, or the solution structure of cytotoxin CTXIIb from Naja mossambica mossambica. PMID:2847926

  2. Regulation of tyrosine hydroxylase transcription by hnRNP K and DNA secondary structure

    PubMed Central

    Banerjee, Kasturi; Wang, Meng; Cai, Elizabeth; Fujiwara, Nana; Baker, Harriet; Cave, John W.

    2014-01-01

    Regulation of tyrosine hydroxylase gene (Th) transcription is critical for specifying and maintaining the dopaminergic neuronal phenotype. Here we define a molecular regulatory mechanism for Th transcription conserved in tetrapod vertebrates. We show that heterogeneous nuclear ribonucleoprotein (hnRNP) K is a transactivator of Th transcription. It binds to previously unreported and evolutionarily conserved G:C-rich regions in the Th proximal promoter. hnRNP K directly binds C-rich single DNA strands within these conserved regions and also associates with double-stranded sequences when proteins, such as CREB, are bound to an adjacent cis-regulatory element. The single DNA strands within the conserved G:C-rich regions adopt either G-quadruplex or i-motif secondary structures. We also show that small molecule-mediated stabilization of these secondary structures represses Th promoter activity. These data suggest that these secondary structures are targets for pharmacological modulation of the dopaminergic phenotype. PMID:25493445

  3. Relationship between chain collapse and secondary structure formation in a partially folded protein.

    PubMed

    Nakagawa, Kanako; Yamada, Yoshiteru; Matsumura, Yoshitaka; Tsukamoto, Seiichi; Yamamoto-Ohtomo, Mio; Ohtomo, Hideaki; Okabe, Takahiro; Fujiwara, Kazuo; Ikeguchi, Masamichi

    2014-06-01

    Chain collapse and secondary structure formation are frequently observed during the early stages of protein folding. Is the chain collapse brought about by interactions between secondary structure units or is it due to polymer behavior in a poor solvent (coil-globule transition)? To answer this question, we measured small-angle X-ray scattering for a series of β-lactoglobulin mutants under conditions in which they assume a partially folded state analogous to the folding intermediates. Mutants that were designed to disrupt the secondary structure units showed the gyration radii similar to that of the wild type protein, indicating that chain collapse is due to coil-globule transitions. PMID:25100622

  4. Dynamics of beta and proliferating cell nuclear antigen sliding clamps in traversing DNA secondary structure.

    PubMed

    Yao, N; Hurwitz, J; O'Donnell, M

    2000-01-14

    Chromosomal replicases of cellular organisms utilize a ring shaped protein that encircles DNA as a mobile tether for high processivity in DNA synthesis. These "sliding clamps" have sufficiently large linear diameters to encircle duplex DNA and are perhaps even large enough to slide over certain DNA secondary structural elements. This report examines the Escherichia coli beta and human proliferating cell nuclear antigen clamps for their ability to slide over various DNA secondary structures. The results show that these clamps are capable of traversing a 13-nucleotide ssDNA loop, a 4-base pair stem-loop, a 4-nucleotide 5' tail, and a 15-mer bubble within the duplex. However, upon increasing the size of these structures (20-nucleotide loop, 12-base pair stem-loop, 28-nucleotide 5' tail, and 20-nucleotide bubble) the sliding motion of the beta and proliferating cell nuclear antigen over these elements is halted. Studies of the E. coli replicase, DNA polymerase III holoenzyme, in chain elongation with the beta clamp demonstrate that upon encounter with an oligonucleotide annealed in its path, it traverses the duplex and resumes synthesis on the 3' terminus of the oligonucleotide. This sliding and resumption of synthesis occurs even when the oligonucleotide contains a secondary structure element, provided the beta clamp can traverse the structure. However, upon encounter with a downstream oligonucleotide containing a large internal secondary structure, the holoenzyme clears the obstacle by strand displacing the oligonucleotide from the template. Implications of these protein dynamics to DNA transactions are discussed. PMID:10625694

  5. RNAmutants: a web server to explore the mutational landscape of RNA secondary structures.

    PubMed

    Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

    2009-07-01

    The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics--indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

  6. Fabrication of experimental three-meter space telescope primary and secondary mirror support structure

    NASA Technical Reports Server (NTRS)

    Mishler, H. W.

    1974-01-01

    The fabrication of prototype titanium alloy primary and secondary mirror support structures for a proposed experimental three-meter space telescope is discussed. The structure was fabricated entirely of Ti-6Al-4V tubing and plate. Fabrication included the development of procedures including welding, forming, and machining. Most of the structures was fabricated by gas-shielding tungsten-arc (GTA) welding with several major components fabricated by high frequency resistance (HFR) welding.

  7. New charge-bearing amino acid residues that promote β-sheet secondary structure.

    PubMed

    Maynard, Stacy J; Almeida, Aaron M; Yoshimi, Yasuharu; Gellman, Samuel H

    2014-11-26

    Proteinogenic amino acid residues that promote β-sheet secondary structure are hydrophobic (e.g., Ile or Val) or only moderately polar (e.g., Thr). The design of peptides intended to display β-sheet secondary structure in water typically requires one set of residues to ensure conformational stability and an orthogonal set, with charged side chains, to ensure aqueous solubility and discourage self-association. Here we describe new amino acids that manifest substantial β-sheet propensity, by virtue of β-branching, and also bear an ionizable group in the side chain. PMID:25393077

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

    PubMed

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

    2015-09-01

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

  9. Secondary Structural Change Can Occur Diffusely and Not Modularly during Protein Folding and Unfolding Reactions.

    PubMed

    Malhotra, Pooja; Udgaonkar, Jayant B

    2016-05-11

    A major goal of protein folding studies is to understand the structural basis of the coupling between stabilizing interactions, which leads to cooperative conformational change. The goal is challenging because of the difficulty in simultaneously measuring global cooperativity by determining population distributions of the conformations present, and the structures of these conformations. Here, hydrogen exchange (HX) into the small protein monellin was carried out under conditions where structure-opening is rate limiting for most backbone amide sites. Detection by mass spectrometry allowed characterization of not only segment-specific structure-opening rates but also the cooperativity of unfolding of the different secondary structural segments of the protein. The segment-specific pattern of HX reveals that the backbone hydrogen-bonding network disassembles in a structurally diffuse, asynchronous manner. A comparison of the site-specific transient opening rates of secondary and tertiary structure in the protein provides a structural rationale for the observation that unfolding is hierarchical and describable by exponential kinetics, despite being diffuse. Since unfolding was studied in native conditions, the sequence of events during folding in the same conditions will be the reverse of the sequence of events observed during unfolding. Hence, the formation of secondary structural units during folding would also occur in a non-cooperative, diffuse, and asynchronous manner. PMID:27093885

  10. Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction

    PubMed Central

    De Leonardis, Eleonora; Lutz, Benjamin; Ratz, Sebastian; Cocco, Simona; Monasson, Rémi; Schug, Alexander; Weigt, Martin

    2015-01-01

    Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via Direct-Coupling Analysis to detect nucleotide-nucleotide contacts. For a representative set of riboswitches, we show that the results of Direct-Coupling Analysis in combination with a generalized Nussinov algorithm systematically improve the results of RNA secondary structure prediction beyond traditional covariance approaches based on mutual information. Even more importantly, we show that the results of Direct-Coupling Analysis are enriched in tertiary structure contacts. By integrating these predictions into molecular modeling tools, systematically improved tertiary structure predictions can be obtained, as compared to using secondary structure information alone. PMID:26420827

  11. Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data.

    PubMed Central

    Quigley, G J; Gehrke, L; Roth, D A; Auron, P E

    1984-01-01

    We present a computer-aided method for determining nucleic acid secondary structure. The method utilizes a program which has the capability to filter matrix diagonal data on the basis of diagonal length, stabilization energy, and chemical and enzymatic data. The program also allows the user to assign selected regions of the structure as uniquely single-stranded or paired, and to filter out "trade-off" structures on the basis of such pairing. In order to demonstrate the utility of the program we present a preliminary secondary structure for the 3' end of alfalfa mosaic virus RNA 4 (AMV-4 RNA). This structure is based on an analysis which includes the use of in vitro partial enzymatic digestion of the RNA. Images PMID:6320093

  12. The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective

    PubMed Central

    Rivas, Elena

    2013-01-01

    Any method for RNA secondary structure prediction is determined by four ingredients. The architecture is the choice of features implemented by the model (such as stacked basepairs, loop length distributions, etc.). The architecture determines the number of parameters in the model. The scoring scheme is the nature of those parameters (whether thermodynamic, probabilistic, or weights). The parameterization stands for the specific values assigned to the parameters. These three ingredients are referred to as “the model.” The fourth ingredient is the folding algorithms used to predict plausible secondary structures given the model and the sequence of a structural RNA. Here, I make several unifying observations drawn from looking at more than 40 years of methods for RNA secondary structure prediction in the light of this classification. As a final observation, there seems to be a performance ceiling that affects all methods with complex architectures, a ceiling that impacts all scoring schemes with remarkable similarity. This suggests that modeling RNA secondary structure by using intrinsic sequence-based plausible “foldability” will require the incorporation of other forms of information in order to constrain the folding space and to improve prediction accuracy. This could give an advantage to probabilistic scoring systems since a probabilistic framework is a natural platform to incorporate different sources of information into one single inference problem. PMID:23695796

  13. Orientation Determination of Protein Helical Secondary Structure Using Linear and Nonlinear Vibrational Spectroscopy

    PubMed Central

    Nguyen, Khoi Tan; Le Clair, Stéphanie V.; Ye, Shuji; Chen, Zhan

    2009-01-01

    In this paper, we systematically presented the orientation determination of protein helical secondary structures using vibrational spectroscopic methods, particularly the nonlinear Sum Frequency Generation (SFG) vibrational spectroscopy, along with linear vibrational spectroscopic techniques such as infrared spectroscopy and Raman scattering. SFG amide I signals can be collected using different polarization combinations of the input laser beams and output signal beam to measure the second order nonlinear optical susceptibility components of the helical amide I modes, which are related to their molecular hyperpolarizability elements through the orientation distribution of these helices. The molecular hyperpolarizability elements of amide I modes of a helix can be calculated based on the infrared transition dipole moment and Raman polarizability tensor of the helix; these quantities are determined by using the bond additivity model to sum over the individual infrared dipole transition moments and Raman polarizability tensors, respectively, of the peptide units (or the amino acid residues). The computed overall infrared transition dipole moment and Raman polarizability tensor of a helix can be validated by experimental data using polarized infrared and polarized Raman spectroscopy on samples with well-aligned helical structures. From the deduced SFG hyperpolarizability elements and measured SFG second order nonlinear susceptibility components, orientation information regarding helical structures can be determined. Even though such orientation information can also be measured using polarized infrared or polarized Raman amide I signals, SFG has a much lower detection limit, which can be used to study the orientation of a helix when its surface coverage is much lower than a monolayer. In addition, the combination of different vibrational spectroscopic techniques, e.g., SFG and Attenuated Total Reflectance – Fourier Transform Infrared spectroscopy, provides more

  14. The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants.

    PubMed

    Mai, J C; Coleman, A W

    1997-03-01

    Sequences of the Internal Transcribed Spacer 2 (ITS-2) regions of the nuclear rDNA repeats from 111 organisms of the family Volvocaceae (Chlorophyta) and unicellular organisms of the Volvocales, including Chlamydomonas reinhardtii, were determined. The use of thermodynamic energy optimization to generate secondary structures and phylogenetic comparative analysis of the spacer regions revealed a common secondary structure that is conserved despite wide intra- and interfamilial primary sequence divergence. The existence of this conserved higher-order structure is supported by the presence of numerous compensating basepair changes as well as by an evolutionary history of insertions and deletions that nevertheless maintains major aspects of the overall structure. Furthermore, this general structure is preserved across broad phylogenetic lines, as it is observed in the ITS-2s of other chlorophytes, including flowering plants; previous reports of common ITS-2 secondary structures in other eukaryotes were restricted to the order level. The reported ITS-2 structure possesses important conserved structural motifs which may help to mediate cleavages in the ITS-2 that occur during rRNA transcript processing. Their recognition can guide further studies of eukaryotic rRNA processing, and their application to sequence alignments may contribute significantly to the value of ITS-2 sequences in phylogenetic analyses at several taxonomic levels, but particularly in characterizing populations and species. PMID:9060392

  15. Synthesis and characterization of nitroaromatic peptoids: fine tuning peptoid secondary structure through monomer position and functionality.

    PubMed

    Fowler, Sarah A; Luechapanichkul, Rinrada; Blackwell, Helen E

    2009-02-20

    N-substituted glycine oligomers, or peptoids, have emerged as an important class of foldamers for the study of biomolecular interactions and for potential use as therapeutic agents. However, the design of peptoids with well-defined conformations a priori remains a formidable challenge. New approaches are required to address this problem, and the systematic study of the role of individual monomer units in the global peptoid folding process represents one strategy. Here, we report our efforts toward this approach through the design, synthesis, and characterization of peptoids containing nitroaromatic monomer units. This work required the synthesis of a new chiral amine building block, (S)-1-(2-nitrophenyl)ethanamine (s2ne), which could be readily installed into peptoids using standard solid-phase peptoid synthesis techniques. We designed a series of peptoid nonamers that allowed us to probe the effects of this relatively electron-deficient and sterically encumbered alpha-chiral side chain on peptoid structure, namely, the peptoid threaded loop and helix. Circular dichroism spectroscopy of the peptoids revealed that the nitroaromatic monomer has a significant effect on peptoid secondary structure. Specifically, the threaded loop structure was disrupted in a nonamer containing alternating N-(S)-1-phenylethylglycine (Nspe) and Ns2ne monomers, and the major conformation was helical instead. Indeed, placement of a single Ns2ne at the N-terminal position of (Nspe)(9) resulted in a destabilized form of the threaded loop structure relative to the homononamer (Nspe)(9). Conversely, we observed that incorporation of N-(S)-1-(4-nitrophenyl)ethylglycine (Nsnp, a p-nitro monomer) at the N-terminal position stabilized the threaded loop structure relative to (Nspe)(9). Additional experiments revealed that nitroaromatic side chains can influence peptoid nonamer folding by modulating the strength of key intramolecular hydrogen bonds in the peptoid threaded loop structure. Steric

  16. [Establishment of industry promotion technology system in Chinese medicine secondary exploitation based on "component structure theory"].

    PubMed

    Cheng, Xu-Dong; Feng, Liang; Zhang, Ming-Hua; Gu, Jun-Fei; Jia, Xiao-Bin

    2014-10-01

    The purpose of the secondary exploitation of Chinese medicine is to improve the quality of Chinese medicine products, enhance core competitiveness, for better use in clinical practice, and more effectively solve the patient suffering. Herbs, extraction, separation, refreshing, preparation and quality control are all involved in the industry promotion of Chinese medicine secondary exploitation of industrial production. The Chinese medicine quality improvement and industry promotion could be realized with the whole process of process optimization, quality control, overall processes improvement. Based on the "component structure theory", "multi-dimensional structure & process dynamic quality control system" and systematic and holistic character of Chinese medicine, impacts of whole process were discussed. Technology systems of Chinese medicine industry promotion was built to provide theoretical basis for improving the quality and efficacy of the secondary development of traditional Chinese medicine products. PMID:25751964

  17. Reactivity of molybdovanadophosphoric acids: Influence of the presence of vanadium in the primary and secondary structure

    SciTech Connect

    Casarini, D.; Centi, G.; Lena, V.; Tvaruzkova, Z. ); Jiru, P. )

    1993-10-01

    The catalytic behavior in butadiene and n-butane oxidation of molybdovanadophosphoric acids with vanadium localized inside the primary (oxoanion) and/or the secondary structure is reported. The samples are characterized by infrared, [sup 31]P-NMR, [sup 51]V-NMR, and UV-visible diffuse reflectance spectroscopies in order to obtain information on the nature and localization of vanadium in the samples before reaction and the possible changes occurring during the course of the catalytic reaction. In particular, it is shown that vanadium localized initially in the secondary structure can exchange with the molybdenum atoms of the oxoanion during the catalytic reaction. Introduction of vanadium in the molybdophosphoric acid structure enhances the selective formation of maleic anhydride from the butadiene when vanadium is present both inside the oxoanion or localized in the secondary structure (before the catalytic tests), but the maximum in catalytic performance is found for different amounts of vanadium, depending on where the vanadium is localized initially. However, when present in the secondary structure, vanadium also has a negative influence on the activity of the heteropoly acid. On the contrary, in n-butane oxidation, the presence of vanadium enhances the rate of alkane activation due to the different rate-determining step. The presence of V ions also affects the maximum selectivity and yield to maleic anhydride from butane. V ions in the secondary structure are more selective at low conversion, while V ions inside the oxoanion are more selective at higher conversions and thus allow better maximum yields to maleic anhydride. 40 refs., 11 figs., 2 tabs.

  18. A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data

    PubMed Central

    Sturm, Marc; Quinten, Sascha; Huber, Christian G.; Kohlbacher, Oliver

    2007-01-01

    We propose a new model for predicting the retention time of oligonucleotides. The model is based on ν support vector regression using features derived from base sequence and predicted secondary structure of oligonucleotides. Because of the secondary structure information, the model is applicable even at relatively low temperatures where the secondary structure is not suppressed by thermal denaturing. This makes the prediction of oligonucleotide retention time for arbitrary temperatures possible, provided that the target temperature lies within the temperature range of the training data. We describe different possibilities of feature calculation from base sequence and secondary structure, present the results and compare our model to existing models. PMID:17567619

  19. Protein-associated water and secondary structure effect removal of blood proteins from metallic substrates.

    PubMed

    Anand, Gaurav; Zhang, Fuming; Linhardt, Robert J; Belfort, Georges

    2011-03-01

    behaved similarly on addition of the alkaline-surfactant cleaning solution, in that platinum and gold exhibited an increase, while tungsten, titanium, and stainless steel showed a decrease in weight. According to dissipation measurements with the QCM-D, the adsorbed layer for platinum and gold was rigid, while that for the tungsten, titanium, and stainless steel was much more flexible. The removal efficiency of adsorbed-protein by alkaline solution of SDS depended on the water content of the adsorbed layers for W, Ti, and SS, while for Pt and Au, it depended on secondary structural content. When protein adsorption was high (Pt, Au), protein-protein interactions and protein-surface interactions were dominant and the removal of protein layers was limited. Water content of the adsorbed protein layer was the determining factor for how efficiently the layer was removed by alkaline SDS when protein adsorption was low. Hence, protein-protein and protein-surface interactions were minimal and protein structure was less perturbed in comparison with those for high protein adsorption. Secondary structural content determined the efficient removal of adsorbed protein for high adsorbed amount. PMID:21182242

  20. RNA secondary structure modeling at consistent high accuracy using differential SHAPE

    PubMed Central

    Rice, Greggory M.; Leonard, Christopher W.; Weeks, Kevin M.

    2014-01-01

    RNA secondary structure modeling is a challenging problem, and recent successes have raised the standards for accuracy, consistency, and tractability. Large increases in accuracy have been achieved by including data on reactivity toward chemical probes: Incorporation of 1M7 SHAPE reactivity data into an mfold-class algorithm results in median accuracies for base pair prediction that exceed 90%. However, a few RNA structures are modeled with significantly lower accuracy. Here, we show that incorporating differential reactivities from the NMIA and 1M6 reagents—which detect noncanonical and tertiary interactions—into prediction algorithms results in highly accurate secondary structure models for RNAs that were previously shown to be difficult to model. For these RNAs, 93% of accepted canonical base pairs were recovered in SHAPE-directed models. Discrepancies between accepted and modeled structures were small and appear to reflect genuine structural differences. Three-reagent SHAPE-directed modeling scales concisely to structurally complex RNAs to resolve the in-solution secondary structure analysis problem for many classes of RNA. PMID:24742934

  1. The Maslach Burnout Inventory: Validating Factorial Structure and Invariance across Intermediate, Secondary, and University Educators.

    ERIC Educational Resources Information Center

    Byrne, Barbara M.

    1991-01-01

    The factorial validity of the Maslach Burnout Inventory (MBI) and the equivalence of factorial measurements and structure across groups were studied for 163 intermediate-grade teachers, 162 secondary school teachers, and 218 university teachers in Canada. Reasons why the MBI may not be appropriate for university educators are discussed. (SLD)

  2. conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure.

    PubMed

    Kieslich, Chris A; Smadbeck, James; Khoury, George A; Floudas, Christodoulos A

    2016-03-28

    Accurate prediction of protein secondary structure remains a crucial step in most approaches to the protein-folding problem, yet the prediction of ordered secondary structure, specifically beta-strands, remains a challenge. We developed a consensus secondary structure prediction method, conSSert, which is based on support vector machines (SVM) and provides exceptional accuracy for the prediction of beta-strands with QE accuracy of over 0.82 and a Q2-EH of 0.86. conSSert uses as input probabilities for the three types of secondary structure (helix, strand, and coil) that are predicted by four top performing methods: PSSpred, PSIPRED, SPINE-X, and RAPTOR. conSSert was trained/tested using 4261 protein chains from PDBSelect25, and 8632 chains from PISCES. Further validation was performed using targets from CASP9, CASP10, and CASP11. Our data suggest that poor performance in strand prediction is likely a result of training bias and not solely due to the nonlocal nature of beta-sheet contacts. conSSert is freely available for noncommercial use as a webservice: http://ares.tamu.edu/conSSert/ . PMID:26928531

  3. Chinese American Post-Secondary Achievement and Attainment: A Cultural and Structural Analysis

    ERIC Educational Resources Information Center

    Pearce, Richard R.; Lin, Zeng

    2007-01-01

    In this article, the authors compare Chinese American post-secondary educational attainment with that of White Americans and, in identifying those factors that most strongly account for success, argue that commonalities exist among social structural factors, while distinct differences are evident among cultural capital factors. The article rejects…

  4. Classroom Structure and Teacher Efficacy in Serving Students with Disabilities: Differences in Elementary and Secondary Teachers

    ERIC Educational Resources Information Center

    Shippen, Margaret E.; Flores, Margaret M.; Crites, Steven A.; Patterson, DaShaunda; Ramsey, Michelle L.; Houchins, David E.; Jolivette, Kristine

    2011-01-01

    The purpose of this study was to investigate the differential classroom structure and efficacy reported by general and special educators at the elementary and secondary level. General and special educators (n = 774, return rate of 37%) from a large school district in the southeast US participated in the study. The participants completed a modified…

  5. EFFECT OF SOLVENT AND TEMPERATURE ON SECONDARY AND TERTIARY STRUCTURE OF ZEIN BY CIRCULAR DICHROISM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Circular dichroism studies were performed on various samples of commercial zein to determine how the secondary and tertiary structure changes with different solvents, temperatures or pH. It was found that alcoholic solvent type and common denaturants, such as SDS and low amounts of urea, had little...

  6. STRUCTURAL CHARACTERIZATION OF SULFONATED AZO DYES USING LIQUID SECONDARY ION MASS SPECTROMETRY/TANDEM MASS SPECTROMETRY

    EPA Science Inventory

    Eight monosulfonated and disulfonated azo dyes were analyzed using liquid secondary ion mass spectrometry/tandem mass spectrometry, in the negative ion mode, under low-energy conditions (110-150 eV). any structurally characteristic fragment ions were obtained, several of which ha...

  7. Secondary School Students' Understanding of Mathematical Induction: Structural Characteristics and the Process of Proof Construction

    ERIC Educational Resources Information Center

    Palla, Marina; Potari, Despina; Spyrou, Panagiotis

    2012-01-01

    In this study, we investigate the meaning students attribute to the structure of mathematical induction (MI) and the process of proof construction using mathematical induction in the context of a geometric recursion problem. Two hundred and thirteen 17-year-old students of an upper secondary school in Greece participated in the study. Students'…

  8. Assessing the impact of secondary structure and solvent accessibility on protein evolution.

    PubMed Central

    Goldman, N; Thorne, J L; Jones, D T

    1998-01-01

    Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution-both above and below the species level-will not be well understood until the physical constraints that affect protein evolution are identified and characterized. PMID:9584116

  9. The Turn of the Screw: An Exercise in Protein Secondary Structure

    ERIC Educational Resources Information Center

    Pikaart, Michael

    2011-01-01

    An exercise using simple paper strips to illustrate protein helical and sheet secondary structures is presented. Drawing on the rich historical context of the use of physical models in protein biochemistry by early practitioners, in particular Linus Pauling, the purpose of this activity is to cultivate in students a hands-on, intuitive sense of…

  10. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

    SciTech Connect

    Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinlzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

    2013-01-24

    The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

  11. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

    PubMed Central

    Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinIzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

    2013-01-01

    The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP–encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence. PMID:23357949

  12. Secondary flow structure in a model curved artery: 3D morphology and circulation budget analysis

    NASA Astrophysics Data System (ADS)

    Bulusu, Kartik V.; Plesniak, Michael W.

    2015-11-01

    In this study, we examined the rate of change of circulation within control regions encompassing the large-scale vortical structures associated with secondary flows, i.e. deformed Dean-, Lyne- and Wall-type (D-L-W) vortices at planar cross-sections in a 180° curved artery model (curvature ratio, 1/7). Magnetic resonance velocimetry (MRV) and particle image velocimetry (PIV) experiments were performed independently, under the same physiological inflow conditions (Womersley number, 4.2) and using Newtonian blood-analog fluids. The MRV-technique performed at Stanford University produced phase-averaged, three-dimensional velocity fields. Secondary flow field comparisons of MRV-data to PIV-data at various cross-sectional planes and inflow phases were made. A wavelet-decomposition-based approach was implemented to characterize various secondary flow morphologies. We hypothesize that the persistence and decay of arterial secondary flow vortices is intrinsically related to the influence of the out-of-plane flow, tilting, in-plane convection and diffusion-related factors within the control regions. Evaluation of these factors will elucidate secondary flow structures in arterial hemodynamics. Supported by the National Science Foundation under Grant Number CBET-0828903, and GW Center for Biomimetics and Bioinspired Engineering (COBRE). The MRV data were acquired at Stanford University in collaboration with Christopher Elkins and John Eaton.

  13. Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM

    PubMed Central

    2013-01-01

    Background Accurate secondary structure prediction provides important information to undefirstafinding the tertiary structures and thus the functions of ncRNAs. However, the accuracy of the native structure derivation of ncRNAs is still not satisfactory, especially on sequences containing pseudoknots. It is recently shown that using the abstract shapes, which retain adjacency and nesting of structural features but disregard the length details of helix and loop regions, can improve the performance of structure prediction. In this work, we use SVM-based feature selection to derive the consensus abstract shape of homologous ncRNAs and apply the predicted shape to structure prediction including pseudoknots. Results Our approach was applied to predict shapes and secondary structures on hundreds of ncRNA data sets with and without psuedoknots. The experimental results show that we can achieve 18% higher accuracy in shape prediction than the state-of-the-art consensus shape prediction tools. Using predicted shapes in structure prediction allows us to achieve approximate 29% higher sensitivity and 10% higher positive predictive value than other pseudoknot prediction tools. Conclusions Extensive analysis of RNA properties based on SVM allows us to identify important properties of sequences and structures related to their shapes. The combination of mass data analysis and SVM-based feature selection makes our approach a promising method for shape and structure prediction. The implemented tools, Knot Shape and Knot Structure are open source software and can be downloaded at: http://www.cse.msu.edu/~achawana/KnotShape. PMID:23369147

  14. Nitrogen and phosphorus addition impact soil N2O emission in a secondary tropical forest of South China

    PubMed Central

    Wang, Faming; Li, Jian; Wang, Xiaoli; Zhang, Wei; Zou, Bi; Neher, Deborah A.; Li, Zhian

    2014-01-01

    Nutrient availability greatly regulates ecosystem processes and functions of tropical forests. However, few studies have explored impacts of N addition (aN), P addition (aP) and N×P interaction on tropical forests N2O fluxes. We established an N and P addition experiment in a tropical forest to test whether: (1) N addition would increase N2O emission and nitrification, and (2) P addition would increase N2O emission and N transformations. Nitrogen and P addition had no effect on N mineralization and nitrification. Soil microbial biomass was increased following P addition in wet seasons. aN increased 39% N2O emission as compared to control (43.3 μgN2O-N m−2h−1). aP did not increase N2O emission. Overall, N2O emission was 60% greater for aNP relative to the control, but significant difference was observed only in wet seasons, when N2O emission was 78% greater for aNP relative to the control. Our results suggested that increasing N deposition will enhance soil N2O emission, and there would be N×P interaction on N2O emission in wet seasons. Given elevated N deposition in future, P addition in this tropical soil will stimulate soil microbial activities in wet seasons, which will further enhance soil N2O emission. PMID:25001013

  15. Secondary structures of rRNAs from all three domains of life.

    PubMed

    Petrov, Anton S; Bernier, Chad R; Gulen, Burak; Waterbury, Chris C; Hershkovits, Eli; Hsiao, Chiaolong; Harvey, Stephen C; Hud, Nicholas V; Fox, George E; Wartell, Roger M; Williams, Loren Dean

    2014-01-01

    Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU) 23S/28S and small subunit (SSU) 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only), Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery). Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision). PMID:24505437

  16. Secondary Structures of rRNAs from All Three Domains of Life

    PubMed Central

    Petrov, Anton S.; Bernier, Chad R.; Gulen, Burak; Waterbury, Chris C.; Hershkovits, Eli; Hsiao, Chiaolong; Harvey, Stephen C.; Hud, Nicholas V.; Fox, George E.; Wartell, Roger M.; Williams, Loren Dean

    2014-01-01

    Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU) 23S/28S and small subunit (SSU) 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only), Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery). Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision). PMID:24505437

  17. A permutation based simulated annealing algorithm to predict pseudoknotted RNA secondary structures.

    PubMed

    Tsang, Herbert H; Wiese, Kay C

    2015-01-01

    Pseudoknots are RNA tertiary structures which perform essential biological functions. This paper discusses SARNA-Predict-pk, a RNA pseudoknotted secondary structure prediction algorithm based on Simulated Annealing (SA). The research presented here extends previous work of SARNA-Predict and further examines the effect of the new algorithm to include prediction of RNA secondary structure with pseudoknots. An evaluation of the performance of SARNA-Predict-pk in terms of prediction accuracy is made via comparison with several state-of-the-art prediction algorithms using 20 individual known structures from seven RNA classes. We measured the sensitivity and specificity of nine prediction algorithms. Three of these are dynamic programming algorithms: Pseudoknot (pknotsRE), NUPACK, and pknotsRG-mfe. One is using the statistical clustering approach: Sfold and the other five are heuristic algorithms: SARNA-Predict-pk, ILM, STAR, IPknot and HotKnots algorithms. The results presented in this paper demonstrate that SARNA-Predict-pk can out-perform other state-of-the-art algorithms in terms of prediction accuracy. This supports the use of the proposed method on pseudoknotted RNA secondary structure prediction of other known structures. PMID:26558299

  18. Protein secondary-structure description with a coarse-grained model.

    PubMed

    Kneller, Gerald R; Hinsen, Konrad

    2015-07-01

    A coarse-grained geometrical model for protein secondary-structure description and analysis is presented which uses only the positions of the C(α) atoms. A space curve connecting these positions by piecewise polynomial interpolation is constructed and the folding of the protein backbone is described by a succession of screw motions linking the Frenet frames at consecutive C(α) positions. Using the ASTRAL subset of the SCOPe database of protein structures, thresholds are derived for the screw parameters of secondary-structure elements and demonstrate that the latter can be reliably assigned on the basis of a C(α) model. For this purpose, a comparative study with the widely used DSSP (Define Secondary Structure of Proteins) algorithm was performed and it was shown that the parameter distribution corresponding to the ensemble of all pure C(α) structures in the RCSB Protein Data Bank matches that of the ASTRAL database. It is expected that this approach will be useful in the development of structure-refinement techniques for low-resolution data. PMID:26143913

  19. An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.

    PubMed

    Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

    2016-01-01

    Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer. PMID:27499762

  20. An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures

    PubMed Central

    Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

    2016-01-01

    Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer. PMID:27499762

  1. miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure

    PubMed Central

    Sperber, Henrik; Beem, Alan; Shannon, Sandra; Jones, Ross; Banik, Pratyusha; Chen, Yu; Ku, Sherman; Varani, Gabriele; Yao, Shuyuan; Ruohola-Baker, Hannele

    2014-01-01

    microRNAs (miRNAs) are crucial for cellular development and homeostasis. In order to better understand regulation of miRNA biosynthesis, we studied cleavage of primary miRNAs by Drosha. While Drosha knockdown triggers an expected decrease of many mature miRNAs in human embryonic stem cells (hESC), a subset of miRNAs are not reduced. Statistical analysis of miRNA secondary structure and fold change of expression in response to Drosha knockdown showed that absence of mismatches in the central region of the hairpin, 5 and 9–12 nt from the Drosha cutting site conferred decreased sensitivity to Drosha knockdown. This suggests that, when limiting, Drosha processes miRNAs without mismatches more efficiently than mismatched miRNAs. This is important because Drosha expression changes over cellular development and the fold change of expression for miRNAs with mismatches in the central region correlates with Drosha levels. To examine the biochemical relationship directly, we overexpressed structural variants of miRNA-145, miRNA-137, miRNA-9, and miRNA-200b in HeLa cells with and without Drosha knockdown; for these miRNAs, elimination of mismatches in the central region increased, and addition of mismatches decreased their expression in an in vitro assay and in cells with low Drosha expression. Change in Drosha expression can be a biologically relevant mechanism by which eukaryotic cells control miRNA profiles. This phenomenon may explain the impact of point mutations outside the seed region of certain miRNAs. PMID:24677349

  2. Male secondary sexual structures and the systematics of the Thereus oppia species group (Lepidoptera, Lycaenidae, Eumaeini)

    PubMed Central

    Robbins, Robert K.; Heredia, María Dolores; Busby, Robert C.

    2015-01-01

    Abstract The Thereus oppia species group includes species with and without a scent pad, which is a histologically and morphologically characterized male secondary sexual structure on the dorsal surface of the forewing. To assess the hypothesis that these structures are lost evolutionarily, but not regained (Dollo’s Law), the taxonomy of this species group is revised. Thereus lomalarga sp. n., and Thereus brocki sp. n., are described. Diagnostic traits, especially male secondary structures, within the Thereus oppia species group are illustrated. Distributional and biological information is summarized for each species. Three species have been reared, and the caterpillars eat Loranthaceae. An inferred phylogeny is consistent with the hypothesis that scent pads in the Thereus oppia species group have been lost evolutionarily twice (in allopatry), and not re-gained. PMID:26448715

  3. Secondary Structural Preferences of Some Antibacterial Cyclooctapeptides in the Presence of Calcium(II)

    PubMed Central

    Stevens, Tarshona; McNeil, Nykia; Lin, Xiuli; Ngu-Schwemlein, Maria

    2012-01-01

    The purpose of this study is to understand the interactions of some antibacterial cationic amphipathic cyclooctapeptides with calcium(II) and their secondary structural preferences. The thermodynamic parameters associated with calcium(II) interactions, between the antibacterial active cyclooctapeptides (COP 1–6) and those that did not exhibit significant activities (COP 7–9), were studied by isothermal titration calorimetry. Calcium(II) binding in the absence and presence of micellar dodecylphosphocholine (DPC), a membrane mimicking detergent, was conducted by circular dichroism (CD). Both groups of cyclopeptides showed weak binding affinities for calcium(II) (Kb ca. 10−3 M−1). However, CD data showed that the antimicrobial peptides COP 1–6 adopted a twisted beta-sheet structure (positive CD absorption band at ca. 203 nm) in the presence of calcium(II) in micellar DPC. In contrast, COP 7–9, which lacked antibacterial activity, adopted a different conformational structure (negative CD absorption band at ca. 203 nm). These results indicate that these cyclopeptides could adopt secondary structural preferences in the presence of calcium(II) amidst a hydrophobic environment to elicit their antibacterial activity. These findings could be useful in facilitating the design of cyclopeptide derivatives that can adopt this beta-sheet-like secondary structure and, thereby, provide a useful molecular template for crafting antibacterial compounds. PMID:25379288

  4. Rigidity of poly-L-glutamic acid scaffolds: Influence of secondary and supramolecular structure

    DOE PAGESBeta

    Nickels, Jonathan D.; Perticaroli, Stefania; Ehlers, Georg; Feygenson, Mikhail; Sokolov, Alexei P.

    2015-03-06

    Poly-L-glutamic acid (PGA) is a widely used biomaterial, with applications ranging from drug delivery and biological glues to food products and as a tissue engineering scaffold. A biodegradable material with flexible conjugation functional groups, tunable secondary structure, and mechanical properties, PGA has potential as a tunable matrix material in mechanobiology. Some recent studies in proteins connecting dynamics, nanometer length scale rigidity, and secondary structure suggest a new point of view from which to analyze and develop this promising material. Our paper characterizes the structure, topology, and rigidity properties of PGA prepared with different molecular weights and secondary structures through variousmore » techniques including scanning electron microscopy, FTIR, light, and neutron scattering spectroscopy. On the length scale of a few nanometers, rigidity is determined by hydrogen bonding interactions in the presence of neutral species and by electrostatic interactions when the polypeptide is negatively charged. Finally, when probed over hundreds of nanometers, the rigidity of these materials is modified by long range intermolecular interactions that are introduced by the supramolecular structure.« less

  5. Rigidity of poly-L-glutamic acid scaffolds: Influence of secondary and supramolecular structure.

    PubMed

    Nickels, Jonathan D; Perticaroli, Stefania; Ehlers, Georg; Feygenson, Mikhail; Sokolov, Alexei P

    2015-09-01

    Poly-l-glutamic acid (PGA) is a widely used biomaterial, with applications ranging from drug delivery and biological glues to food products and as a tissue engineering scaffold. A biodegradable material with flexible conjugation functional groups, tunable secondary structure, and mechanical properties, PGA has potential as a tunable matrix material in mechanobiology. Recent studies in proteins connecting dynamics, nanometer length scale rigidity, and secondary structure suggest a new point of view from which to analyze and develop this promising material. We have characterized the structure, topology, and rigidity properties of PGA prepared with different molecular weights and secondary structures through various techniques including scanning electron microscopy, FTIR, light, and neutron scattering spectroscopy. On the length scale of a few nanometers, rigidity is determined by hydrogen bonding interactions in the presence of neutral species and by electrostatic interactions when the polypeptide is negatively charged. When probed over hundreds of nanometers, the rigidity of these materials is modified by long range intermolecular interactions that are introduced by the supramolecular structure. PMID:25690698

  6. Conserved RNA secondary structures and long-range interactions in hepatitis C viruses.

    PubMed

    Fricke, Markus; Dünnes, Nadia; Zayas, Margarita; Bartenschlager, Ralf; Niepmann, Michael; Marz, Manja

    2015-07-01

    Hepatitis C virus (HCV) is a hepatotropic virus with a plus-strand RNA genome of ∼9.600 nt. Due to error-prone replication by its RNA-dependent RNA polymerase (RdRp) residing in nonstructural protein 5B (NS5B), HCV isolates are grouped into seven genotypes with several subtypes. By using whole-genome sequences of 106 HCV isolates and secondary structure alignments of the plus-strand genome and its minus-strand replication intermediate, we established refined secondary structures of the 5' untranslated region (UTR), the cis-acting replication element (CRE) in NS5B, and the 3' UTR. We propose an alternative structure in the 5' UTR, conserved secondary structures of 5B stem-loop (SL)1 and 5BSL2, and four possible structures of the X-tail at the very 3' end of the HCV genome. We predict several previously unknown long-range interactions, most importantly a possible circularization interaction between distinct elements in the 5' and 3' UTR, reminiscent of the cyclization elements of the related flaviviruses. Based on analogy to these viruses, we propose that the 5'-3' UTR base-pairing in the HCV genome might play an important role in viral RNA replication. These results may have important implications for our understanding of the nature of the cis-acting RNA elements in the HCV genome and their possible role in regulating the mutually exclusive processes of viral RNA translation and replication. PMID:25964384

  7. Rigidity of poly-L-glutamic acid scaffolds: Influence of secondary and supramolecular structure

    SciTech Connect

    Nickels, Jonathan D.; Perticaroli, Stefania; Ehlers, Georg; Feygenson, Mikhail; Sokolov, Alexei P.

    2015-03-06

    Poly-L-glutamic acid (PGA) is a widely used biomaterial, with applications ranging from drug delivery and biological glues to food products and as a tissue engineering scaffold. A biodegradable material with flexible conjugation functional groups, tunable secondary structure, and mechanical properties, PGA has potential as a tunable matrix material in mechanobiology. Some recent studies in proteins connecting dynamics, nanometer length scale rigidity, and secondary structure suggest a new point of view from which to analyze and develop this promising material. Our paper characterizes the structure, topology, and rigidity properties of PGA prepared with different molecular weights and secondary structures through various techniques including scanning electron microscopy, FTIR, light, and neutron scattering spectroscopy. On the length scale of a few nanometers, rigidity is determined by hydrogen bonding interactions in the presence of neutral species and by electrostatic interactions when the polypeptide is negatively charged. Finally, when probed over hundreds of nanometers, the rigidity of these materials is modified by long range intermolecular interactions that are introduced by the supramolecular structure.

  8. Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera

    PubMed Central

    2008-01-01

    Background The cytoplasmic ribosomal small subunit (SSU, 18S) ribosomal RNA (rRNA) is the most frequently-used gene for molecular phylogenetic studies. However, information regarding its secondary structure is neglected in most phylogenetic analyses. Incorporation of this information is essential in order to apply specific rRNA evolutionary models to overcome the problem of co-evolution of paired sites, which violates the basic assumption of the independent evolution of sites made by most phylogenetic methods. Information about secondary structure also supports the process of aligning rRNA sequences across taxa. Both aspects have been shown to increase the accuracy of phylogenetic reconstructions within various taxa. Here, we explore SSU rRNA secondary structures from the three extant classes of Phylum Porifera (Grant, 1836), a pivotal, but largely unresolved taxon of early branching Metazoa. This is the first phylogenetic study of poriferan SSU rRNA data to date that includes detailed comparative secondary structure information for all three sponge classes. Results We found base compositional and structural differences in SSU rRNA among Demospongiae, Hexactinellida (glass sponges) and Calcarea (calcareous sponges). We showed that analyses of primary rRNA sequences, including secondary structure-specific evolutionary models, in combination with reconstruction of the evolution of unusual structural features, reveal a substantial amount of additional information. Of special note was the finding that the gene tree topologies of marine haplosclerid demosponges, which are inconsistent with the current morphology-based classification, are supported by our reconstructed evolution of secondary structure features. Therefore, these features can provide alternative support for sequence-based topologies and give insights into the evolution of the molecule itself. To encourage and facilitate the application of rRNA models in phylogenetics of early metazoans, we present 52 SSU r

  9. Review: Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants

    PubMed Central

    Silverman, Ian M.; Li, Fan; Gregory, Brian D.

    2014-01-01

    The eukaryotic transcriptome is regulated both transcriptionally and post-transcriptionally. Transcriptional control was the major focus of early research efforts, while more recently post-transcriptional mechanisms have gained recognition for their significant regulatory importance. At the heart of post-transcriptional regulatory pathways are cis- and trans-acting features and factors including RNA secondary structure as well as RNA-binding proteins and their recognition sites on target RNAs. Recent advances in genomic methodologies have significantly improved our understanding of both RNA secondary structure and RNA-binding proteins and their regulatory effects within the eukaryotic transcriptome. In this review, we focus specifically on the collection of these regulatory moieties in plant transcriptomes. We describe the approaches for studying RNA secondary structure and RNA-protein interaction sites, with an emphasis on recent methodological advances that produce transcriptome-wide datasets. We discuss how these methods that include genome-wide RNA secondary structure determination and RNA-protein interaction site mapping are significantly improving our understanding of the functions of these two elements in post-transcriptional regulation. Finally, we delineate the need for additional genome-wide studies of RNA secondary structure and RNA-protein interactions in plants. PMID:23498863

  10. An atomic view of additive mutational effects in a protein structure

    SciTech Connect

    Skinner, M.M.; Terwilliger, T.C.

    1996-04-01

    Substitution of a single amino acid in a protein will often lead to substantial changes in properties. If these properties could be altered in a rational way then proteins could be readily generated with functions tailored to specific uses. When amino acid substitutions are made at well-separated locations in a single protein, their effects are generally additive. Additivity of effects of amino acid substitutions is very useful because the properties of proteins with any combination of substitutions can be inferred directly from those of the proteins with single changes. It would therefore be of considerable interest to have a means of knowing whether substitutions at a particular pair of sites in a protein are likely to lead to additive effects. The structural basis for additivity of effects of mutations on protein function was examined by determining crystal structures of single and double mutants in the hydrophobic core of gene V protein. Structural effects of mutations were found to be cumulative when two mutations were made in a single protein. Additivity occurs in this case because the regions structurally affected by mutations at the two sites do not overlap even though the sites are separated by only 9 {angstrom}. Structural distortions induced by mutations in gene V protein decrease rapidly, but not isotropically, with distance from the site of mutation. It is anticipated that cases where structural and functional effects of mutations will be additive could be identified simply by examining whether the regions structurally affected by each component mutation overlap.

  11. Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides

    NASA Astrophysics Data System (ADS)

    Monticelli, Luca; Simões, Carlos; Belvisi, Laura; Colombo, Giorgio

    2006-04-01

    Electrostatic interactions play a fundamental role in determining the structure and dynamics of biomolecules in solution. However the accurate representation of electrostatics in classical mechanics based simulation approaches such as molecular dynamics (MD) is a challenging task. Given the growing importance that MD simulation methods are taking on in the study of protein folding, protein stability and dynamics, and in structure prediction and design projects, it is important to evaluate the influence that different electrostatic schemes have on the results of MD simulations. In this paper we performed long timescale simulations (500 ns) of two peptides, beta3 and RN24 forming different secondary structures, using for each peptide four different electrostatic schemes (namely PME, reaction field correction, and cut-off schemes with and without neutralizing counterions) for a total of eight 500 ns long MD runs. The structural and conformational features of each peptide under the different conditions were evaluated in terms of the time dependence of the flexibility, secondary structure evolution, hydrogen-bonding patterns, and several other structural parameters. The degree of sampling for each simulation as a function of the electrostatic scheme was also critically evaluated. Our results suggest that, while in the case of the short peptide RN24 the performances of the four methods are comparable, PME and RF schemes perform better in maintaining the structure close to the native one for the β-sheet peptide beta3, in which long range contacts are mostly responsible for the definition of the native structure.

  12. Sizing up long non-coding RNAs: do lncRNAs have secondary and tertiary structure?

    PubMed

    Novikova, Irina V; Hennelly, Scott P; Sanbonmatsu, Karissa Y

    2012-01-01

    Long noncoding RNAs (lncRNAs) play a key role in many important areas of epigenetics, stem cell biology, cancer, signaling and brain function. This emerging class of RNAs constitutes a large fraction of the transcriptome, with thousands of new lncRNAs reported each year. The molecular mechanisms of these RNAs are not well understood. Currently, very little structural data exist. We review the available lncRNA sequence and secondary structure data. Since almost no tertiary information is available for lncRNAs, we review crystallographic structures for other RNA systems and discuss the possibilities for lncRNAs in the context of existing constraints. PMID:23267412

  13. 3S: shotgun secondary structure determination of long non-coding RNAs.

    PubMed

    Novikova, Irina V; Dharap, Ashutosh; Hennelly, Scott P; Sanbonmatsu, Karissa Y

    2013-09-15

    Long non-coding RNAs (lncRNAs) have emerged as an important class of RNAs playing key roles in development, disease and epigenetics. Knowledge of lncRNA structure may be critical in understanding function for many lncRNA systems. Due to the enormous number of possible folds for these sequences, secondary structure determination presents a significant challenge, both experimentally and computationally. Here, we present a new strategy capable of determining the RNA secondary structure in the wet lab without significant reliance on computational predictions. First, we chemically probe the entire lncRNA. Next, using a shotgun approach, we divide the RNA into overlapping fragments and probe these fragments. We then compare probing profiles of fragments with the profiles of the full RNA and identify similarities. Sequence regions with profiles that are similar in the fragment and full-length transcript possess only base pairing partners within the fragment. Thus, by experimentally folding smaller and smaller fragments of the full RNA and probing these chemically, we are able to isolate modular sub-domains, dramatically reducing the number of possible folds. The method also eliminates the possibility of pseudoknots within a modular sub-domain. The 3S technique is ideally suited for lncRNAs because it is designed for long RNA sequences. The 3S-determined secondary structure of a specific lncRNA in one species (e.g., human) enables searches for instances of the same lncRNA in other species. PMID:23927838

  14. Determination of Protein Secondary Structure from Infrared Spectra Using Partial Least-Squares Regression.

    PubMed

    Wilcox, Kieaibi E; Blanch, Ewan W; Doig, Andrew J

    2016-07-12

    Infrared (IR) spectra contain substantial information about protein structure. This has previously most often been exploited by using known band assignments. Here, we convert spectral intensities in bins within Amide I and II regions to vectors and apply machine learning methods to determine protein secondary structure. Partial least squares was performed on spectra of 90 proteins in H2O. After preprocessing and removal of outliers, 84 proteins were used for this work. Standard normal variate and second-derivative preprocessing methods on the combined Amide I and II data generally gave the best performance, with root-mean-square values for prediction of ∼12% for α-helix, ∼7% for β-sheet, 7% for antiparallel β-sheet, and ∼8% for other conformations. Analysis of Fourier transform infrared (FTIR) spectra of 16 proteins in D2O showed that secondary structure determination was slightly poorer than in H2O. Interval partial least squares was used to identify the critical regions within spectra for secondary structure prediction and showed that the sides of bands were most valuable, rather than their peak maxima. In conclusion, we have shown that multivariate analysis of protein FTIR spectra can give α-helix, β-sheet, other, and antiparallel β-sheet contents with good accuracy, comparable to that of circular dichroism, which is widely used for this purpose. PMID:27322779

  15. Two-photon circular dichroism of molecular structures simulating L-tryptophan residues in proteins with secondary structures

    NASA Astrophysics Data System (ADS)

    Vesga, Yuly; Diaz, Carlos; Higgs, Mary; Hernandez, Florencio E.

    2014-05-01

    Herein, we report on the calculation and the comparative analysis of the theoretical two-photon circular dichroism (TPCD) spectra of L-tryptophan (Trp) residues in proteins with secondary structures (α-helix, β-strand and random coil) conformation, down to the far-UV region (FUV). The examination of the TPCD spectra of the different conformers in each configuration reveals distinctive fingerprints in the FUV, a dark spectral region for electronic circular dichroism (ECD). Our results show the potential of FUV-TPCD to identify and study protein structures in a region never assessed before but filled with important structural information.

  16. Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS)☟

    PubMed Central

    Xin, Dongyue; Ko, Eunhwa; Perez, Lisa M.; Ioerger, Thomas R.; Burgess, Kevin

    2013-01-01

    Peptide mimics that display amino acid side-chains on semi-rigid scaffolds (not peptide polyamides) can be referred to as minimalist mimics. Accessible conformations of these scaffolds may overlay with secondary structures giving, for example, “minimalist helical mimics”. It is difficult for researchers who want to apply minimalist mimics to decide which one to use because there is no widely accepted protocol for calibrating how closely these compounds mimic secondary structures. Moreover, it is also difficult for potential practitioners to evaluate which ideal minimalist helical mimics are preferred for a particular set of side-chains. For instance, what mimic presents i, i+4, i+7 side-chains in orientations that best resemble an ideal α-helix, and is a different mimic required for a i, i+3, i+7 helical combination? This article describes a protocol for fitting each member of an array of accessible scaffold conformations on secondary structures. The protocol involves: (i) use quenched molecular dynamics (QMD) to generate an ensemble consisting of hundreds of accessible, low energy conformers of the mimics; (ii) representation of each of these as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds;(iii) similar representation of each combination of three side-chains in each ideal secondary structure as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; and, (iv) overlay Cα and Cβ coordinates of all the conformers on all the sets of side-chain “triads” in the ideal secondary structures and express the goodness of fit in terms of root mean squared deviation (RMSD, Å) for each overlay. We refer to this process as Exploring Key Orientations on Secondary structures (EKOS). Application of this procedure reveals the relative bias of a scaffold to overlay on different secondary structures, the “side-chain correspondences” (eg i, i+4, i+7 or i, i+3

  17. Leader length and secondary structure modulate mRNA function under conditions of stress

    SciTech Connect

    Kozak, M.

    1988-07-01

    Simina virus 40-based plasmids that direct the synthesis of preproinsulin in cultured monkey cells were used to study the effects of mRNA structure on translational efficiency. Lengthening the leader sequence enhanced translation in this system. The enhancement was most obvious when an unstructured sequence (two, four, or eight copies of the oligonculeotide AGCTAAGTAAGTAAGTA) was inserted upstream from a region of deliberate secondary structure; the degree of enhancement was proportional to the number of copies of the inserted oligonucleotide. Lengthening the leader sequence on the 3' side of a stem-and-loop structure, in contrast, did not offset the potentially inhibitory effect of the hairpin structure. Both the facilitating effect of length and the inhibitory effect of secondary structure were demonstrated most easily under conditions of mRNA competition, which was brought about by an abrupt shift in the tonicity of the culture medium. These experiments suggest a simple structural basis for the long-recognized differential response of viral and cellular mRNAs to hypertonic stress. The fact that the translatability of structure-prone mRNAs varies with changes in the environment may also have general implications for gene expression in eucaryotic cells.

  18. Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures

    SciTech Connect

    Fang, Xianyang; Stagno, Jason R.; Bhandari, Yuba R.; Zuo, Xiaobing; Wang, Yun-Xing

    2015-02-01

    Whereas the structures of small to medium-sized well folded RNA molecules often can be determined by either X-ray crystallography or NMR spectroscopy, obtaining structural information for large RNAs using experimental, computational, or combined approaches remains a major interest and challenge. RNA is very sensitive to small-angle X-ray scattering (SAXS) due to high electron density along phosphate-sugar backbones, whose scattering contribution dominates SAXS intensity. For this reason, SAXS is particularly useful in obtaining global RNA structural information that outlines backbone topologies and, therefore, molecular envelopes. Such information is extremely valuable in bridging the gap between the secondary structures and three-dimensional topological structures of RNAmolecules, particularly those that have proven difficult to study using other structuredetermination methods. Here we review published results of RNA topological structures derived from SAXS data or in combination with other experimental data, as well as details on RNA sample preparation for SAXS experiments.

  19. An overview of the secondary structure of the V4 region of eukaryotic small-subunit ribosomal RNA.

    PubMed Central

    Nickrent, D L; Sargent, M L

    1991-01-01

    The V4 region of the small subunit (18S) ribosomal RNA was examined in 72 different sequences representing a broad sample eukaryotic diversity. This domain is the most variable region of the 18S rRNA molecule and ranges in length from ca. 230 to over 500 bases. Based upon comparative analysis, secondary structural models were constructed for all sequences and the resulting generalized model shows that most organisms possess seven helices for this region. The protists and two insects show from one to as many as four helices in addition to the above seven. In this report, we summarize secondary structure information presented elsewhere for the V4 region, describe the general features for helical and apical regions, and identify signature sequences useful in helix identification. Our model generally agrees with other current concepts; however, we propose modifications or alternative structures for the start of the V4 region, the large protist inserts, and the sector that may possibly contain a pseudoknot. PMID:2014163

  20. NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea.

    PubMed Central

    Aitio, H.; Annila, A.; Heikkinen, S.; Thulin, E.; Drakenberg, T.; Kilpeläinen, I.

    1999-01-01

    Calerythrin is a 20 kDa calcium-binding protein isolated from gram-positive bacterium Saccharopolyspora erythraea. Based on amino acid sequence homology, it has been suggested that calerythrin belongs to the family of invertebrate sarcoplasmic EF-hand calcium-binding proteins (SCPs), and therefore it is expected to function as a calcium buffer. NMR spectroscopy was used to obtain structural information on the protein in solution. Backbone and side chain 1H, 13C, and 15N assignments were obtained from triple resonance experiments HNCACB, HN(CO)CACB, HNCO, CC(CO)NH, and [15N]-edited TOCSY, and HCCH-TOCSY. Secondary structure was determined by using secondary chemical shifts and characteristic NOEs. In addition, backbone N-H residual dipolar couplings were measured from a spin-state selective [1H, 15N] correlation spectrum acquired from a sample dissolved in a dilute liquid crystal. Four EF-hand motifs with characteristic helix-loop-helix patterns were observed. Three of these are typical calcium-binding EF-hands, whereas site 2 is an atypical nonbinding site. The global fold of calerythrin was assessed by dipolar couplings. Measured dipolar couplings were compared with values calculated from four crystal structures of proteins with sequence homology to calerythrin. These data allowed us to recognize an overall similarity between the folds of calerythrin and sarcoplasmic calcium-binding proteins from the sandworm Nereis diversicolor and the amphioxus Branchiostoma lanceolatum. PMID:10631973

  1. A generalized threading model using integer programming that allows for secondary structure element deletion.

    PubMed

    Ellrott, Kyle; Guo, Jun-tao; Olman, Victor; Xu, Ying

    2006-01-01

    Integer programming is a combinatorial optimization method that has been successfully applied to the protein threading problem. We seek to expand the model optimized by this technique to allow for a more accurate description of protein threading. We have developed and implemented an expanded model of integer programming that has the capability to model secondary structure element deletion, which was not possible in previous version of integer programming based optimization. PMID:17503397

  2. TMPyP4, a Stabilizer of Nucleic Acid Secondary Structure, Is a Novel Acetylcholinesterase Inhibitor

    PubMed Central

    Fujiwara, Nana; Mazzola, Michael; Cai, Elizabeth; Wang, Meng; Cave, John W.

    2015-01-01

    The porphyrin compound, TMPyP4 (5,10,15,20-Tetrakis-(N-methyl-4-pyridyl)porphine), is widely used as a photosensitizer and a modulator of nucleic acid secondary structure stability. Our group recently showed in cultured cells and forebrain slice cultures that this compound can also down regulate expression of Tyrosine hydroxylase (Th), which encodes the rate-limiting enzyme in catecholamine biosynthesis, by stabilizing DNA secondary structures in the Th proximal promoter. The current study sought to establish whether treatment with TMPyP4 could modify mouse Th expression levels in vivo. Intraperitoneal administration of low TMPyP4 doses (10mg/kg), similar to those used for photosensitization, did not significantly reduce Th transcript levels in several catecholaminergic regions. Administration of a high dose (40 mg/kg), similar to those used for tumor xenograph reduction, unexpectedly induced flaccid paralysis in an age and sex-dependent manner. In vitro analyses revealed that TMPyP4, but not putative metabolites, inhibited Acetylcholinesterase activity and pre-treatment of TMPyP4 with Hemeoxygenase-2 (HO-2) rescued Acetylcholinesterase function. Age-dependent differences in HO-2 expression levels may account for some of the variable in vivo effects of high TMPyP4 doses. Together, these studies indicate that only low doses of TMPyP4, such as those typically used for photosensitization, are well tolerated in vivo. Thus, despite its widespread use in vitro, TMPyP4 is not ideal for modifying neuronal gene expression in vivo by manipulating nucleic acid secondary structure stability, which highlights the need to identify more clinically suitable compounds that can modulate nucleic acid secondary structure and gene expression. PMID:26402367

  3. Extremely Slow Dynamics of an Abiotic Helical Assembly: Unusual Relevance to the Secondary Structure of Proteins.

    PubMed

    Avinash, M B; Govindaraju, T

    2013-02-21

    Serendipitously, we found that isoleucine methylester functionalized perylenediimide 1 undergoes an extremely slow supramolecular helical assembly over a day's time. Surprisingly, heating led to irreversible chiral denaturation. However, reversible helical assembly could be achieved only in the presence of nondenatured aggregates of 1, which act as seeds. The intriguing functional relevance deduced from 1 was employed to draw parallels with the secondary structure of proteins, envisaging its plausible implications. PMID:26281870

  4. On the control of secondary carbanion structure utilising ligand effects during directed metallation.

    PubMed

    Wheatley, Andrew E H; Clayden, Jonathan; Hillier, Ian H; Campbell Smith, Alison; Vincent, Mark A; Taylor, Laurence J; Haywood, Joanna

    2012-01-01

    N,N-Diisopropyl-2-propylbenzamide 6-H undergoes lateral deprotonation by t-BuLi in the presence of the Lewis base PMDTA (N,N,N',N″,N″-pentamethyldiethylenetriamine) to give a benzyllithium 6-Li(l)·PMDTA that incorporates a trigonal planar secondary carbanion. In the solid state, the amide directing group and the PMDTA additive work together to abstract the metal ion from the deprotonated α-C of the propyl group (4.107(4) Å). A short distance of 1.376(3) Å is observed between the deprotonated carbon centre and a planar aromatic system that shows a pattern of bond lengths which contrasts with that reported for related tertiary carbanion systems. Analogous benzylic deprotonation is seen if 6-H is treated with t-BuLi in the presence of diglyme to give 6-Li(l)·DGME. X-ray crystallography now shows that the metal ion more closely approaches the tertiary carbanion (2.418(6) Å) but that the planarity of the deprotonated carbon centre and the bonding pattern in the organic anion seen in the PMDTA complex are retained. DFT analysis corroborates both the short distance between aromatic ring and carbanion centre and the unperturbed nature of aromaticity in 6-Li(l)·L (L = Lewis base). The observation of two structure-types for the carbanion in solution is explained theoretically and by NMR spectroscopy in terms of cis and trans isomerism imparted by partial double bond character in the arene-(α-C) bond. PMID:22423271

  5. Secondary relaxation dynamics in rigid glass-forming molecular liquids with related structures.

    PubMed

    Li, Xiangqian; Wang, Meng; Liu, Riping; Ngai, Kia L; Tian, Yongjun; Wang, Li-Min; Capaccioli, Simone

    2015-09-14

    The dielectric relaxation in three glass-forming molecular liquids, 1-methylindole (1MID), 5H-5-Methyl-6,7-dihydrocyclopentapyrazine (MDCP), and Quinaldine (QN) is studied focusing on the secondary relaxation and its relation to the structural α-relaxation. All three glass-formers are rigid and more or less planar molecules with related chemical structures but have dipoles of different strengths at different locations. A strong and fast secondary relaxation is detected in the dielectric spectra of 1MID, while no resolved β-relaxation is observed in MDCP and QN. If the observed secondary relaxation in 1MID is identified with the Johari-Goldstein (JG) β-relaxation, then apparently the relation between the α- and β-relaxation frequencies of 1MID is not in accord with the Coupling Model (CM). The possibility of the violation of the prediction in 1MID as due to either the formation of hydrogen-bond induced clusters or the involvement of intramolecular degree of freedom is ruled out. The violation is explained by the secondary relaxation originating from the in-plane rotation of the dipole located on the plane of the rigid molecule, contributing to dielectric loss at higher frequencies and more intense than the JG β-relaxation generated by the out-of-plane rotation. MDCP has smaller dipole moment located in the plane of the molecule; however, presence of the change of curvature of dielectric loss, ε″(f), at some frequency on the high-frequency flank of the α-relaxation reveals the JG β-relaxation in MDCP and which is in accord with the CM prediction. QN has as large an in-plane dipole moment as 1MID, and the absence of the resolved secondary relaxation is explained by the smaller coupling parameter than the latter in the framework of the CM. PMID:26374048

  6. Secondary relaxation dynamics in rigid glass-forming molecular liquids with related structures

    NASA Astrophysics Data System (ADS)

    Li, Xiangqian; Wang, Meng; Liu, Riping; Ngai, Kia L.; Tian, Yongjun; Wang, Li-Min; Capaccioli, Simone

    2015-09-01

    The dielectric relaxation in three glass-forming molecular liquids, 1-methylindole (1MID), 5H-5-Methyl-6,7-dihydrocyclopentapyrazine (MDCP), and Quinaldine (QN) is studied focusing on the secondary relaxation and its relation to the structural α-relaxation. All three glass-formers are rigid and more or less planar molecules with related chemical structures but have dipoles of different strengths at different locations. A strong and fast secondary relaxation is detected in the dielectric spectra of 1MID, while no resolved β-relaxation is observed in MDCP and QN. If the observed secondary relaxation in 1MID is identified with the Johari-Goldstein (JG) β-relaxation, then apparently the relation between the α- and β-relaxation frequencies of 1MID is not in accord with the Coupling Model (CM). The possibility of the violation of the prediction in 1MID as due to either the formation of hydrogen-bond induced clusters or the involvement of intramolecular degree of freedom is ruled out. The violation is explained by the secondary relaxation originating from the in-plane rotation of the dipole located on the plane of the rigid molecule, contributing to dielectric loss at higher frequencies and more intense than the JG β-relaxation generated by the out-of-plane rotation. MDCP has smaller dipole moment located in the plane of the molecule; however, presence of the change of curvature of dielectric loss, ɛ″(f), at some frequency on the high-frequency flank of the α-relaxation reveals the JG β-relaxation in MDCP and which is in accord with the CM prediction. QN has as large an in-plane dipole moment as 1MID, and the absence of the resolved secondary relaxation is explained by the smaller coupling parameter than the latter in the framework of the CM.

  7. The Role of Secondary Structure in the Entropically Driven Amelogenin Self-Assembly

    PubMed Central

    Lakshminarayanan, Rajamani; Fan, Daming; Du, Chang; Moradian-Oldak, Janet

    2007-01-01

    Amelogenin, the major extracellular enamel matrix protein, plays critical roles in controlling enamel mineralization. This generally hydrophobic protein self-assembles to form nanosphere structures under certain solution conditions. To gain clearer insight into the mechanisms of amelogenin self-assembly, we first investigated the occurrences of secondary structures within its sequence. By applying isothermal titration calorimetry (ITC), we determined the thermodynamic parameters associated with protein-protein interactions and with conformational changes during self-assembly. The recombinant porcine full length (rP172) and a truncated amelogenin lacking the hydrophilic C-terminal (rP148) were used. Circular dichroism (CD) measurements performed at low concentrations (<5 μM) revealed the presence of the polyproline-type II (PPII) conformation in both amelogenins in addition to α-helix and unordered conformations. Structural transition from PPII/unordered to β-sheet was observed for both proteins at higher concentrations (>62.5 μM) and upon self-assembly. ITC measurements indicated that the self-assembly of rP172 and rP148 is entropically driven (+ΔSA) and energetically favorable (−ΔGA). The magnitude of enthalpy (ΔHA) and entropy changes of assembly (ΔSA) were smaller for rP148 than rP172, whereas the Gibbs free energy change of assembly (ΔGA) was not significantly different. It was found that rP172 had higher PPII content than rP148, and the monomer-multimer equilibrium for rP172 was observed in a narrower protein concentration range when compared to rP148. The large positive enthalpy and entropy changes in both cases are attributed to the release of ordered water molecules and the associated entropy gain (due to the hydrophobic effect). These findings suggest that PPII conformation plays an important role in amelogenin self-assembly and that rP172 assembly is more favorable than rP148. The data are direct evidence for the notion that hydrophobic

  8. CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction applications

    PubMed Central

    2012-01-01

    Background Prediction of ribonucleic acid (RNA) secondary structure remains one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization for RNA secondary structure prediction. Thus far, few studies have been reported on the acceleration of the Zuker algorithm on general-purpose processors or on extra accelerators such as Field Programmable Gate-Array (FPGA) and Graphics Processing Units (GPU). To the best of our knowledge, no implementation combines both CPU and extra accelerators, such as GPUs, to accelerate the Zuker algorithm applications. Results In this paper, a CPU-GPU hybrid computing system that accelerates Zuker algorithm applications for RNA secondary structure prediction is proposed. The computing tasks are allocated between CPU and GPU for parallel cooperate execution. Performance differences between the CPU and the GPU in the task-allocation scheme are considered to obtain workload balance. To improve the hybrid system performance, the Zuker algorithm is optimally implemented with special methods for CPU and GPU architecture. Conclusions Speedup of 15.93× over optimized multi-core SIMD CPU implementation and performance advantage of 16% over optimized GPU implementation are shown in the experimental results. More than 14% of the sequences are executed on CPU in the hybrid system. The system combining CPU and GPU to accelerate the Zuker algorithm is proven to be promising and can be applied to other bioinformatics applications. PMID:22369626

  9. Mechanical properties of amyloid-like fibrils defined by secondary structures.

    PubMed

    Bortolini, C; Jones, N C; Hoffmann, S V; Wang, C; Besenbacher, F; Dong, M

    2015-05-01

    Amyloid and amyloid-like fibrils represent a generic class of highly ordered nanostructures that are implicated in some of the most fatal neurodegenerative diseases. On the other hand, amyloids, by possessing outstanding mechanical robustness, have also been successfully employed as functional biomaterials. For these reasons, physical and chemical factors driving fibril self-assembly and morphology are extensively studied - among these parameters, the secondary structures and the pH have been revealed to be crucial, since a variation in pH changes the fibril morphology and net chirality during protein aggregation. It is important to quantify the mechanical properties of these fibrils in order to help the design of effective strategies for treating diseases related to the presence of amyloid fibrils. In this work, we show that by changing pH the mechanical properties of amyloid-like fibrils vary as well. In particular, we reveal that these mechanical properties are strongly related to the content of secondary structures. We analysed and estimated the Young's modulus (E) by comparing the persistence length (Lp) - measured from the observation of TEM images by using statistical mechanics arguments - with the mechanical information provided by peak force quantitative nanomechanical property mapping (PF-QNM). The secondary structure content and the chirality are investigated by means of synchrotron radiation circular dichroism (SR-CD). Results arising from this study could be fruitfully used as a protocol to investigate other medical or engineering relevant peptide fibrils. PMID:25839069

  10. The Use of Additive Manufacturing for Fabrication of Multi-Function Small Satellite Structures

    SciTech Connect

    Horais, Brian J; Love, Lonnie J; Dehoff, Ryan R

    2013-01-01

    The use of small satellites in constellations is limited only by the growing functionality of smallsats themselves. Additive manufacturing provides exciting new design opportunities for development of multifunction CubeSat structures that integrate such functions as propulsion and thermal control into the satellite structures themselves. Manufacturing of these complex multifunction structures is now possible in lightweight, high strength, materials such as titanium by using existing electron beam melting additive manufacturing processes. However, the use of today's additive manufacturing capabilities is often cost-prohibitive for small companies due to the large capital investments required. To alleviate this impediment the U.S. Department of Energy has established a Manufacturing Demonstration Facility (MDF) at their Oak Ridge National Laboratory (ORNL) in Tennessee that provides industry access to a broad range of energy-efficient additive manufacturing equipment for collaborative use by both small and large organizations. This paper presents a notional CubeSat multifunction design that integrates the propulsion system into a three-unit (3U) CubeSat structure. The full-scale structure has been designed and fabricated at the ORNL MDF. The use of additive manufacturing for spacecraft fabrication is opening up many new possibilities in design and fabrication capabilities for what had previously been impossible structures to fabricate.

  11. Peptide Length Determines Equilibrium Secondary Structure in Protein-Analogous Micelles

    NASA Astrophysics Data System (ADS)

    Tirrell, Matthew; Marullo, Rachel; Kastantin, Mark

    2013-03-01

    This work seeks improved bottom-up design of bioinspired materials built from peptide-amphiphiles, which are a class of bioconjugates whereby a biofunctional peptide is covalently attached to a hydrophobic moiety that drives self-assembly in aqueous solution. Specifically, this work highlights the importance of peptide length (i.e. molecular weight) in determining the equilibrium secondary structure of the peptide as well as the self-assembled (i.e. micelle) geometry. Peptides used here repeat a seven-amino acid sequence between one and four times to vary peptide length while maintaining similar peptide-peptide interactions. Without a hydrophobic tail, these peptides all exhibit a combination of random coil and α-helical structure. Upon self-assembly, however, short peptides are prone to β-sheet structure and cylindrical geometry while longer peptides remain helical in spheroidal micelles. The transition to β-sheets in short peptides is kinetic, whereby amphiphiles first self-assemble with helical peptide structure, then overcome an activation barrier as they transition to their equilibrium β-sheet structure at a rate that depends on both temperature and ionic strength. These results identify peptide length as an important control over equilibrium peptide secondary structure and micelle geometry. Furthermore, the kinetic nature of the helix-to-sheet transition opens the door for shape-changing bioinspired materials with tunable conversion rates.

  12. Dissolved organic matter removal during coal slag additive soil aquifer treatment for secondary effluent recharging: Contribution of aerobic biodegradation.

    PubMed

    Wei, Liangliang; Li, Siliang; Noguera, Daniel R; Qin, Kena; Jiang, Junqiu; Zhao, Qingliang; Kong, Xiangjuan; Cui, Fuyi

    2015-06-01

    Recycling wastewater treatment plant (WWTP) effluent at low cost via the soil aquifer treatment (SAT), which has been considered as a renewable approach in regenerating potable and non-potable water, is welcome in arid and semi-arid regions throughout the world. In this study, the effect of a coal slag additive on the bulk removal of the dissolved organic matter (DOM) in WWTP effluent during SAT operation was explored via the matrix configurations of both coal slag layer and natural soil layer. Azide inhibition and XAD-resins fractionation experiments indicated that the appropriate configuration designing of an upper soil layer (25 cm) and a mixture of soil/coal slag underneath would enhance the removal efficiency of adsorption and anaerobic biodegradation to the same level as that of aerobic biodegradation (31.7% vs 32.2%), while it was only 29.4% compared with the aerobic biodegradation during traditional 50 cm soil column operation. The added coal slag would preferentially adsorb the hydrophobic DOM, and those adsorbed organics could be partially biodegraded by the biomass within the SAT systems. Compared with the relatively lower dissolved organic carbon (DOC), ultraviolet light adsorption at 254 nm (UV-254) and trihalomethane formation potential (THMFP) removal rate of the original soil column (42.0%, 32.9%, and 28.0%, respectively), SSL2 and SSL4 columns would enhance the bulk removal efficiency to more than 60%. Moreover, a coal slag additive in the SAT columns could decline the aromatic components (fulvic-like organics and tryptophan-like proteins) significantly. PMID:25845997

  13. Correlation between protein secondary structure, backbone bond angles, and side-chain orientations

    NASA Astrophysics Data System (ADS)

    Lundgren, Martin; Niemi, Antti J.

    2012-08-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central Cα carbon of a protein backbone, and for this we develop new visualization techniques to analyze high-resolution x-ray structures in the Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse-grained energy function to describe the ensuing side-chain geometry in terms of the Cβ carbon orientations. The energy function can model the side-chain geometry with a subatomic precision. As an example we construct the Cα-Cβ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 Å in root-mean-square distance from the experimental x-ray structure.

  14. One-pot synthesis of 3,4,5-trisubstituted 1,2,4-triazoles via the addition of hydrazides to activated secondary amides.

    PubMed

    Bechara, William S; Khazhieva, Inna S; Rodriguez, Elsa; Charette, André B

    2015-03-01

    A general approach has been developed for the one-pot synthesis of 3,4,5-trisubstituted 1,2,4-triazoles from secondary amides and hydrazides via triflic anhydride activation followed by microwave-induced cyclodehydration. In addition, the 1,2,4-triazole moiety is shown to be a useful directing group for Ru-catalyzed C-H arylation. Access to 1,2,4-triazolophenanthridine can be achieved from the reaction products using a Pd-catalyzed intramolecular C-H functionalization reaction. PMID:25700199

  15. Using probe secondary structure information to enhance Affymetrix GeneChip background estimates

    PubMed Central

    Gharaibeh, Raad Z.; Fodor, Anthony A.; Gibas, Cynthia J.

    2007-01-01

    High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data. A number of statistical techniques have been developed to correct for this background noise. Here, we demonstrate that probe minimum folding energy and structure can be used to enhance a previously existing model for background noise correction. We estimate that probe secondary structure accounts for up to 3% of all variation on Affymetrix microarrays. PMID:17387043

  16. The influence of the secondary relaxation processes on the structural relaxation in glass-forming materials

    NASA Astrophysics Data System (ADS)

    Khamzin, A. A.; Popov, I. I.; Nigmatullin, R. R.

    2013-06-01

    In the frame of fractional-kinetic approach, the model of the structural α-relaxation in the presence of the secondary β-relaxation processes is suggested. The model is based on the rigorous bond between β-processes with α-process and leads to the generalized and justified expression for the complex dielectric permittivity (CDP). It allows to form a new sight on the problem of the fitting of multi-peak structure of the dielectric loss spectra in glass-forming materials. The consistency of the CDP expressions obtained is based on a good fit of experimental data for binary methanol-water mixtures.

  17. The influence of the secondary relaxation processes on the structural relaxation in glass-forming materials.

    PubMed

    Khamzin, A A; Popov, I I; Nigmatullin, R R

    2013-06-28

    In the frame of fractional-kinetic approach, the model of the structural α-relaxation in the presence of the secondary β-relaxation processes is suggested. The model is based on the rigorous bond between β-processes with α-process and leads to the generalized and justified expression for the complex dielectric permittivity (CDP). It allows to form a new sight on the problem of the fitting of multi-peak structure of the dielectric loss spectra in glass-forming materials. The consistency of the CDP expressions obtained is based on a good fit of experimental data for binary methanol-water mixtures. PMID:23822251

  18. VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program

    PubMed Central

    Yahyavi, Masoumeh; Falsafi-Zadeh, Sajad; Karimi, Zahra; Kalatarian, Giti; Galehdari, Hamid

    2014-01-01

    The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its trajectories during simulation for known structures available at the Protein Data Bank (PDB). The program helps to calculate (1) percentage SS, (2) SS occurrence in each residue, (3) percentage SS during simulation, and (4) percentage residues in all SS types during simulation. The VMD-SS plug-in was designed using TCL script and stride to calculate secondary structure features. Availability The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755 PMID:25258493

  19. A novel secondary structure based on fused five-membered rings motif

    PubMed Central

    Dhar, Jesmita; Kishore, Raghuvansh; Chakrabarti, Pinak

    2016-01-01

    An analysis of protein structures indicates the existence of a novel, fused five-membered rings motif, comprising of two residues (i and i + 1), stabilized by interresidue Ni+1–H∙∙∙Ni and intraresidue Ni+1–H∙∙∙O=Ci+1 hydrogen bonds. Fused-rings geometry is the common thread running through many commonly occurring motifs, such as β-turn, β-bulge, Asx-turn, Ser/Thr-turn, Schellman motif, and points to its structural robustness. A location close to the beginning of a β-strand is rather common for the motif. Devoid of side chain, Gly seems to be a key player in this motif, occurring at i, for which the backbone torsion angles cluster at ~(−90°, −10°) and (70°, 20°). The fused-rings structures, distant from each other in sequence, can hydrogen bond with each other, and the two segments aligned to each other in a parallel fashion, give rise to a novel secondary structure, topi, which is quite common in proteins, distinct from two major secondary structures, α-helix and β-sheet. Majority of the peptide segments making topi are identified as aggregation-prone and the residues tend to be conserved among homologous proteins. PMID:27511362

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

    PubMed Central

    Lorenzo, J. Ramiro; Alonso, Leonardo G.; Sánchez, Ignacio E.

    2015-01-01

    Asparagine residues in proteins undergo spontaneous deamidation, a post-translational modification that may act as a molecular clock for the regulation of protein function and turnover. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding. We present NGOME, an algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. Compared to previous algorithms, NGOME does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Four case studies of specific proteins show how NGOME may help the user identify deamidation-prone asparagine residues, often related to protein gain of function, protein degradation or protein misfolding in pathological processes. A fifth case study applies NGOME at a proteomic scale and unveils a correlation between asparagine deamidation and protein degradation in yeast. NGOME is freely available as a webserver at the National EMBnet node Argentina, URL: http://www.embnet.qb.fcen.uba.ar/ in the subpage “Protein and nucleic acid structure and sequence analysis”. PMID:26674530

  1. Secondary structure and domain architecture of the 23S and 5S rRNAs

    PubMed Central

    Petrov, Anton S.; Bernier, Chad R.; Hershkovits, Eli; Xue, Yuzhen; Waterbury, Chris C.; Hsiao, Chiaolong; Stepanov, Victor G.; Gaucher, Eric A.; Grover, Martha A.; Harvey, Stephen C.; Hud, Nicholas V.; Wartell, Roger M.; Fox, George E.; Williams, Loren Dean

    2013-01-01

    We present a de novo re-determination of the secondary (2°) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2° structure, the center of the 23S rRNA is an extended single strand, which in 3D is seen to be compact and double helical. Accurately assigning nucleotides to helices compels a revision of the 23S rRNA 2° structure. Unlike the traditional 2° structure, the revised 2° structure of the 23S rRNA shows architectural similarity with the 16S rRNA. The revised 2° structure also reveals a clear relationship with the 3D structure and is generalizable to rRNAs of other species from all three domains of life. The 2° structure revision required us to reconsider the domain architecture. We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness. The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed. Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted. Editable 2° structures mapped with various data are provided (http://apollo.chemistry.gatech.edu/RibosomeGallery). PMID:23771137

  2. Secondary structure components and properties of the melibiose permease from Escherichia coli: a fourier transform infrared spectroscopy analysis.

    PubMed

    Dave, N; Troullier, A; Mus-Veteau, I; Duñach, M; Leblanc, G; Padrós, E

    2000-08-01

    The structure of the melibiose permease from Escherichia coli has been investigated by Fourier transform infrared spectroscopy, using the purified transporter either in the solubilized state or reconstituted in E. coli lipids. In both instances, the spectra suggest that the permease secondary structure is dominated by alpha-helical components (up to 50%) and contains beta-structure (20%) and additional components assigned to turns, 3(10) helix, and nonordered structures (30%). Two distinct and strong absorption bands are recorded at 1660 and 1653 cm(-1), i.e., in the usual range of absorption of helices of membrane proteins. Moreover, conditions that preserve the transporter functionality (reconstitution in liposomes or solubilization with dodecyl maltoside) make possible the detection of two separate alpha-helical bands of comparable intensity. In contrast, a single intense band, centered at approximately 1656 cm(-1), is recorded from the inactive permease in Triton X-100, or a merged and broader signal is recorded after the solubilized protein is heated in dodecyl maltoside. It is suggested that in the functional permease, distinct signals at 1660 and 1653 cm(-1) arise from two different populations of alpha-helical domains. Furthermore, the sodium- and/or melibiose-induced changes in amide I line shape, and in particular, in the relative amplitudes of the 1660 and 1653 cm(-1) bands, indicate that the secondary structure is modified during the early step of sugar transport. Finally, the observation that approximately 80% of the backbone amide protons can be exchanged suggests high conformational flexibility and/or a large accessibility of the membrane domains to the aqueous solvent. PMID:10920008

  3. Crumple: a method for complete enumeration of all possible pseudoknot-free RNA secondary structures.

    PubMed

    Bleckley, Samuel; Stone, Jonathan W; Schroeder, Susan J

    2012-01-01

    The diverse landscape of RNA conformational space includes many canyons and crevices that are distant from the lowest minimum free energy valley and remain unexplored by traditional RNA structure prediction methods. A complete description of the entire RNA folding landscape can facilitate identification of biologically important conformations. The Crumple algorithm rapidly enumerates all possible non-pseudoknotted structures for an RNA sequence without consideration of thermodynamics while filtering the output with experimental data. The Crumple algorithm provides an alternative approach to traditional free energy minimization programs for RNA secondary structure prediction. A complete computation of all non-pseudoknotted secondary structures can reveal structures that would not be predicted by methods that sample the RNA folding landscape based on thermodynamic predictions. The free energy minimization approach is often successful but is limited by not considering RNA tertiary and protein interactions and the possibility that kinetics rather than thermodynamics determines the functional RNA fold. Efficient parallel computing and filters based on experimental data make practical the complete enumeration of all non-pseudoknotted structures. Efficient parallel computing for Crumple is implemented in a ring graph approach. Filters for experimental data include constraints from chemical probing of solvent accessibility, enzymatic cleavage of paired or unpaired nucleotides, phylogenetic covariation, and the minimum number and lengths of helices determined from crystallography or cryo-electron microscopy. The minimum number and length of helices has a significant effect on reducing conformational space. Pairing constraints reduce conformational space more than single nucleotide constraints. Examples with Alfalfa Mosaic Virus RNA and Trypanosome brucei guide RNA demonstrate the importance of evaluating all possible structures when pseduoknots, RNA-protein interactions

  4. Structural effects of liana presence in secondary tropical dry forests using ground LiDAR

    NASA Astrophysics Data System (ADS)

    Sánchez-Azofeifa, A.; Portillo-Quintero, C.; Durán, S. M.

    2015-10-01

    Lianas, woody vines, are a key component of tropical forest because they may reduce carbon storage potential. Lianas are increasing in density and biomass in tropical forests, but it is unknown what the potential consequences of these increases are for forest dynamics. Lianas may proliferate in disturbed areas, such as regenerating forests, but little is known about the role of lianas in secondary succession. In this study, we evaluated the potential of the ground LiDAR to detect differences in the vertical structure of stands of different ages with and without lianas in tropical dry forests. Specifically, we used a terrestrial laser scanner called VEGNET to assess whether liana presence influences the vertical signature of stands of different ages, and whether successional trajectories as detected by the VEGNET could be altered by liana presence. We deployed the VEGNET ground LiDAR system in 15 secondary forests of different ages early (21 years old since land abandonment), intermediate (32-35 years old) and late stages (> 80 years old) with and without lianas. We compared laser-derived vegetation components such as Plant Area Index (PAI), plant area volume density (PAVD), and the radius of gyration (RG) across forest stands between liana and no-liana treatments. In general forest stands without lianas show a clearer distinction of vertical strata and the vertical height of accumulated PAVD. A significant increase of PAI was found from intermediate to late stages in stands without lianas, but in stands where lianas were present there was not a significant trend. This suggests that lianas may be influencing successional trajectories in secondary forests, and these effects can be captured by terrestrial laser scanners such as the VEGNET. This research contributes to estimate the potential effects of lianas in secondary dry forests and highlight the role of ground LiDAR to monitor structural changes in tropical forests due to liana presence.

  5. The Interplay between Adolescent Needs and Secondary School Structures: Fostering Developmentally Responsive Middle and High School Environments across the Transition

    ERIC Educational Resources Information Center

    Ellerbrock, Cheryl R.; Kiefer, Sarah M.

    2013-01-01

    Understanding the developmental responsiveness of secondary school environments may be an important factor in supporting students as they make the transition from one school to the next. Students' needs may or may not be met depending on the nature of the fit between their basic and developmental needs and secondary school structures at the…

  6. Quantification of protein secondary structure by (13)C solid-state NMR.

    PubMed

    Andrade, Fabiana Diuk; Forato, Lucimara Aparecida; Bernardes Filho, Rubens; Colnago, Luiz Alberto

    2016-05-01

    High-resolution (13)C solid-state NMR stands out as one of the most promising techniques to solve the structure of insoluble proteins featuring biological and technological importance. The simplest nuclear magnetic resonance (NMR) spectroscopy method to quantify the secondary structure of proteins uses the areas of carbonyl and alpha carbon peaks. The quantification obtained by fitting procedures depends on the assignment of the peaks to the structure, type of line shape, number of peaks to be used, and other parameters that are set by the operator. In this paper, we demonstrate that the analysis of (13)C NMR spectra by a pattern recognition method-based on the singular value decomposition (SVD) regression, which does not depend on the operator-shows higher correlation coefficients for α-helix and β-sheet (0.96 and 0.91, respectively) than Fourier transform infrared spectroscopy (FTIR) method. Therefore, the use of (13)C solid-state NMR spectra and SVD is a simple and reliable method for quantifying the secondary structures of insoluble proteins in solid-state. PMID:27068694

  7. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

    PubMed Central

    Mathews, David H.; Disney, Matthew D.; Childs, Jessica L.; Schroeder, Susan J.; Zuker, Michael; Turner, Douglas H.

    2004-01-01

    A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. Furthermore, free energy parameters are revised to account for recent experimental results for terminal mismatches and hairpin, bulge, internal, and multibranch loops. To demonstrate the applicability of this method, in vivo modification was performed on 5S rRNA in both Escherichia coli and Candida albicans with 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate, dimethyl sulfate, and kethoxal. The percentage of known base pairs in the predicted structure increased from 26.3% to 86.8% for the E. coli sequence by using modification constraints. For C. albicans, the accuracy remained 87.5% both with and without modification data. On average, for these sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, accuracy improves from 67% to 76%. This enhancement primarily reflects improvement for three sequences that are predicted with <40% accuracy on the basis of energetics alone. For these sequences, inclusion of chemical modification constraints improves the average accuracy from 28% to 78%. For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs. PMID:15123812

  8. Unit-cell intergrowth of pyrochlore and hexagonal tungsten bronze structures in secondary tungsten minerals

    SciTech Connect

    Grey, Ian E. . E-mail: ian.grey@csiro.au; Birch, William D.; Bougerol, Catherine

    2006-12-15

    Structural relations between secondary tungsten minerals with general composition A{sub x}[(W,Fe)(O,OH){sub 3}]{sub .y}H{sub 2}O are described. Phyllotungstite (A=predominantly Ca) is hexagonal, a=7.31(3)A, c=19.55(1)A, space group P6{sub 3}/mmc. Pittongite, a new secondary tungsten mineral from a wolframite deposit near Pittong in Victoria, southeastern Australia (A=predominantly Na) is hexagonal, a=7.286(1)A, c=50.49(1)A, space group P-6m2. The structures of both minerals can be described as unit-cell scale intergrowths of (111){sub py} pyrochlore slabs with pairs of hexagonal tungsten bronze (HTB) layers. In phyllotungstite, the (111){sub py} blocks have the same thickness, 6A, whereas pittongite contains pyrochlore blocks of two different thicknesses, 6 and 12A. The structures can alternatively be described in terms of chemical twinning of the pyrochlore structure on (111){sub py} oxygen planes. At the chemical twin planes, pairs of HTB layers are corner connected as in hexagonal WO{sub 3}.

  9. Discrete state model and accurate estimation of loop entropy of RNA secondary structures.

    PubMed

    Zhang, Jian; Lin, Ming; Chen, Rong; Wang, Wei; Liang, Jie

    2008-03-28

    Conformational entropy makes important contribution to the stability and folding of RNA molecule, but it is challenging to either measure or compute conformational entropy associated with long loops. We develop optimized discrete k-state models of RNA backbone based on known RNA structures for computing entropy of loops, which are modeled as self-avoiding walks. To estimate entropy of hairpin, bulge, internal loop, and multibranch loop of long length (up to 50), we develop an efficient sampling method based on the sequential Monte Carlo principle. Our method considers excluded volume effect. It is general and can be applied to calculating entropy of loops with longer length and arbitrary complexity. For loops of short length, our results are in good agreement with a recent theoretical model and experimental measurement. For long loops, our estimated entropy of hairpin loops is in excellent agreement with the Jacobson-Stockmayer extrapolation model. However, for bulge loops and more complex secondary structures such as internal and multibranch loops, we find that the Jacobson-Stockmayer extrapolation model has large errors. Based on estimated entropy, we have developed empirical formulae for accurate calculation of entropy of long loops in different secondary structures. Our study on the effect of asymmetric size of loops suggest that loop entropy of internal loops is largely determined by the total loop length, and is only marginally affected by the asymmetric size of the two loops. Our finding suggests that the significant asymmetric effects of loop length in internal loops measured by experiments are likely to be partially enthalpic. Our method can be applied to develop improved energy parameters important for studying RNA stability and folding, and for predicting RNA secondary and tertiary structures. The discrete model and the program used to calculate loop entropy can be downloaded at http://gila.bioengr.uic.edu/resources/RNA.html. PMID:18376982

  10. Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures.

    PubMed

    Fu, Yinghan; Xu, Zhenjiang Zech; Lu, Zhi J; Zhao, Shan; Mathews, David H

    2015-01-01

    Recently, non-coding RNAs (ncRNAs) have been discovered with novel functions, and it has been appreciated that there is pervasive transcription of genomes. Moreover, many novel ncRNAs are not conserved on the primary sequence level. Therefore, de novo computational ncRNA detection that is accurate and efficient is desirable. The purpose of this study is to develop a ncRNA detection method based on conservation of structure in more than two genomes. A new method called Multifind, using Multilign, was developed. Multilign predicts the common secondary structure for multiple input sequences. Multifind then uses measures of structure conservation to estimate the probability that the input sequences are a conserved ncRNA using a classification support vector machine. Multilign is based on Dynalign, which folds and aligns two sequences simultaneously using a scoring scheme that does not include sequence identity; its structure prediction quality is therefore not affected by input sequence diversity. Additionally, ensemble defect was introduced to Multifind as an additional discriminating feature that quantifies the compactness of the folding space for a sequence. Benchmarks showed Multifind performs better than RNAz and LocARNATE+RNAz, a method that uses RNAz on structure alignments generated by LocARNATE, on testing sequences extracted from the Rfam database. For de novo ncRNA discovery in three genomes, Multifind and LocARNATE+RNAz had an advantage over RNAz in low similarity regions of genome alignments. Additionally, Multifind and LocARNATE+RNAz found different subsets of known ncRNA sequences, suggesting the two approaches are complementary. PMID:26075601

  11. Generic properties of combinatory maps: Neutral networks of RNA secondary structures

    SciTech Connect

    Reidys, C. |; Stadler, P.F. |; Schuster, P. ||

    1997-03-01

    Random graph theory is used to model and analyze the relationships between sequences and secondary structures of RNA molecules, which are understood as mappings from sequence space into shape space. These maps are non-invertible since there are always many orders of magnitude more sequences than structures. Sequences folding into identical structures form neutral networks. A neutral network is embedded in the set of sequences that are compatible with the given structure. Networks are modeled as graphs and constructed by random choice of vertices from the space of compatible sequences. The theory characterizes neutral networks by the mean fraction of neutral neighbors ({lambda}). The networks are connected and percolate sequence space if the fraction of neutral nearest neighbors exceeds a threshold value ({lambda} > {lambda}*). Below threshold ({lambda} < {lambda}*), the networks are partitioned into a largest giant component and several smaller components. Structures are classified as common or rare according to the sizes of their pre-images, i.e. according to the fractions of sequences folding into them. The neutral networks of any pair of two different common structures almost touch each other, and, as expressed by the conjecture of shape space covering sequences folding into almost all common structures, can be found in a small ball of an arbitrary location in sequence space. The results from random graph theory are compared to data obtained by folding large samples of RNA sequences. Differences are explained in terms of specific features of RNA molecular structures.

  12. Modeling proteins using a super-secondary structure library and NMR chemical shift information

    PubMed Central

    Menon, Vilas; Vallat, Brinda; Dybas, Joseph M.; Fiser, Andras

    2013-01-01

    Summary A remaining challenge in protein modeling is to predict structures for sequences that do not share recognizable sequence similarity to any experimentally solved structure. This challenge can be addressed by hybrid algorithms that utilize easily obtainable experimental data and carry a limited amount of indirect structural information. Based on earlier observations, the library of protein super-secondary structure motifs (Smotifs) saturated about a decade ago, and new folds discovered since then are novel combinations of existing Smotifs. This observation suggests that it should be possible to build any structure, of either a known or yet to be discovered fold, from a combination of existing Smotifs derived from already known structures. In the absence of any sequence similarity signal, limited experimental data can be used to relate the backbone conformations of Smotifs between target proteins and known experimental structures. Here we present a modeling algorithm that relies on an exhaustive Smotif library and on NMR chemical shift patterns without any input of primary sequence information. In a test of 102 proteins with unique folds, the algorithm delivered 90 homology model quality models, among them 24 high quality ones, and a topologically correct solution for almost all cases. Detailed analysis of the method’s performance suggests that further improvement can be achieved by improving sampling algorithms and developing more precise tools that predict dihedral angle preferences from chemical shift assignments. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available. PMID:23685209

  13. Computer analysis of phytochrome sequences and reevaluation of the phytochrome secondary structure by Fourier transform infrared spectroscopy.

    PubMed

    Sühnel, J; Hermann, G; Dornberger, U; Fritzsche, H

    1997-07-18

    A repertoire of various methods of computer sequence analysis was applied to phytochromes in order to gain new insights into their structure and function. A statistical analysis of 23 complete phytochrome sequences revealed regions of non-random amino acid composition, which are supposed to be of particular structural or functional importance. All phytochromes other than phyD and phyE from Arabidopsis have at least one such region at the N-terminus between residues 2 and 35. A sequence similarity search of current databases indicated striking homologies between all phytochromes and a hypothetical 84.2-kDa protein from the cyanobacterium Synechocystis. Furthermore, scanning the phytochrome sequences for the occurrence of patterns defined in the PROSITE database detected the signature of the WD repeats of the beta-transducin family within the functionally important 623-779 region (sequence numbering of phyA from Avena) in a number of phytochromes. A multiple sequence alignment performed with 23 complete phytochrome sequences is made available via the IMB Jena World-Wide Web server (http://www.imb-jena.de/PHYTO.html). It can be used as a working tool for future theoretical and experimental studies. Based on the multiple alignment striking sequence differences between phytochromes A and B were detected directly at the N-terminal end, where all phytochromes B have an additional stretch of 15-42 amino acids. There is also a variety of positions with totally conserved but different amino acids in phytochromes A and B. Most of these changes are found in the sequence segment 150-200. It is, therefore, suggested that this region might be of importance in determining the photosensory specificity of the two phytochromes. The secondary structure prediction based on the multiple alignment resulted in a small but significant beta-sheet content. This finding is confirmed by a reevaluation of the secondary structure using FTIR spectroscopy. PMID:9252112

  14. The recognition of multi-class protein folds by adding average chemical shifts of secondary structure elements

    PubMed Central

    Feng, Zhenxing; Hu, Xiuzhen; Jiang, Zhuo; Song, Hangyu; Ashraf, Muhammad Aqeel

    2015-01-01

    The recognition of protein folds is an important step in the prediction of protein structure and function. Recently, an increasing number of researchers have sought to improve the methods for protein fold recognition. Following the construction of a dataset consisting of 27 protein fold classes by Ding and Dubchak in 2001, prediction algorithms, parameters and the construction of new datasets have improved for the prediction of protein folds. In this study, we reorganized a dataset consisting of 76-fold classes constructed by Liu et al. and used the values of the increment of diversity, average chemical shifts of secondary structure elements and secondary structure motifs as feature parameters in the recognition of multi-class protein folds. With the combined feature vector as the input parameter for the Random Forests algorithm and ensemble classification strategy, we propose a novel method to identify the 76 protein fold classes. The overall accuracy of the test dataset using an independent test was 66.69%; when the training and test sets were combined, with 5-fold cross-validation, the overall accuracy was 73.43%. This method was further used to predict the test dataset and the corresponding structural classification of the first 27-protein fold class dataset, resulting in overall accuracies of 79.66% and 93.40%, respectively. Moreover, when the training set and test sets were combined, the accuracy using 5-fold cross-validation was 81.21%. Additionally, this approach resulted in improved prediction results using the 27-protein fold class dataset constructed by Ding and Dubchak. PMID:26980999

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

    PubMed Central

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

    1989-01-01

    The Columnea latent viroid (CLV) occurs latently in certain Columnea erythrophae plants grown commercially. In potato and tomato, CLV causes potato spindle tuber viroid (PSTV)-like symptoms. Its nucleotide sequence and proposed secondary structure reveal that CLV consists of a single-stranded circular RNA of 370 nucleotides which can assume a rod-like structure with extensive base-pairing characteristic of all known viroids. The electrophoretic mobility of circular CLV under nondenaturing conditions suggests a potential tertiary structure. CLV contains extensive sequence homologies to the PSTV group of viroids but contains a central conserved region identical to that of hop stunt viroid (HSV). CLV also shares some biological properties with each of the two types of viroids. Most probably, CLV is the result of intracellular RNA recombination between an HSV-type and one or more PSTV-type viroids replicating in the same plant. Images PMID:2602114

  16. Neural-network design applied to protein-secondary-structure predictions

    SciTech Connect

    Yu, R.C.; Head-Gordon, T.

    1995-04-01

    The success of neural networks is often limited by a sparse database of training examples, deficient neural-network architectures, and nonglobal optimization of the network variables. The convolution of these three problems has curtailed the application of network models to protein-structure predictions, where homology modeling or information theory approaches are considered better controlled alternatives. This paper introduces our broad objective of disentangling the three degrading features of neural networks cited above, beginning with improved designs of network architectures used in the prediction of protein secondary structure. This work demonstrates that network architecture design considerations greatly improve generalization and more efficiently extract complex sequence-structure relationships from the existing database, as compared to arbitrary architectures with the same size input window.

  17. Structural evaluation of mixer pump installed in Tank 241-AN-107 for caustic addition project

    SciTech Connect

    Leshikar, G.A.

    1995-06-16

    This report documents the structural analysis and evaluation of a mixer pump and caustic addition system to be used in Tank 107-AN. This pump will be installed in the central pump pit of this double- shell tank for the purpose of bringing the hydroxide ion concentration into compliance with Tank Farm operating specifications.

  18. Profiles and Majority Voting-Based Ensemble Method for Protein Secondary Structure Prediction

    PubMed Central

    Bouziane, Hafida; Messabih, Belhadri; Chouarfia, Abdallah

    2011-01-01

    Machine learning techniques have been widely applied to solve the problem of predicting protein secondary structure from the amino acid sequence. They have gained substantial success in this research area. Many methods have been used including k-Nearest Neighbors (k-NNs), Hidden Markov Models (HMMs), Artificial Neural Networks (ANNs) and Support Vector Machines (SVMs), which have attracted attention recently. Today, the main goal remains to improve the prediction quality of the secondary structure elements. The prediction accuracy has been continuously improved over the years, especially by using hybrid or ensemble methods and incorporating evolutionary information in the form of profiles extracted from alignments of multiple homologous sequences. In this paper, we investigate how best to combine k-NNs, ANNs and Multi-class SVMs (M-SVMs) to improve secondary structure prediction of globular proteins. An ensemble method which combines the outputs of two feed-forward ANNs, k-NN and three M-SVM classifiers has been applied. Ensemble members are combined using two variants of majority voting rule. An heuristic based filter has also been applied to refine the prediction. To investigate how much improvement the general ensemble method can give rather than the individual classifiers that make up the ensemble, we have experimented with the proposed system on the two widely used benchmark datasets RS126 and CB513 using cross-validation tests by including PSI-BLAST position-specific scoring matrix (PSSM) profiles as inputs. The experimental results reveal that the proposed system yields significant performance gains when compared with the best individual classifier. PMID:22058650

  19. The secondary structure of the 7SL RNA in the signal recognition particle: functional implications.

    PubMed Central

    Zwieb, C

    1985-01-01

    The secondary structure of the 7SL RNA in the signal recognition particle was determined by applying both a theoretical and an experimental approach. The compensatory base change approach was taken comparing the published sequences of human, Drosophila and Xenopus 7SL RNA's. The deduced secondary structure was confirmed by post-labeling of an RNase V1-nicked dog SRP with P32-pCp and RNA-ligase and analysis of the labeled RNA-fragments by non-denaturing/denaturing 2D polyacrylamide gel electrophoresis. Two interesting features in the secondary structure were revealed: Firstly, bases at positions 122 to 127 of the human 7SL RNA are not only able to pair with bases at positions 167 to 170, but also with a single-stranded region of the bases at positions 223 to 228, suggesting an alternative base pairing scheme for the 7SL RNA in all three organisms. In agreement with this finding, four different conformations were identified after transcription of the 7SL RNA from the genomic human clone. The involvement of the particular basepairing interaction postulated was confirmed by the analysis of a 7SL RNA deletion mutant (Sma1-409). Secondly, a significant sequence homology of the paired bases at positions 236 to 255 and 104 to 109 in 7SL RNA with bases in 5S ribosomal RNA at the positions 84 to 110 was noticed, suggesting that 5S ribosomal and 7SL RNA interact with the same target during protein biosynthesis. These findings are summarized by proposing a mechanism for the translational arrest of protein synthesis by the signal recognition particle using specific sequences and an alternative configuration in the 7SL RNA. Images PMID:2413423

  20. Secondary Plant Products Causing Photosensitization in Grazing Herbivores: Their Structure, Activity and Regulation

    PubMed Central

    Quinn, Jane C.; Kessell, Allan; Weston, Leslie A.

    2014-01-01

    Photosensitivity in animals is defined as a severe dermatitis that results from a heightened reactivity of skin cells and associated dermal tissues upon their exposure to sunlight, following ingestion or contact with UV reactive secondary plant products. Photosensitivity occurs in animal cells as a reaction that is mediated by a light absorbing molecule, specifically in this case a plant-produced metabolite that is heterocyclic or polyphenolic. In sensitive animals, this reaction is most severe in non-pigmented skin which has the least protection from UV or visible light exposure. Photosensitization in a biological system such as the epidermis is an oxidative or other chemical change in a molecule in response to light-induced excitation of endogenous or exogenously-delivered molecules within the tissue. Photo-oxidation can also occur in the plant itself, resulting in the generation of reactive oxygen species, free radical damage and eventual DNA degradation. Similar cellular changes occur in affected herbivores and are associated with an accumulation of photodynamic molecules in the affected dermal tissues or circulatory system of the herbivore. Recent advances in our ability to identify and detect secondary products at trace levels in the plant and surrounding environment, or in organisms that ingest plants, have provided additional evidence for the role of secondary metabolites in photosensitization of grazing herbivores. This review outlines the role of unique secondary products produced by higher plants in the animal photosensitization process, describes their chemistry and localization in the plant as well as impacts of the environment upon their production, discusses their direct and indirect effects on associated animal systems and presents several examples of well-characterized plant photosensitization in animal systems. PMID:24451131

  1. Secondary plant products causing photosensitization in grazing herbivores: their structure, activity and regulation.

    PubMed

    Quinn, Jane C; Kessell, Allan; Weston, Leslie A

    2014-01-01

    Photosensitivity in animals is defined as a severe dermatitis that results from a heightened reactivity of skin cells and associated dermal tissues upon their exposure to sunlight, following ingestion or contact with UV reactive secondary plant products. Photosensitivity occurs in animal cells as a reaction that is mediated by a light absorbing molecule, specifically in this case a plant-produced metabolite that is heterocyclic or polyphenolic. In sensitive animals, this reaction is most severe in non-pigmented skin which has the least protection from UV or visible light exposure. Photosensitization in a biological system such as the epidermis is an oxidative or other chemical change in a molecule in response to light-induced excitation of endogenous or exogenously-delivered molecules within the tissue. Photo-oxidation can also occur in the plant itself, resulting in the generation of reactive oxygen species, free radical damage and eventual DNA degradation. Similar cellular changes occur in affected herbivores and are associated with an accumulation of photodynamic molecules in the affected dermal tissues or circulatory system of the herbivore. Recent advances in our ability to identify and detect secondary products at trace levels in the plant and surrounding environment, or in organisms that ingest plants, have provided additional evidence for the role of secondary metabolites in photosensitization of grazing herbivores. This review outlines the role of unique secondary products produced by higher plants in the animal photosensitization process, describes their chemistry and localization in the plant as well as impacts of the environment upon their production, discusses their direct and indirect effects on associated animal systems and presents several examples of well-characterized plant photosensitization in animal systems. PMID:24451131

  2. Effects of high hydrostatic pressure on secondary structure and emulsifying behavior of sweet potato protein

    NASA Astrophysics Data System (ADS)

    Mehmood Khan, Nasir; Mu, Tai-Hua; Sun, Hong-Nan; Zhang, Miao; Chen, Jing-Wang

    2015-04-01

    In this study, secondary structures of sweet potato protein (SPP) after high hydrostatic pressure (HHP) treatment (200-600 MPa) were evaluated and emulsifying properties of emulsions with HHP-treated SPP solutions in different pH values (3, 6, and 9) were investigated. Circular dichroism analysis confirmed the modification of the SPP secondary structure. Surface hydrophobicity increased at pH 3 and decreased at 6 and 9. Emulsifying activity index at pH 6 increased with an increase in pressure, whereas emulsifying stability index increased at pH 6 and 9. Oil droplet sizes decreased, while volume frequency distribution of the smaller droplets increased at pH 3 and 6 with the HHP treatment. Emulsion viscosity increased at pH 6 and 9 and pseudo-plastic flow behaviors were not altered for all emulsions produced with HHP-treated SPP. These results suggested that HHP could modify the SPP structure for better emulsifying properties, which could increase the use of SPP emulsion in the food industry.

  3. Interplay between desolvation and secondary structure in mediating cosolvent and temperature induced alpha-synuclein aggregation

    NASA Astrophysics Data System (ADS)

    Anderson, V. L.; Webb, W. W.; Eliezer, D.

    2012-10-01

    Both increased temperature and moderate concentrations of fluorinated alcohols enhance aggregation of the Parkinson's disease-associated protein α-synuclein (αS). Here, we investigate the secondary structural rearrangements induced by heating and trifluoroethanol [TFE]. At low TFE concentrations, CD spectra feature a negative peak characteristic of disordered polypeptides near 200 nm and a slight shoulder around 220 nm suggesting some polyproline-II content. Upon heating, these peaks weaken, while a weak negative signal develops at 222 nm. At high TFE concentrations, the spectra show distinct minima at 208 and 222 nm, indicative of considerable α-helical structure, which diminish upon heating. We observe a crossover between the low-TFE and high-TFE behavior near 15% TFE, where we previously showed that a partially helical intermediate is populated. We postulate that the protein is well solvated by water at low TFE concentrations and by TFE at high TFE concentrations, but may become desolvated at the crossover point. We discuss the potential roles and interplay of desolvation and helical secondary structure in driving αS aggregation.

  4. A global sampling approach to designing and reengineering RNA secondary structures

    PubMed Central

    Levin, Alex; Lis, Mieszko; Ponty, Yann; O’Donnell, Charles W.; Devadas, Srinivas; Berger, Bonnie; Waldispühl, Jérôme

    2012-01-01

    The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.e. mutated) to adopt the desired folding properties. Although computationally inexpensive, this approach raises several questions such as (i) the influence of the seed; and (ii) the efficiency of single-path directed searches that may be affected by energy barriers in the mutational landscape. In this article, we present RNA-ensign, a novel paradigm for RNA design. Instead of taking a progressive adaptive walk driven by local search criteria, we use an efficient global sampling algorithm to examine large regions of the mutational landscape under structural and thermodynamical constraints until a solution is found. When considering the influence of the seeds and the target secondary structures, our results show that, compared to single-path directed searches, our approach is more robust, succeeds more often and generates more thermodynamically stable sequences. An ensemble approach to RNA design is thus well worth pursuing as a complement to existing approaches. RNA-ensign is available at http://csb.cs.mcgill.ca/RNAensign. PMID:22941632

  5. Secondary structure of corona proteins determines the cell surface receptors used by nanoparticles.

    PubMed

    Fleischer, Candace C; Payne, Christine K

    2014-12-11

    Nanoparticles used for biological and biomedical applications encounter a host of extracellular proteins. These proteins rapidly adsorb onto the nanoparticle surface, creating a protein corona. Poly(ethylene glycol) can reduce, but not eliminate, the nonspecific adsorption of proteins. As a result, the adsorbed proteins, rather than the nanoparticle itself, determine the cellular receptors used for binding, the internalization mechanism, the intracellular transport pathway, and the subsequent immune response. Using fluorescence microscopy and flow cytometry, we first characterize a set of polystyrene nanoparticles in which the same adsorbed protein, bovine serum albumin, leads to binding to two different cell surface receptors: native albumin receptors and scavenger receptors. Using a combination of circular dichroism spectroscopy, isothermal titration calorimetry, and fluorescence spectroscopy, we demonstrate that the secondary structure of the adsorbed bovine serum albumin protein controls the cellular receptors used by the protein-nanoparticle complexes. These results show that protein secondary structure is a key parameter in determining the cell surface receptor used by a protein-nanoparticle complex. We expect this link between protein structure and cellular outcomes will provide a molecular basis for the design of nanoparticles for use in biological and biomedical applications. PMID:24779411

  6. Comparative structure and biomechanics of plant primary and secondary cell walls

    PubMed Central

    Cosgrove, Daniel J.; Jarvis, Michael C.

    2012-01-01

    Recent insights into the physical biology of plant cell walls are reviewed, summarizing the essential differences between primary and secondary cell walls and identifying crucial gaps in our knowledge of their structure and biomechanics. Unexpected parallels are identified between the mechanism of expansion of primary cell walls during growth and the mechanisms by which hydrated wood deforms under external tension. There is a particular need to revise current “cartoons” of plant cell walls to be more consistent with data from diverse approaches and to go beyond summarizing limited aspects of cell walls, serving instead as guides for future experiments and for the application of new techniques. PMID:22936943

  7. Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce

    PubMed Central

    2013-01-01

    Background Ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Their secondary structures are crucial for the RNA functionality, and the prediction of the secondary structures is widely studied. Our previous research shows that cutting long sequences into shorter chunks, predicting secondary structures of the chunks independently using thermodynamic methods, and reconstructing the entire secondary structure from the predicted chunk structures can yield better accuracy than predicting the secondary structure using the RNA sequence as a whole. The chunking, prediction, and reconstruction processes can use different methods and parameters, some of which produce more accurate predictions than others. In this paper, we study the prediction accuracy and efficiency of three different chunking methods using seven popular secondary structure prediction programs that apply to two datasets of RNA with known secondary structures, which include both pseudoknotted and non-pseudoknotted sequences, as well as a family of viral genome RNAs whose structures have not been predicted before. Our modularized MapReduce framework based on Hadoop allows us to study the problem in a parallel and robust environment. Results On average, the maximum accuracy retention values are larger than one for our chunking methods and the seven prediction programs over 50 non-pseudoknotted sequences, meaning that the secondary structure predicted using chunking is more similar to the real structure than the secondary structure predicted by using the whole sequence. We observe similar results for the 23 pseudoknotted sequences, except for the NUPACK program using the centered chunking method. The performance analysis for 14 long RNA sequences from the Nodaviridae virus family outlines how the coarse-grained mapping of chunking and predictions in the MapReduce framework exhibits shorter turnaround times for short RNA sequences. However

  8. GraphClust: alignment-free structural clustering of local RNA secondary structures

    PubMed Central

    Rose, Dominic; Backofen, Rolf

    2012-01-01

    Motivation: Clustering according to sequence–structure similarity has now become a generally accepted scheme for ncRNA annotation. Its application to complete genomic sequences as well as whole transcriptomes is therefore desirable but hindered by extremely high computational costs. Results: We present a novel linear-time, alignment-free method for comparing and clustering RNAs according to sequence and structure. The approach scales to datasets of hundreds of thousands of sequences. The quality of the retrieved clusters has been benchmarked against known ncRNA datasets and is comparable to state-of-the-art sequence–structure methods although achieving speedups of several orders of magnitude. A selection of applications aiming at the detection of novel structural ncRNAs are presented. Exemplarily, we predicted local structural elements specific to lincRNAs likely functionally associating involved transcripts to vital processes of the human nervous system. In total, we predicted 349 local structural RNA elements. Availability: The GraphClust pipeline is available on request. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22689765

  9. Ten-Structure as Strategy of Addition 1-20 by Involving Spatial Structuring Ability for First Grade Students

    ERIC Educational Resources Information Center

    Salmah, Ummy; Putri, Ratu Ilma Indra; Somakim

    2015-01-01

    The aim of this study is to design learning activities that can support students to develop strategies for the addition of number 1 to 20 in the first grade by involving students' spatial structuring ability. This study was conducted in Indonesia by involving 27 students. In this paper, one of three activities is discussed namely ten-box activity.…

  10. Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta).

    PubMed

    Petrou, E L; Hauser, L; Waples, R S; Seeb, J E; Templin, W D; Gomez-Uchida, D; Seeb, L W

    2013-12-01

    Numerous empirical studies have reported lack of migration-drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ~13,000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years. PMID:24118255

  11. Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)

    PubMed Central

    Petrou, E L; Hauser, L; Waples, R S; Seeb, J E; Templin, W D; Gomez-Uchida, D; Seeb, L W

    2013-01-01

    Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ∼13 000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years. PMID:24118255

  12. Students' Understanding of Primary and Secondary Protein Structure: Drawing Secondary Protein Structure Reveals Student Understanding Better than Simple Recognition of Structures

    ERIC Educational Resources Information Center

    Harle, Marissa; Towns, Marcy H.

    2013-01-01

    The interdisciplinary nature of biochemistry courses requires students to use both chemistry and biology knowledge to understand biochemical concepts. Research that has focused on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations in addition to a fragmented…

  13. Secondary Airflow Structure around Clustered Shrubs and Its Significance for Vegetated Dune Evolution

    NASA Astrophysics Data System (ADS)

    Luo, Wanyin; Dong, Zhibao; Qian, Guangqiang; Lu, Junfeng

    2016-04-01

    Shrubs have an important significance in aeolian processes due to their disturbance of the local airflow. In the formation of vegetated dunes, there is an iterative interaction between shrub geometry, the structure of the secondary airflow, and the interaction between neighboring shrubs. Understanding the dynamics of vegetated dunes thus requires an insight into the airflow fields around shrubs. Based on aerodynamic and aeolian sand physics theory, this project measured the complex secondary flow field and aeolian sand deposition pattern around single and cluster shrubs with varied densities (i.e., 0.05, 0.08, 0.15, 0.20) and gap ratios (the ratio of the gap spacing between the shrub models to the center-to-center distance for the shrub models, ranged from 1.1 to 1.8 with side-by-side arrangement and 1.2 to 4.3 with tandem arrangement) using the particle image velocimetry system through wind tunnle simulation. The relationship between the secondary airflow structure and the shrub's porosity and arrangement was analyzed quantitatively. Research results revealed that porosity (density) is the key parameter to affect the flow patterns around single shrub. Compared to solid obstacles, bleed flow through the shrubs has great influence on the secondary airflow patterns around itself. Under cluster modes, the distance between two adjacent shrubs has great influence on flow field structures around them. The flow patterns around two side-by-side arranged shrubs can be classified into three kinds of modes, that is: single-bluff-body, biased flow pattern and parallel vortex streets. The flow patterns around two tandem arranged shrubs can be classified into three regimes, that is: the extended body regime, reattachment regime and co-shedding regime. The "shadow zone" with low velocity in the lee of shrubs is the optimal position for sand deposition, but its form, size and orientation would varied with the shrub porosity and gap ratio between them. With the increase of the gap

  14. Experiences and Reflections about Teaching Atomic Structure in a Jigsaw Classroom in Lower Secondary School Chemistry Lessons

    NASA Astrophysics Data System (ADS)

    Eilks, Ingo

    2005-02-01

    This article describes and discusses an example of how atomic structure can be taught in lower secondary chemistry using a modified jigsaw-classroom method. The lesson was taught in grades 9 and 10 (age range 15 17 years) chemistry in 13 learning groups with a total of 313 students in various grammar, middle, and comprehensive schools in Germany. The written evaluation of the lesson focused on determining the students’ opinions on the teaching methods that were used. Emphasis was on gathering information from the students’ viewpoint. Did the students think that these methods could make science lessons more attractive? Could these methods help to promote more active student learning, cooperative learning, or communicative and social abilities? Additional data that were derived from a cognitive test and teacher feedback are also presented. The results of the study show that teaching methods like the jigsaw classroom have potential to improve students’ attitude towards science. The results may also indicate that it is appropriate to demand that student-oriented and cooperative-learning methods be used more often in secondary level science education.

  15. Secondary structural analysis of the carboxyl-terminal domain from different connexin isoforms.

    PubMed

    Spagnol, Gaëlle; Al-Mugotir, Mona; Kopanic, Jennifer L; Zach, Sydney; Li, Hanjun; Trease, Andrew J; Stauch, Kelly L; Grosely, Rosslyn; Cervantes, Matthew; Sorgen, Paul L

    2016-03-01

    The connexin carboxyl-terminal (CxCT) domain plays a role in the trafficking, localization, and turnover of gap junction channels, as well as the level of gap junction intercellular communication via numerous post-translational modifications and protein-protein interactions. As a key player in the regulation of gap junctions, the CT presents itself as a target for manipulation intended to modify function. Specific to intrinsically disordered proteins, identifying residues whose secondary structure can be manipulated will be critical toward unlocking the therapeutic potential of the CxCT domain. To accomplish this goal, we used biophysical methods to characterize CxCT domains attached to their fourth transmembrane domain (TM4). Circular dichroism and nuclear magnetic resonance were complementary in demonstrating the connexin isoforms that form the greatest amount of α-helical structure in their CT domain (Cx45 > Cx43 > Cx32 > Cx50 > Cx37 ≈ Cx40 ≈ Cx26). Studies compared the influence of 2,2,2-trifluoroethanol, pH, phosphorylation, and mutations (Cx32, X-linked Charcot-Marie Tooth disease; Cx26, hearing loss) on the TM4-CxCT structure. While pH modestly influences the CT structure, a major structural change was associated with phosphomimetic substitutions. Since most connexin CT domains are phosphorylated throughout their life cycle, studies of phospho-TM4-CxCT isoforms will be critical toward understanding the role that structure plays in regulating gap junction function. PMID:26542351

  16. Characterization of Effect of Support Structures in Laser Additive Manufacturing of Stainless Steel

    NASA Astrophysics Data System (ADS)

    Järvinen, Jukka-Pekka; Matilainen, Ville; Li, Xiaoyun; Piili, Heidi; Salminen, Antti; Mäkelä, Ismo; Nyrhilä, Olli

    Laser additive manufacturing (LAM) of stainless steel is a layer wisetechnology for fabricating 3D parts from metal powder via selectively melting powder with laser beam. Support structures play a significant role in LAM process as they help to remove heat away from the process and on the other hand hold the work piece in its place. A successful design of support structures can help to achievea building process fast and inexpensive with high quality. Aimof this study was to characterize the usability of two types of support structures: web and tube supports. Purpose of this studywas also to analyze how suitable they are in two industrial application cases: case for dental application and case for jewelry application. It was concluded that the removability of web supports was much better than tube supports. It was noticed that support structures are an important part of LAM process and they strongly affect the manufacturability and the end quality of the part.

  17. The influence of residual water on the secondary structure and crystallinity of freeze-dried fibrinogen.

    PubMed

    Wahl, Verena; Scheibelhofer, Otto; Roessl, Ulrich; Leitgeb, Stefan; De Beer, Thomas; Khinast, Johannes

    2015-04-30

    The purpose of this work was to investigate the influence of water content on the secondary structure of a freeze-dried protein (fibrinogen) after a storage period of two weeks. To that end, attenuated reflectance Fourier transformed infrared (ATR-FTIR) and Raman spectra were generated and evaluated and the crystalline state of the fibrinogen bulks was determined via X-ray diffraction. First, a PCA (principal component analysis) of the spectral data was performed. While the α-helix and β-turn contents were increasing with the increasing water content, the β-sheet content was decreasing. A partial least squares (PLS) model was developed to correlate the mid-infrared and Raman spectral changes with the degree of crystallinity. The obtained R(2) value of 0.953 confirmed a correlation between changes in the secondary structure and crystallinity of the samples. The results demonstrated that the combined ATR-FTIR and Raman approach could be used to predict the crystalline state in freeze-dried fibrinogen products. PMID:25701629

  18. Modeling the influence of alkane molecular structure on secondary organic aerosol formation.

    PubMed

    Aumont, Bernard; Camredon, Marie; Mouchel-Vallon, Camille; La, Stéphanie; Ouzebidour, Farida; Valorso, Richard; Lee-Taylor, Julia; Madronich, Sasha

    2013-01-01

    Secondary Organic Aerosols (SOA) production and ageing is a multigenerational oxidation process involving the formation of successive organic compounds with higher oxidation degree and lower vapor pressure. Intermediate Volatility Organic Compounds (IVOC) emitted to the atmosphere are expected to be a substantial source of SOA. These emitted IVOC constitute a complex mixture including linear, branched and cyclic alkanes. The explicit gas-phase oxidation mechanisms are here generated for various linear and branched C10-C22 alkanes using the GECKO-A (Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere) and SOA formation is investigated for various homologous series. Simulation results show that both the size and the branching of the carbon skeleton are dominant factors driving the SOA yield. However, branching appears to be of secondary importance for the particle oxidation state and composition. The effect of alkane molecular structure on SOA yields appears to be consistent with recent laboratory observations. The simulated SOA composition shows, however, an unexpected major contribution from multifunctional organic nitrates. Most SOA contributors simulated for the oxidation of the various homologous series are far too reduced to be categorized as highly oxygenated organic aerosols (OOA). On a carbon basis, the OOA yields never exceeded 10% regardless of carbon chain length, molecular structure or ageing time. This version of the model appears clearly unable to explain a large production of OOA from alkane precursors. PMID:24600999

  19. Analysis of secondary structural and physicochemical changes in protein-protein complexes.

    PubMed

    Saranya, N; Saravanan, K M; Michael Gromiha, M; Selvaraj, S

    2016-03-01

    Conformation switching in protein-protein complexes is considered important for the molecular recognition process. Overall analysis of 123 protein-protein complexes in a benchmark data-set showed that 6.8% of residues switched over their secondary structure conformation upon complex formation. Amino acid residue-wise preference for conformation change has been analyzed in binding and non-binding site residues separately. In this analysis, residues such as Ser, Leu, Glu, and Lys had higher frequency of secondary structural conformation change. The change of helix to coil and sheet to coil conformation and vice versa has been observed frequently, whereas the conformation change of helix to extended sheet occurred rarely in the studied complexes. Influence of conformation change toward the N and C terminal on either side of the binding site residues has been analyzed. Further, analysis on φ and ψ angle variation, conservation, stability, and solvent accessibility have been performed on binding site residues. Knowledge obtained from the present study could be effectively employed in the protein-protein modeling and docking studies. PMID:25990569

  20. Evolutionary conservation of sequence and secondary structures inCRISPR repeats

    SciTech Connect

    Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

    2006-09-01

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

  1. Secondary flow structures under simple harmonic inflow in a bent pipe model for curved arteries

    NASA Astrophysics Data System (ADS)

    Glenn, Autumn; Seagrave, Penelope; Shu, Fangjun; Bulusu, Kartik; Plesniak, Michael W.

    2010-11-01

    Inward centrifuging of fluid in the inviscid core of a 180 degree curved pipe leads to Lyne-type vortices under zero-mean harmonic oscillations, along with the formation of vortices in the Stokes' layer, that rotate in the same directional sense as their steady flow counterpart (Dean vortices). Under physiological conditions, the development of the Lyne-type vortices is believed to be influenced by the systolic pulse, and its associated rapid acceleration and deceleration. Experimental data acquired using Particle Image Velocimetry (PIV) for three harmonic waveforms of different frequencies clarify the conditions under which Lyne vortices form. Multiple vortex pairs were observed for all waveforms and frequencies investigated, including Dean and Lyne-type vortex structures at a Womersley number of 4.22, much lower than previously reported. Hence, frequency alone is not an adequate governing parameter to characterize secondary flow structures in pulsatile flows. A regime map of the secondary flow was sought by using an acceleration-based parameter and the Dean number.

  2. Addition of three-dimensional isoparametric elements to NASA structural analysis program (NASTRAN)

    NASA Technical Reports Server (NTRS)

    Field, E. I.; Johnson, S. E.

    1973-01-01

    Implementation is made of the three-dimensional family of linear, quadratic and cubic isoparametric solid elements into the NASA Structural Analysis program, NASTRAN. This work included program development, installation, testing, and documentation. The addition of these elements to NASTRAN provides a significant increase in modeling capability particularly for structures requiring specification of temperatures, material properties, displacements, and stresses which vary throughout each individual element. Complete program documentation is presented in the form of new sections and updates for direct insertion to the three NASTRAN manuals. The results of demonstration test problems are summarized. Excellent results are obtained with the isoparametric elements for static, normal mode, and buckling analyses.

  3. Secondary Structure Prediction of Protein Constructs Using Random Incremental Truncation and Vacuum-Ultraviolet CD Spectroscopy

    PubMed Central

    Pukáncsik, Mária; Orbán, Ágnes; Nagy, Kinga; Matsuo, Koichi; Gekko, Kunihiko; Maurin, Damien; Hart, Darren; Kézsmárki, István; Vertessy, Beata G.

    2016-01-01

    A novel uracil-DNA degrading protein factor (termed UDE) was identified in Drosophila melanogaster with no significant structural and functional homology to other uracil-DNA binding or processing factors. Determination of the 3D structure of UDE is excepted to provide key information on the description of the molecular mechanism of action of UDE catalysis, as well as in general uracil-recognition and nuclease action. Towards this long-term aim, the random library ESPRIT technology was applied to the novel protein UDE to overcome problems in identifying soluble expressing constructs given the absence of precise information on domain content and arrangement. Nine constructs of UDE were chosen to decipher structural and functional relationships. Vacuum ultraviolet circular dichroism (VUVCD) spectroscopy was performed to define the secondary structure content and location within UDE and its truncated variants. The quantitative analysis demonstrated exclusive α-helical content for the full-length protein, which is preserved in the truncated constructs. Arrangement of α-helical bundles within the truncated protein segments suggested new domain boundaries which differ from the conserved motifs determined by sequence-based alignment of UDE homologues. Here we demonstrate that the combination of ESPRIT and VUVCD spectroscopy provides a new structural description of UDE and confirms that the truncated constructs are useful for further detailed functional studies. PMID:27273007

  4. SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data.

    PubMed

    Ouyang, Zhengqing; Snyder, Michael P; Chang, Howard Y

    2013-02-01

    We present an integrative approach, SeqFold, that combines high-throughput RNA structure profiling data with computational prediction for genome-scale reconstruction of RNA secondary structures. SeqFold transforms experimental RNA structure information into a structure preference profile (SPP) and uses it to select stable RNA structure candidates representing the structure ensemble. Under a high-dimensional classification framework, SeqFold efficiently matches a given SPP to the most likely cluster of structures sampled from the Boltzmann-weighted ensemble. SeqFold is able to incorporate diverse types of RNA structure profiling data, including parallel analysis of RNA structure (PARS), selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), fragmentation sequencing (FragSeq) data generated by deep sequencing, and conventional SHAPE data. Using the known structures of a wide range of mRNAs and noncoding RNAs as benchmarks, we demonstrate that SeqFold outperforms or matches existing approaches in accuracy and is more robust to noise in experimental data. Application of SeqFold to reconstruct the secondary structures of the yeast transcriptome reveals the diverse impact of RNA secondary structure on gene regulation, including translation efficiency, transcription initiation, and protein-RNA interactions. SeqFold can be easily adapted to incorporate any new types of high-throughput RNA structure profiling data and is widely applicable to analyze RNA structures in any transcriptome. PMID:23064747

  5. Structure of the velocity distribution of sheath-accelerated secondary electrons in an asymmetric RF-dc discharge

    NASA Astrophysics Data System (ADS)

    Khrabrov, Alexander V.; Kaganovich, Igor D.; Ventzek, Peter L. G.; Ranjan, Alok; Chen, Lee

    2015-10-01

    Low-pressure capacitively-coupled discharges with additional dc bias applied to a separate electrode are utilized in plasma-assisted etching for semiconductor device manufacturing. Measurements of the electron velocity distribution function (EVDF) of the flux impinging on the wafer, as well as in the plasma bulk, show a thermal population and additional peaks within a broad range of energies. That range extends from the thermal level up to the value for the ‘ballistic’ peak, corresponding to the bias potential. The non-thermal electron flux has been correlated to alleviating the electron shading effect and providing etch-resistance properties to masking photoresist layers. ‘Middle-energy peak electrons’ at energies of several hundred eV may provide an additional sustaining mechanism for the discharge. These features in the electron velocity (or energy) distribution functions are possibly caused by secondary electrons emitted from the electrodes and interacting with two high-voltage sheaths: a stationary sheath at the dc electrode and an oscillating self-biased sheath at the powered electrode. Since at those energies the mean free path for large-angle scattering (momentum relaxation length) is comparable to, or exceeds the size of the discharge gap, these ‘ballistic’ electrons will not be fully scattered by the background gas as they traverse the inter-electrode space. We have performed test-particle simulations in which the features in the EVDF of electrons impacting the RF electrode are fully resolved at all energies. An analytical model has been developed to predict existence of peaked and step-like structures in the EVDF. Those features can be explained by analyzing the kinematics of electron trajectories in the discharge gap. Step-like structures in the EVDF near the powered electrode appear due to accumulation of electrons emitted from the dc electrode within a portion of the RF cycle, and their subsequent release. Trapping occurs when the RF

  6. Ammonium addition (and aerosol pH) has a dramatic impact on the volatility and yield of glyoxal secondary organic aerosol.

    PubMed

    Ortiz-Montalvo, Diana L; Häkkinen, Silja A K; Schwier, Allison N; Lim, Yong B; McNeill, V Faye; Turpin, Barbara J

    2014-01-01

    Glyoxal is an important precursor to secondary organic aerosol (SOA) formed through aqueous chemistry in clouds, fogs, and wet aerosols, yet the gas-particle partitioning of the resulting mixture is not well understood. This work characterizes the volatility behavior of the glyoxal precursor/product mix formed after aqueous hydroxyl radical oxidation and droplet evaporation under cloud-relevant conditions for 10 min, thus aiding the prediction of SOA via this pathway (SOACld). This work uses kinetic modeling for droplet composition, droplet evaporation experiments and temperature-programmed desorption aerosol-chemical ionization mass spectrometer analysis of gas-particle partitioning. An effective vapor pressure (p'L,eff) of ∼10(-7) atm and an enthalpy of vaporization (ΔHvap,eff) of ∼70 kJ/mol were estimated for this mixture. These estimates are similar to those of oxalic acid, which is a major product. Addition of ammonium until the pH reached 7 (with ammonium hydroxide) reduced the p'L,eff to <10(-9) atm and increased the ΔHvap,eff to >80 kJ/mol, at least in part via the formation of ammonium oxalate. pH 7 samples behaved like ammonium oxalate, which has a vapor pressure of ∼10(-11) atm. We conclude that ammonium addition has a large effect on the gas-particle partitioning of the mixture, substantially enhancing the yield of SOACld from glyoxal. PMID:24328102

  7. An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

    PubMed Central

    Tsagkogeorga, Georgia; Turon, Xavier; Hopcroft, Russell R; Tilak, Marie-Ka; Feldstein, Tamar; Shenkar, Noa; Loya, Yossi; Huchon, Dorothée; Douzery, Emmanuel JP; Delsuc, Frédéric

    2009-01-01

    Background Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea. Results Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister

  8. 5-Azacytidine and RNA secondary structure increase the retrovirus mutation rate.

    PubMed Central

    Pathak, V K; Temin, H M

    1992-01-01

    A broad spectrum of mutations occurs at a high rate during a single round of retrovirus replication (V.K. Pathak and H. M. Temin, Proc. Natl. Acad. Sci. USA 87:6019-6023, 1990). We have now determined that this high rate of spontaneous mutation can be further increased by 5-azacytidine (AZC) treatment or by regions of potential RNA secondary structure. We found a 13-fold increase in the mutation rate after AZC treatment of retrovirus-producing cells and target cells. The AZC-induced substitutions were located at the same target sites as previously identified spontaneous substitutions. The concordance of the AZC-induced and spontaneous substitutions indicates the presence of reverse transcription "pause sites," where the growing point is error prone. An analysis of nucleotides that neighbored substitutions revealed that transversions occur primarily by transient template misalignment, whereas transitions occur primarily by misincorporation. We also introduced a 34-bp potential stem-loop structure as an in-frame insertion within a lacZ alpha gene that was inserted in the long terminal repeat (LTR) U3 region and determined whether this potential secondary structure increased the rate of retrovirus mutations. We found a threefold increase in the retrovirus mutation rate. Fifty-seven of 96 mutations were deletions associated with the potential stem-loop. We also determined that these deletion mutations occurred primarily during minus-strand DNA synthesis by comparing the frequencies of mutations in recovered provirus plasmids containing both LTRs and in provirus plasmids containing only one LTR. PMID:1373201

  9. Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the Brassicaceae (mustards).

    PubMed

    Edger, Patrick P; Tang, Michelle; Bird, Kevin A; Mayfield, Dustin R; Conant, Gavin; Mummenhoff, Klaus; Koch, Marcus A; Pires, J Chris

    2014-01-01

    The internal transcribed spacers of the nuclear ribosomal RNA gene cluster, termed ITS1 and ITS2, are the most frequently used nuclear markers for phylogenetic analyses across many eukaryotic groups including most plant families. The reasons for the popularity of these markers include: 1.) Ease of amplification due to high copy number of the gene clusters, 2.) Available cost-effective methods and highly conserved primers, 3.) Rapidly evolving markers (i.e. variable between closely related species), and 4.) The assumption (and/or treatment) that these sequences are non-functional, neutrally evolving phylogenetic markers. Here, our analyses of ITS1 and ITS2 for 50 species suggest that both sequences are instead under selective constraints to preserve proper secondary structure, likely to maintain complete self-splicing functions, and thus are not neutrally-evolving phylogenetic markers. Our results indicate the majority of sequence sites are co-evolving with other positions to form proper secondary structure, which has implications for phylogenetic inference. We also found that the lowest energy state and total number of possible alternate secondary structures are highly significantly different between ITS regions and random sequences with an identical overall length and Guanine-Cytosine (GC) content. Lastly, we review recent evidence highlighting some additional problematic issues with using these regions as the sole markers for phylogenetic studies, and thus strongly recommend additional markers and cost-effective approaches for future studies to estimate phylogenetic relationships. PMID:24984034

  10. Impact of Microscale and Pilot-Scale Freeze-Drying on Protein Secondary Structures: Sucrose Formulations of Lysozyme and Catalase.

    PubMed

    Peters, Björn-Hendrik; Leskinen, Jari T T; Molnár, Ferdinand; Ketolainen, Jarkko

    2015-11-01

    Microscale (MS) freeze-drying offers rapid process cycles for early-stage formulation development. The effects of the MS approach on the secondary structures of two model proteins, lysozyme and catalase, were compared with pilot-scale (PS) vial freeze-drying. The secondary structures were assessed by attenuated total reflection Fourier transformed infrared spectroscopy. Formulations were made with increasing sucrose-protein ratios. Freeze-drying protocols involved regular cooling without thermal treatment and annealing with MS and PS equipment, and cooling rate variations with the MS. Principal component analysis of smoothed second-derivative amide I spectra revealed sucrose-protein ratio-dependent shifts toward α-helical structures. Transferability of sucrose-protein formulations from MS to PS vial freeze-drying was evidenced at regular cooling rates. Local differences in protein secondary structures between the bottom and top of sucrose-catalase samples could be detected at the sucrose-catalase ratios of 1 and 2, this being related to the initial filling height and ice crystal morphology. Annealing revealed temperature, protein, formulation, and sample location-dependent effects influencing surface morphology at the top, or causing protein secondary structure perturbation at the bottom. With the MS approach, protein secondary structure differences at different cooling rates could be detected for sucrose-lysozyme samples at the sucrose-lysozyme ratio of 1. PMID:26305147

  11. Structure of cellulose-deficient secondary cell walls from the irx3 mutant of Arabidopsis thaliana.

    PubMed

    Ha, Marie-Ann; MacKinnon, Iain M; Sturcová, Adriana; Apperley, David C; McCann, Maureen C; Turner, Simon R; Jarvis, Michael C

    2002-09-01

    In the Arabidopsis mutant irx3, truncation of the AtCesA7 gene encoding a xylem-specific cellulose synthase results in reduced cellulose synthesis in the affected xylem cells and collapse of mature xylem vessels. Here we describe spectroscopic experiments to determine whether any cellulose, normal or abnormal, remained in the walls of these cells and whether there were consequent effects on other cell-wall polysaccharides. Xylem cell walls from irx3 and its wild-type were prepared by anatomically specific isolation and were examined by solid-state NMR spectroscopy and FTIR microscopy. The affected cell walls of irx3 contained low levels of crystalline cellulose, probably associated with primary cell walls. There was no evidence that crystalline cellulose was replaced by less ordered glucans. From the molecular mobility of xylans and lignin it was deduced that these non-cellulosic polymers were cross-linked together in both irx3 and the wild-type. The disorder previously observed in the spatial pattern of non-cellulosic polymer deposition in the secondary walls of irx3 xylem could not be explained by any alteration in the structure or cross-linking of these polymers and may be attributed directly to the absence of cellulose microfibrils which, in the wild-type, scaffold the organisation of the other polymers into a coherent secondary cell wall. PMID:12165296

  12. Suppression of secondary electron yield by micro-porous array structure

    SciTech Connect

    Ye, M.; He, Y. N.; Hu, S. G.; Wang, R.; Hu, T. C.; Yang, J.; Cui, W. Z.

    2013-02-21

    We study secondary electron yield (SEY) suppression for metal materials using a roughened surface with a micro-porous array. First, we perform a Monte Carlo simulation of the electron trajectory in a single cylindrical well using a phenomenological model of secondary electron emission and the SEY suppression efficiency of a micro-porous array. The simulation results show that the SEY of a roughened surface is affected significantly by the aspect ratio of the micro-pores and the surface porosity of the metal plate. Then, to verify the simulation results, we produce a micro-porous array on metal plates using photolithography and measure their SEYs. We show that the micro-porous array structure can efficiently suppress the SEY of metal materials, and the measurements agree quantitatively with the corresponding simulation results. Finally, we derive an analytical formula to evaluate easily the SEY suppression efficiency of the Ag micro-porous array. In total, the micro-porous array proposed in this paper offers an alternative to SEY suppression in related areas such as multipactor effects in satellite payloads or electron cloud effects in accelerators.

  13. Role of secondary long wavelength structures in the saturation of electron temperature gradient driven turbulence

    SciTech Connect

    Li Jiquan; Kishimoto, Y.

    2008-11-15

    The dynamics of secondary long wavelength structures (LWSs) in electron temperature gradient (ETG) driven turbulence are investigated by performing gyrofluid simulations and modeling analyses in a slab geometry with an emphasis of the underlying nonlinear interaction processes. It is shown that the back-reaction of the secondary LWS on the ambient fluctuations essentially contributes to saturating ETG instability and limiting the electron transport. The LWS is nonlinearly generated mainly through the beating of the most unstable ETG modes, even a weak modulation instability. The back-reaction is identified as the enhanced stabilization of the ETG modes due to the streamer-type feature of the LWS, which dominantly produces a local poloidal mode coupling among unstable and highly damped spectral components to form a global mode, besides the suppression effect of the LWS due to the radial shearing decorrelation and/or the radial mode coupling. Finally, the correspondence between the LWS in the slab model and the quasimode observed in toroidal ETG simulation [Z. Lin et al., Phys. Plasmas 12, 056125 (2005)] and the importance of the nonlinear mode coupling in the multiscale turbulence interaction are discussed.

  14. Poly(L-lysine) and Clay Nanocomposite with Desired Matrix Secondary Structure: Effects of Polypeptide Molecular Weight

    SciTech Connect

    Hule,R.; Pochan, D.

    2007-01-01

    Nanocomposites (NC) were formed using cationic poly(L-lysine) (PLL), a semicrystalline polypeptide, that was reinforced by sodium montmorillonite (MMT) clay via solution intercalation technique. By varying solution conditions such as pH, temperature, and polypeptide concentration in the presence of clay platelets, the secondary structure of PLL was controllably altered into {alpha}-helical, {beta}-sheet, and random coil. The high molecular weight polypeptide shows a strong propensity to fold into the {beta}-sheet structure when cast as films, irrespective of the initial secondary structure in solution. Nanocomposite local morphology confirms intercalated MMT platelets with PLL over a wide range of compositions.

  15. Is the structural diversity of tripeptides sufficient for developing functional food additives with satisfactory multiple bioactivities?

    NASA Astrophysics Data System (ADS)

    Wang, Jian-Hui; Liu, Yong-Le; Ning, Jing-Heng; Yu, Jian; Li, Xiang-Hong; Wang, Fa-Xiang

    2013-05-01

    Multifunctional peptides have attracted increasing attention in the food science community because of their therapeutic potential, low toxicity and rapid intestinal absorption. However, previous study demonstrated that the limited structural variations make it difficult to optimize dipeptide molecules in a good balance between desirable and undesirable properties (F. Tian, P. Zhou, F. Lv, R. Song, Z. Li, J. Pept. Sci. 13 (2007) 549-566). In the present work, we attempt to answer whether the structural diversity is sufficient for a tripeptide to have satisfactory multiple bioactivities. Statistical test, structural examination and energetic analysis confirm that peptides of three amino acids long can bind tightly to human angiotensin converting enzyme (ACE) and thus exert significant antihypertensive efficacy. Further quantitative structure-activity relationship (QSAR) modeling and prediction of all 8000 possible tripeptides reveal that their ACE-inhibitory potency exhibits a good (positive) relationship to antioxidative activity, but has only a quite modest correlation with bitterness. This means that it is possible to find certain tripeptide entities possessing the optimal combination of strong ACE-inhibitory potency, high antioxidative activity and weak bitter taste, which are the promising candidates for developing multifunctional food additives with satisfactory multiple bioactivities. The marked difference between dipeptide and tripeptide can be attributed to the fact that the structural diversity of peptides increases dramatically with a slight change in sequence length.

  16. Design and analysis of supporting structure between the primary mirror and the secondary mirror on a space telescope

    NASA Astrophysics Data System (ADS)

    Wang, Chenjie; Chai, Wenyi; Feng, Liangjie; Yang, Wengang; Wang, Wei; Fan, Xuewu

    2015-10-01

    Mechanical stability is a significant segment for an on-axis space telescope to assure its assembly accuracy as well as the image quality in the rigorous space environment, supporting structure between the primary mirror and the secondary mirror as a main structure of the on-axis space telescope must be designed reasonably to meet the mission requirements of the space telescope. Meanwhile, in view of the limitation of the satellite launching cost, it is necessary to reduce the weight and power compensation during the supporting structure design based on the satisfaction of telescope performance. Two types of supporting structure for a space telescope are designed, one is three-tripod structure which has three tripods located on the optical bench to support the secondary mirror assemblies and keep the distance between the primary mirror and the secondary mirror, the other is barrel supporting structure which includes a tube and a secondary mirror support with four spider struts. To compare the mechanical performance and launching cost of the two kinds of supporting structure, both structural and thermal analysis model are established. The analysis results indicates that the three-tripod support is lighter, has better mechanical performance and needs less power compensation than the barrel support.

  17. Factors that Affect Mathematics-Science (MS) Scores in the Secondary Education Institutional Exam: An Application of Structural Equation Modeling

    ERIC Educational Resources Information Center

    Yavuz, Mustafa

    2009-01-01

    Discovering what determines students' success in the Secondary Education Institutional Exam is very important to parents and it is also critical for students, teachers, directors, and researchers. Research was carried out by studying the related literature and structural equation modeling techniques. A structural model was created that consisted…

  18. A role of BNLT compound addition on structure and properties of PZT ceramics

    NASA Astrophysics Data System (ADS)

    Jaita, P.; Watcharapasorn, A.; Jiansirisomboon, S.

    2010-09-01

    In this research, effects of lead-free bismuth sodium lanthanum titanate (BNLT) addition on structure and properties of lead zirconate titanate (PZT) ceramics were investigated. PZT ceramics with addition of 0.1-3.0 wt%BNLT were fabricated by a solid-state mixed oxide method and sintering at 1050-1200 °C for 2 h to obtain dense ceramics with at least 96% of theoretical density. X-ray diffraction indicated that complete solid solution occurred for all compositions. Phase identification showed both tetragonal and rhombohedral perovskite structure of PZT with no BNLT phase detected. Scanning electron micrographs of fractured PZT/BNLT ceramics showed equiaxed grain shape with both transgranular and intergranular fracture modes. Addition of BNLT was also found to reduce densification and effectively limited grain growth of PZT ceramic. Optimum Hv and KIC values were found to be 4.85 GPa and 1.56 MPa.m 1/2 for PZT/0.5 wt%BNLT sample. Among PZT/BNLT samples, room temperature dielectric constant seemed to be improved with increasing BNLT content. The maximum piezoelectric coefficient values were observed in pure PZT ceramic and were slightly decreased in BNLT-added samples. Small reduction of remanent polarization and coercive field in hysteresis loops was observed in BNLT-added samples, indicating a slightly suppressed ferroelectric interaction in this material system.

  19. Class Anxiety in Secondary Education: Exploring Structural Relations with Perceived Control, Engagement, Disaffection, and Performance.

    PubMed

    González, Antonio; Faílde Garrido, José María; Rodríguez Castro, Yolanda; Carrera Rodríguez, María Victoria

    2015-01-01

    The aim of this study was to assess the relationships between class-related anxiety with perceived control, teacher-reported behavioral engagement, behavioral disaffection, and academic performance. Participants were 355 compulsory secondary students (9th and 10th grades; Mean age = 15.2 years; SD = 1.8 years). Structural equation models revealed performance was predicted by perceived control, anxiety, disaffection, and engagement. Perceived control predicted anxiety, disaffection, and engagement. Anxiety predicted disaffection and engagement, and partially mediated the effects from control on disaffection (β = -.277, p < .005; CI = -.378, -.197) and engagement (β = .170, p < .002; CI = .103 .258). The negative association between anxiety and performance was mediated by engagement and disaffection (β = -.295, p < .002; CI = -.439, -.182). Anxiety, engagement, and disaffection mediated the effects of control on performance (β = .352, p < .003; CI = .279, .440). The implications of these results are discussed in the light of current theory and educational interventions. PMID:26364673

  20. Phylogenetic study of nine species of freshwater monogeneans using secondary structure and motif prediction from India

    PubMed Central

    Chaudhary, Anshu; Singh, Hridaya Shanker

    2012-01-01

    The present study was performed to identify and validate monogenean species from different piscine hosts using molecular tools. Nine species of freshwater monogeneans were collected from gills and skin of freshwater fishes at Hastinapur, Meerut, India. After microscopic examination, molecular analysis was performed utilizing 28S gene marker. Phylogenetic analysis indicated the validation and systematic position of these nine different monogeneans belongs to the Dactylogyridae and Gyrodactylidae families. The findings also confirm that the 28S rDNA sequence is highly conserved and may prove to be useful in taxonomic studies of parasitic platyhelminthes. Besides this, the study is also supplemented by molecular morphometrics that is based on 28S secondary structure homologies of nine monogenean species. The data indicate that 28S motifs i.e., ≤ 50bp in size can also be considered a promising tool for monogenean species identification and their validation. PMID:23144541

  1. Translation with secondary structure: Dynamic blockages in totally asymmetric simple exclusion process

    NASA Astrophysics Data System (ADS)

    Shaw, Leah

    2011-03-01

    The totally asymmetric simple exclusion process (TASEP) is often used as a model for protein synthesis, with the lattice and particles representing the mRNA and ribosomes, respectively. Here we model the effect of secondary structure (folding) of the mRNA by introducing a dynamic blockage region in the lattice. If the region is unoccupied by particles, the blockage can close and prevent upstream particles from moving into it, representing the folding of that section of mRNA. Reopening of the blockage, allowing particles to pass, represents unfolding. We study the effects of the blockage size, closing/opening probabilities, and TASEP parameters on the particle current and blockage switching rates.

  2. Secondary-structure characterization by far-UV CD of highly purified uncoupling protein 1 expressed in yeast.

    PubMed Central

    Douette, Pierre; Navet, Rachel; Bouillenne, Fabrice; Brans, Alain; Sluse-Goffart, Claudine; Matagne, André; Sluse, Francis E

    2004-01-01

    The rat UCP1 (uncoupling protein 1) is a mitochondrial inner-membrane carrier involved in energy dissipation and heat production. We expressed UCP1 carrying a His6 epitope at its C-terminus in Saccharomyces cerevisiae mitochondria. The recombinant-tagged UCP1 was purified by immobilized metal-ion affinity chromatography to homogeneity (>95%). This made it suitable for subsequent biophysical characterization. Fluorescence resonance energy transfer experiments showed that n-dodecyl-beta-D-maltoside-solubilized UCP1-His6 retained its PN (purine nucleotide)-binding capacity. The far-UV CD spectrum of the functional protein clearly indicated the predominance of alpha-helices in the UCP1 secondary structure. The UCP1 secondary structure exhibited an alpha-helical degree of approx. 68%, which is at least 25% higher than the previously reported estimations based on computational predictions. Moreover, the helical content remained unchanged in free and PN-loaded UCP1. A homology model of the first repeat of UCP1, built on the basis of X-ray-solved close parent, the ADP/ATP carrier, strengthened the CD experimental results. Our experimental and computational results indicate that (i) alpha-helices are the major component of UCP1 secondary structure; (ii) PN-binding mechanism does not involve significant secondary-structure rearrangement; and (iii) UCP1 shares similar secondary-structure characteristics with the ADP/ATP carrier, at least for the first repeat. PMID:14766012

  3. Effect of Secondary Cooling Conditions on Solidification Structure and Central Macrosegregation in Continuously Cast High-Carbon Rectangular Billet

    NASA Astrophysics Data System (ADS)

    Zeng, Jie; Chen, Weiqing

    2015-10-01

    Solidification structures of high carbon rectangular billet with a size of 180 mm × 240 mm in different secondary cooling conditions were simulated using cellular automaton-finite element (CAFE) coupling model. The adequacy of the model was compared with the simulated and the actual macrostructures of 82B steel. Effects of the secondary cooling water intensity on solidification structures including the equiaxed grain ratio and the equiaxed grain compactness were discussed. It was shown that the equiaxed grain ratio and the equiaxed grain compactness changed in the opposite direction at different secondary cooling water intensities. Increasing the secondary cooling water intensity from 0.9 or 1.1 to 1.3 L/kg could improve the equiaxed grain compactness and decrease the equiaxed grain ratio. Besides, the industrial test was conducted to investigate the effect of different secondary cooling water intensities on the center carbon macrosegregation of 82B steel. The optimum secondary cooling water intensity was 0.9 L/kg, while the center carbon segregation degree was 1.10. The relationship between solidification structure and center carbon segregation was discussed based on the simulation results and the industrial test.

  4. An identification method for enclosed voids restriction in manufacturability design for additive manufacturing structures

    NASA Astrophysics Data System (ADS)

    Liu, Shutian; Li, Quhao; Chen, Wenjiong; Tong, Liyong; Cheng, Gengdong

    2015-06-01

    Additive manufacturing (AM) technologies, such as selective laser sintering (SLS) and fused deposition modeling (FDM), have become the powerful tools for direct manufacturing of complex parts. This breakthrough in manufacturing technology makes the fabrication of new geometrical features and multiple materials possible. Past researches on designs and design methods often focused on how to obtain desired functional performance of the structures or parts, specific manufacturing capabilities as well as manufacturing constraints of AM were neglected. However, the inherent constraints in AM processes should be taken into account in design process. In this paper, the enclosed voids, one type of manufacturing constraints of AM, are investigated. In mathematics, enclosed voids restriction expressed as the solid structure is simplyconnected. We propose an equivalent description of simply-connected constraint for avoiding enclosed voids in structures, named as virtual temperature method (VTM). In this method, suppose that the voids in structure are filled with a virtual heating material with high heat conductivity and solid areas are filled with another virtual material with low heat conductivity. Once the enclosed voids exist in structure, the maximum temperature value of structure will be very high. Based upon this method, the simplyconnected constraint is equivalent to maximum temperature constraint. And this method can be easily used to formulate the simply-connected constraint in topology optimization. The effectiveness of this description method is illustrated by several examples. Based upon topology optimization, an example of 3D cantilever beam is used to illustrate the trade-off between manufacturability and functionality. Moreover, the three optimized structures are fabricated by FDM technology to indicate further the necessity of considering the simply-connected constraint in design phase for AM.

  5. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence.

    PubMed

    Rice, D W; Eisenberg, D

    1997-04-11

    In protein fold recognition, a probe amino acid sequence is compared to a library of representative folds of known structure to identify a structural homolog. In cases where the probe and its homolog have clear sequence similarity, traditional residue substitution matrices have been used to predict the structural similarity. In cases where the probe is sequentially distant from its homolog, we have developed a (7 x 3 x 2 x 7 x 3) 3D-1D substitution matrix (called H3P2), calculated from a database of 119 structural pairs. Members of each pair share a similar fold, but have sequence identity less than 30%. Each probe sequence position is defined by one of seven residue classes and three secondary structure classes. Each homologous fold position is defined by one of seven residue classes, three secondary structure classes, and two burial classes. Thus the matrix is five-dimensional and contains 7 x 3 x 2 x 7 x 3 = 882 elements or 3D-1D scores. The first step in assigning a probe sequence to its homologous fold is the prediction of the three-state (helix, strand, coil) secondary structure of the probe; here we use the profile based neural network prediction of secondary structure (PHD) program. Then a dynamic programming algorithm uses the H3P2 matrix to align the probe sequence with structures in a representative fold library. To test the effectiveness of the H3P2 matrix a challenging, fold class diverse, and cross-validated benchmark assessment is used to compare the H3P2 matrix to the GONNET, PAM250, BLOSUM62 and a secondary structure only substitution matrix. For distantly related sequences the H3P2 matrix detects more homologous structures at higher reliabilities than do these other substitution matrices, based on sensitivity versus specificity plots (or SENS-SPEC plots). The added efficacy of the H3P2 matrix arises from its information on the statistical preferences for various sequence-structure environment combinations from very distantly related proteins. It

  6. Distinct Secondary Structures of the Leucine-Rich Repeat Proteoglycans Decorin and Biglycan: Glycosylation-Dependent Conformational Stability

    NASA Technical Reports Server (NTRS)

    Krishnan, Priya; Hocking, Anne M.; Scholtz, J. Martin; Pace, C. Nick; Holik, Kimberly K.; McQuillan, David J.

    1998-01-01

    Biglycan and decorin, closely related small leucine-rich repeat proteoglycans, have been overexpressed in eukaryotic cers and two major glycoforms isolated under native conditions: a proteoglycan substituted with glycosaminoglycan chains; and a core protein form secreted devoid of glycosaminoglycans. A comparative biophysical study of these glycoforms has revealed that the overall secondary structures of biglycan and decorin are different. Far-UV Circular Dichroism (CD) spectroscopy of decorin and biglycan proteoglycans indicates that, although they are predominantly Beta-sheet, biglycan has a significantly higher content of alpha-helical structure. Decorin proteoglycan and core protein are very similar, whereas the biglycan core protein exhibits closer similarity to the decorin glycoforms than to. the biglycan proteoglycan form. However, enzymatic removal of the chondroitin sulfate chains from biglycan proteoglycan does not induce a shift to the core protein structure, suggesting that the fmal form is influenced by polysaccharide addition only during biosynthesis. Fluorescence emission spectroscopy demonstrated that the single tryptophan residue, which is at a conserved position at the C-terminal domain of both biglycan and decorin, is found in similar microenvironments. This indicates that at least in this specific domain, the different glycoforms do exhibit apparent conservation of structure. Exposure of decorin and biglycan to 10 M urea resulted in an increase in fluorescent intensity, which indicates that the emission from tryptophan in the native state is quenched. Comparison of urea-induced protein unfolding curves provided further evidence that decorin and biglycan assume different structures in solution. Decorin proteoglycan and core protein unfold in a manner similar to a classic two-state model, in which there is a steep transition to an unfolded state between 1-2 M urea. The biglycan core protein also shows a similar steep transition. However, biglycan

  7. Mutational analysis of the central domain of adenovirus virus-associated RNA mandates a revision of the proposed secondary structure.

    PubMed Central

    Pe'ery, T; Mellits, K H; Mathews, M B

    1993-01-01

    Protein synthesis in adenovirus-infected cells is regulated during the late phase of infection. The rate of initiation is maintained by a small viral RNA, virus-associated (VA) RNAI, which prevents the phosphorylation of eukaryotic initiation factor eIF-2 by a double-stranded RNA-activated protein kinase, DAI. On the basis of nuclease sensitivity analysis, a secondary-structure model was proposed for VA RNA. The model predicts a complex stem-loop structure in the central part of the molecule, the central domain, joining two duplexed stems. The central domain is required for the inhibition of DAI activation and participates in the binding of VA RNA to DAI. To assess the significance of the postulated stem-loop structure in the central domain, we generated compensating, deletion, and substitution mutations. A substitution mutation which disrupts the structure in the central domain abolishes VA RNA function in vitro and in vivo. Base-compensating mutations failed to restore the function or structure of the mutant, implying that the stem-loop structure may not exist. To confirm this observation, we tested mutants with alterations in the hypothetical loop and short stem that constitute the main features of the wild-type model structure. The upper part of the hypothetical loop could be deleted without abolishing the ability of the RNA to block DAI activation in vitro, whereas other loop mutations were deleterious for function and caused major rearrangements in the molecule. Base-compensating mutations in the stem did not restore the expected base pairing, even though the mutant RNAs were still functional in vitro. Surprisingly, a mutant with a noncompensating substitution mutation in the stem was more effective than wild-type VA RNAI in DAI inhibition assays but was ineffective in vivo. The structural and functional consequences of these mutations do not support the proposed model structure for the central domain, and we therefore suggest an alternative structure in

  8. Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques

    PubMed Central

    Wang, Hsin-Wei; Hsu, Yen-Chu; Hwang, Jenn-Kang; Lyu, Ping-Chiang; Pai, Tun-Wen; Tang, Chuan Yi

    2010-01-01

    This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had “opened” their “closed” structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge

  9. Interactive effects between N addition and disturbance on boreal forest ecosystem structure and function

    NASA Astrophysics Data System (ADS)

    Nordin, Annika; Strengbom, Joachim; From, Fredrik

    2014-05-01

    In management of boreal forests, nitrogen (N) enrichment from atmospheric deposition or from forest fertilization can appear in combination with land-use related disturbances, i.e. tree harvesting by clear-felling. Long-term interactive effects between N enrichment and disturbance on boreal forest ecosystem structure and function are, however, poorly known. We investigated effects of N enrichment by forest fertilization done > 25 years ago on forest understory species composition in old-growth (undisturbed) forests, and in forests clear-felled 10 years ago (disturbed). In clear-felled forests we also investigated effects of the previous N addition on growth of tree saplings. The results show that the N enrichment effect on the understory species composition was strongly dependent on the disturbance caused by clear-felling. In undisturbed forests, there were small or no effects on understory species composition from N addition. In contrast, effects were large in forests first exposed to N addition and subsequently disturbed by clear-felling. Effects of N addition differed among functional groups of plants. Abundance of graminoids increased (+232%) and abundance of dwarf shrubs decreased (-44%) following disturbance in N fertilized forests. For vascular plants, the two perturbations had contrasting effects on α-(within forests) and β-diversity (among forests): in disturbed forests, N addition reduced, or had no effect on α-diversity, while β-diversity increased. For bryophytes, negative effects of disturbance on α-diversity were smaller in N fertilized forests than in forests not fertilized, while neither N addition nor disturbance had any effects on β-diversity. Moreover, sapling growth in forests clear-felled 10 years ago was significantly higher in previously N fertilized forests than in forests not fertilized. Our study show that effects of N addition on plant communities may appear small, short-lived, or even absent until exposed to a disturbance. This

  10. SHAPE Analysis of the RNA Secondary Structure of the Mouse Hepatitis Virus 5′ Untranslated Region and N-Terminal Nsp1 Coding Sequences

    PubMed Central

    Yang, Dong; Liu, Pinghua; Wudeck, Elyse V.; Giedroc, David P.; Leibowitz, Julian L.

    2014-01-01

    SHAPE technology was used to analyze RNA secondary structure of the 5′ most 474 nts of the MHV-A59 genome encompassing the minimal 5′ cis-acting region required for defective interfering RNA replication. The structures generated were in agreement with previous characterizations of SL1 through SL4 and two recently predicted secondary structure elements, S5 and SL5A. SHAPE provided biochemical support for four additional stem-loops not previously functionally investigated in MHV. Secondary structure predictions for 5′ regions of MHV-A59, BCoV and SARS-CoV were similar despite high sequence divergence. The pattern of SHAPE reactivity of in virio genomic RNA, ex virio genomic RNA, and in vitro synthesized RNA were similar, suggesting that binding of N protein or other proteins to virion RNA fails to protect the RNA from reaction with lipid permeable SHAPE reagent. Reverse genetic experiments suggested that SL5C and SL6 within the nsp1 coding sequence are not required for viral replication. PMID:25462342

  11. Content-Related Knowledge of Biology Teachers from Secondary Schools: Structure and learning opportunities

    NASA Astrophysics Data System (ADS)

    Großschedl, Jörg; Mahler, Daniela; Kleickmann, Thilo; Harms, Ute

    2014-09-01

    Teachers' content-related knowledge is a key factor influencing the learning progress of students. Different models of content-related knowledge have been proposed by educational researchers; most of them take into account three categories: content knowledge, pedagogical content knowledge, and curricular knowledge. As there is no consensus about the empirical separability (i.e. empirical structure) of content-related knowledge yet, a total of 134 biology teachers from secondary schools completed three tests which were to capture each of the three categories of content-related knowledge. The empirical structure of content-related knowledge was analyzed by Rasch analysis, which suggests content-related knowledge to be composed of (1) content knowledge, (2) pedagogical content knowledge, and (3) curricular knowledge. Pedagogical content knowledge and curricular knowledge are highly related (rlatent = .70). The latent correlations between content knowledge and pedagogical content knowledge (rlatent = .48)-and curricular knowledge, respectively (rlatent = .35)-are moderate to low (all ps < .001). Beyond the empirical structure of content-related knowledge, different learning opportunities for teachers were investigated with regard to their relationship to content knowledge, pedagogical content knowledge, and curricular knowledge acquisition. Our results show that an in-depth training in teacher education, professional development, and teacher self-study are positively related to particular categories of content-related knowledge. Furthermore, our results indicate that teaching experience is negatively related to curricular knowledge, compared to no significant relationship with content knowledge and pedagogical content knowledge.

  12. Mod-seq: A High-Throughput Method for Probing RNA Secondary Structure.

    PubMed

    Lin, Yizhu; May, Gemma E; Joel McManus, C

    2015-01-01

    It has become increasingly clear that large RNA molecules, especially long noncoding RNAs, function in almost all gene regulatory processes (Cech & Steitz, 2014). Many large RNAs appear to be structural scaffolds for assembly of important RNA/protein complexes. However, the structures of most large cellular RNA molecules are currently unknown (Hennelly & Sanbonmatsu, 2012). While chemical probing can reveal single-stranded regions of RNA, traditional approaches to identify sites of chemical modification are time consuming. Mod-seq is a high-throughput method used to map chemical modification sites on RNAs of any size, including complex mixtures of RNA. In this protocol, we describe preparation of Mod-seq high-throughput sequencing libraries from chemically modified RNA. We also describe a software package "Mod-seeker," which is a compilation of scripts written in Python, for the analysis of Mod-seq data. Mod-seeker returns statistically significant modification sites, which can then be used to aid in secondary structure prediction. PMID:26068740

  13. Secondary structure of splice sites in adenovirus mRNA precursors.

    PubMed Central

    Munroe, S H

    1984-01-01

    In order to investigate the possible role of RNA secondary structure in determining the efficiency and specificity of mRNA splicing, the structures of sequences at three acceptor splice sites in adenovirus were studied. Transcripts spanning intron-exon junctions were synthesized using SP6 RNA polymerase and analyzed using single and double-strand specific nucleases. Distinctive patterns of nuclease cleavage were observed for each of the 3 sites examined. At both sites in the E2a region sequences adjacent to the splice sites were particularly susceptible to digestion with T1 and S1 nucleases. In contrast, a splice site for hexon mRNA was largely resistant to these nucleases. The results obtained suggest that the conformation of the RNA at some, but not all, acceptor sites may enhance the accessibility of these sites to factors involved in splicing nuclear RNA and confirm the presence of a large, previously predicted hairpin structure centered on the acceptor site at 67 map units. Images PMID:6095200

  14. Resolving detailed molecular structures in complex organic mixtures and modeling their secondary organic aerosol formation

    NASA Astrophysics Data System (ADS)

    Goodman-Rendall, Kevin A. S.; Zhuang, Yang R.; Amirav, Aviv; Chan, Arthur W. H.

    2016-03-01

    Characterization of unresolved complex mixtures (UCMs) remains an ongoing challenge towards developing detailed and accurate inputs for modeling secondary organic aerosol (SOA) formation. Traditional techniques based on gas chromatography/electron impact-mass spectrometry induce excessive fragmentation, making it difficult to speciate and quantify isomers precisely. The goal of this study is to identify individual organic isomers by gas chromatography/mass spectrometry with supersonic molecular beam (SMB-GC/MS, also known as GC/MS with Cold EI) and to incorporate speciated isomers into an SOA model that accounts for the specific structures elucidated. Two samples containing atmospherically relevant UCMs are analyzed. The relative isomer distributions exhibit remarkably consistent trends across a wide range of carbon numbers. Constitutional isomers of different alkanes are speciated and individually quantified as linear, branched - for the first time by position of branching - multiply branched, or unsaturated - by degree of ring substitution and number of rings. Relative amounts of exact molecular structures are used as input parameters in an SOA box model to study the effects of molecular structures on SOA yields and volatility evolution. Highly substituted cyclic, mono-substituted cyclic, and linear species have the highest SOA yields while branched alkanes formed the least SOA. The rate of functionalization of a representative UCM is found to be in agreement with current volatility basis set (VBS) parameterizations based on detailed knowledge of composition and known oxidation mechanisms, confirming the validity of VBS parameters currently used in air quality models.

  15. On The Dissolution Kinetics Of Positive Photoresists: The Secondary Structure Model

    NASA Astrophysics Data System (ADS)

    Templeton, Michael K.; Szmanda, Charles R.; Zampini, Anthony

    1987-08-01

    Dissolution kinetics of several model resins with well defined molecular structures were studied extensively. These include a pure m-cresol formaldehyde novolac resin and an alternating m,R-cresol novolac. Other phenolic materials, such as poly(4-hydroxy-styrene), were also examined. Secondary structures of these materials were predicted by molecular mechanics energy minimization techniques and corroborated by comparison with existing experimentally determined X-ray crystallographic data, where available. The excellent agreement between theory and experiment for simple systems lends credence to structural predictions for our model systems. The salient conformational features of these molecules are manifested in the variety of inter- and intramolecular hydrogen bonding interactions which influence strongly the dissolution properties of a given resin. Dissolution kinetics were studied as a function of cation type, developer ionic strength, normality and temperature. The results are explained in terms of the inter- and intramolecular interactions predicted for these resins. Finally we show results which indicate the utility of our model to the design of resist/developer systems.

  16. Linker histone partial phosphorylation: effects on secondary structure and chromatin condensation.

    PubMed

    Lopez, Rita; Sarg, Bettina; Lindner, Herbert; Bartolomé, Salvador; Ponte, Inma; Suau, Pedro; Roque, Alicia

    2015-05-19

    Linker histones are involved in chromatin higher-order structure and gene regulation. We have successfully achieved partial phosphorylation of linker histones in chicken erythrocyte soluble chromatin with CDK2, as indicated by HPCE, MALDI-TOF and Tandem MS. We have studied the effects of linker histone partial phosphorylation on secondary structure and chromatin condensation. Infrared spectroscopy analysis showed a gradual increase of β-structure in the phosphorylated samples, concomitant to a decrease in α-helix/turns, with increasing linker histone phosphorylation. This conformational change could act as the first step in the phosphorylation-induced effects on chromatin condensation. A decrease of the sedimentation rate through sucrose gradients of the phosphorylated samples was observed, indicating a global relaxation of the 30-nm fiber following linker histone phosphorylation. Analysis of specific genes, combining nuclease digestion and qPCR, showed that phosphorylated samples were more accessible than unphosphorylated samples, suggesting local chromatin relaxation. Chromatin aggregation was induced by MgCl2 and analyzed by dynamic light scattering (DLS). Phosphorylated chromatin had lower percentages in volume of aggregated molecules and the aggregates had smaller hydrodynamic diameter than unphosphorylated chromatin, indicating that linker histone phosphorylation impaired chromatin aggregation. These findings provide new insights into the effects of linker histone phosphorylation in chromatin condensation. PMID:25870416

  17. Effect of boron addition on the structure and magnetic properties of CoPt nanoparticles

    SciTech Connect

    Khemjeen, Yutthaya; Pinitsoontorn, Supree Chompoosor, Apiwat

    2015-05-07

    The effect of B addition on CoPt nanoparticles was investigated. The CoPt-B nanoparticles were synthesized by means of the polyol process. Transmission electron microscopy has shown that the as-synthesized particles have a spherical morphology with average size about 2–3 nm. The X-ray absorption spectroscopy and the X-ray diffraction technique showed the effect of B concentration on phase transformation. The addition of B at up to 60% promoted the formation of the L1{sub 0} phase when the nanoparticles were subjected to annealing at 600 °C. If the B content is higher than 60%, the phase transition is suppressed. The evidence of B addition on the structure of CoPt nanoparticles was further supported by the magnetic measurements. The results show that the coercivity of the annealed CoPt-B nanoparticles was enhanced by the B additions from 20% to 60%, with the maximum coercivity of 12 000 Oe for the CoPt-40%B sample.

  18. Hybrid Residual Flexibility/Mass-Additive Method for Structural Dynamic Testing

    NASA Technical Reports Server (NTRS)

    Tinker, M. L.

    2003-01-01

    A large fixture was designed and constructed for modal vibration testing of International Space Station elements. This fixed-base test fixture, which weighs thousands of pounds and is anchored to a massive concrete floor, initially utilized spherical bearings and pendulum mechanisms to simulate Shuttle orbiter boundary constraints for launch of the hardware. Many difficulties were encountered during a checkout test of the common module prototype structure, mainly due to undesirable friction and excessive clearances in the test-article-to-fixture interface bearings. Measured mode shapes and frequencies were not representative of orbiter-constrained modes due to the friction and clearance effects in the bearings. As a result, a major redesign effort for the interface mechanisms was undertaken. The total cost of the fixture design, construction and checkout, and redesign was over $2 million. Because of the problems experienced with fixed-base testing, alternative free-suspension methods were studied, including the residual flexibility and mass-additive approaches. Free-suspension structural dynamics test methods utilize soft elastic bungee cords and overhead frame suspension systems that are less complex and much less expensive than fixed-base systems. The cost of free-suspension fixturing is on the order of tens of thousands of dollars as opposed to millions, for large fixed-base fixturing. In addition, free-suspension test configurations are portable, allowing modal tests to be done at sites without modal test facilities. For example, a mass-additive modal test of the ASTRO-1 Shuttle payload was done at the Kennedy Space Center launch site. In this Technical Memorandum, the mass-additive and residual flexibility test methods are described in detail. A discussion of a hybrid approach that combines the best characteristics of each method follows and is the focus of the study.

  19. FPGA accelerator for protein secondary structure prediction based on the GOR algorithm

    PubMed Central

    2011-01-01

    Background Protein is an important molecule that performs a wide range of functions in biological systems. Recently, the protein folding attracts much more attention since the function of protein can be generally derived from its molecular structure. The GOR algorithm is one of the most successful computational methods and has been widely used as an efficient analysis tool to predict secondary structure from protein sequence. However, the execution time is still intolerable with the steep growth in protein database. Recently, FPGA chips have emerged as one promising application accelerator to accelerate bioinformatics algorithms by exploiting fine-grained custom design. Results In this paper, we propose a complete fine-grained parallel hardware implementation on FPGA to accelerate the GOR-IV package for 2D protein structure prediction. To improve computing efficiency, we partition the parameter table into small segments and access them in parallel. We aggressively exploit data reuse schemes to minimize the need for loading data from external memory. The whole computation structure is carefully pipelined to overlap the sequence loading, computing and back-writing operations as much as possible. We implemented a complete GOR desktop system based on an FPGA chip XC5VLX330. Conclusions The experimental results show a speedup factor of more than 430x over the original GOR-IV version and 110x speedup over the optimized version with multi-thread SIMD implementation running on a PC platform with AMD Phenom 9650 Quad CPU for 2D protein structure prediction. However, the power consumption is only about 30% of that of current general-propose CPUs. PMID:21342582

  20. Architecture and Secondary Structure of an Entire HIV-1 RNA Genome

    PubMed Central

    Watts, Joseph M.; Dang, Kristen K.; Gorelick, Robert J.; Leonard, Christopher W.; Bess, Julian W.; Swanstrom, Ronald; Burch, Christina L.; Weeks, Kevin M.

    2009-01-01

    Single-stranded RNA viruses encompass broad classes of infectious agents and cause the common cold, cancer, AIDS, and other serious health threats. Viral replication is regulated at many levels, including using conserved genomic RNA structures. Most potential regulatory elements within viral RNA genomes are uncharacterized. Here we report the structure of an entire HIV-1 genome at single nucleotide resolution using SHAPE, a high-throughput RNA analysis technology. The genome encodes protein structure at two levels. In addition to the correspondence between RNA and protein primary sequences, a correlation exists between high levels of RNA structure and sequences that encode inter-domain loops in HIV proteins. This correlation suggests RNA structure modulates ribosome elongation to promote native protein folding. Some simple genome elements previously shown to be important, including the ribosomal gag-pol frameshift stem-loop, are components of larger RNA motifs. We also identify organizational principles for unstructured RNA regions. Highly used splice acceptors lie in unstructured motifs and hypervariable regions are sequestered from flanking genome regions by stable insulator helices. These results emphasize that the HIV-1 genome and, potentially, many coding RNAs are punctuated by numerous previously unrecognized regulatory motifs and that extensive RNA structure may constitute an additional level of the genetic code. PMID:19661910

  1. Structural features of helical secondary structures and leucine-rich repeat superhelix in proteins as revealed by HELFIT analyses

    NASA Astrophysics Data System (ADS)

    Matsushima, Norio; Enkhbayar, Purevjav

    2012-09-01

    The HELFIT program determines the helical parameters - pitch, residues per turn (n), radius, and handedness - and p = rmsd / (N - 1)1/2 estimating helical regularity, where "rmsd" is the root mean square deviation from the best fit helix or superhelix and "N" is helix/superhelix length. Helical secondary structures - α-helix and 310-helix - and solenoid structures of leucine rich repeats (LRRs) in The Protein Data Bank (PDB) were analyzed by the HELFIT program. The results indicate that the definition of 310-helices in terms of average, uniform dihedral angles is not appropriate and that it is inherently unstable for a polypeptide to form an extended, regular 310-helix. The 310-helices observed in proteins are better referred to parahelices. A modification of the α-helix, termed the ω-helix, that has four residues in one turn of a helix, has been identified only in synthetic polypeptides. The results also demonstrate that the right-handed ω-helix occur really in proteins. The solenoid structures of LRR domains in brasinosteroid insensitive 1 (BRI1), internalin J (InlJ), and internalin A (InlA) are well represented by a superhelix rather than by a circular arc.

  2. Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules

    NASA Astrophysics Data System (ADS)

    Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy

    2011-03-01

    We have performed an atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme at room temperature with explicit water molecules. Several analyses have been carried out to explore the differential flexibility of the secondary structural segments of the protein and the structure and ordering of water around them. It is found that the overall flexibility of the protein molecule is primarily controlled by few large-amplitude bistable motions exhibited by two coils; one connecting two α-helical segments in domain-1 and the other connecting a 310 helix and a β-sheet in domain-2 of the protein. The heterogeneous structuring of water around the segments of the protein has been found to depend on the degree of exposure of the segments to water. The ordering of water molecules around the protein segments and their tagged potential energies have been found to be anticorrelated with each other. Some of these findings can be verified by suitable experimental studies.

  3. Phylogenetic hypotheses of gorgoniid octocorals according to ITS2 and their predicted RNA secondary structures.

    PubMed

    Aguilar, Catalina; Sánchez, Juan Armando

    2007-06-01

    Gorgoniid octocorals taxonomy (Cnidaria; Octocorallia; Gorgoniidae) includes diagnostic characters not well defined at the generic level, and based on the family diagnosis some species could be classified in either Gorgoniidae or Plexauridae. In this study, we used sequences from the Internal Transcribed Spacer 2 (ITS2) and their predicted RNA secondary structure to both correct the alignment and reconstruct phylogenies using molecular morphometrics for 24 octocorals mostly from the Atlantic. ITS2 exhibited the six-helicoidal ring-model structure found in eukaryotes, and provided 38 parsimony-informative characters. The proposed phylogenies, though differing between sequence- and structure-base results, provided consistent support for several clades. Genera considered part of the polyphyletic genus Leptogorgia, such as Filigorgia, were distantly related to the former in all phylogenetic hypotheses. Main differences among the hypotheses consisted in the placement of Muriceopsis (previously considered from the Plexauridae family) and Filigorgia. Excluding Muriceopsis and an undescribed octocoral from Tobago, Plexaurella and Pterogorgia grouped together as a sister branch of Pinnigorgia spp. but long-branch attraction was evident for the grouping of Plexaurella nutans (another plexaurid) and Pterogorgia citrina. Unexpected results were the divergence between Caribbean genera, Gorgonia and Pseudopterogorgia, which were placed basal respect to Pacifigorgia and Leptogorgia (=Lophogorgia). ITS2 provided support to corroborate observations based on sclerite morphology: species with "capstan sclerites" (e.g., Pacifigorgia and Leptogorgia) were characterized by a long helix IV with one internal loop and a helix V with four internal loops; "scaphoid sclerites" had a predominantly long helix V if compared to helix IV; "asymmetric spiny sclerites" (Muriceopsis, Pinnigorgia and the undescribed octocoral) exhibited one or two lateral bulges in the V helix. Remarkably, Muriceopsis

  4. The structure of secondary cell wall polymers: how Gram-positive bacteria stick their cell walls together.

    PubMed

    Schäffer, Christina; Messner, Paul

    2005-03-01

    The cell wall of Gram-positive bacteria has been a subject of detailed chemical study over the past five decades. Outside the cytoplasmic membrane of these organisms the fundamental polymer is peptidoglycan (PG), which is responsible for the maintenance of cell shape and osmotic stability. In addition, typical essential cell wall polymers such as teichoic or teichuronic acids are linked to some of the peptidoglycan chains. In this review these compounds are considered as 'classical' cell wall polymers. In the course of recent investigations of bacterial cell surface layers (S-layers) a different class of 'non-classical' secondary cell wall polymers (SCWPs) has been identified, which is involved in anchoring of S-layers to the bacterial cell surface. Comparative analyses have shown considerable differences in chemical composition, overall structure and charge behaviour of these SCWPs. This review discusses the progress that has been made in understanding the structural principles of SCWPs, which may have useful applications in S-layer-based 'supramolecular construction kits' in nanobiotechnology. PMID:15758211

  5. An infrared sensor analysing label-free the secondary structure of the Abeta peptide in presence of complex fluids.

    PubMed

    Nabers, Andreas; Ollesch, Julian; Schartner, Jonas; Kötting, Carsten; Genius, Just; Haußmann, Ute; Klafki, Hans; Wiltfang, Jens; Gerwert, Klaus

    2016-03-01

    The secondary structure change of the Abeta peptide to beta-sheet was proposed as an early event in Alzheimer's disease. The transition may be used for diagnostics of this disease in an early state. We present an Attenuated Total Reflection (ATR) sensor modified with a specific antibody to extract minute amounts of Abeta peptide out of a complex fluid. Thereby, the Abeta peptide secondary structure was determined in its physiological aqueous environment by FTIR-difference-spectroscopy. The presented results open the door for label-free Alzheimer diagnostics in cerebrospinal fluid or blood. It can be extended to further neurodegenerative diseases. An immunologic ATR-FTIR sensor for Abeta peptide secondary structure analysis in complex fluids is presented. PMID:25808829

  6. EBSD analysis of magnesium addition on inclusion formation in SS400 structural steel

    SciTech Connect

    Luo, Sin-Jie; Su, Yen-Hao Frank; Lu, Muh-Jung; Kuo, Jui-Chao

    2013-08-15

    In this study, the effect of magnesium addition on the inclusion formation in SS400 steel was investigated. The experimental specimens with and without Mg addition treatment were compared. The microstructure was observed using optical microscopy after etching with 3% nital. The morphology and chemical composition of the inclusions were analyzed via scanning electron microscopy and energy dispersive spectrometry. The lattice structure and orientation of the inclusions were identified by electron backscattering diffraction. The average size of inclusions in SS400 was between 0.67 and 0.75 μm, and between 0.65 and 0.68 μm in SS400 + Mg. The 2 ppm Mg addition resulted in the oxide formation change from Al{sub 2}O{sub 3} to MgO·Al{sub 2}O{sub 3} and in the inclusion formation change from Al{sub 2}O{sub 3}–MnS to MgO·Al{sub 2}O{sub 3}–MnS. Moreover, a simple-phase MnS with an average grain size of 1 μm to 2 μm was observed in rod-like, globular, and polyhedron forms. - Highlights: • The effect of magnesium addition was investigated for SS400 steel. • 2 ppm Mg addition changes the inclusion formation from Al2O3-MnS to MgO·Al2O3-MnS. • MnS observed in inclusions exhibits rod-like, globular, and polyhedron forms.

  7. ITS2 Secondary Structure Improves Discrimination between Medicinal “Mu Tong” Species when Using DNA Barcoding

    PubMed Central

    Zhang, Wei; Yuan, Yuan; Yang, Shuo; Huang, Jianjun; Huang, Luqi

    2015-01-01

    DNA barcoding is a promising species identification method, but it has proved difficult to find a standardized DNA marker in plant. Although the ITS/ITS2 RNA transcript has been proposed as the core barcode for seed plants, it has been criticized for being too conserved in some species to provide enough information or too variable in some species to align it within the different taxa ranks. We selected 30 individuals, representing 16 species and four families, to explore whether ITS2 can successfully resolve species in terms of secondary structure. Secondary structure was predicted using Mfold software and sequence-structure was aligned by MARNA. RNAstat software transformed the secondary structures into 28 symbol code data for maximum parsimony (MP) analysis. The results showed that the ITS2 structures in our samples had a common four-helix folding type with some shared motifs. This conserved structure facilitated the alignment of ambiguous sequences from divergent families. The structure alignment yielded a MP tree, in which most topological relationships were congruent with the tree constructed using nucleotide sequence data. When the data was combined, we obtained a well-resolved and highly supported phylogeny, in which individuals of a same species were clustered together into a monophyletic group. As a result, the different species that are often referred to as the herb “Mu tong” were successfully identified using short fragments of 250 bp ITS2 sequences, together with their secondary structure. Thus our analysis strengthens the potential of ITS2 as a promising DNA barcode because it incorporates valuable secondary structure information that will help improve discrimination between species. PMID:26132382

  8. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data

    PubMed Central

    Wu, Yang; Shi, Binbin; Ding, Xinqiang; Liu, Tong; Hu, Xihao; Yip, Kevin Y.; Yang, Zheng Rong; Mathews, David H.; Lu, Zhi John

    2015-01-01

    Recently, several experimental techniques have emerged for probing RNA structures based on high-throughput sequencing. However, most secondary structure prediction tools that incorporate probing data are designed and optimized for particular types of experiments. For example, RNAstructure-Fold is optimized for SHAPE data, while SeqFold is optimized for PARS data. Here, we report a new RNA secondary structure prediction method, restrained MaxExpect (RME), which can incorporate multiple types of experimental probing data and is based on a free energy model and an MEA (maximizing expected accuracy) algorithm. We first demonstrated that RME substantially improved secondary structure prediction with perfect restraints (base pair information of known structures). Next, we collected structure-probing data from diverse experiments (e.g. SHAPE, PARS and DMS-seq) and transformed them into a unified set of pairing probabilities with a posterior probabilistic model. By using the probability scores as restraints in RME, we compared its secondary structure prediction performance with two other well-known tools, RNAstructure-Fold (based on a free energy minimization algorithm) and SeqFold (based on a sampling algorithm). For SHAPE data, RME and RNAstructure-Fold performed better than SeqFold, because they markedly altered the energy model with the experimental restraints. For high-throughput data (e.g. PARS and DMS-seq) with lower probing efficiency, the secondary structure prediction performances of the tested tools were comparable, with performance improvements for only a portion of the tested RNAs. However, when the effects of tertiary structure and protein interactions were removed, RME showed the highest prediction accuracy in the DMS-accessible regions by incorporating in vivo DMS-seq data. PMID:26170232

  9. Investigations of primary and secondary impact structures on the moon and laboratory experiments to study the ejecta of secondary particles. Ph.D. Thesis - Ruprecht Karl Univ.

    NASA Technical Reports Server (NTRS)

    Koenig, B.

    1977-01-01

    Young lunar impact structures were investigated by using lunar orbiter, Apollo Metric and panorama photographs. Measurements on particularly homogeneous areas low in secondary craters made possible an expansion of primary crater distribution to small diameters. This is now sure for a range between 20m or = D or = 20km and this indicates that the size and velocity distribution of the impacting bodies in the last 3 billion years has been constant. A numerical approximation in the form of a 7th degree polynomial was obtained for the distribution.

  10. 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 Cα 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 φ and ψ angles, respectively, and 8° and 32° for mean absolute errors of Cα-based θ and τ 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

  11. Investigating the secondary structures for long oligonucleotides using attenuated-total-reflection nanoplasmon-enhanced Raman scattering

    NASA Astrophysics Data System (ADS)

    Chiu, K.-C.; Yu, L.-Y.; Lin, C.-Y.; Chen, S.-J.

    2007-09-01

    This study utilizes a nanoplasmon-enhanced Raman scattering based on the attenuated-total-reflection (ATR) method to investigate the secondary structures of long oligonucleotides and their influence on the DNA hybridization. It is found that the ring-breathing modes of adenine, thymine, guanine, and cytosine in Raman fingerprint associated with three 60mer oligonucleotides with prominent secondary structures are lower than those observed for the two oligonucleotides with no obvious secondary structures. It is also determined that increasing the DNA hybridization temperature from 35 °C to 45 °C reduces secondary structure effects. The kinetics of biomolecular interaction analysis can be performed by using surface plasmons resonance biosensor, but the structural information of the oligonucleotides can not observed directly. The ATR-Raman spectrum can provide the structural information of the oligonucleotide monolayer on the sensing surface with the help of a silver patterned nanostructure film based on the finite-difference time-domain simulation and the e-beam lithography fabrication adapted as an ATR-Raman active substrate.

  12. Determination of Endosperm Protein Secondary Structure in Hard Wheat Breeding Lines using Synchrotron Infrared Microspectroscopy

    SciTech Connect

    Bonwell,E.; Fisher, T.; Fritz, A.; Wetzel, D.

    2008-01-01

    One molecular aspect of mature hard wheat protein quality for breadmaking is the relative amount of endosperm protein in the a-helix form compared with that in other secondary structure forms including {beta}-sheet. Modeling of a-helix and {beta}-sheet absorption bands that contribute to the amide I band at 1650 cm-1 was applied to more than 1500 spectra in this study. The microscopic view of wheat endosperm is dominated by many large starch granules with protein in between. The spectrum produced from in situ microspectroscopy of this mixture is dominated by carbohydrate bands from the large starch granules that fill up the field. The high spatial resolution achievable with synchrotron infrared microspectroscopy enables revealing good in situ spectra of the protein located interstitially. Synchrotron infrared microspectroscopic mapping of 4 {mu}m thick frozen sections of endosperm in the subaleurone region provides spectra from a large number of pixels. Pixels with protein-dominated spectra are sorted out from among adjacent pixels to minimize the starch absorption and scattering contributions. Subsequent data treatment to extract information from the amide I band requires a high signal to noise ratio. Although spectral interference of the carbohydrate band on the amide band is not a problem, the scattering produced by the large starch granules diminishes the signal to noise ratio throughout the spectrum. High density mapping was done on beamlines U2B and U10B at the National Synchrotron Light Source at Brookhaven National Laboratory, Upton, NY. Mapping with a single masked spot size of 5.5 {mu}m diameter or confocal 5 {mu}m x 5 {mu}m spot size, respectively, on the two beamlines used produced spectra for new breeding lines under current consideration. Appropriate data treatment allows calculation of a numerical estimate of the a-helix population relative to other secondary protein structures from the position and shape of the amide I absorption band. Current

  13. Determination of Endosperm Protein Secondary Structure in Hard Wheat Breeding Lines using Synchrotron Infrared Microspectroscopy

    SciTech Connect

    Wetzel, D.; Bonwell, E; Fritz, T; Fritz, A

    2008-01-01

    One molecular aspect of mature hard wheat protein quality for breadmaking is the relative amount of endosperm protein in the {alpha}-helix form compared with that in other secondary structure forms including {beta}-sheet. Modeling of {alpha}-helix and {beta}-sheet absorption bands that contribute to the amide I band at 1650 cm{sup -1} was applied to more than 1500 spectra in this study. The microscopic view of wheat endosperm is dominated by many large starch granules with protein in between. The spectrum produced from in situ microspectroscopy of this mixture is dominated by carbohydrate bands from the large starch granules that fill up the field. The high spatial resolution achievable with synchrotron infrared microspectroscopy enables revealing good in situ spectra of the protein located interstitially. Synchrotron infrared microspectroscopic mapping of 4 {mu}m thick frozen sections of endosperm in the subaleurone region provides spectra from a large number of pixels. Pixels with protein-dominated spectra are sorted out from among adjacent pixels to minimize the starch absorption and scattering contributions. Subsequent data treatment to extract information from the amide I band requires a high signal to noise ratio. Although spectral interference of the carbohydrate band on the amide band is not a problem, the scattering produced by the large starch granules diminishes the signal to noise ratio throughout the spectrum. High density mapping was done on beamlines U2B and U10B at the National Synchrotron Light Source at Brookhaven National Laboratory, Upton, NY. Mapping with a single masked spot size of 5.5 {mu}m diameter or confocal 5 {mu}mX5{mu}m spot size, respectively, on the two beamlines used produced spectra for new breeding lines under current consideration. Appropriate data treatment allows calculation of a numerical estimate of the {alpha}-helix population relative to other secondary protein structures from the position and shape of the amide I

  14. Fine Structure in the Secondary Electron Emission Peak for Diamond Crystal with (100) Negative Electron Affinity Surface

    NASA Technical Reports Server (NTRS)

    Asnin, V. M.; Krainsky, I. L.

    1998-01-01

    A fine structure was discovered in the low-energy peak of the secondary electron emission spectra of the diamond surface with negative electron affinity. We studied this structure for the (100) surface of the natural type-IIb diamond crystal. We have found that the low-energy peak consists of a total of four maxima. The relative energy positions of three of them could be related to the electron energy minima near the bottom of the conduction band. The fourth peak, having the lowest energy, was attributed to the breakup of the bulk exciton at the surface during the process of secondary electron emission.

  15. Prediction of protein secondary structure based on residue pair types and conformational states using dynamic programming algorithm.

    PubMed

    Sadeghi, Mehdi; Parto, Sahar; Arab, Shahriar; Ranjbar, Bijan

    2005-06-20

    We have used a statistical approach for protein secondary structure prediction based on information theory and simultaneously taking into consideration pairwise residue types and conformational states. Since the prediction of residue secondary structure by one residue window sliding make ambiguity in state prediction, we used a dynamic programming algorithm to find the path with maximum score. A score system for residue pairs in particular conformations is derived for adjacent neighbors up to ten residue apart in sequence. The three state overall per-residue accuracy, Q3, of this method in a jackknife test with dataset created from PDBSELECT is more than 70%. PMID:15936021

  16. Capped mRNAs with reduced secondary structure can function in extracts from poliovirus-infected cells

    SciTech Connect

    Sonenberg, N.; Guertin, D.; Lee, K.A.W.

    1982-12-01

    Extracts form poliovirus-infected HeLa cells were used to study ribosome binding of native and denatured reovirus mRNAs and translation of capped mRNAs with different degrees of secondary structure. Here, the authors demonstrate that ribosomes in extracts from poliovirus-infected cells could form initiation complexes with denatured reovirus mRNA, in contrast to their inability to bind native reovirus mRNA. Furthermore, the capped alfalfa mosiac virus 4 RNA, which is most probable devoid of stable secondary structure at its 5' end, could be translated at much higher efficiency than could other capped mRNAs in extracts from poliovirus-infected cells.

  17. Soil microbial community structure and nitrogen cycling responses to agroecosystem management and carbon substrate addition

    NASA Astrophysics Data System (ADS)

    Berthrong, S. T.; Buckley, D. H.; Drinkwater, L. E.

    2011-12-01

    Fertilizer application in conventional agriculture leads to N saturation and decoupled soil C and N cycling, whereas organic practices, e.g. complex rotations and legume incorporation, often results in increased SOM and tightly coupled cycles of C and N. These legacy effects of management on soils likely affect microbial community composition and microbial process rates. This project tested if agricultural management practices led to distinct microbial communities and if those communities differed in ability to utilize labile plant carbon substrates and to produce more plant available N. We addressed several specific questions in this project. 1) Do organic and conventional management legacies on similar soils produce distinct soil bacterial and fungal community structures and abundances? 2) How do these microbial community structures change in response to carbon substrate addition? 3) How do the responses of the microbial communities influence N cycling? To address these questions we conducted a laboratory incubation of organically and conventionally managed soils. We added C-13 labelled glucose either in one large dose or several smaller pulses. We extracted genomic DNA from soils before and after incubation for TRFLP community fingerprinting. We measured C in soil pools and respiration and N in soil extracts and leachates. Management led to different compositions of bacteria and fungi driven by distinct components in organic soils. Biomass did not differ across treatments indicating that differences in cycling were due to composition rather than abundance. C substrate addition led to convergence in bacterial communities; however management still strongly influenced the difference in communities. Fungal communities were very distinct between managements and plots with substrate addition not altering this pattern. Organic soils respired 3 times more of the glucose in the first week than conventional soils (1.1% vs 0.4%). Organic soils produced twice as much

  18. DNA secondary structures are associated with recombination in major Plasmodium falciparum variable surface antigen gene families

    PubMed Central

    Sander, Adam F.; Lavstsen, Thomas; Rask, Thomas S.; Lisby, Michael; Salanti, Ali; Fordyce, Sarah L.; Jespersen, Jakob S.; Carter, Richard; Deitsch, Kirk W.; Theander, Thor G.; Pedersen, Anders Gorm; Arnot, David E.

    2014-01-01

    Many bacterial, viral and parasitic pathogens undergo antigenic variation to counter host immune defense mechanisms. In Plasmodium falciparum, the most lethal of human malaria parasites, switching of var gene expression results in alternating expression of the adhesion proteins of the Plasmodium falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome-wide recombination hotspots in var genes, we show that during the parasite’s sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum-erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens. PMID:24253306

  19. Secondary structure and conformational change of mushroom polyphenol oxidase during thermosonication treatment by using FTIR spectroscopy.

    PubMed

    Baltacıoğlu, Hande; Bayındırlı, Alev; Severcan, Feride

    2017-01-01

    To understand the conformational changes of mushroom PPO, the secondary structural change of the enzyme during thermosonication treatment at different power (60, 80 and 100%), temperature (20-60°C) and time (0-30min) combinations was investigated by using FTIR spectroscopy and compared with the change in enzyme activity. The enzyme inactivation higher than 99% was obtained at 100% amplitude at 60°C for 10min. FTIR studies showed that marked spectral changes were noted after ultrasound treatment at 20°C. The α-helix and β-sheet contents decreased, while aggregated β-sheet, turns and random coil contents increased as temperature increased up to 60°C during thermosonication treatment for 10min indicating protein denaturation. Aggregated bands located at 1683 and 1616cm(-1) became evident after ultrasound treatment at 40°C. When temperature was lowered back to 25°C, from ultrasound treatment at 60°C, these bands were still observed, indicating the irreversible change in the structure. PMID:27507504

  20. The influence of viral RNA secondary structure on interactions with innate host cell defences

    PubMed Central

    Witteveldt, Jeroen; Blundell, Richard; Maarleveld, Joris J.; McFadden, Nora; Evans, David J.; Simmonds, Peter

    2014-01-01

    RNA viruses infecting vertebrates differ fundamentally in their ability to establish persistent infections with markedly different patterns of transmission, disease mechanisms and evolutionary relationships with their hosts. Although interactions with host innate and adaptive responses are complex and persistence mechanisms likely multi-factorial, we previously observed associations between bioinformatically predicted RNA secondary formation in genomes of positive-stranded RNA viruses with their in vivo fitness and persistence. To analyse this interactions functionally, we transfected fibroblasts with non-replicating, non-translated RNA transcripts from RNA viral genomes with differing degrees of genome-scale ordered RNA structure (GORS). Single-stranded RNA transcripts induced interferon-β mediated though RIG-I and PKR activation, the latter associated with rapid induction of antiviral stress granules. A striking inverse correlation was observed between induction of both cellular responses with transcript RNA structure formation that was independent of both nucleotide composition and sequence length. The consistent inability of cells to recognize RNA transcripts possessing GORS extended to downstream differences from unstructured transcripts in expression of TNF-α, other interferon-stimulated genes and induction of apoptosis. This functional association provides novel insights into interactions between virus and host early after infection and provides evidence for a novel mechanism for evading intrinsic and innate immune responses. PMID:24335283

  1. Sheath structure transition controlled by secondary electron emission at low gas pressure

    NASA Astrophysics Data System (ADS)

    Schweigert, Irina; Langendorf, Samuel J.; Keidar, Michael; Walker, Mitchell L. R.

    2014-10-01

    Previously the experiments demonstrated that the growth of the electron temperature with power in the Hall thruster is restricted by plasma-wall interaction if the wall has an enhanced secondary electron emission (SEE) yield. It is known that the plasma and wall is separated by the sheath potential drop to provide the condition of zero-current on the surface with floating potential. The rearrangement of the sheath structure near the plate with enhanced SEE is the subject of our experimental and theoretical study. The experiment was carried out in multidipole plasma device, where plasma is maintained by the negatively-biased emissive filament. The plate with sapphire surface is placed 50 cm apart from the filament. The plasma parameters were measured for different negative biases Ub and discharge currents J at P = 10-4 Torr. In our PIC simulations the plasma was calculated for the experimental conditions. We solved self-consistently the Boltzmann equations for the electron and ion distribution functions and Poisson equation for electrical field. Both in the experiment and simulation we found non-monotonic change in sheath structure near the plate depending on Ub and J. The kinetic simulations allowed us to describe the sheath rearrangement in terms of the electron energy distribution function.

  2. FTIR Study On The Secondary Structure Of Mucin From Mucinous Cystadenoma Of The Ovary

    NASA Astrophysics Data System (ADS)

    Shen, Keng; Wu, Paochen; Zhou, Weij in; Liu, Fuan; Guo, Hai; Wu, Jinguang

    1989-12-01

    The mucinous cystadenoma, a common benign neoplasm of the ovary, may sometime bring about a fatal outcome known as pseudomyxoma peritonei which is characterized by massive accumulation of mucinous substance in the peritoneal cavity, resulting in extensive adhesions, chronic progressive intestinal obstruction and finally death of the patient. Surgical approach to this condition proves to be a palliative procedure. Repeated operation can only remove part of the geletinous material and reaccumulation of mucus within 1-2 years after the initial surgery is almost a rule. In view of the benign histologic nature of the disease, chemotherapy, either systemic or intraperitoneal, and radiotherapy are generally ineffective in arresting the progression of the pathologic process and preventing the reaccumulation of mucus. Therefore, the only hope lies on the introduction into the peritoneal cavity some agents which may dissolve the accumulated mucin, relieve the intestinal obstruction, and consequently, prolong and even save the life f the patient. Based on this conception, sporadic articles by a few authors(1,2)ap-peared in the literature reporting their clinical experience with different mucolytic agents. However, some blindness would inevitably be involved in such investigations due to the lack of a comprehensive understanding of the chemical structures of the substance. The purpose of the present paper is to report our preliminary results of study of the secondary structures of mucin secreted by this special type of tumor.

  3. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

    PubMed Central

    Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin

    2014-01-01

    Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80% and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test data set of 198 proteins, achieving a Q3 accuracy of 80.7% and a Sov accuracy of 74.2%. PMID:25750595

  4. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.

    PubMed

    Spencer, Matt; Eickholt, Jesse; Jianlin Cheng

    2015-01-01

    Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80 percent and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test dataset of 198 proteins, achieving a Q3 accuracy of 80.7 percent and a Sov accuracy of 74.2 percent. PMID:25750595

  5. Formation of secondary structures in heat-resistant steels under sliding friction

    NASA Astrophysics Data System (ADS)

    Lad'yanov, V. I.; Goncharov, O. Yu.; Malenko, P. I.; Nikonova, R. M.; Gilmutdinov, F. Z.; Mokrushina, M. I.; Tereshkina, S. A.; Leonov, A. Yu.; Relmasira, K. J.

    2015-12-01

    The formation of secondary structures in nicotrated layers on surfaces of complex-alloy heatresistant 25Kh3M3NBTsA and 30KhN2MFA structural steels under the effect of sliding friction with resource lubrication has been studied using metallography, X-ray diffraction, X-ray photoelectron spectroscopy, and thermodynamic modeling. It has been found that, under friction, the nicotrated layer on the steels oxidizes to produce iron oxides, which is substantially less pronounced for 25Kh3M3NBTsA steel than for 30KhN2MFA steel. It has been shown using thermodynamic modeling that, under equilibrium conditions, the heating of both steels to a temperature of ~300°C leads to the formation of an internal-oxidation layer, which consists of FeO with MoO2, Cr2O3, and carbon impurities, a Fe3O4 interlayer with MoO2 and Cr2O3 impurities, and a top layer of Fe2O3 with Cr2O3 impurity. The heating of steels to a temperature of ~700°C leads to the formation of an internal-oxidation layer, which consists of FeO with MoO2 and carbon impurities, a Fe3O4 interlayer with MoO2 impurity, and a top layer of Cr2O3 with Fe2MnO4 and SiO2 impurities.

  6. Duplex formation and secondary structure of γ-PNA observed by NMR and CD.

    PubMed

    Viéville, J M P; Barluenga, S; Winssinger, N; Delsuc, M A

    2016-03-01

    Peptide nucleic acids (PNAs) are non-natural oligonucleotides mimics, wherein the phosphoribose backbone has been replaced by a peptidic moiety (N-(2-aminoethyl)glycine). This peptidic backbone lends itself to substitution and the γ-position has proven to yield oligomers with enhanced hybridization properties. In this study, we use Nuclear Magnetic Resonance (NMR) and Circular Dichroism (CD) to explore the properties of the supramolecular duplexes formed by these species. We show that standard Watson-Crick base pair as well as non-standard ones are formed in solution. The duplexes thus formed present marked melting transition temperatures substantially higher than their nucleic acid homologs. Moreover, the presence of a chiral group on the γ-peptidic backbone increases further this transition temperature, leading to very stable duplexes. PNA duplexes with a chiral backbone present a marked chiral secondary structure, observed by CD, and showing a common folding pattern for all studied structures. Nevertheless small differences are observed depending on the details of the nucleobase sequence. PMID:26493008

  7. Structural and Ferromagnetic Properties of an Orthorhombic Phase of MnBi Stabilized with Rh Additions

    NASA Astrophysics Data System (ADS)

    Taufour, Valentin; Thimmaiah, Srinivasa; March, Stephen; Saunders, Scott; Sun, Kewei; Lamichhane, Tej Nath; Kramer, Matthew J.; Bud'ko, Sergey L.; Canfield, Paul C.

    2015-07-01

    The article addresses the possibility of alloy elements in MnBi which may modify the thermodynamic stability of the NiAs-type structure without significantly degrading the magnetic properties. The addition of small amounts of Rh and Mn provides an improvement in the thermal stability with some degradation of the magnetic properties. The small amounts of Rh and Mn additions in MnBi stabilize an orthorhombic phase whose structural and magnetic properties are closely related to the ones of the previously reported high-temperature phase of MnBi (HT MnBi). To date, the properties of the HT MnBi, which is stable between 613 and 719 K, have not been studied in detail because of its transformation to the stable low-temperature MnBi (LT MnBi), making measurements near and below its Curie temperature difficult. The Rh-stabilized MnBi with chemical formula Mn1.0625 -xRhx Bi [x =0.02 (1 ) ] adopts a new superstructure of the NiAs /Ni2In structure family. It is ferromagnetic below a Curie temperature of 416 K. The critical exponents of the ferromagnetic transition are not of the mean-field type but are closer to those associated with the Ising model in three dimensions. The magnetic anisotropy is uniaxial; the anisotropy energy is rather large, and it does not increase when raising the temperature, contrary to what happens in LT MnBi. The saturation magnetization is approximately 3 μB/f .u . at low temperatures. While this exact composition may not be application ready, it does show that alloying is a viable route to modifying the stability of this class of rare-earth-free magnet alloys.

  8. Structural and ferromagnetic properties of an orthorhombic phase of MnBi stabilized with Rh additions

    DOE PAGESBeta

    Taufour, Valentin; Thimmaiah, Srinivasa; March, Stephen; Saunders, Scott; Sun, Kewei; Lamichhane, Tej Nath; Kramer, Matthew J.; Bud’ko, Sergey L.; Canfield, Paul C.

    2015-07-28

    The article addresses the possibility of alloy elements in MnBi which may modify the thermodynamic stability of the NiAs-type structure without significantly degrading the magnetic properties. The addition of small amounts of Rh and Mn provides an improvement in the thermal stability with some degradation of the magnetic properties. The small amounts of Rh and Mn additions in MnBi stabilize an orthorhombic phase whose structural and magnetic properties are closely related to the ones of the previously reported high-temperature phase of MnBi (HT MnBi). The properties of the HT MnBi, which is stable between 613 and 719 K, have notmore » been studied in detail because of its transformation to the stable low-temperature MnBi (LT MnBi), making measurements near and below its Curie temperature difficult. The Rh-stabilized MnBi with chemical formula Mn1.0625–xRhxBi [x=0.02(1)] adopts a new superstructure of the NiAs/Ni2In structure family. It is ferromagnetic below a Curie temperature of 416 K. The critical exponents of the ferromagnetic transition are not of the mean-field type but are closer to those associated with the Ising model in three dimensions. The magnetic anisotropy is uniaxial; the anisotropy energy is rather large, and it does not increase when raising the temperature, contrary to what happens in LT MnBi. The saturation magnetization is approximately 3μB/f.u. at low temperatures. Thus, while this exact composition may not be application ready, it does show that alloying is a viable route to modifying the stability of this class of rare-earth-free magnet alloys.« less

  9. Structural and ferromagnetic properties of an orthorhombic phase of MnBi stabilized with Rh additions

    SciTech Connect

    Taufour, Valentin; Thimmaiah, Srinivasa; March, Stephen; Saunders, Scott; Sun, Kewei; Lamichhane, Tej Nath; Kramer, Matthew J.; Bud’ko, Sergey L.; Canfield, Paul C.

    2015-07-28

    The article addresses the possibility of alloy elements in MnBi which may modify the thermodynamic stability of the NiAs-type structure without significantly degrading the magnetic properties. The addition of small amounts of Rh and Mn provides an improvement in the thermal stability with some degradation of the magnetic properties. The small amounts of Rh and Mn additions in MnBi stabilize an orthorhombic phase whose structural and magnetic properties are closely related to the ones of the previously reported high-temperature phase of MnBi (HT MnBi). The properties of the HT MnBi, which is stable between 613 and 719 K, have not been studied in detail because of its transformation to the stable low-temperature MnBi (LT MnBi), making measurements near and below its Curie temperature difficult. The Rh-stabilized MnBi with chemical formula Mn1.0625–xRhxBi [x=0.02(1)] adopts a new superstructure of the NiAs/Ni2In structure family. It is ferromagnetic below a Curie temperature of 416 K. The critical exponents of the ferromagnetic transition are not of the mean-field type but are closer to those associated with the Ising model in three dimensions. The magnetic anisotropy is uniaxial; the anisotropy energy is rather large, and it does not increase when raising the temperature, contrary to what happens in LT MnBi. The saturation magnetization is approximately 3μB/f.u. at low temperatures. Thus, while this exact composition may not be application ready, it does show that alloying is a viable route to modifying the stability of this class of rare-earth-free magnet alloys.

  10. Insight into the secondary structure of chloramphenicol acetyltransferase type I — computer analysis and FT-IR spectroscopic characterization of the protein structure

    NASA Astrophysics Data System (ADS)

    Andreeva, A. E.; Karamancheva, I. R.

    2001-05-01

    The secondary structure of chloramphenicol O-acetyltransferase type I (CAT I) and an N-terminal deleted mutant has been studied by Fourier transform infrared spectroscopy. The analysis of the amide I band of different samples (KBr, hydrated films and buffer solution) by Fourier self-deconvolution followed by a curve fitting was performed. The spectroscopic data have been utilized to determine the α-helix and β-structure % contents, which depend strongly on the protein sample preparation. Furthermore, the secondary structure of the enzyme-inhibitor Crystal Violet complex was analyzed. The observed difference in the secondary structural contents suggests that some conformational changes of the enzyme are induced by the inhibitor after binding.

  11. Biomechanical investigation into the structural design of porous additive manufactured cages using numerical and experimental approaches.

    PubMed

    Tsai, Pei-I; Hsu, Ching-Chi; Chen, San-Yuan; Wu, Tsung-Han; Huang, Chih-Chieh

    2016-09-01

    Traditional solid cages have been widely used in posterior lumbar interbody fusion (PLIF) surgery. However, solid cages significantly affect the loading mechanism of the human spine due to their extremely high structural stiffness. Previous studies proposed and investigated porous additive manufactured (AM) cages; however, their biomechanical performances were analyzed using oversimplified bone-implant numerical models. Thus, the aim of this study was to investigate the outer shape and inner porous structure of the AM cages. The outer shape of the AM cages was discovered using a simulation-based genetic algorithm; their inner porous structure was subsequently analyzed parametrically using T10-S1 multilevel spine models. Finally, six types of the AM cages, which were manufactured using selective laser melting, were tested to validate the numerical outcomes. The subsidence resistance of the optimum design was superior to the conventional cage designs. A porous AM cage with a pillar diameter of 0.4mm, a pillar angle of 40°, and a porosity of between 69% and 80% revealed better biomechanical performances. Both the numerical and experimental outcomes can help surgeons to understand the biomechanics of PLIF surgery combined with the use of AM cages. PMID:27392226

  12. Amyloid-β-Secondary Structure Distribution in Cerebrospinal Fluid and Blood Measured by an Immuno-Infrared-Sensor: A Biomarker Candidate for Alzheimer's Disease.

    PubMed

    Nabers, Andreas; Ollesch, Julian; Schartner, Jonas; Kötting, Carsten; Genius, Just; Hafermann, Henning; Klafki, Hans; Gerwert, Klaus; Wiltfang, Jens

    2016-03-01

    The misfolding of the Amyloid-beta (Aβ) peptide into β-sheet enriched conformations was proposed as an early event in Alzheimer's Disease (AD). Here, the Aβ peptide secondary structure distribution in cerebrospinal fluid (CSF) and blood plasma of 141 patients was measured with an immuno-infrared-sensor. The sensor detected the amide I band, which reflects the overall secondary structure distribution of all Aβ peptides extracted from the body fluid. We observed a significant downshift of the amide I band frequency of Aβ peptides in Dementia Alzheimer type (DAT) patients, which indicated an overall shift to β-sheet. The secondary structure distribution of all Aβ peptides provides a better marker for DAT detection than a single Aβ misfold or the concentration of a specific oligomer. The discrimination between DAT and disease control patients according to the amide I frequency was in excellent agreement with the clinical diagnosis (accuracy 90% for CSF and 84% for blood). The amide I band maximum above or below the decisive marker frequency appears as a novel spectral biomarker candidate of AD. Additionally, a preliminary proof-of-concept study indicated an amide I band shift below the marker band already in patients with mild cognitive impairment due to AD. The presented immuno-IR-sensor method represents a promising, simple, robust, and label-free diagnostic tool for CSF and blood analysis. PMID:26828829

  13. Effects of essential oil treatments on the secondary protein structure of Vicia faba: A mid-infrared spectroscopic study supported by two-dimensional correlation analysis

    NASA Astrophysics Data System (ADS)

    Mecozzi, Mauro; Sturchio, Elena

    2015-02-01

    In this study we investigated the effects of essential oil treatments on the secondary protein structure of the Vicia faba roots, a bioindicator plant, in order to obtain information for the potential allelopathic uses of these oils as alternative to the use of pesticides in agriculture. We tested two mixtures of essential oils consisting of Tween 20-emulsions of tea tree oil (TTO) and Tween 20-emulsion of Clove and Rosemary (GARROM) essential oils respectively at three different oil concentrations each. The molecular modifications caused in Vicia faba by exposure to oil emulsions were investigated by FTIR spectroscopy in diffuse reflectance (DRIFT) mode. We considered the specific Amide I, Amide II and Amide VI bands by ordinary and second derivative spectroscopy and the results showed that both Tween 20-emulsion of GARROM and Tween 20-emulsion of TTO oils cause transitions among the secondary (α-helix, β-sheet and β-turn) structures with in addition the appearance of random coil structures in exposed samples. The Amide VI bands, placed between 500 and 600 cm-1, confirmed the structural transitions observed for the Amide I bands. In addition we observed the presence of a protein oxidation effect for TTO treated samples, oxidation which resulted negligible instead for the GARROM oil samples. At last, FTIR spectra were also submitted to two-dimensional correlation analysis (2DCORR) and double two-dimensional correlation analysis (D2DCORR); the results confirmed the different effects caused by the two typologies of essential oils on the secondary protein structures of Vicia faba roots.

  14. Effects of essential oil treatments on the secondary protein structure of Vicia faba: a mid-infrared spectroscopic study supported by two-dimensional correlation analysis.

    PubMed

    Mecozzi, Mauro; Sturchio, Elena

    2015-02-25

    In this study we investigated the effects of essential oil treatments on the secondary protein structure of the Vicia faba roots, a bioindicator plant, in order to obtain information for the potential allelopathic uses of these oils as alternative to the use of pesticides in agriculture. We tested two mixtures of essential oils consisting of Tween 20-emulsions of tea tree oil (TTO) and Tween 20-emulsion of Clove and Rosemary (GARROM) essential oils respectively at three different oil concentrations each. The molecular modifications caused in Vicia faba by exposure to oil emulsions were investigated by FTIR spectroscopy in diffuse reflectance (DRIFT) mode. We considered the specific Amide I, Amide II and Amide VI bands by ordinary and second derivative spectroscopy and the results showed that both Tween 20-emulsion of GARROM and Tween 20-emulsion of TTO oils cause transitions among the secondary (α-helix, β-sheet and β-turn) structures with in addition the appearance of random coil structures in exposed samples. The Amide VI bands, placed between 500 and 600 cm(-1), confirmed the structural transitions observed for the Amide I bands. In addition we observed the presence of a protein oxidation effect for TTO treated samples, oxidation which resulted negligible instead for the GARROM oil samples. At last, FTIR spectra were also submitted to two-dimensional correlation analysis (2DCORR) and double two-dimensional correlation analysis (D2DCORR); the results confirmed the different effects caused by the two typologies of essential oils on the secondary protein structures of Vicia faba roots. PMID:25203214

  15. Residual Structure of Streptococcus mutans Biofilm following Complete Disinfection Favors Secondary Bacterial Adhesion and Biofilm Re-Development

    PubMed Central

    Ohsumi, Tatsuya; Takenaka, Shoji; Wakamatsu, Rika; Sakaue, Yuuki; Narisawa, Naoki; Senpuku, Hidenobu; Ohshima, Hayato; Terao, Yutaka; Okiji, Takashi

    2015-01-01

    Chemical disinfection of oral biofilms often leaves biofilm structures intact. This study aimed to examine whether the residual structure promotes secondary bacterial adhesion. Streptococcus mutans biofilms generated on resin-composite disks in a rotating disc reactor were disinfected completely with 70% isopropyl alcohol, and were again cultured in the same reactor after resupplying with the same bacterial solution. Specimens were subjected to fluorescence confocal laser scanning microscopy, viable cell counts and PCR-Invader assay in order to observe and quantify secondarily adhered cells. Fluorescence microscopic analysis, particularly after longitudinal cryosectioning, demonstrated stratified patterns of viable cells on the disinfected biofilm structure. Viable cell counts of test specimens were significantly higher than those of controls, and increased according to the amount of residual structure and culture period. Linear regression analysis exhibited a high correlation between viable and total cell counts. It was concluded that disinfected biofilm structures favored secondary bacterial adhesion. PMID:25635770

  16. Secondary structure, stability and tetramerisation of recombinant K(V)1.1 potassium channel cytoplasmic N-terminal fragment.

    PubMed

    Abbott, G W; Bloemendal, M; Van Stokkum, I H; Mercer, E A; Miller, R T; Sewing, S; Wolters, M; Pongs, O; Srai, S K

    1997-08-15

    The recombinant N-terminal fragment (amino acids 14-162) of a tetrameric voltage-gated potassium channel (K(V)1.1) has been studied using spectroscopic techniques. Evidence is presented that it forms a tetramer in aqueous solution, whereas when solubilised in 1% Triton X-100 it remains monomeric. The secondary structure content of both monomeric and tetrameric K(V)1.1 N-terminal fragment has been estimated from FTIR and CD spectroscopy to be 20-25% alpha-helix, 20-25% beta-sheet, 20% turns and 30-40% random coil. Solubilisation of the protein in detergent is shown by hydrogen-deuterium exchange analysis to alter tertiary structure rather than secondary structure and this may be the determining factor in tetramerisation ability. Using molecular modelling we propose a supersecondary structure consisting of two structural domains. PMID:9300810

  17. CMB topography and electrical conductivity as additional constraints for the lowermost mantle thermo-chemical structure

    NASA Astrophysics Data System (ADS)

    Deschamps, F.; Yin, Y.; Tackley, P. J.

    2013-12-01

    A variety of seismic observations, including tomographic models, indicate that the lowermost mantle is strongly heterogeneous. Seismic observations further support a thermo-chemical origin for the large scale heterogeneities. In particular, the large low-shear wave velocity provinces (LLSVP) observed by global tomographic images are better explained by a combination of thermal and chemical anomalies. Despite the accuracy of seismic information, uncertainties and trade-off still prevent the determination of a detailed lower mantle thermo-chemical structure. For instance, the nature of chemical heterogeneities and the exact role played by the post-perovskite phase transition are still debated. Additional constraints are needed to discriminate between the possible models of structure and dynamics of the lower mantle. Here, we consider two potential additional constraints, the electrical conductivity and the dynamic topography at the core-mantle boundary (CMB). Unlike density and seismic velocities, electrical conductivity increases with temperature. In addition, it strongly varies with the iron and silicate content. Using appropriate mineral physics data, we calculated a 3D distribution of electrical conductivity in lower mantle from the thermo-chemical structure inferred by probabilistic tomography, which maps iron and silicate excess in the LLSVP. In the lowermost mantle, we observe a belt of high conductivity, with maximum values around 20 S/m located in the LLSVP. Such a belt may trigger electric currents in the lowermost mantle and induce magnetic field variations with period of one year or more. It may thus be seen by global models of electrical conductivity. Unfortunately, such models do not sample yet regions deeper than 2000 km. A second, independent constraint we explored is the dynamic topography at the CMB. We used stagYY to calculate the dynamic topography associated with several models of thermo-chemical convection, and observe strong differences

  18. The role of additional computed tomography in the decision-making process on the secondary prevention in patients after systemic cerebral thrombolysis

    PubMed Central

    Sobolewski, Piotr; Kozera, Grzegorz; Szczuchniak, Wiktor; Nyka, Walenty M

    2016-01-01

    Introduction Patients with ischemic stroke undergoing intravenous (iv)-thrombolysis are routinely controlled with computed tomography on the second day to assess stroke evolution and hemorrhagic transformation (HT). However, the benefits of an additional computed tomography (aCT) performed over the next days after iv-thrombolysis have not been determined. Methods We retrospectively screened 287 Caucasian patients with ischemic stroke who were consecutively treated with iv-thrombolysis from 2008 to 2012. The results of computed tomography performed on the second (control computed tomography) and seventh (aCT) day after iv-thrombolysis were compared in 274 patients (95.5%); 13 subjects (4.5%), who died before the seventh day from admission were excluded from the analysis. Results aCTs revealed a higher incidence of HT than control computed tomographies (14.2% vs 6.6%; P=0.003). Patients with HT in aCT showed higher median of National Institutes of Health Stroke Scale score on admission than those without HT (13.0 vs 10.0; P=0.01) and higher presence of ischemic changes >1/3 middle cerebral artery territory (66.7% vs 35.2%; P<0.01). Correlations between presence of HT in aCT and National Institutes of Health Stroke Scale score on admission (rpbi 0.15; P<0.01), and the ischemic changes >1/3 middle cerebral artery (phi=0.03) existed, and the presence of HT in aCT was associated with 3-month mortality (phi=0.03). Conclusion aCT after iv-thrombolysis enables higher detection of HT, which is related to higher 3-month mortality. Thus, patients with severe middle cerebral artery infarction may benefit from aCT in the decision-making process on the secondary prophylaxis. PMID:26730196

  19. The characteristics of effective secondary math and science instructional facilitators and the necessary support structures as perceived by practitioners and principals

    NASA Astrophysics Data System (ADS)

    Mahagan, Vikki Lynn

    Instructional facilitators are known by a variety of titles depending on the school district in which they are employed. They are sometimes called instructional coaches, teacher leaders, lead teachers, and instructional specialist (Denton & Hasbrouck, 2009). Throughout this study, the title instructional facilitator was used and will refer to secondary math or science instructional facilitators who are housed at least one day per week on a campus. This study is a mixed-methods descriptive study which has identified character traits, specials skill, and talents possessed by effective secondary math and science instructional facilitators as perceived by practicing facilitators and principals and assistant principals who work along side instructional facilitators. Specific job training to help ensure the success of a facilitator was identified as viewed by both facilitators and principals. Additionally, this study compared the perceptions of practicing facilitators and principals to determine if significant differences exist with respect to perceptions of staff development opportunities, support structures, and resources available for instructional facilitators.

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

    PubMed Central

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

    2001-01-01

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

  1. Properties of Inconel 625 Mesh Structures Grown by Electron Beam Additive Manufacturing

    SciTech Connect

    List III, Frederick Alyious; Dehoff, Ryan R; Lowe, Larry E; Sames, William J

    2014-01-01

    Relationships between electron beam parameters (beam current, beam speed, and beam focus) and physical properties (mass, diameter, elastic modulus, and yield strength) have been investigated for Inconel 625 mesh cubes fabricated using an additive manufacturing technology based on electron beam melting. The elastic modulus and yield strength of the mesh cubes have been systematically varied by approximately a factor of ten by changing the electron beam parameters. Simple models have been used to understand better these relationships. Structural anisotropies of the mesh associated with the layered build architecture have been observed and may contribute, along with microstructural anisotropies, to the anisotropic mechanical properties of the mesh. Knowledge of this kind is likely applicable to other metal and alloy systems and is essential to rapidly realize the full potential of this burgeoning technology.

  2. Application and testing of additive manufacturing for mirrors and precision structures

    NASA Astrophysics Data System (ADS)

    Sweeney, Michael; Acreman, Martyn; Vettese, Tom; Myatt, Ray; Thompson, Mike

    2015-09-01

    Additive Manufacturing (aka AM, and 3-D printing) is widely touted in the media as the foundation for the next industrial revolution. Beneath the hype, AM does indeed offer profound advantages in lead-time, dramatically reduced consumption of expensive raw materials, while enabling new and innovative design forms that cannot be produced by other means. General Dynamics and their industry partners have begun to embrace this technology for mirrors and precision structures used in the aerospace, defense, and precision optical instrumentation industries. Aggressively lightweighted, open and closed back test mirror designs, 75-150 mm in size, were first produced by AM from several different materials. Subsequent optical finishing and test experiments have exceeded expectations for density, surface finish, dimensional stability and isotropy of thermal expansion on the optical scale of measurement. Materials currently under examination include aluminum, titanium, beryllium, aluminum beryllium, Inconel 625, stainless steel/bronze, and PEKK polymer.

  3. Tailoring of Boehmite-Derived Aluminosilicate Aerogel Structure and Properties: Influence of Ti Addition

    NASA Technical Reports Server (NTRS)

    Hurwitz, Frances I.; Guo, Haiquan; Sheets, Erik J.; Miller, Derek R.; Newlin, Katy N.

    2010-01-01

    Aluminosilicate aerogels offer potential for extremely low thermal conductivities at temperatures greater than 900 C, beyond where silica aerogels reach their upper temperature limits. Aerogels have been synthesized at various Al:Si ratios, including mullite compositions, using Boehmite (AlOOH) as the Al source, and tetraethoxy orthosilicate as the Si precursor. The Boehmite-derived aerogels are found to form by a self-assembly process of AlOOH crystallites, with Si-O groups on the surface of an alumina skeleton. Morphology, surface area and pore size varies with the crystallite size of the starting Boehmite powder, as well as with synthesis parameters. Ternary systems, including Al-Si-Ti aerogels incorporating a soluble Ti precursor, are possible with careful control of pH. The addition of Ti influences sol viscosity, gelation time pore structure and pore size distribution, as well as phase formation on heat treatment.

  4. Effect of calcium chloride addition on ice cream structure and quality.

    PubMed

    Costa, F F; Resende, J V; Abreu, L R; Goff, H D

    2008-06-01

    The influence of calcium fortification by the addition of calcium chloride on quality parameters of ice cream based on physical properties was investigated, as was the effect of kappa-carrageenan at modifying the effects of this calcium fortification. Four ice cream mixes of conventional composition, with added kappa-carrageenan (0 or 0.025%) and added calcium chloride (0 or 4.4 g L(-1) = 40 mM of added Ca(2+)), were prepared. Modulated temperature-differential scanning calorimetry was used to investigate the effect of calcium chloride on the nucleation temperature, enthalpy of melting, and freezing point depression. The protein composition of 15.4% (wt/wt) reconstituted skim milk powder solutions with or without 4.4 g L(-1) added CaCl(2) and in the supernatant after ultracentrifugation was determined. Fat particle size distributions in ice cream were characterized by light scattering. Ice crystal sizes before and after temperature cycling were determined by cold-stage light microscopy. The results demonstrated that the addition of calcium chloride led to a substantial increase in ice crystal sizes and in fat partial coalescence, which were exacerbated by the addition of kappa-carrageenan. These results can be explained by the interaction between Ca(2+) ions and casein micelles, rather than any effects on freezing point depression. The calcium ions led to a more compact micelle, less serum beta-casein, and high fat destabilization, all of which would be expected to reduce macromolecular structure and volume occupancy in the unfrozen phase, which led to increased rates of ice recrystallization. PMID:18487638

  5. Computational and molecular analysis of conserved influenza A virus RNA secondary structures involved in infectious virion production.

    PubMed

    Kobayashi, Yuki; Dadonaite, Bernadeta; van Doremalen, Neeltje; Suzuki, Yoshiyuki; Barclay, Wendy S; Pybus, Oliver G

    2016-09-01

    As well as encoding viral proteins, genomes of RNA viruses harbor secondary and tertiary RNA structures that have been associated with functions essential for successful replication and propagation. Here, we identified stem-loop structures that are extremely conserved among 1,884 M segment sequences of influenza A virus (IAV) strains from various subtypes and host species using computational and evolutionary methods. These structures were predicted within the 3' and 5' ends of the coding regions of M1 and M2, respectively, where packaging signals have been previously proposed to exist. These signals are thought to be required for the incorporation of a single copy of 8 different negative-strand RNA segments (vRNAs) into an IAV particle. To directly test the functionality of conserved stem-loop structures, we undertook reverse genetic experiments to introduce synonymous mutations designed to disrupt secondary structures predicted at 3 locations and found them to attenuate infectivity of recombinant virus. In one mutant, predicted to disrupt stem loop structure at nucleotide positions 219-240, attenuation was more evident at increased temperature and was accompanied by an increase in the production of defective virus particles. Our results suggest that the conserved secondary structures predicted in the M segment are involved in the production of infectious viral particles during IAV replication. PMID:27399914

  6. Addition of cement to lime-based mortars: Effect on pore structure and vapor transport

    SciTech Connect

    Mosquera, M.J. . E-mail: mariajesus.mosquera@uca.es; Silva, B.; Prieto, B.; Ruiz-Herrera, E.

    2006-09-15

    The main focus of this work is to determine the effect of cement addition, a common practice in many restorations, on the pore structure of lime-based mortars. A second target is to establish correlations between microstructure and water vapor transport across the mortar, which is a key characteristic of building decay. In order to achieve these objectives, we prepared a set of mortars consisting of air-hardening lime with a progressively increasing cement content, as well as a mortar containing hydraulic lime. Several different techniques, most notably mercury intrusion porosimetry and scanning electron microscopy in the backscatter mode, were used to investigate the pore structure. The results from these procedures led to the conclusion that porosity and pore size are progressively reduced as cement content increases. Moreover, an excellent correlation between pore radius parameter and the vapor diffusion coefficient was established. Hydraulic lime mortar exhibited textural parameters and diffusivity values halfway between those of the different lime/cement mixes studied.

  7. Children's Understanding of the Additive Composition of Number and of the Decimal Structure: What Is the Relationship?

    ERIC Educational Resources Information Center

    Krebs, Georgina; Squire, Sarah; Bryant, Peter

    2003-01-01

    Nunes and Bryant (Children doing mathematics, Blackwell, Oxford, 1996) proposed that an understanding of the additive composition of number could be a precursor to an understanding of the decimal structure. If this is so, children should achieve an understanding of additive composition before they can handle the decimal structure. The aim of our…

  8. DNA secondary structure of the released strand stimulates WRN helicase action on forked duplexes without coordinate action of WRN exonuclease

    SciTech Connect

    Ahn, Byungchan; Bohr, Vilhelm A.

    2011-08-12

    Highlights: {yields} In this study, we investigated the effect of a DNA secondary structure on the two WRN activities. {yields} We found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. {yields} These results imply that WRN helicase and exonuclease activities can act independently. -- Abstract: Werner syndrome (WS) is an autosomal recessive premature aging disorder characterized by aging-related phenotypes and genomic instability. WS is caused by mutations in a gene encoding a nuclear protein, Werner syndrome protein (WRN), a member of the RecQ helicase family, that interestingly possesses both helicase and exonuclease activities. Previous studies have shown that the two activities act in concert on a single substrate. We investigated the effect of a DNA secondary structure on the two WRN activities and found that a DNA secondary structure of the displaced strand during unwinding stimulates WRN helicase without coordinate action of WRN exonuclease. These results imply that WRN helicase and exonuclease activities can act independently, and we propose that the uncoordinated action may be relevant to the in vivo activity of WRN.

  9. Decentralization and Structural Change in Secondary Education in Argentina: The Case of the Province of Buenos Aires

    ERIC Educational Resources Information Center

    Acedo, Clementina; Gorostiaga, Jorge M.; Senen-Gonzalez, Silvia

    2007-01-01

    Over the past decade, Argentina created and implemented a compulsory lower-secondary education level, within an ambitious educational reform programme. This article addresses the reform at the national level, diverse provincial responses, and the particular way that the powerful province of Buenos Aires appropriated the structural change. The…

  10. Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures1[w

    PubMed Central

    Loke, Johnny C.; Stahlberg, Eric A.; Strenski, David G.; Haas, Brian J.; Wood, Paul Chris; Li, Qingshun Quinn

    2005-01-01

    Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3′-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3′-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a single-nucleotide profile scan on the 3′-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly(A) signals and to develop tools to predict 3′-ends for gene annotation. PMID:15965016

  11. Effect of Programmed Instruction on Students' Attitude towards Structure of the Atom and the Periodic Table among Kenyan Secondary Schools

    ERIC Educational Resources Information Center

    Wangila, M. J.; Martin, W.; Ronald, M.

    2015-01-01

    This study examined the effect of Programmed Instruction on students' attitude towards Structure of the Atom and the Periodic Table (SAPT) among mixed (co-educational) secondary schools of Butere district, Kakamega county, Kenya. The quasi-experimental research design was adopted, using the nonrandomized Solomon four-group as a model. The sample…

  12. effect of hydrogen addition and burner diameter on the stability and structure of lean, premixed flames

    NASA Astrophysics Data System (ADS)

    Kaufman, Kelsey Leigh

    Low swirl burners (LSBs) have gained popularity in heating and gas power generation industries, in part due to their proven capacity for reducing the production of NOx, which in addition to reacting to form smog and acid rain, plays a central role in the formation of the tropospheric ozone layer. With lean operating conditions, LSBs are susceptible to combustion instability, which can result in flame extinction or equipment failure. Extensive work has been performed to understand the nature of LSB combustion, but scaling trends between laboratory- and industrial-sized burners have not been established. Using hydrogen addition as the primary method of flame stabilization, the current work presents results for a 2.54 cm LSB to investigate potential effects of burner outlet diameter on the nature of flame stability, with focus on flashback and lean blowout conditions. In the lean regime, the onset of instability and flame extinction have been shown to occur at similar equivalence ratios for both the 2.54 cm and a 3.81 cm LSB and depend on the resolution of equivalence ratios incremented. Investigations into flame structures are also performed. Discussion begins with a derivation for properties in a multicomponent gas mixture used to determine the Reynolds number (Re) to develop a condition for turbulent intensity similarity in differently-sized LSBs. Based on this requirement, operating conditions are chosen such that the global Reynolds number for the 2.54 cm LSB is within 2% of the Re for the 3.81 cm burner. With similarity obtained, flame structure investigations focus on flame front curvature and flame surface density (FSD). As flame structure results of the current 2.54 cm LSB work are compared to results for the 3.81 cm LSB, no apparent relationship is shown to exist between burner diameter and the distribution of flame surface density. However, burner diameter is shown to have a definite effect on the flame front curvature. In corresponding flow conditions, a

  13. Secondary dislocation structures in a Ni-TiN system from the GMS and O-lattice theory

    NASA Astrophysics Data System (ADS)

    Tang, Yiru; Dai, Fuzhi; Gu, Xinfu; Wang, Zhongchang; Zhang, Wenzheng

    2016-03-01

    The preferred state in an interface is the key to evaluating misfit strain, especially for the interphase interfaces in secondary preferred state. The structure of good matching site (GMS) in a GMS clusters offers a guidance for the preferred state, especially for identifying the coincidence site lattice in two dimension for secondary preferred state and the Burgers vectors in a large misfit system. Here, we combine the GMS with O-lattice theory to calculate the secondary dislocation structure in the habit planes of the type II and III TiN precipitates in a Ni-TiN system. We find that under a slight elastic strain, the type III habit plane contains a single set of secondary dislocations, consistent with the experimental observation. The type II habit plane contains three sets of secondary dislocations, two of which can be relaxed to be nearly parallel and another of which may be invisible in diffraction contrast due to its short Burgers vector. The present study provides a reasonable interpretation to the observed interfacial dislocations, and also suggests Burgers vectors for the dislocations that are not determined experimentally.

  14. Identification of WD40 repeats by secondary structure-aided profile-profile alignment.

    PubMed

    Wang, Chuan; Dong, Xiaobao; Han, Lei; Su, Xiao-Dong; Zhang, Ziding; Li, Jinyan; Song, Jiangning

    2016-06-01

    A WD40 protein typically contains four or more repeats of ~40 residues ended with the Trp-Asp dipeptide, which folds into β-propellers with four β strands in each repeat. They often function as scaffolds for protein-protein interactions and are involved in numerous fundamental biological processes. Despite their important functional role, the "velcro" closure of WD40 propellers and the diversity of WD40 repeats make their identification a difficult task. Here we develop a new WD40 Repeat Recognition method (WDRR), which uses predicted secondary structure information to generate candidate repeat segments, and further employs a profile-profile alignment to identify the correct WD40 repeats from candidate segments. In particular, we design a novel alignment scoring function that combines dot product and BLOSUM62, thereby achieving a great balance of sensitivity and accuracy. Taking advantage of these strategies, WDRR could effectively reduce the false positive rate and accurately identify more remote homologous WD40 repeats with precise repeat boundaries. We further use WDRR to re-annotate the Pfam families in the β-propeller clan (CL0186) and identify a number of WD40 repeat proteins with high confidence across nine model organisms. The WDRR web server and the datasets are available at http://protein.cau.edu.cn/wdrr/. PMID:27021623

  15. Line-Based Object Recognition using Hausdorff Distance: From Range Images to Molecular Secondary Structure

    SciTech Connect

    Guerra, C; Pascucci, V

    2004-12-13

    Object recognition algorithms are fundamental tools in automatic matching of geometric shapes within a background scene. Many approaches have been proposed in the past to solve the object recognition problem. Two of the key aspects that distinguish them in terms of their practical usability are: (i) the type of input model description and (ii) the comparison criteria used. In this paper we introduce a novel scheme for 3D object recognition based on line segment representation of the input shapes and comparison using the Hausdor distance. This choice of model representation provides the flexibility to apply the scheme in different application areas. We define several variants of the Hausdor distance to compare the models within the framework of well defined metric spaces. We present a matching algorithm that efficiently finds a pattern in a 3D scene. The algorithm approximates a minimization procedure of the Hausdor distance. The output error due to the approximation is guaranteed to be within a known constant bound. Practical results are presented for two classes of objects: (i) polyhedral shapes extracted from segmented range images and (ii) secondary structures of large molecules. In both cases the use of our approximate algorithm allows to match correctly the pattern in the background while achieving the efficiency necessary for practical use of the scheme. In particular the performance is improved substantially with minor degradation of the quality of the matching.

  16. GADIS: Algorithm for designing sequences to achieve target secondary structure profiles of intrinsically disordered proteins.

    PubMed

    Harmon, Tyler S; Crabtree, Michael D; Shammas, Sarah L; Posey, Ammon E; Clarke, Jane; Pappu, Rohit V

    2016-09-01

    Many intrinsically disordered proteins (IDPs) participate in coupled folding and binding reactions and form alpha helical structures in their bound complexes. Alanine, glycine, or proline scanning mutagenesis approaches are often used to dissect the contributions of intrinsic helicities to coupled folding and binding. These experiments can yield confounding results because the mutagenesis strategy changes the amino acid compositions of IDPs. Therefore, an important next step in mutagenesis-based approaches to mechanistic studies of coupled folding and binding is the design of sequences that satisfy three major constraints. These are (i) achieving a target intrinsic alpha helicity profile; (ii) fixing the positions of residues corresponding to the binding interface; and (iii) maintaining the native amino acid composition. Here, we report the development of a G: enetic A: lgorithm for D: esign of I: ntrinsic secondary S: tructure (GADIS) for designing sequences that satisfy the specified constraints. We describe the algorithm and present results to demonstrate the applicability of GADIS by designing sequence variants of the intrinsically disordered PUMA system that undergoes coupled folding and binding to Mcl-1. Our sequence designs span a range of intrinsic helicity profiles. The predicted variations in sequence-encoded mean helicities are tested against experimental measurements. PMID:27503953

  17. Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing

    NASA Astrophysics Data System (ADS)

    Weber, Jeffrey K.; Pande, Vijay S.

    2013-09-01

    The protein folding problem has long represented a "holy grail" in statistical physics due to its physical complexity and its relevance to many human diseases. While past theoretical work has yielded apt descriptions of protein folding landscapes, recent large-scale simulations have provided insights into protein folding that were impractical to obtain from early theories. In particular, the role that non-native contacts play in protein folding, and their relation to the existence of misfolded, β-sheet rich trap states on folding landscapes, has emerged as a topic of interest in the field. In this paper, we present a modified model of heteropolymer freezing that includes explicit secondary structural characteristics which allow observations of "intramolecular amyloid" states to be probed from a theoretical perspective. We introduce a variable persistence length-based energy penalty to a model Hamiltonian, and we illustrate how this modification alters the phase transitions present in the theory. We find, in particular, that inclusion of this variable persistence length increases both generic freezing and folding temperatures in the model, allowing both folding and glass transitions to occur in a more highly optimized fashion. We go on to discuss how these changes might relate to protein evolution, misfolding, and the emergence of intramolecular amyloid states.

  18. The accessory helix of complexin functions by stabilizing central helix secondary structure

    PubMed Central

    Radoff, Daniel T; Dong, Yongming; Snead, David; Bai, Jihong; Eliezer, David; Dittman, Jeremy S

    2014-01-01

    The presynaptic protein complexin (CPX) is a critical regulator of synaptic vesicle fusion, but the mechanisms underlying its regulatory effects are not well understood. Its highly conserved central helix (CH) directly binds the ternary SNARE complex and is required for all known CPX functions. The adjacent accessory helix (AH) is not conserved despite also playing an important role in CPX function, and numerous models for its mechanism have been proposed. We examined the impact of AH mutations and chimeras on CPX function in vivo and in vitro using C. elegans. The mouse AH fully restored function when substituted into worm CPX suggesting its mechanism is evolutionarily conserved. CPX inhibitory function was impaired when helix propagation into the CH was disrupted whereas replacing the AH with a non-native helical sequence restored CPX function. We propose that the AH operates by stabilizing CH secondary structure rather than through protein or lipid interactions. DOI: http://dx.doi.org/10.7554/eLife.04553.001 PMID:25383924

  19. Spontaneous deposition of polylysine on surfaces: role of the secondary structure to optimize noncovalent coating strategies.

    PubMed

    Di Mauro, Alessandro; Mirabella, Francesca; D'Urso, Alessandro; Randazzo, Rosalba; Purrello, Roberto; Fragalà, Maria Elena

    2015-01-01

    Understanding the factors that governs spontaneous molecular transfer from solution to solid surface is fundamental to control noncovalent surface functionalization strategies, both in term of robustness and reproducibility. The comprehension of the nature of interaction involved in the mechanism of spontaneous adsorption will allow for a fine modulation of the deposition process. Herein, we provide experimental evidences to demonstrate that poly-lysine secondary structure represents a crucial factor profoundly influencing the outcome of its spontaneous deposition on quartz surfaces. In particular, random coil to α-helix transition is required to drive an effective transfer of the poly-l-lysine at the liquid-solid interface. β-sheet deposition requires longer times to be accomplished, while random-coil deposition is highly unfavored. Accordingly, polylysine deposition on quartz and silicon is effective when α-helix is formed in solution (pH>10). This surface noncovalent functionalization represents a simple strategy to fabricate hybrid organic-inorganic or biocompatible materials. In fact, the proposed methodology is proven robust and repeatable and compatible for combination with solution or vapor phases (i.e. MOCVD) nanomaterial deposition approaches. PMID:25441360

  20. Regulation of Fibronectin EDA Exon Alternative Splicing: Possible Role of RNA Secondary Structure for Enhancer Display

    PubMed Central

    Muro, Andrés F.; Caputi, Massimo; Pariyarath, Rajalakshmi; Pagani, Franco; Buratti, Emanuele; Baralle, Francisco E.

    1999-01-01

    The fibronectin primary transcript undergoes alternative splicing in three noncoordinated sites: the cassette-type EDA and EDB exons and the more complex IIICS region. We have shown previously that an 81-nucleotide region within the EDA exon is necessary for exon recognition and that this region contains at least two splicing-regulatory elements: a polypurinic enhancer (exonic splicing enhancer [ESE]) and a nearby silencer element (exonic splicing silencer [ESS]). Here, we have analyzed the function of both elements in different cell types. We have mapped the ESS to the nucleotide level, showing that a single base change is sufficient to abolish its function. Testing of the ESE and ESS elements in heterologous exons, individually or as part of the complete EDA regulatory region, showed that only the ESE element is active in different contexts. Functional studies coupled to secondary-structure enzymatic analysis of the EDA exon sequence variants suggest that the role of the ESS element may be exclusively to ensure the proper RNA conformation and raise the possibility that the display of the ESE element in a loop position may represent a significant feature of the exon splicing-regulatory region. PMID:10082532

  1. A new criterion to evaluate water vapor interference in protein secondary structural analysis by FTIR spectroscopy.

    PubMed

    Zou, Ye; Ma, Gang

    2014-01-01

    Second derivative and Fourier self-deconvolution (FSD) are two commonly used techniques to resolve the overlapped component peaks from the often featureless amide I band in Fourier transform infrared (FTIR) curve-fitting approach for protein secondary structural analysis. Yet, the reliability of these two techniques is greatly affected by the omnipresent water vapor in the atmosphere. Several criteria are currently in use as quality controls to ensure the protein absorption spectrum is negligibly affected by water vapor interference. In this study, through a second derivative study of liquid water, we first argue that the previously established criteria cannot guarantee a reliable evaluation of water vapor interference due to a phenomenon that we refer to as sample's absorbance-dependent water vapor interference. Then, through a comparative study of protein and liquid water, we show that a protein absorption spectrum can still be significantly affected by water vapor interference even though it satisfies the established criteria. At last, we propose to use the comparison between the second derivative spectra of protein and liquid water as a new criterion to better evaluate water vapor interference for more reliable second derivative and FSD treatments on the protein amide I band. PMID:24901531

  2. Spatial structure of neuronal receptive field in awake monkey secondary visual cortex (V2).

    PubMed

    Liu, Lu; She, Liang; Chen, Ming; Liu, Tianyi; Lu, Haidong D; Dan, Yang; Poo, Mu-ming

    2016-02-16

    Visual processing depends critically on the receptive field (RF) properties of visual neurons. However, comprehensive characterization of RFs beyond the primary visual cortex (V1) remains a challenge. Here we report fine RF structures in secondary visual cortex (V2) of awake macaque monkeys, identified through a projection pursuit regression analysis of neuronal responses to natural images. We found that V2 RFs could be broadly classified as V1-like (typical Gabor-shaped subunits), ultralong (subunits with high aspect ratios), or complex-shaped (subunits with multiple oriented components). Furthermore, single-unit recordings from functional domains identified by intrinsic optical imaging showed that neurons with ultralong RFs were primarily localized within pale stripes, whereas neurons with complex-shaped RFs were more concentrated in thin stripes. Thus, by combining single-unit recording with optical imaging and a computational approach, we identified RF subunits underlying spatial feature selectivity of V2 neurons and demonstrated the functional organization of these RF properties. PMID:26839410

  3. The Structure of Educational Costs: Multiproduct Cost Functions for Primary and Secondary Schools in Latin America.

    ERIC Educational Resources Information Center

    Jimenez, Emmanuel

    1986-01-01

    Relying heavily on equations and tabular data, this paper analyzes the educational cost functions of primary and secondary schooling levels in Latin America. Economies of scale are found for both levels in Bolivian and Paraguayan urban schools; schools combining primary and secondary school services are shown to be less cost effective. (23…

  4. Polymorphism, population structure, and multivariate relationships among secondary traits in open-pollinated corn heterotic groups

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant, ear and kernel traits directly or indirectly associated with grain yield in corn (Zea mays) were suggested as "secondary" traits to select for larger grain yield, especially in open-pollinated corn varieties (OPVs) and their hybrids (OPVhs). Thirty-four secondary traits, besides grain yield, ...

  5. Scoping the Duals: Structural Challenges of Combining Further and Higher Education in Post-Secondary Institutions

    ERIC Educational Resources Information Center

    Garrod, Neil; Macfarlane, Bruce

    2007-01-01

    Dual sector universities (or duals) are a growing international phenomenon that cut across the divide that typically exists in post-secondary education. Duals combine "further" and "higher" education within a single institution providing enhanced opportunities for student transition between post-secondary sectors. This paper reports the results of…

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

    PubMed

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

    2013-01-01

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

  7. A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

    PubMed

    Rivas, Elena; Lang, Raymond; Eddy, Sean R

    2012-02-01

    The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases. PMID:22194308

  8. Using cuttlefish ink as an additive to produce -non-iridescent structural colors of high color visibility.

    PubMed

    Zhang, Yafeng; Dong, Biqin; Chen, Ang; Liu, Xiaohan; Shi, Lei; Zi, Jian

    2015-08-26

    Non-iridescent structural colors of high color visibility are produced by amorphous photonic structures, in which -natural cuttlefish ink is used as an additive to break down the long-range order of the structures. The color hue and its spectral purity can be tuned by adjusting the diameter of the polystyrene (PS) spheres and the proportion of ink particles. PMID:26175211

  9. Secondary structure confirmation and localization of Mg2+ ions in the mammalian CPEB3 ribozyme.

    PubMed

    Skilandat, Miriam; Rowinska-Zyrek, Magdalena; Sigel, Roland K O

    2016-05-01

    Most of today's knowledge of the CPEB3 ribozyme, one of the few small self-cleaving ribozymes known to occur in humans, is based on comparative studies with the hepatitis delta virus (HDV) ribozyme, which is highly similar in cleavage mechanism and probably also in structure. Here we present detailed NMR studies of the CPEB3 ribozyme in order to verify the formation of the predicted nested double pseudoknot in solution. In particular, the influence of Mg(2+), the ribozyme's crucial cofactor, on the CPEB3 structure is investigated. NMR titrations, Tb(3+)-induced cleavage, as well as stoichiometry determination by hydroxyquinoline sulfonic acid fluorescence and equilibrium dialysis, are used to evaluate the number, location, and binding mode of Mg(2+)ions. Up to eight Mg(2+)ions interact site-specifically with the ribozyme, four of which are bound with high affinity. The global fold of the CPEB3 ribozyme, encompassing 80%-90% of the predicted base pairs, is formed in the presence of monovalent ions alone. Low millimolar concentrations of Mg(2+)promote a more compact fold and lead to the formation of additional structures in the core of the ribozyme, which contains the inner small pseudoknot and the active site. Several Mg(2+)binding sites, which are important for the functional fold, appear to be located in corresponding locations in the HDV and CPEB3 ribozyme, demonstrating the particular relevance of Mg(2+)for the nested double pseudoknot structure. PMID:26966151

  10. Critical review of the safety assessment of nano-structured silica additives in food.

    PubMed

    Winkler, Hans Christian; Suter, Mark; Naegeli, Hanspeter

    2016-01-01

    The development of nano-materials is viewed as one of the most important technological advances of the 21st century and new applications of nano-sized particles in the production, processing, packaging or storage of food are expected to emerge soon. This trend of growing commercialization of engineered nano-particles as part of modern diet will substantially increase oral exposure. Contrary to the proven benefits of nano-materials, however, possible adverse health effects have generally received less attention. This problem is very well illustrated by nano-structured synthetic amorphous silica (SAS), which is a common food additive since several decades although the relevant risk assessment has never been satisfactorily completed. A no observed adverse effect level of 2500 mg SAS particles/kg body weight per day was derived from the only available long-term administration study in rodents. However, extrapolation to a safe daily intake for humans is problematic due to limitations of this chronic animal study and knowledge gaps as to possible local intestinal effects of SAS particles, primarily on the gut-associated lymphoid system. This uncertainty is aggravated by digestion experiments indicating that dietary SAS particles preserve their nano-sized structure when reaching the intestinal lumen. An important aspect is whether food-borne particles like SAS alter the function of dendritic cells that, embedded in the intestinal mucosa, act as first-line sentinels of foreign materials. We conclude that nano-particles do not represent a completely new threat and that most potential risks can be assessed following procedures established for conventional chemical hazards. However, specific properties of food-borne nano-particles should be further examined and, for that purpose, in vitro tests with decision-making cells of the immune system are needed to complement existing in vivo studies. PMID:27287345

  11. A secondary structural common core in the ribosomal ITS2 (internal transcribed spacer) of Culexspecies from diverse geographical locations

    PubMed Central

    Bhargavi, Ryavarapu; Vishwakarma, Siddharth; Murty, Upadhyayula Suryanarayana

    2005-01-01

    In the present study, sequence and structural analysis of ITS2 region (the spacer segment between 5.8S and 28S rRNA of mature rRNA sequences) of 7 Culex species belonging to 5 different geographical locations was carried out. Alignment of the ITS2 sequence from the 7 species revealed 8 homologous domains. Four species namely C. vishnui, C. annulus, C. pipiens, C. quiquefasciatusshowed high sequence (98­100%) and RNA secondary structure similarity. The ITS2 similarity among different species is high despite their varying geographical locations. Several common features of secondary structure are shared among these species, with some of them supported by compensatory changes, suggesting the significant role by ITS2 as an RNA domain during ribosome biogenesis. PMID:17597853

  12. Two-dimensional sup 1 H NMR studies on HPr protein from Staphylococcus aureus: Complete sequential assignments and secondary structure

    SciTech Connect

    Kalbitzer, H.R.; Neidig, K.P. ); Hengstenberg, W. )

    1991-11-19

    Complete sequence-specific assignments of the {sup 1}H NMR spectrum of HPr protein from Staphylococcus aureus were obtained by two-dimensional NMR methods. Important secondary structure elements that can be derived from the observed nuclear Overhauser effects are a large antiparallel {beta}-pleated sheet consisting of four strands, A, B, C, D, a segment S{sub AB} consisting of an extended region around the active-center histidine (His-15) and an {alpha}-helix, a half-turn between strands B and C, a segment S{sub CD} which shows no typical secondary structure, and the {alpha}-helical, C-terminal segment S{sub term}. These general structural features are similar to those found earlier in HPr proteins from different microorganisms such as Escherichia coli, Bacillus subtilis, and Streptococcus faecalis.

  13. Influencing the structure of block copolymer micelles with small molecule additives

    NASA Astrophysics Data System (ADS)

    Robertson, Megan; Singh, Avantika; Cooksey, Tyler; Kidd, Bryce; Piemonte, Rachele; Wang, Shu; Mai Le, Kim; Madsen, Louis

    Amphiphilic block copolymer micelles in water are under broad exploration for drug delivery applications due to their high loading capacity and targeted drug delivery. We aim to understand the kinetic and thermodynamic processes that underlie the self-assembly of diblock copolymer micelle systems. The present work focuses on diblock copolymers containing poly(ethylene oxide) (a hydrophilic polymer) and polycaprolactone (a hydrophobic polymer), which spontaneously self-assemble into spherical micelles in water. Addition of a common good solvent (a co-solvent) for both of the constituting blocks, such as tetrahydrofuran (THF), reduces the interfacial tension at the core-corona interface. We are currently investigating the effect of this phenomenon on the micelle structural properties, using small-angle scattering and nuclear magnetic resonance. We have characterized the hydrodynamic radius, core radius, corona thickness, aggregation number, degree of swelling of the micelle core with the co-solvent, and unimer (free chain) concentration, as a function of the co-solvent concentration. Fundamental knowledge from these studies will inform design of drug delivery systems by allowing us to tailor micelle properties for optimal cargo loading.

  14. Aggregation and secondary loop structure of oligonucleotides do not determine their ability to inhibit TLR9.

    PubMed

    Ashman, Robert F; Goeken, J Adam; Lenert, Petar S

    2011-08-01

    Toll-like receptor 9 (TLR9) is an endosomal DNA sensor that warns us of the presence of infectious danger and triggers a rapid pro-inflammatory response in dendritic cells, macrophages, and B cells. The consequences of uncontrolled TLR9 activation can be detrimental for the host, contributing to the pathogenesis of bacterial septic shock or autoimmune diseases, such as systemic lupus erythematosus. Therefore, we need to develop TLR9 antagonists. We and others have created inhibitory oligonucleotides (INH-ODN) that are capable of sequence-dependent inhibition of TLR9-induced activation in both human and mouse cells. However, it is not clear whether marked differences in INH-ODN activity related to base sequence derived from polymerization of INH-ODNs or their ability to complex with stimulatory CpG-oligonucleotides (ST-ODN). Furthermore, the 5' end of INH-ODNs may assume a particular loop configuration that may be needed for binding to a critical site on TLR9. Here, we show that 1) G-tetrads required for ODN stacking were compatible with INH-ODN activity but were not necessary; 2) there was no relationship between activity and self-association at endosomal pH; 3) there was no evidence for direct binding between ST-ODNs and INH-ODNs; 4) when a 3G sequence was disrupted, despite a preserved stem-loop formation, INH-ODN activity was abolished. These results support the conclusion that certain features of the primary linear sequence are critical for TLR9 inhibition, but changes in secondary structure or in ODN aggregation are irrelevant. PMID:21376154

  15. Secondary Structures of Ubiquitin Ions Soft-Landed onto Self-Assembled Monolayer Surfaces.

    PubMed

    Hu, Qichi; Laskin, Julia

    2016-06-01

    The secondary structures of multiply charged ubiquitin ions soft-landed onto self-assembled monolayer (SAM) surfaces were studied using in situ infrared reflection-absorption spectroscopy (IRRAS). Two charge states of ubiquitin, 5+ and 13+, were mass selected separately from a mixture of different charge states produced by electrospray ionization (ESI). The low 5+ charge state represents a nativelike folded state of ubiquitin, while the high 13+ charge state assumes an extended, almost linear conformation. Each of the two charge states was soft-landed onto a CH3- and COOH-terminated SAM of alkanethiols on gold (HSAM and COOH-SAM). HSAM is a hydrophobic surface known to stabilize helical conformations of soft-landed protonated peptides, whereas COOH-SAM is a hydrophilic surface that preferentially stabilizes β-sheet conformations. IRRAS spectra of the soft-landed ubiquitin ions were acquired as a function of time during and after ion soft-landing. Similar to smaller peptide ions, helical conformations of ubiquitin are found to be more abundant on HSAM, while the relative abundance of β-sheet conformations increases on COOH-SAM. The initial charge state of ubiquitin also has a pronounced effect on its conformation on the surface. Specifically, on both surfaces, a higher relative abundance of helical conformations and a lower relative abundance of β-sheet conformations are observed for the 13+ charge state compared to the 5+ charge state. Time-resolved experiments indicate that the α-helical band in the spectrum of the 13+ charge state slowly increases with time on the HSAM surface and decreases in the spectrum of the 13+ charge state on COOH-SAM. These results further support the preference of the hydrophobic HSAM surface toward helical conformations and demonstrate that soft-landed protein ions may undergo slow conformational changes during and after deposition. PMID:27192353

  16. Aerobic addition of secondary phosphine oxides to vinyl sulfides: a shortcut to 1-hydroxy-2-(organosulfanyl)ethyl(diorganyl)phosphine oxides

    PubMed Central

    Malysheva, Svetlana F; Artem’ev, Alexander V; Gusarova, Nina K; Belogorlova, Nataliya A; Albanov, Alexander I; Liu, C W

    2015-01-01

    Summary Secondary phosphine oxides react with vinyl sulfides (both alkyl- and aryl-substituted sulfides) under aerobic and solvent-free conditions (80 °C, air, 7–30 h) to afford 1-hydroxy-2-(organosulfanyl)ethyl(diorganyl)phosphine oxides in 70–93% yields. PMID:26664618

  17. Can Families in Rural India Bear the Additional Burden of Secondary Education? Investigating the Determinants of Transition. CREATE Pathways to Access. Research Monograph No. 50

    ERIC Educational Resources Information Center

    Siddhu, Gaurav

    2010-01-01

    India has witnessed a major expansion in participation in basic education in recent years, in the context of a major programme for its promotion: Sarva Shiksha Abhiyan (SSA). Despite a significantly improved picture at the basic level, a considerable proportion of children continue to drop out before reaching the secondary level. Over half of…

  18. Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs

    PubMed Central

    Meyer, Irmtraud M.; Miklós, István

    2005-01-01

    Owing to the degeneracy of the genetic code, protein-coding regions of mRNA sequences can harbour more than only amino acid information. We search the mRNA sequences of 11 human protein-coding genes for evolutionarily conserved secondary structure elements using RNA-Decoder, a comparative secondary structure prediction program that is capable of explicitly taking the known protein-coding context of the mRNA sequences into account. We detect well-defined, conserved RNA secondary structure elements in the coding regions of the mRNA sequences and show that base-paired codons strongly correlate with sparse codons. We also investigate the role of repetitive elements in the formation of secondary structure and explain the use of alternate start codons in the caveolin-1 gene by a conserved secondary structure element overlapping the nominal start codon. We discuss the functional roles of our novel findings in regulating the gene expression on mRNA level. We also investigate the role of secondary structure on the correct splicing of the human CFTR gene. We study the wild-type version of the pre-mRNA as well as 29 variants with synonymous mutations in exon 12. By comparing our predicted secondary structures to the experimentally determined splicing efficiencies, we find with weak statistical significance that pre-mRNAs with high-splicing efficiencies have different predicted secondary structures than pre-mRNAs with low-splicing efficiencies. PMID:16275783

  19. Secondary structure of expansion segment D1 in LSU rDNA from Arachnida and its phylogenetic application in Eriophyoid mites and in Acari.

    PubMed

    Wang, Zheng-Hang; Zhao, Ya-E; Xu, Yang; Hu, Li; Chen, Yi-Meng

    2015-12-01

    An increasing number of researchers have applied secondary-structure based multiple alignments of rDNA genes in phylogeny. These studies mostly depended on a few valuable divergent domains in LSU and SSU rDNA. Yet other divergent domains, e.g. D1, were poorly investigated and rarely used. However, these domains might contain additional evolutionary data and play a vital role in DNA-based phylogenetic study. Here, we investigated all available D1 sequences of Arachnida taxa and predicted corresponding secondary structures to help identify homologous positions in the D1 region. Long insertions were found exclusive to Eriophyoidea and folded into three newly proposed helices. Non-Acari taxa were all GC rich. In Acari, most Trombidiformes and all Mesostigmata (Parasitiformes) taxa were AT rich and Ixodida (Parasitiformes) GC rich; however there was no consistent base bias in Sarcoptiformes sequences. For Eriophyoid mites, genera Cecidophyopsis and Aceria were both well supported in MP, NJ, ME and ML tress based on D1 sequences, and clusters of Cecidophyopsis species were identical with former study. This demonstrated that the D1 region could act as a valuable molecular marker in phylogenetic reconstruction of Eriophyoidea. Additionally, D1 has been proven suitable in phylogenetic analysis at the family and genus level in Acari, but not in Opiliones. PMID:26420464

  20. Determination of secondary structural changes in gluten proteins during mixing using Fourier transform horizontal attenuated total reflectance spectroscopy.

    PubMed

    Seabourn, Bradford W; Chung, Okkyung K; Seib, Paul A; Mathewson, Paul R

    2008-06-11

    Fourier transform horizontal attenuated total reflectance (FT-HATR) was used to examine changes in the secondary structure of gluten proteins in a flour-water dough system during mixing. Midinfrared spectra of mixed dough revealed changes in four bands in the amide III region associated with secondary structure in proteins: 1317 (alpha-helix), 1285 (beta-turn), 1265 (random coil), and 1242 cm (-1) (beta-sheet). The largest band, which also showed the greatest change in second derivative band area (SDBA) during mixing, was located at 1242 cm (-1). The bands at 1317 and 1285 cm (-1) also showed an increase in SDBA over time. Conversely, the band at 1265 cm (-1) showed a corresponding decrease over time as the doughs were mixed. All bands reached an optimum corresponding to the minimum mobility of the dough as determined by the mixograph. Increases in alpha-helix, beta-turn, and beta-sheet secondary structures during mixing suggest that the dough proteins assume a more ordered conformation. These results demonstrate that it is possible, using infrared spectroscopic techniques, to relate the rheological behavior of developing dough in a mixograph directly to changes in the structure of the gluten protein system. PMID:18489117

  1. Effects of frit addition on the surface morphology and structural properties of ZnO-Bi2O3-Mn2O3 discs

    NASA Astrophysics Data System (ADS)

    Shahardin, Ahmad Hajidi; Mahmud, Shahrom; Sendi, Rabab Khalid

    2015-04-01

    ZnO-Bi2O3-Mn2O3 discs were prepared using conventional ceramic processing method and sintered at 1000°C. The different percentages of frit on the ZnO-Bi2O3-Mn2O3 discs were 0.0%, 0.5%, 1.0% and 3.0%. From FESEM observation, the grain structure and grain growth were more uniformly constructed and well distributed. Frit addition was found to cause a big drop in the average grain size from 4.59 µm to 2.76 µm even with an addition of 0.5 mol%. The Si and Al content in the frit recipe might have played a role as inhibiting agents in grain growth during sintering. RAMAN intensity and phase shifting were not affected by frit addition except at 3 mol%. Frit addition did not affect the formation of secondary phases. Frit addition below 3 mol% in ZnO-Bi2O3-Mn2O3 varistor discs can be used as a method in controlling grain size without affecting other properties.

  2. Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus.

    PubMed

    Schaak, Janell E; Babitzke, Paul; Bevilacqua, Philip C

    2003-12-01

    Expression of the trpEDCFBA operon of Bacillus subtilis is regulated by transcription attenuation and translation control mechanisms. We recently determined that the B. subtilis trp leader readthrough transcript can adopt a Mg(2+)-dependent tertiary structure that appears to interfere with TRAP-mediated translation control of trpE. In the present study, sequence comparisons to trp leaders from three other Bacillus sp. were made, suggesting that RNA secondary and tertiary structures are phylogenetically conserved. To test this hypothesis, experiments were carried out with the trp leader transcript from Bacillus stearothermophilus. Structure mapping experiments confirmed the predicted secondary structure. Native gel experiments identified a faster mobility species in the presence of Mg(2+), suggesting that a Mg(2+)-dependent tertiary structure forms. Mg(2+)-dependent protection of residues within the first five triplet repeats of the TRAP binding target and a pyrimidine-rich internal loop were observed, consistent with tertiary structure formation between these regions. Structure mapping in the presence of a competitor DNA oligonucleotide allowed the interacting partners to be identified as a single-stranded portion of the purine-rich TRAP binding target and the large downstream pyrimidine-rich internal loop. Thermal denaturation experiments revealed a Mg(2+)- and pH-dependent unfolding transition that was absent for a transcript missing the first five triplet repeats. The stability of several mutant transcripts allowed a large portion of the base-pairing register for the tertiary interaction to be determined. These data indicate that RNA secondary and tertiary structures involved in TRAP-mediated translation control are conserved in at least four Bacillus species. PMID:14624006

  3. Structured additive regression modeling of age of menarche and menopause in a breast cancer screening program.

    PubMed

    Duarte, Elisa; de Sousa, Bruno; Cadarso-Suarez, Carmen; Rodrigues, Vitor; Kneib, Thomas

    2014-05-01

    Breast cancer risk is believed to be associated with several reproductive factors, such as early menarche and late menopause. This study is based on the registries of the first time a woman enters the screening program, and presents a spatio-temporal analysis of the variables age of menarche and age of menopause along with other reproductive and socioeconomic factors. The database was provided by the Portuguese Cancer League (LPCC), a private nonprofit organization dealing with multiple issues related to oncology of which the Breast Cancer Screening Program is one of its main activities. The registry consists of 259,652 records of women who entered the screening program for the first time between 1990 and 2007 (45-69-year age group). Structured Additive Regression (STAR) models were used to explore spatial and temporal correlations with a wide range of covariates. These models are flexible enough to deal with a variety of complex datasets, allowing us to reveal possible relationships among the variables considered in this study. The analysis shows that early menarche occurs in younger women and in municipalities located in the interior of central Portugal. Women living in inland municipalities register later ages for menopause, and those born in central Portugal after 1933 show a decreasing trend in the age of menopause. Younger ages of menarche and late menopause are observed in municipalities with a higher purchasing power index. The analysis performed in this study portrays the time evolution of the age of menarche and age of menopause and their spatial characterization, adding to the identification of factors that could be of the utmost importance in future breast cancer incidence research. PMID:24615881

  4. Use of complementary DNA oligomers to probe trp leader transcript secondary structures involved in transcription pausing and termination.

    PubMed Central

    Fisher, R; Yanofsky, C

    1984-01-01

    DNA oligomers were synthesized that are perfectly complementary to different segments of the tryptophan (trp) operon leader transcript. These 15 nucleotide long oligomers were used as probes of the involvement of transcript secondary structures in two processes: transcription pausing at the pause site located near base pair 90 in the leader region, and transcription termination at the attenuator. The 15-mers were complementary to the four segments of the trp leader transcript which have been shown to form the alternative secondary structures that are believed to be responsible for pausing, termination, and antitermination. Oligomers complementary to RNA segments 1 and 3 relieved termination while the 15-mer complementary to RNA segment 1 relieved pausing. 15-mers complementary to segment 2 had no effect on pausing and the oligomer complementary to segment 4 had virtually no effect on termination. PMID:6201827

  5. The Response of Greek Key Proteins to Changes in Connectivity Depends on the Nature of Their Secondary Structure

    PubMed Central

    Kemplen, Katherine R.; De Sancho, David; Clarke, Jane

    2015-01-01

    What governs the balance between connectivity and topology in regulating the mechanism of protein folding? We use circular permutation to vary the order of the helices in the all-α Greek key protein FADD (Fas-associated death domain) to investigate this question. Unlike all-β Greek key proteins, where changes in the order of secondary structure cause a shift in the folding nucleus, the position of the nucleus in FADD is unchanged, even when permutation reduces the complexity significantly. We suggest that this is because local helical contacts are so dominant that permutation has little effect on the entropic cost of forming the folding nucleus whereas, in all-β Greek key proteins, all interactions in the nucleus are long range. Thus, the type of secondary structure modulates the sensitivity of proteins to changes in connectivity. PMID:25861761

  6. [Skeleton or mummy: practices and structures for secondary burial in southern Italy in modern and contemporary age].

    PubMed

    Fornaciari, Antonio

    2013-01-01

    The ancient concepts of death as duration and the practices of secondary burial,first analysed by Robert Hertz, still survive in many areas of southern Italy. According to these beliefs death was perceived not as a sudden event, but as a long-lasting process, during which the deceased person had to go through a transitory phase, passing from one state of existence to another. Recent archeological research documents the persistence of secondary burial rites in Southern Italy during the Modern Age. A survey conducted in the province of Messina in Eastern Sicily has identified two surviving architectural structures appointed for the treatment of the bodies: the 'sitting colatoio' aimed at favoring the skeletonisation and the 'horizontal colatoio' used to obtain mummification by dehydration. Both these structures controlled the corpse's decay and transformed the body in a stable and durable simulacra of the dead. PMID:25807706

  7. Plasmodesmata during development: re-examination of the importance of primary, secondary, and branched plasmodesmata structure versus function

    PubMed Central

    Burch-Smith, Tessa M.; Stonebloom, Solomon; Xu, Min

    2010-01-01

    Plasmodesmata (PD) structure and function vary temporally and spatially during all stages of plant development. PD that originate during, or post, cell division are designated as primary or secondary according to classical terminology. PD structure may be simple, twinned, or branched. Studies of PD during leaf, root, and embryo development have lead to the generalization that cells in less mature tissues contain predominantly simple PD. New quantitative analyses reveal that twinned and branched PD also occur in immature tissues. New data also highlight the versatility of viral movement proteins as tags for labeling PD in immature tissues as well as PD in mature tissues. A summary of the formation and function of primary, secondary, and branched PD during leaf, trichome, embryo, apical meristem, vascular cambium, and root development underscores the remarkable and indispensible plant-specific intercellular communication system that is mediated by PD. PMID:21174132

  8. a High Efficiency Dye-Sensitized Solar Cell with NANO-TiO2 Secondary Structure in the Photoanode

    NASA Astrophysics Data System (ADS)

    Lan, Zhang; Wu, Jihuai; Lin, Jianming; Huang, Miaoliang

    2013-04-01

    A high efficiency dye-sensitized solar cell (DSC) with nanocrystallite TiO2 (nano-TiO2) secondary structure in the photoanode was successfully fabricated via a simple one step doctor blade printing method with a special nano-TiO2 paste containing micro-sized nano-TiO2 aggregates formed in situ. The special secondary structure in the photoanode shows improved optical absorption, increased light scattering ability, and enhanced electron transport and collection efficiency, resulting in high power conversion efficiency of 7.30% with 6 μm thin nano-TiO2 film in the photoanode, and the highest value of 9.28% by increasing the thickness of the nano-TiO2 film to 11 μm.

  9. Kohonen map as a visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures.

    PubMed

    Hanke, J; Reich, J G

    1996-12-01

    The method of Kohonen maps, a special form of neural networks, was applied as a visualization tool for the analysis of protein sequence similarity. The procedure converts sequence (domains, aligned sequences, segments of secondary structure) into a characteristic signal matrix. This conversion depends on the property or replacement score vector selected by the user. Similar sequences have small distance in the signal space. The trained Kohonen network is functionally equivalent to an unsupervised non-linear cluster analyzer. Protein families, or aligned sequences, or segments of similar secondary structure, aggregate as clusters, and their proximity may be inspected on a color screen or on paper. Pull-down menus permit access to background information in the established text-oriented way. PMID:9021261

  10. Intrusive growth of primary and secondary phloem fibres in hemp stem determines fibre-bundle formation and structure.

    PubMed

    Snegireva, Anastasia; Chernova, Tatyana; Ageeva, Marina; Lev-Yadun, Simcha; Gorshkova, Tatyana

    2015-01-01

    Plant fibres-cells with important mechanical functions and a widely used raw material-are usually identified in microscopic sections only after reaching a significant length or after developing a thickened cell wall. We characterized the early developmental stages of hemp (Cannabis sativa) stem phloem fibres, both primary (originating from the procambium) and secondary (originating in the cambium), when they still had only a primary cell wall. We gave a major emphasis to the role of intrusive elongation, the specific type of plant cell growth by which fibres commonly attain large cell length. We could identify primary phloem fibres at a distance of only 1.2-1.5 mm from the shoot apical meristem when they grew symplastically with the surrounding tissues. Half a millimeter further downwards along the stem, fibres began their intrusive elongation, which led to a sharp increase in fibre numbers visible within the stem cross-sections. The intrusive elongation of primary phloem fibres was completed within the several distal centimetres of the growing stem, before the onset of their secondary cell wall formation. The formation of secondary phloem fibres started long after the beginning of secondary xylem formation. Our data indicate that only a small portion of the fusiform cambial initials (<10 %) give rise directly or via their derivatives to secondary phloem fibres. The key determinant of final bundle structure, both for primary and secondary phloem fibres, is intrusive growth. Through bi-directional elongation, fibres join other fibres initiated individually in other stem levels, thus forming the bundles. Our results provide the specific developmental basis for further biochemical and molecular-genetic studies of phloem fibre development in hemp, but may be applied to many other species. PMID:26019229

  11. Intrusive growth of primary and secondary phloem fibres in hemp stem determines fibre-bundle formation and structure

    PubMed Central

    Snegireva, Anastasia; Chernova, Tatyana; Ageeva, Marina; Lev-Yadun, Simcha; Gorshkova, Tatyana

    2015-01-01

    Plant fibres—cells with important mechanical functions and a widely used raw material—are usually identified in microscopic sections only after reaching a significant length or after developing a thickened cell wall. We characterized the early developmental stages of hemp (Cannabis sativa) stem phloem fibres, both primary (originating from the procambium) and secondary (originating in the cambium), when they still had only a primary cell wall. We gave a major emphasis to the role of intrusive elongation, the specific type of plant cell growth by which fibres commonly attain large cell length. We could identify primary phloem fibres at a distance of only 1.2–1.5 mm from the shoot apical meristem when they grew symplastically with the surrounding tissues. Half a millimeter further downwards along the stem, fibres began their intrusive elongation, which led to a sharp increase in fibre numbers visible within the stem cross-sections. The intrusive elongation of primary phloem fibres was completed within the several distal centimetres of the growing stem, before the onset of their secondary cell wall formation. The formation of secondary phloem fibres started long after the beginning of secondary xylem formation. Our data indicate that only a small portion of the fusiform cambial initials (<10 %) give rise directly or via their derivatives to secondary phloem fibres. The key determinant of final bundle structure, both for primary and secondary phloem fibres, is intrusive growth. Through bi-directional elongation, fibres join other fibres initiated individually in other stem levels, thus forming the bundles. Our results provide the specific developmental basis for further biochemical and molecular-genetic studies of phloem fibre development in hemp, but may be applied to many other species. PMID:26019229

  12. Secondary structure and (1)H, (13)C, (15)N resonance assignments of the endosomal sorting protein sorting nexin 3.

    PubMed

    Overduin, Michael; Rajesh, Sandya; Gruenberg, Jean; Lenoir, Marc

    2015-10-01

    Sorting nexin 3 (SNX3) belongs to a sub-family of sorting nexins that primarily contain a single Phox homology domain capable of binding phosphoinositides and membranes. We report the complete (1)H, (13)C and (15)N resonance assignments of the full-length human SNX3 protein and identification of its secondary structure elements, revealing a canonical fold and unstructured termini. PMID:25893673

  13. A Pilot Study to Examine the Effect of Additional Structured Outdoor Playtime on Preschoolers' Physical Activity Levels

    ERIC Educational Resources Information Center

    Alhassan, Sofiya; Nwaokelemeh, Ogechi; Lyden, Kate; Goldsby, TaShauna; Mendoza, Albert

    2013-01-01

    The impact of additional structured outdoor playtime on preschoolers'; physical activity (PA) level is unclear. The purpose of this pilot study was to explore the effects of increasing structured outdoor playtime on preschoolers'; PA levels. Eight full-day classrooms (n = 134 children) from two preschool programmes were randomised into a treatment…

  14. Effect of template secondary structure on the inhibition of HIV-1 reverse transcriptase by a pyridinone non-nucleoside inhibitor.

    PubMed Central

    Olsen, D B; Carroll, S S; Culberson, J C; Shafer, J A; Kuo, L C

    1994-01-01

    The importance of RNA secondary structure on HIV-1 reverse transcriptase catalyzed polymerization and on the potency of the pyridin-2-one inhibitor 3-(4,7-dichlorobenzoxazol-2-ylmethylamino)-5-ethyl-6-meth ylpyridin-2(1H)-one, L-697,661, were investigated by employing heteromeric primer-template systems. Our data revealed that a stem-loop hairpin secondary structure in the RNA template could lead to strong hindrance of reverse transcription in the reaction catalyzed by HIV-1 reverse transcriptase resulting in the build up of intermediate-length (pause) polymerization products. The presence of L-697,661 greatly enhanced the accumulation of the pause products suggesting that the rate of enzyme translocation from the pause product might be more potently inhibited than polymerization up to the pause site. Model experiments using a synthetic RNA template containing a stem-loop hairpin revealed that the inhibitory potency of L-697, 661 increased 2-fold upon polymerization to within four bases of the secondary structure. Inhibitor potency was enhanced over 6-fold when primer-extension proceeded through the duplex region of the stem-loop. Images PMID:7514786

  15. Secondary School Students’ LLL Competencies, and Their Relation with Classroom Structure and Achievement

    PubMed Central

    Klug, Julia; Lüftenegger, Marko; Bergsmann, Evelyn; Spiel, Christiane; Schober, Barbara

    2016-01-01

    There is a strong urge to foster lifelong learning (LLL) competencies with its key components – motivation and self-regulated learning – from early on in the education system. School in general is presently not considered to be successful in systematically imparting motivation and self-regulated learning strategies. There is strong evidence that decisive motivational determinants decrease the longer students stay in school. At present, the central sources of information about the situation in Austria are international monitoring studies, which only examine selected aspects of specific target groups, and their interpretability concerning mean values is constricted due to cultural differences. Thus, it is important to conduct additional and more differentiated national surveys of the actual state. This is why this study aimed at answering the following questions: (1) how well are Austrian students equipped for the future, in terms of their lifelong learning competencies, (2) can perceived classroom structure predict students’ LLL, and (3) is there a correlation of students’ LLL with their achievement in the school subjects math and German language. 5366 students (52.1% female) from 36 Austrian schools took part in the online-questionnaire (mean age 15.35 years, SD = 2.45), which measured their perceived LLL competencies in the subjects math and German language, their perceived classroom structure and their achievement. Results showed that the great majority of Austrian students – independent from domain and sex – know and are able to apply cognitive as well as metacognitive learning strategies. With regard to motivation the picture is less satisfactory: whilst students’ self-efficacy is not the problem, there is a lack of interest in the school subjects and they often report to follow performance approach goals. Classroom structure positively predicted students’ goals, interest, self-efficacy and learning strategies. Self-efficacy, performance

  16. Secondary School Students' LLL Competencies, and Their Relation with Classroom Structure and Achievement.

    PubMed

    Klug, Julia; Lüftenegger, Marko; Bergsmann, Evelyn; Spiel, Christiane; Schober, Barbara

    2016-01-01

    There is a strong urge to foster lifelong learning (LLL) competencies with its key components - motivation and self-regulated learning - from early on in the education system. School in general is presently not considered to be successful in systematically imparting motivation and self-regulated learning strategies. There is strong evidence that decisive motivational determinants decrease the longer students stay in school. At present, the central sources of information about the situation in Austria are international monitoring studies, which only examine selected aspects of specific target groups, and their interpretability concerning mean values is constricted due to cultural differences. Thus, it is important to conduct additional and more differentiated national surveys of the actual state. This is why this study aimed at answering the following questions: (1) how well are Austrian students equipped for the future, in terms of their lifelong learning competencies, (2) can perceived classroom structure predict students' LLL, and (3) is there a correlation of students' LLL with their achievement in the school subjects math and German language. 5366 students (52.1% female) from 36 Austrian schools took part in the online-questionnaire (mean age 15.35 years, SD = 2.45), which measured their perceived LLL competencies in the subjects math and German language, their perceived classroom structure and their achievement. Results showed that the great majority of Austrian students - independent from domain and sex - know and are able to apply cognitive as well as metacognitive learning strategies. With regard to motivation the picture is less satisfactory: whilst students' self-efficacy is not the problem, there is a lack of interest in the school subjects and they often report to follow performance approach goals. Classroom structure positively predicted students' goals, interest, self-efficacy and learning strategies. Self-efficacy, performance approach goals, meta

  17. Effect of addition of pore expanding agent on changes of structure characteristics of ordered mesoporous silicas

    NASA Astrophysics Data System (ADS)

    Derylo-Marczewska, A.; Marczewski, A. W.; Skrzypek, I.; Pikus, S.; Kozak, M.

    2008-12-01

    A series of mesoporous silica materials were synthesized by applying two types of Pluronic copolymers as pore creating agents. Differentiation of pore structure of the obtained sorbents was attained by changing the amount of trimethylbenzene as pore expander introduced to a reacting mixture. The parameters characterizing porous structure were estimated from nitrogen adsorption/desorption isotherms. The changes of pore arrangement in the synthesized materials were investigated by using X-ray diffraction. The structural transformations were found at the TMB/polymer ratio of 0.8 and 1. Correlations between the values of structure parameters and the content of TMB were found.

  18. The Structure of Scientific Arguments by Secondary Science Teachers: Comparison of Experimental and Historical Science Topics

    ERIC Educational Resources Information Center

    Gray, Ron; Kang, Nam-Hwa

    2014-01-01

    Just as scientific knowledge is constructed using distinct modes of inquiry (e.g. experimental or historical), arguments constructed during science instruction may vary depending on the mode of inquiry underlying the topic. The purpose of this study was to examine whether and how secondary science teachers construct scientific arguments during…

  19. The Maslach Burnout Inventory: Testing for Invariant Factorial Structure across Gender for Elementary and Secondary Teachers.

    ERIC Educational Resources Information Center

    Byrne, Barbara M.

    A study was conducted to: (1) test for the factorial validity of the 22-item Maslach Burnout Inventory (MBI) separately for 742 male and 801 female elementary school teachers and 659 male and 721 female secondary school teachers in Central Canada; (2) cross-validate findings across a second independent sample for each teacher group; and (3) test…

  20. The Tension between Organisational Sub-structures in Secondary Schools and Educational Reform.

    ERIC Educational Resources Information Center

    Imants, Jeroen; Sleegers, Peter; Witziers, Bob

    2001-01-01

    Explores how Dutch secondary schools can provide supportive working contexts that promote teacher learning, focusing on integration of two substructures (subject departments and student guidance units). Analyzes tensions between the substructures, summarizes insights into teacher learning communities, and discusses integrated teacher teams'…

  1. Impact of zeolite-based nanomodified additive on the structure and strength of the cement stone

    NASA Astrophysics Data System (ADS)

    Egorova, A. D.; Filippova, K. E.

    2015-01-01

    Portland cement is the main binder in the building materials industry; its properties strongly influence properties of mortars and concretes. Some regions experience difficulties with delivery and storage of Portland cement, raising the need to develop an effective additive from the available raw materials. Such materials for the Republic of Sakha (Yakutia) are zeolite-containing rocks. Studies have shown that introducing of dibutylphthalate to the composition of modified additive during mechanochemical activation leads to achievement of up to 11% of total amount particles with the size of 3-30 nm. After introducing 0.5% of the obtained additives, the compressive strength of cement-sand slurry samples increases up to 28%. Positive effect of additives introduction is also observed at high flow rate of water (W / C = 0.7). Gaining strength reaches 23%, allowing the efficient use of additive for movable mixtures with enhanced strength properties. In general, the proposed supplement allows reducing the water flow in the solution without decreasing its mobility, and increasing strength properties, which makes it possible to obtain a whole class of solutions of modified cement binder. The market value of the developed additives is 18 rubles per 1 kg, making sound competition in the market of modifying additives.

  2. Effects of meat addition on pasta structure, nutrition and in vitro digestibility.

    PubMed

    Liu, Tingting; Hamid, Nazimah; Kantono, Kevin; Pereira, Loveena; Farouk, Mustafa M; Knowles, Scott O

    2016-12-15

    In our study, semolina flour was substituted with beef emulsion (EM) at three different levels of 15, 30 and 45% (w/w) to develop a pasta with enhanced nutritional profile. The protein, fat, and water content significantly increased with addition of meat. The addition of meat enhanced the pasta gluten network. The redness and yellowness of cooked pasta increased with meat addition. Tensile strength increased from 0.018N/mm(2) in the control sample to 0.046N/mm(2) in 45% beef emulsion (45EM) sample. All meat-containing samples had significantly higher elasticity than control (0.039N/mm(2)). GI significantly decreased and IVPD value increased in 45EM sample. Five essential amino acids (leucine, lysine, methionine, threonine, tryptophan) in pasta digesta increased significantly with increasing meat addition. PMID:27451161

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

    NASA Astrophysics Data System (ADS)

    Wu, Hong; Li, Peng; Li, Yulong

    2016-02-01

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

  4. hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

    PubMed Central

    Sugimoto, Yoichiro; Vigilante, Alessandra; Darbo, Elodie; Zirra, Alexandra; Militti, Cristina; D’Ambrogio, Andrea; Luscombe, Nicholas M; Ule, Jernej

    2015-01-01

    mRNA structure is important for post-transcriptional regulation, largely because it affects binding of trans-acting factors1. However, little is known about the in vivo structure of full-length mRNAs. Here we present hiCLIP, a high-throughput technique to identify RNA secondary structures interacting with RNA-binding proteins (RBPs) in vivo. Using this technique to investigate RNA structures bound by Staufen 1 (STAU1), we uncover a dominance of intra-molecular RNA duplexes, a depletion of duplexes from coding regions of highly translated mRNAs, an unforeseen prevalence of long-range duplexes in 3′ untranslated regions (UTRs), and a decreased incidence of SNPs in duplex-forming regions. We also discover a duplex spanning 858nts in the 3′ UTR of the X-box binding Protein 1 (XBP1) mRNA that regulates its cytoplasmic splicing and stability. Our study reveals the fundamental role of mRNA secondary structures in gene regulation and introduces hiCLIP as a widely applicable method for discovering novel, especially long-range, RNA duplexes. PMID:25799984

  5. Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints

    PubMed Central

    2015-01-01

    Knowledge of RNA structure is necessary to determine structure–function relationships and to facilitate design of potential therapeutics. RNA secondary structure prediction can be improved by applying constraints from nuclear magnetic resonance (NMR) experiments to a dynamic programming algorithm. Imino proton walks from NOESY spectra reveal double-stranded regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs, UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to identify constraints for the 5′ to 3′ directionality of base pairs in helices. The 5′ to 3′ directionality constraints were incorporated into an NMR-assisted prediction of secondary structure (NAPSS-CS) program. When it was tested on 18 structures, including nine pseudoknots, the sensitivity and positive predictive value were improved relative to those of three unrestrained programs. The prediction accuracy for the pseudoknots improved the most. The program also facilitates assignment of chemical shifts to individual nucleotides, a necessary step for determining three-dimensional structure. PMID:26451676

  6. Magnesium and manganese binding sites on proteins have the same predominant motif of secondary structure.

    PubMed

    Khrustalev, Vladislav Victorovich; Barkovsky, Eugene Victorovich; Khrustaleva, Tatyana Aleksandrovna

    2016-04-21

    Manganese ion (Mn(2+)) can substitute magnesium ion (Mg(2+)) in active sites of numerous enzymes. Binding sites for these two ions have been studied in two sets of protein 3D structures from the Protein Data Bank with the homology level lower than 25%. The structural motif "beta strand - binder - random coil" is predominant in both Mn(2+) and Mg(2+) coordination spheres, especially in functionally relevant ones. That predominant motif works as an active binder of those divalent cations which can then attract additional ligands, such as different phosphate-containing compounds. In contrast, such Mg(2+) and Mn(2+) binding motif as "GK(T/S)T" being the N-terminal part of alpha helices works as an active binder of phosphates which can then attract divalent cations. There are few differences between Mg(2+) and Mn(2+) coordination spheres responsible of the cation specificity. His residues are underrepresented in certain positions around Asp and Glu residues involved in Mg(2+) coordination, while they are overrepresented in certain positions around Asp and Glu residues coordinating Mn(2+). The random coil region in the "beta strand - random coil - alpha helix" motif for Mg(2+) binding is usually shorter than that in the same motif for Mn(2+) coordination. This feature is associated with the lower number of binding amino acids (and lower levels of usage of such "major" binders as Asp and Glu) for Mg(2+) (which is a hard Lewis acid) in comparison with those for Mn(2+) (an intermediate Lewis acid). PMID:26876751

  7. B2 structure of high-entropy alloys with addition of Al

    SciTech Connect

    Li, C.; Zhao, M.; Li, J. C.; Jiang, Q.

    2008-12-01

    A series of AlCrCoNiFe based alloys with equal percentage of principal components (high-entropy alloys or HE alloys) is fabricated. The related crystalline structures of the alloys are measured and calculated. Results show that the formed bcc phase is a compound based B2 structure where there is partial ionic bonding between Al and other transition metals. Thus, the bcc structure of the alloys should be a B2 instead of an A2 due to the large difference in electronegativities among the components consisting of the HE alloys.

  8. Influence of Ni nanoparticle addition and spark plasma sintering on the TiNiSn–Ni system: Structure, microstructure, and thermoelectric properties

    SciTech Connect

    Birkel, Christina S.; Douglas, Jason E.; Lettiere, Bethany R.; Seward, Gareth; Zhang, Yichi; Pollock, Tresa M.; Seshadri, Ram; Stucky, Galen D.

    2013-12-01

    The electronic and thermal properties of thermoelectric materials are highly dependent on their microstructure and therefore on the preparation conditions, including the initial synthesis and, if applicable, densification of the obtained powders. Introduction of secondary phases on the nano- and/or microscale is widely used to improve the thermoelectric figure of merit by reduction of the thermal conductivity. In order to understand the effect of the preparation technique on structure and properties, we have studied the thermoelectric properties of the well-known half-Heusler TiNiSn with addition of a small amount of nickel nanoparticles. The different parameters are the initial synthesis (levitation melting and microwave heating), the amount of nickel nanoparticles added and the exact pressing profile using spark plasma sintering. The resulting materials have been characterized by synchrotron X-ray diffraction and microprobe measurements and their thermoelectric properties are investigated. We found the lowest (lattice) thermal conductivity in samples with full-Heusler TiNi2Sn and Ni3Sn4 as secondary phases.

  9. Telomere Capping Proteins are Structurally Related to RPA with an additional Telomere-Specific Domain

    SciTech Connect

    Gelinas, A.; Paschini, M; Reyes, F; Heroux, A; Batey, R; Lundblad, V; Wuttke, D

    2009-01-01

    Telomeres must be capped to preserve chromosomal stability. The conserved Stn1 and Ten1 proteins are required for proper capping of the telomere, although the mechanistic details of how they contribute to telomere maintenance are unclear. Here, we report the crystal structures of the C-terminal domain of the Saccharomyces cerevisiae Stn1 and the Schizosaccharomyces pombe Ten1 proteins. These structures reveal striking similarities to corresponding subunits in the replication protein A complex, further supporting an evolutionary link between telomere maintenance proteins and DNA repair complexes. Our structural and in vivo data of Stn1 identify a new domain that has evolved to support a telomere-specific role in chromosome maintenance. These findings endorse a model of an evolutionarily conserved mechanism of DNA maintenance that has developed as a result of increased chromosomal structural complexity.

  10. Structure of influenza virus RNP. I. Influenza virus nucleoprotein melts secondary structure in panhandle RNA and exposes the bases to the solvent.

    PubMed Central

    Baudin, F; Bach, C; Cusack, S; Ruigrok, R W

    1994-01-01

    The influenza virus genome consists of eight segments of negative-sense RNA, i.e. the viral (v) RNA forms the template for the mRNA. Each segment is encapsidated by the viral nucleoprotein to form a ribonucleoprotein (RNP) particle and each RNP carries its own polymerase complex. We studied the interaction of purified nucleoprotein with RNA in vitro, by using a variety of enzymatic and chemical probes for RNA conformation. Our results suggest that the nucleoprotein binds to the vRNA backbone without apparent sequence specificity, exposing the bases to the outside and melting all secondary structure. In this way, the viral polymerase may transcribe the RNA without the need for dissociating the nucleoprotein and without being stopped by RNA secondary structure, and the viral RNPs are ready to start transcription as soon as they enter the host cell. Images PMID:8039508

  11. Factor Structure of the Test Anxiety Inventory for Children and Adolescents (TAICA) Scores across Gender among Students in Elementary and Secondary School Settings

    ERIC Educational Resources Information Center

    Lowe, Patricia A.; Lee, Steven W.

    2008-01-01

    The factor structure of the Test Anxiety Inventory for Children and Adolescents, a new multidimensional measure used to assess test anxiety in elementary and secondary school students, is examined across gender. The sample consisted of 696 elementary and secondary school students (391 girls and 305 boys). Coefficient of congruence and salient…

  12. Secondary structure of Tetrahymena thermophilia 5S ribosomal RNA as revealed by enzymatic digestion and microdensitometric analysis.

    PubMed Central

    Sneath, B; Vary, C; Pavlakis, G; Vournakis, J

    1986-01-01

    The secondary structure of [32P] end-labeled 5S rRNA from Tetrahymena thermophilia (strain B) has been investigated using the enzymes S1 nuclease, cobra venom ribonuclease and T2 ribonuclease. The results, analyzed by scanning microdensitometry and illustrated by three-dimensional computer graphics, support the secondary structure model of Curtiss and Vournakis for 5S rRNA. Aberrent mobility of certain RNA fragments on sequencing gels was observed as regions of band compression. These regions are postulated to be caused by stable internal base-pairing. The molecule was probed with T2 RNase in neutral (pH 7.5) and acidic (pH 4.5) buffers and only minor structural differences were revealed. One of the helices was found to be susceptible to enzymatic attack by both the single-strand and double-strand specific enzymes. These observations are evidence for the existence of dynamic structural equilibria in 5S rRNA. Images PMID:3005972

  13. Effects of Very Low Dose Fast Neutrons on Cell Membrane And Secondary Protein Structure in Rat Erythrocytes

    PubMed Central

    Nafee, Sherif S.; Shaheen, Salem A.; Al-Hadeethi, Y.

    2015-01-01

    The effects of ionizing radiation on biological cells have been reported in several literatures. Most of them were mainly concerned with doses greater than 0.01 Gy and were also concerned with gamma rays. On the other hand, the studies on very low dose fast neutrons (VLDFN) are rare. In this study, we have investigated the effects of VLDFN on cell membrane and protein secondary structure of rat erythrocytes. Twelve female Wistar rats were irradiated with neutrons of total dose 0.009 Gy (241Am-Be, 0.2 mGy/h) and twelve others were used as control. Blood samples were taken at the 0, 4th, 8th, and 12th days postirradiation. Fourier transform infrared (FTIR) spectra of rat erythrocytes were recorded. Second derivative and curve fitting were used to analysis FTIR spectra. Hierarchical cluster analysis (HCA) was used to classify group spectra. The second derivative and curve fitting of FTIR spectra revealed that the most significant alterations in the cell membrane and protein secondary structure upon neutron irradiation were detected after 4 days postirradiation. The increase in membrane polarity, phospholipids chain length, packing, and unsaturation were noticed from the corresponding measured FTIR area ratios. This may be due to the membrane lipid peroxidation. The observed band shift in the CH2 stretching bands toward the lower frequencies may be associated with the decrease in membrane fluidity. The curve fitting of the amide I revealed an increase in the percentage area of α-helix opposing a decrease in the β-structure protein secondary structure, which may be attributed to protein denaturation. The results provide detailed insights into the VLDFN effects on erythrocytes. VLDFN can cause an oxidative stress to the irradiated erythrocytes, which appears clearly after 4 days postirradiation. PMID:26436416

  14. IDENTIFICATION AND REMOVAL OF PROTEINS THAT CO-PURIFY WITH INFECTIOUS PRION PROTEIN IMPROVES THE ANALYSIS OF ITS SECONDARY STRUCTURE

    PubMed Central

    Moore, Roger A.; Timmes, Andrew; Wilmarth, Phillip A.; Safronetz, David; Priola, Suzette A.

    2013-01-01

    Prion diseases are neurodegenerative disorders associated with the accumulation of an abnormal isoform of the mammalian prion protein (PrP). Fourier transform infrared spectroscopy (FTIR) has previously been used to show that the conformation of aggregated, infectious PrP (PrPSc) varies between prion strains and these unique conformations may determine strain-specific disease phenotypes. However, the relative amounts of α-helix, β-sheet and other secondary structures have not always been consistent between studies suggesting that other proteins might be confounding the analysis of PrPSc secondary structure. We have used FTIR and tandem mass spectrometry to analyze enriched PrPSc from mouse and hamster prion strains both before and after the removal of protein contaminants that commonly co-purify with PrPSc. Our data show that non-PrP proteins do contribute to absorbances that have been associated with α-helical, loop, turn, and β-sheet structures attributed to PrPSc. The major contaminant, the α-helical protein ferritin, absorbs strongly at 1652cm−1 in the FTIR spectrum associated with PrPSc. However, even the removal of greater than 99% of the ferritin from PrPSc did not completely abolish absorbance at 1652cm−1. Our results show that contaminating proteins alter the FTIR spectrum attributed to PrPSc and suggest that the α-helical, loop/turn, and β-sheet secondary structure that remains following their removal are derived from PrPSc itself. PMID:21805638

  15. The secondary structure and the thermal unfolding parameters of the S-layer protein from Lactobacillus salivarius.

    PubMed

    Lighezan, Liliana; Georgieva, Ralitsa; Neagu, Adrian

    2016-09-01

    Surface layer (S-layer) proteins have been identified in the cell envelope of many organisms, such as bacteria and archaea. They self-assemble, forming monomolecular crystalline arrays. Isolated S-layer proteins are able to recrystallize into regular lattices, which proved useful in biotechnology. Here we investigate the structure and thermal unfolding of the S-layer protein isolated from Lactobacillus salivarius 16 strain of human origin. Using circular dichroism (CD) spectroscopy, and the software CDSSTR from DICHROWEB, CONTINLL from CDPro, as well as CDNN, we assess the fractions of the protein's secondary structural elements at temperatures ranging between 10 and 90 °C, and predict the tertiary class of the protein. To study the thermal unfolding of the protein, we analyze the temperature dependence of the CD signal in the far- and near-UV domains. Fitting the experimental data by two- and three-state models of thermal unfolding, we infer the midpoint temperatures, the temperature dependence of the changes in Gibbs free energy, enthalpy, and entropy of the unfolding transitions in standard conditions, and the temperature dependence of the equilibrium constant. We also estimate the changes in heat capacity at constant pressure in standard conditions. The results indicate that the thermal unfolding of the S-layer protein from L. salivarius is highly cooperative, since changes in the secondary and tertiary structures occur simultaneously. The thermodynamic analysis predicts a "cold" transition, at about -3 °C, of both the secondary and tertiary structures. Our findings may be important for the use of S-layer proteins in biotechnology and in biomedical applications. PMID:26992716

  16. Influence of Additive and Multiplicative Structure and Direction of Comparison on the Reversal Error

    ERIC Educational Resources Information Center

    González-Calero, José Antonio; Arnau, David; Laserna-Belenguer, Belén

    2015-01-01

    An empirical study has been carried out to evaluate the potential of word order matching and static comparison as explanatory models of reversal error. Data was collected from 214 undergraduate students who translated a set of additive and multiplicative comparisons expressed in Spanish into algebraic language. In these multiplicative comparisons…

  17. Studies on the Food Additive Propyl Gallate: Synthesis, Structural Characterization, and Evaluation of the Antioxidant Activity

    ERIC Educational Resources Information Center

    Garrido, Jorge; Garrido, E. Manuela; Borges, Fernanda

    2012-01-01

    Antioxidants are additives largely used in industry for delaying, retarding, or preventing the development of oxidative deterioration. Propyl gallate (E310) is a phenolic antioxidant extensively used in the food, cosmetics, and pharmaceutical industries. A series of lab experiments have been developed to teach students about the importance and…

  18. Factor analysis models for structuring covariance matrices of additive genetic effects: a Bayesian implementation

    PubMed Central

    de los Campos, Gustavo; Gianola, Daniel

    2007-01-01

    Multivariate linear models are increasingly important in quantitative genetics. In high dimensional specifications, factor analysis (FA) may provide an avenue for structuring (co)variance matrices, thus reducing the number of parameters needed for describing (co)dispersion. We describe how FA can be used to model genetic effects in the context of a multivariate linear mixed model. An orthogonal common factor structure is used to model genetic effects under Gaussian assumption, so that the marginal likelihood is multivariate normal with a structured genetic (co)variance matrix. Under standard prior assumptions, all fully conditional distributions have closed form, and samples from the joint posterior distribution can be obtained via Gibbs sampling. The model and the algorithm developed for its Bayesian implementation were used to describe five repeated records of milk yield in dairy cattle, and a one common FA model was compared with a standard multiple trait model. The Bayesian Information Criterion favored the FA model. PMID:17897592

  19. Accurate prediction of protein structural classes by incorporating predicted secondary structure information into the general form of Chou's pseudo amino acid composition.

    PubMed

    Kong, Liang; Zhang, Lichao; Lv, Jinfeng

    2014-03-01

    Extracting good representation from protein sequence is fundamental for protein structural classes prediction tasks. In this paper, we propose a novel and powerful method to predict protein structural classes based on the predicted secondary structure information. At the feature extraction stage, a 13-dimensional feature vector is extracted to characterize general contents and spatial arrangements of the secondary structural elements of a given protein sequence. Specially, four segment-level features are designed to elevate discriminative ability for proteins from the α/β and α+β classes. After the features are extracted, a multi-class non-linear support vector machine classifier is used to implement protein structural classes prediction. We report extensive experiments comparing the proposed method to the state-of-the-art in protein structural classes prediction on three widely used low-similarity benchmark datasets: FC699, 1189 and 640. Our method achieves competitive performance on prediction accuracies, especially for the overall prediction accuracies which have exceeded the best reported results on all of the three datasets. PMID:24316044

  20. Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2.

    PubMed

    Aloy, P; Mas, J M; Martí-Renom, M A; Querol, E; Avilés, F X; Oliva, B

    2000-01-01

    Knowledge-based energy profiles combined with secondary structure prediction have been applied to molecular modelling refinement. To check the procedure, three different models of human procarboxypeptidase A2 (hPCPA2) have been built using the 3D structures of procarboxypeptidase A1 (pPCPA1) and bovine procarboxypeptidase A (bPCPA) as templates. The results of the refinement can be tested against the X-ray structure of hPCPA2 which has been recently determined. Regions miss-modelled in the activation segment of hPCPA2 were detected by means of pseudo-energies using Prosa II and modified afterwards according to the secondary structure prediction. Moreover, models obtained by automated methods as COMPOSER, MODELLER and distance restraints have also been compared, where it was found possible to find out the best model by means of pseudo-energies. Two general conclusions can be elicited from this work: (1) on a given set of putative models it is possible to distinguish among them the one closest to the crystallographic structure, and (2) within a given structure it is possible to find by means of pseudo-energies those regions that have been defectively modelled. PMID:10702927

  1. Secondary structure model of the Mason-Pfizer monkey virus 5' leader sequence: identification of a structural motif common to a variety of retroviruses.

    PubMed Central

    Harrison, G P; Hunter, E; Lever, A M

    1995-01-01

    A stable secondary structure model is presented for the region 3' of the primer-binding site to 130 bases into the gag sequence of the prototype type D retrovirus Mason-Pfizer monkey virus. Using biochemical probing of RNA from this region in association with free energy minimization, we have identified a stem-loop structure in the region, which from other studies has been shown to be important for genomic RNA encapsidation. The structure involves a highly stable stem of five G-C pairs terminating in a heptaloop. Comparison of the Mason-Pfizer monkey virus structure with one predicted for squirrel monkey retrovirus demonstrates an identical stem and a common ACC motif in the loop. Free energy studies of the secondary structure of the 5' regions of eight other retroviruses predict stem loops which have similar GAYC motifs. We believe this may represent a common structural and sequence motif which among other functions may be involved in genomic RNA packaging in these viruses. PMID:7884866

  2. Induced Secondary Structure and Polymorphism in an Intrinsically Disordered Structural Linker of the CNS: Solid-State NMR and FTIR Spectroscopy of Myelin Basic Protein Bound to Actin

    PubMed Central

    Ahmed, Mumdooh A.M.; Bamm, Vladimir V.; Shi, Lichi; Steiner-Mosonyi, Marta; Dawson, John F.; Brown, Leonid; Harauz, George; Ladizhansky, Vladimir

    2009-01-01

    Abstract The 18.5 kDa isoform of myelin basic protein (MBP) is a peripheral membrane protein that maintains the structural integrity of the myelin sheath of the central nervous system by conjoining the cytoplasmic leaflets of oligodendrocytes and by linking the myelin membrane to the underlying cytoskeleton whose assembly it strongly promotes. It is a multifunctional, intrinsically disordered protein that behaves primarily as a structural stabilizer, but with elements of a transient or induced secondary structure that represent binding sites for calmodulin or SH3-domain-containing proteins, inter alia. In this study we used solid-state NMR (SSNMR) and Fourier transform infrared (FTIR) spectroscopy to study the conformation of 18.5 kDa MBP in association with actin microfilaments and bundles. FTIR spectroscopy of fully 13C,15N-labeled MBP complexed with unlabeled F-actin showed induced folding of both protein partners, viz., some increase in β-sheet content in actin, and increases in both α-helix and β-sheet content in MBP, albeit with considerable extended structure remaining. Solid-state NMR spectroscopy revealed that MBP in MBP-actin assemblies is structurally heterogeneous but gains ordered secondary structure elements (both α-helical and β-sheet), particularly in the terminal fragments and in a central immunodominant epitope. The overall conformational polymorphism of MBP is consistent with its in vivo roles as both a linker (membranes and cytoskeleton) and a putative signaling hub. PMID:19134474

  3. Nucleophilic additions of primary and secondary amines to pentacyclo[5.4.0.0{sup 2,6}.0{sup 3,10}.0{sup 5,9}]undecane-8,11-dione

    SciTech Connect

    Bott, S.G.; Marchand, A.P.; Kumar, K.A.

    1995-10-01

    The crystal structures of three compounds formed via nucleophilic attack of a heterocyclic secondary amine on PCU-8,11-dione, with the concomitant intramolecular attack of one keto oxygen on the carbon of the other ketone, are presented. In all three compounds, the bridging oxygen contains substantial p-character, and the bonds to the {open_quotes}attacking{close_quotes} nitrogen are significantly shorter than would be expected.

  4. Structure/property (constitutive and dynamic strength/damage) characterization of additively manufactured 316L SS

    NASA Astrophysics Data System (ADS)

    Gray, G. T., III; Livescu, V.; Rigg, P. A.; Trujillo, C. P.; Cady, C. M.; Chen, S. R.; Carpenter, J. S.; Lienert, T. J.; Fensin, S.

    2015-09-01

    For additive manufacturing (AM), the certification and qualification paradigm needs to evolve as there exists no "ASTM-type" additive manufacturing certified process or AM-material produced specifications. Accordingly, utilization of AM materials to meet engineering applications requires quantification of the constitutive properties of these evolving materials in comparison to conventionally-manufactured metals and alloys. Cylinders of 316L SS were produced using a LENS MR-7 laser additive manufacturing system from Optomec (Albuquerque, NM) equipped with a 1kW Yb-fiber laser. The microstructure of the AM-316L SS is detailed in both the as-built condition and following heat-treatments designed to obtain full recrystallization. The constitutive behavior as a function of strain rate and temperature is presented and compared to that of nominal annealed wrought 316L SS plate. The dynamic damage evolution and failure response of all three materials was probed using flyer-plate impact driven spallation experiments at a peak stress of 4.5 GPa to examine incipient spallation response. The spall strength of AM-produced 316L SS was found to be very similar for the peak shock stress studied to that of annealed wrought or AM-316L SS following recrystallization. The damage evolution as a function of microstructure was characterized using optical metallography.

  5. Secondary impact hazard assessment

    NASA Technical Reports Server (NTRS)

    1986-01-01

    A series of light gas gun shots (4 to 7 km/sec) were performed with 5 mg nylon and aluminum projectiles to determine the size, mass, velocity, and spatial distribution of spall and ejecta from a number of graphite/epoxy targets. Similar determinations were also performed on a few aluminum targets. Target thickness and material were chosen to be representative of proposed Space Station structure. The data from these shots and other information were used to predict the hazard to Space Station elements from secondary particles resulting from impacts of micrometeoroids and orbital debris on the Space Station. This hazard was quantified as an additional flux over and above the primary micrometeoroid and orbital debris flux that must be considered in the design process. In order to simplify the calculations, eject and spall mass were assumed to scale directly with the energy of the projectile. Other scaling systems may be closer to reality. The secondary particles considered are only those particles that may impact other structure immediately after the primary impact. The addition to the orbital debris problem from these primary impacts was not addressed. Data from this study should be fed into the orbital debris model to see if Space Station secondaries make a significant contribution to orbital debris. The hazard to a Space Station element from secondary particles above and beyond the micrometeoroid and orbital debris hazard is categorized in terms of two factors: (1) the 'view factor' of the element to other Space Station structure or the geometry of placement of the element, and (2) the sensitivity to damage, stated in terms of energy. Several example cases were chosen, the Space Station module windows, windows of a Shuttle docked to the Space Station, the habitat module walls, and the photovoltaic solar cell arrays. For the examples chosen the secondary flux contributed no more than 10 percent to the total flux (primary and secondary) above a given calculated

  6. Secondary impact hazard assessment

    NASA Astrophysics Data System (ADS)

    1986-06-01

    A series of light gas gun shots (4 to 7 km/sec) were performed with 5 mg nylon and aluminum projectiles to determine the size, mass, velocity, and spatial distribution of spall and ejecta from a number of graphite/epoxy targets. Similar determinations were also performed on a few aluminum targets. Target thickness and material were chosen to be representative of proposed Space Station structure. The data from these shots and other information were used to predict the hazard to Space Station elements from secondary particles resulting from impacts of micrometeoroids and orbital debris on the Space Station. This hazard was quantified as an additional flux over and above the primary micrometeoroid and orbital debris flux that must be considered in the design process. In order to simplify the calculations, eject and spall mass were assumed to scale directly with the energy of the projectile. Other scaling systems may be closer to reality. The secondary particles considered are only those particles that may impact other structure immediately after the primary impact. The addition to the orbital debris problem from these primary impacts was not addressed. Data from this study should be fed into the orbital debris model to see if Space Station secondaries make a significant contribution to orbital debris. The hazard to a Space Station element from secondary particles above and beyond the micrometeoroid and orbital debris hazard is categorized in terms of two factors: (1) the 'view factor' of the element to other Space Station structure or the geometry of placement of the element, and (2) the sensitivity to damage, stated in terms of energy. Several example cases were chosen, the Space Station module windows, windows of a Shuttle docked to the Space Station, the habitat module walls, and the photovoltaic solar cell arrays. For the examples chosen the secondary flux contributed no more than 10 percent to the total flux (primary and secondary) above a given calculated

  7. Primary and secondary structure of 5.8S rRNA from the silkgland of Bombyx mori.

    PubMed Central

    Fujiwara, H; Kawata, Y; Ishikawa, H

    1982-01-01

    Nucleotide sequence of 5.8S rRNA of the silkworm, Bombyx mori has been determined by gel sequencing methods. The 5.8S rRNA was the longest so far reported, with the 5'-terminal sequence several nucleotides longer than those of the other organisms. Upon constructing the secondary structure in accordance with the "burp gun" model (12), the Bombyx 5.8S rRNA formed a wide-open "muzzle" due to several unpaired bases at the ends. The overall structure also appeared less stable with less G . C pairs and more unpaired bases than that of the HeLa 5.8S rRNA. These structural features may be essential for those 5.8S rRNAs which interact with 28S rRNAs containing the hidden break to form a stable complex. PMID:7088713

  8. Structure alterations in Al-Y-based metallic glasses with La and Ni addition

    NASA Astrophysics Data System (ADS)

    Shi, X. M.; Wang, X. D.; Yu, Q.; Cao, Q. P.; Zhang, D. X.; Zhang, J.; Hu, T. D.; Lai, L. H.; Xie, H. L.; Xiao, T. Q.; Jiang, J. Z.

    2016-03-01

    The atomic structures of Al89Y11, Al90Y6.5La3.5, and Al82.8Y6.07Ni8La3.13 metallic glasses have been studied by using high energy X-ray diffraction, X-ray absorption fine structure combined with the ab initio molecular dynamics and reverse Monte Carlo simulations. It is demonstrated that the partial replacement of Y atoms by La has limited improvement of the glass forming ability (GFA), although La atoms reduce the ordering around Y atoms and also the fractions of icosahedron-like polyhedra centered by Al atoms. In contrast, Ni atoms can significantly improve the GFA, which are inclined to locate in the shell of polyhedra centered by Al, Y, and La atoms, mainly forming Ni-centered icosahedron-like polyhedra to enhance the spatial connectivity between clusters and suppress the crystallization.

  9. Structure-property effects of tantalum additions to nickel-base superalloys

    NASA Technical Reports Server (NTRS)

    Heckel, R. W.; Pletka, B. J.; Koss, D. A.; Jackson, M. R.

    1982-01-01

    The characterization of the effect of Ta on the structure of Ni base superalloys, the determination of the effects of Ta (structure) variations on the mechanical, thermal, and oxidation behavior, and the identification of alloying elements which have potential as substitutes for Ta are investigated. Mar M247 type alloys are emphasized; nominal and analyzed compositions of ten alloys under study are given. X-ray and composition analysis are being used to determine the partitioning of alloying elements between gamma, gamma primes, and MC (cubic) as a function of Ta content. The diffusional interactions of the Mar M247-type alloys with as cast beta + gamma alloys are studied to determine the effects of Ta on alloy/coating degradation.

  10. Experiments to Populate and Validate a Processing Model for Polyurethane Foam: Additional Data for Structural Foams.

    SciTech Connect

    Rao, Rekha R.; Celina, Mathias C.; Giron, Nicholas Henry; Long, Kevin Nicholas; Russick, Edward M.

    2015-01-01

    We are developing computational models to help understand manufacturing processes, final properties and aging of structural foam, polyurethane PMDI. Th e resulting model predictions of density and cure gradients from the manufacturing process will be used as input to foam heat transfer and mechanical models. BKC 44306 PMDI-10 and BKC 44307 PMDI-18 are the most prevalent foams used in structural parts. Experiments needed to parameterize models of the reaction kinetics and the equations of motion during the foam blowing stages were described for BKC 44306 PMDI-10 in the first of this report series (Mondy et al. 2014). BKC 44307 PMDI-18 is a new foam that will be used to make relatively dense structural supports via over packing. It uses a different catalyst than those in the BKC 44306 family of foams; hence, we expect that the reaction kineti cs models must be modified. Here we detail the experiments needed to characteriz e the reaction kinetics of BKC 44307 PMDI-18 and suggest parameters for the model based on these experiments. In additi on, the second part of this report describes data taken to provide input to the preliminary nonlinear visco elastic structural response model developed for BKC 44306 PMDI-10 foam. We show that the standard cu re schedule used by KCP does not fully cure the material, and, upon temperature elevation above 150 o C, oxidation or decomposition reactions occur that alter the composition of the foam. These findings suggest that achieving a fully cured foam part with this formulation may be not be possible through therma l curing. As such, visco elastic characterization procedures developed for curing thermosets can provide only approximate material properties, since the state of the material continuously evolves during tests.

  11. New recombinant cyclohexylamine oxidase variants for deracemization of secondary amines by orthogonally assaying designed mutants with structurally diverse substrates

    NASA Astrophysics Data System (ADS)

    Li, Guangyue; Yao, Peiyuan; Cong, Peiqian; Ren, Jie; Wang, Lei; Feng, Jinhui; Lau, Peter C. K.; Wu, Qiaqing; Zhu, Dunming

    2016-05-01

    To further expand the substrate range of the cyclohexylamine oxidase (CHAO) from Brevibacterium oxydans, a library of diverse mutants was created and assayed toward a group of structurally diverse substrates. Among them, mutants T198A and M226A exhibited enhanced activity relative to wt CHAO for most (S)-enantiomers of primary amines and some secondary amines. While mutants T198I, L199I, L199F, M226I and M226T were more active than wt CHAO toward the primary amines, mutants T198F, L199T, Y321A, Y321T, Y321I and Y321F enhanced the enzyme activity toward the secondary amines. In particular, mutant Y321I displayed an enhanced catalytic efficiency toward 1-(4-methoxybenzyl)-1, 2, 3, 4, 5, 6, 7, 8-octahydroisoquinoline (13). Whereas a double mutant, Y321I/M226T, acted on (S)-N-(prop-2-yn-1-yl)-2, 3-dihydro-1H-inden-1-amine [(S)-8]. Since (R)-8 is an irreversible inhibitor of monoamine oxidase and (S)-13 is an intermediate of dextromethorphan, a cough suppressant drug, deracemizations of 8 and 13 were carried out with crude enzyme extracts of the respective mutants. This resulted in 51% and 78% isolated yields of (R)-8 and (S)-13, respectively, each with high enantiomeric excess (93% and 99% ee). The results demonstrated the application potential of the evolved CHAO mutants in drug synthesis requiring chiral secondary amines.

  12. New recombinant cyclohexylamine oxidase variants for deracemization of secondary amines by orthogonally assaying designed mutants with structurally diverse substrates.

    PubMed

    Li, Guangyue; Yao, Peiyuan; Cong, Peiqian; Ren, Jie; Wang, Lei; Feng, Jinhui; Lau, Peter C K; Wu, Qiaqing; Zhu, Dunming

    2016-01-01

    To further expand the substrate range of the cyclohexylamine oxidase (CHAO) from Brevibacterium oxydans, a library of diverse mutants was created and assayed toward a group of structurally diverse substrates. Among them, mutants T198A and M226A exhibited enhanced activity relative to wt CHAO for most (S)-enantiomers of primary amines and some secondary amines. While mutants T198I, L199I, L199F, M226I and M226T were more active than wt CHAO toward the primary amines, mutants T198F, L199T, Y321A, Y321T, Y321I and Y321F enhanced the enzyme activity toward the secondary amines. In particular, mutant Y321I displayed an enhanced catalytic efficiency toward 1-(4-methoxybenzyl)-1, 2, 3, 4, 5, 6, 7, 8-octahydroisoquinoline (13). Whereas a double mutant, Y321I/M226T, acted on (S)-N-(prop-2-yn-1-yl)-2, 3-dihydro-1H-inden-1-amine [(S)-8]. Since (R)-8 is an irreversible inhibitor of monoamine oxidase and (S)-13 is an intermediate of dextromethorphan, a cough suppressant drug, deracemizations of 8 and 13 were carried out with crude enzyme extracts of the respective mutants. This resulted in 51% and 78% isolated yields of (R)-8 and (S)-13, respectively, each with high enantiomeric excess (93% and 99% ee). The results demonstrated the application potential of the evolved CHAO mutants in drug synthesis requiring chiral secondary amines. PMID:27138090

  13. New recombinant cyclohexylamine oxidase variants for deracemization of secondary amines by orthogonally assaying designed mutants with structurally diverse substrates

    PubMed Central

    Li, Guangyue; Yao, Peiyuan; Cong, Peiqian; Ren, Jie; Wang, Lei; Feng, Jinhui; Lau, Peter C.K.; Wu, Qiaqing; Zhu, Dunming

    2016-01-01

    To further expand the substrate range of the cyclohexylamine oxidase (CHAO) from Brevibacterium oxydans, a library of diverse mutants was created and assayed toward a group of structurally diverse substrates. Among them, mutants T198A and M226A exhibited enhanced activity relative to wt CHAO for most (S)-enantiomers of primary amines and some secondary amines. While mutants T198I, L199I, L199F, M226I and M226T were more active than wt CHAO toward the primary amines, mutants T198F, L199T, Y321A, Y321T, Y321I and Y321F enhanced the enzyme activity toward the secondary amines. In particular, mutant Y321I displayed an enhanced catalytic efficiency toward 1-(4-methoxybenzyl)-1, 2, 3, 4, 5, 6, 7, 8-octahydroisoquinoline (13). Whereas a double mutant, Y321I/M226T, acted on (S)-N-(prop-2-yn-1-yl)-2, 3-dihydro-1H-inden-1-amine [(S)-8]. Since (R)-8 is an irreversible inhibitor of monoamine oxidase and (S)-13 is an intermediate of dextromethorphan, a cough suppressant drug, deracemizations of 8 and 13 were carried out with crude enzyme extracts of the respective mutants. This resulted in 51% and 78% isolated yields of (R)-8 and (S)-13, respectively, each with high enantiomeric excess (93% and 99% ee). The results demonstrated the application potential of the evolved CHAO mutants in drug synthesis requiring chiral secondary amines. PMID:27138090

  14. Secondary RNA structure and nucleotide specificity contribute to internal initiation mediated by the human tau 5′ leader

    PubMed Central

    Veo, Bethany L.; Krushel, Leslie A.

    2012-01-01

    Mechanisms by which eukaryotic internal ribosomal entry sites (IRESs) initiate translation have not been well described. Viral IRESs utilize a combination of secondary/tertiary structure concomitant with sequence specific elements to initiate translation. Eukaryotic IRESs are proposed to utilize the same components, although it appears that short sequence specific elements are more common. In this report we perform an extensive analysis of the IRES in the human tau mRNA. We demonstrate that the tau IRES exhibits characteristics similar to viral IRESs. It contains two main structural domains that exhibit secondary interactions, which are essential for internal initiation. Moreover, the tau IRES is extremely sensitive to small nucleotide substitutions. Our data also indicates that the 40S ribosome is recruited to the middle of the IRES, but whether it scans to the initiation codon in a linear fashion is questioned. Overall, these results identify structural and sequence elements critical for tau IRES activity and consequently, provide a novel target to regulate tau protein expression in disease states including Alzheimer disease and other tauopathies. PMID:22995835

  15. Population structure and secondary production of Siriella clausii, a dominant detritus feeding mysid in Posidonia oceanica meadows (W Mediterranean Sea)

    NASA Astrophysics Data System (ADS)

    Barberá, Carmen; Sanchez-Jerez, Pablo; Sorbe, Jean Claude

    2013-10-01

    Temporal trends in abundance, demographic structure of the population and secondary production of Siriella clausii were studied at three different sectors of Posidonia oceanica meadows in the SE Iberian Peninsula, with different levels of habitat complexity. Secondary production was calculated through three methods widely employed in marine invertebrates: the Hynes method (based on demographic structure data) and models by Morin-Bourassa and Brey (based on biomass data). This filter/grazer and detritus feeder is the most abundant mysid in P. oceanica seagrass meadows in the Mediterranean. The population structure was similar in the three sectors, but the temporal pattern of abundance was different, at times even opposite. This pattern may be related to the aggregated spatial distribution, metapopulation dynamics or stochastic factors, but other potential factors could be involved, such as habitat features or predation rates. The values of production oscillated between 25 and 60 mgAFDW/m2/year, depending on the calculation method that was applied, and showed differences between sites and seagrass complexity. The present values are intermediate between those characterising highly productive systems, such as estuaries, and systems of limited productivity (bathyal habitats). Compared to other peracarids, mysid production is greater than that of isopods and less than amphipod production. This is possibly related to the life cycle and reproductive strategies. Detritus feeders such as S. clausii may play an important trophic role due their capacity to use as food the biomass associated to detritus, which constitutes larges reservoirs of carbon derived from seagrass primary production.

  16. Extracting Infrared Spectra of Protein Secondary Structures Using a Library of Protein Spectra and the Ramachandran Plot.

    PubMed

    Coe, James V; Nystrom, Steven V; Chen, Zhaomin; Li, Ran; Verreault, Dominique; Hitchcock, Charles L; Martin, Edward W; Allen, Heather C

    2015-10-15

    Infrared (IR) spectra from 1200 to 1800 cm(-1) of the pure α-helix and β-sheet secondary structures have been extracted using a covariant least-squares procedure which relates a library of 40 infrared (IR) solution protein spectra from the work of Dong, Carpenter, and Caughey and amino acid fractions of the proteins based on assignments by STRIDE (secondary structure identification) of Eisenhaber and Argos. The excitonic splitting of the β-sheet structures is determined for this library of solution proteins. The method is extended to find a set of spectral basis functions that analyze IR spectra of protein samples for α-helix and β-sheet content. A rigorous error analysis including covariance, the correlations between the input library spectra, was used to justify the results and avoid less meaningful results. The utility of the results on α-helix and β-sheet regions is demonstrated by detecting protein changes due to cancer in imaging Fourier transform IR (FTIR) spectra of liver tissue slices. This work ends with a method to extract IR spectra of less prominent torsional angle distributions. PMID:26397941

  17. Protein secondary structure of the isolated photosystem II reaction center and conformational changes studied by Fourier transform infrared spectroscopy.

    PubMed

    He, W Z; Newell, W R; Haris, P I; Chapman, D; Barber, J

    1991-05-01

    The secondary structure of the photosystem II (PSII) reaction center isolated from pea chloroplasts has been characterized by Fourier transform infrared (FTIR) spectroscopy. Spectra were recorded in aqueous buffers containing H2O or D2O; the detergent present for most measurements was dodecyl maltoside. The broad amide I and amide II bands were analyzed by using second-derivative and deconvolution procedures. Absorption bands were assigned to the presence of alpha-helices, beta-sheets, turns, or random structure. Quantitative analysis revealed that this complex contained a high proportion of alpha-helices (67%) and some antiparallel beta-sheets (9%) and turns (11%). An irreversible decrease in the intensity of the band associated with the alpha-helices occurs upon exposure of the isolated PSII reaction center to bright illumination. This loss of alpha-helical content gave rise to an increase in other secondary structures, particularly beta-sheets. After similar pretreatment with light, sodium dodecyl sulfate polyacrylamide gel electrophoresis reveals lower mobility and solubility of constituent D1 and D2 polypeptides of the PSII reaction center. Some degradation of these polypeptides also occurs. In contrast, there is no change in the mobility of the two subunits of cytochrome b559. In the absence of illumination, the PSII reaction center exchanged into dodecyl maltoside shows good thermal stability as compared with samples in Triton X-100. Only at a temperature of about 60 degrees C do spectral changes take place that are indicative of denaturation. PMID:1850626

  18. Pausing of reverse transcriptase on retroviral RNA templates is influenced by secondary structures both 5' and 3' of the catalytic site.

    PubMed Central

    Harrison, G P; Mayo, M S; Hunter, E; Lever, A M

    1998-01-01

    In the most extensive examination to date of the relationship between the pausing of reverse transcrip-tase (RT) and RNA secondary structures, pause events were found to be correlated to inverted repeats both ahead of, and behind the catalytic site in vitro. In addition pausing events were strongly associated with polyadenosine sequences and to a lesser degree diadenosines and monoadenosine residues. Pausing was also inversely proportional to the potential bond strength between the nascent strand and the template at the point of termination, for both mono and dinucleotides. A run of five adenosine and four uridine residues caused most pausing on the HIV-1 template, a region which is the site of much sequence heterogeneity in HIV-1. We propose that homopolyadenosine tracts can act as termination signals for RT in the context of inverted repeats as they do for certain RNA polymerases. PMID:9649630

  19. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota

    PubMed Central

    SCHULTZ, JÖRG; MAISEL, STEFANIE; GERLACH, DANIEL; MÜLLER, TOBIAS; WOLF, MATTHIAS

    2005-01-01

    The ongoing characterization of novel species creates the need for a molecular marker which can be used for species- and, simultaneously, for mega-systematics. Recently, the use of the internal transcribed spacer 2 (ITS2) sequence was suggested, as it shows a high divergence in sequence with an assumed conservation in structure. This hypothesis was mainly based on small-scale analyses, comparing a limited number of sequences. Here, we report a large-scale analysis of more than 54,000 currently known ITS2 sequences with the goal to evaluate the hypothesis of a conserved structural core and to assess its use for automated large-scale phylogenetics. Structure prediction revealed that the previously described core structure can be found for more than 5000 sequences in a wide variety of taxa within the eukaryotes, indicating that the core secondary structure is indeed conserved. This conserved structure allowed an automated alignment of extremely divergent sequences as exemplified for the ITS2 sequences of a ctenophorean eumetazoon and a volvocalean green alga. All classified sequences, together with their structures can be accessed at http://www.biozentrum.uni-wuerzburg.de/bioinformatik/projects/ITS2.html. Furthermore, we found that, although sample sequences are known for most major taxa, there exists a profound divergence in coverage, which might become a hindrance for general usage. In summary, our analysis strengthens the potential of ITS2 as a general phylogenetic marker and provides a data source for further ITS2-based analyses. PMID:15769870

  20. Secondary Structure of a Conserved Domain in an Intron of Influenza A M1 mRNA

    PubMed Central

    2014-01-01

    Influenza A virus utilizes RNA throughout infection. Little is known, however, about the roles of RNA structures. A previous bioinformatics survey predicted multiple regions of influenza A virus that are likely to generate evolutionarily conserved and stable RNA structures. One predicted conserved structure is in the pre-mRNA coding for essential proteins, M1 and M2. This structure starts 79 nucleotides downstream of the M2 mRNA 5′ splice site. Here, a combination of biochemical structural mapping, mutagenesis, and NMR confirms the predicted three-way multibranch structure of this RNA. Imino proton NMR spectra reveal no change in secondary structure when 80 mM KCl is supplemented with 4 mM MgCl2. Optical melting curves in 1 M NaCl and in 100 mM KCl with 10 mM MgCl2 are very similar, with melting temperatures ∼14 °C higher than that for 100 mM KCl alone. These results provide a firm basis for designing experiments and potential therapeutics to test for function in cell culture. PMID:25026548

  1. Effect of reduction of strategic Columbium addition in 718 Alloy on the structure and properties

    NASA Technical Reports Server (NTRS)

    Ziegler, K. R.; Wallace, J. F.

    1985-01-01

    A series of alloys was developed having a base composition similar to Inconel 718, with reduced Cb levels of 3.00 and 1.10 wt% Cb. Substitutions of 3.0% W, 3.0W + 0.9V or Mo increased from 3.0% to 5.8% were made for the Cb in these alloys. Two additional alloys, one containing 3.49% Cb and 1.10% Ti and another containing 3.89% Cb and 1.29% Ti were also studied. Tensile properties at rooom and elevated temperatures, stress-rupture tests, and an analysis of extracted phases were carried out for each of the alloys. Additions of solid solution elements to a reduced Cb alloy had no significant effect on the properties of the alloys under either process condition. The solution and age alloys with substitutions of 1.27% i at 3.89% Cb had tensile properties similar top hose of the original alloy and stress-rupture properties superior to the original alloy. The improved stress-rupture properties were the result of significant precipitation of Ni3Ti-gamma prime in the alloy, which is more stable than gamma' at the elevated temperatures. At lower temperatures, the new alloy benefits from gamma' strengthening. With more precise control and proper processing, the reduced Cb direct-age alloy could substitute for Alloy 718 in high strength applications.

  2. Characterization of embedded fiber optic strain sensors into metallic structures via ultrasonic additive manufacturing

    NASA Astrophysics Data System (ADS)

    Schomer, John J.; Hehr, Adam J.; Dapino, Marcelo J.

    2016-04-01

    Fiber Bragg Grating (FBG) sensors measure deviation in a reflected wavelength of light to detect in-situ strain. These sensors are immune to electromagnetic interference, and the inclusion of multiple FBGs on the same fiber allows for a seamlessly integrated sensing network. FBGs are attractive for embedded sensing in aerospace applications due to their small noninvasive size and prospect of constant, real-time nondestructive evaluation. In this study, FBG sensors are embedded in aluminum 6061 via ultrasonic additive manufacturing (UAM), a rapid prototyping process that uses high power ultrasonic vibrations to weld similar and dissimilar metal foils together. UAM was chosen due to the desire to embed FBG sensors at low temperatures, a requirement that excludes other additive processes such as selective laser sintering or fusion deposition modeling. In this paper, the embedded FBGs are characterized in terms of birefringence losses, post embedding strain shifts, consolidation quality, and strain sensing performance. Sensors embedded into an ASTM test piece are compared against an exterior surface mounted foil strain gage at both room and elevated temperatures using cyclic tensile tests.

  3. Influence of additives on the structure of surfactant-free microemulsions.

    PubMed

    Marcus, J; Touraud, D; Prévost, S; Diat, O; Zemb, T; Kunz, W

    2015-12-28

    We study the addition of electrolytes to surfactant-free microemulsions in the domain where polydisperse pre-Ouzo aggregates are present. As in previous studies, the microemulsion is the ternary system water/ethanol/1-octanol, where ethanol acts as co-solvent. Addition of electrolytes modifies the static X-ray and neutron scattering, and dynamic light scattering patterns, as well as the position of the miscibility gap, where spontaneous emulsification occurs upon dilution with water. All observations can be rationalized considering that electrolytes are either "salting out" the ethanol, which is the main component of the interface stabilizing the aggregates, or producing charge separation via the antagonistic ion effect discovered by Onuki et al. Amphiphilic electrolytes, such as sodium dodecylsulfate or sodium dietheylhexylphosphate, induce a gradual transition towards monodisperse ionic micelles with their characteristic broad scattering "peak". In these micelles the ethanol plays then the role of a cosurfactant. Dynamic light scattering can only be understood by combination of fluctuations of aggregate concentration due to the vicinity of a critical point and in-out fluctuations of ethanol. PMID:26593697

  4. Modifying structure-sensitive reactions by addition of Zn to Pd

    SciTech Connect

    Childers, David J.; Schweitzer, Neil M.; Kamali Shahari, Seyed Mehdi; Rioux, Robert M.; Miller, Jeffrey T.; Meyer, Randall J.

    2014-10-01

    Silica-supported Pd and PdZn nanoparticles of a similar size were evaluated for neopentane hydrogenolysis/isomerization and propane hydrogenolysis/dehydrogenation. Monometallic Pd showed high neopentane hydrogenolysis selectivity. Addition of small amounts of Zn to Pd lead Pd–Zn scatters in the EXAFS spectrum and an increase in the linear bonded CO by IR. In addition, the neopentane turnover rate decreased by nearly 10 times with little change in the selectivity. Increasing amounts of Zn lead to greater Pd–Zn interactions, higher linear-to-bridging CO ratios by IR and complete loss of neopentane conversion. Pd NPs also had high selectivity for propane hydrogenolysis and thus were poorly selective for propylene. The PdZn bimetallic catalysts, however, were able to preferentially catalyze dehydrogenation, were not active for propane hydrogenolysis, and thus were highly selective for propylene formation. The decrease in hydrogenolysis selectivity was attributed to the isolation of active Pd atoms by inactive metallic Zn,demonstrating that hydrogenolysis requires a particular reactive ensemble whereas propane dehydrogenation does not.

  5. Highly Aligned Carbon Fiber in Polymer Composite Structures via Additive Manufacturing

    DOE PAGESBeta

    Tekinalp, Halil L; Kunc, Vlastimil; Velez-Garcia, Gregorio M; Duty, Chad E; Love, Lonnie J; Naskar, Amit K; Blue, Craig A; Ozcan, Soydan

    2014-01-01

    Additive manufacturing, diverging from traditional manufacturing techniques, such as casting and machining materials, can handle complex shapes with great design flexibility without the typical waste. Although this technique has been mainly used for rapid prototyping, interest is growing in using this method to directly manufacture actual parts of complex shape. To use 3D-printing additive manufacturing in wide spread applications, the technique and the feedstock materials require improvements to meet the mechanical requirements of load-bearing components. Thus, we investigated the short fiber (0.2 mm to 0.4 mm) reinforced acrylonitrile-butadiene-styrene composites as a feedstock for 3D-printing in terms of their processibility, microstructuremore » and mechanical performance; and also provided comparison with traditional compression molded composites. The tensile strength and modulus of 3D-printed samples increased ~115% and ~700%, respectively. 3D-printer yielded samples with very high fiber orientation in printing direction (up to 91.5 %), whereas, compression molding process yielded samples with significantly less fiber orientation. Microstructure-mechanical property relationships revealed that although the relatively high porosity is observed in the 3D-printed composites as compared to those produced by the conventional compression molding technique, they both exhibited comparable tensile strength and modulus. This phenomena is explained based on the changes in fiber orientation, dispersion and void formation.« less

  6. Unexpected Michael Additions on the Way to 2.3,8.9-Dibenzanthanthrenes with Interesting Structural Properties.

    PubMed

    Reus, Christian; Lechner, Marc P; Schulze, Matthias; Lungerich, Dominik; Diner, Colin; Gruber, Marco; Stryker, Jeffrey M; Hampel, Frank; Jux, Norbert; Tykwinski, Rik R

    2016-06-27

    The synthesis and properties of a new polycyclic aromatic hydrocarbon containing eight annulated rings and based on the anthanthrene core is described. An unexpected, nucleophile-dependent Michael addition to a dibenzanthanthrene-1,7-dione is found, giving a product with three triisopropylsilylacetylene units and a remarkable solid-state structure (as determined by X-ray crystallography). PMID:27140668

  7. Correlation of second