WorldWideScience

Sample records for base pairing motif

  1. Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs

    DEFF Research Database (Denmark)

    van Beest, M; Dooijes, D; van De Wetering, M; Kjaerulff, S; Bonvin, A; Nielsen, O; Clevers, H; Nielsen, Olaf

    2000-01-01

    promoter elements controlled by the yeast genes ste11 and Rox1 has indicated strict conservation of a larger DNA motif. By site selection, we identify a highly specific 12-base pair motif for Ste11, AGAACAAAGAAA. Similarly, we show that Tcf1, MatMc, and Sox4 bind unique, highly specific DNA motifs of 12...

  2. 2',4'-BNA bearing a 2-pyridine nucleobase for CG base pair recognition in the parallel motif triplex DNA.

    Science.gov (United States)

    Hari, Yoshiyuki; Matsugu, Sachiko; Inohara, Hiroyasu; Hatanaka, Yuri; Akabane, Masaaki; Imanishi, Takeshi; Obika, Satoshi

    2010-09-21

    We succeeded in the synthesis of triplex-forming oligonucleotides (TFOs) that contain a deoxyribonucleotide (Py) bearing a 2-pyridine nucleobase or the 2',4'-BNA congener (Py(B)). By UV melting experiments, it was found that 2-pyridine was a very promising nucleobase for the sequence-selective recognition of a CG base pair within double-stranded DNA (dsDNA) in a parallel motif triplex. Moreover, Py(B) in TFOs showed stronger affinity to a CG base pair than Py with further increase in the selectivity. Using TFO including multiple Py(B) units, triplex formation with dsDNA containing three CG base pairs was observed. PMID:20648389

  3. Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m5dCyd: Implications for the Stability of DNA i-Motif Conformations

    Science.gov (United States)

    Yang, Bo; Rodgers, M. T.

    2015-08-01

    Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m5dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m5dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m5dCyd)H+(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

  4. Sheared-type G(anti).C(syn) base-pair: a unique d(GXC) loop closure motif.

    Science.gov (United States)

    Chin, Ko-Hsin; Chou, Shan-Ho

    2003-05-30

    Stable DNA loop structures closed by a novel G.C base-pair have been determined for the single-residue d(GXC) loops (X=A, T, G or C) in low-salt solution by high-resolution nuclear magnetic resonance (NMR) techniques. The closing G.C base-pair in these loops is not of the canonical Watson-Crick type, but adopts instead a unique sheared-type (trans Watson-Crick/sugar-edge) pairing, like those occurring in the sheared mismatched G.A or A.C base-pair, to draw the two opposite strands together. The cytidine residue in the closing base-pair is transformed into the rare syn domain to form two H-bonds with the guanine base and to prevent the steric clash between the G 2NH(2) and the C H-5 protons. Besides, the sugar pucker of the syn cytidine is still located in the regular C2'-endo domain, unlike the C3'-endo domain adopted for the pyrimidines of the out-of-alternation left-handed Z-DNA structure. The facile formation of the compact d(GXC) loops closed by a unique sheared-type G(anti).C(syn) base-pair demonstrates the great potential of the single-stranded d(GXC) triplet repeats to fold into stable hairpins. PMID:12758081

  5. Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes – A comparative study of group-I intron structures

    Indian Academy of Sciences (India)

    K Chandrasekhar; R Malathi

    2003-09-01

    In recent decades studies on RNA structure and function have gained significance due to discoveries on diversified functions of RNA. A common element for RNA secondary structure formed by series of non-Watson/Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural motifs in ribozymes, playing a crucial role in their enzymatic activity. To understand the functional significance of these non-canonical base pairs in catalytic RNA, we analysed the sequences of group-I introns from nuclear genes. The results suggest that they might form the building blocks of folded RNA motifs which are crucial to the catalytic activity of the ribozyme. The conservation of these, as observed from divergent organisms, argues for the presence of non-canonical base pairs as an important requisite for the structure and enzymatic property of ribozymes by enabling them to carry out functions such as replication, polymerase activity etc. in primordial conditions in the absence of proteins.

  6. Elucidation of the sequence-specific third-strand recognition of four Watson-Crick base pairs in a pyrimidine triple-helix motif: T.AT, C.GC, T.CG, and G.TA.

    OpenAIRE

    Yoon, K; Hobbs, C. A.; Koch, J.; Sardaro, M; Kutny, R; Weis, A L

    1992-01-01

    We report a specific pattern of recognition by third-strand bases for each of the four Watson-Crick base pairs within a pyrimidine triple-helix motif as determined by PAGE: T.AT, C.GC, T.CG, and G.TA. Our recognition scheme for base triplets is in agreement with previous studies. In addition, we identified another triplet, T.CG, under physiological conditions, in which formation of triple helix was observed at equimolar ratios of the third strand and duplex target. Although different nearest-...

  7. Social Network Analysis Based on Network Motifs

    OpenAIRE

    Xu Hong-lin; Yan Han-bing; Gao Cui-fang; Zhu Ping

    2014-01-01

    Based on the community structure characteristics, theory, and methods of frequent subgraph mining, network motifs findings are firstly introduced into social network analysis; the tendentiousness evaluation function and the importance evaluation function are proposed for effectiveness assessment. Compared with the traditional way based on nodes centrality degree, the new approach can be used to analyze the properties of social network more fully and judge the roles of the nodes effectively. I...

  8. Identifying discriminative classification-based motifs in biological sequences

    OpenAIRE

    Vens, Celine; Rosso, Marie-Noëlle; Danchin, Etienne

    2011-01-01

    Motivation: Identification of conserved motifs in biological sequences is crucial to unveil common shared functions. Many tools exist for motif identification, including some that allow degenerate positions with multiple possible nucleotides or amino acids. Most efficient methods available today search conserved motifs in a set of sequences, but do not check for their specificity regarding to a set of negative sequences. Results: We present a tool to identify degenerate motifs, based on a giv...

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

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The structure-based sequence motif of the distant proteins in evolution, protein tyrosine phosphatases (PTP) Ⅰ and Ⅱ superfamilies, as an example, has been defined by the structural comparison, structure-based sequence alignment and analyses on substitution patterns of residues in common sequence conserved regions. And the phosphatases Ⅰ and Ⅱ can be correctly identified together by the structure-based PTP sequence motif from SWISS-PROT and TrEBML databases. The results show that the correct rates of identification are over 98%. This is the first time to identify PTP Ⅰ and Ⅱ together by this motif.

  10. An algorithm for motif-based network design

    CERN Document Server

    Mäki-Marttunen, Tuomo

    2016-01-01

    A determinant property of the structure of a biological network is the distribution of local connectivity patterns, i.e., network motifs. In this work, a method for creating directed, unweighted networks while promoting a certain combination of motifs is presented. This motif-based network algorithm starts with an empty graph and randomly connects the nodes by advancing or discouraging the formation of chosen motifs. The in- or out-degree distribution of the generated networks can be explicitly chosen. The algorithm is shown to perform well in producing networks with high occurrences of the targeted motifs, both ones consisting of 3 nodes as well as ones consisting of 4 nodes. Moreover, the algorithm can also be tuned to bring about global network characteristics found in many natural networks, such as small-worldness and modularity.

  11. MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs

    Directory of Open Access Journals (Sweden)

    Tsunoda Tatsuhiko

    2007-03-01

    Full Text Available Abstract Background A combination of multiple types of transcription factors and cis-regulatory elements is often required for gene expression in eukaryotes, and the combinatorial regulation confers specific gene expression to tissues or environments. To reveal the combinatorial regulation, computational methods are developed that efficiently infer combinations of cis-regulatory motifs that are important for gene expression as measured by DNA microarrays. One promising type of computational method is to utilize regression analysis between expression levels and scores of motifs in input sequences. This type takes full advantage of information on expression levels because it does not require that the expression level of each gene be dichotomized according to whether or not it reaches a certain threshold level. However, there is no web-based tool that employs regression methods to systematically search for motif combinations and that practically handles combinations of more than two or three motifs. Results We here introduced MotifCombinator, an online tool with a user-friendly interface, to systematically search for combinations composed of any number of motifs based on regression methods. The tool utilizes well-known regression methods (the multivariate linear regression, the multivariate adaptive regression spline or MARS, and the multivariate logistic regression method for this purpose, and uses the genetic algorithm to search for combinations composed of any desired number of motifs. The visualization systems in this tool help users to intuitively grasp the process of the combination search, and the backup system allows users to easily stop and restart calculations that are expected to require large computational time. This tool also provides preparatory steps needed for systematic combination search – i.e., selecting single motifs to constitute combinations and cutting out redundant similar motifs based on clustering analysis. Conclusion

  12. Motifs in Triadic Random Graphs based on Steiner Triple Systems

    CERN Document Server

    Winkler, Marco

    2013-01-01

    Conventionally, pairwise relationships between nodes are considered to be the fundamental building blocks of complex networks. However, over the last decade the overabundance of certain sub-network patterns, so called motifs, has attracted high attention. It has been hypothesized, these motifs, instead of links, serve as the building blocks of network structures. Although the relation between a network's topology and the general properties of the system, such as its function, its robustness against perturbations, or its efficiency in spreading information is the central theme of network science, there is still a lack of sound generative models needed for testing the functional role of subgraph motifs. Our work aims to overcome this limitation. We employ the framework of exponential random graphs (ERGMs) to define novel models based on triadic substructures. The fact that only a small portion of triads can actually be set independently poses a challenge for the formulation of such models. To overcome this obst...

  13. Report on Pairing-based Cryptography.

    Science.gov (United States)

    Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

    2015-01-01

    This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST's position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed. PMID:26958435

  14. Leucine-based receptor sorting motifs are dependent on the spacing relative to the plasma membrane

    DEFF Research Database (Denmark)

    Geisler, C; Dietrich, J; Nielsen, B L;

    1998-01-01

    amino acid, is constitutively active. In this study, we have investigated how the spacing relative to the plasma membrane affects the function of both types of leucine-based motifs. For phosphorylation-dependent leucine-based motifs, a minimal spacing of 7 residues between the plasma membrane and the...... phospho-acceptor was required for phosphorylation and thereby activation of the motifs. For constitutively active leucine-based motifs, a minimal spacing of 6 residues between the plasma membrane and the acidic residue was required for optimal activity of the motifs. In addition, we found that the acidic......Many integral membrane proteins contain leucine-based motifs within their cytoplasmic domains that mediate internalization and intracellular sorting. Two types of leucine-based motifs have been identified. One type is dependent on phosphorylation, whereas the other type, which includes an acidic...

  15. Application of PCR amplicon sequencing using a single primer pair in PCR amplification to assess variations in Helicobacter pylori CagA EPIYA tyrosine phosphorylation motifs

    Directory of Open Access Journals (Sweden)

    Karlsson Anneli

    2010-02-01

    Full Text Available Abstract Background The presence of various EPIYA tyrosine phosphorylation motifs in the CagA protein of Helicobacter pylori has been suggested to contribute to pathogenesis in adults. In this study, a unique PCR assay and sequencing strategy was developed to establish the number and variation of cagA EPIYA motifs. Findings MDA-DNA derived from gastric biopsy specimens from eleven subjects with gastritis was used with M13- and T7-sequence-tagged primers for amplification of the cagA EPIYA motif region. Automated capillary electrophoresis using a high resolution kit and amplicon sequencing confirmed variations in the cagA EPIYA motif region. In nine cases, sequencing revealed the presence of AB, ABC, or ABCC (Western type cagA EPIYA motif, respectively. In two cases, double cagA EPIYA motifs were detected (ABC/ABCC or ABC/AB, indicating the presence of two H. pylori strains in the same biopsy. Conclusion Automated capillary electrophoresis and Amplicon sequencing using a single, M13- and T7-sequence-tagged primer pair in PCR amplification enabled a rapid molecular typing of cagA EPIYA motifs. Moreover, the techniques described allowed for a rapid detection of mixed H. pylori strains present in the same biopsy specimen.

  16. Direct Updating of an RNA Base-Pairing Probability Matrix with Marginal Probability Constraints

    OpenAIRE

    Hamada, Michiaki

    2012-01-01

    A base-pairing probability matrix (BPPM) stores the probabilities for every possible base pair in an RNA sequence and has been used in many algorithms in RNA informatics (e.g., RNA secondary structure prediction and motif search). In this study, we propose a novel algorithm to perform iterative updates of a given BPPM, satisfying marginal probability constraints that are (approximately) given by recently developed biochemical experiments, such as SHAPE, PAR, and FragSeq. The method is easily ...

  17. A Comparative Study of Bases for Motif Inference

    OpenAIRE

    Pisanti, Nadia; Crochemore, Maxime; Grossi, Roberto; Sagot, Marie-France

    2005-01-01

    International audience Motif inference is at the heart of several time-demanding computational tasks, such as in molecular biology, data mining and identification of structured motifs in sequences, and in data compression, to name a few. In this scenario, a motif is a pattern that appears repeated at least a certain number of times (the quorum), to be of interest. The pattern can be approximated in that some of its characters can be left unspecified (the don't cares). Motif inference is not ...

  18. PETModule: a motif module based approach for enhancer target gene prediction.

    Science.gov (United States)

    Zhao, Changyong; Li, Xiaoman; Hu, Haiyan

    2016-01-01

    The identification of enhancer-target gene (ETG) pairs is vital for the understanding of gene transcriptional regulation. Experimental approaches such as Hi-C have generated valuable resources of ETG pairs. Several computational methods have also been developed to successfully predict ETG interactions. Despite these progresses, high-throughput experimental approaches are still costly and existing computational approaches are still suboptimal and not easy to apply. Here we developed a motif module based approach called PETModule that predicts ETG pairs. Tested on eight human cell types and two mouse cell types, we showed that a large number of our predictions were supported by Hi-C and/or ChIA-PET experiments. Compared with two recently developed approaches for ETG pair prediction, we shown that PETModule had a much better recall, a similar or better F1 score, and a larger area under the receiver operating characteristic curve. The PETModule tool is freely available at http://hulab.ucf.edu/research/projects/PETModule/. PMID:27436110

  19. Automated protein motif generation in the structure-based protein function prediction tool ProMOL.

    Science.gov (United States)

    Osipovitch, Mikhail; Lambrecht, Mitchell; Baker, Cameron; Madha, Shariq; Mills, Jeffrey L; Craig, Paul A; Bernstein, Herbert J

    2015-12-01

    ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. We developed an algorithm and workflow for the automation of motif building and testing routines in ProMOL. The algorithm uses a set of empirically derived parameters for optimization and requires little user intervention. The automated motif generation algorithm was first tested in a performance comparison with a set of manually generated motifs based on identical active sites from the same 112 PDB entries. The two sets of motifs were equally effective in identifying alignments with homologs and in rejecting alignments with unrelated structures. A second set of 296 active site motifs were generated automatically, based on Catalytic Site Atlas entries with literature citations, as an expansion of the library of existing manually generated motif templates. The new motif templates exhibited comparable performance to the existing ones in terms of hit rates against native structures, homologs with the same EC and Pfam designations, and randomly selected unrelated structures with a different EC designation at the first EC digit, as well as in terms of RMSD values obtained from local structural alignments of motifs and query structures. This research is supported by NIH grant GM078077. PMID:26573864

  20. Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses

    Science.gov (United States)

    Liu, Bingqiang; Zhou, Chuan; Li, Guojun; Zhang, Hanyuan; Zeng, Erliang; Liu, Qi; Ma, Qin

    2016-03-01

    Regulons are the basic units of the response system in a bacterial cell, and each consists of a set of transcriptionally co-regulated operons. Regulon elucidation is the basis for studying the bacterial global transcriptional regulation network. In this study, we designed a novel co-regulation score between a pair of operons based on accurate operon identification and cis regulatory motif analyses, which can capture their co-regulation relationship much better than other scores. Taking full advantage of this discovery, we developed a new computational framework and built a novel graph model for regulon prediction. This model integrates the motif comparison and clustering and makes the regulon prediction problem substantially more solvable and accurate. To evaluate our prediction, a regulon coverage score was designed based on the documented regulons and their overlap with our prediction; and a modified Fisher Exact test was implemented to measure how well our predictions match the co-expressed modules derived from E. coli microarray gene-expression datasets collected under 466 conditions. The results indicate that our program consistently performed better than others in terms of the prediction accuracy. This suggests that our algorithms substantially improve the state-of-the-art, leading to a computational capability to reliably predict regulons for any bacteria.

  1. SALAD database: a motif-based database of protein annotations for plant comparative genomics

    OpenAIRE

    Mihara, Motohiro; Itoh, Takeshi; Izawa, Takeshi

    2009-01-01

    Proteins often have several motifs with distinct evolutionary histories. Proteins with similar motifs have similar biochemical properties and thus related biological functions. We constructed a unique comparative genomics database termed the SALAD database (http://salad.dna.affrc.go.jp/salad/) from plant-genome-based proteome data sets. We extracted evolutionarily conserved motifs by MEME software from 209 529 protein-sequence annotation groups selected by BLASTP from the proteome data sets o...

  2. Distance-based identification of structure motifs in proteins using constrained frequent subgraph mining.

    Science.gov (United States)

    Huan, Jun; Bandyopadhyay, Deepak; Prins, Jan; Snoeyink, Jack; Tropsha, Alexander; Wang, Wei

    2006-01-01

    Structure motifs are amino acid packing patterns that occur frequently within a set of protein structures. We define a labeled graph representation of protein structure in which vertices correspond to amino acid residues and edges connect pairs of residues and are labeled by (1) the Euclidian distance between the C(alpha) atoms of the two residues and (2) a boolean indicating whether the two residues are in physical/chemical contact. Using this representation, a structure motif corresponds to a labeled clique that occurs frequently among the graphs representing the protein structures. The pairwise distance constraints on each edge in a clique serve to limit the variation in geometry among different occurrences of a structure motif. We present an efficient constrained subgraph mining algorithm to discover structure motifs in this setting. Compared with contact graph representations, the number of spurious structure motifs is greatly reduced. Using this algorithm, structure motifs were located for several SCOP families including the Eukaryotic Serine Proteases, Nuclear Binding Domains, Papain-like Cysteine Proteases, and FAD/NAD-linked Reductases. For each family, we typically obtain a handful of motifs within seconds of processing time. The occurrences of these motifs throughout the PDB were strongly associated with the original SCOP family, as measured using a hyper-geometric distribution. The motifs were found to cover functionally important sites like the catalytic triad for Serine Proteases and co-factor binding sites for Nuclear Binding Domains. The fact that many motifs are highly family-specific can be used to classify new proteins or to provide functional annotation in Structural Genomics Projects. PMID:17369641

  3. Arithmetic Operators for Pairing-Based Cryptography

    OpenAIRE

    Beuchat, Jean-Luc; Brisebarre, Nicolas; Detrey, Jérémie; Okamoto, Eiji

    2007-01-01

    Since their introduction in constructive cryptographic applications, pairings over (hyper)elliptic curves are at the heart of an ever increasing number of protocols. Software implementations being rather slow, the study of hardware architectures became an active research area. In this paper, we first study an accelerator for the eta_T pairing over F_3[x]/(x^97 + x^12 + 2). Our architecture is based on a unified arithmetic operator which performs addition, multiplication, and cubing over F_3^9...

  4. Metagenome fragment classification based on multiple motif-occurrence profiles

    Directory of Open Access Journals (Sweden)

    Naoki Matsushita

    2014-09-01

    Full Text Available A vast amount of metagenomic data has been obtained by extracting multiple genomes simultaneously from microbial communities, including genomes from uncultivable microbes. By analyzing these metagenomic data, novel microbes are discovered and new microbial functions are elucidated. The first step in analyzing these data is sequenced-read classification into reference genomes from which each read can be derived. The Naïve Bayes Classifier is a method for this classification. To identify the derivation of the reads, this method calculates a score based on the occurrence of a DNA sequence motif in each reference genome. However, large differences in the sizes of the reference genomes can bias the scoring of the reads. This bias might cause erroneous classification and decrease the classification accuracy. To address this issue, we have updated the Naïve Bayes Classifier method using multiple sets of occurrence profiles for each reference genome by normalizing the genome sizes, dividing each genome sequence into a set of subsequences of similar length and generating profiles for each subsequence. This multiple profile strategy improves the accuracy of the results generated by the Naïve Bayes Classifier method for simulated and Sargasso Sea datasets.

  5. A structural-alphabet-based strategy for finding structural motifs across protein families.

    Science.gov (United States)

    Wu, Chih Yuan; Chen, Yao Chi; Lim, Carmay

    2010-08-01

    Proteins with insignificant sequence and overall structure similarity may still share locally conserved contiguous structural segments; i.e. structural/3D motifs. Most methods for finding 3D motifs require a known motif to search for other similar structures or functionally/structurally crucial residues. Here, without requiring a query motif or essential residues, a fully automated method for discovering 3D motifs of various sizes across protein families with different folds based on a 16-letter structural alphabet is presented. It was applied to structurally non-redundant proteins bound to DNA, RNA, obligate/non-obligate proteins as well as free DNA-binding proteins (DBPs) and proteins with known structures but unknown function. Its usefulness was illustrated by analyzing the 3D motifs found in DBPs. A non-specific motif was found with a 'corner' architecture that confers a stable scaffold and enables diverse interactions, making it suitable for binding not only DNA but also RNA and proteins. Furthermore, DNA-specific motifs present 'only' in DBPs were discovered. The motifs found can provide useful guidelines in detecting binding sites and computational protein redesign. PMID:20525797

  6. The Annotation of RNA Motifs

    Directory of Open Access Journals (Sweden)

    Eric Westhof

    2006-04-01

    Full Text Available The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNA–RNA and quaternary RNA–protein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-Watson–Crick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s. The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a decomposition of each motif into non-Watson–Crick base-pairs; (b geometric classification of each basepair; (c identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e acceptance or rejection of the null hypothesis that the motif is conserved.

  7. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

    KAUST Repository

    Chawla, Mohit

    2015-06-27

    Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.

  8. iTriplet, a rule-based nucleic acid sequence motif finder

    Directory of Open Access Journals (Sweden)

    Gunderson Samuel I

    2009-10-01

    Full Text Available Abstract Background With the advent of high throughput sequencing techniques, large amounts of sequencing data are readily available for analysis. Natural biological signals are intrinsically highly variable making their complete identification a computationally challenging problem. Many attempts in using statistical or combinatorial approaches have been made with great success in the past. However, identifying highly degenerate and long (>20 nucleotides motifs still remains an unmet challenge as high degeneracy will diminish statistical significance of biological signals and increasing motif size will cause combinatorial explosion. In this report, we present a novel rule-based method that is focused on finding degenerate and long motifs. Our proposed method, named iTriplet, avoids costly enumeration present in existing combinatorial methods and is amenable to parallel processing. Results We have conducted a comprehensive assessment on the performance and sensitivity-specificity of iTriplet in analyzing artificial and real biological sequences in various genomic regions. The results show that iTriplet is able to solve challenging cases. Furthermore we have confirmed the utility of iTriplet by showing it accurately predicts polyA-site-related motifs using a dual Luciferase reporter assay. Conclusion iTriplet is a novel rule-based combinatorial or enumerative motif finding method that is able to process highly degenerate and long motifs that have resisted analysis by other methods. In addition, iTriplet is distinguished from other methods of the same family by its parallelizability, which allows it to leverage the power of today's readily available high-performance computing systems.

  9. An Identity Based Aggregate Signature from Pairings

    Directory of Open Access Journals (Sweden)

    Yike Yu

    2011-04-01

    Full Text Available An aggregate signature is a useful digital signature that supports aggregation: Given n signatures on n distinct messages from n distinct users, aggregate signature scheme is possible to aggregate all these signature into a single short signature. This single signature, along with the n original messages will convince any verifier that the n users did indeed sign the n original messages respectively (i.e., for i=1,...,n user i signed message  mi. In this paper, we propose an identity based aggregate signature scheme which requires constant pairing operations in the verification and the size of aggregate signature is independent of the number of signers. We prove that the proposed signature scheme is secure against existential forgery under adaptively chosen message and identity attack in the random oracle model assuming the intractability of the computational Diffie-Hellman problem.

  10. Natural versus artificial creation of base pairs in DNA: origin of nucleobases from the perspectives of unnatural base pair studies.

    Science.gov (United States)

    Hirao, Ichiro; Kimoto, Michiko; Yamashige, Rie

    2012-12-18

    Since life began on Earth, the four types of bases (A, G, C, and T(U)) that form two sets of base pairs have remained unchanged as the components of nucleic acids that replicate and transfer genetic information. Throughout evolution, except for the U to T modification, the four base structures have not changed. This constancy within the genetic code raises the question of how these complicated nucleotides were generated from the molecules in a primordial soup on the early Earth. At some prebiotic stage, the complementarity of base pairs might have accelerated the generation and accumulation of nucleotides or oligonucleotides. We have no clues whether one pair of nucleobases initially appeared on the early Earth during this process or a set of two base pairs appeared simultaneously. Recently, researchers have developed new artificial pairs of nucleobases (unnatural base pairs) that function alongside the natural base pairs. Some unnatural base pairs in duplex DNA can be efficiently and faithfully amplified in a polymerase chain reaction (PCR) using thermostable DNA polymerases. The addition of unnatural base pair systems could expand the genetic alphabet of DNA, thus providing a new mechanism for the generation novel biopolymers by the site-specific incorporation of functional components into nucleic acids and proteins. Furthermore, the process of unnatural base pair development might provide clues to the origin of the natural base pairs in a primordial soup on the early Earth. In this Account, we describe the development of three representative types of unnatural base pairs that function as a third pair of nucleobases in PCR and reconsider the origin of the natural nucleic acids. As researchers developing unnatural base pairs, they use repeated "proof of concept" experiments. As researchers design new base pairs, they improve the structures that function in PCR and eliminate those that do not. We expect that this process is similar to the one functioning in the

  11. Motif Statistics

    OpenAIRE

    Nicodème, Pierre; Salvy, Bruno; Flajolet, Philippe

    1999-01-01

    We present a complete analysis of the statistics of number of occurrences of a regular expression pattern in a random text. This covers «motifs» widely used in computational biology. Our approach is based on: (i) a constructive approach to classical results in theoretical computer science (automata and formal language theory), in particular, the rationality of generating functions of regular languages; (ii) analytic combinatorics that is used for deriving asymptotic properties from generating...

  12. An ensemble of SVM classifiers based on gene pairs.

    Science.gov (United States)

    Tong, Muchenxuan; Liu, Kun-Hong; Xu, Chungui; Ju, Wenbin

    2013-07-01

    In this paper, a genetic algorithm (GA) based ensemble support vector machine (SVM) classifier built on gene pairs (GA-ESP) is proposed. The SVMs (base classifiers of the ensemble system) are trained on different informative gene pairs. These gene pairs are selected by the top scoring pair (TSP) criterion. Each of these pairs projects the original microarray expression onto a 2-D space. Extensive permutation of gene pairs may reveal more useful information and potentially lead to an ensemble classifier with satisfactory accuracy and interpretability. GA is further applied to select an optimized combination of base classifiers. The effectiveness of the GA-ESP classifier is evaluated on both binary-class and multi-class datasets. PMID:23668348

  13. Higher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAs

    KAUST Repository

    Chawla, Mohit

    2013-10-10

    The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. 2013 The Author(s).

  14. (φ,ψ)2-motifs: a purely conformation-based, fine-grained enumeration of protein parts at the two-residue level

    OpenAIRE

    Hollingsworth, Scott A; Lewis, Matthew C.; Berkholz, Donald S.; Wong, Weng-Keen; Karplus, P. Andrew

    2011-01-01

    A deep understanding of protein structure benefits from the use of a variety of classification strategies that enhance our ability to effectively describe local patterns of conformation. Here, we use a clustering algorithm to analyze 76,533 all-trans segments from protein structures solved at 1.2 Å resolution or better to create a purely φ,ψ-based comprehensive empirical categorization of common conformations adopted by two adjacent φ,ψ-pairs (i.e. (φ,ψ)2-motifs). The clustering algorithm wor...

  15. SPIC: A novel similarity metric for comparing transcription factor binding site motifs based on information contents

    OpenAIRE

    Zhang, Shaoqiang; Zhou, Xiguo; Du, Chuanbin; Su, Zhengchang

    2013-01-01

    Background Discovering transcription factor binding sites (TFBS) is one of primary challenges to decipher complex gene regulatory networks encrypted in a genome. A set of short DNA sequences identified by a transcription factor (TF) is known as a motif, which can be expressed accurately in matrix form such as a position-specific scoring matrix (PSSM) and a position frequency matrix. Very frequently, we need to query a motif in a database of motifs by seeking its similar motifs, merge similar ...

  16. A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs

    Directory of Open Access Journals (Sweden)

    Seitzer Phillip

    2012-11-01

    Full Text Available Abstract Background Discovery of functionally significant short, statistically overrepresented subsequence patterns (motifs in a set of sequences is a challenging problem in bioinformatics. Oftentimes, not all sequences in the set contain a motif. These non-motif-containing sequences complicate the algorithmic discovery of motifs. Filtering the non-motif-containing sequences from the larger set of sequences while simultaneously determining the identity of the motif is, therefore, desirable and a non-trivial problem in motif discovery research. Results We describe MotifCatcher, a framework that extends the sensitivity of existing motif-finding tools by employing random sampling to effectively remove non-motif-containing sequences from the motif search. We developed two implementations of our algorithm; each built around a commonly used motif-finding tool, and applied our algorithm to three diverse chromatin immunoprecipitation (ChIP data sets. In each case, the motif finder with the MotifCatcher extension demonstrated improved sensitivity over the motif finder alone. Our approach organizes candidate functionally significant discovered motifs into a tree, which allowed us to make additional insights. In all cases, we were able to support our findings with experimental work from the literature. Conclusions Our framework demonstrates that additional processing at the sequence entry level can significantly improve the performance of existing motif-finding tools. For each biological data set tested, we were able to propose novel biological hypotheses supported by experimental work from the literature. Specifically, in Escherichia coli, we suggested binding site motifs for 6 non-traditional LexA protein binding sites; in Saccharomyces cerevisiae, we hypothesize 2 disparate mechanisms for novel binding sites of the Cse4p protein; and in Halobacterium sp. NRC-1, we discoverd subtle differences in a general transcription factor (GTF binding site motif

  17. Attribute pair-based visual recognition and memory.

    Directory of Open Access Journals (Sweden)

    Masahiko Morita

    Full Text Available BACKGROUND: In the human visual system, different attributes of an object, such as shape, color, and motion, are processed separately in different areas of the brain. This raises a fundamental question of how are these attributes integrated to produce a unified perception and a specific response. This "binding problem" is computationally difficult because all attributes are assumed to be bound together to form a single object representation. However, there is no firm evidence to confirm that such representations exist for general objects. METHODOLOGY/PRINCIPAL FINDINGS: Here we propose a paired-attribute model in which cognitive processes are based on multiple representations of paired attributes. In line with the model's prediction, we found that multiattribute stimuli can produce an illusory perception of a multiattribute object arising from erroneous integration of attribute pairs, implying that object recognition is based on parallel perception of paired attributes. Moreover, in a change-detection task, a feature change in a single attribute frequently caused an illusory perception of change in another attribute, suggesting that multiple pairs of attributes are stored in memory. CONCLUSIONS/SIGNIFICANCE: The paired-attribute model can account for some novel illusions and controversial findings on binocular rivalry and short-term memory. Our results suggest that many cognitive processes are performed at the level of paired attributes rather than integrated objects, which greatly facilitates the binding problem and provides simpler solutions for it.

  18. Model-based Comparative Prediction of Transcription-Factor Binding Motifs in Anabolic Responses in Bone

    Institute of Scientific and Technical Information of China (English)

    Andy B. Chen; Kazunori Hamamura; Guohua Wang; Weirong Xing; Subburaman Mohan; Hiroki Yokota; Yunlong Liu

    2007-01-01

    Understanding the regulatory mechanism that controls the alteration of global gene expression patterns continues to be a challenging task in computational biology. We previously developed an ant algorithm, a biologically-inspired computational technique for microarray data, and predicted putative transcription-factor binding motifs (TFBMs) through mimicking interactive behaviors of natural ants. Here we extended the algorithm into a set of web-based software, Ant Modeler, and applied it to investigate the transcriptional mechanism underlying bone formation. Mechanical loading and administration of bone morphogenic proteins (BMPs) are two known treatments to strengthen bone. We addressed a question: Is there any TFBM that stimulates both "anabolic responses of mechanical loading" and "BMP-mediated osteogenic signaling"? Although there is no significant overlap among genes in the two responses, a comparative model-based analysis suggests that the two independent osteogenic processes employ common TFBMs, such as a stress responsive element and a motif for peroxisome proliferator-activated recep- tor (PPAR). The post-modeling in vitro analysis using mouse osteoblast cells sup- ported involvements of the predicted TFBMs such as PPAR, Ikaros 3, and LMO2 in response to mechanical loading. Taken together, the results would be useful to derive a set of testable hypotheses and examine the role of specific regulators in complex transcriptional control of bone formation.

  19. ID-Based Signature Scheme with Weil Pairing

    Directory of Open Access Journals (Sweden)

    Neetu Sharma

    2013-09-01

    Full Text Available Digital signature is an essential component in cryptography. Digital signaturesguarantee end-to-end message integrity and authentication information about the origin of a message. In this paper we propose a new identification based digital signature scheme with weil pairing. Also we analyze security and efficiency of our scheme. Security of our scheme is based on expressing the torsion point of curve into linear combination of its basis points; it is more complicated than solving ECDLP(Elliptic Curve Discrete Logarithm Problem. We claim that our new identification based digital signature scheme is more secure and efficient than the existing scheme of Islam et al(S. K. Hafizul Islam, G.P. Biswas, An Efficient and Provably-secure Digital signature Scheme based on Elliptic Curve Bilinear Pairings, Theoretical and Applied Informatics ISSN 18965334 Vol.24, no. 2, 2012, pp. 109 118 based on bilinear pairing.

  20. Calix[4]pyrrole-based ion pair receptors.

    Science.gov (United States)

    Kim, Sung Kuk; Sessler, Jonathan L

    2014-08-19

    Ion pair receptors, which are able to bind concurrently both a cation and an anion, often display higher selectivity and affinity for specific ion pairs than simple ion receptors capable of recognizing primarily either a cation or an anion. This enhancement in recognition function is attributable to direct or indirect cooperative interactions between cobound ions via electrostatic attractions between oppositely charged ions, as well as to positive allosteric effects. In addition, by virtue of binding the counterions of the targeted ion, ion pair receptors can minimize the solvation of the counterions, which can otherwise have a negative effect on the interactions between the receptors and the targeted ions. As a result of their more favorable interactions, ion pair receptors are attractive for use in applications, such as extraction and sensing, where control of the binding interactions is advantageous. In this Account, we illustrate this potential in the context of ion pair receptors based on the calix[4]pyrrole scaffold. Both simple ditopic ion pair receptors, containing sites for the recognition of a single anion and single cation, and so-called multitopic ion pair receptors will be discussed. The latter systems differ from conventional, so-called ditopic ion pair receptors in that they contain more than one binding site for a given targeted ion (e.g., a cation). This permits a level of selectivity and control over binding function not normally seen for simple ion or ion pair receptors containing one or two binding sites, respectively. Calix[4]pyrroles are macrocyclic compounds consisting of four pyrrole units linked via fully substituted sp(3) hybridized meso carbon atoms. They are effective receptors for Lewis basic anions (e.g., halides) in typical organic media and under certain conditions will recognize ion pairs containing charge diffuse cations, such as a small alkylammonium, imidazolium, or cesium cations. The calix[4]pyrrole framework is further

  1. Transduction motif analysis of gastric cancer based on a human signaling network

    Energy Technology Data Exchange (ETDEWEB)

    Liu, G.; Li, D.Z.; Jiang, C.S.; Wang, W. [Fuzhou General Hospital of Nanjing Command, Department of Gastroenterology, Fuzhou, China, Department of Gastroenterology, Fuzhou General Hospital of Nanjing Command, Fuzhou (China)

    2014-04-04

    To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD) scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs.

  2. Transduction motif analysis of gastric cancer based on a human signaling network

    International Nuclear Information System (INIS)

    To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD) scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs

  3. Motif-Based Text Mining of Microbial Metagenome Redundancy Profiling Data for Disease Classification.

    Science.gov (United States)

    Wang, Yin; Li, Rudong; Zhou, Yuhua; Ling, Zongxin; Guo, Xiaokui; Xie, Lu; Liu, Lei

    2016-01-01

    Background. Text data of 16S rRNA are informative for classifications of microbiota-associated diseases. However, the raw text data need to be systematically processed so that features for classification can be defined/extracted; moreover, the high-dimension feature spaces generated by the text data also pose an additional difficulty. Results. Here we present a Phylogenetic Tree-Based Motif Finding algorithm (PMF) to analyze 16S rRNA text data. By integrating phylogenetic rules and other statistical indexes for classification, we can effectively reduce the dimension of the large feature spaces generated by the text datasets. Using the retrieved motifs in combination with common classification methods, we can discriminate different samples of both pneumonia and dental caries better than other existing methods. Conclusions. We extend the phylogenetic approaches to perform supervised learning on microbiota text data to discriminate the pathological states for pneumonia and dental caries. The results have shown that PMF may enhance the efficiency and reliability in analyzing high-dimension text data. PMID:27057545

  4. The thermodynamics and kinetics of a nucleotide base pair

    Science.gov (United States)

    Wang, Yujie; Gong, Sha; Wang, Zhen; Zhang, Wenbing

    2016-03-01

    The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.

  5. Ultrafast dynamics in DNA base pairs following ultraviolet excitation.

    Science.gov (United States)

    Orr-Ewing, Andrew

    2015-03-01

    Photo-protective mechanisms in DNA are essential to maintain the integrity of the genetic code by preventing damage from absorption of solar ultraviolet (UV) radiation. We have used time-resolved infra-red (TRIR) spectroscopy to observe the dynamics of Watson-Crick nucleobase pairs following absorption of femtosecond UV laser pulses. The base pairs are prepared as nucleosides in solution, and photo-induced dynamics are probed in the carbonyl and N-H bond stretching regions using broadband IR pulses with picosecond time resolution. Results will be presented for the guanine-cytosine (G-C) base pair, contrasting the rapid recovery of ground-state products (the photo-protection pathway) with formation of other photoproducts which might represent photo-damage mechanisms. This work is a collaboration with the group of Prof F. Temps (Christian-Albrechts-Universitat zu Kiel). This research is supported by ERC Advanced Grant 290966 CAPRI.

  6. Density functional calculations of planar DNA base-pairs

    CERN Document Server

    Machado, M V T; Artacho, E; Sánchez-Portál, D; Soler, J M; Machado, Maider; Ordejon, Pablo; Artacho, Emilio; Sanchez-Portal, Daniel; Soler, Jose M.

    1999-01-01

    We present a systematic Density Functional Theory (DFT) study of geometries and energies of the nucleic acid DNA bases (guanine, adenine, cytosine and thymine) and 30 different DNA base-pairs. We use a recently developed linear-scaling DFT scheme, which is specially suited for systems with large numbers of atoms. As a first step towards the study of large DNA systems, in this work: (i) We establish the reliability of the approximations of our method (including pseudopotentials and basis sets) for the description of the hydrogen-bonded base pairs, by comparing our results with those of former calculations. We show that the interaction energies at Hartree-Fock geometries are in very good agreement with those of second order M{ø}ller-Plesset (MP2) perturbation theory (the most accurate technique that can be applied at present for system of the sizes of the base-pairs). (ii) We perform DFT structural optimizations for the 30 different DNA base-pairs, only three of which had been previously studied with DFT. Our ...

  7. Theoretical analysis of noncanonical base pairing interactions in RNA molecules

    Indian Academy of Sciences (India)

    Dhananjay Bhattacharyya; Siv Chand Koripella; Abhijit Mitra; Vijay Babu Rajendran; Bhabdyuti Sinha

    2007-08-01

    Noncanonical base pairs in RNA have strong structural and functional implications but are currently not considered for secondary structure predictions. We present results of comparative ab initio studies of stabilities and interaction energies for the three standard and 24 selected unusual RNA base pairs reported in the literature. Hydrogen added models of isolated base pairs, with heavy atoms frozen in their ‘away from equilibrium’ geometries, built from coordinates extracted from NDB, were geometry optimized using HF/6-31G** basis set, both before and after unfreezing the heavy atoms. Interaction energies, including BSSE and deformation energy corrections, were calculated, compared with respective single point MP2 energies, and correlated with occurrence frequencies and with types and geometries of hydrogen bonding interactions. Systems having two or more N-H…O/N hydrogen bonds had reasonable interaction energies which correlated well with respective occurrence frequencies and highlighted the possibility of some of them playing important roles in improved secondary structure prediction methods. Several of the remaining base pairs with one N-H…O/N and/or one C-H…O/N interactions respectively, had poor interaction energies and negligible occurrences. High geometry variations on optimization of some of these were suggestive of their conformational switch like characteristics.

  8. Social Networks-Based Adaptive Pairing Strategy for Cooperative Learning

    Science.gov (United States)

    Chuang, Po-Jen; Chiang, Ming-Chao; Yang, Chu-Sing; Tsai, Chun-Wei

    2012-01-01

    In this paper, we propose a grouping strategy to enhance the learning and testing results of students, called Pairing Strategy (PS). The proposed method stems from the need of interactivity and the desire of cooperation in cooperative learning. Based on the social networks of students, PS provides members of the groups to learn from or mimic…

  9. NEW ID-BASED GROUP SIGNATURE FROM PAIRINGS

    Institute of Scientific and Technical Information of China (English)

    Chen Xiaofeng; Zhang Fangguo; Kwangjo Kim

    2006-01-01

    We argue that traditional identity-based systems from pairings seem unsuitable for designing group signature schemes due to the problem of key escrow. In this paper we first propose new ID-based public key systems without trusted PKG (Private Key Generator) from bilinear pairings. In our new ID-based systems, if the dishonest PKG impersonates an honest user to communicate with others, the user can provide a proof of treachery of the PKG afterwards, which is similar to certificate-based systems. Therefore, our systems reach the Girault's trusted level 3. We then propose a group signature scheme under the new ID-based systems, the security and performance of which rely on the new systems. The size of the group public key and the length of the signature are independent on the numbers of the group.

  10. Waveguide-based OPO source of entangled photon pairs

    International Nuclear Information System (INIS)

    In this paper, we present a compact source of narrow-band energy-time-entangled photon pairs in the telecom regime based on a Ti-indiffused periodically poled lithium niobate (PPLN) waveguide resonator, i.e. a waveguide with end-face dielectric multi-layer mirrors. This is a monolithic doubly resonant optical parametric oscillator (OPO) far below threshold, which generates photon pairs by spontaneous parametric down-conversion (SPDC) at around 1560 nm with a 117 MHz (0.91 pm)-bandwidth. A coherence time of 2.7 ns is estimated by a time correlation measurement and a high quality of the entangled states is confirmed by a Bell-type experiment. Since highly coherent energy-time-entangled photon pairs in the telecom regime are suitable for long distance transmission and manipulation, this source is well suited to the requirements of quantum communication.

  11. Partition function and base pairing probabilities of RNA heterodimers

    Directory of Open Access Journals (Sweden)

    Stadler Peter F

    2006-03-01

    Full Text Available Abstract Background RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. Methods The standard dynamic programming algorithms for computing secondary structures of linear single-stranded RNA molecules are extended to the co-folding of two interacting RNAs. Results We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures. Availability RNAcofold is distributed as part of the Vienna RNA Package, http://www.tbi.univie.ac.at/RNA/. Contact Stephan H. Bernhart – berni@tbi.univie.ac.at

  12. Isoindigo-based polymer photovoltaics: modifying polymer molecular structures to control the nanostructural packing motif.

    Science.gov (United States)

    Kim, Yu Jin; Lee, Yun-Ji; Kim, Yun-Hi; Park, Chan Eon

    2016-07-21

    Donor molecular structures, and their packing aspects in donor:acceptor active blends, play a crucial role in the photovoltaic performance of polymer solar cells. We systematically investigated a series of isoindigo-based donor polymers within the framework of a three-dimensional (3D) crystalline motif by modifying their chemical structures, thereby affecting device performances. Although our isoindigo-based polymer series contained polymers that differed only by their alkyl side chains and/or donating units, they showed quite different nanoscale morphological properties, which resulted in significantly different device efficiencies. Notably, blends of our isoindigo-based donor polymer systems with an acceptor compound, whereby the blends had more intermixed network morphologies and stronger face-on orientations of the polymer crystallites, provided better-performing photovoltaic devices. This behavior was analyzed using atomic force microscopy (AFM) and two-dimensional grazing incidence wide angle X-ray diffraction (2D-GIWAXD). To the best of our knowledge, no correlation has been reported previously between 3D nano-structural donor crystallites and device performances, particularly for isoindigo-based polymer systems. PMID:27326694

  13. Dispom: a discriminative de-novo motif discovery tool based on the jstacs library.

    Science.gov (United States)

    Grau, Jan; Keilwagen, Jens; Gohr, André; Paponov, Ivan A; Posch, Stefan; Seifert, Michael; Strickert, Marc; Grosse, Ivo

    2013-02-01

    DNA-binding proteins are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in target regions of genomic DNA. However, de-novo discovery of these binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not yet been solved satisfactorily. Here, we present a detailed description and analysis of the de-novo motif discovery tool Dispom, which has been developed for finding binding sites of DNA-binding proteins that are differentially abundant in a set of target regions compared to a set of control regions. Two additional features of Dispom are its capability of modeling positional preferences of binding sites and adjusting the length of the motif in the learning process. Dispom yields an increased prediction accuracy compared to existing tools for de-novo motif discovery, suggesting that the combination of searching for differentially abundant motifs, inferring their positional distributions, and adjusting the motif lengths is beneficial for de-novo motif discovery. When applying Dispom to promoters of auxin-responsive genes and those of ABI3 target genes from Arabidopsis thaliana, we identify relevant binding motifs with pronounced positional distributions. These results suggest that learning motifs, their positional distributions, and their lengths by a discriminative learning principle may aid motif discovery from ChIP-chip and gene expression data. We make Dispom freely available as part of Jstacs, an open-source Java library that is tailored to statistical sequence analysis. To facilitate extensions of Dispom, we describe its implementation using Jstacs in this manuscript. In addition, we provide a stand-alone application of Dispom at http://www.jstacs.de/index.php/Dispom for instant use. PMID:23427988

  14. The effect of base pair mismatch on DNA strand displacement

    CERN Document Server

    Broadwater, Bo

    2016-01-01

    DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single base pair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration, and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term, the concurrent displacement model, and used the first passage t...

  15. SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

    Science.gov (United States)

    Davey, Norman E.; Cowan, Joanne L.; Shields, Denis C.; Gibson, Toby J.; Coldwell, Mark J.; Edwards, Richard J.

    2012-01-01

    Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (short linear motif fingerprints), a de novo motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional motifs. Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E. PMID:22977176

  16. T cell receptor zeta allows stable expression of receptors containing the CD3gamma leucine-based receptor-sorting motif

    DEFF Research Database (Denmark)

    Dietrich, J; Geisler, C

    1998-01-01

    that the leucine-based motif in these complexes was inactive. In contrast, the CD4/CD3gamma chimeras did not associate with TCRzeta, and the leucine-based motif in these chimeras was constitutively active resulting in a high spontaneous internalization rate and low expression of the chimeras at the cell surface...

  17. Graphene/Lead (Pb)-based Cooper -pair splitter

    Science.gov (United States)

    Borzenets, Ivan; Shimazaki, Yuya; Jones, Gareth; Russo, Saverio; Yamamoto, Michihisa; Tarucha, Seigo

    2015-03-01

    We have fabricated a Cooper-pair splitter device based on a superconductor- two normal leads, ``Y'' shaped junction with graphene as the base material. (Compared to nanowire-based devices, the two dimensional nature of graphene allows for the normal leads to be placed arbitrarily close together and in a non-parallel arrangement.) The superconducting lead is created by contacting graphene with lead (Pb), thus inducing a supercurrent via the proximity effect. The normal metal leads are patterned into quantum dots by etching nano-constrictions with self-aligned side gates. Quantum dots strongly suppress two electron processes, allowing only one electron to pass at a time. Thus, the Cooper-pair splitting efficiency is enhanced as the split electrons must necessarily tunnel through different quantum dots. Using a DC measurement we have demonstrated enhanced currents though both normal leads when both quantum dots are in resonance and the input lead is in the superconducting regime: demonstrating Cooper-pair splitting. (This is contrary to the classical regime of currents though a three resistor junction.) Shot noise measurements would demonstrate that the split electrons tunnel at the same time. Demonstrating that the split electrons have opposite spin would show that such a device could be used as a source of quantum entangled electrons.

  18. Coherent Pair Production in Deformed Crystals with a Complex Base

    Science.gov (United States)

    Mkrtchyan, A. R.; Saharian, A. A.; Parazian, V. V.

    We investigate the coherent electron-positron pair creation by high-energy photons in a periodically deformed single crystal with a complex base. The formula for the corresponding differential cross-section is derived for an arbitrary deformation field. The conditions are specified under which the influence of the deformation is considerable. The case is considered in detail when the photon enters into the crystal at small angles with respect to a crystallographic axis. The results of the numerical calculations are presented for SiO2 single crystal and Moliere parametrization of the screened atomic potentials in the case of the deformation field generated by the acoustic wave of S type. In dependence of the parameters, the presence of deformation can either enhance or reduce the pair creation cross-section. This can be used to control the parameters of the positron sources for storage rings and colliders.

  19. Coherent pair production in deformed crystals with a complex base

    CERN Document Server

    Mkrtchyan, A R; Saharian, A A

    2006-01-01

    We investigate the coherent electron-positron pair creation by high-energy photons in a periodically deformed single crystal with a complex base. The formula for the corresponding differential cross-section is derived for an arbitrary deformation field. The conditions are specified under which the influence of the deformation is considerable. The case is considered in detail when the photon enters into the crystal at small angles with respect to a crystallographic axis. The results of the numerical calculations are presented for $\\mathrm{SiO}_{2}$ single crystal and Moliere parametrization of the screened atomic potentials in the case of the deformation field generated by the acoustic wave of $S$ type. In dependence of the parameters, the presence of deformation can either enhance or reduce the pair creation cross-section. This can be used to control the parameters of the positron sources for storage rings and colliders.

  20. An ID-based Blind Signature Scheme from Bilinear Pairings

    Directory of Open Access Journals (Sweden)

    B.Umaprasada Rao

    2010-03-01

    Full Text Available Blind signatures, introduced by Chaum, allow a user to obtain a signature on a message without revealing any thing about the message to the signer. Blind signatures play on important role in plenty of applications such as e-voting, e-cash system where anonymity is of great concern. Identity based(ID-based public key cryptography can be a good alternative for certified based public key setting, especially when efficient key management and moderate security are required. In this paper, we propose an ID-based blind signature scheme from bilinear pairings. The proposed scheme is based on the Hess ID- based digital signature scheme. Also we analyze security and efficiency of the proposed scheme.

  1. Three 3D hybrid networks based on octamolybdates and different CuI/CuII-bis(triazole) motifs

    International Nuclear Information System (INIS)

    Three 3D compounds based on octamolybdate clusters and various CuI/CuII-bis(triazole) motifs, [CuI2btb][β-Mo8O26]0.5 (1), [CuI2btpe][β-Mo8O26]0.5 (2), and [CuII(btpe)2][β-Mo8O26]0.5 (3) [btb=1,4-bis(1,2,4-triazol-1-yl)butane, btpe=1,5-bis(1,2,4-triazol-1-yl)pentane], were isolated via tuning flexible ligand spacer length and metal coordination preferences. In 1, the copper(I)-btb motif is a one-dimensional (1D) chain which is further linked by hexadentate β-[Mo8O26]4- clusters via coordinating to CuI cations giving a 3D structure. In 2, the copper(I)-btpe motif exhibits a 'stairs'-like [CuI2btpe]2+ sheet, and the tetradentate β-[Mo8O26]4- clusters interact with two neighboring [CuI2btpe]2+ sheets constructing a 3D framework. In 3, the copper(II)-btpe motif possesses a novel (2D→3D) interdigitated structure, which is further connected by the tetradentate β-[Mo8O26]4- clusters forming a 3D framework. The thermal stability and luminescent properties of 1-3 are investigated in the solid state. -- Graphical abstract: Three 3D compounds based on β-[Mo8O26]4- clusters with different CuI/CuII-bis(triazole) motifs were synthesized by regularly tuning flexible ligand spacer length and metal coordination preferences. Display Omitted

  2. ExactSearch: a web-based plant motif search tool

    OpenAIRE

    Gunasekara, Chathura; Subramanian, Avinash; Avvari, Janaki Venkata Ram Kumar; Li, Bin; Chen, Su; Wei, Hairong

    2016-01-01

    Background Plant biologists frequently need to examine if a sequence motif bound by a specific transcription or translation factor is present in the proximal promoters or 3′ untranslated regions (3′ UTR) of a set of plant genes of interest. To achieve such a task, plant biologists have to not only identify an appropriate algorithm for motif searching, but also manipulate the large volume of sequence data, making it burdensome to carry out or fulfill. Result In this study, we developed a web p...

  3. Physics of base-pairing dynamics in DNA

    Science.gov (United States)

    Manghi, Manoel; Destainville, Nicolas

    2016-05-01

    As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque-driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain orientational degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain orientational degrees of freedom can be integrated out, and the quasi-static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.

  4. Mining protein sequences for motifs.

    Science.gov (United States)

    Narasimhan, Giri; Bu, Changsong; Gao, Yuan; Wang, Xuning; Xu, Ning; Mathee, Kalai

    2002-01-01

    We use methods from Data Mining and Knowledge Discovery to design an algorithm for detecting motifs in protein sequences. The algorithm assumes that a motif is constituted by the presence of a "good" combination of residues in appropriate locations of the motif. The algorithm attempts to compile such good combinations into a "pattern dictionary" by processing an aligned training set of protein sequences. The dictionary is subsequently used to detect motifs in new protein sequences. Statistical significance of the detection results are ensured by statistically determining the various parameters of the algorithm. Based on this approach, we have implemented a program called GYM. The Helix-Turn-Helix motif was used as a model system on which to test our program. The program was also extended to detect Homeodomain motifs. The detection results for the two motifs compare favorably with existing programs. In addition, the GYM program provides a lot of useful information about a given protein sequence. PMID:12487759

  5. Large-scale organization of rat sensorimotor cortex based on a motif of large activation spreads.

    Science.gov (United States)

    Frostig, Ron D; Xiong, Ying; Chen-Bee, Cynthia H; Kvasnák, Eugen; Stehberg, Jimmy

    2008-12-01

    Parcellation according to function (e.g., visual, somatosensory, auditory, motor) is considered a fundamental property of sensorimotor cortical organization, traditionally defined from cytoarchitectonics and mapping studies relying on peak evoked neuronal activity. In the adult rat, stimulation of single whiskers evokes peak activity at topographically appropriate locations within somatosensory cortex and provides an example of cortical functional specificity. Here, we show that single whisker stimulation also evokes symmetrical areas of suprathreshold and subthreshold neuronal activation that spread extensively away from peak activity, effectively ignoring cortical borders by spilling deeply into multiple cortical territories of different modalities (auditory, visual and motor), where they were blocked by localized neuronal activity blocker injections and thus ruled out as possibly caused by "volume conductance." These symmetrical activity spreads were supported by underlying border-crossing, long-range horizontal connections as confirmed with transection experiments and injections of anterograde neuronal tracer experiments. We found such large evoked activation spreads and their underlying connections regardless of whisker identity, cortical layer, or axis of recorded responses, thereby revealing a large scale nonspecific organization of sensorimotor cortex based on a motif of large symmetrical activation spreads. Because the large activation spreads and their underlying horizontal connections ignore anatomical borders between cortical modalities, sensorimotor cortex could therefore be viewed as a continuous entity rather than a collection of discrete, delineated unimodal regions, an organization that could coexist with established specificity of cortical organization and that could serve as a substrate for associative learning, direct multimodal integration and recovery of function after injury. PMID:19052219

  6. Treatment of pairing correlations based on the equations of motion for zero-coupled pair operators

    International Nuclear Information System (INIS)

    The pairing problem is treated by means of the equations of motion for zero-coupled pair operators. Exact equations for the seniority-v states of N particles are derived. These equations can be solved by a step-by-step procedure which consists of progressively adding pairs of particles to a core. The theory can be applied at several levels of approximation depending on the number of core states which are taken into account. Some numerical applications to the treatment of v = 0, v = 1, and v = 2 states in the Ni isotopes are performed. The accuracy of various approximations is tested by comparison with exact results. For the seniority-one and seniority-two problems it turns out that the results obtained from the first-order theory are very accurate, while those of higher order calculations are practically exact. Concerning the seniority-zero problem, a fifth-order calculation reproduces quite well the three lowest states

  7. Treatment of pairing correlations based on the equations of motion for zero-coupled pair operators

    Energy Technology Data Exchange (ETDEWEB)

    Andreozzi, F.; Covello, A.; Gargano, A.; Ye, L.J.; Porrino, A.

    1985-07-01

    The pairing problem is treated by means of the equations of motion for zero-coupled pair operators. Exact equations for the seniority-v states of N particles are derived. These equations can be solved by a step-by-step procedure which consists of progressively adding pairs of particles to a core. The theory can be applied at several levels of approximation depending on the number of core states which are taken into account. Some numerical applications to the treatment of v = 0, v = 1, and v = 2 states in the Ni isotopes are performed. The accuracy of various approximations is tested by comparison with exact results. For the seniority-one and seniority-two problems it turns out that the results obtained from the first-order theory are very accurate, while those of higher order calculations are practically exact. Concerning the seniority-zero problem, a fifth-order calculation reproduces quite well the three lowest states.

  8. Single base pair mutation analysis by PNA directed PCR clamping

    DEFF Research Database (Denmark)

    Ørum, H.; Nielsen, P.E.; Egholm, M.; Berg, R.H.; Buchardt, O.; Stanley, C.

    1993-01-01

    A novel method that allows direct analysis of single base mutation by the polymerase chain reaction (PCR) is described. The method utilizes the finding that PNAs (peptide nucleic acids) recognize and bind to their complementary nucleic acid sequences with higher thermal stability and specificity...... than the corresponding deoxyribooligonucleotides and that they cannot function as primers for DNA polymerases. We show that a PNA/DNA complex can effectively block the formation of a PCR product when the PNA is targeted against one of the PCR primer sites. Furthermore, we demonstrate that this blockage...... allows selective amplification/suppression of target sequences that differ by only one base pair. Finally we show that PNAs can be designed in such a way that blockage can be accomplished when the PNA target sequence is located between the PCR primers....

  9. Nonclassically paired photons from sources based on cold atoms

    Science.gov (United States)

    Głódź, Małgorzata; Janowicz, Maciej; Kowalski, Krzysztof; Szonert, Jerzy

    2015-01-01

    In this short review some essentials concerning creation and testing of nonclassically correlated photons (biphotons) are given. In the introduction we remind the role which the experimentally produced entangled states have been playing for the foundations of the quantum physics, by witnessing against the model of local hidden variables. The well established sources of biphotons are based on spontaneous parametric down conversion in nonlinear crystals. A popular source with two BBO crystals is described, which generates pairs of photons nearly maximally entangled in polarization. Crystalbased sources rely on intrinsically broadband transitions, therefore thus produced biphotons are also broadband. Additional efforts (like applying optical cavities) are needed to reach narrowband biphotons which would comply with the requirements of some implementations in the quantum communication science. The topical issue of our article is a review of another, more recent approaches based on narrowband transitions between levels in cold atoms. Such method provides naturally narrowband biphotons. First, the principles are given of an atomic source of nonclassically paired photons, which is operated in a pulsed write-read mode. Such source is based on two separated in time Raman transitions triggered successively in two Λ-schemes. Next, cw-mode sources based (mainly) on spontaneous four wave mixing process (SFWM) are presented in a generic four-level scheme. Some underlying physics is sketched and profiles of biphoton correlation functions in the time domain are explained. Among other presented SFWM sources, one proves in testing high degree entanglement of generated biphotons, both in time-frequency and polarization (hyperentanglement).

  10. SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

    OpenAIRE

    Davey, Norman E.; Cowan, Joanne L; Shields, Denis C.; Gibson, Toby J.; Coldwell, Mark J; Edwards, Richard J

    2012-01-01

    Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use ...

  11. HMM-based prediction for protein structural motifs' two local properties: solvent accessibility and backbone torsion angles.

    Science.gov (United States)

    Yu, Jianyong; Xiang, Leijun; Hong, Jiang; Zhang, Weidong

    2013-02-01

    Protein structure prediction is often assisted by predicting one-dimensional structural properties including relative solvent accessibility (RSA) surface and backbone torsion angles (BTA) of residues, and these two properties are continuously varying variables because proteins can move freely in a three-dimensional space. Instead of subdividing them into a few arbitrarily defined states that many popular approaches used, this paper proposes an integrated system for realvalue prediction of protein structural motifs' two local properties, based on the modified Hidden Markov Model that we previously presented. The model was used to capture the relevance of RSA and the dependency of BTA between adjacent residues along the local protein chain in motifs with definite probabilities. These two properties were predicted according to their own probability distribution. The method was applied to a protein fragment library. For nine different classes of motifs, real values of RSA were predicted with mean absolute error (MAE) of 0.122-0.175 and Pearson's correlation coefficient (PCC) of 0.623-0.714 between predicted and actual RSA. Meanwhile, real values of BTA were obtained with MAE of 8.5⁰-29.4⁰ for Φ angles, 11.2⁰-38.5⁰ for ψ angles and PCC of 0.601-0.716 for Φ, 0.597-0.713 for ψ. The results were compared with well-known Real-SPINE Server, and indicate the proposed method may at least serve as the foundation to obtain better local properties from structural motifs for protein structure prediction. PMID:22894152

  12. Paired structures and other opposite-based models

    DEFF Research Database (Denmark)

    Rodríguez, J. Tinguaro; Franco, Camilo; Gómez, Daniel;

    2015-01-01

    In this paper we present a new class of fuzzy sets, paired fuzzy sets, that tries to overcome any conflict between families of fuzzy sets that share a main characteristic: that they are generated from two basic opposite fuzzy sets. Hence, the first issue is to formalize the notion of opposition, ...... viewed as a particular paired structure when the classical fuzzy negation is considered; on the other hand, the relationship of this model with bipolarity is reconsidered from our paired view....

  13. Structure, stability, and dynamics of canonical and noncanonical base pairs: quantum chemical studies.

    Science.gov (United States)

    Roy, Ashim; Panigrahi, Swati; Bhattacharyya, Malyasri; Bhattacharyya, Dhananjay

    2008-03-27

    The importance of non-Watson-Crick base pairs in the three-dimensional structure of RNA is now well established. The structure and stability of these noncanonical base pairs are, however, poorly understood. We have attempted to understand structural features of 33 frequently occurring base pairs using density functional theory. These are of three types, namely (i) those stabilized by two or more polar hydrogen bonds between the bases, (ii) those having one polar and another C-H...O/N type interactions, and (iii) those having one H-bond between the bases and another involving one of the sugars linked to the bases. We found that the base pairs having two polar H-bonds are very stable as compared to those having one C-H...O/N interaction. Our quantitatively analysis of structures of these optimized base pairs indicates that they possess a different amount of nonplanarity with large propeller or buckle values as also observed in the crystal structures. We further found that geometry optimization does not modify the hydrogen-bonding pattern, as values of shear and open angle of the base pairs remain conserved. The structures of initial crystal geometry and final optimized geometry of some base pairs having only one polar H-bond and a C-H...O/N interaction, however, are significantly different, indicating the weak nature of the nonpolar interaction. The base pair flexibility, as measured from normal-mode analysis, in terms of the intrinsic standard deviations of the base pair structural parameters are in conformity with those calculated from RNA crystal structures. We also noticed that deformation of a base pair along the stretch direction is impossible for all of the base pairs, and movements of the base pairs along shear and open are also quite restricted. The base pair opening mode through alteration of propeller or buckle is considerably less restricted for most of the base pairs. PMID:18318519

  14. Base pairing in RNA structures: A computational analysis of structural aspects and interaction energies

    Indian Academy of Sciences (India)

    Purshotam Sharma; Abhijit Mitra; Sitansh Sharma; Harjinder Singh

    2007-09-01

    The base pairing patterns in RNA structures are more versatile and completely different as compared to DNA. We present here results of ab-initio studies of structures and interaction energies of eight selected RNA base pairs reported in literature. Interaction energies, including BSSE correction, of hydrogen added crystal geometries of base pairs have been calculated at the HF/6-31G∗∗ level. The structures and interaction energies of the base pairs in the crystal geometry are compared with those obtained after optimization of the base pairs. We find that the base pairs become more planar on full optimization. No change in the hydrogen bonding pattern is seen. It is expected that the inclusion of appropriate considerations of many of these aspects of RNA base pairing would significantly improve the accuracy of RNA secondary structure prediction.

  15. Detecting the bipartite World Trade Web evolution across 2007: a motifs-based analysis

    CERN Document Server

    Saracco, Fabio; Gabrielli, Andrea; Squartini, Tiziano

    2015-01-01

    In the present paper we employ the theoretical tools developed in network theory, in order to shed light on the response of world wide trade to the financial crisis of 2007. In particular, we have explored the evolution of the bipartite country-product World Trade Web across the years 1995-2010, monitoring the behaviour of the system both before and after 2007. Remarkably, our results indicate that, from 2003 on, the abundances of a recently-defined class of bipartite motifs assume values progressively closer to the ones predicted by a null model which preserves only basic features of the observed structure, completely randomizing the rest. In other words, as 2007 approaches the World Trade Web becomes more and more compatible with the picture of a bipartite network where correlations between countries and products are progressively lost. Moreover, the trends characterizing the z-scores of the considered family of motifs suggest that the most evident modification in the structure of the world trade network ca...

  16. Spliceosomal small nuclear RNAs of Tetrahymena thermophila and some possible snRNA-snRNA base-pairing interactions

    DEFF Research Database (Denmark)

    Orum, H; Nielsen, Henrik; Engberg, J

    1991-01-01

    We have identified and characterized the full set of spliceosomal small nuclear RNAs (snRNAs; U1, U2, U4, U5 and U6) from the ciliated protozoan Tetrahymena thermophila. With the exception of U4 snRNA, the sizes of the T. thermophila snRNAs are closely similar to their metazoan homologues. The T....... thermophila snRNAs all have unique 5' ends, which start with an adenine residue. In contrast, with the exception of U6, their 3' ends show some size heterogeneity. The primary sequences of the T. thermophila snRNAs contain the sequence motifs shown, or proposed, to be of functional importance in other...... organisms. Furthermore, secondary structures closely similar to phylogenetically proven models can be inferred from the T. thermophila data. Analysis of the snRNA sequences identifies three potential snRNA-snRNA base-pairing interactions, all of which are consistent with available phylogenetic data. Two of...

  17. Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family.

    Science.gov (United States)

    Sponer, Judit E; Spacková, Nad'a; Kulhanek, Petr; Leszczynski, Jerzy; Sponer, Jirí

    2005-03-17

    Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/6-31G and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2'-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearly isoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2'-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions. PMID:16838999

  18. A fluorescence glucose sensor based on pH induced conformational switch of i-motif DNA.

    Science.gov (United States)

    Ke, Qingqing; Zheng, Yu; Yang, Fan; Zhang, Hanchang; Yang, Xiurong

    2014-11-01

    A facile fluorescence biosensor for the detection of glucose is proposed based on the pH-induced conformational switch of i-motif DNA in this paper. Glucose can be oxidized by oxygen (O2) in the presence of glucose oxidase (GOD), and the generated gluconic acid can decrease the pH value of the solution and then induce the fluorophore- and quencher-labeled cytosine-rich single-stranded DNA to fold into a close-packed i-motif structure. As a result, the fluorescence quenching occurs because of the resonance energy transfer between fluorophore and quencher. Based on this working principle, the concentration of glucose can be detected by the decrease of fluorescence density. Under the optimal experimental conditions, the assay shows a linear response range of 5-100 µM for the glucose concentration with a detection limit of 4 µM. This glucose biosensor was applied to determine glucose in real samples successfully, suggesting its potential in the practical applicability. PMID:25127630

  19. Structural alphabet motif discovery and a structural motif database.

    Science.gov (United States)

    Ku, Shih-Yen; Hu, Yuh-Jyh

    2012-01-01

    This study proposes a general framework for structural motif discovery. The framework is based on a modular design in which the system components can be modified or replaced independently to increase its applicability to various studies. It is a two-stage approach that first converts protein 3D structures into structural alphabet sequences, and then applies a sequence motif-finding tool to these sequences to detect conserved motifs. We named the structural motif database we built the SA-Motifbase, which provides the structural information conserved at different hierarchical levels in SCOP. For each motif, SA-Motifbase presents its 3D view; alphabet letter preference; alphabet letter frequency distribution; and the significance. SA-Motifbase is available at http://bioinfo.cis.nctu.edu.tw/samotifbase/. PMID:22099701

  20. Flexibility of short DNA helices with finite-length effect: from base pairs to tens of base pairs

    CERN Document Server

    Wu, Yuan-Yan; Zhang, Xi; Tan, Zhi-Jie

    2015-01-01

    Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5 to 50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ~6 bps at each helix end. Correspondingly, the apparent persistence length lp of short DNAs increases gradually from ~29nm to ~45nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ~6 bps at each helix end have...

  1. Design of potent inhibitors of human RAD51 recombinase based on BRC motifs of BRCA2 protein: modeling and experimental validation of a chimera peptide.

    KAUST Repository

    Nomme, Julian

    2010-08-01

    We have previously shown that a 28-amino acid peptide derived from the BRC4 motif of BRCA2 tumor suppressor inhibits selectively human RAD51 recombinase (HsRad51). With the aim of designing better inhibitors for cancer treatment, we combined an in silico docking approach with in vitro biochemical testing to construct a highly efficient chimera peptide from eight existing human BRC motifs. We built a molecular model of all BRC motifs complexed with HsRad51 based on the crystal structure of the BRC4 motif-HsRad51 complex, computed the interaction energy of each residue in each BRC motif, and selected the best amino acid residue at each binding position. This analysis enabled us to propose four amino acid substitutions in the BRC4 motif. Three of these increased the inhibitory effect in vitro, and this effect was found to be additive. We thus obtained a peptide that is about 10 times more efficient in inhibiting HsRad51-ssDNA complex formation than the original peptide.

  2. Raising the barrier for photoinduced DNA charge injection with a cyclohexyl artificial base pair.

    Science.gov (United States)

    Singh, Arunoday P N; Harris, Michelle A; Young, Ryan M; Miller, Stephen A; Wasielewski, Michael R; Lewis, Frederick D

    2015-01-01

    The effects of an artificial cyclohexyl base pair on the quantum yields of fluorescence and dynamics of charge separation and charge recombination have been investigated for several synthetic DNA hairpins. The hairpins possess stilbenedicarboxamide, perylenediimide, or naphthalenediimide linkers and base-paired stems. In the absence of the artificial base pair hole injection into both adenine and guanine purine bases is exergonic and irreversible, except in the case of stilbene with adenine for which it is slightly endergonic and reversible. Insertion of the artificial base pair renders hole injection endergonic or isoergonic except in the case of the powerful naphthalene acceptor for which it remains exergonic. Both hole injection and charge recombination are slower for the naphthalene acceptor in the presence of the artificial base pair than in its absence. The effect of an artificial base pair on charge separation and charge recombination in hairpins possessing stilbene and naphthalene acceptor linkers and a stilbenediether donor capping group has also been investigated. In the case of the stilbene acceptor-stilbene donor capped hairpins photoinduced charge separation across six base pairs is efficient in the absence of the artificial base pair but does not occur in its presence. In the case of the naphthalene acceptor-stilbene donor capped hairpins the artificial base pair slows but does not stop charge separation and charge recombination, leading to the formation of long-lived charge separated states. PMID:26442603

  3. Comparable Stability of Hoogsteen and Watson–Crick Base Pairs in Ionic Liquid Choline Dihydrogen Phosphate

    OpenAIRE

    Hisae Tateishi-Karimata; Miki Nakano; Naoki Sugimoto

    2014-01-01

    The instability of Hoogsteen base pairs relative to Watson–Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson–Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stabi...

  4. Predicting kinase activity in angiotensin receptor phosphoproteomes based on sequence-motifs and interactions.

    Directory of Open Access Journals (Sweden)

    Rikke Bøgebo

    Full Text Available Recent progress in the understanding of seven-transmembrane receptor (7TMR signalling has promoted the development of a new generation of pathway selective ligands. The angiotensin II type I receptor (AT1aR is one of the most studied 7TMRs with respect to selective activation of the β-arrestin dependent signalling. Two complimentary global phosphoproteomics studies have analyzed the complex signalling induced by the AT1aR. Here we integrate the data sets from these studies and perform a joint analysis using a novel method for prediction of differential kinase activity from phosphoproteomics data. The method builds upon NetworKIN, which applies sophisticated linear motif analysis in combination with contextual network modelling to predict kinase-substrate associations with high accuracy and sensitivity. These predictions form the basis for subsequently nonparametric statistical analysis to identify likely activated kinases. This suggested that AT1aR-dependent signalling activates 48 of the 285 kinases detected in HEK293 cells. Of these, Aurora B, CLK3 and PKG1 have not previously been described in the pathway whereas others, such as PKA, PKB and PKC, are well known. In summary, we have developed a new method for kinase-centric analysis of phosphoproteomes to pinpoint differential kinase activity in large-scale data sets.

  5. MODIS: an audio motif discovery software

    OpenAIRE

    Catanese, Laurence; Souviraà-Labastie, Nathan; Qu, Bingqing; Campion, Sébastien; Gravier, Guillaume; Vincent, Emmanuel; Bimbot, Frédéric

    2013-01-01

    International audience MODIS is a free speech and audio motif discovery software developed at IRISA Rennes. Motif discovery is the task of discovering and collecting occurrences of repeating patterns in the absence of prior knowledge, or training material. MODIS is based on a generic approach to mine repeating audio sequences, with tolerance to motif variability. The algorithm implementation allows to process large audio streams at a reasonable speed where motif discovery often requires hu...

  6. Stabilization of i-motif structures by 2′-β-fluorination of DNA

    Science.gov (United States)

    Assi, Hala Abou; Harkness, Robert W.; Martin-Pintado, Nerea; Wilds, Christopher J.; Campos-Olivas, Ramón; Mittermaier, Anthony K.; González, Carlos; Damha, Masad J.

    2016-01-01

    i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH+). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies. At neutral and basic pH values, the cytosine bases deprotonate and the structure unfolds into single strands. To avoid this limitation and expand the range of environmental conditions supporting i-motif folding, we replaced the sugar in DNA by 2-deoxy-2-fluoroarabinose. We demonstrate that such a modification significantly stabilizes i-motif formation over a wide pH range, including pH 7. Nuclear magnetic resonance experiments reveal that 2-deoxy-2-fluoroarabinose adopts a C2′-endo conformation, instead of the C3′-endo conformation usually found in unmodified i-motifs. Nevertheless, this substitution does not alter the overall i-motif structure. This conformational change, together with the changes in charge distribution in the sugar caused by the electronegative fluorine atoms, leads to a number of favorable sequential and inter-strand electrostatic interactions. The availability of folded i-motifs at neutral pH will aid investigations into the biological function of i-motifs in vitro, and will expand i-motif applications in nanotechnology. PMID:27166371

  7. Predicting the Mechanism and Kinetics of the Watson-Crick to Hoogsteen Base Pairing Transition

    NARCIS (Netherlands)

    J. Vreede; P.G. Bolhuis; D.W.H. Swenson

    2016-01-01

    DNA duplexes predominantly contain Watson-Crick (WC) base pairs. Yet, a non-negligible number of base pairs converts to the Hoogsteen (HG) hydrogen bonding pattern, involving a 180° rotation of the purine base relative to Watson-Crick. These WC to HG conversions alter the conformation of DNA, and ma

  8. Roles of ion pairing on electroreduction of carbon dioxide based on imidazolium-based salts

    International Nuclear Information System (INIS)

    Highlights: • The significant electrocatalytic effects of imidazolium salts are due to a strong ion-pairing. • DFT calculation predicts the ion pair [BMIM+][CO2.−] conformation. • The extent of ion-pairing decreases with increasing the size of the alkyl substituent. - Abstract: The roles of ion pairing on CO2 electroreduction involving imidazolium-based salts are explored on an Ag electrode in a DMF solution. The electroreductive behaviours of CO2 and the IR results establish the dominant role of the cation of imidazolium-based salts in CO2 electrocatalytic reduction process. Density functional theory (DFT) calculations predict that the ion pair formation is mainly driven by the attraction of the four nearby and positively charged hydrogen atoms which are at the C2, N1 and N3-positions of an imidazolium cation for the negatively charged oxygen atoms in the CO2.− species. The electrostatic interaction between an imidazolium cation and the CO2.− species decreases with increasing the size of the alkyl substituent at the N1-position of that imidazolium cation

  9. Plasmodium vivax antigen discovery based on alpha-helical coiled coil protein motif.

    Directory of Open Access Journals (Sweden)

    Nora Céspedes

    Full Text Available Protein α-helical coiled coil structures that elicit antibody responses, which block critical functions of medically important microorganisms, represent a means for vaccine development. By using bioinformatics algorithms, a total of 50 antigens with α-helical coiled coil motifs orthologous to Plasmodium falciparum were identified in the P. vivax genome. The peptides identified in silico were chemically synthesized; circular dichroism studies indicated partial or high α-helical content. Antigenicity was evaluated using human sera samples from malaria-endemic areas of Colombia and Papua New Guinea. Eight of these fragments were selected and used to assess immunogenicity in BALB/c mice. ELISA assays indicated strong reactivity of serum samples from individuals residing in malaria-endemic regions and sera of immunized mice, with the α-helical coiled coil structures. In addition, ex vivo production of IFN-γ by murine mononuclear cells confirmed the immunogenicity of these structures and the presence of T-cell epitopes in the peptide sequences. Moreover, sera of mice immunized with four of the eight antigens recognized native proteins on blood-stage P. vivax parasites, and antigenic cross-reactivity with three of the peptides was observed when reacted with both the P. falciparum orthologous fragments and whole parasites. Results here point to the α-helical coiled coil peptides as possible P. vivax malaria vaccine candidates as were observed for P. falciparum. Fragments selected here warrant further study in humans and non-human primate models to assess their protective efficacy as single components or assembled as hybrid linear epitopes.

  10. Tunnel Conductance of Watson-Crick Nucleoside-Base Pairs from Telegraph Noise

    OpenAIRE

    Chang, Shuai; He, Jin; Lin, Lisha; Zhang, Peiming; Liang, Feng; Young, Michael; Huang, Shuo; Lindsay, Stuart

    2009-01-01

    The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base-pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive ...

  11. lsosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin Ricin Internal Loop

    Czech Academy of Sciences Publication Activity Database

    Havrila, Marek; Réblová, Kamila; Zirbel, C.L.; Leontis, B. N.; Šponer, Jiří

    2013-01-01

    Roč. 117, č. 46 (2013), s. 14302-14319. ISSN 1520-6106 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : 23S RIBOSOMAL-RNA * PARTICLE MESH EWALD * NUCLEIC-ACIDS Subject RIV: BO - Biophysics Impact factor: 3.377, year: 2013

  12. lsosteric and Nonisosteric Base Pairs in RNA Motifs: Molecular Dynamics and Bioinformatics Study of the Sarcin Ricin Internal Loop

    Czech Academy of Sciences Publication Activity Database

    Havrila, Marek; Réblová, K.; Zirbel, C.L.; Leontis, N. B.

    2013-01-01

    Roč. 117, č. 46 (2013), s. 14302-14319. ISSN 1520-6106 R&D Projects: GA ČR GBP305/12/G034; GA MŠk ED1.1.00/02.0068 Institutional research plan: CEZ:AV0Z50040702 Institutional support: RVO:68081707 Keywords : 23S RIBOSOMAL-RNA * PARTICLE MESH EWALD * NUCLEIC-ACIDS Subject RIV: BO - Biophysics Impact factor: 3.377, year: 2013

  13. Conducting Task-Based Interviews with Pairs of Children: Consensus, Conflict, Knowledge Construction and Turn Taking

    Science.gov (United States)

    Houssart, Jenny; Evens, Hilary

    2011-01-01

    This article explores theoretical and methodological issues associated with task-based interviews conducted with pairs of children. We explore different approaches to interviews from sociological, psychological and subject-based perspectives. Our interviews, concerning mathematical questions and carried out with pairs of 10 and 11-year-olds, are…

  14. A novel pseudo-complementary PNA G-C base pair

    DEFF Research Database (Denmark)

    Olsen, Anne G.; Dahl, Otto; Petersen, Asger Bjørn; Nielsen, John; Nielsen, Peter E.

    2011-01-01

    Pseudo-complementary oligonucleotide analogues and mimics provide novel opportunities for targeting duplex structures in RNA and DNA. Previously, a pseudo-complementary A-T base pair has been introduced. Towards sequence unrestricted targeting, a pseudo-complementary G-C base pair consisting of the...

  15. Development of artificial nucleic acid that recognizes a CG base pair in triplex DNA formation.

    Science.gov (United States)

    Hari, Yoshiyuki

    2013-01-01

    An oligonucleotide that can form a triplex with double-stranded DNA is called a triplex-forming oligonucleotide (TFO). TFOs have gained considerable attention because of their potential as gene targeting tools. However, triplex DNA formation involves inherent problems for practical use. The most important problem is that natural nucleotides in TFO do not have sufficient affinity and base pair-selectivity to pyrimidine-purine base pair, like a CG or TA base pair, within dsDNA. This suggests that dsDNA region including a CG or TA base pair cannot be targeted. Therefore, artificial nucleotides, especially with non-natural nucleobases, capable of direct recognition of a CG or TA base pair via hydrogen bond formation have been developed; however, nucleotides with better selectivity and stronger affinity are necessary for implementing this dsDNA-targeting technology using TFOs. Under such a background, we considered that facile and efficient synthesis of various nucleobase derivatives in TFOs would be useful for finding an ideal nucleobase for recognition of a CG or TA base pair because detailed and rational exploration of nucleobase structures is facilitated. Recently, to develop a nucleobase recognizing a CG base pair, we have used post-elongation modification, i.e., modification after oligonucleotide synthesis, for the facile synthesis of nucleobase derivatives. This review mainly summarizes our recent findings on the development of artificial nucleobases and nucleotides for recognition of a CG base pair in triplexes formed between dsDNA and TFOs. PMID:24189561

  16. The Impact of a Peer-Learning Agent Based on Pair Programming in a Programming Course

    Science.gov (United States)

    Han, Keun-Woo; Lee, EunKyoung; Lee, YoungJun

    2010-01-01

    This paper analyzes the educational effects of a peer-learning agent based on pair programming in programming courses. A peer-learning agent system was developed to facilitate the learning of a programming language through the use of pair programming strategies. This system is based on the role of a peer-learning agent from pedagogical and…

  17. Theory of tunneling across hydrogen-bonded base pairs for DNA recognition and sequencing

    Science.gov (United States)

    Lee, Myeong H.; Sankey, Otto F.

    2009-05-01

    We present the results of first-principles calculations for the electron tunnel current through hydrogen-bonded DNA base pairs and for (deoxy)nucleoside-nucleobase pairs. Electron current signals either through a base pair or through a deoxynucleoside-nucleobase pair are a potential mechanism for recognition or identification of the DNA base on a single-stranded DNA polymer. Four hydrogen-bonded complexes are considered: guanine-cytosine, diaminoadenine-thymine, adenine-thymine, and guanine-thymine. First, the electron tunneling properties are examined through their complex band structure (CBS) and the metal contact’s Fermi-level alignment. For gold contacts, the metal Fermi level lies near the highest occupied molecular orbital for all DNA base pairs. The decay constant determined by the complex band structure at the gold Fermi level shows that tunnel current decays more slowly for base pairs with three hydrogen bonds (guanine-cytosine and diaminoadenine-thymine) than for base pairs with two hydrogen bonds (adenine-thymine and guanine-thymine). The decay length and its dependence on hydrogen-bond length are examined. Second, the conductance is computed using density functional theory Green’s-function scattering methods and these results agree with estimates made from the tunneling decay constant obtained from the CBS. Changing from a base pair to a deoxynucleoside-nucleobase complex shows a significant decrease in conductance. It also becomes difficult to distinguish the current signal by only the number of hydrogen bonds.

  18. A Project Risk Ranking Approach Based on Set Pair Analysis

    Institute of Scientific and Technical Information of China (English)

    Gao Feng; Chen Yingwu

    2006-01-01

    Set Pair Analysis (SPA) is a new methodology to describe and process system uncertainty. It is different from stochastic or fuzzy methods in reasoning and operation, and it has been applied in many areas recently. In this paper, the application of SPA in risk ranking is presented, which includes review of risk ranking, introduction of Connecting Degree (CD) that is a key role in SPA., Arithmetic and Tendency Grade (TG) of CDs, and a risk ranking approach proposed. Finally a case analysis is presented to illustrate the reasonability of this approach. It is found that this approach is very convenient to operate, while the ranking result is more comprehensible.

  19. Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing

    Directory of Open Access Journals (Sweden)

    Shu-ichi Nakano

    2014-08-01

    Full Text Available The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I and 2'-deoxyribo-2,6-diaminopurine (D as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G•C > D•T ≈ I•C > A•T > G•T > I•T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.

  20. Covering All the Bases in Genetics: Simple Shorthands and Diagrams for Teaching Base Pairing to Biology Undergraduates

    Directory of Open Access Journals (Sweden)

    Sergei Kuchin

    2011-03-01

    Full Text Available Explaining base pairing is an important element in teaching undergraduate genetics. I propose a teaching approach that aims to close the gap between the mantra “A pairs with T, and G pairs with C” and the “intimidating” chemical diagrams. The approach offers a set of simple “shorthands” for the key bases that can be used to quickly deduce all canonical and wobble pairs that the students need to know. The approach can be further developed to analyze mutagenic mismatch pairing.

  1. Lewis pair polymerization by classical and frustrated Lewis pairs: Acid, base and monomer scope and polymerization mechanism

    KAUST Repository

    Zhang, Yuetao

    2012-01-01

    Classical and frustrated Lewis pairs (LPs) of the strong Lewis acid (LA) Al(C 6F 5) 3 with several Lewis base (LB) classes have been found to exhibit exceptional activity in the Lewis pair polymerization (LPP) of conjugated polar alkenes such as methyl methacrylate (MMA) as well as renewable α-methylene-γ-butyrolactone (MBL) and γ-methyl- α-methylene-γ-butyrolactone (γ-MMBL), leading to high molecular weight polymers, often with narrow molecular weight distributions. This study has investigated a large number of LPs, consisting of 11 LAs as well as 10 achiral and 4 chiral LBs, for LPP of 12 monomers of several different types. Although some more common LAs can also be utilized for LPP, Al(C 6F 5) 3-based LPs are far more active and effective than other LA-based LPs. On the other hand, several classes of LBs, when paired with Al(C 6F 5) 3, can render highly active and effective LPP of MMA and γ-MMBL; such LBs include phosphines (e.g., P tBu 3), chiral chelating diphosphines, N-heterocyclic carbenes (NHCs), and phosphazene superbases (e.g., P 4- tBu). The P 4- tBu/Al(C 6F 5) 3 pair exhibits the highest activity of the LP series, with a remarkably high turn-over frequency of 9.6 × 10 4 h -1 (0.125 mol% catalyst, 100% MMA conversion in 30 s, M n = 2.12 × 10 5 g mol -1, PDI = 1.34). The polymers produced by LPs at RT are typically atactic (P γMMBL with ∼47% mr) or syndio-rich (PMMA with ∼70-75% rr), but highly syndiotactic PMMA with rr ∼91% can be produced by chiral or achiral LPs at -78 °C. Mechanistic studies have identified and structurally characterized zwitterionic phosphonium and imidazolium enolaluminates as the active species of the current LPP system, which are formed by the reaction of the monomer·Al(C 6F 5) 3 adduct with P tBu 3 and NHC bases, respectively. Kinetic studies have revealed that the MMA polymerization by the tBu 3P/ Al(C 6F 5) 3 pair is zero-order in monomer concentration after an initial induction period, and the polymerization

  2. Steady-State Fluorescence and Lifetime Emission Study of pH-Sensitive Probes Based on i-motif Forming Oligonucleotides Single and Double Labeled with Pyrene

    OpenAIRE

    Anna Dembska; Patrycja Rzepecka; Bernard Juskowiak

    2015-01-01

    Cytosine-rich nucleic acids undergo pH-stimulated structural transitions leading to formation of an i-motif architecture at an acidic pH. Thus, i-motifs are good foundation for designing simple pH-sensitive fluorescent probes. We report here steady-state and time-resolved fluorescence studies of pyrene-labeled probes based on RET sequence: C4GC4GC4GC4TA (RET21), AC4GC4GC4GC4TA (RET21A) and C4GC4GC4GC4T (RET20). Comparative studies with single- and double-labeled i-motif probes were carried o...

  3. rMotifGen: random motif generator for DNA and protein sequences

    Directory of Open Access Journals (Sweden)

    Hardin C Timothy

    2007-08-01

    Full Text Available Abstract Background Detection of short, subtle conserved motif regions within a set of related DNA or amino acid sequences can lead to discoveries about important regulatory domains such as transcription factor and DNA binding sites as well as conserved protein domains. In order to help assess motif detection algorithms on motifs with varying properties and levels of conservation, we have developed a computational tool, rMotifGen, with the sole purpose of generating a number of random DNA or protein sequences containing short sequence motifs. Each motif consensus can be user-defined, randomly generated, or created from a position-specific scoring matrix (PSSM. Insertions and mutations within these motifs are created according to user-defined parameters and substitution matrices. The resulting sequences can be helpful in mutational simulations and in testing the limits of motif detection algorithms. Results Two implementations of rMotifGen have been created, one providing a graphical user interface (GUI for random motif construction, and the other serving as a command line interface. The second implementation has the added advantages of platform independence and being able to be called in a batch mode. rMotifGen was used to construct sample sets of sequences containing DNA motifs and amino acid motifs that were then tested against the Gibbs sampler and MEME packages. Conclusion rMotifGen provides an efficient and convenient method for creating random DNA or amino acid sequences with a variable number of motifs, where the instance of each motif can be incorporated using a position-specific scoring matrix (PSSM or by creating an instance mutated from its corresponding consensus using an evolutionary model based on substitution matrices. rMotifGen is freely available at: http://bioinformatics.louisville.edu/brg/rMotifGen/.

  4. THE CONSTRUCTIONS OF ALMOST BINARY SEQUENCE PAIRS WITH THREE-LEVEL CORRELATION BASED ON CYCLOTOMY

    Institute of Scientific and Technical Information of China (English)

    Peng Xiuping; Xu Chengqian

    2012-01-01

    In this paper,a new class of almost binary sequence pair with a single zero element is presented.The almost binary sequence pairs with three-level correlation are constructed based on cyclotomic numbers of order 2,4,and 6.Most of them have good correlation and balance property,whose maximum nontrivial correlation magnitudes are 2 and the difference between the numbers of occurrence of +1's and -1's are 0 or 1.In addition,the corresponding binary sequence pairs are investigated as well and we can also get some kinds of binary sequence pairs with optimum balance and good correlation.

  5. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.

    Science.gov (United States)

    Sarver, Michael; Zirbel, Craig L; Stombaugh, Jesse; Mokdad, Ali; Leontis, Neocles B

    2008-01-01

    New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, "Find RNA 3D" (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose

  6. Thermodynamics of the formation of Ag(I)-mediated azole base pairs in DNA duplexes.

    Science.gov (United States)

    Schweizer, Kristina; Léon, J Christian; Ravoo, Bart Jan; Müller, Jens

    2016-07-01

    Isothermal titration calorimetry was applied to determine the thermodynamic parameters for the specific binding of Ag(I) ions to a series of DNA duplexes comprising Im:Im or Tr:Tr mispairs to form metal-mediated Im-Ag(I)-Im or Tr-Ag(I)-Tr base pairs (Im=imidazole nucleoside; Tr=1.2,4-triazole nucleoside). A total of seven different duplexes are discussed, incorporating one to three artificial base pairs in neighboring or non-neighboring positions. The association constant related to the formation of Tr-Ag(I)-Tr base pairs is estimated to be <10(3)M(-1). In contrast, Im-Ag(I)-Im base pairs are much more stable. The intrinsic association constant for their formation is in the order of 10(6)M(-1) and is therefore larger than that for the formation of T-Hg(II)-T and C-Ag(I)-C base pairs consisting of natural nucleobases. Two neighboring Im-Ag(I)-Im base pairs form cooperatively, whereas two remotely located Im-Ag(I)-Im base pairs form non-cooperatively. In general, the specific binding of Ag(I) to Im:Im-containing duplexes is enthalpically driven, with a significant additional entropic contribution in most cases. PMID:27032292

  7. The conserved dileucine- and tyrosine-based motifs in MLV and MPMV envelope glycoproteins are both important to regulate a common Env intracellular trafficking

    Directory of Open Access Journals (Sweden)

    Lopez-Vergès Sandra

    2006-09-01

    Full Text Available Abstract Background Retrovirus particles emerge from the assembly of two structural protein components, Gag that is translated as a soluble protein in the cytoplasm of the host cells, and Env, a type I transmembrane protein. Because both components are translated in different intracellular compartments, elucidating the mechanisms of retrovirus assembly thus requires the study of their intracellular trafficking. Results We used a CD25 (Tac chimera-based approach to study the trafficking of Moloney murine leukemia virus and Mason-Pfizer monkey virus Env proteins. We found that the cytoplasmic tails (CTs of both Env conserved two major signals that control a complex intracellular trafficking. A dileucine-based motif controls the sorting of the chimeras from the trans-Golgi network (TGN toward endosomal compartments. Env proteins then follow a retrograde transport to the TGN due to the action of a tyrosine-based motif. Mutation of either motif induces the mis-localization of the chimeric proteins and both motifs are found to mediate interactions of the viral CTs with clathrin adaptors. Conclusion This data reveals the unexpected complexity of the intracellular trafficking of retrovirus Env proteins that cycle between the TGN and endosomes. Given that Gag proteins hijack endosomal host proteins, our work suggests that the endosomal pathway may be used by retroviruses to ensure proper encountering of viral structural Gag and Env proteins in cells, an essential step of virus assembly.

  8. Mining Conditional Phosphorylation Motifs.

    Science.gov (United States)

    Liu, Xiaoqing; Wu, Jun; Gong, Haipeng; Deng, Shengchun; He, Zengyou

    2014-01-01

    Phosphorylation motifs represent position-specific amino acid patterns around the phosphorylation sites in the set of phosphopeptides. Several algorithms have been proposed to uncover phosphorylation motifs, whereas the problem of efficiently discovering a set of significant motifs with sufficiently high coverage and non-redundancy still remains unsolved. Here we present a novel notion called conditional phosphorylation motifs. Through this new concept, the motifs whose over-expressiveness mainly benefits from its constituting parts can be filtered out effectively. To discover conditional phosphorylation motifs, we propose an algorithm called C-Motif for a non-redundant identification of significant phosphorylation motifs. C-Motif is implemented under the Apriori framework, and it tests the statistical significance together with the frequency of candidate motifs in a single stage. Experiments demonstrate that C-Motif outperforms some current algorithms such as MMFPh and Motif-All in terms of coverage and non-redundancy of the results and efficiency of the execution. The source code of C-Motif is available at: https://sourceforge. net/projects/cmotif/. PMID:26356863

  9. A cohesin-based structural platform supporting homologous chromosome pairing in meiosis.

    Science.gov (United States)

    Ding, Da-Qiao; Haraguchi, Tokuko; Hiraoka, Yasushi

    2016-08-01

    The pairing and recombination of homologous chromosomes during the meiotic prophase is necessary for the accurate segregation of chromosomes in meiosis. However, the mechanism by which homologous chromosomes achieve this pairing has remained an open question. Meiotic cohesins have been shown to affect chromatin compaction; however, the impact of meiotic cohesins on homologous pairing and the fine structures of cohesion-based chromatin remain to be determined. A recent report using live-cell imaging and super-resolution microscopy demonstrated that the lack of meiotic cohesins alters the chromosome axis structures and impairs the pairing of homologous chromosomes. These results suggest that meiotic cohesin-based chromosome axis structures are crucial for the pairing of homologous chromosomes. PMID:26856595

  10. Self-organised criticality in base-pair breathing in DNA with a defect

    CERN Document Server

    Duduiala, Ciprian-Ionut; Laughton, Charles A

    2011-01-01

    We analyse base-pair breathing in a DNA sequence of 12 base-pairs with a defective base at its centre. We use both all-atom molecular dynamics (MD) simulations and a system of stochastic differential equations (SDE). In both cases, Fourier analysis of the trajectories reveals self-organised critical behaviour in the breathing of base-pairs. The Fourier Transforms (FT) of the interbase distances show power-law behaviour with gradients close to -1. The scale-invariant behaviour we have found provides evidence for the view that base-pair breathing corresponds to the nucleation stage of large-scale DNA opening (or 'melting') and that this process is a (second-order) phase transition. Although the random forces in our SDE system were introduced as white noise, FTs of the displacements exhibit pink noise, as do the displacements in the AMBER/MD simulations.

  11. A new improved ID-based proxy ring signature scheme from bilinear pairings

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Ring signature and proxy signature are of vital importance to secure electronic commerce. Recently,the bilinear pairing such as Weil pairing or Tate pairing on elliptic curves and hyperelliptic curves is playing an important role in security solutions. Several ID-based signature schemes have been put forward, many of which are based on bilinear pairings. In key management and moderate security demand scenarios, ID-based public key cryptosystem is more preferable than other public key infrastructure based systems. In this paper, an improved ID-based proxy ring signature scheme from bilinear pairings is proposed which combines the advantages of proxy signature and of ring signatures. Our scheme can guarantee the profits of the proxy signer via preventing the original signer form generating the proxy ring signature. Furthermore, bilinear pairings are introduced to minimize the computation overhead and to improve the related performance of our scheme. In contrast with Zhang's scheme, our scheme is a computational efficiency improvement for signature verification because the computational cost of bilinear pairings required is reduced from O(n) to O( 1 ). In addition, the proxy ring signature presented in this paper can perfectly satisfy all the security requirements of proxy ring signature, i.e.signer-ambiguity, non-forgeability, verification, non-deniability and distinguishability.

  12. Intelligent Music Composition using Genetic Algorithm based on Motif Uniform Mutation

    Directory of Open Access Journals (Sweden)

    Faria Nassiri-Mofakham

    2015-03-01

    Full Text Available Nowadays, fields of music and artificial intelligence are closer together through research in both areas. Music composition using artificial intelligence (AI solutions has created a challenging research area. Automatic music composition will not only help researchers understand human’s musical thinking, but also helps composers and musicians improve music theory significantly by using the computing power of computers. In this study, an automatic music composition is presented. The system is implemented by using Markov chain and Lindenmayer systems as well as genetic algorithm. Fitness evaluation of the generated music is achord-based. The evaluations show the fast evolution of the results by genetic algorithm using uniform mutation. Creativity in music composition is beyond the present borders of AI and much work is still ahead in this field.

  13. An ID-based Blind Signature Scheme from Bilinear Pairings

    OpenAIRE

    B. Umaprasada Rao; K.A.Ajmath

    2010-01-01

    Blind signatures, introduced by Chaum, allow a user to obtain a signature on a message without revealing any thing about the message to the signer. Blind signatures play on important role in plenty of applications such as e-voting, e-cash system where anonymity is of great concern. Identity based(ID-based) public key cryptography can be a good alternative for certified based public key setting, especially when efficient key management and moderate security are required. In this paper, we prop...

  14. Conserved function of the lysine-based KXD/E motif in Golgi retention for endomembrane proteins among different organisms.

    Science.gov (United States)

    Woo, Cheuk Hang; Gao, Caiji; Yu, Ping; Tu, Linna; Meng, Zhaoyue; Banfield, David K; Yao, Xiaoqiang; Jiang, Liwen

    2015-11-15

    We recently identified a new COPI-interacting KXD/E motif in the C-terminal cytosolic tail (CT) of Arabidopsis endomembrane protein 12 (AtEMP12) as being a crucial Golgi retention mechanism for AtEMP12. This KXD/E motif is conserved in CTs of all EMPs found in plants, yeast, and humans and is also present in hundreds of other membrane proteins. Here, by cloning selective EMP isoforms from plants, yeast, and mammals, we study the localizations of EMPs in different expression systems, since there are contradictory reports on the localizations of EMPs. We show that the N-terminal and C-terminal GFP-tagged EMP fusions are localized to Golgi and post-Golgi compartments, respectively, in plant, yeast, and mammalian cells. In vitro pull-down assay further proves the interaction of the KXD/E motif with COPI coatomer in yeast. COPI loss of function in yeast and plants causes mislocalization of EMPs or KXD/E motif-containing proteins to vacuole. Ultrastructural studies further show that RNA interference (RNAi) knockdown of coatomer expression in transgenic Arabidopsis plants causes severe morphological changes in the Golgi. Taken together, our results demonstrate that N-terminal GFP fusions reflect the real localization of EMPs, and KXD/E is a conserved motif in COPI interaction and Golgi retention in eukaryotes. PMID:26378254

  15. Theory of nodal s ± -wave pairing symmetry in the Pu-based 115 superconductor family.

    Science.gov (United States)

    Das, Tanmoy; Zhu, Jian-Xin; Graf, Matthias J

    2015-01-01

    The spin-fluctuation mechanism of superconductivity usually results in the presence of gapless or nodal quasiparticle states in the excitation spectrum. Nodal quasiparticle states are well established in copper-oxide, and heavy-fermion superconductors, but not in iron-based superconductors. Here, we study the pairing symmetry and mechanism of a new class of plutonium-based high-Tc superconductors and predict the presence of a nodal s(±) wave pairing symmetry in this family. Starting from a density-functional theory (DFT) based electronic structure calculation we predict several three-dimensional (3D) Fermi surfaces in this 115 superconductor family. We identify the dominant Fermi surface "hot-spots" in the inter-band scattering channel, which are aligned along the wavevector Q = (π, π, π), where degeneracy could induce sign-reversal of the pairing symmetry. Our calculation demonstrates that the s(±) wave pairing strength is stronger than the previously thought d-wave pairing; and more importantly, this pairing state allows for the existence of nodal quasiparticles. Finally, we predict the shape of the momentum- and energy-dependent magnetic resonance spectrum for the identification of this pairing symmetry. PMID:25721375

  16. Triple helix formation: binding avidity of acridine-conjugated AG motif third strands containing natural, modified and surrogate bases opposed to pyrimidine interruptions in a polypurine target.

    OpenAIRE

    Orson, F M; Klysik, J; Bergstrom, D E; Ward, B; Glass, G A; P. Hua; Kinsey, B M

    1999-01-01

    A critical issue for the general application of triple-helix-forming oligonucleotides (TFOs) as modulators of gene expression is the dramatically reduced binding of short TFOs to targets that contain one or two pyrimidines within an otherwise homopurine sequence. Such targets are often found in gene regulatory regions, which represent desirable sites for triple helix formation. Using intercalator-conjugated AG motif TFOs, we compared the efficacy and base selectivity of 13 different bases or ...

  17. Tunnel conductance of Watson-Crick nucleoside-base pairs from telegraph noise

    International Nuclear Information System (INIS)

    The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive to the geometry of the junction, but a subset of the data appears to come from unstrained molecular pairs. The conductances determined from these pairs are within a factor of two of the predictions of density functional calculations. The experimental data reproduces the counterintuitive theoretical prediction that guanine-deoxycytidine pairs (3 H-bonds) have a smaller conductance than adenine-thymine pairs (2 H-bonds). A bimodal distribution of switching lifetimes shows that both H-bonds and molecule-metal contacts break.

  18. Tunnel conductance of Watson-Crick nucleoside-base pairs from telegraph noise.

    Science.gov (United States)

    Chang, Shuai; He, Jin; Lin, Lisha; Zhang, Peiming; Liang, Feng; Young, Michael; Huang, Shuo; Lindsay, Stuart

    2009-05-01

    The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive to the geometry of the junction, but a subset of the data appears to come from unstrained molecular pairs. The conductances determined from these pairs are within a factor of two of the predictions of density functional calculations. The experimental data reproduces the counterintuitive theoretical prediction that guanine-deoxycytidine pairs (3 H-bonds) have a smaller conductance than adenine-thymine pairs (2 H-bonds). A bimodal distribution of switching lifetimes shows that both H-bonds and molecule-metal contacts break. PMID:19420603

  19. On the internal d-wave structure of s+/- pairs in Iron-based Superconductors

    Science.gov (United States)

    Ong, Tze Tzen; Coleman, Piers

    2014-03-01

    A key issue in understanding the high temperature iron-based superconductors concerns the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. Whereas electronically paired superconductors generally avoid the Coulomb interaction through the formation of higher angular momentum pairs, iron based superconductors involve s-wave (s+/-) pairs with zero angular momentum. By taking account of the orbital degrees of freedom of the iron atoms, here we show that the s+/- pairs in these materials possess hidden d-wave symmetry, forming orbital triplets in which the the d-wave angular momentum of the pairs is compensated by the internal angular momentum of the orbitals. The recent observation of a gap with octahedral structure in KFe2As2 materials can be understood as a transition to a ``high spin'' configuration of the d-wave orbital triplets, through the alignment of the two angular momentum components of the pair. We acknowledge funding from DOE grant DE-FG02-99ER45790.

  20. Tunnel conductance of Watson-Crick nucleoside-base pairs from telegraph noise

    Science.gov (United States)

    Chang, Shuai; He, Jin; Lin, Lisha; Zhang, Peiming; Liang, Feng; Young, Michael; Huang, Shuo; Lindsay, Stuart

    2009-05-01

    The use of tunneling signals to sequence DNA is presently hampered by the small tunnel conductance of a junction spanning an entire DNA molecule. The design of a readout system that uses a shorter tunneling path requires knowledge of the absolute conductance across base pairs. We have exploited the stochastic switching of hydrogen-bonded DNA base-nucleoside pairs trapped in a tunnel junction to determine the conductance of individual molecular pairs. This conductance is found to be sensitive to the geometry of the junction, but a subset of the data appears to come from unstrained molecular pairs. The conductances determined from these pairs are within a factor of two of the predictions of density functional calculations. The experimental data reproduces the counterintuitive theoretical prediction that guanine-deoxycytidine pairs (3 H-bonds) have a smaller conductance than adenine-thymine pairs (2 H-bonds). A bimodal distribution of switching lifetimes shows that both H-bonds and molecule-metal contacts break.

  1. Entanglement and Sources of Magnetic Anisotropy in Radical Pair-Based Avian Magnetoreceptors

    CERN Document Server

    Hogben, Hannah J; Hore, P J

    2012-01-01

    One of the principal models of magnetic sensing in migratory birds rests on the quantum spin-dynamics of transient radical pairs created photochemically in ocular cryptochrome proteins. We consider here the role of electron spin entanglement and coherence in determining the sensitivity of a radical pair-based geomagnetic compass and the origins of the directional response. It emerges that the anisotropy of radical pairs formed from spin-polarized molecular triplets could form the basis of a more sensitive compass sensor than one founded on the conventional hyper?ne-anisotropy model. This property offers new and more flexible opportunities for the design of biologically inspired magnetic compass sensors.

  2. Distribution of Primes and of Interval Prime Pairs Based on $\\Theta$ Function

    CERN Document Server

    Fan, Yifang

    2010-01-01

    $\\Theta$ function is defined based upon Kronecher symbol. In light of the principle of inclusion-exclusion, $\\Theta$ function of sine function is used to denote the distribution of composites and primes. The structure of Goldbach Conjecture has been analyzed, and $\\Xi$ function is brought forward by the linear diophantine equation; by relating to $\\Theta$ function, the interval distribution of composite pairs and prime pairs (i.e. the Goldbach Conjecture) is thus obtained. In the end, Abel's Theorem (Multiplication of Series) is used to discuss the lower limit of the distribution of the interval prime pairs.

  3. Rule Based Ensembles Using Pair Wise Neural Network Classifiers

    Directory of Open Access Journals (Sweden)

    Moslem Mohammadi Jenghara

    2015-03-01

    Full Text Available In value estimation, the inexperienced people's estimation average is good approximation to true value, provided that the answer of these individual are independent. Classifier ensemble is the implementation of mentioned principle in classification tasks that are investigated in two aspects. In the first aspect, feature space is divided into several local regions and each region is assigned with a highly competent classifier and in the second, the base classifiers are applied in parallel and equally experienced in some ways to achieve a group consensus. In this paper combination of two methods are used. An important consideration in classifier combination is that much better results can be achieved if diverse classifiers, rather than similar classifiers, are combined. To achieve diversity in classifiers output, the symmetric pairwise weighted feature space is used and the outputs of trained classifiers over the weighted feature space are combined to inference final result. In this paper MLP classifiers are used as the base classifiers. The Experimental results show that the applied method is promising.

  4. Multi-hop teleportation based on W state and EPR pairs

    Science.gov (United States)

    Hai-Tao, Zhan; Xu-Tao, Yu; Pei-Ying, Xiong; Zai-Chen, Zhang

    2016-05-01

    Multi-hop teleportation has significant value due to long-distance delivery of quantum information. Many studies about multi-hop teleportation are based on Bell pairs, partially entangled pairs or W state. The possibility of multi-hop teleportation constituted by partially entangled pairs relates to the number of nodes. The possibility of multi-hop teleportation constituted by double W states is after n-hop teleportation. In this paper, a multi-hop teleportation scheme based on W state and EPR pairs is presented and proved. The successful possibility of quantum information transmitted hop by hop through intermediate nodes is deduced. The possibility of successful transmission is after n-hop teleportation. Project supported by the National Natural Science Foundation of China (Grant No. 61571105), the Prospective Future Network Project of Jiangsu Province, China (Grant No. BY2013095-1-18), and the Independent Project of State Key Laboratory of Millimeter Waves, China (Grant No. Z201504).

  5. Distribution of Primes and of Interval Prime Pairs Based on $\\Theta$ Function

    OpenAIRE

    Fan, Yifang; Li, Zhiyu

    2010-01-01

    $\\Theta$ function is defined based upon Kronecher symbol. In light of the principle of inclusion-exclusion, $\\Theta$ function of sine function is used to denote the distribution of composites and primes. The structure of Goldbach Conjecture has been analyzed, and $\\Xi$ function is brought forward by the linear diophantine equation; by relating to $\\Theta$ function, the interval distribution of composite pairs and prime pairs (i.e. the Goldbach Conjecture) is thus obtained. In the end, Abel's ...

  6. Intra-inter band pairing, order parameter symmetry in Fe-based superconductors: A model study

    International Nuclear Information System (INIS)

    Highlights: • MS deals with exciting research fields of condensed matter physics, the Fe-based superconductors. • Fe-based superconductors with multiple gaps, it is important to show why it have a singleTc. • We show the essestial requirement of both the intra and inter-band pairing channels. • Signature of the above shown in characteristic ratio, thermal behaviour of specific heat jump. - Abstract: In the quest of why there should be a single transition temperature in a multi-gapped system like Fe-based materials we use two band model for simplicity. The model comprises of spin density wave (SDW), orbital density wave (ODW) arising due to nested pieces of the electron and hole like Fermi surfaces; together with superconductivity of different pairing symmetries around electron and hole like Fermi surfaces. We show that either only intra or only inter band pairing is insufficient to describe some of the experimental results like large to small gap ratio, thermal behaviour of electronic specific heat jump etc. It is shown that the inter-band pairing is essential in Fe-based materials having multiple gaps to produce a single global Tc. Some of our results in this scenario, matches with the earlier published work (Dolgov et al., 2009), and also have differences. The origin of difference between the two is also discussed. Combined intra–inter band pairing mechanism produces the specific heat jump to superconducting transition temperature ratio proportional to square of the transition temperature, both in the electron and hole doped regime, for sign changing s± wave symmetry which takes the d + s pairing symmetry form. Our work thus demonstrates the importance of combined intra-inter band pairing irrespective of the pairing mechanism

  7. Physical implementation of pair-based spike timing dependent plasticity

    International Nuclear Information System (INIS)

    Full text: Objective Spike-timing-dependent plasticity (STOP) is one of several plasticity rules which leads to learning and memory in the brain. STOP induces synaptic weight changes based on the timing of the pre- and post-synaptic neurons. A neural network which can mimic the adaptive capability of biological brains in the temporal domain, requires the weight of single connections to be altered by spike timing. To physically realise this network into silicon, a large number of interconnected STOP circuits on the same substrate is required. This imposes two significant limitations in terms of power and area. To cover these limitations, very large scale integrated circuit (VLSI) technology provides attractive features in terms of low power and small area requirements. An example is demonstrated by (lndiveli et al. 2006). The objective of this paper is to present a new implementation of the STOP circuit which demonstrates better power and area in comparison to previous implementations. Methods The proposed circuit uses complementary metal oxide semiconductor (CMOS) technology as depicted in Fig. I. The synaptic weight can be stored on a capacitor and charging/discharging current can lead to potentiation and depression. HSpice simulation results demonstrate that the average power, peak power, and area of the proposed circuit have been reduced by 6, 8 and 15%, respectively, in comparison with Indiveri's implementation. These improvements naturally lead to packing more STOP circuits onto the same substrate, when compared to previous proposals. Hence, this new implementation is quite interesting for real-world large neural networks.

  8. Biochemical evidence for the requirement of Hoogsteen base pairing for replication by human DNA polymerase iota.

    Science.gov (United States)

    Johnson, Robert E; Prakash, Louise; Prakash, Satya

    2005-07-26

    Because of the near geometric identity of Watson-Crick (W-C) GxC and AxT base pairs, a given DNA polymerase forms the four possible correct base pairs with nearly identical catalytic efficiencies. However, human DNA polymerase iota (Pol iota), a member of the Y family of DNA polymerases, exhibits a marked template specificity, being more efficient at incorporating the correct nucleotide opposite template purines than opposite pyrimidines. By using 7-deazaadenine and 7-deazaguanine as the templating residues, which disrupt Hoogsteen base pair formation, we show that, unlike the other DNA polymerases belonging to the A, B, or Y family, DNA synthesis by Pol iota is severely inhibited by these N7-modified bases. These observations provide biochemical evidence that, during normal DNA synthesis, template purines adopt a syn conformation in the Pol iota active site, enabling the formation of a Hoogsteen base pair with the incoming pyrimidine nucleotide. Additionally, mutational studies with Leu-62, which lies in close proximity to the templating residue in the Pol iota ternary complex, have indicated that both factors, steric constraints within the active site and the stability provided by the hydrogen bonds in the Hoogsteen base pair, contribute to the efficiency of correct nucleotide incorporation opposite template purines by Pol iota. PMID:16014707

  9. Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data

    Directory of Open Access Journals (Sweden)

    de los Reyes Benildo G

    2008-04-01

    Full Text Available Abstract Background Integrating data from multiple global assays and curated databases is essential to understand the spatio-temporal interactions within cells. Different experiments measure cellular processes at various widths and depths, while databases contain biological information based on established facts or published data. Integrating these complementary datasets helps infer a mutually consistent transcriptional regulatory network (TRN with strong similarity to the structure of the underlying genetic regulatory modules. Decomposing the TRN into a small set of recurring regulatory patterns, called network motifs (NM, facilitates the inference. Identifying NMs defined by specific transcription factors (TF establishes the framework structure of a TRN and allows the inference of TF-target gene relationship. This paper introduces a computational framework for utilizing data from multiple sources to infer TF-target gene relationships on the basis of NMs. The data include time course gene expression profiles, genome-wide location analysis data, binding sequence data, and gene ontology (GO information. Results The proposed computational framework was tested using gene expression data associated with cell cycle progression in yeast. Among 800 cell cycle related genes, 85 were identified as candidate TFs and classified into four previously defined NMs. The NMs for a subset of TFs are obtained from literature. Support vector machine (SVM classifiers were used to estimate NMs for the remaining TFs. The potential downstream target genes for the TFs were clustered into 34 biologically significant groups. The relationships between TFs and potential target gene clusters were examined by training recurrent neural networks whose topologies mimic the NMs to which the TFs are classified. The identified relationships between TFs and gene clusters were evaluated using the following biological validation and statistical analyses: (1 Gene set enrichment

  10. Looped out and perpendicular: Deformation of Watson–Crick base pair associated with actinomycin D binding

    OpenAIRE

    Chou, Shan-Ho; Chin, Ko-Hsin; Chen, Fu-Ming

    2002-01-01

    Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5′-GXC/CYG-5′ complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson–Crick X/Y base pairs are looped ou...

  11. A regenerated electrochemical biosensor for label-free detection of glucose and urea based on conformational switch of i-motif oligonucleotide probe.

    Science.gov (United States)

    Gao, Zhong Feng; Chen, Dong Mei; Lei, Jing Lei; Luo, Hong Qun; Li, Nian Bing

    2015-10-15

    Improving the reproducibility of electrochemical signal remains a great challenge over the past decades. In this work, i-motif oligonucleotide probe-based electrochemical DNA (E-DNA) sensor is introduced for the first time as a regenerated sensing platform, which enhances the reproducibility of electrochemical signal, for label-free detection of glucose and urea. The addition of glucose or urea is able to activate glucose oxidase-catalyzed or urease-catalyzed reaction, inducing or destroying the formation of i-motif oligonucleotide probe. The conformational switch of oligonucleotide probe can be recorded by electrochemical impedance spectroscopy. Thus, the difference of electron transfer resistance is utilized for the quantitative determination of glucose and urea. We further demonstrate that the E-DNA sensor exhibits high selectivity, excellent stability, and remarkable regenerated ability. The human serum analysis indicates that this simple and regenerated strategy holds promising potential in future biosensing applications. PMID:26515000

  12. Discrimination of Single Base Pair Differences Among Individual DNA Molecules Using a Nanopore

    Science.gov (United States)

    Vercoutere, Wenonah; DeGuzman, Veronica

    2003-01-01

    The protein toxin alpha-hemolysin form nanometer scale channels across lipid membranes. Our lab uses a single channel in an artificial lipid bilayer in a patch clamp device to capture and examine individual DNA molecules. This nanopore detector used with a support vector machine (SVM) can analyze DNA hairpin molecules on the millisecond time scale. We distinguish duplex stem length, base pair mismatches, loop length, and single base pair differences. The residual current fluxes also reveal structural molecular dynamics elements. DNA end-fraying (terminal base pair dissociation) can be observed as near full blockades, or spikes, in current. This technique can be used to investigate other biological processes dependent on DNA end-fraying, such as the processing of HIV DNA by HIV integrase.

  13. A quantum theoretical study of reactions of methyldiazonium ion with DNA base pairs

    International Nuclear Information System (INIS)

    Graphical abstract: Reactions of methyldiazonium ion at the different sites of the DNA bases in the Watson-Crick GC and AT base pairs were investigated employing density functional and second order Moller-Plesset (MP2) perturbation theories. Display Omitted Highlights: → Methylation of the DNA bases is important as it can cause mutation and cancer. → Methylation reactions of the GC and AT base pairs with CH3N2+ were not studied earlier theoretically. → Experimental observations have been explained using theoretical methods. - Abstract: Methylation of the DNA bases in the Watson-Crick GC and AT base pairs by the methyldiazonium ion was investigated employing density functional and second order Moller-Plesset (MP2) perturbation theories. Methylation at the N3, N7 and O6 sites of guanine, N1, N3 and N7 sites of adenine, O2 and N3 sites of cytosine and the O2 and O4 sites of thymine were considered. The computed reactivities for methylation follow the order N7(guanine) > N3(adenine) > O6(guanine) which is in agreement with experiment. The base pairing in DNA is found to play a significant role with regard to reactivities of the different sites.

  14. Sub-base-pair resolution during DNA separation in an optofluidic chip

    OpenAIRE

    Pollnau, Markus; Hammer, Manfred; Dongre, Chaitanya; Hoekstra, Hugo J.W.M.

    2014-01-01

    DNA sequencing in a lab-on-a-chip aims at providing cheap, high-speed analysis of low reagent volumes to, e.g., identify genomic deletions or insertions associated with genetic illnesses. Detecting single base-pair insertions or deletions from DNA fragments in the diagnostically relevant range of 150-1000 base-pairs requires a sizing accuracy of S < 10^-3, while only S < 10^-2 were reported. Here we demonstrate a sizing accuracy of S = 4 x 10^-4, thereby paving the way for the envisaged appli...

  15. Solvent effect on the anharmonic vibrational frequencies in guanine-cytosine base pair

    Science.gov (United States)

    Bende, A.; Muntean, C. M.

    2012-02-01

    We present an ab initio study of the vibrational properties of cytosine and guanine in the Watson-Crick and Hoogsteen base pair configurations. The results are obtained by considering the DFT method together with the Polarizable Continuum Model (PCM) using PBE and B3PW91 exchange-correlation functionals and triple-ζ valence basis set. We investigate the importance of anharmonic corrections for the vibrational modes taking into account the solvent effect of the water environment. In particular, the unusual anharmonic effect of the H+ vibration in the case of the Hoogsteen base pair configuration is discussed.

  16. Fine-tuning of T-cell development by the CD3γ di-leucine-based TCR-sorting motif

    DEFF Research Database (Denmark)

    Lauritsen, Jens Peter H; Boding, Lasse; Buus, Terkild B; Kongsbak, Martin; Levring, Trine B; Rode, Anna K O; Bonefeld, Charlotte Menné; Geisler, Carsten

    2015-01-01

    negative (DN) 4 cells in CD3γLLAA mice. This was not caused by reduced proliferation but most probably by increased down-regulation of the antiapoptotic molecule Bcl-2 causing enhanced apoptosis during the transition from the DN3 to the DN4 stage. In contrast, proliferation of immature CD8 single positive...... (ISP) thymocytes was increased resulting in normal numbers of ISP in CD3γLLAA mice. Despite the normal numbers of ISP, CD3γLLAA mice had reduced numbers of double positive and SP thymocytes indicating that the CD3γ diL motif also affected later stages of T-cell development. In accordance, we found that......The CD3γ di-leucine-based (diL) receptor-sorting motif plays a central role in TCR down-regulation and in clonal expansion of virus-specific T cells. However, the role of the CD3γ diL motif in T-cell development is not known. In this study, we show that protein kinase C-induced TCR down...

  17. Comparison, Analysis and Optimization of Motif Finding Based on Different Algorithms%基于不同算法的Motif预测比较分析与优化

    Institute of Scientific and Technical Information of China (English)

    张斐; 谭军; 谢竞博

    2009-01-01

    研究转录因子结合位点(TFBs)的主要预测模型及其预测的算法,通过基于调控元件预测的3种代表性的算法MEME、Gibbs采样和Weeder预测拟南芥基因组.比较结果表明,Gibbs采样算法和Weeder算法预测长、短motif效率较高.重点分析MEME算法,提出结合不同算法查找motif的优化方法,并以实验验证该方法能有效提高预测效率.%This paper studies some models and discrimination algorithms of Transcription Factor Binding sites(TFBs). Experiment compares advantages and disadvantages in three representative discrimination algorithms which are based on regulation elements, including MEME, Gibbs sample and Weeder through predicting arabidopsis thaliana genome, against Gibbs sampling algorithm and Weeder algorithms are forecast long and short motif of the characteristics of high efficiency, MEME is intensively analyzed, and proposed an effective way to forecast motifs through MEME binding other discrimination algorithms. Experimental result proves that the method can improve the efficiency of motif finding efficiently.

  18. Strong enhancement of vibrational relaxation by Watson-Crick base pairing.

    Science.gov (United States)

    Woutersen, Sander; Cristalli, Gloria

    2004-09-15

    We have studied the ultrafast dynamics of NH-stretch vibrational excitations in Watson-Crick base pairs consisting of adenine and uracil derivatives. To estimate the influence of the A:U hydrogen bonding on the vibrational dynamics, we have also studied the uracil derivative in monomeric form. The vibrational relaxation of the NH-stretching mode is found to occur much faster in the Watson-Crick base pair than in monomeric uracil. From the delay dependence of the transient vibrational spectra, it can be concluded that both in base-paired and monomeric uracil, the energy relaxation takes place in two steps, the first step being a rapid transfer of energy from the NH-stretching mode to an accepting mode, the second step the relaxation of this accepting mode. The transient spectra show evidence that in the base pair the hydrogen bond between the nucleobases acts as the accepting mode, and that the hydrogen bonding between the bases is responsible for the extremely fast vibrational relaxation in this system. PMID:15352831

  19. Strong enhancement of vibrational relaxation by Watson-Crick base pairing

    Science.gov (United States)

    Woutersen, Sander; Cristalli, Gloria

    2004-09-01

    We have studied the ultrafast dynamics of NH-stretch vibrational excitations in Watson-Crick base pairs consisting of adenine and uracil derivatives. To estimate the influence of the A:U hydrogen bonding on the vibrational dynamics, we have also studied the uracil derivative in monomeric form. The vibrational relaxation of the NH-stretching mode is found to occur much faster in the Watson-Crick base pair than in monomeric uracil. From the delay dependence of the transient vibrational spectra, it can be concluded that both in base-paired and monomeric uracil, the energy relaxation takes place in two steps, the first step being a rapid transfer of energy from the NH-stretching mode to an accepting mode, the second step the relaxation of this accepting mode. The transient spectra show evidence that in the base pair the hydrogen bond between the nucleobases acts as the accepting mode, and that the hydrogen bonding between the bases is responsible for the extremely fast vibrational relaxation in this system.

  20. Efficient replication bypass of size-expanded DNA base pairs in bacterial cells

    OpenAIRE

    Delaney, James C.; GAO, JIANMIN; Liu, Haibo; Shrivastav, Nidhi; Essigmann, John M.; Kool, Eric T.

    2009-01-01

    Supersize me! Size-expanded DNA bases (xDNA) are able to encode natural DNA sequences in replication. In vitro experiments with a DNA polymerase show nucleotide incorporation opposite the xDNA bases with correct pairing. In vivo experiments using E. coli show that two xDNA bases (xA and xC, see picture) encode the correct replication partners.

  1. Live demonstration: Gesture-Based remote control using stereo pair of dynamic vision sensors

    OpenAIRE

    J. Lee; Delbruck, T; Park, P K J; Pfeiffer, M.; Shin, C W; Ryu, H; Kang, B C

    2012-01-01

    This demonstration shows a natural gesture interface for console entertainment devices using as input a stereo pair of dynamic vision sensors. The event-based processing of the sparse sensor output allows fluid interaction at a laptop processor load of less than 3%.

  2. DNA electronic circular dichroism on the inter-base pair scale

    DEFF Research Database (Denmark)

    Di Meo, Florent; Nørby, Morten Steen; Rubio-Magnieto, Jenifer;

    2015-01-01

    A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the...

  3. Genome filtering using methylation-sensitive restriction enzymes with six-base pair recognition sites

    Science.gov (United States)

    The large fraction of repetitive DNA in many plant genomes has complicated all aspects of DNA sequencing and assembly, and thus techniques that enrich for genes and low-copy sequences have been employed to isolate gene space. Methyl sensitive restriction enzymes with six base pair recognition sites...

  4. Free energy analysis and mechanism of base pair stacking in nicked DNA.

    Science.gov (United States)

    Häse, Florian; Zacharias, Martin

    2016-09-01

    The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and stability and its sequence dependence. Free energy simulations have been conducted on a series of double stranded DNA molecules with a central strand break (nick) in one strand. The change in free energy upon unstacking was calculated for all ten possible base pair steps using umbrella sampling along a center-of-mass separation coordinate and including a comparison of different water models. Comparison to experimental studies indicates qualitative agreement of the stability order but a general overestimation of base pair stacking interactions in the simulations. A significant dependence of calculated nucleobase stacking free energies on the employed water model was observed with the tendency of stacking free energies being more accurately reproduced by more complex water models. The simulation studies also suggest a mechanism of stacking/unstacking that involves significant motions perpendicular to the reaction coordinate and indicate that the equilibrium nicked base pair step may slightly differ from regular B-DNA geometry in a sequence-dependent manner. PMID:27407106

  5. 6-Pyrazolylpurine as an Artificial Nucleobase for Metal-Mediated Base Pairing in DNA Duplexes

    Science.gov (United States)

    Léon, J. Christian; Sinha, Indranil; Müller, Jens

    2016-01-01

    The artificial nucleobase 6-pyrazol-1-yl-purine (6PP) has been investigated with respect to its usability in metal-mediated base pairing. As was shown by temperature-dependent UV spectroscopy, 6PP may form weakly stabilizing 6PP–Ag(I)–6PP homo base pairs. Interestingly, 6PP can be used to selectively recognize a complementary pyrimidine nucleobase. The addition of Ag(I) to a DNA duplex comprising a central 6PP:C mispair (C = cytosine) leads to a slight destabilization of the duplex. In contrast, a stabilizing 6PP–Ag(I)–T base pair is formed with a complementary thymine (T) residue. It is interesting to note that 6PP is capable of differentiating between the pyrimidine moieties despite the fact that it is not as sterically crowded as 6-(3,5-dimethylpyrazol-1-yl)purine, an artificial nucleobase that had previously been suggested for the recognition of nucleic acid sequences via the formation of a metal-mediated base pair. Hence, the additional methyl groups of 6-(3,5-dimethylpyrazol-1-yl)purine may not be required for the specific recognition of the complementary nucleobase. PMID:27089326

  6. Assessment of composite motif discovery methods

    Directory of Open Access Journals (Sweden)

    Johansen Jostein

    2008-02-01

    Full Text Available Abstract Background Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have addressed the problem of single motif discovery – discovering binding motifs for individual transcription factors. In higher organisms, however, transcription factors usually act in combination with nearby bound factors to induce specific regulatory behaviours. Hence, recent focus has shifted from single motifs to the discovery of sets of motifs bound by multiple cooperating transcription factors, so called composite motifs or cis-regulatory modules. Given the large number and diversity of methods available, independent assessment of methods becomes important. Although there have been several benchmark studies of single motif discovery, no similar studies have previously been conducted concerning composite motif discovery. Results We have developed a benchmarking framework for composite motif discovery and used it to evaluate the performance of eight published module discovery tools. Benchmark datasets were constructed based on real genomic sequences containing experimentally verified regulatory modules, and the module discovery programs were asked to predict both the locations of these modules and to specify the single motifs involved. To aid the programs in their search, we provided position weight matrices corresponding to the binding motifs of the transcription factors involved. In addition, selections of decoy matrices were mixed with the genuine matrices on one dataset to test the response of programs to varying levels of noise. Conclusion Although some of the methods tested tended to score somewhat better than others overall, there were still large variations between individual datasets and no single method performed consistently better than the rest in all situations. The variation in performance on individual

  7. Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding.

    Science.gov (United States)

    Chou, Shan-Ho; Chin, Ko-Hsin; Chen, Fu-Ming

    2002-05-14

    Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5'-GXC/CYG-5' complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson-Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition. PMID:12011426

  8. Looped out and perpendicular: Deformation of Watson–Crick base pair associated with actinomycin D binding

    Science.gov (United States)

    Chou, Shan-Ho; Chin, Ko-Hsin; Chen, Fu-Ming

    2002-01-01

    Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5′-GXC/CYG-5′ complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson–Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition. PMID:12011426

  9. The Sentiment Trend Analysis of Twitter Based on Set Pair Contact Degree

    Directory of Open Access Journals (Sweden)

    Chunying Zhang

    2013-01-01

    Full Text Available Sentiment trend of twitter users have a great influence on their friends and the crowd listened. This paper directs at the user sentiment state of twitter, the unique medium, and applies set pair analysis method for trend analysis. First, we begin with set pair contact degree, then based on set pair affective computing model to make comparison with the size relationship of same degree, difference degree, opposition degree of the emotion, to build the user sentiment trend analysis model; Secondly, we analyze the influence for the user's own sentiment trend when the value changed of difference coefficient ; thirdly, after analyze to obtain one user's sentiment orientation threshold as prerequisite for user behavior prediction. Finally, setting an example to calculate the sentiment trend of one twitter, then to get the conclusion is that the analysis of user emotion from a three-dimensional angle is more realistic than the single angle.

  10. Identification of DNA base-pairing via tunnel-current decay

    OpenAIRE

    He, Jin; Lin, Lisha; Zhang, Peiming; Lindsay, Stuart

    2007-01-01

    We propose a new approach for reading the sequence of a DNA molecule passing between electrodes on a nanopore, using hydrogen-bond mediated tunneling signals. The base-electrode interaction is modeled using a nucleobase functionalized STM probe that is pulled away from a nucleoside monolayer. Watson-Crick recognition results in slow-decay of the tunnel current, uniquely characteristic of the base-pair in over half the reads. Thirteen independent reads would yield the desired 99.99% accuracy.

  11. Acid-Base Pairs in Lewis Acidic Zeolites Promote Direct Aldol Reactions by Soft Enolization.

    Science.gov (United States)

    Lewis, Jennifer D; Van de Vyver, Stijn; Román-Leshkov, Yuriy

    2015-08-17

    Hf-, Sn-, and Zr-Beta zeolites catalyze the cross-aldol condensation of aromatic aldehydes with acetone under mild reaction conditions with near quantitative yields. NMR studies with isotopically labeled molecules confirm that acid-base pairs in the Si-O-M framework ensemble promote soft enolization through α-proton abstraction. The Lewis acidic zeolites maintain activity in the presence of water and, unlike traditional base catalysts, in acidic solutions. PMID:26138135

  12. The CD3 gamma leucine-based receptor-sorting motif is required for efficient ligand-mediated TCR down-regulation

    DEFF Research Database (Denmark)

    von Essen, Marina; Menné, Charlotte; Nielsen, Bodil L;

    2002-01-01

    other pathway is dependent on protein kinase C (PKC)-mediated activation of the CD3 gamma di-leucine-based receptor-sorting motif. Previous studies have failed to demonstrate a connection between ligand- and PKC-induced TCR down-regulation. Thus, although an apparent paradox, the dogma has been that...... ligand- and PKC-induced TCR down-regulations are not interrelated. By analyses of a newly developed CD3 gamma-negative T cell variant, freshly isolated and PHA-activated PBMC, and a mouse T cell line, we challenged this dogma and demonstrate in this work that PKC activation and the CD3 gamma di...

  13. Fluorescence 'on-off-on' chemosensor for sequential recognition of Fe(3+) and Hg(2+) in water based on tetraphenylethylene motif.

    Science.gov (United States)

    Yan, Yuanyuan; Che, Zhiping; Yu, Xiang; Zhi, Xiaoyan; Wang, Juanjuan; Xu, Hui

    2013-01-15

    A novel selective and sensitive fluorescence 'on-off-on' probe based on tetraphenylethylene (TPE) motif for sequential recognition of Fe(3+) and Hg(2+) in water has been developed. Especially the complex 6-Fe(3+) could behave as a 'turn on' fluorescent sensor over a wide-range pH value for detection of Hg(2+). The selectivity of this complex for Hg(2+) over other heavy and transition metal ions is excellent, and its sensitivity for Hg(2+) is at 2 ppb in water. PMID:23218869

  14. Site-Specific Incorporation of Functional Components into RNA by an Unnatural Base Pair Transcription System

    Directory of Open Access Journals (Sweden)

    Rie Kawai

    2012-03-01

    Full Text Available Toward the expansion of the genetic alphabet, an unnatural base pair between 7-(2-thienylimidazo[4,5-b]pyridine (Ds and pyrrole-2-carbaldehyde (Pa functions as a third base pair in replication and transcription, and provides a useful tool for the site-specific, enzymatic incorporation of functional components into nucleic acids. We have synthesized several modified-Pa substrates, such as alkylamino-, biotin-, TAMRA-, FAM-, and digoxigenin-linked PaTPs, and examined their transcription by T7 RNA polymerase using Ds-containing DNA templates with various sequences. The Pa substrates modified with relatively small functional groups, such as alkylamino and biotin, were efficiently incorporated into RNA transcripts at the internal positions, except for those less than 10 bases from the 3′-terminus. We found that the efficient incorporation into a position close to the 3′-terminus of a transcript depended on the natural base contexts neighboring the unnatural base, and that pyrimidine-Ds-pyrimidine sequences in templates were generally favorable, relative to purine-Ds-purine sequences. The unnatural base pair transcription system provides a method for the site-specific functionalization of large RNA molecules.

  15. DNA Aptamer Generation by Genetic Alphabet Expansion SELEX (ExSELEX) Using an Unnatural Base Pair System.

    Science.gov (United States)

    Kimoto, Michiko; Matsunaga, Ken-ichiro; Hirao, Ichiro

    2016-01-01

    Genetic alphabet expansion of DNA using unnatural base pair systems is expected to provide a wide variety of novel tools and methods. Recent rapid progress in this area has enabled the creation of several types of unnatural base pairs that function as a third base pair in polymerase reactions. Presently, a major topic is whether the genetic alphabet expansion system actually increases nucleic acid functionalities. We recently applied our unnatural base pair system to in vitro selection (SELEX), using a DNA library containing four natural bases and an unnatural base, and succeeded in the generation of high-affinity DNA aptamers that specifically bind to target proteins. Only a few hydrophobic unnatural bases greatly augmented the affinity of the aptamers. Here, we describe a new approach (genetic alphabet Expansion SELEX, ExSELEX), using our hydrophobic unnatural base pair system for high affinity DNA aptamer generation. PMID:26552815

  16. Aviram-Ratner rectifying mechanism for DNA base-pair sequencing through graphene nanogaps

    Science.gov (United States)

    Agapito, Luis A.; Gayles, Jacob; Wolowiec, Christian; Kioussis, Nicholas

    2012-04-01

    We demonstrate that biological molecules such as Watson-Crick DNA base pairs can behave as biological Aviram-Ratner electrical rectifiers because of the spatial separation and weak hydrogen bonding between the nucleobases. We have performed a parallel computational implementation of the ab initio non-equilibrium Green’s function (NEGF) theory to determine the electrical response of graphene—base-pair—graphene junctions. The results show an asymmetric (rectifying) current-voltage response for the cytosine-guanine base pair adsorbed on a graphene nanogap. In sharp contrast we find a symmetric response for the thymine-adenine case. We propose applying the asymmetry of the current-voltage response as a sensing criterion to the technological challenge of rapid DNA sequencing via graphene nanogaps.

  17. A quantum theoretical study of reactions of methyldiazonium ion with DNA base pairs

    Science.gov (United States)

    Shukla, P. K.; Ganapathy, Vinay; Mishra, P. C.

    2011-09-01

    Methylation of the DNA bases in the Watson-Crick GC and AT base pairs by the methyldiazonium ion was investigated employing density functional and second order Møller-Plesset (MP2) perturbation theories. Methylation at the N3, N7 and O6 sites of guanine, N1, N3 and N7 sites of adenine, O2 and N3 sites of cytosine and the O2 and O4 sites of thymine were considered. The computed reactivities for methylation follow the order N7(guanine) > N3(adenine) > O6(guanine) which is in agreement with experiment. The base pairing in DNA is found to play a significant role with regard to reactivities of the different sites.

  18. Theoretical investigation of the molecular structure of the pi kappa DNA base pair.

    Science.gov (United States)

    Florián, J; Leszczyński, J

    1995-04-01

    The structure of the nonclassical pi kappa base pair (7-methyl-oxoformycin B. . .2,4-diaminopyrimidine) was studied at the ab initio Hartree-Fock (HF) and MP2 levels using the 6-31G* and 6-31G** basis sets. The pi kappa base pair is bound by three parallel hydrogen bonds with the donor-acceptor-donor recognition pattern. Recently, these bases were proposed as an extension of the genetic alphabet from four to six letters (Piccirilli et al, Nature 343,33 (1990)). By the HF/6-31G* method with full geometry optimization we calculated the 12 degree propeller twist for the minimum energy structure of this complex. The linearity of hydrogen bonds is preserved in the twisted structure by virtue of the pyramidal arrangement of the kappa-base amino groups. The rings of both the pi and kappa molecules remain nearly planar. This nonplanar structure of the pi kappa base pair is only 0.1 kcal/mol more stable than the planar (Cs) conformation. The HF/6-31G* level gas-phase interaction energy of pi kappa (-13.5 kcal/mol) calculated by us turned out to be nearly the same as the interaction energy obtained previously for the adenine-thymine base pair (-13.4 kcal/mol) at the same computational level. The inclusion of p-polarization functions on hydrogens, electron correlation effects (MP2/6-31G** level), and the correction for the basis set superposition error (BSSE) increase this energy to -14.0 kcal/mol. PMID:7626240

  19. The Motif Tracking Algorithm

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The search for patterns or motifs in data represents a problem area of key interest to finance and economic researchers. In this paper, we introduce the motif tracking algorithm (MTA), a novel immune inspired (IS) pattern identification tool that is able to identify unknown motifs of a non specified length which repeat within time series data. The power of the algorithm comes from the fact that it uses a small number of parameters with minimal assumptions regarding the data being examined or the underlying motifs. Our interest lies in applying the algorithm to financial time series data to identify unknown patterns that exist. The algorithm is tested using three separate data sets. Particular suitability to financial data is shown by applying it to oil price data. In all cases, the algorithm identifies the presence of a motif population in a fast and efficient manner due to the utilization of an intuitive symbolic representation.The resulting population of motifs is shown to have considerable potential value for other applications such as forecasting and algorithm seeding.

  20. The Motif Tracking Algorithm

    CERN Document Server

    Wilson, William; Aickelin, Uwe; 10.1007/s11633.008.0032.0

    2010-01-01

    The search for patterns or motifs in data represents a problem area of key interest to finance and economic researchers. In this paper we introduce the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify unknown motifs of a non specified length which repeat within time series data. The power of the algorithm comes from the fact that it uses a small number of parameters with minimal assumptions regarding the data being examined or the underlying motifs. Our interest lies in applying the algorithm to financial time series data to identify unknown patterns that exist. The algorithm is tested using three separate data sets. Particular suitability to financial data is shown by applying it to oil price data. In all cases the algorithm identifies the presence of a motif population in a fast and efficient manner due to the utilisation of an intuitive symbolic representation. The resulting population of motifs is shown to have considerable potential value for other ap...

  1. Genetic interaction motif finding by expectation maximization – a novel statistical model for inferring gene modules from synthetic lethality

    Directory of Open Access Journals (Sweden)

    Ye Ping

    2005-12-01

    Full Text Available Abstract Background Synthetic lethality experiments identify pairs of genes with complementary function. More direct functional associations (for example greater probability of membership in a single protein complex may be inferred between genes that share synthetic lethal interaction partners than genes that are directly synthetic lethal. Probabilistic algorithms that identify gene modules based on motif discovery are highly appropriate for the analysis of synthetic lethal genetic interaction data and have great potential in integrative analysis of heterogeneous datasets. Results We have developed Genetic Interaction Motif Finding (GIMF, an algorithm for unsupervised motif discovery from synthetic lethal interaction data. Interaction motifs are characterized by position weight matrices and optimized through expectation maximization. Given a seed gene, GIMF performs a nonlinear transform on the input genetic interaction data and automatically assigns genes to the motif or non-motif category. We demonstrate the capacity to extract known and novel pathways for Saccharomyces cerevisiae (budding yeast. Annotations suggested for several uncharacterized genes are supported by recent experimental evidence. GIMF is efficient in computation, requires no training and automatically down-weights promiscuous genes with high degrees. Conclusion GIMF effectively identifies pathways from synthetic lethality data with several unique features. It is mostly suitable for building gene modules around seed genes. Optimal choice of one single model parameter allows construction of gene networks with different levels of confidence. The impact of hub genes the generic probabilistic framework of GIMF may be used to group other types of biological entities such as proteins based on stochastic motifs. Analysis of the strongest motifs discovered by the algorithm indicates that synthetic lethal interactions are depleted between genes within a motif, suggesting that synthetic

  2. Molecular evolution of epizootic hemorrhagic disease viruses in North America based on historical isolates using motif fingerprints.

    Science.gov (United States)

    Wilson, W C; Ruder, M G; Jasperson, D; Smith, T P L; Naraghi-Arani, P; Lenhoff, R; Stallknecht, D E; Valdivia-Granda, W A; Sheoran, D

    2016-08-01

    Epizootic hemorrhagic disease virus (EHDV) is an orbivirus of the Reoviridae family that has significant impact on wild and captive white-tailed deer. Although closely related to bluetongue virus that can cause disease in sheep and cattle, North American EHDV historically has not been associated with disease in cattle or sheep. Severe disease in cattle has been reported with other EHDV strains from East Asia and the Middle East. To understand the potential role of viral genetics in the epidemiology of epizootic hemorrhagic disease, a molecular characterization of North American EHDV strains from 1955 to 2012 was conducted via conventional phylogenetic analysis and a new classification approach using motif fingerprint patterns. Overall, this study indicates that the genetic make-up of EHDV populations in North America have slowly evolved over time. The data also suggested limited reassortment events between serotypes 1 and 2 and introduces a new analysis tool for more detailed sequence pattern analysis. PMID:27107856

  3. Motif-Optimized Subtype A HIV Envelope-based DNA Vaccines Rapidly Elicit Neutralizing Antibodies When Delivered Sequentially

    Science.gov (United States)

    Pissani, Franco; Malherbe, Delphine C.; Robins, Harlan; DeFilippis, Victor R.; Park, Byung; Sellhorn, George; Stamatatos, Leonidas; Overbaugh, Julie; Haigwood, Nancy L.

    2012-01-01

    HIV-1 infection results in the development of a diverging quasispecies unique to each infected individual. Envelope (Env)-specific neutralizing antibodies (NAbs) typically develop over months to years after infection and initially are limited to the infecting virus. In some subjects, antibody responses develop that neutralize heterologous isolates (HNAbs), a phenomenon termed broadening of the NAb response. Studies of co-crystalized antibodies and proteins have facilitated the identification of some targets of broadly neutralizing monoclonal antibodies (NmAbs) capable of neutralizing many or most heterologous viruses; however, the ontogeny of these antibodies in vivo remains elusive. We hypothesize that Env protein escape variants stimulate broad NAb development in vivo and could generate such NAbs when used as immunogens. Here we test this hypothesis in rabbits using HIV Env vaccines featuring: (1) use of individual quasispecies env variants derived from an HIV-1 subtype A-infected subject exhibiting high levels of NAbs within the first year of infection that increased and broadened with time; (2) motif optimization of envs to enhance in vivo expression of DNA formulated as vaccines; and (3) a combined DNA plus protein boosting regimen. Vaccines consisted of multiple env variants delivered sequentially and a simpler regimen that utilized only the least and most divergent clones. The simpler regimen was as effective as the more complex approach in generating modest HNAbs and was more efficient when modified, motif-optimized DNA was used in combination with trimeric gp140 protein. This is a rationally designed strategy that facilitates future vaccine design by addressing the difficult problem of generating HNAbs to HIV by empirically testing the immunogenicity of naturally occurring quasispecies env variants. PMID:22749601

  4. A light scattering study of the evolution of pairing in Fe-based superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Hackl, Rudi; Kretzschmar, Florian; Muschler, Bernhard; Boehm, Thomas [Walther-Meissner-Institut, DE-85748 Garching (Germany); Wen, Hai-Hu [Nanjing University, Nanjing 210093 (China); Tsurkan, Vladimir [University of Augsburg, DE-86159 Augsburg (Germany); Academy of Sciences of Moldova, MD-2028 Chisinau (Moldova, Republic of); Deisenhofer, Joachim; Loidl, Alois [University of Augsburg, DE-86159 Augsburg (Germany)

    2013-07-01

    The iron-based superconductors are a laboratory for exploring the relevance of electron-electron interactions beyond electron-phonon coupling, being at work in conventional superconductors, since the Fermi surfaces can be varied systematically by atomic substitution. This enables one to systematically study magnetism and superconductivity as a function of the Fermi surface topology. Inelastic light scattering affords a window into the electronic properties of the ordered states. In particular, the evolution of the superconducting pairing upon doping can be probed since light scattering allows access to the anisotropy of the energy gap and, in some cases, of the pairing potential. Ba{sub 1-x}K{sub x}Fe{sub 2}As{sub 2} is one of those cases since the competition between s- and d-wave pairing leads to the appearance of exciton-like modes below the gap edges of the various bands. Along with the results from other materials having different Fermi surface cross-sections the data in Ba{sub 1-x}K{sub x}Fe{sub 2}As{sub 2} support the spin fluctuation scenario driven by interband coupling. The experiments show that there exist alternative routes for the analysis of the pairing interaction in superconductors with unconventional coupling and anisotropic gaps.

  5. Comparison of NIR FRET pairs for quantitative transferrin-based assay

    Science.gov (United States)

    Sinsuebphon, Nattawut; Bevington, Travis; Zhao, Lingling; Ken, Abe; Barroso, Margarida; Intes, Xavier

    2014-02-01

    Transferrin (Tfn) is commonly used as a drug delivery carrier for cancer treatment. Tfn cellular internalization can be observed by Förster resonance energy transfer (FRET), which occurs when two fluorophores - donor and acceptor - are a few nanometers apart. Donor fluorescence lifetime can be used to sense and quantify FRET occurrence. In FRET state, the donor is quenched leading to a significant reduction in its lifetime. In this study, donor and acceptor near-infrared (NIR) fluorophore-labeled Tfn were used to quantify cellular internalization in breast cancer cell line (T47D). Based on donor lifetime, quantum yield and spectral data, seven NIR FRET pairs were chosen for this comparison. Performance of the different NIR FRET pairs was evaluated in vitro in multiwell plate settings and by analyzing the relationship between quenched donor fraction and acceptor:donor ratio. Additionally, we performed brightness comparison between each pairs. Several parameters, such as brightness, lifetime, R0 and FRET donor population values are used to identify the most suitable NIR FRET pair for in vivo studies in preclinical settings.

  6. Spontaneous formation and base pairing of plausible prebiotic nucleotides in water.

    Science.gov (United States)

    Cafferty, Brian J; Fialho, David M; Khanam, Jaheda; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

    2016-01-01

    The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life. PMID:27108699

  7. Spontaneous formation and base pairing of plausible prebiotic nucleotides in water

    Science.gov (United States)

    Cafferty, Brian J.; Fialho, David M.; Khanam, Jaheda; Krishnamurthy, Ramanarayanan; Hud, Nicholas V.

    2016-01-01

    The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life. PMID:27108699

  8. Automated motif discovery from glycan array data.

    Science.gov (United States)

    Cholleti, Sharath R; Agravat, Sanjay; Morris, Tim; Saltz, Joel H; Song, Xuezheng; Cummings, Richard D; Smith, David F

    2012-10-01

    Assessing interactions of a glycan-binding protein (GBP) or lectin with glycans on a microarray generates large datasets, making it difficult to identify a glycan structural motif or determinant associated with the highest apparent binding strength of the GBP. We have developed a computational method, termed GlycanMotifMiner, that uses the relative binding of a GBP with glycans within a glycan microarray to automatically reveal the glycan structural motifs recognized by a GBP. We implemented the software with a web-based graphical interface for users to explore and visualize the discovered motifs. The utility of GlycanMotifMiner was determined using five plant lectins, SNA, HPA, PNA, Con A, and UEA-I. Data from the analyses of the lectins at different protein concentrations were processed to rank the glycans based on their relative binding strengths. The motifs, defined as glycan substructures that exist in a large number of the bound glycans and few non-bound glycans, were then discovered by our algorithm and displayed in a web-based graphical user interface ( http://glycanmotifminer.emory.edu ). The information is used in defining the glycan-binding specificity of GBPs. The results were compared to the known glycan specificities of these lectins generated by manual methods. A more complex analysis was also carried out using glycan microarray data obtained for a recombinant form of human galectin-8. Results for all of these lectins show that GlycanMotifMiner identified the major motifs known in the literature along with some unexpected novel binding motifs. PMID:22877213

  9. Optimization of the pyridyl nucleobase scaffold for polymerase recognition and unnatural base pair replication

    Czech Academy of Sciences Publication Activity Database

    Hari, Y.; Hwang, G. T.; Leconte, A. M.; Joubert, Nicolas; Hocek, Michal; Romesberg, F. E.

    2008-01-01

    Roč. 9, č. 17 (2008), s. 2796-2799. ISSN 1439-4227 R&D Projects: GA MŠk LC512 Grant ostatní: NIH(US) GM60005 Institutional research plan: CEZ:AV0Z40550506 Keywords : pyridines * C-nucleosides * base-pairs * DNA polymerase * replication Subject RIV: CC - Organic Chemistry Impact factor: 3.322, year: 2008

  10. Does base-pairing strength play a role in microRNA repression?

    Science.gov (United States)

    Carmel, Ido; Shomron, Noam; Heifetz, Yael

    2012-11-01

    MicroRNAs (miRNAs) are short, single-stranded RNAs that silence gene expression by either degrading mRNA or repressing translation. Each miRNA regulates a specific set of mRNA "targets" by binding to complementary sequences in their 3' untranslated region. In this study, we examined the importance of the base-pairing strength of the miRNA-target duplex to repression. We hypothesized that if base-pairing strength affects the functionality of miRNA repression, organisms with higher body temperature or that live at higher temperatures will have miRNAs with higher G/C content so that the miRNA-target complex will remain stable. In the nine model organisms examined, we found a significant correlation between the average G/C content of miRNAs and physiological temperature, supporting our hypothesis. Next, for each organism examined, we compared the average G/C content of miRNAs that are conserved among distant organisms and that of miRNAs that are evolutionarily recent. We found that the average G/C content of ancient miRNAs is lower than recent miRNAs in homeotherms, whereas the trend was inversed in poikilotherms, suggesting that G/C content is associated with temperature, thus further supporting our hypothesis. In the organisms examined, the average G/C content of miRNA "seed" sequences was higher than that of mature miRNAs, which was higher than pre-miRNA loops, suggesting an association between the degree of functionality of the sequence and its average G/C content. Our analyses show a possible association between the base-pairing strength of miRNA-targets and the temperature of an organism, suggesting that base-pairing strength plays a role in repression by miRNAs. PMID:23019592

  11. Spontaneous formation and base pairing of plausible prebiotic nucleotides in water

    OpenAIRE

    Cafferty, Brian J.; Fialho, David M.; Khanam, Jaheda; Krishnamurthy, Ramanarayanan; Hud, Nicholas V.

    2016-01-01

    The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ...

  12. Application of Set Pair Analysis-Based Similarity Forecast Model and Wavelet Denoising for Runoff Forecasting

    OpenAIRE

    Chien-Ming Chou

    2014-01-01

    This study presents the application of a set pair analysis-based similarity forecast (SPA-SF) model and wavelet denoising to forecast annual runoff. The SPA-SF model was built from identical, discrepant and contrary viewpoints. The similarity between estimated and historical data can be obtained. The weighted average of the annual runoff values characterized by the highest connection coefficients was regarded as the predicted value of the estimated annual runoff. In addition, runoff time seri...

  13. Chlamydomonas reinhardtii telomere repeats form unstable structures involving guanine-guanine base pairs.

    OpenAIRE

    Petracek, M E; Berman, J.

    1992-01-01

    Unusual DNA structures involving four guanines in a planar formation (guanine tetrads) are formed by guanine-rich (G-rich) telomere DNA and other G-rich sequences (reviewed in (1)) and may be important in the structure and function of telomeres. These structures result from intrastrand and/or interstrand Hoogsteen base pairs between the guanines. We used the telomeric repeat of Chlamydomonas reinhardtii, TTTTAGGG, which contains 3 guanines and has a long interguanine A + T tract, to determine...

  14. Pairing-Free ID-Based Key-Insulated Signature Scheme

    Institute of Scientific and Technical Information of China (English)

    Guo-Bin Zhu; Hu Xiong; Zhi-Guang Qin

    2015-01-01

    Abstract⎯Without the assumption that the private keys are kept secure perfectly, cryptographic primitives cannot be deployed in the insecure environments where the key leakage is inevitable. In order to reduce the damage caused by the key exposure in the identity-based (ID-based) signature scenarios efficiently, we propose an ID-based key-insulated signature scheme in this paper, which eliminates the expensive bilinear pairing operations. Compared with the previous work, our scheme minimizes the computation cost without any extra cost. Under the discrete logarithm (DL) assumption, a security proof of our scheme in the random oracle model has also been given.

  15. Iron-based superconductors: Current status of materials and pairing mechanism

    International Nuclear Information System (INIS)

    Highlight: • An up-to-date review by the discoverer and a theoretical pioneer of iron-based superconductor. - Abstract: Since the discovery of high Tc iron-based superconductors in early 2008, more than 15,000 papers have been published as a result of intensive research. This paper describes the current status of iron-based superconductors (IBSC) covering most up-to-date research progress along with the some background research, focusing on materials (bulk and thin film) and pairing mechanism

  16. Recognition of base pair inversions in duplex by chimeric (alpha,beta) triplex-forming oligonucleotides.

    Science.gov (United States)

    Timofeev, Edward N; Goryaeva, Baira V; Florentiev, Vladimir L

    2006-10-01

    DNA recognition by triplex-forming oligonucleotides (TFOs) is usually limited by homopurine-homopyrimidine sequence in duplexes. Modifications of the third strand may overcome this limitation. Chimeric alpha-beta TFOs are expected to form triplex DNA upon binding to non-regular sequence duplexes. In the present study we describe binding properties of chimeric alpha-beta oligodeoxynucleotides in the respect to short DNA duplexes with one, three, and five base pair inversions. Non-natural chimeric TFO's contained alpha-thymidine residues inside (GT) or (GA) core sequences. Modified residues were addressed to AT/TA inversions in duplexes. It was found in the non-denaturing gel-electrophoresis experiments that single or five adjacent base pair inversions in duplexes may be recognized by chimeric alpha-beta TFO's at 10 degrees C and pH 7.8. Three dispersed base pair inversions in the double stranded DNA prevented triplex formation by either (GT) or (GA) chimeras. Estimation of thermal stability of chimeric alpha-beta triplexes showed decrease in T(m) values as compared with unmodified complexes. PMID:16928141

  17. Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

    Science.gov (United States)

    Swasey, Steven M.; Gwinn, Elisabeth G.

    2016-04-01

    The thermal and chemical fragility of DNA nanomaterials assembled by Watson–Crick (WC) pairing constrain the settings in which these materials can be used and how they can be functionalized. Here we investigate use of the silver cation, Ag+, as an agent for more robust, metal-mediated self-assembly, focusing on the simplest duplex building blocks that would be required for more elaborate Ag+–DNA nanostructures. Our studies of Ag+-induced assembly of non-complementary DNA oligomers employ strands of 2–24 bases, with varied base compositions, and use electrospray ionization mass spectrometry to determine product compositions. High yields of duplex products containing narrowly distributed numbers of Ag+ can be achieved by optimizing solution conditions. These Ag+-mediated duplexes are stable to at least 60 mM Mg2+, higher than is necessary for WC nanotechnology schemes such as tile assemblies and DNA origami, indicating that sequential stages of Ag+-mediated and WC-mediated assembly may be feasible. Circular dichroism spectroscopy suggests simple helical structures for Ag+-mediated duplexes with lengths to at least 20 base pairs, and further indicates that the structure of cytosine-rich duplexes is preserved at high urea concentrations. We therefore propose an approach towards dynamic DNA nanomaterials with enhanced thermal and chemical stability through designs that combine sturdy silver-mediated ‘frames’ with WC paired ‘pictures’.

  18. CHEM-PATH-TRACKER: An automated tool to analyze chemical motifs in molecular structures.

    Science.gov (United States)

    Ribeiro, João V; Cerqueira, N M F S A; Fernandes, Pedro A; Ramos, Maria J

    2014-07-01

    In this article, we propose a method for locating functionally relevant chemical motifs in protein structures. The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three-dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed chem-path-tracker. This software is a VMD plug-in that allows the user to highlight and reveal potential chemical motifs requiring only a few selections. The analysis is based on atoms/residues pair distances applying a modified version of Dijkstra's algorithm, and it makes possible to monitor the distances of a large pathway, even during a molecular dynamics simulation. This tool turned out to be very useful, fast, and user-friendly in the performed tests. The chem-path-tracker package is distributed as an independent platform and can be found at http://www.fc.up.pt/PortoBioComp/database/doku.php?id=chem-path-tracker. PMID:24775806

  19. Prediction of plant promoters based on hexamers and random triplet pair analysis

    Directory of Open Access Journals (Sweden)

    Noman Nasimul

    2011-06-01

    Full Text Available Abstract Background With an increasing number of plant genome sequences, it has become important to develop a robust computational method for detecting plant promoters. Although a wide variety of programs are currently available, prediction accuracy of these still requires further improvement. The limitations of these methods can be addressed by selecting appropriate features for distinguishing promoters and non-promoters. Methods In this study, we proposed two feature selection approaches based on hexamer sequences: the Frequency Distribution Analyzed Feature Selection Algorithm (FDAFSA and the Random Triplet Pair Feature Selecting Genetic Algorithm (RTPFSGA. In FDAFSA, adjacent triplet-pairs (hexamer sequences were selected based on the difference in the frequency of hexamers between promoters and non-promoters. In RTPFSGA, random triplet-pairs (RTPs were selected by exploiting a genetic algorithm that distinguishes frequencies of non-adjacent triplet pairs between promoters and non-promoters. Then, a support vector machine (SVM, a nonlinear machine-learning algorithm, was used to classify promoters and non-promoters by combining these two feature selection approaches. We referred to this novel algorithm as PromoBot. Results Promoter sequences were collected from the PlantProm database. Non-promoter sequences were collected from plant mRNA, rRNA, and tRNA of PlantGDB and plant miRNA of miRBase. Then, in order to validate the proposed algorithm, we applied a 5-fold cross validation test. Training data sets were used to select features based on FDAFSA and RTPFSGA, and these features were used to train the SVM. We achieved 89% sensitivity and 86% specificity. Conclusions We compared our PromoBot algorithm to five other algorithms. It was found that the sensitivity and specificity of PromoBot performed well (or even better with the algorithms tested. These results show that the two proposed feature selection methods based on hexamer frequencies

  20. Visibility graph motifs

    CERN Document Server

    Iacovacci, Jacopo

    2015-01-01

    Visibility algorithms transform time series into graphs and encode dynamical information in their topology, paving the way for graph-theoretical time series analysis as well as building a bridge between nonlinear dynamics and network science. In this work we introduce and study the concept of visibility graph motifs, smaller substructures that appear with characteristic frequencies. We develop a theory to compute in an exact way the motif profiles associated to general classes of deterministic and stochastic dynamics. We find that this simple property is indeed a highly informative and computationally efficient feature capable to distinguish among different dynamics and robust against noise contamination. We finally confirm that it can be used in practice to perform unsupervised learning, by extracting motif profiles from experimental heart-rate series and being able, accordingly, to disentangle meditative from other relaxation states. Applications of this general theory include the automatic classification a...

  1. DNA replication through G-quadruplex motifs is promoted by the S. cerevisiae Pif1 DNA helicase

    OpenAIRE

    Paeschke, Katrin; Capra, John A.; Zakian, Virginia A.

    2011-01-01

    G-quadruplex (G4) DNA structures are extremely stable four-stranded secondary structures held together by non-canonical G-G base pairs. Genome-wide chromatin immuno-precipitation was used to determine the in vivo binding sites of the multi-functional S. cerevisiae Pif1 DNA helicase, a potent unwinder of G4 structures in vitro. G4 motifs were a significant subset of the high confidence Pif1 binding sites. Replication slowed in the vicinity of these motifs, and they were prone to breakage in Pi...

  2. Detecting seeded motifs in DNA sequences

    OpenAIRE

    Pizzi, Cinzia; Bortoluzzi, Stefania; Bisognin, Andrea; Coppe, Alessandro; Danieli, Gian Antonio

    2005-01-01

    The problem of detecting DNA motifs with functional relevance in real biological sequences is difficult due to a number of biological, statistical and computational issues and also because of the lack of knowledge about the structure of searched patterns. Many algorithms are implemented in fully automated processes, which are often based upon a guess of input parameters from the user at the very first step. In this paper, we present a novel method for the detection of seeded DNA motifs, compo...

  3. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

    Indian Academy of Sciences (India)

    Surjit B Dixit; Mihaly Mezei; David L Beveridge

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute–solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interactmore strongly with watermolecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning’s counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 Å from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general

  4. Efficient and provable secure pairing-free security-mediated identity-based identification schemes.

    Science.gov (United States)

    Chin, Ji-Jian; Tan, Syh-Yuan; Heng, Swee-Huay; Phan, Raphael C-W

    2014-01-01

    Security-mediated cryptography was first introduced by Boneh et al. in 2001. The main motivation behind security-mediated cryptography was the capability to allow instant revocation of a user's secret key by necessitating the cooperation of a security mediator in any given transaction. Subsequently in 2003, Boneh et al. showed how to convert a RSA-based security-mediated encryption scheme from a traditional public key setting to an identity-based one, where certificates would no longer be required. Following these two pioneering papers, other cryptographic primitives that utilize a security-mediated approach began to surface. However, the security-mediated identity-based identification scheme (SM-IBI) was not introduced until Chin et al. in 2013 with a scheme built on bilinear pairings. In this paper, we improve on the efficiency results for SM-IBI schemes by proposing two schemes that are pairing-free and are based on well-studied complexity assumptions: the RSA and discrete logarithm assumptions. PMID:25207333

  5. Efficient and Provable Secure Pairing-Free Security-Mediated Identity-Based Identification Schemes

    Directory of Open Access Journals (Sweden)

    Ji-Jian Chin

    2014-01-01

    Full Text Available Security-mediated cryptography was first introduced by Boneh et al. in 2001. The main motivation behind security-mediated cryptography was the capability to allow instant revocation of a user’s secret key by necessitating the cooperation of a security mediator in any given transaction. Subsequently in 2003, Boneh et al. showed how to convert a RSA-based security-mediated encryption scheme from a traditional public key setting to an identity-based one, where certificates would no longer be required. Following these two pioneering papers, other cryptographic primitives that utilize a security-mediated approach began to surface. However, the security-mediated identity-based identification scheme (SM-IBI was not introduced until Chin et al. in 2013 with a scheme built on bilinear pairings. In this paper, we improve on the efficiency results for SM-IBI schemes by proposing two schemes that are pairing-free and are based on well-studied complexity assumptions: the RSA and discrete logarithm assumptions.

  6. [Personal motif in art].

    Science.gov (United States)

    Gerevich, József

    2015-01-01

    One of the basic questions of the art psychology is whether a personal motif is to be found behind works of art and if so, how openly or indirectly it appears in the work itself. Analysis of examples and documents from the fine arts and literature allow us to conclude that the personal motif that can be identified by the viewer through symbols, at times easily at others with more difficulty, gives an emotional plus to the artistic product. The personal motif may be found in traumatic experiences, in communication to the model or with other emotionally important persons (mourning, disappointment, revenge, hatred, rivalry, revolt etc.), in self-searching, or self-analysis. The emotions are expressed in artistic activity either directly or indirectly. The intention nourished by the artist's identity (Kunstwollen) may stand in the way of spontaneous self-expression, channelling it into hidden paths. Under the influence of certain circumstances, the artist may arouse in the viewer, consciously or unconsciously, an illusionary, misleading image of himself. An examination of the personal motif is one of the important research areas of art therapy. PMID:26202617

  7. Detecting seeded motifs in DNA sequences.

    Science.gov (United States)

    Pizzi, Cinzia; Bortoluzzi, Stefania; Bisognin, Andrea; Coppe, Alessandro; Danieli, Gian Antonio

    2005-01-01

    The problem of detecting DNA motifs with functional relevance in real biological sequences is difficult due to a number of biological, statistical and computational issues and also because of the lack of knowledge about the structure of searched patterns. Many algorithms are implemented in fully automated processes, which are often based upon a guess of input parameters from the user at the very first step. In this paper, we present a novel method for the detection of seeded DNA motifs, composed by regions with a different extent of variability. The method is based on a multi-step approach, which was implemented in a motif searching web tool (MOST). Overrepresented exact patterns are extracted from input sequences and clustered to produce motifs core regions, which are then extended and scored to generate seeded motifs. The combination of automated pattern discovery algorithms and different display tools for the evaluation and selection of results at several analysis steps can potentially lead to much more meaningful results than complete automation can produce. Experimental results on different yeast and human real datasets proved the methodology to be a promising solution for finding seeded motifs. MOST web tool is freely available at http://telethon.bio.unipd.it/bioinfo/MOST. PMID:16141193

  8. Detecting seeded motifs in DNA sequences

    Science.gov (United States)

    Pizzi, Cinzia; Bortoluzzi, Stefania; Bisognin, Andrea; Coppe, Alessandro; Danieli, Gian Antonio

    2005-01-01

    The problem of detecting DNA motifs with functional relevance in real biological sequences is difficult due to a number of biological, statistical and computational issues and also because of the lack of knowledge about the structure of searched patterns. Many algorithms are implemented in fully automated processes, which are often based upon a guess of input parameters from the user at the very first step. In this paper, we present a novel method for the detection of seeded DNA motifs, composed by regions with a different extent of variability. The method is based on a multi-step approach, which was implemented in a motif searching web tool (MOST). Overrepresented exact patterns are extracted from input sequences and clustered to produce motifs core regions, which are then extended and scored to generate seeded motifs. The combination of automated pattern discovery algorithms and different display tools for the evaluation and selection of results at several analysis steps can potentially lead to much more meaningful results than complete automation can produce. Experimental results on different yeast and human real datasets proved the methodology to be a promising solution for finding seeded motifs. MOST web tool is freely available at . PMID:16141193

  9. Charge Transport in DNA Oligonucleotides with Various Base-Pairing Patterns

    Czech Academy of Sciences Publication Activity Database

    Kratochvílová, Irena; Todorciuc, Tatiana; Král, Karel; Němec, Hynek; Bunček, M.; Šebera, Jakub; Záliš, Stanislav; Vokáčová, Zuzana; Sychrovský, Vladimír; Bednárová, Lucie; Mojzeš, P.; Schneider, Bohdan

    2010-01-01

    Roč. 17, 1a (2010), L7-L7. ISSN 1211-5894. [Discussions in Structural Molecular Biology /8./. 18.03.2010-20.03.2010, Nové Hrady] R&D Projects: GA AV ČR KAN401770651; GA ČR GA203/08/1594 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z40550506; CEZ:AV0Z10100520; CEZ:AV0Z40400503; CEZ:AV0Z50520701 Keywords : base-pairing patterns * oligonucleotides * DNA Subject RIV: CF - Physical ; Theoretical Chemistry

  10. DFT Description of Intermolecular Forces between 9-Aminoacridines and DNA Base Pairs

    Directory of Open Access Journals (Sweden)

    Sandra Cotes Oyaga

    2013-01-01

    Full Text Available The B3LYP method with 6-31G* basis set was used to predict the geometries of five 9-aminoacridines (9-AA 1(a–e, DNA base pairs, and respective complexes. Polarizabilities, charge distribution, frontier molecular orbital (FMO, and dipole moments were used to analyze the nature of interactions that allow reasonable drug diffusion levels. The results showed that charge delocalization, high polarizabilities, and high dipole moments play an important role in intermolecular interactions with DNA. The interactions of 9-AA 1(a–e with GC are the strongest. 9-AA 1(d displayed the strongest interaction and 9-AA 1(b the weakest.

  11. Unconventional pairing originating from disconnected Fermi surfaces in the iron-based superconductor

    Energy Technology Data Exchange (ETDEWEB)

    Kuroki, Kazuhiko; Usui, Hidetomo [Department of Applied Physics and Chemistry, The University of Electro-Communications, Chofu, Tokyo 182-8585 (Japan); Onari, Seiichiro; Tanaka, Yukio [Department of Applied Physics, Nagoya University, Nagoya 464-8603 (Japan); Arita, Ryotaro [Department of Applied Physics, University of Tokyo, Hongo, Tokyo 113-8656 (Japan); Kontani, Hiroshi [Department of Physics, Nagoya University, Nagoya 464-8602 (Japan); Aoki, Hideo [Department of Physics, University of Tokyo, Hongo, Tokyo 113-0033 (Japan)], E-mail: kuroki@vivace.e-one.uec.ac.jp

    2009-02-15

    For an iron-based high T{sub c} superconductor LaFeAsO{sub 1-x}F{sub x}, we construct a minimal model where all of the five Fe d bands turn out to be involved. We then investigate the origin of superconductivity with a five-band random-phase approximation by solving the Eliashberg equation. We conclude that the spin fluctuation modes arising from the nesting between the disconnected Fermi pockets realize basically an extended s-wave pairing, where the gap changes sign across the nesting vector.

  12. Superior coexistence: systematicALLY regulatING land subsidence BASED on set pair theory

    Science.gov (United States)

    Chen, Y.; Gong, S.-L.

    2015-11-01

    Anthropogenic land subsidence is an environmental side effect of exploring and using natural resources in the process of economic development. The key points of the system for controlling land subsidence include cooperation and superior coexistence while the economy develops, exploring and using natural resources, and geological environmental safety. Using the theory and method of set pair analysis (SPA), this article anatomises the factors, effects, and transformation of land subsidence. Based on the principle of superior coexistence, this paper promotes a technical approach to the system for controlling land subsidence, in order to improve the prevention and control of geological hazards.

  13. A Multiparty Controlled Bidirectional Quantum Secure Direct Communication and Authentication Protocol Based on EPR Pairs

    Science.gov (United States)

    Chang, Yan; Zhang, Shi-Bin; Yan, Li-Li; Sheng, Zhi-Wei

    2013-06-01

    A multiparty controlled bidirectional quantum secure direct communication and authentication protocol is proposed based on EPR pair and entanglement swapping. The legitimate identities of communicating parties are encoded to Bell states which act as a detection sequence. Secret messages are transmitted by using the classical XOR operation, which serves as a one-time-pad. No photon with secret information transmits in the quantum channel. Compared with the protocols proposed by Wang et al. [Acta Phys. Sin. 56 (2007) 673; Opt. Commun. 266 (2006) 732], the protocol in this study implements bidirectional communication and authentication, which defends most attacks including the ‘man-in-the-middle’ attack efficiently.

  14. Theoretical study of metal ion binding in modified and natural cytosine-cytosine base pairs

    Czech Academy of Sciences Publication Activity Database

    Šebera, Jakub; Sugiyama, K.; Ono, A.; Mulder, J.; Bickelhaupt, F. M.; Tanaka, Y.; Sychrovský, Vladimír; Guerra, C. F.

    2013-01-01

    Roč. 20, č. 1 (2013), s. 39-39. ISSN 1211-5894. [Discussions in Structural Molecular Biology. Annual Meeting of the Czech Society for Structural Biology /11./. 14.03.2013-16.03.2013, Nové Hrady] R&D Projects: GA ČR GAP205/10/0228; GA ČR(CZ) GAP304/10/1951; GA TA ČR TA01011165 Institutional support: RVO:61388963 Keywords : DFT * NMR * base pair * metal-mediated Subject RIV: CF - Physical ; Theoretical Chemistry

  15. AISMOTIF-An Artificial Immune System for DNA Motif Discovery

    Directory of Open Access Journals (Sweden)

    Seeja K R

    2011-03-01

    Full Text Available Discovery of transcription factor binding sites is a much explored and still exploring area of research in functional genomics. Many computational tools have been developed for finding motifs and each of them has their own advantages as well as disadvantages. Most of these algorithms need prior knowledge about the data to construct background models. However there is not a single technique that can be considered as best for finding regulatory motifs. This paper proposes an artificial immune system based algorithm for finding the transcription factor binding sites or motifs and two new weighted scores for motif evaluation. The algorithm is enumerative, but sufficient pruning of the pattern search space has been incorporated using immune system concepts. The performance of AISMOTIF has been evaluated by comparing it with eight state of art composite motif discovery algorithms and found that AISMOTIF predicts known motifs as well as new motifs from the benchmark dataset without any prior knowledge about the data.

  16. AISMOTIF-An Artificial Immune System for DNA Motif Discovery

    CERN Document Server

    Seeja, K R

    2011-01-01

    Discovery of transcription factor binding sites is a much explored and still exploring area of research in functional genomics. Many computational tools have been developed for finding motifs and each of them has their own advantages as well as disadvantages. Most of these algorithms need prior knowledge about the data to construct background models. However there is not a single technique that can be considered as best for finding regulatory motifs. This paper proposes an artificial immune system based algorithm for finding the transcription factor binding sites or motifs and two new weighted scores for motif evaluation. The algorithm is enumerative, but sufficient pruning of the pattern search space has been incorporated using immune system concepts. The performance of AISMOTIF has been evaluated by comparing it with eight state of art composite motif discovery algorithms and found that AISMOTIF predicts known motifs as well as new motifs from the benchmark dataset without any prior knowledge about the data...

  17. Theoretical investigation of the hydrogen atom transfer in the hydrated A–T base pair

    International Nuclear Information System (INIS)

    Highlights: ► We study the hydrated A–T base pair with 2 and 4 water molecules. ► We consider the dynamics of hydrogen transfer in the hydrogen bridges. ► We compare this study with experimental data and simple schemes. - Abstract: The hydrated A–T base pair has been studied in order to understand the structural modifications and their electronic rearrangements induced by the movement of the hydrogen atoms in the H-bonds. The comparison of these results with that of the nonhydrated system can explain the role of the H-bonds of the water molecules in this system. Two naïve schemes have been considered, one where the hydrogen bonds of the water molecules are only indirectly involved in the hydrogen atoms transfer between the bases and another where the water molecules are directly involved in this transfer. The results support the idea that the real mechanisms are more complexes than these schemes. Some new stable structures of the A–T(H2O)2 and the A–T(H2O)4 systems have been found and the mechanisms of their generations have been analysed.

  18. Thiazole orange as a fluorescent probe: Label-free and selective detection of silver ions based on the structural change of i-motif DNA at neutral pH.

    Science.gov (United States)

    Kang, Bei Hua; Gao, Zhong Feng; Li, Na; Shi, Yan; Li, Nian Bing; Luo, Hong Qun

    2016-08-15

    Silver ions have been widely applied to many fields and have harmful effects on environments and human health. Herein, a label-free optical sensor for Ag(+) detection is constructed based on thiazole orange (TO) as a fluorescent probe for the recognition of i-motif DNA structure change at neutral pH. Ag(+) can fold a C-rich single stranded DNA sequence into i-motif DNA structure at neutral pH and that folding is reversible by chelation with cysteine (Cys). The DNA folding process can be indicated by the fluorescence change of TO, which is non-fluorescent in free molecule state and emits strong fluorescence after the incorporation with i-motif DNA. Thus, a rapid, sensitive, and selective method for the detection of Ag(+) and Cys is developed with a detection limit of 17 and 280nM, respectively. It is worth noting that the mechanism underlying the increase of the fluorescence of thiazole orange in the presence of i-motif structure is explained. Moreover, a fluorescent DNA logic gate is successfully designed based on the Ag(+)/Cys-mediated reversible fluorescence changes. The proposed detection strategy is label-free and economical. In addition, this system shows a great promise for i-motif/TO complex to analyze Ag(+) in the real samples. PMID:27260446

  19. Computational analyses of synergism in small molecular network motifs.

    Directory of Open Access Journals (Sweden)

    Yili Zhang

    2014-03-01

    Full Text Available Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically to alter the responses of the motifs to stimuli. Synergism (or antagonism was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions.

  20. A model for avian magnetoreception by coupling magnetite-based mechanism with radical-pair-based mechanism

    CERN Document Server

    Lu, Yan

    2012-01-01

    Many species of animals have been testified to use the geomagnetic field for their navigation, but the biophysical mechanism of magnetoreception has remained enigmatic. This paper presents a biophysical model consisting of magnetite-based mechanism and radical-pair-based mechanism for the avian magnetoreception. The amplitude of resultant magnetic field outside the magnetic particles correspond to the geomagnetic field direction and effect the yield of singlet/triplet state products in the radical pair reactions, therefore the yield of singlet/triplet state products can connect with the geomagnetic field information for orientational detection by the proposed model. The resultant magnetic fields corresponds to two materials with different magnetic properties were analysed under different directions of the geomagnetic field. The results shown that the ferromagnetic particles in organisms could provide more significant change of singlet state products than that of superparamagnetic particles, and the period of ...

  1. Excited States of DNA Base Pairs Using Long-Range Corrected Time-Dependent Density Functional Theory

    Science.gov (United States)

    Jensen, Lasse; Govind, Niranjan

    2009-08-01

    In this work, we present a study of the excitation energies of adenine, cytosine, guanine, thymine, and the adenine-thymine (AT) and guanine-cytosine (GC) base pairs using long-range corrected (LC) density functional theory. We compare three recent LC functionals, BNL, CAM-B3LYP, and LC-PBE0, with B3LYP and coupled cluster results from the literature. We find that the best overall performance is for the BNL functional based on LDA. However, in order to achieve this good agreement, a smaller attenuation parameter is needed, which leads to nonoptimum performance for ground-state properties. B3LYP, on the other hand, severely underestimates the charge-transfer (CT) transitions in the base pairs. Surprisingly, we also find that the CAM-B3LYP functional also underestimates the CT excitation energy for the GC base pair but correctly describes the AT base pair. This illustrates the importance of retaining the full long-range exact exchange even at distances as short as that of the DNA base pairs. The worst overall performance is obtained with the LC-PBE0 functional, which overestimates the excitations for the individual bases as well as the base pairs. It is therefore crucial to strike a good balance between the amount of local and long-range exact exchange. Thus, this work highlights the difficulties in obtained LC functionals, which provides a good description of both ground- and excited-state properties.

  2. Damage mechanism of hydroxyl radicals toward adenine—thymine base pair

    International Nuclear Information System (INIS)

    The adenine—thymine base pair was studied in the presence of hydroxyl radicals in order to probe the hydrogen bond effect. The results show that the hydrogen bonds have little effect on the hydroxylation and dehydrogenation happened at the sites, which are not involved in a hydrogen bond, while at the sites involved in hydrogen bond formation in the base pair, the reaction becomes more difficult, both in view of the free energy barrier and the exothermicity. With a 6–311++G(d,p) level of description, both B3LYP and MP2 methods confirm that the C8 site of isolated adenine has the highest possibility to form covalent bond with the hydroxyl radicals, though with different energetics: B3LYP predicts a barrierless pathway, while MP2 finds a transition state with an energy of 106.1 kJ/mol. For the dehydrogenation reactions, B3LYP method predicts that the free energy barrier increases in the order of HN9 < HN61 < HN62 < H2 < H8. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  3. A Bilinear Pairing-Based Dynamic Key Management and Authentication for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Chin-Ling Chen

    2015-01-01

    Full Text Available In recent years, wireless sensor networks have been used in a variety of environments; a wireless network infrastructure, established to communicate and exchange information in a monitoring area, has also been applied in different environments. However, for sensitive applications, security is the paramount issue. In this paper, we propose using bilinear pairing to design dynamic key management and authentication scheme of the hierarchical sensor network. We use the dynamic key management and the pairing-based cryptography (PBC to establish the session key and the hash message authentication code (HMAC to support the mutual authentication between the sensors and the base station. In addition, we also embed the capability of the Global Positioning System (GPS to cluster nodes to find the best path of the sensor network. The proposed scheme can also provide the requisite security of the dynamic key management, mutual authentication, and session key protection. Our scheme can defend against impersonation attack, replay attack, wormhole attack, and message manipulation attack.

  4. Gapped graphene-based Josephson junction with d-wave pair coupling

    Energy Technology Data Exchange (ETDEWEB)

    Goudarzi, H., E-mail: h.goudarzi@urmia.ac.ir; Khezerlou, M., E-mail: m.khezerlou@urmia.ac.ir; Dezhaloud, T.

    2013-06-15

    Highlights: • We aim to study the influence of the Josephson current passing through a d-wave S/I/S gapped graphene-based junction. • We investigate how the Andreev bound states and the Josephson current are affected by characteristic of d-wave pairing asymmetry. • It is shown that the Josephson current for special range of phase vanishes and the position of the maximum current depends on the mass gap of graphene. -- Abstract: The Josephson current passing through a S/I/S gapped graphene-based junction, where superconductivity in the S region is induced by depositing unconventional d-wave superconductor is investigated. The energy levels of massive Dirac fermions are exactly found for Andreev bound states. We illustrate the effect of characteristic of d-wave pairing symmetry on the Andreev bound states and the Josephson current. It is shown that the Josephson current vanishes for special range of superconductivity phase, φ = φ{sub 1} − φ{sub 2} and the position of the maximum current depends on the mass gap of graphene. The critical supercurrent varies in an oscillatory manner as function of the barrier strength, so that the period of oscillations does not change by increasing the effective mass of quasiparticles.

  5. Gapped graphene-based Josephson junction with d-wave pair coupling

    International Nuclear Information System (INIS)

    Highlights: • We aim to study the influence of the Josephson current passing through a d-wave S/I/S gapped graphene-based junction. • We investigate how the Andreev bound states and the Josephson current are affected by characteristic of d-wave pairing asymmetry. • It is shown that the Josephson current for special range of phase vanishes and the position of the maximum current depends on the mass gap of graphene. -- Abstract: The Josephson current passing through a S/I/S gapped graphene-based junction, where superconductivity in the S region is induced by depositing unconventional d-wave superconductor is investigated. The energy levels of massive Dirac fermions are exactly found for Andreev bound states. We illustrate the effect of characteristic of d-wave pairing symmetry on the Andreev bound states and the Josephson current. It is shown that the Josephson current vanishes for special range of superconductivity phase, φ = φ1 − φ2 and the position of the maximum current depends on the mass gap of graphene. The critical supercurrent varies in an oscillatory manner as function of the barrier strength, so that the period of oscillations does not change by increasing the effective mass of quasiparticles

  6. Structure-Based Analysis of Toxoplasma gondii Profilin: A Parasite-Specific Motif Is Required for Recognition by Toll-Like Receptor 11

    Energy Technology Data Exchange (ETDEWEB)

    K Kucera; A Koblansky; L Saunders; K Frederick; E De La Cruz; S Ghosh; Y Modis

    2011-12-31

    Profilins promote actin polymerization by exchanging ADP for ATP on monomeric actin and delivering ATP-actin to growing filament barbed ends. Apicomplexan protozoa such as Toxoplasma gondii invade host cells using an actin-dependent gliding motility. Toll-like receptor (TLR) 11 generates an innate immune response upon sensing T. gondii profilin (TgPRF). The crystal structure of TgPRF reveals a parasite-specific surface motif consisting of an acidic loop, followed by a long {beta}-hairpin. A series of structure-based profilin mutants show that TLR11 recognition of the acidic loop is responsible for most of the interleukin (IL)-12 secretion response to TgPRF in peritoneal macrophages. Deletion of both the acidic loop and the {beta}-hairpin completely abrogates IL-12 secretion. Insertion of the T. gondii acidic loop and {beta}-hairpin into yeast profilin is sufficient to generate TLR11-dependent signaling. Substitution of the acidic loop in TgPRF with the homologous loop from the apicomplexan parasite Cryptosporidium parvum does not affect TLR11-dependent IL-12 secretion, while substitution with the acidic loop from Plasmodium falciparum results in reduced but significant IL-12 secretion. We conclude that the parasite-specific motif in TgPRF is the key molecular pattern recognized by TLR11. Unlike other profilins, TgPRF slows nucleotide exchange on monomeric rabbit actin and binds rabbit actin weakly. The putative TgPRF actin-binding surface includes the {beta}-hairpin and diverges widely from the actin-binding surfaces of vertebrate profilins.

  7. A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria

    Directory of Open Access Journals (Sweden)

    Axmann Ilka M

    2007-10-01

    Full Text Available Abstract Background Non-coding RNAs (ncRNA are regulators of gene expression in all domains of life. They control growth and differentiation, virulence, motility and various stress responses. The identification of ncRNAs can be a tedious process due to the heterogeneous nature of this molecule class and the missing sequence similarity of orthologs, even among closely related species. The small ncRNA Yfr1 has previously been found in the Prochlorococcus/Synechococcus group of marine cyanobacteria. Results Here we show that screening available genome sequences based on an RNA motif and followed by experimental analysis works successfully in detecting this RNA in all lineages of cyanobacteria. Yfr1 is an abundant ncRNA between 54 and 69 nt in size that is ubiquitous for cyanobacteria except for two low light-adapted strains of Prochlorococcus, MIT 9211 and SS120, in which it must have been lost secondarily. Yfr1 consists of two predicted stem-loop elements separated by an unpaired sequence of 16–20 nucleotides containing the ultraconserved undecanucleotide 5'-ACUCCUCACAC-3'. Conclusion Starting with an ncRNA previously found in a narrow group of cyanobacteria only, we show here the highly specific and sensitive identification of its homologs within all lineages of cyanobacteria, whereas it was not detected within the genome sequences of E. coli and of 7 other eubacteria belonging to the alpha-proteobacteria, chlorobiaceae and spirochaete. The integration of RNA motif prediction into computational pipelines for the detection of ncRNAs in bacteria appears as a promising step to improve the quality of such predictions.

  8. Effect of base-pair inhomogeneities on charge transport along the DNA molecule, mediated by twist and radial polarons

    International Nuclear Information System (INIS)

    Some recent results for a three-dimensional, semi-classical, tight-binding model for DNA show that there are two types of polarons, namely radial and twist polarons, which can transport charge along the DNA molecule. However, the existence of two types of base pairs in real DNA makes it crucial to find out if charge transport also exists in DNA chains with different base pairs. In this paper, we address this problem in its simple case, a homogeneous chain except for a single different base pair, which we call a base-pair inhomogeneity, and its effect on charge transport. Radial polarons experience either reflection or trapping. However, twist polarons are good candidates for charge transport along real DNA. This transport is also very robust with respect to weak parametric and diagonal disorder

  9. The MHC motif viewer

    DEFF Research Database (Denmark)

    Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole;

    2010-01-01

    In vertebrates, the onset of cellular immune reactions is controlled by presentation of peptides in complex with major histocompatibility complex (MHC) molecules to T cell receptors. In humans, MHCs are called human leukocyte antigens (HLAs). Different MHC molecules present different subsets of...... peptides, and knowledge of their binding specificities is important for understanding differences in the immune response between individuals. Algorithms predicting which peptides bind a given MHC molecule have recently been developed with high prediction accuracy. The utility of these algorithms is...... binding motif for each MHC molecule is predicted using state-of-the-art, pan-specific peptide-MHC binding-prediction methods, and is visualized as a sequence logo, in a format that allows for a comprehensive interpretation of binding motif anchor positions and amino acid preferences....

  10. MHC motif viewer

    OpenAIRE

    Rapin, Nicolas; Hoof, Ilka; Lund, Ole; Nielsen, Morten

    2008-01-01

    In vertebrates the major histocompatibility complex (MHC) presents peptides to the immune system. In humans MHCs are called human leukocyte antigens (HLAs), and some of the loci encoding them are the most polymorphic in the human genome. Different MHC molecules present different subsets of peptides, and knowledge of their binding specificities is important for understanding the differences in the immune response between individuals. Knowledge of motifs may be used to identify epitopes, unders...

  11. Nucleic Acid Base Analog FRET-Pair Facilitating Detailed Structural Measurements in Nucleic Acid Containing Systems

    DEFF Research Database (Denmark)

    Börjesson, Karl; Preus, Søren; El-Sagheer, Afaf;

    2009-01-01

    We present the first nucleobase analog fluorescence resonance energy transfer (FRET)-pair. The pair consists of tCO, 1,3-diaza-2-oxophenoxazine, as an energy donor and the newly developed tC(nitro), 7-nitro-1,3-diaza-2-oxophenothiazine, as an energy acceptor. The FRET-pair successfully monitors d...

  12. Cloud Base Height Measurements at Manila Observatory: Initial Results from Constructed Paired Sky Imaging Cameras

    Science.gov (United States)

    Lagrosas, N.; Tan, F.; Antioquia, C. T.

    2014-12-01

    Fabricated all sky imagers are efficient and cost effective instruments for cloud detection and classification. Continuous operation of this instrument can result in the determination of cloud occurrence and cloud base heights for the paired system. In this study, a fabricated paired sky imaging system - consisting two commercial digital cameras (Canon Powershot A2300) enclosed in weatherproof containers - is developed in Manila Observatory for the purpose of determining cloud base heights at the Manila Observatory area. One of the cameras is placed on the rooftop of Manila Observatory and the other is placed on the rooftop of the university dormitory, 489m from the first camera. The cameras are programmed to simultaneously gather pictures every 5 min. Continuous operation of these cameras were implemented since the end of May of 2014 but data collection started end of October 2013. The data were processed following the algorithm proposed by Kassianov et al (2005). The processing involves the calculation of the merit function that determines the area of overlap of the two pictures. When two pictures are overlapped, the minimum of the merit function corresponds to the pixel column positions where the pictures have the best overlap. In this study, pictures of overcast sky prove to be difficult to process for cloud base height and were excluded from processing. The figure below shows the initial results of the hourly average of cloud base heights from data collected from November 2013 to July 2014. Measured cloud base heights ranged from 250m to 1.5km. These are the heights of cumulus and nimbus clouds that are dominant in this part of the world. Cloud base heights are low in the early hours of the day indicating low convection process during these times. However, the increase in the convection process in the atmosphere can be deduced from higher cloud base heights in the afternoon. The decrease of cloud base heights after 15:00 follows the trend of decreasing solar

  13. Ionic force field optimization based on single-ion and ion-pair solvation properties

    CERN Document Server

    Fyta, Maria; Dzubiella, Joachim; Vrbka, Lubos; Netz, Roland R

    2009-01-01

    Molecular dynamics simulations of ionic solutions depend sensitively on the force fields employed for the ions. To resolve the fine differences between ions of the same valence and roughly similar size and in particular to correctly describe ion-specific effects, it is clear that accurate force fields are necessary. In the past, optimization strategies for ionic force fields either considered single-ion properties (such as the solvation free energy at infinite dilution or the ion-water structure) or ion-pair properties (in the form of ion-ion distribution functions). In this paper we investigate strategies to optimize ionic force fields based on single-ion and ion-pair properties simultaneously. To that end, we simulate five different salt solutions, namely CsCl, KCl, NaI, KF, and CsI, at finite ion concentration. The force fields of these ions are systematically varied under the constraint that the single-ion solvation free energy matches the experimental value, which reduces the two-dimensional $\\{\\sigma,\\e...

  14. GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor.

    Science.gov (United States)

    Nemoto, Wataru; Yamanishi, Yoshihiro; Limviphuvadh, Vachiranee; Saito, Akira; Toh, Hiroyuki

    2016-09-01

    G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-dimers or higher-order molecular complexes. Many GPCRs exert a wide variety of molecular functions by forming specific combinations of GPCR subtypes. In addition, some GPCRs are reportedly associated with diseases. GPCR oligomerization is now recognized as an important event in various biological phenomena, and many researchers are investigating this subject. We have developed a support vector machine (SVM)-based method to predict interacting pairs for GPCR oligomerization, by integrating the structure and sequence information of GPCRs. The performance of our method was evaluated by the Receiver Operating Characteristic (ROC) curve. The corresponding area under the curve was 0.938. As far as we know, this is the only prediction method for interacting pairs among GPCRs. Our method could accelerate the analyses of these interactions, and contribute to the elucidation of the global structures of the GPCR networks in membranes. Proteins 2016; 84:1224-1233. © 2016 Wiley Periodicals, Inc. PMID:27191053

  15. Extruded polymer films pigmented with a heterogeneous ion-pair based lumophore for O2 sensing.

    Science.gov (United States)

    Mills, Andrew; Graham, Ashleigh

    2013-11-01

    A novel approach to polymeric Ru(II)-diimine luminescent O2 sensors is described. The Ru(II)-diimine, tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride ([Ru(dpp)3](2+)), is first ion-paired to the surface of heterogeneous TiO2 particles, rendered negatively charged due to the alkali nature of the aqueous solution, to produce an O2 sensitive pigment with a strikingly high oxygen sensitivity (i.e. PO2 (S = 1/2) = 0.002 atm, where PO2 (S = 1/2) is defined as the amount of oxygen required to reduce the initial, oxygen free luminescence by 50%), and a rapid response to oxygen. The pigment is extruded in low density polyethylene (LDPE) to produce a thin (60 μm), flexible, O2 sensing plastic film, with an O2 sensitivity (PO2 (S = 1/2) = 0.84 atm) comparable to the more traditional homogeneous lumophore ion-pair based O2 sensor ink films reported in the literature. PMID:24040643

  16. Exploiting bounded signal flow for graph orientation based on cause-effect pairs

    Directory of Open Access Journals (Sweden)

    Niedermeier Rolf

    2011-08-01

    Full Text Available Abstract Background We consider the following problem: Given an undirected network and a set of sender-receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting edge directions. This problem has applications in understanding protein interaction based cell regulation mechanisms. Since this problem is NP-hard, research so far concentrated on polynomial-time approximation algorithms and tractable special cases. Results We take the viewpoint of parameterized algorithmics and examine several parameters related to the maximum signal flow over vertices or edges. We provide several fixed-parameter tractability results, and in one case a sharp complexity dichotomy between a linear-time solvable case and a slightly more general NP-hard case. We examine the value of these parameters for several real-world network instances. Conclusions Several biologically relevant special cases of the NP-hard problem can be solved to optimality. In this way, parameterized analysis yields both deeper insight into the computational complexity and practical solving strategies.

  17. Homosexual Pairing within a Swarm-Based Mating System: The Case of the Chironomid Midge

    Directory of Open Access Journals (Sweden)

    Athol J. McLachlan

    2011-01-01

    Full Text Available Homosexuality has been dubbed the Darwinian paradox, because it raises the question of how behaviour that would seem to reduce the chance of successful mating can be maintained by natural selection. This question rests on the assumption that same sex mating is the result of active choice of partner, hardwired into the mating behaviour, but there is an alternative explanation for such behaviour. I refer to the possibility that same-sex mating is the result, not of adaptive behaviour at all, but rather of errors due to imprecise sensory machinery. Such an explanation finds support within the mating system of insects with swarm-based mating systems. To explore this case, I turn to the common chironomid midge. I show that homosexual pairing here, exclusively involving male/male pairs, is common. I attempt to show that this observation, together with data on insect predators of swarming midges, can be used to penetrate the mysteries of this fascinating but elusive mating system.

  18. Clamping down on weak terminal base pairs: oligonucleotides with molecular caps as fidelity-enhancing elements at the 5′- and 3′-terminal residues

    OpenAIRE

    Narayanan, Sukunath; Gall, Julia; Richert, Clemens

    2004-01-01

    The base-pairing fidelity of oligonucleotides depends on the identity of the nucleobases involved and the position of matched or mismatched base pairs in the duplex. Nucleobases forming weak base pairs, as well as a terminal position favor mispairing. We have searched for 5′-appended acylamido caps that enhance the stability and base-pairing fidelity of oligonucleotides with a 5′-terminal 2′-deoxyadenosine residue using combinatorial synthesis and MALDI-monitored nuclease selections. This pro...

  19. D-MATRIX: A web tool for constructing weight matrix of conserved DNA motifs

    OpenAIRE

    Sen, Naresh; Mishra, Manoj; Khan, Feroz; Meena, Abha; Sharma, Ashok

    2009-01-01

    Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based o...

  20. Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition

    Science.gov (United States)

    Kuznetsov, Nikita A.; Bergonzo, Christina; Campbell, Arthur J.; Li, Haoquan; Mechetin, Grigory V.; de los Santos, Carlos; Grollman, Arthur P.; Fedorova, Olga S.; Zharkov, Dmitry O.; Simmerling, Carlos

    2015-01-01

    Formamidopyrimidine-DNA glycosylase (Fpg) excises 8-oxoguanine (oxoG) from DNA but ignores normal guanine. We combined molecular dynamics simulation and stopped-flow kinetics with fluorescence detection to track the events in the recognition of oxoG by Fpg and its mutants with a key phenylalanine residue, which intercalates next to the damaged base, changed to either alanine (F110A) or fluorescent reporter tryptophan (F110W). Guanine was sampled by Fpg, as evident from the F110W stopped-flow traces, but less extensively than oxoG. The wedgeless F110A enzyme could bend DNA but failed to proceed further in oxoG recognition. Modeling of the base eversion with energy decomposition suggested that the wedge destabilizes the intrahelical base primarily through buckling both surrounding base pairs. Replacement of oxoG with abasic (AP) site rescued the activity, and calculations suggested that wedge insertion is not required for AP site destabilization and eversion. Our results suggest that Fpg, and possibly other DNA glycosylases, convert part of the binding energy into active destabilization of their substrates, using the energy differences between normal and damaged bases for fast substrate discrimination. PMID:25520195

  1. Fingerprint Identification Using SIFT-Based Minutia Descriptors and Improved All Descriptor-Pair Matching

    Directory of Open Access Journals (Sweden)

    Jiuqiang Han

    2013-03-01

    Full Text Available The performance of conventional minutiae-based fingerprint authentication algorithms degrades significantly when dealing with low quality fingerprints with lots of cuts or scratches. A similar degradation of the minutiae-based algorithms is observed when small overlapping areas appear because of the quite narrow width of the sensors. Based on the detection of minutiae, Scale Invariant Feature Transformation (SIFT descriptors are employed to fulfill verification tasks in the above difficult scenarios. However, the original SIFT algorithm is not suitable for fingerprint because of: (1 the similar patterns of parallel ridges; and (2 high computational resource consumption. To enhance the efficiency and effectiveness of the algorithm for fingerprint verification, we propose a SIFT-based Minutia Descriptor (SMD to improve the SIFT algorithm through image processing, descriptor extraction and matcher. A two-step fast matcher, named improved All Descriptor-Pair Matching (iADM, is also proposed to implement the 1:N verifications in real-time. Fingerprint Identification using SMD and iADM (FISiA achieved a significant improvement with respect to accuracy in representative databases compared with the conventional minutiae-based method. The speed of FISiA also can meet real-time requirements.

  2. Factors influencing the extent and selectivity of alkylation within triplexes by reactive G/A motif oligonucleotides.

    OpenAIRE

    Lampe, J N; Kutyavin, I V; Rhinehart, R; Reed, M W; Meyer, R. B.; Gamper, H B

    1997-01-01

    G/A motif triplex-forming oligonucleotides (TFOs) complementary to a 21 base pair homopurine/homopyrimidine run were conjugated at one or both ends to chlorambucil. These TFOs were incubated with several synthetic duplexes containing the targeted homopurine run flanked by different sequences. The extent of mono and interstrand cross-linking was compared with the level of binding at equilibrium. Covalent modification took place within a triple-stranded complex and usually occurred at guanine r...

  3. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs.

    Science.gov (United States)

    Fang, Wei; Chen, Ji; Rossi, Mariana; Feng, Yexin; Li, Xin-Zheng; Michaelides, Angelos

    2016-06-01

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

  4. Theoretical studies on the intermolecular interactions of potentially primordial base-pair analogues

    Czech Academy of Sciences Publication Activity Database

    Šponer, Judit E.; Vázquez-Mayagoitia, Á.; Sumpter, B.G.; Leszczynski, J.; Šponer, Jiří; Otyepka, M.; Banáš, P.; Fuentes-Cabrera, M.

    2010-01-01

    Roč. 16, č. 10 (2010), s. 3057-3065. ISSN 0947-6539 R&D Projects: GA MŠk(CZ) LC06030; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400040802; GA ČR(CZ) GA203/09/1476 Grant ostatní: GA MŠk(CZ) LC512; GA AV ČR(CZ) IAA400550701; GA ČR(CZ) GD203/09/H046 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : quantum chemistry * base pairing * origin of life Subject RIV: BO - Biophysics Impact factor: 5.476, year: 2010

  5. POINT PATTERN MATCHING ALGORITHM BASED ON POINT PAIR TOPOLOGICAL CHARACTERISTICS AND SPECTRAL MATCHING

    Institute of Scientific and Technical Information of China (English)

    Lu Chunyan; Zou Huanxin; Zhao Jian; Zhou Shilin

    2012-01-01

    Most of the Point Pattern Matching (PPM) algorithm performs poorly when the noise of the point's position and outliers exist.This paper presents a novel and robust PPM algorithm which combined Point Pair Topological Characteristics (PPTC) and Spectral Matching (SM) together to solve the afore mentioned issues.In which PPTC,a new shape descriptor,is firstly proposed.A new comparability measurement based on PPTC is defined as the matching probability.Finally,the correct matching results are achieved by the spectral matching method.The synthetic data experiments show its robustness by comparing with the other state-of-art algorithms and the real world data experiments show its effectiveness.

  6. Gapped graphene-based Josephson junction with d-wave pair coupling

    Science.gov (United States)

    Goudarzi, H.; Khezerlou, M.; Dezhaloud, T.

    2013-06-01

    The Josephson current passing through a S/I/S gapped graphene-based junction, where superconductivity in the S region is induced by depositing unconventional d-wave superconductor is investigated. The energy levels of massive Dirac fermions are exactly found for Andreev bound states. We illustrate the effect of characteristic of d-wave pairing symmetry on the Andreev bound states and the Josephson current. It is shown that the Josephson current vanishes for special range of superconductivity phase, φ = φ1 - φ2 and the position of the maximum current depends on the mass gap of graphene. The critical supercurrent varies in an oscillatory manner as function of the barrier strength, so that the period of oscillations does not change by increasing the effective mass of quasiparticles.

  7. Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

    Science.gov (United States)

    2016-01-01

    Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

  8. Comment Fail-Stop Blind Signature Scheme Design Based on Pairings

    Institute of Scientific and Technical Information of China (English)

    HU Xiaoming; HUANG Shangteng

    2006-01-01

    Fail-stop signature schemes provide security for a signer against forgeries of an enemy with unlimited computational power by enabling the signer to provide a proof of forgery when a forgery happens. Chang et al proposed a robust fail-stop blind signature scheme based on bilinear pairings. However, in this paper, it will be found that there are several mistakes in Chang et al' fail-stop blind signature scheme. Moreover, it will be pointed out that this scheme doesn' meet the property of a fail-stop signature: unconditionally secure for a signer. In Chang et al' scheme, a forger can forge a valid signature that can' be proved by a signer using the "proof of forgery". The scheme also doesn' possess the unlinkability property of a blind signature.

  9. RMOD: a tool for regulatory motif detection in signaling network.

    Science.gov (United States)

    Kim, Jinki; Yi, Gwan-Su

    2013-01-01

    Regulatory motifs are patterns of activation and inhibition that appear repeatedly in various signaling networks and that show specific regulatory properties. However, the network structures of regulatory motifs are highly diverse and complex, rendering their identification difficult. Here, we present a RMOD, a web-based system for the identification of regulatory motifs and their properties in signaling networks. RMOD finds various network structures of regulatory motifs by compressing the signaling network and detecting the compressed forms of regulatory motifs. To apply it into a large-scale signaling network, it adopts a new subgraph search algorithm using a novel data structure called path-tree, which is a tree structure composed of isomorphic graphs of query regulatory motifs. This algorithm was evaluated using various sizes of signaling networks generated from the integration of various human signaling pathways and it showed that the speed and scalability of this algorithm outperforms those of other algorithms. RMOD includes interactive analysis and auxiliary tools that make it possible to manipulate the whole processes from building signaling network and query regulatory motifs to analyzing regulatory motifs with graphical illustration and summarized descriptions. As a result, RMOD provides an integrated view of the regulatory motifs and mechanism underlying their regulatory motif activities within the signaling network. RMOD is freely accessible online at the following URL: http://pks.kaist.ac.kr/rmod. PMID:23874612

  10. RMOD: a tool for regulatory motif detection in signaling network.

    Directory of Open Access Journals (Sweden)

    Jinki Kim

    Full Text Available Regulatory motifs are patterns of activation and inhibition that appear repeatedly in various signaling networks and that show specific regulatory properties. However, the network structures of regulatory motifs are highly diverse and complex, rendering their identification difficult. Here, we present a RMOD, a web-based system for the identification of regulatory motifs and their properties in signaling networks. RMOD finds various network structures of regulatory motifs by compressing the signaling network and detecting the compressed forms of regulatory motifs. To apply it into a large-scale signaling network, it adopts a new subgraph search algorithm using a novel data structure called path-tree, which is a tree structure composed of isomorphic graphs of query regulatory motifs. This algorithm was evaluated using various sizes of signaling networks generated from the integration of various human signaling pathways and it showed that the speed and scalability of this algorithm outperforms those of other algorithms. RMOD includes interactive analysis and auxiliary tools that make it possible to manipulate the whole processes from building signaling network and query regulatory motifs to analyzing regulatory motifs with graphical illustration and summarized descriptions. As a result, RMOD provides an integrated view of the regulatory motifs and mechanism underlying their regulatory motif activities within the signaling network. RMOD is freely accessible online at the following URL: http://pks.kaist.ac.kr/rmod.

  11. Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.

    Directory of Open Access Journals (Sweden)

    Miguel M Fonseca

    Full Text Available BACKGROUND: Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick base pairing between two nucleotides in RNA molecules to recognize one or more synonymous codons. Different hypotheses have been proposed to explain the factors that determine the nucleotide composition of wobble sites in vertebrate mitochondrial tRNA anticodons. Until now, the two major postulates--the "codon-anticodon adaptation hypothesis" and the "wobble versatility hypothesis"--have not been formally tested in vertebrate mitochondria because both make the same predictions regarding the composition of anticodon wobble sites. The same is true for the more recent "wobble cost hypothesis". PRINCIPAL FINDINGS: In this study we have analyzed the occurrence of synonymous codons and tRNA anticodon wobble sites in 1553 complete vertebrate mitochondrial genomes, focusing on three fish species with mtDNA codon usage bias reversal (L-strand is GT-rich. These mitogenomes constitute an excellent opportunity to study the evolution of the wobble nucleotide composition of tRNA anticodons because due to the reversal the predictions for the anticodon wobble sites differ between the existing hypotheses. We observed that none of the wobble sites of tRNA anticodons in these unusual mitochondrial genomes coevolved to match the new overall codon usage bias, suggesting that nucleotides at the wobble sites of tRNA anticodons in vertebrate mitochondrial genomes are determined by wobble versatility. CONCLUSIONS/SIGNIFICANCE: Our results suggest that, at wobble sites of tRNA anticodons in vertebrate mitogenomes, selection favors the most versatile nucleotide in terms of wobble base-pairing stability and that wobble site composition is not influenced by codon usage. These results are in agreement with the "wobble versatility hypothesis".

  12. Alpha Beta Monitoring System Based on a Pair of Simultaneous Multi Wire Proportional Counters

    International Nuclear Information System (INIS)

    A new approach for a simultaneous alpha beta contamination monitoring system is presented. In nuclear environments or laboratories working with open radioactive sources there exists a risk of contamination. In order to avoid external contamination hazards, hand & foot alpha beta monitoring systems are needed. Usually, monitoring systems are based on large area Multi Wire Proportional Counters (MWPC).Generally, in the MWPC detectors the filling gas is supplied by a continuous gas supply system. The filling gas should not exhibit appreciable electron attachment coefficient. Typically, a noble gas such as Argon Methane, 90%Ar+10%CH4 is in use. This method of measurement is effective, yet it requires expensive maintenance costs due to gas flow control and periodical replacements. Several hand held commercial detectors such as Rotem Ind. PA-100, are based on free air flow alpha MWPC. Due to the energy released from the alpha particles in the filling gas a large number of ion pairs are formed. Despite the electron attachment coefficient of free air, a measurable pulse is obtained. Contrary to alpha sources, beta emitters deposit only a small part of their energy. In order to obtain a measurable pulse from beta interactions, oxygen free gas is required. Gas sealed detectors which are appropriate for beta measurements, require a relative thick entrance window in order to avoid gas leakage. Thick windows absorb alpha particles so that they are not appropriate for alpha measurement. The presented approach combines a pair of simultaneous MWPC assembled in a ôpancakeö type configuration; the sealed gas beta counter is located behind a free air alpha detector. This approach enables simultaneous alpha-beta measurement without needing continuous gas supply

  13. Detecting DNA regulatory motifs by incorporating positional trendsin information content

    Energy Technology Data Exchange (ETDEWEB)

    Kechris, Katherina J.; van Zwet, Erik; Bickel, Peter J.; Eisen,Michael B.

    2004-05-04

    On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, we propose a simple extension to the model-based motif discovery methods. We assign position-specific prior distributions to the frequency parameters of the model, penalizing deviations from a specified conservation profile. Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif.

  14. Discriminative Motif Finding for Predicting Protein Subcellular Localization

    OpenAIRE

    Lin, Tien-ho; Murphy, Robert F.; Bar-Joseph, Ziv

    2011-01-01

    Many methods have been described to predict the subcellular location of proteins from sequence information. However, most of these methods either rely on global sequence properties or use a set of known protein targeting motifs to predict protein localization. Here we develop and test a novel method that identifies potential targeting motifs using a discriminative approach based on hidden Markov models (discriminative HMMs). These models search for motifs that are present in a compartment but...

  15. Protein functional-group 3D motif and its applications

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Representing and recognizing protein active sites sequence motif (1D motif) and structural motif (3D motif) is an important topic for predicting and designing protein function. Prevalent methods for extracting and searching 3D motif always consider residue as the minimal unit, which have limited sensitivity. Here we present a new spatial representation of protein active sites, called "functional-group 3D motif ", based on the fact that the functional groups inside a residue contribute mostly to its function. Relevant algorithm and computer program are developed, which could be widely used in the function prediction and the study of structural-function relationship of proteins. As a test, we defined a functional-group 3D motif of the catalytic triad and oxyanion hole with the structure of porcine trypsin (PDB code: 1mct) as the template. With our motif-searching program, we successfully found similar sub-structures in trypsins, subtilisins and a/b hydrolases, which show distinct folds but share similar catalytic mechanism. Moreover, this motif can be used to elucidate the structural basis of other proteins with variant catalytic triads by comparing it to those proteins. Finally, we scanned this motif against a non-redundant protein structure database to find its matches, and the results demonstrated the potential application of functional group 3D motif in function prediction. Above all, compared with the other 3D-motif representations on residues, the functional group 3D motif achieves better representation of protein active region, which is more sensitive for protein function prediction.

  16. Initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction for logic operations and amplified biosensing.

    Science.gov (United States)

    Bi, Sai; Yue, Shuzhen; Wu, Qiang; Ye, Jiayan

    2016-09-15

    Here we program an initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction. Due to the recycling of initiator and performance in a cascade manner, this system is versatilely extended to logic operations, including the construction of concatenated logic circuits with a feedback function and a biocomputing keypad-lock security system. Compared with previously reported molecular security systems, the prominent feature of our keypad lock is that it can be spontaneously reset and recycled with no need of any external stimulus and human intervention. Moreover, through integrating with an isothermal amplification technique of rolling circle amplification (RCA), this programming catalytic DNA self-assembly strategy readily achieves sensitive and selective biosensing of initiator. Importantly, a magnetic graphene oxide (MGO) is introduced to remarkably reduced background, which plays an important role in enhancing the signal-to-noise ratio and improving the detection sensitivity. Therefore, the proposed sophisticated DNA strand displacement-based methodology with engineering dynamic functions may find broad applications in the construction of programming DNA nanostructures, amplification biosensing platform, and large-scale DNA circuits. PMID:27132002

  17. MHC motif viewer

    DEFF Research Database (Denmark)

    Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole;

    2008-01-01

    In vertebrates, the major histocompatibility complex (MHC) presents peptides to the immune system. In humans, MHCs are called human leukocyte antigens (HLAs), and some of the loci encoding them are the most polymorphic in the human genome. Different MHC molecules present different subsets of....... Algorithms that predict which peptides MHC molecules bind have recently been developed and cover many different alleles, but the utility of these algorithms is hampered by the lack of tools for browsing and comparing the specificity of these molecules. We have, therefore, developed a web server, MHC motif...

  18. Novel H+-Ion Sensor Based on a Gated Lateral BJT Pair

    Directory of Open Access Journals (Sweden)

    Heng Yuan

    2015-12-01

    Full Text Available An H+-ion sensor based on a gated lateral bipolar junction transistor (BJT pair that can operate without the classical reference electrode is proposed. The device is a special type of ion-sensitive field-effect transistor (ISFET. Classical ISFETs have the advantage of miniaturization, but  they are difficult to fabricate by a single fabrication process because of the bulky and brittle reference electrode materials. Moreover, the reference electrodes need to be separated from the sensor device in some cases. The proposed device is composed of two gated lateral BJT components, one of which had a silicide layer while the other was without the layer. The two components were operated under the metal-oxide semiconductor field-effect transistor (MOSFET-BJT hybrid mode, which can be controlled by emitter voltage and base current. Buffer solutions with different pH values were used as the sensing targets to verify the characteristics of the proposed device. Owing to their different sensitivities, both components could simultaneously detect the H+-ion concentration and function as a reference to each other. Per the experimental results, the sensitivity of the proposed device was found to be approximately 0.175 μA/pH. This experiment demonstrates enormous potential to lower the cost of the ISFET-based sensor technology.

  19. Effect of base-pair inhomogeneities on charge transport along DNA mediated by twist and radial polarons

    OpenAIRE

    Palmero, F.; Archilla, J. F. R.; Hennig, D.; Romero, F. R.

    2003-01-01

    Some recent results for a three--dimensional, semi--classical, tight--binding model for DNA show that there are two types of polarons, named radial and twist polarons, that can transport charge along the DNA molecule. However, the existence of two types of base pairs in real DNA, makes it crucial to find out if charge transport also exist in DNA chains with different base pairs. In this paper we address this problem in its simple case, an homogeneous chain except for a single different base p...

  20. Effect of Interior Loop Length on the Thermal Stability and pKa of i-Motif DNA

    OpenAIRE

    Reilly, Samantha M.; Morgan, Rhianna K.; Brooks, Tracy A.; Randy M. Wadkins

    2015-01-01

    The four-stranded i-motif (iM) conformation of cytosine-rich DNA has importance to a wide variety of biochemical systems that range from its use in nanomaterials to a potential role in oncogene regulation. An iM is stabilized by acidic pH that allows hemiprotonated cytidines to form a C•C+ base pair. Fundamental studies to understand how the length of loops connecting the protonated C•C+ pairs affect intramolecular iM physical properties are described in this report. We characterized both the...

  1. Simulation-based investigation of the paired-gear method in cod-end selectivity studies

    DEFF Research Database (Denmark)

    Herrmann, Bent; Frandsen, Rikke; Holst, René; O'Neill, F.G.

    had a small mesh cover. Thus, estimates of the selectivity parameters of the test cod-end can be made using both the paired-gear method and the covered cod-end method. These estimates are compared and, as it is assumed that the covered cod-end method is objective, we conclude that the paired...

  2. Pairing symmetries of several iron-based superconductor families and some similarities with cuprates and heavy-fermions

    Directory of Open Access Journals (Sweden)

    Das Tanmoy

    2012-03-01

    Full Text Available We show that, by using the unit-cell transformation between 1 Fe per unit cell to 2 Fe per unit cell, one can qualitatively understand the pairing symmetry of several families of iron-based superconductors. In iron-pnictides and iron-chalcogenides, the nodeless s±-pairing and the resulting magnetic resonance mode transform nicely between the two unit cells, while retaining all physical properties unchanged. However, when the electron-pocket disappears from the Fermi surface with complete doping in KFe2As2, we find that the unit-cell invariant requirement prohibits the occurrence of s±-pairing symmetry (caused by inter-hole-pocket nesting. However, the intra-pocket nesting is compatible here, which leads to a nodal d-wave pairing. The corresponding Fermi surface topology and the pairing symmetry are similar to Ce-based heavy-fermion superconductors. Furthermore, when the Fermi surface hosts only electron-pockets in KyFe2-xSe2, the inter-electron-pocket nesting induces a nodeless and isotropic d-wave pairing. This situation is analogous to the electron-doped cuprates, where the strong antiferromagnetic order creates similar disconnected electron-pocket Fermi surface, and hence nodeless d-wave pairing appears. The unit-cell transformation in KyFe2-xSe2 exhibits that the d-wave pairing breaks the translational symmetry of the 2 Fe unit cell, and thus cannot be realized unless a vacancy ordering forms to compensate for it. These results are consistent with the coexistence picture of a competing order and nodeless d-wave superconductivity in both cuprates and KyFe1.6Se2.

  3. Cryptanalysis on Identity-based Authenticated Key Agreement Protocols from Pairings

    Directory of Open Access Journals (Sweden)

    Mengbo Hou

    2010-07-01

    Full Text Available Two-party authenticated key agreement protocol is used to authenticate entities and establish session keys in an open network in order to provide secure communications between two parties. Several security attributes are highly desired for such protocols, such as perfect forward secrecy (the corruption of long-term keys of all the entities should not compromise any session key, PKG forward secrecy (the corruption of the PKG's master key in the ID-based system should not compromise the established session keys, and known session-key specific temporary information secrecy (The exposure of private temporary information should not compromise the secrecy of generated session keys. In 2005, Choie et al. proposed three identity-based authenticated key agreement protocols from pairings. Our analysis shows that they all didn't provide protection against known session-key specific temporary information attack and some of them are vulnerable against man-in-the-middle attack, such as the key replicating attack. We analyze some of the attacks under the BR93 security model.

  4. Pair Frames

    OpenAIRE

    Fereydooni, Abolhassan; Safapour, Ahmad

    2011-01-01

    In this paper a new concept related to the frame theory is introduced; the notion of pair frame. By investigating some properties of such frames, it is shown that pair frames are a generalization of ordinary frames. Some classes of of them are introduced such as (p, q)-pair frames and near identity pair frames.

  5. Nucleon-pair states of even-even Sn isotopes based on realistic effective interactions

    Science.gov (United States)

    Cheng, Y. Y.; Qi, C.; Zhao, Y. M.; Arima, A.

    2016-08-01

    In this paper we study yrast states of 128,126,124Sn and 104,106,108Sn by using the monopole-optimized realistic interactions in terms of both the shell model (SM) and the nucleon-pair approximation (NPA). For yrast states of 128,126Sn and 104,106Sn, we calculate the overlaps between the wave functions obtained in the full SM space and those obtained in the truncated NPA space, and find that most of these overlaps are very close to 1. Very interestingly, for most of these states with positive parity and even spin or with negative parity and odd spin, the SM wave function is found to be well represented by one nucleon-pair basis state, viz., a simple picture of "nucleon-pair states" (nucleon-pair configuration without mixings) emerges. In 128,126Sn, the positive-parity (or negative-parity) yrast states with spin J >10 (or J >7 ) are found to be well described by breaking one or two S pairs in the 101+ (or 71-) state, i.e., the yrast state of seniority-two, spin-maximum, and positive-parity (or negative-parity), into non-S pair(s). Similar regularity is also pointed out for 104,106Sn. The evolution of E 2 transition rates between low-lying states in 128,126,124Sn is discussed in terms of the seniority scheme.

  6. Interfacial molecular recognition of adenine, adenosine and ATP by a C60-uracil adduct via complementary base pairing

    Science.gov (United States)

    Marczak, Renata; Hoang, Vu T.; Noworyta, Krzysztof; Zandler, Melvin E.; Kutner, Wlodzimierz; D'Souza, Francis

    2002-10-01

    A new C60-uracil adduct was demonstrated to recognize adenine, adenosine, or adenosine 5'-triphosphate (ATP) via complementary base pairing which led to complex formation. The base-pairing mechanism was modeled by ab initio B3LYP/3-21G(*) calculations which revealed the Watson-Crick (A-T) interactions. Stable "expanded liquid" Langmuir films of the complexes were prepared with the limiting area per molecule increasing for different subphase composition in the order: water < adenine < adenosine < ATP solution. Comparison of experimental and calculated areas per molecule and dipole moments suggest both prevailing horizontal orientation of the complexes in films.

  7. Polarization entangled photon-pair source based on a type-II PPLN waveguide emitting at a telecom wavelength

    CERN Document Server

    Martin, A; Herrmann, H; Sohler, W; Ostrowsky, D B; Alibart, O; Tanzilli, S

    2010-01-01

    We report the realization of a fiber coupled polarization entangled photon-pair source at 1310 nm based on a birefringent titanium in-diffused waveguide integrated on periodically poled lithium niobate. By taking advantage of an original setup, we characterized the quantum properties of the pairs by measuring two-photon interference in both Hong-Ou-Mandel and standard Bell inequality configurations. We obtained, for the two sets of measurements, interference net visibilities reaching nearly 100%, which represent the best results ever reported for similar waveguide-based configurations. These results prove the relevance of our approach as an enabling technology for long-distance quantum communication.

  8. Aztec, Incan and Mayan Motifs...Lead to Distinctive Designs.

    Science.gov (United States)

    Shields, Joanne

    2001-01-01

    Describes an art project for seventh-grade students in which they choose motifs based on Incan, Aztec, and Mayan Indian materials to incorporate into two-dimensional designs. Explains that the activity objective is to create a unified, balanced and pleasing composition using a minimum of three motifs. (CMK)

  9. Probing structural changes of self assembled i-motif DNA

    KAUST Repository

    Lee, Iljoon

    2015-01-01

    We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change. This journal is

  10. In vivo dynamics of enterovirus protease revealed by fluorescence resonance emission transfer (FRET) based on a novel FRET pair

    International Nuclear Information System (INIS)

    An in vivo protease assay suitable for analysis by fluorescence resonance energy transfer (FRET) was developed on the basis of a novel FRET pair. The specifically designed fusion substrate consists of green fluorescent protein 2 (GFP2)-peptide-red fluorescent protein 2 (DsRed2), with a cleavage motif for the enterovirus 2A protease (2Apro) embedded within the peptide region. FRET can be readily visualized in real-time from cells expressing the fusion substrate until a proteolytic cleavage by 2Apro from the input virus. The level of FRET decay is a function of the amount and infection duration of the inoculated virus as measured by a fluorometer assay. The FRET biosensor also responded well to other related enteroviruses but not to a phylogenetically distant virus. Western blot analysis confirmed the physical cleavage of the fusion substrate upon the infections. The study provides proof of principle for applying the FRET technology to diagnostics, screening procedures, and cell biological research

  11. Epitope-based vaccines with the Anaplasma marginale MSP1a functional motif induce a balanced humoral and cellular immune response in mice.

    Directory of Open Access Journals (Sweden)

    Paula S Santos

    Full Text Available Bovine anaplasmosis is a hemoparasitic disease that causes considerable economic loss to the dairy and beef industries. Cattle immunized with the Anaplasma marginale MSP1 outer membrane protein complex presents a protective humoral immune response; however, its efficacy is variable. Immunodominant epitopes seem to be a key-limiting factor for the adaptive immunity. We have successfully demonstrated that critical motifs of the MSP1a functional epitope are essential for antibody recognition of infected animal sera, but its protective immunity is yet to be tested. We have evaluated two synthetic vaccine formulations against A. marginale, using epitope-based approach in mice. Mice infection with bovine anaplasmosis was demonstrated by qPCR analysis of erythrocytes after 15-day exposure. A proof-of-concept was obtained in this murine model, in which peptides conjugated to bovine serum albumin were used for immunization in three 15-day intervals by intraperitoneal injections before challenging with live bacteria. Blood samples were analyzed for the presence of specific IgG2a and IgG1 antibodies, as well as for the rickettsemia analysis. A panel containing the cytokines' transcriptional profile for innate and adaptive immune responses was carried out through qPCR. Immunized BALB/c mice challenged with A. marginale presented stable body weight, reduced number of infected erythrocytes, and no mortality; and among control groups mortality rates ranged from 15% to 29%. Additionally, vaccines have significantly induced higher IgG2a than IgG1 response, followed by increased expression of pro-inflammatory cytokines. This is a successful demonstration of epitope-based vaccines, and protection against anaplasmosis may be associated with elicitation of effector functions of humoral and cellular immune responses in murine model.

  12. Model construction and pairing symmetry for the iron-based oxypnictides

    Energy Technology Data Exchange (ETDEWEB)

    Aoki, Hideo, E-mail: aoki@phys.s.u-tokyo.ac.j [Department of Physics, University of Tokyo, Hongo, Tokyo 113-0033 (Japan)

    2009-10-15

    PC-19-INV: In order to clarify the mechanism of superconductivity in the iron-based compound recently discovered by Hosono's group, we have first constructed a tight-binding model in terms of the maximally localized Wannier orbitals from a first-principles electronic structure calculation. The model has turned out to involve all the five Fe 3d bands. This is used to calculate the spin and charge susceptibilities with the five-band random-phase approximation, which are then plugged into the linearised Eliashberg equation. For a doped system we obtain an unconventional s-wave pairing with sign-reversing gap functions. To be more precise, the gap function is a 5x5 matrix, for which the diagonal elements mainly comprise d{sub x}{sup 2}{sub -y}{sup 2} and d{sub yz},d{sub xz} orbital components. The strong dependence of the gap between different orbitals may be observed experimentally.

  13. Simplified Aircraft-Based Paired Approach: Concept Definition and Initial Analysis

    Science.gov (United States)

    Johnson, Sally C.; Lohr, Gary W.; McKissick, Burnell T.; Abbott, Terence S.; Geurreiro, Nelson M.; Volk, Paul

    2013-01-01

    Simplified Aircraft-based Parallel Approach (SAPA) is an advanced concept proposed by the Federal Aviation Administration (FAA) to support dependent parallel approach operations to runways with lateral spacing closer than 2500 ft. At the request of the FAA, NASA performed an initial assessment of the potential performance and feasibility of the SAPA concept, including developing and assessing an operational implementation of the concept and conducting a Monte Carlo wake simulation study to examine the longitudinal spacing requirements. The SAPA concept was shown to have significant operational advantages in supporting the pairing of aircraft with dissimilar final approach speeds. The wake simulation study showed that support for dissimilar final approach speeds could be significantly enhanced through the use of a two-phased altitudebased longitudinal positioning requirement, with larger longitudinal positioning allowed for higher altitudes out of ground effect and tighter longitudinal positioning defined for altitudes near and in ground effect. While this assessment is preliminary and there are a number of operational issues still to be examined, it has shown the basic SAPA concept to be technically and operationally feasible.

  14. Decentralized supervisory based switching control for uncertain multivariable plants with variable input-output pairing.

    Science.gov (United States)

    Namaki-Shoushtari, Omid; Khaki-Sedigh, Ali

    2012-01-01

    In this paper, the design of decentralized switching control for uncertain multivariable plants is considered. In the proposed strategy, the uncertainty region is divided into smaller regions with a nominal model and specific control structure. The underlying design is based on the quantitative feedback theory (QFT). It is assumed that a MIMO-QFT controller exists for robust stability and performance of the individual uncertain sets. The proposed control structure is made up by these local decentralized controllers, which commute among themselves in accordance with the decision of a high level decision maker called the supervisor. The supervisor makes the decision by comparing the local models' behaviors with the one of the plant and selects the controller corresponding to the best fitted model. A hysteresis switching logic is used to slow down the switching to guarantee the overall closed loop stability. It is shown that this strategy provides a stable and robust adaptive controller to deal with complex multivariable plants with input-output pairing changes during the plant operation, which can facilitate the development of a reconfigurable decentralized control. Also, the multirealization technique is used to implement a family of controllers to achieve bumpless transfer. Simulation results are employed to show the effectiveness of the proposed method. PMID:21999896

  15. All-pairs Shortest Path Algorithm based on MPI+CUDA Distributed Parallel Programming Model

    Directory of Open Access Journals (Sweden)

    Qingshuang Wu

    2013-12-01

    Full Text Available In view of the problem that computing shortest paths in a graph is a complex and time-consuming process, and the traditional algorithm that rely on the CPU as computing unit solely can't meet the demand of real-time processing, in this paper, we present an all-pairs shortest paths algorithm using MPI+CUDA hybrid programming model, which can take use of the overwhelming computing power of the GPU cluster to speed up the processing. This proposed algorithm can combine the advantages of MPI and CUDA programming model, and can realize two-level parallel computing. In the cluster-level, we take use of the MPI programming model to achieve a coarse-grained parallel computing between the computational nodes of the GPU cluster. In the node-level, we take use of the CUDA programming model to achieve a GPU-accelerated fine grit parallel computing in each computational node internal. The experimental results show that the MPI+CUDA-based parallel algorithm can take full advantage of the powerful computing capability of the GPU cluster, and can achieve about hundreds of time speedup; The whole algorithm has good computing performance, reliability and scalability, and it is able to meet the demand of real-time processing of massive spatial shortest path analysis

  16. Doppler Broadening Analysis of Steel Specimens Using Accelerator Based In Situ Pair Production

    International Nuclear Information System (INIS)

    Positron Annihilation Spectroscopy (PAS) techniques can be utilized as a sensitive probe of defects in materials. Studying these microscopic defects is very important for a number of industries in order to predict material failure or structural integrity. We have been developing gamma-induced pair-production techniques to produce positrons in thick samples (∼4-40 g/cm2, or ∼0.5-5 cm in steel). These techniques are called 'Accelerator-based Gamma-induced Positron Annihilation Spectroscopy'(AG-PAS). We have begun testing the capabilities of this technique for imaging of defect densities in thick structural materials. As a first step, a linear accelerator (LINAC) was employed to produce photon beams by stopping 15 MeV electrons in a 1 mm thick tungsten converter. The accelerator is capable of operating with 30-60 ns pulse width, up to 200 mA peak current at 1 kHz repetition rate. The highly collimated bremsstrahlung beam impinged upon our steel tensile specimens, after traveling through a 1.2 m thick concrete wall. Annihilation radiation was detected by a well-shielded and collimated high-purity germanium detector (HPGe). Conventional Doppler broadening spectrometry (DBS) was performed to determine S, W and T parameters for our samples.

  17. Identification of a novel calcium binding motif based on the detection of sequence insertions in the animal peroxidase domain of bacterial proteins.

    Directory of Open Access Journals (Sweden)

    Saray Santamaría-Hernando

    Full Text Available Proteins of the animal heme peroxidase (ANP superfamily differ greatly in size since they have either one or two catalytic domains that match profile PS50292. The orf PP_2561 of Pseudomonas putida KT2440 that we have called PepA encodes a two-domain ANP. The alignment of these domains with those of PepA homologues revealed a variable number of insertions with the consensus G-x-D-G-x-x-[GN]-[TN]-x-D-D. This motif has also been detected in the structure of pseudopilin (pdb 3G20, where it was found to be involved in Ca(2+ coordination although a sequence analysis did not reveal the presence of any known calcium binding motifs in this protein. Isothermal titration calorimetry revealed that a peptide containing this consensus motif bound specifically calcium ions with affinities ranging between 33-79 µM depending on the pH. Microcalorimetric titrations of the purified N-terminal ANP-like domain of PepA revealed Ca(2+ binding with a K(D of 12 µM and stoichiometry of 1.25 calcium ions per protein monomer. This domain exhibited peroxidase activity after its reconstitution with heme. These data led to the definition of a novel calcium binding motif that we have termed PERCAL and which was abundantly present in animal peroxidase-like domains of bacterial proteins. Bacterial heme peroxidases thus possess two different types of calcium binding motifs, namely PERCAL and the related hemolysin type calcium binding motif, with the latter being located outside the catalytic domains and in their C-terminal end. A phylogenetic tree of ANP-like catalytic domains of bacterial proteins with PERCAL motifs, including single domain peroxidases, was divided into two major clusters, representing domains with and without PERCAL motif containing insertions. We have verified that the recently reported classification of bacterial heme peroxidases in two families (cd09819 and cd09821 is unrelated to these insertions. Sequences matching PERCAL were detected in all kingdoms of

  18. Universal quantum gates for Single Cooper Pair Box based quantum computing

    Science.gov (United States)

    Echternach, P.; Williams, C. P.; Dultz, S. C.; Braunstein, S.; Dowling, J. P.

    2000-01-01

    We describe a method for achieving arbitrary 1-qubit gates and controlled-NOT gates within the context of the Single Cooper Pair Box (SCB) approach to quantum computing. Such gates are sufficient to support universal quantum computation.

  19. Uncertainty evaluation for three-dimensional scanning electron microscope reconstructions based on the stereo-pair technique

    DEFF Research Database (Denmark)

    Carli, Lorenzo; Genta, G; Cantatore, Angela; Barbato, G; De Chiffre, Leonardo; Levi, R

    2011-01-01

    multiple-view reconstructions of the cylindrical item under consideration. Uncertainty evaluation was performed starting from a modified version of the Piazzesi equation, enabling the calculation of the z-coordinate from a given stereo-pair. The metrological characteristics of each input variable have been......3D-SEM is a method, based on the stereophotogrammetry technique, which obtains three-dimensional topographic reconstructions starting typically from two SEM images, called the stereo-pair. In this work, a theoretical uncertainty evaluation of the stereo-pair technique, according to GUM (Guide to...... the Expression of Uncertainty in Measurement), was carried out, considering 3D-SEM reconstructions of a wire gauge with a reference diameter of 250 µm. Starting from the more commonly used tilting strategy, one based on the item rotation inside the SEM chamber was also adopted. The latter enables...

  20. Metal-semiconductor pair nanoparticles by a physical route based on bipolar mixing

    Science.gov (United States)

    Kala, Shubhra; Theissmann, Ralf; Rouenhoff, Marcel; Kruis, Frank Einar

    2016-03-01

    In this report a methodology is described and demonstrated for preparing Au-Ge pair nanoparticles with known compositions by extending and modifying the basic steps normally used to synthesize nanoparticles in carrier gas. For the formation of pair nanoparticles by bipolar mixing, two oppositely charged aerosols of nanoparticles having the desired size are produced with the help of two differential mobility analyzers. Then both are allowed to pass through a tube, which provides sufficient residence time to result in nanoparticle pair formation due to Brownian collisions influenced by Coulomb forces. The effect of residence time on the formation of nanoparticle pairs as well as the influence of diffusion and discharging is described. Subsequently, necessary modifications to the experimental setup are demonstrated systematically. The kinetics of nanoparticles pair formation in a carrier gas is also calculated and compared with measurements made with the help of an online aerosol size analysis technique. This synthesis of nanoparticle pairs can be seen as a possible route towards Janus-type nanoparticles.

  1. Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs

    Energy Technology Data Exchange (ETDEWEB)

    Patra, Amritraj [Vanderbilt Univ., Nashville, TN (United States); Harp, Joel [Vanderbilt Univ., Nashville, TN (United States); Pallan, Pradeep S. [Vanderbilt Univ., Nashville, TN (United States); Zhao, Linlin [Vanderbilt Univ., Nashville, TN (United States); Abramov, Mikhail [Rega Inst. for Medical Research (Belgium); Herdewijn, Piet [Rega Inst. for Medical Research (Belgium); Univ. of Evry-Val-d' Essonne (France); Egli, Martin [Vanderbilt Univ., Nashville, TN (United States)

    2012-12-28

    The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli strain relies on the four building blocks 5-chloro-2'-deoxyuridine (ClU), A, C and G instead of the standard T, A, C, G alphabet [Marlière,P., Patrouix,J., Döring,V., Herdewijn,P., Tricot,S., Cruveiller,S., Bouzon,M. and Mutzel,R. (2011) Chemical evolution of a bacterium’s genome. Angew. Chem. Int. Ed., 50, 7109–7114]. The residual fraction of T in the DNA of adapted bacteria was <2% and the switch from T to ClU was accompanied by a massive number of mutations, including >1500 A to G or G to A transitions in a culture. The former is most likely due to wobble base pairing between ClU and G, which may be more common for ClU than T. To identify potential changes in the geometries of base pairs and duplexes as a result of replacement of T by ClU, we determined four crystal structures of a B-form DNA dodecamer duplex containing ClU:A or ClU:G base pairs. The structures reveal nearly identical geometries of these pairs compared with T:A or T:G, respectively, and no consequences for stability and cleavage by an endonuclease (EcoRI). The lack of significant changes in the geometry of ClU:A and ClU:G base pairs relative to the corresponding native pairs is consistent with the sustained unlimited self-reproduction of E. coli strains with virtually complete T→ClU genome substitution.

  2. Universal Quantitative Kinase Assay Based on Diagonal SCX Chromatography and Stable Isotope Dimethyl Labeling Provides High-definition Kinase Consensus Motifs for PKA and Human Mps1

    NARCIS (Netherlands)

    Hennrich, Marco L.; Marino, Fabio; Groenewold, Vincent; Kops, Geert J. P. L.; Mohammed, Shabaz; Heck, Albert J. R.

    2013-01-01

    In order to understand cellular signaling, a clear understanding of kinase-substrate relationships is essential. Some of these relationships are defined by consensus recognition motifs present in substrates making them amendable for phosphorylation by designated kinases. Here, we explore a method th

  3. Photoinduced electron transfer in a Watson-Crick base-paired, 2-aminopurine:uracil-C60 hydrogen bonding conjugate.

    Science.gov (United States)

    D'Souza, Francis; Gadde, Suresh; Islam, D-M Shafiqul; Pang, Siew-Cheng; Schumacher, Amy Lea; Zandler, Melvin E; Horie, Rumiko; Araki, Yasuyaki; Ito, Osamu

    2007-02-01

    A fluorescent reporter molecule, 2-aminopurine was self-assembled via Watson-Crick base-pairing to a uracil appended fullerene to form a donor-acceptor conjugate; efficient photoinduced charge separation was confirmed by time-resolved emission and transient absorption spectral studies. PMID:17252101

  4. A 3-base pair deletion, c.9711_9713del, in DMD results in intellectual disability without muscular dystrophy

    NARCIS (Netherlands)

    de Brouwer, Arjan P. M.; Nabuurs, Sander B.; Verhaart, Ingrid E. C.; Oudakker, Astrid R.; Hordijk, Roel; Yntema, Helger G.; Hordijk-Hos, Jannet M.; Voesenek, Krysta; de Vries, Bert B. A.; van Essen, Ton; Chen, Wei; Hu, Hao; Chelly, Jamel; den Dunnen, Johan T.; Kalscheuer, Vera M.; Aartsma-Rus, Annemieke M.; Hamel, Ben C. J.; van Bokhoven, Hans; Kleefstra, Tjitske

    2014-01-01

    We have identified a deletion of 3 base pairs in the dystrophin gene (DMD), c.9711_9713del, in a family with nonspecific X-linked intellectual disability (ID) by sequencing of the exons of 86 known X-linked ID genes. This in-frame deletion results in the deletion of a single-amino-acid residue, Leu3

  5. Intrastrand base pairing in single-stranded deoxyribonucleic acid from ColE1-derived plasmid pCR1.

    OpenAIRE

    Edlind, T D; Ihler, G M

    1981-01-01

    Single strands of EcoRI-cleaved pCR1 deoxyribonucleic acid were examined by electron microscopy for intrastrand base pairing by using partial denaturing conditions. The locations of three stem and loop structures were mapped relative to the inverted repeat of Tn903. Potential roles and origins of these loops are discussed.

  6. Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

    Directory of Open Access Journals (Sweden)

    Farré Domènec

    2007-12-01

    Full Text Available Abstract Background The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.

  7. Comparison of Three Cre-LoxP Based Paired-End Library Construction Methods

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Ze; Nath, Nandita; Tritt, Andrew; Liang, Shoudan; Han, James; Pennacchio, Len; Chen, Feng

    2013-03-26

    Paired-end library sequencing has been proven useful in scaffold construction during de novo whole genome shotgun assembly. The ability of generating mate pairs with > 8 Kb insert sizes is especially important for genomes containing long repeats. To make mate paired libraries for next generation sequencing, DNA fragments need to be circularized to bring the ends together. There are several methods that can be used for DNA circulation, namely ligation, hybridization and Cre-LoxP recombination. With higher circularization efficiency with large insert DNA fragments, Cre-LoxP recombination method generally has been used for constructing >8 kb insert size paired-end libraries. Second fragmentation step is also crucial for maintaining high library complexity and uniform genome coverage. Here we will describe the following three fragmentation methods: restriction enzyme digestion, random shearing and nick translation. We will present the comparison results for these three methods. Our data showed that all three methods are able to generate paired-end libraries with greater than 20 kb insert. Advantages and disadvantages of these three methods will be discussed as well.

  8. Plant trials of an on-stream iron ore analyser based on pair production

    International Nuclear Information System (INIS)

    An on-stream iron ore analyser, called Ironscan, has been developed in collaboration with Hamersley Iron Pty Limited for measuring the iron content of iron ore on conveyor belts. The analyser is based on pair production and irradiates the ore with gamma rays from a 226Ra source. A big advantage of the analyser is that it can be mounted under existing conveyor belts with minimal modifications to the conveyor structure, and the presence of steel reinforcement cables in the belt does not interfere once the analyser has been correctly calibrated. After dynamic trials of a laboratory prototype on a small conveyor facility at Port Melbourne to demonstrate the viability of the method for lumps (-30 + 6 mm particle size) and fines (-6 mm particle size), an industrial prototype was manufactured by Mineral Control Instrumentation Limited in Adelaide (now the Commonwealth Scientific and Industrial Research Organisation licensee) and extensively tested at the Hamersley Iron operations in Dampier and Mount Tom Price, Western Australia. At Dampier, it was installed on the main shiploading conveyor to assess its performance on the normal lumps and fines that are exported. The root mean square (RMS) deviation between single Ironscan measurements and conventional chemical analyses was about 0.4% Fe. The analyser was then evaluated on -150 mm ore from the primary crusher at Mount Tom Price. While it was clear that ore grade could be measured even at this coarse particle size, it was very difficult to obtain comparable chemical analyses and there was insufficient data to estimate the RMS deviation. (author). 6 refs, 7 figs, 1 tab

  9. Carcinogenesis of asbestos switched on by inducing cross-linkage between DNA complementary pair bases

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Since the beginning of the 1980s, Dai Qianhuan predicted based upon his di-region theory that the carcinogenesis switched on by the so-called physical carcinogenic factors including radiation, asbestos and foreign matter implantation, is just initiated through the cross-linking between DNA complementary pair bases induced by them. In this note, it was evidenced with the DNA filter elution method that the oxygenase activated by asbestos induces the cross-linking between DNA inter-strands and DNA-protein with dosage correlation, in which over 80% of DNA inter-strand cross-link ratio account for the total cross-link ratio. Obviously, both of the cross-linkages are just induced by hydroxyl free radical, HO@, because the ferrous ion increased the cross-link ratios up to several times through Fenton reaction and vitamin C inhibited the cross-link ratios with factors of 8-9 by destroying the hydroxyl radical. Non-carcinogen but with lower free radical formation energy, pyrene, by culturing with asbestos gave 3-4 times cross-link ratios than the original ratios induced by asbestos only. Estradiol, an endogenous carcinogen, as a bio-electrophilic species but with higher free radical formation energy by culturing with asbestos, gave only 1.2 time cross-link ratios than expected ones. Ferrous ion which can increase HO@ concentration through Fenton reaction, increased the ratios to 2-2.5 times in the former case but only 1.2 time in the latter case. Vitamin C, a free radical scavenger, gave a powerful inhibition to the cross-linking with a factor of 8-11 in the former case but a weak inhibition with a factor of 1.2 only in the latter case. So, it is evidenced further that the cross-linkages induced by asbestos are originated from hydroxyl radical. Reasonable structures of the cross-linking products induced by asbestos or hydroxyl radical have been depicted based upon AM1 MO theory. These structures have been verified further by a reasonable explanation of the mutational

  10. A structure filter for the Eukaryotic Linear Motif Resource

    Directory of Open Access Journals (Sweden)

    Gemünd Christine

    2009-10-01

    Full Text Available Abstract Background Many proteins are highly modular, being assembled from globular domains and segments of natively disordered polypeptides. Linear motifs, short sequence modules functioning independently of protein tertiary structure, are most abundant in natively disordered polypeptides but are also found in accessible parts of globular domains, such as exposed loops. The prediction of novel occurrences of known linear motifs attempts the difficult task of distinguishing functional matches from stochastically occurring non-functional matches. Although functionality can only be confirmed experimentally, confidence in a putative motif is increased if a motif exhibits attributes associated with functional instances such as occurrence in the correct taxonomic range, cellular compartment, conservation in homologues and accessibility to interacting partners. Several tools now use these attributes to classify putative motifs based on confidence of functionality. Results Current methods assessing motif accessibility do not consider much of the information available, either predicting accessibility from primary sequence or regarding any motif occurring in a globular region as low confidence. We present a method considering accessibility and secondary structural context derived from experimentally solved protein structures to rectify this situation. Putatively functional motif occurrences are mapped onto a representative domain, given that a high quality reference SCOP domain structure is available for the protein itself or a close relative. Candidate motifs can then be scored for solvent-accessibility and secondary structure context. The scores are calibrated on a benchmark set of experimentally verified motif instances compared with a set of random matches. A combined score yields 3-fold enrichment for functional motifs assigned to high confidence classifications and 2.5-fold enrichment for random motifs assigned to low confidence classifications

  11. A terrain-based paired-site sampling design to assess biodiversity losses from eastern hemlock decline

    Science.gov (United States)

    Young, J.A.; Smith, D.R.; Snyder, C.D.; Lemarie, D.P.

    2002-01-01

    Biodiversity surveys are often hampered by the inability to control extraneous sources of variability introduced into comparisons of populations across a heterogenous landscape. If not specifically accounted for a priori, this noise can weaken comparisons between sites, and can make it difficult to draw inferences about specific ecological processes. We developed a terrain-based, paired-site sampling design to analyze differences in aquatic biodiversity between streams draining eastern hemlock (Tsuga canadensis) forests, and those draining mixed hardwood forests in Delaware Water Gap National Recreation Area (USA). The goal of this design was to minimize variance due to terrain influences on stream communities, while representing the range of hemlock dominated stream environments present in the park. We used geographic information systems (GIS) and cluster analysis to define and partition hemlock dominated streams into terrain types based on topographic variables and stream order. We computed similarity of forest stands within terrain types and used this information to pair hemlock-dominated streams with hardwood counterparts prior to sampling. We evaluated the effectiveness of the design through power analysis and found that power to detect differences in aquatic invertebrate taxa richness was highest when sites were paired and terrain type was included as a factor in the analysis. Precision of the estimated difference in mean richness was nearly doubled using the terrain-based, paired site design in comparison to other evaluated designs. Use of this method allowed us to sample stream communities representative of park-wide forest conditions while effectively controlling for landscape variability.

  12. Quantum heat engine based on photon-assisted Cooper pair tunneling

    Science.gov (United States)

    Hofer, Patrick P.; Souquet, J.-R.; Clerk, A. Â. A.

    2016-01-01

    We propose and analyze a simple mesoscopic quantum heat engine that exhibits both high power and high efficiency. The system consists of a biased Josephson junction coupled to two microwave cavities, with each cavity coupled to a thermal bath. Resonant Cooper pair tunneling occurs with the exchange of photons between cavities, and a temperature difference between the baths can naturally lead to a current against the voltage, and hence work. As a consequence of the unique properties of Cooper-pair tunneling, the heat current is completely separated from the charge current. This combined with the strong energy selectivity of the process leads to an extremely high efficiency.

  13. Salt dependent premelting base pair opening probabilities of B and Z DNA Poly [d(G-C)] and significance for the B-Z transition

    OpenAIRE

    Chen, Y. Z.; Prohofsky, E W

    1993-01-01

    We calculate room temperature thermal fluctuational base pair opening probabilities of B and Z DNA Poly[d(G-C)] at various salt concentrations and discuss the significance of thermal fluctuation in facilitating base pair disruption during B to Z transition. Our calculated base pair opening probability of the B DNA at lower salt concentrations and the probability of the Z DNA at high salt concentrations are in agreement with observations. The salt dependence of the probabilities indicates a B ...

  14. Automatic annotation of protein motif function with Gene Ontology terms

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Vanathi

    2004-09-01

    Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.

  15. Adjusted Wald Confidence Interval for a Difference of Binomial Proportions Based on Paired Data

    Science.gov (United States)

    Bonett, Douglas G.; Price, Robert M.

    2012-01-01

    Adjusted Wald intervals for binomial proportions in one-sample and two-sample designs have been shown to perform about as well as the best available methods. The adjusted Wald intervals are easy to compute and have been incorporated into introductory statistics courses. An adjusted Wald interval for paired binomial proportions is proposed here and…

  16. Ferrocene-based Lewis acids and Lewis pairs: Synthesis and structural characterization

    Indian Academy of Sciences (India)

    Pagidi Sudhakar; Pakkirisamy Thilagar

    2013-01-01

    Optically active Lewis acids and Lewis pairs were synthesized and characterized by multinuclear NMR, UV/Vis spectroscopy and elemental analysis. Optical rotation measurements were carried out and the absolute configuration of the new chiral molecules confirmed by single crystal X-ray diffraction.

  17. Classification between normal and tumor tissues based on the pair-wise gene expression ratio

    International Nuclear Information System (INIS)

    Precise classification of cancer types is critically important for early cancer diagnosis and treatment. Numerous efforts have been made to use gene expression profiles to improve precision of tumor classification. However, reliable cancer-related signals are generally lacking. Using recent datasets on colon and prostate cancer, a data transformation procedure from single gene expression to pair-wise gene expression ratio is proposed. Making use of the internal consistency of each expression profiling dataset this transformation improves the signal to noise ratio of the dataset and uncovers new relevant cancer-related signals (features). The efficiency in using the transformed dataset to perform normal/tumor classification was investigated using feature partitioning with informative features (gene annotation) as discriminating axes (single gene expression or pair-wise gene expression ratio). Classification results were compared to the original datasets for up to 10-feature model classifiers. 82 and 262 genes that have high correlation to tissue phenotype were selected from the colon and prostate datasets respectively. Remarkably, data transformation of the highly noisy expression data successfully led to lower the coefficient of variation (CV) for the within-class samples as well as improved the correlation with tissue phenotypes. The transformed dataset exhibited lower CV when compared to that of single gene expression. In the colon cancer set, the minimum CV decreased from 45.3% to 16.5%. In prostate cancer, comparable CV was achieved with and without transformation. This improvement in CV, coupled with the improved correlation between the pair-wise gene expression ratio and tissue phenotypes, yielded higher classification efficiency, especially with the colon dataset – from 87.1% to 93.5%. Over 90% of the top ten discriminating axes in both datasets showed significant improvement after data transformation. The high classification efficiency achieved suggested

  18. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun

    2013-06-29

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors\\' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  19. A luminescence switch-on probe for terminal deoxynucleotidyl transferase (TdT) activity detection by using an iridium(III)-based i-motif probe.

    Science.gov (United States)

    Lu, Lihua; Wang, Modi; Liu, Li-Juan; Wong, Chun-Yuen; Leung, Chung-Hang; Ma, Dik-Lung

    2015-06-21

    An iridium(III) complex exhibiting higher responce towards i-motif DNA over dsDNA and ssDNA was employed for the construction of a TdT activity detection platform. The assay exhibited a linear signal enhancement for TdT in the concentration range of 0 to 8 U mL(-1), and the limit of detection for TdT was 0.25 U mL(-1). PMID:25999030

  20. RNAMotifScanX: a graph alignment approach for RNA structural motif identification

    OpenAIRE

    Zhong, Cuncong; Zhang, Shaojie

    2015-01-01

    RNA structural motifs are recurrent three-dimensional (3D) components found in the RNA architecture. These RNA structural motifs play important structural or functional roles and usually exhibit highly conserved 3D geometries and base-interaction patterns. Analysis of the RNA 3D structures and elucidation of their molecular functions heavily rely on efficient and accurate identification of these motifs. However, efficient RNA structural motif search tools are lacking due to the high complexit...

  1. A Point Pairing Method Based on the Principle of Material Frame Indifference for the Characterization of Unknown Space Objects using Space-Based Non-Resolved Photometry Data

    Science.gov (United States)

    Chaudhary, A.; Payne, T.; Dao, P.; Murray-Krezan, J.; Lucas, K.; Mutschler, S.

    2013-09-01

    The point pairing method in this paper is based on set of simple physical truths for three-axis stabilized space objects in the geosynchronous orbit (GEO). It defines a method for the calculation of pairs of observation conditions (i.e. point pairs) that have a special property for three-axis stabilized GEO object characterization. An observation condition is defined to be the geometry of illumination for the solar panel and the body of the satellite and the geometry of its observation by a sensor. The physical truths are due to observation conditions that are equivalent with respect to either the solar panel or body for a pair of points, which can be identified analytically. When the observation conditions are equivalent for the solar panel, the contribution to the GEO object brightness by the solar panel at those pair of points is identical. Then the difference between the pair of brightness values cancels the solar panel contribution unconditionally and the remainder is only due to the body. Similarly, when the contribution of the body to the observed brightness is same for the point pair, the difference between the two brightness values cancels the body contribution unconditionally and the remainder is only due to the solar panels. This enables separation of the observed brightness data into contributions by the solar panels and the body, which is fundamental to space-object characterization. This separation of the solar panel or body contributions is feasible in each waveband of observation. Thus the point pairing is useful for the analysis of panchromatic as well as multi-spectral data. The desired observation conditions for point pairing occur routinely, typically within a week of each other. This work is supported by the Space Vehicles Directorate of the Air Force Materials Laboratory.

  2. A model for 3:2 HFQPO pairs in black hole binaries based on cosmic battery

    CERN Document Server

    Huang, Chang-Yin; Wang, Ding-Xiong; Li, Yang

    2016-01-01

    A model for 3:2 high-frequency quasi-periodic oscillations (HFQPOs) with 3:2 pairs observed in four black hole X-ray binaries (BHXBs) is proposed by invoking the epicyclic resonances with the magnetic connection (MC) between a spinning black hole (BH) with a relativistic accretion disc. It turns out that the MC can be worked out due to Poynting-Robertson cosmic battery (PRCB), and the 3:2 HFQPO pairs associated with the steep power-law states can be fitted in this model. Furthermore, the severe damping problem in the epicyclic resonance model can be overcome by transferring energy from the BH to the inner disc via the MC process for emitting X-rays with sufficient amplitude and coherence to produce the HFQPOs. In addition, we discuss the important role of the magnetic field in state transition of BHXBs.

  3. 3D broadband isotropic NRI metamaterial based on metallic cross-pairs

    International Nuclear Information System (INIS)

    In this paper, a new type of 3D metamaterial composed of double periodic array of metallic cross-pairs printed on the six sides of a cubic dielectric substrate was proposed to obtain the characteristics of broadband NRI and isotropy for the applications of super lenses. The behaviors of NRI, isotropy and polarization were analyzed using the CST Microwave Studio. The results show that the proposed metamaterial exhibits not only a broadband NRI whose relative bandwidth can be up to 56.7%, but also polarization-independence and isotropy. Thus, the proposed metamaterial is a good candidate material for 3D broadband isotropic NRI metamaterial. - Highlights: → 3D metamaterial is composed of double periodic array of metallic cross-pairs printed on the six sides of a cubic dielectric substrate. → Broadband negative refraction index (NRI) with relative bandwidth of 56.7%. → Polarization-independence and isotropy.

  4. Watson-Crick Base Pairing, Electronic and Photophysical Properties of Triazole Modified Adenine Analogues: A Computational Study

    KAUST Repository

    Das, Shubhajit

    2015-09-17

    We employ first-principles Density Functional Theory (DFT) and time-dependent DFT (TDDFT) to elucidate structural, electronic and optical properties of a few recently reported triazole adenine nucleobase analogues. The results are compared against the findings obtained for both natural adenine nucleobase and available experimental data. The optical absorption of these adenine analogues are calculated both in gas-phase and in solvent (methanol) using Polarized Continuum Model (PCM). We find that all the analogues show a red-shifted absorption profile as compared to adenine. Our simulated emission spectra in solvent compare fairly well with experimentally observed results. We investigate base paring ability of these adenine analogues with thymine. The calculations on the intrinsic stability of these base pairs ascertain that all the adenine analogues form the hydrogen bonded Watson-Crick base pair with similar H-bonding energy as obtained for natural adenine-thymine base pair. In our study, we provide a microscopic origin of the low-energy absorption and emission peaks, observed experimentally.

  5. A Practical Parallel Algorithm for All-Pair Shortest Path Based on Pipelining

    Institute of Scientific and Technical Information of China (English)

    Hua Wang; Ling Tian; Chun-Hua Jiang

    2008-01-01

    On the basis of Floyd algorithm with theextended path matrix, a parallel algorithm whichresolves all-pair shortest path (APSP) problem oncluster environment is analyzed and designed.Meanwhile, the parallel APSP pipelining algorithmmakes full use of overlapping technique betweencomputation and communication. Compared withbroadcast operation, the parallel algorithm reducescommunication cost. This algorithm has beenimplemented on MPI on PC-cluster. The theoreticalanalysis and experimental results show that the parallelalgorithm is an efficient and scalable algorithm.

  6. A polarization entangled photon-pair source based on a type-II PPLN waveguide emitting at a telecom wavelength

    International Nuclear Information System (INIS)

    We report the realization of a fiber-coupled polarization entangled photon-pair source at 1310 nm based on a birefringent titanium in-diffused waveguide integrated into periodically poled lithium niobate. By making use of a dedicated and high-performance setup, we characterized the quantum properties of the pairs by measuring two-photon interference in both Hong-Ou-Mandel and standard Bell inequality configurations. For the two sets of measurements we obtained interference net visibilities reaching nearly 100%, which represent important and competitive results compared to those for the similar waveguide-based configurations already reported. These results prove the relevance of our approach as an enabling technology for long-distance quantum communication.

  7. Electronic structure of an anticancer drug DC81 and its interaction with DNA base pairs

    Science.gov (United States)

    Tiwari, Gargi; Sharma, Dipendra; Dwivedi, K. K.; Dwivedi, M. K.

    2016-05-01

    The drug, 8-Hydroxy-7-methoxy-pyrrolo-[2,1-c][1,4] benzodiazepine-5-one, commonly christened as DC81 belongs to the pyrrolo-[2,1-c][1,4]benzodiazepine (PBDs) family. It is a member of the group of naturally occurring antitumour antibiotics produced by various Streptomyces species. The antitumour activity of DC81 is attributed to its sequence specific interaction with G-C rich DNA region in particular, for Pu-G-Pu motifs. In the present paper, physico-chemical properties DC81 have been carried out using an ab-initio method, HF/6-31G(d,p) with GAMESS program. MEP, HOMO and LUMO surfaces have been scanned. Ionization potential, electron affinity, electronegativity, global hardness and softness of the drug have been calculated. Further, drug-DNA interactions have been examined using modified second order perturbation theory along with multicentred-multipole expansion technique. Results have been discussed in the light of other theoretical and experimental observations. Efforts have been made to elucidate the binding patterns and thereby biological properties of the drug.

  8. Motif-specific sampling of phosphoproteomes

    OpenAIRE

    Ruse, Cristian I.; McClatchy, Daniel B.; Lu, Bingwen; Cociorva, Daniel; Motoyama, Akira; Kyu Park, Sung; Yates, John R.

    2008-01-01

    Phosphoproteomics, the targeted study of a subfraction of the proteome which is modified by phosphorylation, has become an indispensable tool to study cell signaling dynamics. We described a methodology that linked phosphoproteome and proteome analysis based on Ba2+ binding properties of amino acids. This technology selected motif-specific phosphopeptides independent of the system under analysis. MudPIT (Multidimensional Identification Technology) identified 1037 precipitated phosphopeptides ...

  9. Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

    Czech Academy of Sciences Publication Activity Database

    Morgado, C.A.; Svozil, D.; Turner, D.H.; Šponer, Jiří

    2012-01-01

    Roč. 14, č. 36 (2012), s. 12580-12591. ISSN 1463-9076 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional research plan: CEZ:AV0Z50040702 Keywords : GA base pairs * base stacking * RNA duplexes Subject RIV: BO - Biophysics Impact factor: 3.829, year: 2012

  10. PhosphoScan: A Probability-Based Method for Phosphorylation Site Prediction Using MS2/MS3 Pair Information

    OpenAIRE

    Wan, Yunhu; Cripps, Diane; Thomas, Stefani; Campbell, Patricia; Ambulos, Nicholas; CHEN Ting; Yang, Austin

    2008-01-01

    Phosphopeptide identification and phosphorylation site localization are crucial aspects of many biological studies. Furthermore, multiple phosphorylations of peptides make site localization even more difficult. We developed a probability-based method to unambiguously determine phosphorylation sites within phosphopeptides using MS2/3 pair information. A comparison test was performed with SEQUEST and MASCOT predictions using a spectral data set from a synthetic doubly phosphorylated peptide, an...

  11. A new image reconstruction method for 3-D PET based upon pairs of near-missing lines of response

    International Nuclear Information System (INIS)

    We formerly introduced a new image reconstruction method for three-dimensional positron emission tomography, which is based upon pairs of near-missing lines of response. This method uses an elementary geometric property of lines of response, namely that two lines of response which originate from radioactive isotopes located within a sufficiently small voxel, will lie within a few millimeters of each other. The effectiveness of this method was verified by performing a simulation using GATE software and a digital Hoffman phantom

  12. Detection of Wuchereria bancrofti DNA in paired serum and urine samples using polymerase chain reaction-based systems

    OpenAIRE

    Camila Ximenes; Eduardo Brandão; Paula Oliveira; Abraham Rocha; Tamisa Rego; Rafael Medeiros; Ana Aguiar-Santos; João Ferraz; Christian Reis; Paulo Araujo; Luiz Carvalho; Melo, Fabio L

    2014-01-01

    The Global Program for the Elimination of Lymphatic Filariasis (GPELF) aims to eliminate this disease by the year 2020. However, the development of more specific and sensitive tests is important for the success of the GPELF. The present study aimed to standardise polymerase chain reaction (PCR)-based systems for the diagnosis of filariasis in serum and urine. Twenty paired biological urine and serum samples from individuals already known to be positive for Wuche...

  13. UvrD Helicase Unwinds DNA One Base Pair At A Time By A Two-Part Power Stroke

    OpenAIRE

    Lee, Jae Young; Yang, Wei

    2006-01-01

    Helicases use the energy derived from nucleoside triphosphate hydrolysis to unwind double helices in essentially every metabolic pathway involving nucleic acids. Earlier crystal structures have suggested that DNA helicases translocate along a single-stranded DNA in an inchworm fashion. We report here a series of crystal structures of the UvrD helicase complexed with DNA and ATP hydrolysis intermediates. These structures reveal that ATP binding alone leads to unwinding of 1 base pair by direct...

  14. A Practical Parallel Algorithm for All-Pair Shortest Path Based on Pipelining

    Institute of Scientific and Technical Information of China (English)

    Hua Wang; Ling Tian; Chun-Hua Jiang

    2008-01-01

    On the basis of Floyd algorithm with the extended path matrix, a parallel algorithm which resolves all-pair shortest path (APSP) problem on cluster environment is analyzed and designed. Meanwhile, the parallel APSP pipelining algorithm makes full use of overlapping technique between computation and communication. Compared with broadcast operation, the parallel algorithm reduces communication cost. This algorithm has been implemented on MPI on PC-cluster. The theoretical analysis and experimental results show that the parallel algorithm is an efficient and scalable algorithm.

  15. All-pairs Shortest Path Algorithm based on MPI+CUDA Distributed Parallel Programming Model

    OpenAIRE

    Qingshuang Wu; Chunya Tong; Qiang Wang; Xiangfu Cheng

    2013-01-01

    In view of the problem that computing shortest paths in a graph is a complex and time-consuming process, and the traditional algorithm that rely on the CPU as computing unit solely can't meet the demand of real-time processing, in this paper, we present an all-pairs shortest paths algorithm using MPI+CUDA hybrid programming model, which can take use of the overwhelming computing power of the GPU cluster to speed up the processing. This proposed algorithm can combine the advantages of MPI and ...

  16. Uncertainty evaluation for three-dimensional scanning electron microscope reconstructions based on the stereo-pair technique

    International Nuclear Information System (INIS)

    3D-SEM is a method, based on the stereophotogrammetry technique, which obtains three-dimensional topographic reconstructions starting typically from two SEM images, called the stereo-pair. In this work, a theoretical uncertainty evaluation of the stereo-pair technique, according to GUM (Guide to the Expression of Uncertainty in Measurement), was carried out, considering 3D-SEM reconstructions of a wire gauge with a reference diameter of 250 µm. Starting from the more commonly used tilting strategy, one based on the item rotation inside the SEM chamber was also adopted. The latter enables multiple-view reconstructions of the cylindrical item under consideration. Uncertainty evaluation was performed starting from a modified version of the Piazzesi equation, enabling the calculation of the z-coordinate from a given stereo-pair. The metrological characteristics of each input variable have been taken into account and a SEM stage calibration has been performed. Uncertainty tables for the cases of tilt and rotation were then produced, leading to the calculation of expanded uncertainty. For the case of rotation, the largest uncertainty contribution resulted to be the rotational angle; however, for the case of tilt it resulted to be the pixel size. A relative expanded uncertainty equal to 5% and 4% was obtained for the case of rotation and tilt, respectively

  17. ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets

    OpenAIRE

    Pope, Bernard J.; Nguyen-Dumont, Tú; Hammet, Fleur; Park, Daniel J

    2014-01-01

    Background We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequencing (MPS), which allows the uniform definition of library size so that subsequent paired-end sequencing can achieve complete overlap of read pairs. Variant calling from Hi-Plex-derived datasets can thus rely on the identification of variants appearing in both reads of read-pairs, permitting stringent filtering of sequencing chemistry-induced errors. These principles ...

  18. A Search for Spectral Galaxy Pairs of Overlapping Galaxies based on Fuzzy Recognition

    CERN Document Server

    Yang, Haifeng; Chen, Xiaoyan; Zhang, Jifu; Hou, Wen; Cai, Jianghui; Wei, Peng; Ren, Juanjuan; Liu, Xiaojie; Zhao, Yongheng

    2014-01-01

    The Spectral Galaxy Pairs (SGPs) are de?ned as the composite galaxy spectra which contain two independent redshift systems. These spectra are useful for studying dust properties of the foreground galaxies. In this paper, a total of 165 spectra of SGPs are mined out from Sloan Digital Sky Survey (SDSS) Data Release 9 (DR9) using the concept of membership degree from the fuzzy set theory particularly de?ned to be suitable for fuzzily identifying emission lines. The spectra and images of this sample are classi?ed according to the membership degree and their image features, respectively. Many of these 2nd redshift systems are too small or too dim to select from the SDSS images alone, making the sample a potentially unique source of information on dust e?ects in low-luminosity or low-surface-brightness galaxies that are underrepresented in morphological pair samples. The dust extinction of the objects with high membership degree is also estimated by Balmer decrement. Additionally, analyses for a series of spectros...

  19. Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs

    OpenAIRE

    Ohkubo, Akihiro; Yamada, Kenji; Ito, Yu; Yoshimura, Kiichi; Miyauchi, Koichiro; Kanamori, Takashi; Masaki, Yoshiaki; Seio, Kohji; Yuasa, Hideya; Sekine, Mitsuo

    2015-01-01

    A triplex-forming oligonucleotide (TFO) could be a useful molecular tool for gene therapy and specific gene modification. However, unmodified TFOs have two serious drawbacks: low binding affinities and high sequence-dependencies. In this paper, we propose a new strategy that uses a new set of modified nucleobases for four-base recognition of TFOs, and thereby overcome these two drawbacks. TFOs containing a 2’-deoxy-4N-(2-guanidoethyl)-5-methylcytidine (dgC) residue for a C-G base pair have hi...

  20. DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water

    International Nuclear Information System (INIS)

    To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH2 group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH2 group of G-C base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes

  1. DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water

    Energy Technology Data Exchange (ETDEWEB)

    Okutsu, N.; Shimamura, K.; Shimizu, E.; Kurita, N., E-mail: kurita@cs.tut.ac.jp [Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580 (Japan); Shulga, S. [Institute for Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv (Ukraine); Danilov, V. I. [Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv (Ukraine)

    2016-02-01

    To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH{sub 2} group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH{sub 2} group of G-C base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes.

  2. Complex based on Isthmin and RGD motif against glioma U251 cells%基于Isthmin和RGD基序的复合物对胶质瘤U251的治疗作用

    Institute of Scientific and Technical Information of China (English)

    陈宏颉; 曹磊; 王守森; 郑兆聪; 王如密; 汪君

    2011-01-01

    Objective To study the effect of complex based on Isthmin and RGD motif against glioma U251 cells.Methods The complex based on Isthmin and RGD motif was prepared,and the glioma U251 cell xenografts were established to observe the antitumor and antiangiogenesis effects of the complex in vivo and in vivo.Results The complex could induce U251 cell apoptosis and attack tumor endothelium cells,which inhibited the growth of glioma U251 cells and improved the lifespan of tumor bearing mice.Conclusion The complex based on Isthmin and RGD motif could dually target tumor and endothelium cells,which provided a promising strategy for glioma gene therapy.%目的 探讨基于Isthmin和BGD基序的复合物对胶质瘤U251的治疗效应.方法 构建Isthmin和RGD基序的复合物,并建立胶质瘤U251移植瘤模型,体内外观察其对U251细胞和血管内皮细胞的影响.结果 该复合物能有效诱导U251细胞的凋亡,抑制肿瘤血管的生成,从而抑制肿瘤的生长和延长荷瘤小鼠的平均生存率.结论 该复合物能同时靶向肿瘤和血管内皮细胞,为胶质瘤的基因治疗提供了较理想的策略.

  3. Sequential visibility-graph motifs

    Science.gov (United States)

    Iacovacci, Jacopo; Lacasa, Lucas

    2016-04-01

    Visibility algorithms transform time series into graphs and encode dynamical information in their topology, paving the way for graph-theoretical time series analysis as well as building a bridge between nonlinear dynamics and network science. In this work we introduce and study the concept of sequential visibility-graph motifs, smaller substructures of n consecutive nodes that appear with characteristic frequencies. We develop a theory to compute in an exact way the motif profiles associated with general classes of deterministic and stochastic dynamics. We find that this simple property is indeed a highly informative and computationally efficient feature capable of distinguishing among different dynamics and robust against noise contamination. We finally confirm that it can be used in practice to perform unsupervised learning, by extracting motif profiles from experimental heart-rate series and being able, accordingly, to disentangle meditative from other relaxation states. Applications of this general theory include the automatic classification and description of physical, biological, and financial time series.

  4. A speedup technique for (l, d-motif finding algorithms

    Directory of Open Access Journals (Sweden)

    Dinh Hieu

    2011-03-01

    Full Text Available Abstract Background The discovery of patterns in DNA, RNA, and protein sequences has led to the solution of many vital biological problems. For instance, the identification of patterns in nucleic acid sequences has resulted in the determination of open reading frames, identification of promoter elements of genes, identification of intron/exon splicing sites, identification of SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have proven to be extremely helpful in domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, etc. Motifs are important patterns that are helpful in finding transcriptional regulatory elements, transcription factor binding sites, functional genomics, drug design, etc. As a result, numerous papers have been written to solve the motif search problem. Results Three versions of the motif search problem have been proposed in the literature: Simple Motif Search (SMS, (l, d-motif search (or Planted Motif Search (PMS, and Edit-distance-based Motif Search (EMS. In this paper we focus on PMS. Two kinds of algorithms can be found in the literature for solving the PMS problem: exact and approximate. An exact algorithm identifies the motifs always and an approximate algorithm may fail to identify some or all of the motifs. The exact version of PMS problem has been shown to be NP-hard. Exact algorithms proposed in the literature for PMS take time that is exponential in some of the underlying parameters. In this paper we propose a generic technique that can be used to speedup PMS algorithms. Conclusions We present a speedup technique that can be used on any PMS algorithm. We have tested our speedup technique on a number of algorithms. These experimental results show that our speedup technique is indeed very

  5. Alpha-beta monitoring system based on pair of simultaneous Multi-Wire Proportional Counters

    Science.gov (United States)

    Wengrowicz, U.; Amidan, D.; Orion, I.

    2016-08-01

    A new approach for a simultaneous alpha-beta Multi-wire Proportional Counter (MWPC) is presented. The popular approach for alpha-beta monitoring systems consists of a large area MWPC using noble gas flow such as Argon Methane. This method of measurement is effective but requires large-scale and expensive maintenance due to the needs of gas flow control and periodic replacements. In this work, a pair of simultaneous MWPCs for alpha-beta measuring is presented. The developed detector consists of a sealed gas MWPC sensor for beta particles, behind a free air alpha sensor. This approach allows effective simultaneous detection and discrimination of both alpha and beta radiation without the maintenance cost noble gas flow required for unsealed detectors.

  6. Headwater thermal response to partial-retention forest harvesting: a process-based paired-catchment experiment

    Science.gov (United States)

    Moore, R. D.; Guenther, S. M.; Gomi, T.

    2008-12-01

    Paired-catchment experiments are the most rigorous empirical research design for estimating the effects of land use on aquatic systems. However, they have recently come under increasing criticism, in part because past studies typically treated catchments as black boxes. As a result, investigators could only speculate about the factors responsible for any observed effects, limiting their ability to generalize the experimental results in space and time. This study used a paired-catchment approach to investigate the effects of partial- retention forest harvesting with no riparian buffer on the thermal regime of a headwater stream in coastal British Columbia. In addition to monitoring stream temperature at three locations within the treatment reach, we monitored above-stream microclimate, water surface evaporation, bed temperature profiles, groundwater temperature, and reach-scale surface-subsurface interaction. Daily maximum stream temperatures increased after harvesting by over 5 °C during summer, with little effect in winter. The major driver of post- harvest warming was an increase in solar radiation, which was partially moderated by the increased effects of hyporheic exchange, bed heat conduction and evaporation. Incorporating process-based measurements into paired-catchment experiments not only allows the causes of treatment response to be assessed, but they provide a valuable data set for testing predictive models.

  7. The ALHAMBRA survey: an empirical estimation of the cosmic variance for merger fraction studies based on close pairs

    CERN Document Server

    López-Sanjuan, C; Hernández-Monteagudo, C; Varela, J; Molino, A; Arnalte-Mur, P; Ascaso, B; Castander, F J; Fernández-Soto, A; Huertas-Company, M; Márquez, I; Martínez, V J; Masegosa, J; Moles, M; Pović, M; Aguerri, J A L; Alfaro, E; Benítez, N; Broadhurst, T; Cabrera-Caño, J; Cepa, J; Cerviño, M; Cristóbal-Hornillos, D; Del Olmo, A; Delgado, R M González; Husillos, C; Infante, L; Perea, J; Prada, F; Quintana, J M

    2014-01-01

    Our goal is to estimate empirically, for the first time, the cosmic variance that affects merger fraction studies based on close pairs. We compute the merger fraction from photometric redshift close pairs with 10h^-1 kpc <= rp <= 50h^-1 kpc and Dv <= 500 km/s, and measure it in the 48 sub-fields of the ALHAMBRA survey. We study the distribution of the measured merger fractions, that follow a log-normal function, and estimate the cosmic variance sigma_v as the intrinsic dispersion of the observed distribution. We develop a maximum likelihood estimator to measure a reliable sigma_v and avoid the dispersion due to the observational errors (including the Poisson shot noise term). The cosmic variance of the merger fraction depends mainly on (i) the number density of the populations under study, both for the principal (n_1) and the companion (n_2) galaxy in the close pair, and (ii) the probed cosmic volume V_c. We find a significant dependence on neither the search radius used to define close companions, t...

  8. Mutagenic Effects Induced by the Attack of NO2 Radical to the Guanine-Cytosine Base Pair

    Science.gov (United States)

    Cerón-Carrasco, José Pedro; Requena, Alberto; Zúñiga, José; Jacquemin, Denis

    2015-03-01

    We investigate the attack of the nitrogen dioxide radical (NO2) to the guanine-cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO2 radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO2-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC-NO2 radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis.

  9. The experimental study of monitoring gene-based therapy with the binding of diglycylcysteine binding motifs and 99Tcm-glucoheptonate

    International Nuclear Information System (INIS)

    Objective: To evaluate the feasibility of monitoring the gene expression of VEGF165 via the diglycylcysteine (GGC) reporter gene system by reporter probe of 99Tcm-GH. Methods: DNA fragments encoding GGC binding motifs were prepared by PCR and positioned at the C end of VEGF165 gene after the linearization of pcDNA3-VEGF165 plasmid. A replication-defective adenovirus vector Ad5-VEGF165 GGC motif-internal ribosomal entry site (IRES) -enhanced green fluorescent protein (EGFP) (Ad5-VIE)was constructed, with a cytomegalovirus (CMV) early promoter driving the expression of VEGF165 gene, GGC motif and EGFP, under the aid of an IRFS. A replication-defective adenovirus carrying the Ad5-EGFP was used as the control. Mesenchymal stem cells (MSC) were infected with the recombinant adenovirus at a multiplicity of infection (MOI) from 0 to 100 infectious units (0, 10, 25, 50, 100). Th e cellular uptake of 99Tcm-GH in infected MSC were then studied at 30, 60, 90 and 120 min. VEGF165 was detected by quantitative reverse transcriptase real-time PCR (RT-PCR), Western-blot, and immunohistochemistry. EGFP was observed by RT-PCR and fluorescence microscopy. The correlation analysis was studied between the cellular uptake of 99Tcm-GH and the expression of VEGF165. SPSS 13.0 was applied for statistical analysis. Independent samples t-test, q-test and Pearson correlation coefficient were used. Results: After infected with different viral titer of Ad-VIE, the cellular uptake of 99Tcm-GH increased with the increasing virus titer(r2 =0.86, P99Tcm-GH in Ad5-VIE-infected cells were significantly higher than those of Ad5 -EGFP-transfected cells at all time points (t =15.10- 54.92, all P165 and EGFP mRNA levels increased with increasing virus titer, and the VEGF165 mRNA correlated well with the EGFP mRNA(r2=0.99, P99Tcm-GH and the expression of VEGF165 protein in MSC(r2=0.90, P165 protein expressed obviously at Ad5-VIE-infected MSC, and the EGFP was observed by fluorescence microscopy

  10. Comprehensive evaluation of medium and long range correlated density functionals in TD-DFT investigation of DNA bases and base pairs: gas phase and water solution study

    Science.gov (United States)

    Shukla, Manoj K.; Leszczynski, Jerzy

    2010-11-01

    A comprehensive analysis of the performance of the TD-DFT method using different density functionals including recently developed medium and long-range correlation corrected density functionals have been carried out for lower-lying electronic singlet valence transitions of nucleic acid bases and the Watson-Crick base pairs in the gas phase and in the water solution. The standard 6-311++G(d,p) basis set was used. Ground state geometries of bases and base pairs were optimized at the M05-2X/6-311++G(d,p) level. The nature of potential energy surfaces (PES) was ascertained through the harmonic vibrational frequency analysis; all geometries were found to be minima at the respective PES. Electronic singlet vertical transition energies were also computed at the CC2/def2-TZVP level in the gas phase. The effect of state-specific water solvation on TD-DFT computed transition energies was considered using the PCM model. For the isolated bases the performance of the B3LYP functional was generally found to be superior among all functionals, but it measurably fails for charge-transfer states in the base pairs. The CC2/def2-TZVP computed transition energies were also revealed to be inferior compared with B3LYP results for the isolated bases. The performance of the ωB97XD, CAM-B3LYP and BMK functionals were found to be similar and comparable with the CC2 results for the isolated bases. However, for the Watson-Crick adenine-thymine and guanine-cytosine base pairs the performance of the ωB97XD functional was found to be the best among all the studied functionals in the present work in predicting the locally excited transitions as well as charge transfer states.

  11. Main: SEF1MOTIF [PLACE

    Lifescience Database Archive (English)

    Full Text Available inding motif; sequence found in 5'-upstream region (-640; -765) of soybean beta-conglicinin (7S globulin) ge...ne; W=A/T; SOYBEAN; STORAGE PROTEIN; 7S; GLOBULIN; BETA-CONGLICININ; seed; soybean (Glycine max) ATATTTAWW ...

  12. A 2×2 SOI mach-zehnder thermo-optical switch based on strongly guided paired multimode interference couplers

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A silicon-on-insulator 2×2 Mach-Zehnder thermo-optical switch is developed based on strongly guided paired multimode interference couplers. The multimode-interference couplers were etched deeply for improving coupler characteristics such as self-imaging quality, uniformity and fabrication tolerance. The proposed switch achieves good performances, including a low insertion loss of -11 .OdB, a fiber-waveguide coupling loss of -4.3dB and a fast response speed measured to be 3.5 and 8.8 μs for raise and fall switching time, respectively.

  13. Unusual glass-forming ability of new Zr-Cu-based bulk glassy alloys containing an immiscible element pair

    International Nuclear Information System (INIS)

    We herein report the unusual glass-forming ability (GFA) of a new series of quinary Zr48Cu36-xNixAg8Al8 (048Cu36Ag8Al8 alloy. By cooper mold casting, an as-cast glassy rod with a diameter of 30 mm can be easily obtained for the representative alloy Zr48Cu32Ni4Ag8Al8. The possible reasons for the excellent GFA of the new quinary alloys with an immiscible element pair are discussed based on the atomic size distribution, chemical compatibility among the components and atomic structure of glassy alloys. (author)

  14. Cryptanalysis and Improvement on "Robust EPR-Pairs-Based Quantum Secure Communication with Authentication Resisting Collective Noise"

    Science.gov (United States)

    Yue, Qiu-Ling; Yu, Chao-Hua; Liu, Bin; Wang, Qing-Le

    2016-05-01

    Recently, Chang et al. [Sci Chin-Phys Mech Astron. 57(10), 1907-1912, 2014] proposed two robust quantum secure communication protocols with authentication based on Einstein-Podolsky-Rosen (EPR) pairs, which can resist collective noise. In this paper, we analyze the security of their protocols, and show that there is a kind of security flaw in their protocols. By a kind of impersonation attack, the eavesdropper can obtain half of the message on average. Furthermore, an improved method of their protocols is proposed to close the security loophole.

  15. Prediction of protein secondary structure based on residue pair types and conformational states using dynamic programming algorithm.

    Science.gov (United States)

    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. Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations

    Czech Academy of Sciences Publication Activity Database

    Mládek, Arnošt; Sharma, P.; Mitra, A.; Bhattacharyya, D.; Šponer, Jiří; Šponer, Judit E.

    2009-01-01

    Roč. 113, č. 6 (2009), s. 1743-1755. ISSN 1520-6106 R&D Projects: GA AV ČR(CZ) IAA400550701; GA AV ČR(CZ) IAA400040802; GA AV ČR(CZ) 1QS500040581; GA MŠk(CZ) LC06030 Grant ostatní: GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702; CEZ:AV0Z40550506 Keywords : quantum chemical calculations * base pairing * RNA Subject RIV: BO - Biophysics Impact factor: 3.471, year: 2009

  17. Seamless Metallic Coating and Surface Adhesion of Self-Assembled Bioinspired Nanostructures Based on Di-(3,4-dihydroxy-l-phenylalanine) Peptide Motif

    Science.gov (United States)

    2015-01-01

    The noncoded aromatic 3,4-dihydroxy-l-phenylalanine (DOPA) amino acid has a pivotal role in the remarkable adhesive properties displayed by marine mussels. These properties have inspired the design of adhesive chemical entities through various synthetic approaches. DOPA-containing bioinspired polymers have a broad functional appeal beyond adhesion due to the diverse chemical interactions presented by the catechol moieties. Here, we harnessed the molecular self-assembly abilities of very short peptide motifs to develop analogous DOPA-containing supramolecular polymers. The DOPA-containing DOPA–DOPA and Fmoc–DOPA–DOPA building blocks were designed by substituting the phenylalanines in the well-studied diphenylalanine self-assembling motif and its 9-fluorenylmethoxycarbonyl (Fmoc)-protected derivative. These peptides self-organized into fibrillar nanoassemblies, displaying high density of catechol functional groups. Furthermore, the Fmoc–DOPA–DOPA peptide was found to act as a low molecular weight hydrogelator, forming self-supporting hydrogel which was rheologically characterized. We studied these assemblies using electron microscopy and explored their applicative potential by examining their ability to spontaneously reduce metal cations into elementary metal. By applying ionic silver to the hydrogel, we observed efficient reduction into silver nanoparticles and the remarkable seamless metallic coating of the assemblies. Similar redox abilities were observed with the DOPA–DOPA assemblies. In an effort to impart adhesiveness to the obtained assemblies, we incorporated lysine (Lys) into the Fmoc–DOPA–DOPA building block. The assemblies of Fmoc–DOPA–DOPA–Lys were capable of gluing together glass surfaces, and their adhesion properties were investigated using atomic force microscopy. Taken together, a class of DOPA-containing self-assembling peptides was designed. These nanoassemblies display unique properties and can serve as multifunctional

  18. Seamless metallic coating and surface adhesion of self-assembled bioinspired nanostructures based on di-(3,4-dihydroxy-L-phenylalanine) peptide motif.

    Science.gov (United States)

    Fichman, Galit; Adler-Abramovich, Lihi; Manohar, Suresh; Mironi-Harpaz, Iris; Guterman, Tom; Seliktar, Dror; Messersmith, Phillip B; Gazit, Ehud

    2014-07-22

    The noncoded aromatic 3,4-dihydroxy-L-phenylalanine (DOPA) amino acid has a pivotal role in the remarkable adhesive properties displayed by marine mussels. These properties have inspired the design of adhesive chemical entities through various synthetic approaches. DOPA-containing bioinspired polymers have a broad functional appeal beyond adhesion due to the diverse chemical interactions presented by the catechol moieties. Here, we harnessed the molecular self-assembly abilities of very short peptide motifs to develop analogous DOPA-containing supramolecular polymers. The DOPA-containing DOPA-DOPA and Fmoc-DOPA-DOPA building blocks were designed by substituting the phenylalanines in the well-studied diphenylalanine self-assembling motif and its 9-fluorenylmethoxycarbonyl (Fmoc)-protected derivative. These peptides self-organized into fibrillar nanoassemblies, displaying high density of catechol functional groups. Furthermore, the Fmoc-DOPA-DOPA peptide was found to act as a low molecular weight hydrogelator, forming self-supporting hydrogel which was rheologically characterized. We studied these assemblies using electron microscopy and explored their applicative potential by examining their ability to spontaneously reduce metal cations into elementary metal. By applying ionic silver to the hydrogel, we observed efficient reduction into silver nanoparticles and the remarkable seamless metallic coating of the assemblies. Similar redox abilities were observed with the DOPA-DOPA assemblies. In an effort to impart adhesiveness to the obtained assemblies, we incorporated lysine (Lys) into the Fmoc-DOPA-DOPA building block. The assemblies of Fmoc-DOPA-DOPA-Lys were capable of gluing together glass surfaces, and their adhesion properties were investigated using atomic force microscopy. Taken together, a class of DOPA-containing self-assembling peptides was designed. These nanoassemblies display unique properties and can serve as multifunctional platforms for various

  19. Suggested Intense Positron Source based on (micropole) undulator induced pair production

    International Nuclear Information System (INIS)

    The construction of an Intense Positron Source (IPS) is suggested. The intensity of the produced positrons is to exceed that of any other existing source by orders of magnitude. The instantaneous intensity is to be 103 to 106 times higher yet. Fast positrons are to be produced in pulses of time duration ∼1 ns to 10 ps. Slow positron pulses of order +e-pairs will be produced by the generated gamma rays; 3) moderators to thermalize the produced positrons; and 4) a transport system through which the slow positrons will move. Spinoff benefits provided by the suggested device include the following: The equipment may be used to create (or destroy) nuclear isotopes in a controlled manner (i.e. without producing unwanted species); to produce (or destroy) in a controlled way chemical elements; to produce well collimated intense photon beams in the multi 100 MeV range for nuclear physics research, with intensities many orders of magnitude higher than can be achieved today; to generate intense bursts of neutrons; to supply fast positrons produced at high intensities (1016 to 1017 s-1) and within a small transverse phase space, to future high energy colliders, thereby perhaps even eliminating the need for damping rings. ((orig.))

  20. Dynamically tunable Fano resonance in planar structures based on periodically asymmetric graphene nanodisk pair

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhengren [School of Science, Chongqing Jiaotong University, Chongqing 400074 (China); Su, Xiaopeng [Department of Physics, Tongji University, Shanghai 200092 (China); Fan, Yuancheng [Key Laboratory of Space Applied Physics and Chemistry, Ministry of Education and Department of Applied Physics, School of Science, Northwestern Polytechnical University, Xi' an 710129 (China); Yin, Pengfei [School of Science, Chongqing Jiaotong University, Chongqing 400074 (China); Zhang, Liwei [School of Physics and Chemistry, Henan Polytechnic University, Jiaozuo 454000 (China); Shi, Xi, E-mail: xishi@tongji.edu.cn [Department of Physics, Tongji University, Shanghai 200092 (China)

    2015-09-15

    We present a dynamically frequency tunable Fano resonance planar device composed of periodically asymmetric graphene nanodisk pair for the mid-infrared region. The two asymmetric graphene nanodisks can be directly excited by the light simultaneously and produce two kinds of reflected light with almost the same spectrum linewidth. By studying the local field distributions of our structure, we find that there are two kinds of modes for the two asymmetric graphene nanodisks, i.e., the symmetric mode and antisymmetric mode. Resonance coupling between the symmetric and antisymmetric modes generates the Fano resonance in our structure. This Fano resonance generation mechanism is different from it in traditional Fano resonance structure. In the traditional Fano resonance structure, the Fano resonance comes from the coupling effect between continuum and discrete structure. Moreover, we find that both of the Fano resonance amplitude and frequency of the structure can be dynamically controlled by varying the Fermi energy of graphene. Resonance transition in the structure is studied to reveal the physical mechanism behind it.

  1. Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs.

    Science.gov (United States)

    Ohkubo, Akihiro; Yamada, Kenji; Ito, Yu; Yoshimura, Kiichi; Miyauchi, Koichiro; Kanamori, Takashi; Masaki, Yoshiaki; Seio, Kohji; Yuasa, Hideya; Sekine, Mitsuo

    2015-07-13

    A triplex-forming oligonucleotide (TFO) could be a useful molecular tool for gene therapy and specific gene modification. However, unmodified TFOs have two serious drawbacks: low binding affinities and high sequence-dependencies. In this paper, we propose a new strategy that uses a new set of modified nucleobases for four-base recognition of TFOs, and thereby overcome these two drawbacks. TFOs containing a 2'-deoxy-4N-(2-guanidoethyl)-5-methylcytidine (d(g)C) residue for a C-G base pair have higher binding and base recognition abilities than those containing 2'-OMe-4N-(2-guanidoethyl)-5-methylcytidine (2'-OMe (g)C), 2'-OMe-4N-(2-guanidoethyl)-5-methyl-2-thiocytidine (2'-OMe (g)Cs), d(g)C and 4S-(2-guanidoethyl)-4-thiothymidine ((gs)T). Further, we observed that N-acetyl-2,7-diamino-1,8-naphtyridine ((DA)Nac) has a higher binding and base recognition abilities for a T-A base pair compared with that of dG and the other DNA derivatives. On the basis of this knowledge, we successfully synthesized a fully modified TFO containing (DA)Nac, d(g)C, 2'-OMe-2-thiothymidine (2'-OMe (s)T) and 2'-OMe-8-thioxoadenosine (2'-OMe (s)A) with high binding and base recognition abilities. To the best of our knowledge, this is the first report in which a fully modified TFO accurately recognizes a complementary DNA duplex having a mixed sequence under neutral conditions. PMID:26013815

  2. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition.

    Science.gov (United States)

    Harika, Narinder K; Paul, Ananya; Stroeva, Ekaterina; Chai, Yun; Boykin, David W; Germann, Markus W; Wilson, W David

    2016-06-01

    Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor-surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a (15)N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents. PMID:27131382

  3. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition

    Science.gov (United States)

    Harika, Narinder K.; Paul, Ananya; Stroeva, Ekaterina; Chai, Yun; Boykin, David W.; Germann, Markus W.; Wilson, W. David

    2016-01-01

    Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor–surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a 15N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents. PMID:27131382

  4. Morpholino spin-labeling for base-pair sequencing of a 3'-terminal RNA stem by proton homonuclear Overhauser enhancements: yeast ribosomal 5S RNA

    International Nuclear Information System (INIS)

    Base-pair sequences for 5S and 5.8S RNAs are not readily extracted from proton homonuclear nuclear Overhauser enhancement (NOE) connectivity experiments alone, due to extensive peak overlap in the downfield (11-15 ppm) proton NMR spectrum. In this paper, we introduce a new method for base-pair proton peak assignment for ribosomal RNAs, based upon the distance-dependent broadening of the resonances of base-pair protons spatially proximal to a paramagnetic group. Introduction of a nitroxide spin-label covalently attached to the 3'-terminal ribose provides an unequivocal starting point for base-pair hydrogen-bond proton NMR assignment. Subsequent NOE connectivities then establish the base-pair sequence for the terminal stem of a 5S RNA. Periodate oxidation of yeast 5S RNA, followed by reaction with 4-amino-2,2,6,6-tetramethylpiperidinyl-1-oxy (TEMPO-NH2) and sodium borohydride reduction, produces yeast 5S RNA specifically labeled with a paramagnetic nitroxide group at the 3'-terminal ribose. Comparison of the 500-MHz 1H NMR spectra of native and 3'-terminal spin-labeled yeast 5S RNA serves to identify the terminal base pair (G1 . C120) and its adjacent base pair (G2 . U119) on the basis of their proximity to the 3'-terminal spin-label. From that starting point, we have then identified (G . C, A . U, or G . U) and sequenced eight of the nine base pairs in the terminal helix via primary and secondary NOE's

  5. Young Foreign Language Learners' Interactions during Task-Based Paired Assessments

    Science.gov (United States)

    Butler, Yuko Goto; Zeng, Wei

    2014-01-01

    Despite the popularity of task-based language teaching (TBLT) in foreign language (FL) education at elementary school, it remains unclear how young learners' FL abilities can best be evaluated with tasks. The present study seeks to understand developmental differences in interactions among elementary-school students during task-based language…

  6. Chain propagation and termination mechanisms for polymerization of conjugated polar alkenes by [Al]-based frustrated Lewis pairs

    KAUST Repository

    He, Jianghua

    2014-11-25

    A combined experimental and theoretical study on mechanistic aspects of polymerization of conjugated polar alkenes by frustrated Lewis pairs (FLPs) based on N-heterocyclic carbene (NHC) and Al(C6F5)3 pairs is reported. This study consists of three key parts: structural characterization of active propagating intermediates, propagation kinetics, and chain-termination pathways. Zwitterionic intermediates that simulate the active propagating species in such polymerization have been generated or isolated from the FLP activation of monomers such as 2-vinylpyridine and 2-isopropenyl-2-oxazoline-one of which, IMes+-CH2C(Me)=(C3H2NO)Al(C6F5)3 - (2), has been structurally characterized. Kinetics performed on the polymerization of 2-vinylpyridine by ItBu/Al(C6F5)3 revealed that the polymerization follows a zero-order dependence on monomer concentration and a first-order dependence on initiator (ItBu) and activator [Al(C6F5)3] concentrations, indicating a bimolecular, activated monomer propagation mechanism. The Lewis pair polymerization of conjugate polar alkenes such as methacrylates is accompanied by competing chain-termination side reactions; between the two possible chain-termination pathways, the one that proceeds via intramolecular backbiting cyclization involving nucleophilic attack of the activated ester group of the growing polymer chain by the O-ester enolate active chain end to generate a six-membered lactone (δ-valerolactone)-terminated polymer chain is kinetically favored, but thermodynamically disfavored, over the pathway leading to the -ketoester-terminated chain, as revealed by computational studies.

  7. Post Hartree-Fock studies of the canonical Watson-Crick DNA base pairs: molecular structure and the nature of stability.

    Science.gov (United States)

    Danilov, Victor I; Anisimov, Victor M

    2005-02-01

    Gas-phase gradient optimization was carried out on the canonical Watson-Crick DNA base pairs using the second-order Møller-Plesset perturbation method at the 6-31G(d) and 6-31G(d,p) basis sets. It is detected that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buckled geometry of G-C and A-T base pairs; while HF and DFT methods predict perfect planar or almost planar geometry of the base pairs. Supposedly the nonplanarity of the pairs is caused by pyramidalization of the amino nitrogen atoms, which is underestimated by the HF and DFT methods. This justifies the importance of geometry optimization at the MP2 level for obtaining reliable prediction of the charge distribution, molecular dipole moments and geometrical structure of the base pairs. The Morokuma-Kitaura and the Reduced Variational Space methods of the decomposition for molecular HF interaction energies were used for investigation of the hydrogen bonding in the Watson-Crick base pairs. It is shown that the HF stability of the hydrogen-bonded DNA base pairs originates mainly from electrostatic interactions. At the same time, the calculated magnitude of the second order intramolecular correlation correction to the Coulomb energy showed that electron correlation reduces the contribution of the electrostatic term to the attractive interaction for the A-T and G-C base pairs. Polarization, charge transfer and dispersion interactions also make considerable contribution to the attraction energy of bases. PMID:15588110

  8. New in silico approach to assessing RNA secondary structures with non-canonical base pairs

    OpenAIRE

    Rybarczyk, Agnieszka; Szostak, Natalia; Antczak, Maciej; Zok, Tomasz; Popenda, Mariusz; Adamiak, Ryszard; Blazewicz, Jacek; Szachniuk, Marta

    2015-01-01

    Background The function of RNA is strongly dependent on its structure, so an appropriate recognition of this structure, on every level of organization, is of great importance. One particular concern is the assessment of base-base interactions, described as the secondary structure, the knowledge of which greatly facilitates an interpretation of RNA function and allows for structure analysis on the tertiary level. The RNA secondary structure can be predicted from a sequence using in silico meth...

  9. Novel coronene-naphthalene dimide-based donor-acceptor pair for tunable charge-transfer nanostructures.

    Science.gov (United States)

    Kumar, Mohit; George, Subi J

    2014-09-01

    Charge-transfer (CT) assemblies of aromatic donor (D) and acceptor (A) molecules have recently gained attention as a promising material for organic electronics and ferroelectrics. Two major factors which govern their functions are the strength of CT interaction and their supramolecular nanostructuring. Here we present coronene-naphthalenediimide (NDI)-based novel D-A pairs that form alternately stacked CT assemblies. Through systematic substitution of the NDI derivatives and studying their CT interactions with coronene, a clear understanding of the secondary forces responsible for controlling their association is gained. Finally, the use of CT-based supramolecular amphiphiles for their nanostructural engineering into ordered one-dimensional (1-D) assemblies is demonstrated. PMID:25045008

  10. A base-paired hairpin structure essential for the functional priming signal for DNA replication of the broad host range plasmid RSF1010.

    OpenAIRE

    Miao, D M; Honda, Y; Tanaka, K.; Higashi, A.; Nakamura, T.(International Center for Elementary Particle Physics and Department of Physics, The University of Tokyo, Tokyo, Japan); TAGUCHI, Y.; Sakai, H.; Komano, T; Bagdasarian, M

    1993-01-01

    The two single-strand DNA initiation signals, ssiA(RSF1010) and ssiB(RSF1010) of the broad host-range plasmid RSF1010 contain proposed stem-loop structures. Nine single base-change mutations in the stem of the ssiA structure, each of which destroyed a relevant base pairing, damaged the ssiA activity. A second single-base change was introduced into each of the nine ssiA mutants in such a way that the base pairing was restored. Only three out of nine second base changes that restored the base p...

  11. Event Networks and the Identification of Crime Pattern Motifs.

    Directory of Open Access Journals (Sweden)

    Toby Davies

    Full Text Available In this paper we demonstrate the use of network analysis to characterise patterns of clustering in spatio-temporal events. Such clustering is of both theoretical and practical importance in the study of crime, and forms the basis for a number of preventative strategies. However, existing analytical methods show only that clustering is present in data, while offering little insight into the nature of the patterns present. Here, we show how the classification of pairs of events as close in space and time can be used to define a network, thereby generalising previous approaches. The application of graph-theoretic techniques to these networks can then offer significantly deeper insight into the structure of the data than previously possible. In particular, we focus on the identification of network motifs, which have clear interpretation in terms of spatio-temporal behaviour. Statistical analysis is complicated by the nature of the underlying data, and we provide a method by which appropriate randomised graphs can be generated. Two datasets are used as case studies: maritime piracy at the global scale, and residential burglary in an urban area. In both cases, the same significant 3-vertex motif is found; this result suggests that incidents tend to occur not just in pairs, but in fact in larger groups within a restricted spatio-temporal domain. In the 4-vertex case, different motifs are found to be significant in each case, suggesting that this technique is capable of discriminating between clustering patterns at a finer granularity than previously possible.

  12. Event Networks and the Identification of Crime Pattern Motifs.

    Science.gov (United States)

    Davies, Toby; Marchione, Elio

    2015-01-01

    In this paper we demonstrate the use of network analysis to characterise patterns of clustering in spatio-temporal events. Such clustering is of both theoretical and practical importance in the study of crime, and forms the basis for a number of preventative strategies. However, existing analytical methods show only that clustering is present in data, while offering little insight into the nature of the patterns present. Here, we show how the classification of pairs of events as close in space and time can be used to define a network, thereby generalising previous approaches. The application of graph-theoretic techniques to these networks can then offer significantly deeper insight into the structure of the data than previously possible. In particular, we focus on the identification of network motifs, which have clear interpretation in terms of spatio-temporal behaviour. Statistical analysis is complicated by the nature of the underlying data, and we provide a method by which appropriate randomised graphs can be generated. Two datasets are used as case studies: maritime piracy at the global scale, and residential burglary in an urban area. In both cases, the same significant 3-vertex motif is found; this result suggests that incidents tend to occur not just in pairs, but in fact in larger groups within a restricted spatio-temporal domain. In the 4-vertex case, different motifs are found to be significant in each case, suggesting that this technique is capable of discriminating between clustering patterns at a finer granularity than previously possible. PMID:26605544

  13. Spin fluctuations and unconventional superconducting pairing in iron-based superconductors

    Institute of Scientific and Technical Information of China (English)

    Yu Shun-Li; Li Jian-Xin

    2013-01-01

    In this article,we review the recent theoretical works on the spin fluctuations and superconductivity in iron-based superconductors.Using the fluctuation exchange approximation and multi-orbital tight-binding models,we study the characteristics of the spin fluctuations and the symmetries of the superconducting gaps for different iron-based superconductors.We explore the systems with both electron-like and hole-like Fermi surfaces (FS) and the systems with only the electronlike FS.We argue that the spin-fluctuation theories are successful in explaining at least the essential part of the problems,indicating that the spin fluctuation is the common origin of superconductivity in iron-based superconductors.

  14. A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers.

    Science.gov (United States)

    Durand, Guillaume; Dausse, Eric; Goux, Emma; Fiore, Emmanuelle; Peyrin, Eric; Ravelet, Corinne; Toulmé, Jean-Jacques

    2016-05-19

    Loop-loop (also known as kissing) interactions between RNA hairpins are involved in several mechanisms in both prokaryotes and eukaryotes such as the regulation of the plasmid copy number or the dimerization of retroviral genomes. The stability of kissing complexes relies on loop parameters (base composition, sequence and size) and base combination at the loop-loop helix - stem junctions. In order to identify kissing partners that could be used as regulatory elements or building blocks of RNA scaffolds, we analysed a pool of 5.2 × 10(6) RNA hairpins with randomized loops. We identified more than 50 pairs of kissing RNA hairpins. Two kissing motifs, 5'CCNY and 5'RYRY, generate highly stable complexes with KDs in the low nanomolar range. Such motifs were introduced in the apical loop of hairpin aptamers that switch between unfolded and folded state upon binding to their cognate target molecule, hence their name aptaswitch. The aptaswitch-ligand complex is specifically recognized by a second RNA hairpin named aptakiss through loop-loop interaction. Taking advantage of our kissing motif repertoire we engineered aptaswitch-aptakiss modules for purine derivatives, namely adenosine, GTP and theophylline and demonstrated that these molecules can be specifically and simultaneously detected by surface plasmon resonance or by fluorescence anisotropy. PMID:27067541

  15. A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations

    Science.gov (United States)

    Lemons, Patrick R.; Marshall, T.C.; McCloskey, Sarah E.; Sethi, S.A.; Schmutz, Joel A.; Sedinger, James S.

    2015-01-01

    Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artifacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad-hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra-pair paternity and conspecific brood parasitism using a likelihood-based approach in a new version of program cervus. We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies.

  16. Demonstration of polarization sensitivity of emulsion-based pair conversion telescope for cosmic gamma-ray polarimetry

    CERN Document Server

    Ozaki, Keita; Aoki, Shigeki; Kamada, Keiki; Kaneyama, Taichi; Nakagawa, Ryo; Rokujo, Hiroki

    2016-01-01

    Linear polarization of high-energy gamma-rays (10 MeV-100 GeV) can be detected by measuring the azimuthal angle of electron-positron pairs and observing the modulation of the azimuthal distribution. To demonstrate the gamma-ray polarization sensitivity of emulsion, we conducted a test using a polarized gamma-ray beam at SPring-8/LEPS. Emulsion tracks were reconstructed using scanning data, and gamma-ray events were selected automatically. Using an optical microscope, out of the 2381 gamma-ray conversions that were observed, 1372 remained after event selection, on the azimuthal angle distribution of which we measured the modulation. From the distribution of the azimuthal angles of the selected events, a modulation factor of 0.21 + 0.11 - 0.09 was measured, from which the detection of a non-zero modulation was established with a significance of 3.06 $\\sigma$. This attractive polarimeter will be applied to the GRAINE project, a balloon-borne experiment that observes cosmic gamma-rays with an emulsion-based pair ...

  17. Detection of Wuchereria bancrofti DNA in paired serum and urine samples using polymerase chain reaction-based systems

    Directory of Open Access Journals (Sweden)

    Camila Ximenes

    2014-12-01

    Full Text Available The Global Program for the Elimination of Lymphatic Filariasis (GPELF aims to eliminate this disease by the year 2020. However, the development of more specific and sensitive tests is important for the success of the GPELF. The present study aimed to standardise polymerase chain reaction (PCR-based systems for the diagnosis of filariasis in serum and urine. Twenty paired biological urine and serum samples from individuals already known to be positive for Wuchereria bancrofti were collected during the day. Conventional PCR and semi-nested PCR assays were optimised. The detection limit of the technique for purified W. bancrofti DNA extracted from adult worms was 10 fg for the internal systems (WbF/Wb2 and 0.1 fg by using semi-nested PCR. The specificity of the primers was confirmed experimentally by amplification of 1 ng of purified genomic DNA from other species of parasites. Evaluation of the paired urine and serum samples by the semi-nested PCR technique indicated only two of the 20 tested individuals were positive, whereas the simple internal PCR system (WbF/Wb2, which has highly promising performance, revealed that all the patients were positive using both samples. This study successfully demonstrated the possibility of using the PCR technique on urine for the diagnosis of W. bancrofti infection.

  18. Rational design and identification of a non-peptidic aggregation inhibitor of amyloid-β based on a pharmacophore motif obtained from cyclo[-Lys-Leu-Val-Phe-Phe-].

    Science.gov (United States)

    Arai, Tadamasa; Araya, Takushi; Sasaki, Daisuke; Taniguchi, Atsuhiko; Sato, Takeshi; Sohma, Youhei; Kanai, Motomu

    2014-07-28

    Inhibition of pathogenic protein aggregation may be an important and straightforward therapeutic strategy for curing amyloid diseases. Small-molecule aggregation inhibitors of Alzheimer's amyloid-β (Aβ) are extremely scarce, however, and are mainly restricted to dye- and polyphenol-type compounds that lack drug-likeness. Based on the structure-activity relationship of cyclic Aβ16-20 (cyclo-[KLVFF]), we identified unique pharmacophore motifs comprising side-chains of Leu(2), Val(3), Phe(4), and Phe(5) residues without involvement of the backbone amide bonds to inhibit Aβ aggregation. This finding allowed us to design non-peptidic, small-molecule aggregation inhibitors that possess potent activity. These molecules are the first successful non-peptidic, small-molecule aggregation inhibitors of amyloids based on rational molecular design. PMID:24931598

  19. Long-Range Vibrational Dynamics Are Directed by Watson-Crick Base Pairing in Duplex DNA.

    Science.gov (United States)

    Hithell, Gordon; Shaw, Daniel J; Donaldson, Paul M; Greetham, Gregory M; Towrie, Michael; Burley, Glenn A; Parker, Anthony W; Hunt, Neil T

    2016-05-01

    Ultrafast two-dimensional infrared (2D-IR) spectroscopy of a 15-mer A-T DNA duplex in solution has revealed structure-dependent vibrational coupling and energy transfer processes linking bases with the sugar-phosphate backbone. Duplex melting induces significant changes in the positions of off-diagonal peaks linking carbonyl and ring-stretching vibrational modes of the adenine and thymine bases with vibrations of the phosphate group and phosphodiester linkage. These indicate that Watson-Crick hydrogen bonding and helix formation lead to a unique vibrational coupling arrangement of base vibrational modes with those of the phosphate unit. On the basis of observations from time-resolved 2D-IR data, we conclude that rapid energy transfer processes occur between base and backbone, mediated by additional modes located on the deoxyribose moiety within the same nucleotide. These relaxation dynamics are insensitive to duplex melting, showing that efficient intramolecular energy relaxation to the solvent via the phosphate groups is the key to excess energy dissipation in both single- and double-stranded DNA. PMID:27079484

  20. Pairing based threshold cryptography improving on Libert-Quisquater and Baek-Zheng

    DEFF Research Database (Denmark)

    Desmedt, Yvo; Lange, Tanja

    In this paper we apply techniques from secret sharing and threshold decryption to show how to properly design an ID-based threshold system in which one assumes no trust in any party. In our scheme: We avoid that any single machine ever knew the master secret s of the trusted authority (TA). Inste...

  1. Stacked base-pair structures of adenine nucleosides stabilized by the formation of hydrogen-bonding network involving the two sugar groups

    International Nuclear Information System (INIS)

    Highlights: ► A combination of laser desorption and supersonic jet-cooling is used to produce base pairs of adenine nucleosides. ► Stacked base-pair structure of N6,N6-dimethyladnosine is identified by IR vibrational spectroscopy. ► Anharmonic vibrational calculation is employed to analyze the vibrational mode coupling in the stacked base pair. - Abstract: We have employed a laser desorption technique combined with supersonic-jet cooling for producing base pairs of adenine nucleosides, adenosine (Ado) and N6,N6-dimethyladenosine (DMAdo) under low-temperature conditions. The resulting base pairs are then ionized through resonant two-photon ionization (R2PI) and analyzed by time-of-flight mass spectrometry. It is found that dimers of these adenine nucleosides are stable, especially in the case of DMAdo, with respect to those of the corresponding bases, i.e., adenine and N6,N6-dimethyladenine. Structural analysis of the DMAdo dimer is performed based on the IR–UV double resonance measurements and theoretical calculations. The result demonstrates that the dimer possesses a stacked structure being stabilized by the formation of hydrogen-bonding network involving the two sugar groups. The occurrence of the frequency shift and broadening is explained satisfactorily based on the anharmonic coupling of the OH stretching modes with specific bending modes and low-frequency modes of base and sugar moieties

  2. Subradiant split Cooper pairs

    OpenAIRE

    Cottet, Audrey; Kontos, Takis; Yeyati, Alfredo Levy

    2011-01-01

    We suggest a way to characterize the coherence of the split Cooper pairs emitted by a double-quantum-dot based Cooper pair splitter (CPS), by studying the radiative response of such a CPS inside a microwave cavity. The coherence of the split pairs manifests in a strongly nonmonotonic variation of the emitted radiation as a function of the parameters controlling the coupling of the CPS to the cavity. The idea to probe the coherence of the electronic states using the tools of Cavity Quantum Ele...

  3. Neuronal synapse as a memristor: modeling pair- and triplet-based STDP rule.

    Science.gov (United States)

    Cai, Weiran; Ellinger, Frank; Tetzlaff, Ronald

    2015-02-01

    We propose a new memristive model for the neuronal synapse based on the spike-timing-dependent plasticity (STDP) protocol, considering both long-term and short-term plasticity in the synapse. Higher-order behavior is modeled by a memristor with adaptive thresholds, which realizes the well-established suppression principle of Froemke. We assume a mechanism of variable thresholds adapting to synaptic potentiation (LTP) and depression (LTD), which reproduces the refractory time in the weight modification. The corresponding dynamical process is governed by a set of ordinary differential equations. Interestingly, the Froemke's model and our memristive model, based on two completely different mechanisms, are found to be quantitatively equivalent for the 'pre-post-pre' case and 'post-pre-post' case. A relation of the adaptive thresholds to short-term plasticity is addressed. PMID:24960611

  4. Determination of the rate of base-pair substitution and insertion mutations in retrovirus replication.

    OpenAIRE

    Dougherty, J P; Temin, H M

    1988-01-01

    We recently described a protocol for determination of retrovirus mutation rates, that is, the mutation frequency in a single cycle of retrovirus replication (J.P. Dougherty and H.M. Temin, Mol. Cell. Biol. 6:4378-4395, 1987; J.P. Dougherty and H.M. Temin, p. 18-23, in J. H. Miller and M. P. Calos, ed., Gene Transfer Vectors for Mammalian Cells, 1987). We used this protocol to determine the mutation rates for defined mutations in a replicating retrovirus by using a spleen necrosis virus-based ...

  5. The Analysis of the Atomic Pair Distribution Function of Pmn-Based Nanopowders by X-Ray Diffraction

    Science.gov (United States)

    Ghasemifard, M.; Khorrami, Gh. H.

    The three-dimensional atomic-scale structure around Mg, Nb, Ti and Zr atoms in a series ferroelectric material such as PMN, PZT, PMN-PZT and PMN-PT has been studied using X-ray diffraction (MoKα), Rietveld refinement and the atomic pair distribution function (PDF) technique. The structure and particle size of the powders was determined by X-ray diffraction and TEM observation. The studies show that the materials are disordered at nanometer length distances. The three-dimensional atomic ordering in PMN-based nanopowders may well be described by a cubic structure of the perovskite type, similar to that occurring in the bulk crystals. At the end, the analyzed data show that the sizes of ZrO6 octahedral are larger than TiO6 octahedral.

  6. Cyanine-based probe\\tag-peptide pair fluorescence protein imaging and fluorescence protein imaging methods

    Science.gov (United States)

    Mayer-Cumblidge, M. Uljana; Cao, Haishi

    2013-01-15

    A molecular probe comprises two arsenic atoms and at least one cyanine based moiety. A method of producing a molecular probe includes providing a molecule having a first formula, treating the molecule with HgOAc, and subsequently transmetallizing with AsCl.sub.3. The As is liganded to ethanedithiol to produce a probe having a second formula. A method of labeling a peptide includes providing a peptide comprising a tag sequence and contacting the peptide with a biarsenical molecular probe. A complex is formed comprising the tag sequence and the molecular probe. A method of studying a peptide includes providing a mixture containing a peptide comprising a peptide tag sequence, adding a biarsenical probe to the mixture, and monitoring the fluorescence of the mixture.

  7. Electron pairing without superconductivity

    Science.gov (United States)

    Levy, Jeremy

    Strontium titanate (SrTiO3) is the first and best known superconducting semiconductor. It exhibits an extremely low carrier density threshold for superconductivity, and possesses a phase diagram similar to that of high-temperature superconductors--two factors that suggest an unconventional pairing mechanism. Despite sustained interest for 50 years, direct experimental insight into the nature of electron pairing in SrTiO3 has remained elusive. Here we perform transport experiments with nanowire-based single-electron transistors at the interface between SrTiO3 and a thin layer of lanthanum aluminate, LaAlO3. Electrostatic gating reveals a series of two-electron conductance resonances--paired electron states--that bifurcate above a critical pairing field Bp of about 1-4 tesla, an order of magnitude larger than the superconducting critical magnetic field. For magnetic fields below Bp, these resonances are insensitive to the applied magnetic field; for fields in excess of Bp, the resonances exhibit a linear Zeeman-like energy splitting. Electron pairing is stable at temperatures as high as 900 millikelvin, well above the superconducting transition temperature (about 300 millikelvin). These experiments demonstrate the existence of a robust electronic phase in which electrons pair without forming a superconducting state. Key experimental signatures are captured by a model involving an attractive Hubbard interaction that describes real-space electron pairing as a precursor to superconductivity. Support from AFOSR, ONR, ARO, NSF, DOE and NSSEFF is gratefully acknowledged.

  8. Finding a Leucine in a Haystack: Searching the Proteome for ambigous Leucine-Aspartic Acid motifs

    KAUST Repository

    Arold, Stefan T.

    2016-01-25

    Leucine-aspartic acid (LD) motifs are short helical protein-protein interaction motifs involved in cell motility, survival and communication. LD motif interactions are also implicated in cancer metastasis and are targeted by several viruses. LD motifs are notoriously difficult to detect because sequence pattern searches lead to an excessively high number of false positives. Hence, despite 20 years of research, only six LD motif–containing proteins are known in humans, three of which are close homologues of the paxillin family. To enable the proteome-wide discovery of LD motifs, we developed LD Motif Finder (LDMF), a web tool based on machine learning that combines sequence information with structural predictions to detect LD motifs with high accuracy. LDMF predicted 13 new LD motifs in humans. Using biophysical assays, we experimentally confirmed in vitro interactions for four novel LD motif proteins. Thus, LDMF allows proteome-wide discovery of LD motifs, despite a highly ambiguous sequence pattern. Functional implications will be discussed.

  9. Maximizing Expected Base Pair Accuracy in RNA Secondary Structure Prediction by Joining Stochastic Context-Free Grammars Method

    Directory of Open Access Journals (Sweden)

    Shahira M. Habashy

    2012-03-01

    Full Text Available The identification of RNA secondary structures has been among the most exciting recent developments in biology and medical science. Prediction of RNA secondary structure is a fundamental problem in computational structural biology. For several decades, free energy minimization has been the most popular method for prediction from a single sequence. It is based on a set of empirical free energy change parameters derived from experiments using a nearest-neighbor model. Accurate prediction of RNA secondary structure from the base sequence is an unsolved computational challenge. The accuracy of predictions made by free energy minimization is limited by the quality of the energy parameters in the underlying free energy model. More recently, stochastic context-free grammars (SCFGs have emerged as an alternative probabilistic methodology for modeling RNA structure. Unlike physics-based methods, which rely on thousands of experimentally -measured thermodynamic parameters, SCFGs use fully-automated statistical learning algorithms to derive model parameters. This paper proposes a new algorithm that computes base pairing pattern for RNA molecule. Complex internal structures in RNA are fully taken into account. It supports the calculation of stochastic context-free grammars (SCFGs, and equilibrium concentrations of duplex structures. This new algorithm is compared with dynamic programming benchmark mfold and algorithms (Tfold, and MaxExpect. The results showed that the proposed algorithm achieved better performance with respect to sensitivity and positive predictive value.

  10. Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways

    DEFF Research Database (Denmark)

    Pandey, A; Fernandez, M M; Steen, H;

    2000-01-01

    molecule containing a Src homology 3 domain as well as an immunoreceptor tyrosine-based activation motif (ITAM). This molecule is 55% identical to a previously isolated molecule designated signal transducing adaptor molecule (STAM) that was identified as an interleukin (IL)-2-induced phosphoprotein and is...... therefore designated STAM2. Tyrosine phosphorylation of STAM2 is induced by growth factors such as epidermal growth factor and platelet-derived growth factor as well as by cytokines like IL-3. Several of the deletion mutants tested except the one containing only the amino-terminal region underwent tyrosine...... phosphorylation upon growth factor stimulation, implying that STAM2 is phosphorylated on several tyrosine residues. STAM2 is downstream of the Jak family of kinases since coexpression of STAM2 with Jak1 or Jak2 but not an unrelated Tec family kinase, Etk, resulted in its tyrosine phosphorylation. In contrast to...

  11. Combinatorial analysis for sequence and spatial motif discovery in short sequence fragments

    OpenAIRE

    Jackups, Ronald; Liang, Jie

    2010-01-01

    Motifs are over-represented sequence or spatial patterns appearing in proteins. They often play important roles in maintaining protein stability and in facilitating protein function. When motifs are located in short sequence fragments, as in transmembrane domains that are only 6–20 residues in length, and when there is only very limited data, it is difficult to identify motifs. In this study, we introduce combinatorial models based on permutation for assessing statistically significant sequen...

  12. Combinatorial analysis for sequence and spatial motif discovery in short sequence fragments

    OpenAIRE

    Jackups, Ronald; Liang, Jie

    2006-01-01

    Motifs are over-represented sequence or spatial patterns appearing in proteins. They often play important roles in maintaining protein stability and in facilitating protein function. When motifs are located in short sequence fragments, as in transmembrane domains that are only 6–20 residues in length, and when there is only very limited data, it is difficult to identify motifs. In this study, we introduce combinatorial models based on permutation for assessing statistically significant sequen...

  13. A model for gamma-ray binaries, based on the effect of pair production feedback in shocked pulsar winds

    CERN Document Server

    Derishev, E

    2016-01-01

    We analyze the model of gamma-ray binaries, consisting of a massive star and a pulsar with ultrarelativistic wind. We consider radiation from energetic particles, accelerated at the pulsar wind termination shock, and feedback of this radiation on the wind through production of secondary electron-positron pairs. We show that the pair feedback limits the Lorentz factor of the pulsar wind and creates a population of very energetic pairs, whose radiation may be responsible for the observed gamma-ray signal.

  14. Novel transmission pricing scheme based on point-to-point tariff and transaction pair matching for pool market

    International Nuclear Information System (INIS)

    Transmission pricing scheme is a key component in the infrastructure of power market, and pool is an indispensable pattern of market organization; meanwhile, pay-as-bid (PAB) serves as a main option to determine market prices in pool. In this paper, a novel transmission pricing scheme is proposed for pool power market based on PAB. The new scheme is developed by utilizing point-to-point (PTP) tariff and introducing an approach of transaction pair matching (TPM). The model and procedure of the new scheme are presented in detail. Apart from the advantages of existing transmission pricing schemes, such as ensuing open, fair and non-discriminatory access, proper recovery for investment as well as transparency, the new scheme provides economic signals to promote the maximum use of the existing transmission network, encourages appropriate bidding behaviors in pool, and helps to reduce the possibility of the enforcement of market power and the appearing of price spikes; thus improves market operation efficiency and trading effects. In order to testify the effectiveness of the proposed scheme, a case based on IEEE 30-bus system is studied. (author)

  15. Design of A 5-Bit Fully Parallel Analog to Digital Converter Using Common Gate Differrential Mos Pair-Based Comparator

    Science.gov (United States)

    Aytar, Oktay

    2015-09-01

    This paper presents a novel comparator structure based on the common gate differential MOS pair. The proposed comparator has been applied to fully parallel analog to digital converter (A/D converter). Furthermore, this article presents 5 bit fully parallel A/D Converter design using the cadence IC5141 design platform and NCSU(North Carolina State University) design kit with 0.18 μm CMOS technology library. The proposed fully parallel A/D converter consist of resistor array block, comparator block, 1-n decoder block and programmable logic array. The 1-n decoder block includes latch block and thermometer code circuit that is implemented using transmission gate based multiplexer circuit. Thus, sampling frequency and analog bandwidth are increased. The INL and DNL of the proposed fully parallel A/D converter are (0/ + 0.63) LSB and (-0.26/ + 0.31) LSB at a sampling frequency of 5 GS/s with an input signal of 50 MHz, respectively. The proposed fully parallel A/D Converter consumes 340 mW from 1.8 V supply.

  16. Effect of single interstitial impurity in iron-based superconductors with sign-changed s-wave pairing symmetry

    Science.gov (United States)

    Yu, Xiang-Long; Liu, Da-Yong; Quan, Ya-Min; Zheng, Xiao-Jun; Zou, Liang-Jian

    2015-12-01

    We employ the self-consistent Bogoliubov-de Gennes (BdG) formulation to investigate the effect of single interstitial nonmagnetic/magnetic impurity in iron-based superconductors with s ± -wave pairing symmetry. We find that both the nonmagnetic and magnetic impurities can induce bound states within the superconducting (SC) gap and a π phase shift of SC order parameter at the impurity site. However, different from the interstitial-nonmagnetic-impurity case characterized by two symmetric peaks with respect to zero energy, the interstitial magnetic one only induces single bound-state peak. In the strong scattering regime this peak can appear at the Fermi level, which has been observed in the recent scanning tunneling microscope (STM) experiment of Fe(Te,Se) superconductor with interstitial Fe impurities (Yin et al. 2015 [44]). This novel single in-gap peak feature also distinguishes the interstitial case from the substitutional one with two peaks. These results provide important information for comparing the different impurity effects in the iron-based superconductors.

  17. Excited state properties of naphtho-homologated xxDNA bases and effect of methanol solution, deoxyribose, and base pairing.

    Science.gov (United States)

    Zhang, Laibin; Ren, Tingqi; Tian, Jianxiang; Yang, Xiuqin; Zhou, Liuzhu; Li, Xiaoming

    2013-04-18

    Design and synthesis of fluorescent nucleobase analogues for studying structures and dynamics of nucleic acids have attracted much attention in recent years. In the present work, a comprehensive theoretical study of electronic transitions of naphtho-homologated base analogues, namely, xxC, xxT, xxA, and xxG, was performed. The nature of the low-lying excited states was discussed, and the results were compared with those of x-bases. Geometrical characteristics of the lowest excited singlet ππ* states were explored using the CIS method. The calculated excitation maxima are 423, 397, 383, and 357 nm for xxA, xxG, xxC, and xxT, respectively, and they are greatly red-shifted compared with x-bases and natural bases, allowing them to be selectively excited in the presence of the natural bases. In the gas phase, the fluorescence from them would be expected to occur around 497, 461, 457, and 417 nm, respectively. The effects of methanol solution, deoxyribose, and base paring with their complementary natural bases on the relevant absorption and emission spectra of these modified bases were also examined. PMID:23531077

  18. Investigation on the ion pair amphiphiles and their in vitro release of amantadine drug based on PLGA–PEG–PLGA gel

    International Nuclear Information System (INIS)

    The amantadine drug and oleic acid surfactant are used to form amantadine-based ion pair amphiphiles based on proton transfer reaction between the drug and the surfactant molecules. The ion pair amphiphiles are characterized by 1H-nuclear magnetic resonance, Fourier transform infrared spectroscopy, and X-ray diffraction. Self-assembly properties of amantadine-based ion pair amphiphiles are studied by surface tension determination, transmission electron microscopy, zeta potential, and dynamic light scattering. The aggregation behavior studies indicate that the as-prepared ion pair amphiphiles can self-assemble into vesicles with the size of 200–300 nm in aqueous solution. The drug release results show that the amantadine release rate could be well controlled by incorporating the amantadine-based ion pair vesicles in poly (lactic-co-glycolic acid)-poly (ethylene glycol)-poly (lactic-co-glycolic acid) (PLGA–PEG–PLGA) copolymer hydrogel. The drug release from the AT–OA vesicle-loaded PLGA–PEG–PLGA hydrogel is significantly inhibited in comparison with the AT-loaded PLGA–PEG–PLGA hydrogel. The present work thus demonstrates that the vesicle-loaded hydrogel is a good candidate for the drug delivery system with long-term controlled drug release behavior

  19. Investigation on the ion pair amphiphiles and their in vitro release of amantadine drug based on PLGA–PEG–PLGA gel

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaoxia, E-mail: yxx-678@163.com; Ji, Xiaoqing; Shi, Chunhuan; Liu, Jing [Shandong University, School of Pharmaceutical Science and Center for Pharmaceutical Research & Drug Delivery Systems (China); Wang, Haiyang [Institute of Materia Medica Shandong Academy of Medical Sciences, Shandong Taitian Newdrug Discovery Co.Ltd (China); Luan, Yuxia, E-mail: yuxialuan@sdu.edu.cn [Shandong University, School of Pharmaceutical Science and Center for Pharmaceutical Research & Drug Delivery Systems (China)

    2014-12-15

    The amantadine drug and oleic acid surfactant are used to form amantadine-based ion pair amphiphiles based on proton transfer reaction between the drug and the surfactant molecules. The ion pair amphiphiles are characterized by {sup 1}H-nuclear magnetic resonance, Fourier transform infrared spectroscopy, and X-ray diffraction. Self-assembly properties of amantadine-based ion pair amphiphiles are studied by surface tension determination, transmission electron microscopy, zeta potential, and dynamic light scattering. The aggregation behavior studies indicate that the as-prepared ion pair amphiphiles can self-assemble into vesicles with the size of 200–300 nm in aqueous solution. The drug release results show that the amantadine release rate could be well controlled by incorporating the amantadine-based ion pair vesicles in poly (lactic-co-glycolic acid)-poly (ethylene glycol)-poly (lactic-co-glycolic acid) (PLGA–PEG–PLGA) copolymer hydrogel. The drug release from the AT–OA vesicle-loaded PLGA–PEG–PLGA hydrogel is significantly inhibited in comparison with the AT-loaded PLGA–PEG–PLGA hydrogel. The present work thus demonstrates that the vesicle-loaded hydrogel is a good candidate for the drug delivery system with long-term controlled drug release behavior.

  20. Identifying motifs in folktales using topic models

    OpenAIRE

    Karsdorp, F.; Bosch, A.P.J. van den

    2013-01-01

    With the undertake of various folktale digitalization initiatives, the need for computational aids to explore these collections is increasing. In this paper we compare Labeled LDA (L-LDA) to a simple retrieval model on the task of identifying motifs in folktales. We show that both methods are well able to successfully discriminate between relevant and irrelevant motifs. L-LDA represents motifs as distributions over words. In a second experiment we compare the quality of these distributions to...

  1. On Candlestick-based Trading Rules Profitability Analysis via Parametric Bootstraps and Multivariate Pair-Copula based Models

    OpenAIRE

    Andreea Röthig; Andreas Röthig; Carl Chiarella

    2015-01-01

    This study analyses the profitability of candlestick-based technical trading rules in currency futures markets. The main feature of this type of technical analysis is that it generates signals based on the relationships between several price series, i.e. open, high, low and close prices. Since the trading rules are not precise and mainly based on causal knowledge of traders, we use a fuzzy-system to mathematize and classify them. The profitability of the trading rules is then tested by means ...

  2. Bridge and brick motifs in complex networks

    Science.gov (United States)

    Huang, Chung-Yuan; Sun, Chuen-Tsai; Cheng, Chia-Ying; Hsieh, Ji-Lung

    2007-04-01

    Acknowledging the expanding role of complex networks in numerous scientific contexts, we examine significant functional and topological differences between bridge and brick motifs for predicting network behaviors and functions. After observing similarities between social networks and their genetic, ecological, and engineering counterparts, we identify a larger number of brick motifs in social networks and bridge motifs in the other three types. We conclude that bridge and brick motif content analysis can assist researchers in understanding the small-world and clustering properties of network structures when investigating network functions and behaviors.

  3. Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition.

    Directory of Open Access Journals (Sweden)

    Edze R Westra

    Full Text Available Discriminating self and non-self is a universal requirement of immune systems. Adaptive immune systems in prokaryotes are centered around repetitive loci called CRISPRs (clustered regularly interspaced short palindromic repeat, into which invader DNA fragments are incorporated. CRISPR transcripts are processed into small RNAs that guide CRISPR-associated (Cas proteins to invading nucleic acids by complementary base pairing. However, to avoid autoimmunity it is essential that these RNA-guides exclusively target invading DNA and not complementary DNA sequences (i.e., self-sequences located in the host's own CRISPR locus. Previous work on the Type III-A CRISPR system from Staphylococcus epidermidis has demonstrated that a portion of the CRISPR RNA-guide sequence is involved in self versus non-self discrimination. This self-avoidance mechanism relies on sensing base pairing between the RNA-guide and sequences flanking the target DNA. To determine if the RNA-guide participates in self versus non-self discrimination in the Type I-E system from Escherichia coli we altered base pairing potential between the RNA-guide and the flanks of DNA targets. Here we demonstrate that Type I-E systems discriminate self from non-self through a base pairing-independent mechanism that strictly relies on the recognition of four unchangeable PAM sequences. In addition, this work reveals that the first base pair between the guide RNA and the PAM nucleotide immediately flanking the target sequence can be disrupted without affecting the interference phenotype. Remarkably, this indicates that base pairing at this position is not involved in foreign DNA recognition. Results in this paper reveal that the Type I-E mechanism of avoiding self sequences and preventing autoimmunity is fundamentally different from that employed by Type III-A systems. We propose the exclusive targeting of PAM-flanked sequences to be termed a target versus non-target discrimination mechanism.

  4. A new Salmonella tester strain (TA102) with A X T base pairs at the site of mutation detects oxidative mutagens.

    OpenAIRE

    Levin, D E; Hollstein, M; Christman, M.F.; Schwiers, E A; Ames, B N

    1982-01-01

    A new tester strain, TA102, is described as an addition to the set of strains for the Salmonella/microsome mutagenicity test. This strain contains A X T base pairs at the site of the mutation (determined by DNA sequence analysis) in contrast to the other Salmonella tester strains that detect mutagens damaging G X C base pairs. This strain differs from previous tester strains in that the mutation has been introduced into a multicopy plasmid, so that approximately equal to 30 copies of the muta...

  5. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2011-06-01

    Full Text Available Abstract Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet, which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i ubiquitous motifs, shared by several superfamilies and (ii superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

  6. RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

    Energy Technology Data Exchange (ETDEWEB)

    Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E. [National Magnetic Resonance Facility at Madison (United States); Eghbalnia, Hamid R., E-mail: eghbalhd@uc.edu [University of Cincinnati, Department of Molecular and Cellular Physiology (United States)

    2012-04-15

    The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ({sup 1}H-{sup 15}N 2D HMQC) and proton-proton nuclear Overhauser enhancement spectroscopy ({sup 1}H-{sup 1}H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino

  7. Implementation of FFT by using MATLAB: SIMULINK on Xilinx Virtex-4 FPGAs: Performance of a Paired Transform Based FFT

    Directory of Open Access Journals (Sweden)

    Ranganadh Narayanam

    2013-06-01

    Full Text Available Discrete Fourier Transform is principal mathematical method for the frequency analysis and is having wide applications in Engineering and Sciences. Because the DFT is so ubiquitous, fast methods for computing DFT have been studied extensively, and continuous to be an active research. The way of splitting the DFT gives out various fast algorithms. In this paper, we present the implementation of two fast algorithms for the DFT for evaluating their performance. One of them is the popular radix-2 Cooley-Tukey fast Fourier transform algorithm (FFT [1] and the other one is the Grigoryan FFT based on the splitting by the paired transform [2]. We evaluate the performance of these algorithms by implementing them on the Xilinx Virtex-4 FPGAs [3], by developing our own FFT processor architectures. Finally we show that the Grigoryan FFT is working faster than Cooley-Tukey FFT, consequently it is useful for higher sampling rates. Operating at higher sampling rates is a challenge in DSP applications.

  8. Spectrophotometric Determination of Cefixime Trihydrate in Pharmaceutical Formulations Based on Ion-Pair Reaction with Bromophenol Blue.

    Science.gov (United States)

    Keskar, Mrudul R; Jugade, Ravin M

    2015-01-01

    Cefixime trihydrate is a broad spectrum cephalosporin antibiotic, effective against gram-positive and gram-negative bacterial infections. Simple and rapid method has been developed for the determination of cefixime trihydrate in bulk and pharmaceutical formulations. This method was based on the formation of bluish-green ion-pair complex of cefixime trihydrate with bromophenol blue in dimethyl sulfoxide (DMSO)-acetonitrile medium. Different parameters were studied and optimized. A 2:1 complex was formed between the drug and reagent almost instantaneously at room temperature which has λmax of 610 nm. Under optimum conditions, calibration curve was found to be linear over the range of 10-130 μg mL(-1). The method was subjected to analytical quality control. The limit of detection was found to be 1.08 μg mL(-1). Recovery studies and interference studies were carried out. The proposed method was successfully applied to the determination of cefixime trihydrate in bulk and pharmaceutical formulations with high precision and accuracy. PMID:26279621

  9. High yield and ultrafast sources of electrically triggered entangled-photon pairs based on strain-tunable quantum dots.

    Science.gov (United States)

    Zhang, Jiaxiang; Wildmann, Johannes S; Ding, Fei; Trotta, Rinaldo; Huo, Yongheng; Zallo, Eugenio; Huber, Daniel; Rastelli, Armando; Schmidt, Oliver G

    2015-01-01

    Triggered sources of entangled photon pairs are key components in most quantum communication protocols. For practical quantum applications, electrical triggering would allow the realization of compact and deterministic sources of entangled photons. Entangled-light-emitting-diodes based on semiconductor quantum dots are among the most promising sources that can potentially address this task. However, entangled-light-emitting-diodes are plagued by a source of randomness, which results in a very low probability of finding quantum dots with sufficiently small fine structure splitting for entangled-photon generation (∼10(-2)). Here we introduce strain-tunable entangled-light-emitting-diodes that exploit piezoelectric-induced strains to tune quantum dots for entangled-photon generation. We demonstrate that up to 30% of the quantum dots in strain-tunable entangled-light-emitting-diodes emit polarization-entangled photons. An entanglement fidelity as high as 0.83 is achieved with fast temporal post selection. Driven at high speed, that is 400 MHz, strain-tunable entangled-light-emitting-diodes emerge as promising devices for high data-rate quantum applications. PMID:26621073

  10. Unravelling the interaction dynamics of a carbonatite-silicate magmatic pair: A numerical approach based on Korteweg Stress theory

    Science.gov (United States)

    Valentini, L.; Moore, K. R.; Chazot, G.

    2009-04-01

    Most of the worldwide carbonatites occur in spatial association with silicate rocks. Even when unquestionable evidence for the associated carbonatite and silicate rocks to represent contemporaneous liquids exists, the modes of interaction between the two liquids can be difficult to infer. In general, the retrieval of information about the mechanisms of interaction between magmas can be complicated by the intrinsic dynamical nature of such systems. The development of new physico-chemical equilibria (e.g. hybridization) can erase any information about the previous stages of interaction. However, the occurrence of magmatic heterogeneities, such as enclaves and flow bands, as well as mineral disequilibrium textures, may serve as dynamic markers for the underlying interaction processes. Small-scale heterogeneities, in the form of micron to millimetre sized globules, characterized by more or less smooth interfaces, are frequently observed in carbonatite-silicate pairs. Textural observation, as well as the lack of suitable mechanisms for the dispersion of a discrete magmatic liquid in the form of a small-scale emulsion, have lead many petrologists to advocate immiscible separation as the process capable of forming such textures. However, the geochemical criteria for liquid immiscibility are not always met, and when not coupled with geochemical and dynamical arguments, textural observation may lead to ambiguous conclusions. In this study we adopted an integrated approach in order to infer the details of magmatic interaction of a carbonatite-silicate pair from Massif Central (France). The studied samples display emulsion-like textures, formed by micro-scale dolomitic globules dispersed in a trachytic glassy matrix. Our approach is based on a novel numerical method, coupled with textural observation and geochemical analyses. The novelty of our numerical model consists in the inclusion, in the adopted advection-diffusion equations, of a term that takes into account the effect

  11. Modified normal-phase ion-pair chromatographic methods for the facile separation and purification of imidazolium-based ionic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Urban, ND; Schenkel, MR; Robertson, LA; Noble, RD; Gin, DL

    2012-07-04

    lmidazolium- and oligo(imidazolium)-based ionic organic compounds are important in the design of room-temperature ionic liquid materials; however, the chromatographic analysis and separation of such compounds are often difficult. A convenient and inexpensive method for effective thin-layer chromatography (TLC) analysis and column chromatography separation of imidazolium-based ionic compounds is presented. Normal-phase ion-pair TLC is used to effectively analyze homologous mixtures of these ionic compounds. Subsequent separation of the mixtures is performed using ion-pair flash chromatography on normal-phase silica gel, yielding high levels of recovery. This method also results in a complete exchange of the counter anion on the imidazolium compounds to the anion of the ion-pair reagent. (C) 2012 Elsevier Ltd. All rights reserved.

  12. Statistical inference about the relative efficiency of a new survey protocol, based on paired-tow survey calibration data

    OpenAIRE

    Cadigan, Noel G.; Dowden, Jeff J.

    2010-01-01

    Paired-tow calibration studies provide information on changes in survey catchability that may occur because of some necessary change in protocols (e.g., change in vessel or vessel gear) in a fish stock survey. This information is important to ensure the continuity of annual time-series of survey indices of stock size that provide the basis for fish stock assessments. There are several statistical models used to analyze the paired-catch data from calibration studies. Our main contribu...

  13. Specific RNA self-assembly with minimal paranemic motifs

    Science.gov (United States)

    Afonin, Kirill A.; Cieply, Dennis J.; Leontis, Neocles B.

    2016-01-01

    The paranemic crossover (PX) is a motif for assembling two nucleic acid molecules using Watson-Crick (WC) basepairing without unfolding pre-formed secondary structure in the individual molecules. Once formed, the paranemic assembly motif comprises adjacent parallel double helices that cross over at every possible point over the length of the motif. The interaction is reversible as it does not require denaturation of basepairs internal to each interacting molecular unit. Paranemic assembly has been demonstrated for DNA but not for RNA, and only for motifs with four or more cross-over points and lengths of five or more helical half-turns. Here we report the design of RNA molecules that paranemically assemble with the minimum number of two cross-overs spanning the major groove to form paranemic motifs with a length of three half-turns (3HT). Dissociation constants (Kds) were measured for series of molecules in which the number of basepairs between the cross-over points was varied from five to eight basepairs. The paranemic 3HT complex with six basepairs (3HT_6M) was found to be the most stable with Kd = 1×10−8 M. The half-time for kinetic exchange of the 3HT_6M complex was determined to be ~100 minutes, from which we calculated association and dissociation rate constants ka = 5.11×103 M−1sec−1 and kd = 5.11×10−5 sec−1. RNA paranemic assembly of 3HT and 5HT complexes is blocked by single-base substitutions that disrupt individual inter-molecular Watson-Crick basepairs and is restored by compensatory substitutions that restore those basepairs. The 3HT motif appears suitable for specific, programmable, and reversible tecto-RNA self-assembly for constructing artificial RNA molecular machines. PMID:18072767

  14. ACL2 Meets the GPU: Formalizing a CUDA-based Parallelizable All-Pairs Shortest Path Algorithm in ACL2

    Directory of Open Access Journals (Sweden)

    David S. Hardin

    2013-04-01

    Full Text Available As Graphics Processing Units (GPUs have gained in capability and GPU development environments have matured, developers are increasingly turning to the GPU to off-load the main host CPU of numerically-intensive, parallelizable computations. Modern GPUs feature hundreds of cores, and offer programming niceties such as double-precision floating point, and even limited recursion. This shift from CPU to GPU, however, raises the question: how do we know that these new GPU-based algorithms are correct? In order to explore this new verification frontier, we formalized a parallelizable all-pairs shortest path (APSP algorithm for weighted graphs, originally coded in NVIDIA's CUDA language, in ACL2. The ACL2 specification is written using a single-threaded object (stobj and tail recursion, as the stobj/tail recursion combination yields the most straightforward translation from imperative programming languages, as well as efficient, scalable executable specifications within ACL2 itself. The ACL2 version of the APSP algorithm can process millions of vertices and edges with little to no garbage generation, and executes at one-sixth the speed of a host-based version of APSP coded in C – a very respectable result for a theorem prover. In addition to formalizing the APSP algorithm (which uses Dijkstra's shortest path algorithm at its core, we have also provided capability that the original APSP code lacked, namely shortest path recovery. Path recovery is accomplished using a secondary ACL2 stobj implementing a LIFO stack, which is proven correct. To conclude the experiment, we ported the ACL2 version of the APSP kernels back to C, resulting in a less than 5% slowdown, and also performed a partial back-port to CUDA, which, surprisingly, yielded a slight performance increase.

  15. Graph animals, subgraph sampling, and motif search in large networks

    Science.gov (United States)

    Baskerville, Kim; Grassberger, Peter; Paczuski, Maya

    2007-09-01

    We generalize a sampling algorithm for lattice animals (connected clusters on a regular lattice) to a Monte Carlo algorithm for “graph animals,” i.e., connected subgraphs in arbitrary networks. As with the algorithm in [N. Kashtan , Bioinformatics 20, 1746 (2004)], it provides a weighted sample, but the computation of the weights is much faster (linear in the size of subgraphs, instead of superexponential). This allows subgraphs with up to ten or more nodes to be sampled with very high statistics, from arbitrarily large networks. Using this together with a heuristic algorithm for rapidly classifying isomorphic graphs, we present results for two protein interaction networks obtained using the tandem affinity purification (TAP) method: one of Escherichia coli with 230 nodes and 695 links, and one for yeast (Saccharomyces cerevisiae) with roughly ten times more nodes and links. We find in both cases that most connected subgraphs are strong motifs ( Z scores >10 ) or antimotifs ( Z scores <-10 ) when the null model is the ensemble of networks with fixed degree sequence. Strong differences appear between the two networks, with dominant motifs in E. coli being (nearly) bipartite graphs and having many pairs of nodes that connect to the same neighbors, while dominant motifs in yeast tend towards completeness or contain large cliques. We also explore a number of methods that do not rely on measurements of Z scores or comparisons with null models. For instance, we discuss the influence of specific complexes like the 26S proteasome in yeast, where a small number of complexes dominate the k cores with large k and have a decisive effect on the strongest motifs with 6-8 nodes. We also present Zipf plots of counts versus rank. They show broad distributions that are not power laws, in contrast to the case when disconnected subgraphs are included.

  16. Paired fuzzy sets

    DEFF Research Database (Denmark)

    Rodríguez, J. Tinguaro; Franco de los Ríos, Camilo; Gómez, Daniel;

    2015-01-01

    In this paper we want to stress the relevance of paired fuzzy sets, as already proposed in previous works of the authors, as a family of fuzzy sets that offers a unifying view for different models based upon the opposition of two fuzzy sets, simply allowing the existence of different types of...

  17. Sampling Motif-Constrained Ensembles of Networks

    Science.gov (United States)

    Fischer, Rico; Leitão, Jorge C.; Peixoto, Tiago P.; Altmann, Eduardo G.

    2015-10-01

    The statistical significance of network properties is conditioned on null models which satisfy specified properties but that are otherwise random. Exponential random graph models are a principled theoretical framework to generate such constrained ensembles, but which often fail in practice, either due to model inconsistency or due to the impossibility to sample networks from them. These problems affect the important case of networks with prescribed clustering coefficient or number of small connected subgraphs (motifs). In this Letter we use the Wang-Landau method to obtain a multicanonical sampling that overcomes both these problems. We sample, in polynomial time, networks with arbitrary degree sequences from ensembles with imposed motifs counts. Applying this method to social networks, we investigate the relation between transitivity and homophily, and we quantify the correlation between different types of motifs, finding that single motifs can explain up to 60% of the variation of motif profiles.

  18. Sampling motif-constrained ensembles of networks

    CERN Document Server

    Fischer, Rico; Peixoto, Tiago P; Altmann, Eduardo G

    2015-01-01

    The statistical significance of network properties is conditioned on null models which satisfy spec- ified properties but that are otherwise random. Exponential random graph models are a principled theoretical framework to generate such constrained ensembles, but which often fail in practice, either due to model inconsistency, or due to the impossibility to sample networks from them. These problems affect the important case of networks with prescribed clustering coefficient or number of small connected subgraphs (motifs). In this paper we use the Wang-Landau method to obtain a multicanonical sampling that overcomes both these problems. We sample, in polynomial time, net- works with arbitrary degree sequences from ensembles with imposed motifs counts. Applying this method to social networks, we investigate the relation between transitivity and homophily, and we quantify the correlation between different types of motifs, finding that single motifs can explain up to 60% of the variation of motif profiles.

  19. Temporal motifs in time-dependent networks

    CERN Document Server

    Kovanen, Lauri; Kaski, Kimmo; Kertész, János; Saramäki, Jari

    2011-01-01

    Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as networks of telecommunication, neural signal processing, biochemical reactions and human social interactions. We introduce the general framework of temporal motifs to study the mesoscale spatio-temporal structure of these networks. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences and to colored directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network.

  20. Temporal motifs in time-dependent networks

    International Nuclear Information System (INIS)

    Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as telecommunication, neural signal processing, biochemical reaction and human social interaction networks. We introduce the framework of temporal motifs to study the mesoscale topological–temporal structure of temporal networks in which the events of nodes do not overlap in time. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences to coloured directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network

  1. Young Learners' Interactional Development in Task-Based Paired-Assessment in Their First and Foreign Languages: A Case of English Learners in China

    Science.gov (United States)

    Butler, Yuko Goto; Zeng, Wei

    2015-01-01

    In response to the growing interest in evaluating young learners' foreign language (FL) performance, this study aims to deepen our understanding of young learners' developmental differences in interaction during task-based paired-language assessments. To examine age effects separately from the effect of general language proficiency, we analysed…

  2. Structures, physicochemical properties, and applications of T-Hg-II-T, C-Ag-I-C, and other metallo-base-pairs

    Czech Academy of Sciences Publication Activity Database

    Tanaka, Y.; Kondo, J.; Sychrovský, Vladimír; Šebera, Jakub; Dairaku, T.; Saneyoshi, H.; Urata, H.; Torigoe, H.; Ono, A.

    2015-01-01

    Roč. 51, č. 98 (2015), s. 17343-17360. ISSN 1359-7345 R&D Projects: GA ČR GAP205/10/0228 Institutional support: RVO:61388963 Keywords : metal-mediated base-pairs * T–Hg–T * C–Ag–C Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.834, year: 2014

  3. Self-deflection of bright soliton in a separate bright-dark screening soliton pair based on higher-order space charge field

    Institute of Scientific and Technical Information of China (English)

    Zhonghua Hao(郝中华); Jinsong Liu(刘劲松)

    2003-01-01

    Based on the interaction of the separate soliton pair, the self-deflection of the bright screening soliton in a bright-dark pair is studied by taking the higher order space charge field into account. Both numerical and analytical methods are adopted to obtain the result that the higher order of space charge field can enhance the deflection process of the bright soliton and varying the peak intensity of the dark soliton can influence the self-deflection strongly. The expression of the deflection distance with the dark soliton's peak intensity is derived, and some corresponding properties of the self-deflection process are figured out.

  4. NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data

    DEFF Research Database (Denmark)

    Andreatta, Massimo; Schafer-Nielsen, Claus; Lund, Ole;

    2011-01-01

    Recent advances in high-throughput technologies have made it possible to generate both gene and protein sequence data at an unprecedented rate and scale thereby enabling entirely new "omics"-based approaches towards the analysis of complex biological processes. However, the amount and complexity of...

  5. Preonset studies of spondyloepiphyseal dysplasia tarda caused by a novel 2-base pair deletion in SEDL encoding sedlin.

    Science.gov (United States)

    Mumm, S; Zhang, X; Gottesman, G S; McAlister, W H; Whyte, M P

    2001-12-01

    Spondyloepiphyseal dysplasia tarda (SEDT), an X-linked recessive skeletal disorder, presents with disproportionate short stature and "barrel-chest" deformity in affected (hemizygous) adolescent boys. In four reported families to date, mutations in a gene designated SEDL (spondyloepiphyseal dysplasia late) cosegregate with SEDT. We diagnosed SEDT in a short-stature, kyphotic 15-year-old boy because of his characteristic vertebral malformations. Clinical manifestations of SEDT were evident in at least four previous generations. A novel 2-base pair (bp) deletion in exon 5 of SEDL was found in the propositus by polymerase chain reaction (PCR) amplification and sequencing of all four coding exons. The mutation ATdel241-242 cosegregated with the kindred's skeletal disease. The deletion is adjacent to a noncanonical splice site for exon 5 but does not alter splicing. Instead, it deletes 2 bp from the coding sequence, causing a frameshift. A maternal aunt and her three young sons were investigated subsequently. Radiographs showed subtle shaping abnormalities of her pelvis and knees, suggesting heterozygosity. X-rays of the spine and pelvis of her 8-year-old son revealed characteristic changes of SEDT, but her younger sons (aged 6 years and 3 years) showed no abnormalities. SEDL analysis confirmed that she and only her eldest boy had the 2-bp deletion. Molecular testing of SEDL enables carrier detection and definitive diagnosis before clinical or radiographic expression of SEDT. Although there is no specific treatment for SEDT, preexpression molecular testing of SEDL could be helpful if avoiding physical activities potentially injurious to the spine and the joints proves beneficial. PMID:11760838

  6. 2012 IUPAP C10 Young Scientist Prize on the Structure and Dynamics of Condensed Matter Lecture: Spin Fluctuations and Pairing in Fe-based Superconductors

    Science.gov (United States)

    Christianson, A. D.

    2012-02-01

    The origin of superconductivity in the Fe-based superconductors, like that in other unconventional superconductors, remains shrouded in mystery. How the pairing bosons emerge either due to or in spite of the strong magnetic interactions found in the Fe-based superconductors is one of the most thoroughly investigated questions in the field. A prominent example of the interplay of superconductivity and magnetism is the dramatic shift of spectral weight from the low energy spin excitations to an energy which is related to the superconducting gap resulting in a peak in the spin excitation spectrum localized in both momentum and energy which occurs at the onset of superconductivity. The appearance of the new peak in the spin excitation spectrum below the superconducting transition temperature is referred to as s spin resonance and is most commonly interpreted as indicating a sign change of the superconducting order parameter on different portions of the Fermi surface and thus is consistent with an extended s-wave or s± pairing symmetry in many Fe-based superconductors. We will review the observations and implications of the spin resonance across the Fe-based superconductors. In particular we will examine the relationship between the resonance energy and the superconducting transition temperature as a function of chemical doping and pressure. While the spin resonance provides important information about pairing symmetry, there does not appear to be sufficient spectral to explain the pairing strength. Thus the remainder of the spin excitation spectrum must be examined to determine if spin fluctuations are ultimately responsible for pairing in the Fe-based materials. Consequently, we will discuss in detail the way in which the spin excitations evolve from the nonsuperconducting compounds to their superconducting relatives as a function of chemical doping.

  7. Huge electric field enhancement and highly sensitive sensing based on the Fano resonance effect in an asymmetric nanorod pair

    International Nuclear Information System (INIS)

    A sharp plasmonic Fano resonance is found to appear in a silver nanorod pair structure with broken length symmetry. It is shown that it arises from strong interference between a narrow plasmon mode of inter-nanorod near-field coupling and broad scattering from the nanorod. The inter-nanorod coupling is the result of the magnetic dipole plasmon resonance induced by the anti-parallel current of the nanorod pair, while the broad scattering is caused by electric dipole oscillation. The numerical results show that a giant local field enhancement (197), a high quality factor (52) and a sensing sensitivity of 1426 nm per refractive index unit in the symmetry-broken nanorod pair with a displacement Δl = 40 nm originated from a pronounced Fano resonance in the near-infrared spectrum. Huge local field enhancement and high sensitivity make this simple structure promising for surface enhanced Raman spectroscopy and sensing applications. (paper)

  8. MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis

    Directory of Open Access Journals (Sweden)

    Klepper Kjetil

    2013-01-01

    Full Text Available Abstract Background Traditional methods for computational motif discovery often suffer from poor performance. In particular, methods that search for sequence matches to known binding motifs tend to predict many non-functional binding sites because they fail to take into consideration the biological state of the cell. In recent years, genome-wide studies have generated a lot of data that has the potential to improve our ability to identify functional motifs and binding sites, such as information about chromatin accessibility and epigenetic states in different cell types. However, it is not always trivial to make use of this data in combination with existing motif discovery tools, especially for researchers who are not skilled in bioinformatics programming. Results Here we present MotifLab, a general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. MotifLab supports comprehensive motif discovery and analysis by allowing users to integrate several popular motif discovery tools as well as different kinds of additional information, including phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, transcription factor interactions and gene expression. MotifLab offers several data-processing operations that can be used to create, manipulate and analyse data objects, and complete analysis workflows can be constructed and automatically executed within MotifLab, including graphical presentation of the results. Conclusions We have developed MotifLab as a flexible workbench for motif analysis in a genomic context. The flexibility and effectiveness of this workbench has been demonstrated on selected test cases, in particular two previously published benchmark data sets for single motifs and modules, and a realistic example of genes responding to treatment with forskolin. MotifLab is freely

  9. Sequence-Based Screening for Rare Enzymes: New Insights into the World of AMDases Reveal a Conserved Motif and 58 Novel Enzymes Clustering in Eight Distinct Families.

    Science.gov (United States)

    Maimanakos, Janine; Chow, Jennifer; Gaßmeyer, Sarah K; Güllert, Simon; Busch, Florian; Kourist, Robert; Streit, Wolfgang R

    2016-01-01

    Arylmalonate Decarboxylases (AMDases, EC 4.1.1.76) are very rare and mostly underexplored enzymes. Currently only four known and biochemically characterized representatives exist. However, their ability to decarboxylate α-disubstituted malonic acid derivatives to optically pure products without cofactors makes them attractive and promising candidates for the use as biocatalysts in industrial processes. Until now, AMDases could not be separated from other members of the aspartate/glutamate racemase superfamily based on their gene sequences. Within this work, a search algorithm was developed that enables a reliable prediction of AMDase activity for potential candidates. Based on specific sequence patterns and screening methods 58 novel AMDase candidate genes could be identified in this work. Thereby, AMDases with the conserved sequence pattern of Bordetella bronchiseptica's prototype appeared to be limited to the classes of Alpha-, Beta-, and Gamma-proteobacteria. Amino acid homologies and comparison of gene surrounding sequences enabled the classification of eight enzyme clusters. Particularly striking is the accumulation of genes coding for different transporters of the tripartite tricarboxylate transporters family, TRAP transporters and ABC transporters as well as genes coding for mandelate racemases/muconate lactonizing enzymes that might be involved in substrate uptake or degradation of AMDase products. Further, three novel AMDases were characterized which showed a high enantiomeric excess (>99%) of the (R)-enantiomer of flurbiprofen. These are the recombinant AmdA and AmdV from Variovorax sp. strains HH01 and HH02, originated from soil, and AmdP from Polymorphum gilvum found by a data base search. Altogether our findings give new insights into the class of AMDases and reveal many previously unknown enzyme candidates with high potential for bioindustrial processes. PMID:27610105

  10. Detecting Motifs in System Call Sequences

    CERN Document Server

    Wilson, William O; Aickelin, Uwe

    2010-01-01

    The search for patterns or motifs in data represents an area of key interest to many researchers. In this paper we present the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify unknown motifs which repeat within time series data. The power of the algorithm is derived from its use of a small number of parameters with minimal assumptions. The algorithm searches from a completely neutral perspective that is independent of the data being analysed, and the underlying motifs. In this paper the motif tracking algorithm is applied to the search for patterns within sequences of low level system calls between the Linux kernel and the operating system's user space. The MTA is able to compress data found in large system call data sets to a limited number of motifs which summarise that data. The motifs provide a resource from which a profile of executed processes can be built. The potential for these profiles and new implications for security research are highlighted. A...

  11. Synthesis of 5-[3-(2-aminopyrimidin-4-yl)aminopropyn-1-yl]uracil derivative that recognizes Ade-Thy base pairs in double-stranded DNA.

    Science.gov (United States)

    Ito, Yu; Masaki, Yoshiaki; Kanamori, Takashi; Ohkubo, Akihiro; Seio, Kohji; Sekine, Mitsuo

    2016-01-01

    5-[3-(2-Aminopyrimidin-4-yl)aminopropyn-1-yl]uracil (Ura(Pyr)) was designed as a new nucleobase to recognize Ade-Thy base pair in double-stranded DNA. We successfully synthesized the dexoynucleoside phosphoramidite having Ura(Pyr) and incorporated it into triplex forming oligonucleotides (TFOs). Melting temperature analysis revealed that introduction of Ura(Pyr) into TFOs could effectively stabilize their triplex structures without loss of base recognition capabilities. PMID:26602276

  12. Change of the sign of superconducting intraband order parameters induced by interband pair hopping interaction in iron-based high-temperature superconductors

    International Nuclear Information System (INIS)

    Iron based superconductors are characterized by the s± gap symmetry, where the gap changes its sign between pockets of the Fermi surface. We discuss another sign change mechanism of the superconducting order parameter (OP)—the interband Cooper pairs hopping interaction. In the minimal two-orbital model of iron based superconductors we show that this interaction can lead to a change of the sign of the intraband superconducting OP regardless of its symmetry. (paper)

  13. Effect of BrU on the transition between wobble Gua-Thy and tautomeric Gua-Thy base-pairs: ab initio molecular orbital calculations

    International Nuclear Information System (INIS)

    We investigated transition states (TS) between wobble Guanine-Thymine (wG-T) and tautomeric G-T base-pair as well as Br-containing base-pairs by MP2 and density functional theory (DFT) calculations. The obtained TS between wG-T and G*-T (asterisk is an enol-form of base) is different from TS got by the previous DFT calculation. The activation energy (17.9 kcal/mol) evaluated by our calculation is significantly smaller than that (39.21 kcal/mol) obtained by the previous calculation, indicating that our TS is more preferable. In contrast, the obtained TS and activation energy between wG-T and G-T* are similar to those obtained by the previous DFT calculation. We furthermore found that the activation energy between wG-BrU and tautomeric G-BrU is smaller than that between wG-T and tautomeric G-T. This result elucidates that the replacement of CH3 group of T by Br increases the probability of the transition reaction producing the enol-form G* and T* bases. Because G* prefers to bind to T rather than to C, and T* to G not A, our calculated results reveal that the spontaneous mutation from C to T or from A to G base is accelerated by the introduction of wG-BrU base-pair.

  14. Effect of BrU on the transition between wobble Gua-Thy and tautomeric Gua-Thy base-pairs: ab initio molecular orbital calculations

    Science.gov (United States)

    Nomura, Kazuya; Hoshino, Ryota; Hoshiba, Yasuhiro; Danilov, Victor I.; Kurita, Noriyuki

    2013-04-01

    We investigated transition states (TS) between wobble Guanine-Thymine (wG-T) and tautomeric G-T base-pair as well as Br-containing base-pairs by MP2 and density functional theory (DFT) calculations. The obtained TS between wG-T and G*-T (asterisk is an enol-form of base) is different from TS got by the previous DFT calculation. The activation energy (17.9 kcal/mol) evaluated by our calculation is significantly smaller than that (39.21 kcal/mol) obtained by the previous calculation, indicating that our TS is more preferable. In contrast, the obtained TS and activation energy between wG-T and G-T* are similar to those obtained by the previous DFT calculation. We furthermore found that the activation energy between wG-BrU and tautomeric G-BrU is smaller than that between wG-T and tautomeric G-T. This result elucidates that the replacement of CH3 group of T by Br increases the probability of the transition reaction producing the enol-form G* and T* bases. Because G* prefers to bind to T rather than to C, and T* to G not A, our calculated results reveal that the spontaneous mutation from C to T or from A to G base is accelerated by the introduction of wG-BrU base-pair.

  15. MOTIFSIM: A web tool for detecting similarity in multiple DNA motif datasets.

    Science.gov (United States)

    Tran, Ngoc Tam L; Huang, Chun-Hsi

    2015-07-01

    Currently, there are a number of motif detection tools available that possess unique functionality. These tools often report different motifs, and therefore use of multiple tools is generally advised since common motifs reported by multiple tools are more likely to be biologically significant. However, results produced by these different tools need to be compared and existing similarity detection tools only allow comparison between two data sets. Here, we describe a motif similarity detection tool (MOTIFSIM) possessing a web-based, user-friendly interface that is capable of detecting similarity from multiple DNA motif data sets concurrently. Results can either be viewed online or downloaded. Users may also download and run MOTIFSIM as a command-line tool in stand-alone mode. The web tool, along with its command-line version, user manuals, and source codes, are freely available at http://biogrid-head.engr.uconn.edu/motifsim/. PMID:26156781

  16. A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation

    Energy Technology Data Exchange (ETDEWEB)

    Bucher, P. [Swiss Institute for Experimental Cancer Research, Lausanne (Switzerland); Bairoch, A. [Centre Medical Universitaire, Geneva (Switzerland)

    1994-12-31

    A general syntax for expressing bimolecular sequence motifs is described, which will be used in future releases of the PROSITE data bank and in a similar collection of nucleic acid sequence motifs currently under development. The central part of the syntax is a regular structure which can be viewed as a generalization of the profiles introduced by Gribskov and coworkers. Accessory features implement specific motif search strategies and provide information helpful for the interpretation of predicted matches. Two contrasting examples, representing E. coli promoters and SH3 domains respectively, are shown to demonstrate the versatility of the syntax, and its compatibility with diverse motif search methods. It is argued, that a comprehensive machine-readable motif collection based on the new syntax, in conjunction with a standard search program, can serve as a general-purpose sequence interpretation and function prediction tool.

  17. Cooper pairs in atomic nuclei

    International Nuclear Information System (INIS)

    We describe recent efforts to study Cooper pairs in atomic nuclei. We consider a self-consistent Hartree Fock mean field for the even Sm isotopes and compare results based on three treatments of pairing correlations: a BCS treatment, a number-projected BCS treatment and an exact treatment using the Richardson Ansatz. Significant differences are seen in the pairing correlation energies. Furthermore, because it does not average over the properties of the fermion pairs, the Richardson solution permits a more meaningful definition of the Cooper wave function and of the fraction of pairs that are collective. Our results confirm that only a few pairs near the Fermi surface in realistic atomic nuclei are collective. (Author)

  18. Cooper pairs in atomic nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Pittel, S. [Bartol Research Institute and Department of Physics and Astronomy, University of Delaware, Newark, 19716 Delaware (United States); Dussel, G. G. [Departamento de Fisica J.J. Giambiagi, Universidad de Buenos Aires, 1428 Buenos Aires (Argentina); Dukelsky, J.; Sarriguren, P. [Instituto de Estructura de la Materia, CSIC, Serrano 123, 28006 Madrid (Spain)

    2008-12-15

    We describe recent efforts to study Cooper pairs in atomic nuclei. We consider a self-consistent Hartree Fock mean field for the even Sm isotopes and compare results based on three treatments of pairing correlations: a BCS treatment, a number-projected BCS treatment and an exact treatment using the Richardson Ansatz. Significant differences are seen in the pairing correlation energies. Furthermore, because it does not average over the properties of the fermion pairs, the Richardson solution permits a more meaningful definition of the Cooper wave function and of the fraction of pairs that are collective. Our results confirm that only a few pairs near the Fermi surface in realistic atomic nuclei are collective. (Author)

  19. Fitness for synchronization of network motifs

    DEFF Research Database (Denmark)

    Vega, Y.M.; Vázquez-Prada, M.; Pacheco, A.F.; Vazquez-Prada Baillet, Miguel

    We study the synchronization of Kuramoto's oscillators in small parts of networks known as motifs. We first report on the system dynamics for the case of a scale-free network and show the existence of a non-trivial critical point. We compute the probability that network motifs synchronize, and fi...... that the fitness for synchronization correlates well with motifs interconnectedness and structural complexity. Possible implications for present debates about network evolution in biological and other systems are discussed. © 2004 Elsevier B.V. All rights reserved....

  20. QM/MM Simulation of the Hydrogen Bond Dynamics of an Adenine:Uracil Base Pair in Solution. Geometric Correlations and Infrared Spectrum

    CERN Document Server

    Yan, Yun-an

    2009-01-01

    Hybrid QM(DFT)/MM molecular dynamics simulations have been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. Trajectories are analyzed putting special attention to the geometric correlations of the $\\NHN$ and $\\NHO$ hydrogen bonds in the base pair. Further, based on empirical correlations between the hydrogen bond bond length and the fundamental NH stretching frequency its fluctuations are obtained along the trajectory. Using the time dependent frequencies the infrared lineshape is determined assuming the validity of a second order cumulant expansion. The deviations for the fundamental transition frequencies are calculated to amount to less than 2% as compared with experiment. The width of the spectrum for the $\\NHN$ bond is in reasonable agreement with experiment while that for the $\\NHO$ case is underestimated by the present model. Comparing the performance of different pseudopotentials it is found that the Troulli...

  1. Oxygen-aromatic contacts in intra-strand base pairs: analysis of high-resolution DNA crystal structures and quantum chemical calculations.

    Science.gov (United States)

    Jain, Alok; Krishna Deepak, R N V; Sankararamakrishnan, Ramasubbu

    2014-07-01

    Three-dimensional structures of biomolecules are stabilized by a large number of non-covalent interactions and some of them such as van der Waals, electrostatic and hydrogen bond interactions are well characterized. Delocalized π-electron clouds of aromatic residues are known to be involved in cation-π, CH-π, OH-π and π-π interactions. In proteins, many examples have been found in which the backbone carbonyl oxygen of one residue makes close contact with the aromatic center of aromatic residues. Quantum chemical calculations suggest that such contacts may provide stability to the protein secondary structures. In this study, we have systematically analyzed the experimentally determined high-resolution DNA crystal structures and identified 91 examples in which the aromatic center of one base is in close contact (interactions between the bases in base pairs with oxygen-aromatic contacts are energetically favorable. Decomposition of interaction energies indicates that dispersion forces are the major cause for energetically stable interaction in these base pairs. We speculate that oxygen-aromatic contacts in intra-strand base pairs in a DNA structure may have biological significance. PMID:24816369

  2. Monte Carlo simulations of biaxial structure in thin hybrid nematic film based upon spatially anisotropic pair potential

    Institute of Scientific and Technical Information of China (English)

    Zhang Zhi-Dong; Chang Chun-Rui; Ma Dong-Lai

    2009-01-01

    Hybrid nematic films have been studied by Monte Carlo simulations using a lattice spin model,in which the pair potential is spatially anisotropic and dependent on elastic constants of liquid crystals.We confirm in the thin hybrid nematic film the existence of a biaxially nonbent structure and the structarc transition from the biaxial to the bent-director structure,which is similar to the result obtained using the Lebwohl-Lasher model.However,the step-like director's profile,characteristic for the biaxial structure,is spatially asymmetric in the film because the pair potential leads to K1≠K3.We estimate the upper cell thickness to be 69 spin layers,in which the biaxial structure can be found.

  3. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Directory of Open Access Journals (Sweden)

    Fauteux François

    2009-10-01

    Full Text Available Abstract Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP gene promoters from three plant families, namely Brassicaceae (mustards, Fabaceae (legumes and Poaceae (grasses using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L. Heynh., soybean (Glycine max (L. Merr. and rice (Oryza sativa L. respectively. We have identified three conserved motifs (two RY-like and one ACGT-like in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination

  4. Structures and Energetics of Four Adjacent G·U Pairs That Stabilize an RNA Helix.

    Science.gov (United States)

    Gu, Xiaobo; Mooers, Blaine H M; Thomas, Leonard M; Malone, Joshua; Harris, Steven; Schroeder, Susan J

    2015-10-22

    Consecutive G·U base pairs inside RNA helices can be destabilizing, while those at the ends of helices are thermodynamically stabilizing. To determine if this paradox could be explained by differences in base stacking, we determined the high-resolution (1.32 Å) crystal structure of (5'-GGUGGCUGUU-3')2 and studied three sequences with four consecutive terminal G·U pairs by NMR spectroscopy. In the crystal structure of (5'-GGUGGCUGUU-3')2, the helix is overwound but retains the overall features of A-form RNA. The penultimate base steps at each end of the helix have high base overlap and contribute to the unexpectedly favorable energetic contribution for the 5'-GU-3'/3'-UG-5' motif in this helix position. The balance of base stacking and helical twist contributes to the positional dependence of G·U pair stabilities. The energetic stabilities and similarity to A-form RNA helices suggest that consecutive G·U pairs would be recognized by RNA helix binding proteins, such as Dicer and Ago. Thus, these results will aid future searches for target sites of small RNAs in gene regulation. PMID:26425937

  5. A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data

    OpenAIRE

    Ngoc Tam L. Tran; Huang, Chun-Hsi

    2014-01-01

    Abstract ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs tha...

  6. Analysing a reading strategy based on the elaboration of questions and the pair of answers and questions

    OpenAIRE

    Wilmo Ernesto Francisco Junior

    2011-01-01

    This paper describes a reading activity developed with chemistry students. The main aim was to analyse the reflections produced after reading three articles about experimentation. This study was performed with 17 chemistry students from a federal university. The reading strategy involved writing productions. Questions and the pair of questions and answers elaborated from articles were analysed, as well as the contribution of the socialization of knowledge by means of discussions and a debate....

  7. Temperature Dependence of the Average Energy Expended Per e-h Pair for Germanium-Based Dark Matter Experiments

    OpenAIRE

    Wei, W. -Z.; Wang, L.; Mei, D.-M.

    2016-01-01

    We report a new method to determine the temperature-dependent average energy expended per electron-hole (e-h) pair, $\\varepsilon$, for germanium detectors. As a result, the Fano factor and $\\varepsilon$ can be determined separately. Subsequently, we illustrate the variation of $\\varepsilon$ as a function of temperature. The impact of $\\varepsilon$ on the energy threshold and energy scale for germanium detectors at a given temperature is evaluated.

  8. Estimation of the Contribution of Intrinsic Currents to Motoneuron Firing Based on Paired Motoneuron Discharge Records in the Decerebrate Cat

    OpenAIRE

    Powers, Randall K.; Nardelli, Paul; Cope, T. C.

    2008-01-01

    Motoneuron activation is strongly influenced by persistent inward currents (PICs) flowing through voltage-sensitive channels. PIC characteristics and their contribution to the control of motoneuron firing rate have been extensively described in reduced animal preparations, but their contribution to rate modulation in human motoneurons is controversial. It has recently been proposed that the analysis of discharge records of a simultaneously recorded pair of motor units can be used to make quan...

  9. Multiple regression approach to mapping of quantitative trait loci (QTL) based on sib-pair data: a theoretical analysis

    OpenAIRE

    Xiong, Momiao; Guo, Sunwei

    2000-01-01

    The interval mapping method has been shown to be a powerful tool for mapping QTL. However, it is still a challenge to perform a simultaneous analysis of several linked QTLs, and to isolate multiple linked QTLs. To circumvent these problems, multiple regression analysis has been suggested for experimental species. In this paper, the multiple regression approach is extended to human sib-pair data through multiple regression of the squared difference in trait values between two...

  10. Discovering sequence motifs in quantitative and qualitative pepetide data

    DEFF Research Database (Denmark)

    Andreatta, Massimo

    analyze and interpret such data. The first paper in this thesis presents a new, publicly available method based on artificial neural networks that allows custom analysis of quantitative peptide data. The online NNAlign web-server provides a simple yet powerful tool for the discovery of sequence motifs in...... thousands of interactions in a single experiment, with virtually unlimited choice of potential targets and variants of these targets. However, the amount and complexity of data produced by high-throughput techniques poses serious challenges to researchers of limited bioinformatics expertise who need to...... this thesis deals with the presence of multiple motifs, due to the experimental setup or the actual poly-specificity of the receptor, in peptide data. A new algorithm, based on Gibbs sampling, identifies multiple specificities by performing two tasks simultaneously: alignment and clustering of peptide...

  11. miRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity

    DEFF Research Database (Denmark)

    Moore, Michael J; Scheel, Troels K H; Luna, Joseph M;

    2015-01-01

    microRNAs (miRNAs) act as sequence-specific guides for Argonaute (AGO) proteins, which mediate posttranscriptional silencing of target messenger RNAs. Despite their importance in many biological processes, rules governing AGO-miRNA targeting are only partially understood. Here we report a modified...... AGO HITS-CLIP strategy termed CLEAR (covalent ligation of endogenous Argonaute-bound RNAs)-CLIP, which enriches miRNAs ligated to their endogenous mRNA targets. CLEAR-CLIP mapped ∼130,000 endogenous miRNA-target interactions in mouse brain and ∼40,000 in human hepatoma cells. Motif and structural...... analysis define expanded pairing rules for over 200 mammalian miRNAs. Most interactions combine seed-based pairing with distinct, miRNA-specific patterns of auxiliary pairing. At some regulatory sites, this specificity confers distinct silencing functions to miRNA family members with shared seed sequences...

  12. Systematic exploration of a class of hydrophobic unnatural base pairs yields multiple new candidates for the expansion of the genetic alphabet

    Czech Academy of Sciences Publication Activity Database

    Dhami, K.; Malyshev, D. A.; Ordoukhanian, P.; Kubelka, Tomáš; Hocek, Michal; Romesberg, F. E.

    2014-01-01

    Roč. 42, č. 16 (2014), s. 10235-10244. ISSN 0305-1048 R&D Projects: GA ČR GBP206/12/G151 Institutional support: RVO:61388963 Keywords : unnatural base pairs * DNA * dTPT3-dNaM Subject RIV: CE - Biochemistry Impact factor: 9.112, year: 2014 http://nar.oxfordjournals.org/content/42/16/10235

  13. DNA Electronic Circular Dichroism on the Inter-Base Pair Scale: An Experimental-Theoretical Case Study of the AT Homo-Oligonucleotide.

    Science.gov (United States)

    Di Meo, Florent; Pedersen, Morten N; Rubio-Magnieto, Jenifer; Surin, Mathieu; Linares, Mathieu; Norman, Patrick

    2015-02-01

    A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment. PMID:26261947

  14. Transcription modulation in vitro of the fibroin gene exerted by a 200-base-pair region upstream from the "TATA" box.

    OpenAIRE

    Tsuda, M; Suzuki, Y

    1983-01-01

    We have previously reported that the 5'-flanking sequence upstream from the "TATA" box modulates the faithful transcription initiation of the fibroin gene in a homologous whole cell extract prepared from the silk glands, whereas such a modulating effect is not observed in a HeLa cell extract. Subsequently we have determined that major signals responsible for the modulating effect are located within a 200-base-pair region upstream from the TATA box, mainly in a distal region between nucleotide...

  15. Growing Right Onto Wellness (GROW): A Family-Centered, Community-Based Obesity Prevention Randomized Controlled Trial for Preschool Child-Parent Pairs

    OpenAIRE

    Po’e, Eli K.; Heerman, William J.; Mistry, Rishi S.; Barkin, Shari L.

    2013-01-01

    Growing Right Onto Wellness (GROW) is a randomized controlled trial that tests the efficacy of a family-centered, community-based, behavioral intervention to prevent childhood obesity among preschool-aged children. Focusing on parent-child pairs, GROW utilizes a multi-level framework, which accounts for macro (i.e., built-environment) and micro (i.e., genetics) level systems that contribute to the childhood obesity epidemic.

  16. Insights into electron tunneling across hydrogen-bonded base-pairs in complete molecular circuits for single-stranded DNA sequencing

    Science.gov (United States)

    Lee, Myeong H.; Sankey, Otto F.

    2009-01-01

    We report a first-principles study of electron ballistic transport through a molecular junction containing deoxycytidine-monophosphate (dCMP) connected to metal electrodes. A guanidinium ion and guanine nucleobase are tethered to gold electrodes on opposite sides to form hydrogen bonds with the dCMP molecule providing an electric circuit. The circuit mimics a component of a potential device for sequencing unmodified single-stranded DNA. The molecular conductance is obtained from DFT Green's function scattering methods and is compared to estimates from the electron tunneling decay constant obtained from the complex band structure. The result is that a complete molecular dCMP circuit of 'linker((CH2)2)-guanidinium-phosphate-deoxyribose-cytosine-guanine' has a very low conductance (of the order of fS) while the hydrogen-bonded guanine-cytosine base-pair has a moderate conductance (of the order of tens to hundreds of nS). Thus, while the transverse electron transfer through base-pairing is moderately conductive, electron transfer through a complete molecular dCMP circuit is not. The gold Fermi level is found to be aligned very close to the HOMO for both the guanine-cytosine base-pair and the complete molecular dCMP circuit. Results for two different plausible geometries of the hydrogen-bonded dCMP molecule reveal that the conductance varies from fS for an extended structure to pS for a slightly compressed structure.

  17. Identification of an RcsA/RcsB recognition motif in the promoters of exopolysaccharide biosynthetic operons from Erwinia amylovora and Pantoea stewartii subspecies stewartii.

    Science.gov (United States)

    Wehland, M; Kiecker, C; Coplin, D L; Kelm, O; Saenger, W; Bernhard, F

    1999-02-01

    The regulation of capsule synthesis (Rcs) regulatory network is responsible for the induction of exopolysaccharide biosynthesis in many enterobacterial species. We have previously shown that two transcriptional regulators, RcsA and RcsB, do bind as a heterodimer to the promoter of amsG, the first reading frame in the operon for amylovoran biosynthesis in the plant pathogenic bacterium Erwinia amylovora. We now identified a 23-base pair fragment from position -555 to -533 upstream of the translational start site of amsG as sufficient for the specific binding of the Rcs proteins. In addition, we could detect an RcsA/RcsB-binding site in a corresponding region of the promoter of cpsA, the homologous counterpart to the E. amylovora amsG gene in the operon for stewartan biosynthesis of Pantoea stewartii. The specificity and characteristic parameters of the protein-DNA interaction were analyzed by DNA retardation, protein-DNA cross-linking, and directed mutagenesis. The central core motif TRVGAAWAWTSYG of the amsG promoter was found to be most important for the specific interaction with RcsA/RcsB, as evaluated by mutational analysis and an in vitro selection approach. The wild type P. stewartii Rcs binding motif is degenerated in two positions and an up-mutation according to our consensus motif resulted in about a 5-fold increased affinity of the RcsA/RcsB proteins. PMID:9920870

  18. A Further Study on Mining DNA Motifs Using Fuzzy Self-Organizing Maps.

    Science.gov (United States)

    Tapan, Sarwar; Wang, Dianhui

    2016-01-01

    Self-organizing map (SOM)-based motif mining, despite being a promising approach for problem solving, mostly fails to offer a consistent interpretation of clusters with respect to the mixed composition of signal and noise in the nodes. The main reason behind this shortcoming comes from the similarity metrics used in data assignment, specially designed with the biological interpretation for this domain, which are not meant to consider the inevitable noise mixture in the clusters. This limits the explicability of the majority of clusters that are supposedly noise dominated, degrading the overall system clarity in motif discovery. This paper aims to improve the explicability aspect of learning process by introducing a composite similarity function (CSF) that is specially designed for the k -mer-to-cluster similarity measure with respect to the degree of motif properties and embedded noise in the cluster. Our proposed motif finding algorithm in this paper is built on our previous work robust elicitation algorithms for discovering (READ) [1] and termed READ Deoxyribonucleic acid motifs using CSFs (READ(csf)), which performs slightly better than READ and shows some remarkable improvements over SOM-based SOMBRERO and SOMEA tools in terms of F-measure on the testing data sets. A real data set containing multiple motifs is used to explore the potential of the READ(csf) for more challenging biological data mining tasks. Visual comparisons with the verified logos extracted from JASPAR database demonstrate that our algorithm is promising to discover multiple motifs simultaneously. PMID:26068877

  19. Observation of H-bond mediated 3hJH2H3coupling constants across Watson-Crick AU base pairs in RNA

    International Nuclear Information System (INIS)

    3hJH2H3trans-hydrogen bond scalar coupling constants have been observed for the first time in Watson-Crick AU base pairs in uniformly 15N-labeled RNA oligonucleotides using a new 2hJNN-HNN-E. COSY experiment. The experiment utilizes adenosine H2 (AH2) for original polarization and detection, while employing 2hJNNcouplings for coherence transfer across the hydrogen bonds (H-bonds). The H3 protons of uracil bases are unperturbed throughout the experiment so that these protons appear as passive spins in E. COSY patterns. 3hJH2H3coupling constants can therefore be accurately measured in the acquisition dimension from the displacement of the E. COSY multiplet components, which are separated by the relatively large 1JH3N3coupling constants in the indirect dimension of the two-dimensional experiment. The 3hJH2H3scalar coupling constants determined for AU base pairs in the two RNA hairpins examined here have been found to be positive and range in magnitude up to 1.8 Hz. Using a molecular fragment representation of an AU base pair, density functional theory/finite field perturbation theory (DFT/FPT) methods have been applied to attempt to predict the relative contributions of H-bond length and angular geometry to the magnitude of 3hJH2H3coupling constants. Although the DFT/FPT calculations did not reproduce the full range of magnitude observed experimentally for the 3hJH2H3coupling constants, the calculations do predict the correct sign and general trends in variation in size of these coupling constants. The calculations suggest that the magnitude of the coupling constants depends largely on H-bond length, but can also vary with differences in base pair geometry. The dependency of the 3hJH2H3coupling constant on H-bond strength and geometry makes it a new probe for defining base pairs in NMR studies of nucleic acids

  20. Prevalent RNA recognition motif duplication in the human genome.

    Science.gov (United States)

    Tsai, Yihsuan S; Gomez, Shawn M; Wang, Zefeng

    2014-05-01

    The sequence-specific recognition of RNA by proteins is mediated through various RNA binding domains, with the RNA recognition motif (RRM) being the most frequent and present in >50% of RNA-binding proteins (RBPs). Many RBPs contain multiple RRMs, and it is unclear how each RRM contributes to the binding specificity of the entire protein. We found that RRMs within the same RBP (i.e., sibling RRMs) tend to have significantly higher similarity than expected by chance. Sibling RRM pairs from RBPs shared by multiple species tend to have lower similarity than those found only in a single species, suggesting that multiple RRMs within the same protein might arise from domain duplication followed by divergence through random mutations. This finding is exemplified by a recent RRM domain duplication in DAZ proteins and an ancient duplication in PABP proteins. Additionally, we found that different similarities between sibling RRMs are associated with distinct functions of an RBP and that the RBPs tend to contain repetitive sequences with low complexity. Taken together, this study suggests that the number of RBPs with multiple RRMs has expanded in mammals and that the multiple sibling RRMs may recognize similar target motifs in a cooperative manner. PMID:24667216

  1. Average Energy Expended Per e-h Pair and Energy Scale Function for Germanium-Based Dark Matter Experiments

    CERN Document Server

    Wei, W -Z; Mei, D -M

    2016-01-01

    We report a new method to determine the temperature-dependent average energy expended per electron-hole (e-h) pair, $\\varepsilon$, for germanium detectors. As a result, the Fano factor and $\\varepsilon$ can be determined separately. Subsequently, we illustrate the variation of $\\varepsilon$ as a function of temperature. The impact of $\\varepsilon$ on the energy threshold and energy scale for germanium detectors at a given temperature is evaluated. We demonstrate an absolute energy scale function of low-energy recoils for germanium detectors in the direct detection of dark matter particles.

  2. Identifying Function, Agent, and Setting Motifs in Some Early Spanish "libros de caballerías"

    OpenAIRE

    NEUMAYER, KRISTIN

    2012-01-01

    The essay presents the methodology of a doctoral thesis (2008, University of Wisconsin-Madison) which classifies plot motifs in some sixteenth-century Castilian books of chivalry. Therein, two critical approaches to the texts are noted: motif studies, which analyze narrative components, and structural studies, which examine whole plotlines. Based on V. Propp’s Morphology of the Folktale, the motif is defined as a unit of plot structure. Propp’s thirty-one functions and seven tale-roles are th...

  3. Atomic-Level Organization of Vicinal Acid-Base Pairs through the Chemisorption of Aniline and Derivatives onto Mesoporous SBA15

    KAUST Repository

    Basset, Jean-Marie

    2016-06-09

    The design of novel heterogeneous catalysts with multiple adjacent functionalities is of high interest for heterogeneous catalysis. Herein, we report a method to obtain a majority bifunctional acid-base pairs on SBA15. Aniline reacts with SBA15 by opening siloxane bridges leading to N-phenylsilanamine-silanol pairs. In contrast with ammonia treated surfaces, the material is stable under air/moisture. Advanced solid state MAS NMR: 2D ¹H-¹H double-quantum, ¹H-¹³C HETCOR experiments and dynamic nuclear polarization enhanced ²⁹Si and ¹⁵N spectra demonstrate both the close proximity between the two moieties and the formation of a covalent Si-N surface bond and confirm the design of vicinal acid-base pairs. This approach was successfully applied to the design of a series of aniline derivatives bifunctional SBA15. A correlation of the substituents effects on the aromatic ring (Hammet parameters) on the kinetics of the model reaction of Knoevenagel is observed.

  4. Structure of Stacked Dimers of N-Methylated Watson–Crick Adenine–Thymine Base Pairs

    Directory of Open Access Journals (Sweden)

    Sándor Suhai

    2003-09-01

    Full Text Available Abstract: The structure of two isomeric stacked dimers of Watson-Crick 9-methyladenine-1-methylthymine pairs was fully optimized using an approximate density functional theory (DFT method augmented with an empirical dispersion interaction. The results of the calculations reveal that head-to-tail (AT-TA and head-to-head (AT-AT dimers possess a significantly different geometry. The structure of both complexes is stabilized by vertical CH…O and C-H…N hydrogen bonds with the participation of the hydrogen atoms of the methyl groups. The energy of hydrogen bonding and stacking interactions was additionally calculated using the MP2/6-31G*(0.25 method. Differences in the mutual arrangement of the base pairs in two isomeric dimers lead to significant changes of intra and interstrand stacking interaction energies.

  5. Fiber-based photon-pair source capable of hybrid entanglement in frequency and transverse mode, controllably scalable to higher dimensions

    Science.gov (United States)

    Cruz-Delgado, D.; Ramirez-Alarcon, R.; Ortiz-Ricardo, E.; Monroy-Ruz, J.; Dominguez-Serna, F.; Cruz-Ramirez, H.; Garay-Palmett, K.; U’Ren, A. B.

    2016-01-01

    We have designed and implemented a photon-pair source, based on the spontaneous four wave mixing (SFWM) process in a few-mode fiber, in a geometry which permits multiple, simultaneous SFWM processes, each associated with a distinct combination of transverse modes for the four participating waves. In our source: i) each process is group-velocity-matched so that it is, by design, nearly-factorable, and ii) the spectral separation between neighboring processes is greater than the marginal spectral width of each process. Consequently, there is a direct correspondence between the joint amplitude of each process and each of the Schmidt mode pairs of the overall two-photon state. Our approach permits hybrid entanglement in discrete frequency and in transverse mode, whereby control of the number of supported fiber transverse modes allows scalability to higher dimensions while spectral filtering may be used for straightforward Schmidt mode discrimination. PMID:27271284

  6. Fiber-based photon-pair source capable of hybrid entanglement in frequency and transverse mode, controllably scalable to higher dimensions

    Science.gov (United States)

    Cruz-Delgado, D.; Ramirez-Alarcon, R.; Ortiz-Ricardo, E.; Monroy-Ruz, J.; Dominguez-Serna, F.; Cruz-Ramirez, H.; Garay-Palmett, K.; U’Ren, A. B.

    2016-06-01

    We have designed and implemented a photon-pair source, based on the spontaneous four wave mixing (SFWM) process in a few-mode fiber, in a geometry which permits multiple, simultaneous SFWM processes, each associated with a distinct combination of transverse modes for the four participating waves. In our source: i) each process is group-velocity-matched so that it is, by design, nearly-factorable, and ii) the spectral separation between neighboring processes is greater than the marginal spectral width of each process. Consequently, there is a direct correspondence between the joint amplitude of each process and each of the Schmidt mode pairs of the overall two-photon state. Our approach permits hybrid entanglement in discrete frequency and in transverse mode, whereby control of the number of supported fiber transverse modes allows scalability to higher dimensions while spectral filtering may be used for straightforward Schmidt mode discrimination.

  7. Dislocation network with pair-coupling structure in {111} γ/γ' interface of Ni-based single crystal superalloy.

    Science.gov (United States)

    Ru, Yi; Li, Shusuo; Zhou, Jian; Pei, Yanling; Wang, Hui; Gong, Shengkai; Xu, Huibin

    2016-01-01

    The γ/γ' interface dislocation network is reported to improve the high temperature creep resistance of single crystal superalloys and is usually found to deposit in {001} interface. In this work, a new type of dislocation network was found in {111} γ/γ' interface at a single crystal model superalloy crept at 1100 °C/100 MPa. The dislocations in the network are screw with Burgers vectors of 1/2 a and most interestingly, they exhibit a pair-coupling structure. Further investigation indicates that the formation of {111} interface dislocation network occurs when the γ' raft structure begins to degrade by the dislocations cutting into the rafted γ' through the interface. In this condition, the pair-coupling structure is established by the dislocations gliding in a single {111} plane of γ', in order to remove the anti-phase boundary in γ'; these dislocations also act as diffusion channels for dissolving of the γ' particle that is unstable under the interfacial stress from lattice misfit, which leads to the formation of {111}-type zigzag interface. The formation of this network arises as a consequence of more negative misfit, low-alloying γ' particle and proper test conditions of temperature and stress. PMID:27511822

  8. WildSpan: mining structured motifs from protein sequences

    Directory of Open Access Journals (Sweden)

    Chen Chien-Yu

    2011-03-01

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

  9. A new motif for inhibitors of geranylgeranyl diphosphate synthase.

    Science.gov (United States)

    Foust, Benjamin J; Allen, Cheryl; Holstein, Sarah A; Wiemer, David F

    2016-08-15

    The enzyme geranylgeranyl diphosphate synthase (GGDPS) is believed to receive the substrate farnesyl diphosphate through one lipophilic channel and release the product geranylgeranyl diphosphate through another. Bisphosphonates with two isoprenoid chains positioned on the α-carbon have proven to be effective inhibitors of this enzyme. Now a new motif has been prepared with one isoprenoid chain on the α-carbon, a second included as a phosphonate ester, and the potential for a third at the α-carbon. The pivaloyloxymethyl prodrugs of several compounds based on this motif have been prepared and the resulting compounds have been tested for their ability to disrupt protein geranylgeranylation and induce cytotoxicity in myeloma cells. The initial biological studies reveal activity consistent with GGDPS inhibition, and demonstrate a structure-function relationship which is dependent on the nature of the alkyl group at the α-carbon. PMID:27338660

  10. MOTIFATOR : detection and characterization of regulatory motifs using prokaryote transcriptome data

    NARCIS (Netherlands)

    Blom, Evert-Jan; Roerdink, Jos B.T.M.; Kuipers, Oscar P.; Hijum, Sacha A.F.T. van

    2009-01-01

    Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processi

  11. The MHC motif viewer: a visualization tool for MHC binding motifs

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Hoof, Ilka; Lund, Ole; Nielsen, Morten

    2010-01-01

    hampered by the lack of tools for browsing and comparing specificity of these molecules. We have developed a Web server, MHC Motif Viewer, which allows the display of the binding motif for MHC class I proteins for human, chimpanzee, rhesus monkey, mouse, and swine, as well as HLA-DR protein sequences. The...

  12. A relational extension of the notion of motifs: application to the common 3D protein substructures searching problem.

    Science.gov (United States)

    Pisanti, Nadia; Soldano, Henry; Carpentier, Mathilde; Pothier, Joel

    2009-12-01

    The geometrical configurations of atoms in protein structures can be viewed as approximate relations among them. Then, finding similar common substructures within a set of protein structures belongs to a new class of problems that generalizes that of finding repeated motifs. The novelty lies in the addition of constraints on the motifs in terms of relations that must hold between pairs of positions of the motifs. We will hence denote them as relational motifs. For this class of problems, we present an algorithm that is a suitable extension of the KMR paradigm and, in particular, of the KMRC as it uses a degenerate alphabet. Our algorithm contains several improvements that become especially useful when-as it is required for relational motifs-the inference is made by partially overlapping shorter motifs, rather than concatenating them. The efficiency, correctness and completeness of the algorithm is ensured by several non-trivial properties that are proven in this paper. The algorithm has been applied in the important field of protein common 3D substructure searching. The methods implemented have been tested on several examples of protein families such as serine proteases, globins and cytochromes P450 additionally. The detected motifs have been compared to those found by multiple structural alignments methods. PMID:20047489

  13. Functional characterization of variations on regulatory motifs.

    Directory of Open Access Journals (Sweden)

    Michal Lapidot

    2008-03-01

    Full Text Available Transcription factors (TFs regulate gene expression through specific interactions with short promoter elements. The same regulatory protein may recognize a variety of related sequences. Moreover, once they are detected it is hard to predict whether highly similar sequence motifs will be recognized by the same TF and regulate similar gene expression patterns, or serve as binding sites for distinct regulatory factors. We developed computational measures to assess the functional implications of variations on regulatory motifs and to compare the functions of related sites. We have developed computational means for estimating the functional outcome of substituting a single position within a binding site and applied them to a collection of putative regulatory motifs. We predict the effects of nucleotide variations within motifs on gene expression patterns. In cases where such predictions could be compared to suitable published experimental evidence, we found very good agreement. We further accumulated statistics from multiple substitutions across various binding sites in an attempt to deduce general properties that characterize nucleotide substitutions that are more likely to alter expression. We found that substitutions involving Adenine are more likely to retain the expression pattern and that substitutions involving Guanine are more likely to alter expression compared to the rest of the substitutions. Our results should facilitate the prediction of the expression outcomes of binding site variations. One typical important implication is expected to be the ability to predict the phenotypic effect of variation in regulatory motifs in promoters.

  14. Sublinear Time Motif Discovery from Multiple Sequences

    Directory of Open Access Journals (Sweden)

    Yunhui Fu

    2013-10-01

    Full Text Available In this paper, a natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are k background sequences, and each character in a background sequence is a random character from an alphabet, Σ. A motif G = g1g2 ... gm is a string of m characters. In each background sequence is implanted a probabilistically-generated approximate copy of G. For a probabilistically-generated approximate copy b1b2 ... bm of G, every character, bi, is probabilistically generated, such that the probability for bi ≠ gi is at most α. We develop two new randomized algorithms and one new deterministic algorithm. They make advancements in the following aspects: (1 The algorithms are much faster than those before. Our algorithms can even run in sublinear time. (2 They can handle any motif pattern. (3 The restriction for the alphabet size is a lower bound of four. This gives them potential applications in practical problems, since gene sequences have an alphabet size of four. (4 All algorithms have rigorous proofs about their performances. The methods developed in this paper have been used in the software implementation. We observed some encouraging results that show improved performance for motif detection compared with other software.

  15. Comparative Analysis of Regulatory Motif Discovery Tools for Transcription Factor Binding Sites

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In the post-genomic era, identification of specific regulatory motifs or transcription factor binding sites (TFBSs) in non-coding DNA sequences, which is essential to elucidate transcriptional regulatory networks, has emerged as an obstacle that frustrates many researchers. Consequently, numerous motif discovery tools and correlated databases have been applied to solving this problem. However, these existing methods, based on different computational algorithms, show diverse motif prediction efficiency in non-coding DNA sequences. Therefore, understanding the similarities and differences of computational algorithms and enriching the motif discovery literatures are important for users to choose the most appropriate one among the online available tools. Moreover, there still lacks credible criterion to assess motif discovery tools and instructions for researchers to choose the best according to their own projects. Thus integration of the related resources might be a good approach to improve accuracy of the application. Recent studies integrate regulatory motif discovery tools with experimental methods to offer a complementary approach for researchers, and also provide a much-needed model for current researches on transcriptional regulatory networks. Here we present a comparative analysis of regulatory motif discovery tools for TFBSs.

  16. QuateXelero: an accelerated exact network motif detection algorithm.

    Science.gov (United States)

    Khakabimamaghani, Sahand; Sharafuddin, Iman; Dichter, Norbert; Koch, Ina; Masoudi-Nejad, Ali

    2013-01-01

    Finding motifs in biological, social, technological, and other types of networks has become a widespread method to gain more knowledge about these networks' structure and function. However, this task is very computationally demanding, because it is highly associated with the graph isomorphism which is an NP problem (not known to belong to P or NP-complete subsets yet). Accordingly, this research is endeavoring to decrease the need to call NAUTY isomorphism detection method, which is the most time-consuming step in many existing algorithms. The work provides an extremely fast motif detection algorithm called QuateXelero, which has a Quaternary Tree data structure in the heart. The proposed algorithm is based on the well-known ESU (FANMOD) motif detection algorithm. The results of experiments on some standard model networks approve the overal superiority of the proposed algorithm, namely QuateXelero, compared with two of the fastest existing algorithms, G-Tries and Kavosh. QuateXelero is especially fastest in constructing the central data structure of the algorithm from scratch based on the input network. PMID:23874498

  17. S-1-Based versus capecitabine-based preoperative chemoradiotherapy in the treatment of locally advanced rectal cancer: a matched-pair analysis.

    Directory of Open Access Journals (Sweden)

    Meng Su

    Full Text Available OBJECTIVE: The aim of this paper was to compare the efficacy and safety of S-1-based and capecitabine-based preoperative chemoradiotherapy regimens in patients with locally advanced rectal cancer through a retrospective matched-pair analysis. MATERIALS AND METHODS: Between Jan 2010 and Mar 2014, 24 patients with locally advanced rectal cancer who received preoperative radiotherapy concurrently with S-1 were individually matched with 24 contemporary patients with locally advanced rectal cancer who received preoperative radiotherapy concurrently with capecitabine according to clinical stage (as determined by pelvic magnetic resonance imaging and computed tomography and age (within five years. All these patients performed mesorectal excision 4-8 weeks after the completion of chemoradiotherapy. RESULTS: The tumor volume reduction rates were 55.9±15.1% in the S-1 group and 53.8±16.0% in the capecitabine group (p = 0.619. The overall downstaging, including both T downstaging and N downstaging, occurred in 83.3% of the S-1 group and 70.8% of the capecitabine group (p = 0.508. The significant tumor regression, including regression grade I and II, occurred in 33.3% of S-1 patients and 25.0% of capecitabine patients (p = 0.754. In the two groups, Grade 4 adverse events were not observed and Grade 3 consisted of only two cases of diarrhea, and no patient suffered hematologic adverse event of Grade 2 or higher. However, the incidence of diarrhea (62.5% vs 33.3%, p = 0.014 and hand-foot syndrome (29.2% vs 0%, p = 0.016 were higher in capecitabine group. Other adverse events did not differ significantly between two groups. CONCLUSIONS: The two preoperative chemoradiotherapy regimens were effective and safe for patients of locally advanced rectal cancer, but regimen with S-1 exhibited a lower incidence of adverse events.

  18. Adjoint of Pair Frames

    OpenAIRE

    Fereydooni, Abolhassan; Safapour, Ahmad; Rahimi , Asghar

    2012-01-01

    The concept of (p,q)-pair frames is generalized to (l,l^*)-pair frames. Adjoint (conjugate) of a pair frames for dual space of a Banach space is introduced and some conditions for the existence of adjoint (conjugate) of pair frames are presented.

  19. Pair-Wise, Deformable Mirror, Image Plane-Based Diversity Electric Field Estimation for High Contrast Coronagraphy

    Science.gov (United States)

    Give'on, Amir; Kern, Brian D.; Shaklan, Stuart

    2011-01-01

    In this paper we describe the complex electric field reconstruction from image plane intensity measurements for high contrast coronagraphic imaging. A deformable mirror (DM) surface is modied with pairs of complementary shapes to create diversity in the image plane of the science camera where the intensity of the light is measured. Along with the Electric Field Conjugation correction algorithm, this estimation method has been used in various high contrast imaging testbeds to achieve the best contrasts to date both in narrow and in broad band light. We present the basic methodology of estimation in easy to follow list of steps, present results from HCIT and raise several open quations we are confronted with using this method.

  20. A pair of novel Cd(II) enantiomers based on lactate derivatives: Synthesis, crystal structures and properties

    Science.gov (United States)

    Xu, Zhong-Xuan; Ao, Ke-Hou; Zhang, Jian

    2016-09-01

    A pair of novel 3D homochiral metal-organic frameworks (HMOFs), namely [Cd2.5((R)-CIA)6(1,4-DIB)(H2O)2]·((CH3)2NH2)·H2O (1-D), [Cd2.5((S)-CIA)6(1,4-DIB)(H2O)2]·((CH3)2NH2)·H2O (1-L), have been synthesized using lactic acid derivative ligands ((R)-H3CIA and (S)-H3CIA) and 1,4-DIB. Crystallographic analyses indicate that the complexes 1-D and 1-L are packed by cage substructures. Some physical characteristics, such as solid-state circular dichroism (CD), thermal stabilities and photoluminescent properties are also investigated. Our results highlight the effective method to apply lactic acid derivative ligands to form interesting HMOFs.

  1. Sequential motif profile of natural visibility graphs

    CERN Document Server

    Iacovacci, Jacopo

    2016-01-01

    The concept of sequential visibility graph motifs -subgraphs appearing with characteristic frequencies in the visibility graphs associated to time series- has been advanced recently along with a theoretical framework to compute analytically the motif profiles associated to Horizontal Visibility Graphs (HVGs). Here we develop a theory to compute the profile of sequential visibility graph motifs in the context of Natural Visibility Graphs (VGs). This theory gives exact results for deterministic aperiodic processes with a smooth invariant density or stochastic processes that fulfil the Markov property and have a continuous marginal distribution. The framework also allows for a linear time numerical estimation in the case of empirical time series. A comparison between the HVG and the VG case (including evaluation of their robustness for short series polluted with measurement noise) is also presented.

  2. Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Hanke, S.; Hinsby, A. M.; Friis, Carsten; Brunak, Søren; Mann, M.; Blom, Nikolaj

    Advances in mass spectrometry-based proteomics have yielded a substantial mapping of the tyrosine phosphoproteome and thus provided an important step toward a systematic analysis of intracellular signaling networks in higher eukaryotes. In this study we decomposed an uncharacterized proteomics data...... set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr...... and validated as a binding motif for the SH2 domain-containing inositol phosphatase SHIP2. Our decomposition of the in vivo Tyr(P) proteome furthermore suggests that two-thirds of the Tyr(P) sites mediate interaction, whereas the remaining third govern processes such as enzyme activation and nucleic...

  3. Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions

    Directory of Open Access Journals (Sweden)

    Aruga Jun

    2010-02-01

    Full Text Available Abstract Background The C2H2 zinc finger (ZF domain is widely conserved among eukaryotic proteins. In Zic/Gli/Zap1 C2H2 ZF proteins, the two N-terminal ZFs form a single structural unit by sharing a hydrophobic core. This structural unit defines a new motif comprised of two tryptophan side chains at the center of the hydrophobic core. Because each tryptophan residue is located between the two cysteine residues of the C2H2 motif, we have named this structure the tandem CWCH2 (tCWCH2 motif. Results Here, we characterized 587 tCWCH2-containing genes using data derived from public databases. We categorized genes into 11 classes including Zic/Gli/Glis, Arid2/Rsc9, PacC, Mizf, Aebp2, Zap1/ZafA, Fungl, Zfp106, Twincl, Clr1, and Fungl-4ZF, based on sequence similarity, domain organization, and functional similarities. tCWCH2 motifs are mostly found in organisms belonging to the Opisthokonta (metazoa, fungi, and choanoflagellates and Amoebozoa (amoeba, Dictyostelium discoideum. By comparison, the C2H2 ZF motif is distributed widely among the eukaryotes. The structure and organization of the tCWCH2 motif, its phylogenetic distribution, and molecular phylogenetic analysis suggest that prototypical tCWCH2 genes existed in the Opisthokonta ancestor. Within-group or between-group comparisons of the tCWCH2 amino acid sequence identified three additional sequence features (site-specific amino acid frequencies, longer linker sequence between two C2H2 ZFs, and frequent extra-sequences within C2H2 ZF motifs. Conclusion These features suggest that the tCWCH2 motif is a specialized motif involved in inter-zinc finger interactions.

  4. New Theoretical Insight into the Interactions and Properties of Formic Acid: Development of a Quantum-Based Pair Potential for Formic Acid.

    Energy Technology Data Exchange (ETDEWEB)

    Roszak, S; Gee, R; Balasubramanian, K; Fried, L

    2005-08-08

    We performed ab initio quantum chemical studies for the development of intra and intermolecular interaction potentials for formic acid for use in molecular dynamics simulations of formic acid molecular crystal. The formic acid structures considered in the ab initio studies include both the cis and trans monomers which are the conformers that have been postulated as part of chains constituting liquid and crystal phases under extreme conditions. Although the cis to trans transformation is not energetically favored, the trans isomer was found as a component of stable gas-phase species. Our decomposition scheme for the interaction energy indicates that the hydrogen bonded complexes are dominated by the Hartree-Fock forces while parallel clusters are stabilized by the electron correlation energy. The calculated three-body and higher interactions are found to be negligible, thus rationalizing the development of an atom-atom pair potential for formic acid based on high-level ab initio calculations of small formic acid clusters. Here we present an atom-atom pair potential that includes both intra- and inter-molecular degrees of freedom for formic acid. The newly developed pair potential is used to examine formic acid in the condensed phase via molecular dynamics simulations. The isothermal compression under hydrostatic pressure obtained from molecular dynamics simulations is in good agreement with experiment. Further, the calculated equilibrium melting temperature is found to be in good agreement with experiment.

  5. New theoretical insight into the interactions and properties of formic acid: development of a quantum-based pair potential for formic acid.

    Science.gov (United States)

    Roszak, Szczepan; Gee, Richard H; Balasubramanian, Krishnan; Fried, Laurence E

    2005-10-01

    We performed ab initio quantum-chemical studies for the development of intra- and intermolecular interaction potentials for formic acid for use in molecular-dynamics simulations of formic acid molecular crystal. The formic acid structures considered in the ab initio studies include both the cis and trans monomers which are the conformers that have been postulated as part of chains constituting liquid and crystal phases under extreme conditions. Although the cis to trans transformation is not energetically favored, the trans isomer was found as a component of stable gas-phase species. Our decomposition scheme for the interaction energy indicates that the hydrogen-bonded complexes are dominated by the Hartree-Fock forces while parallel clusters are stabilized by the electron correlation energy. The calculated three-body and higher interactions are found to be negligible, thus rationalizing the development of an atom-atom pair potential for formic acid based on high-level ab initio calculations of small formic acid clusters. Here we present an atom-atom pair potential that includes both intra- and inter molecular degrees of freedom for formic acid. The newly developed pair potential is used to examine formic acid in the condensed phase via molecular-dynamics simulations. The isothermal compression under hydrostatic pressure obtained from molecular-dynamics simulations is in good agreement with experiment. Further, the calculated equilibrium melting temperature is found to be in good agreement with experiment. PMID:16238411

  6. Solvation of deoxynucleosides in aqueous mixtures of organic solvents probed through their intrinsic fluorescence: Implications for open base pair states in DNA

    Science.gov (United States)

    Ababneh, Anas Mohammad

    Because of the importance of solvation in the function of DNA, there is considerable interest in understanding the solvation network of its constituent components. This is of particular importance in connection with the closing of base pairs that have been disrupted as a result of structural fluctuations. Following the opening of a base pair, the open base is exposed to a heterogeneous environment which involves polar as well as nonpolar interactions. Toward the goal of understanding how the open bases interact with such a heterogeneous environment, we have studied the intrinsic fluorescence properties of the purine and pyrimidine nucleosides (dG, dA, dT, and dC) in organic solvents in the presence of small amounts of water. Exposure of the nucleoside to water was done by preparing solutions in three different ways: (i) "premixed" solution in which the nucleoside is dissolved in a water-organic solvent mixture, (ii) "carry its own water" solution in which the nucleoside is first dissolved in water and then diluted in the organic solvent, and (iii) "injected" solution in which water is added to a solution of the nucleoside in the organic solvent. The organic solvents used in the present study were: n-butanol, acetonitrile, methanol, n-propanol, isopropanol, and isobutanol. We find that for n-butanol and acetonitrile, which have a high degree of amphiphilicity and weak hydrogen bonding ability, respectively, the fluorescence spectral properties of the purines are found to depend on the sequence of the steps in which the aqueous mixture was formed. By contrast, no such dependence was observed in the other organic solvents. On the other hand, no such dependence was observed for the pyrimidines in any of the organic solvents used in the present study. These findings suggest that the final solvation network around the purines is dependent on the nature of the environment to which they were initially exposed. This would tend to present an impediment to the closing of

  7. The Phe-Phe Motif for Peptide Self-Assembly in Nanomedicine

    OpenAIRE

    Silvia Marchesan; Vargiu, Attilio V.; Katie E. Styan

    2015-01-01

    Since its discovery, the Phe-Phe motif has gained in popularity as a minimalist building block to drive the self-assembly of short peptides and their analogues into nanostructures and hydrogels. Molecules based on the Phe-Phe motif have found a range of applications in nanomedicine, from drug delivery and biomaterials to new therapeutic paradigms. Here we discuss the various production methods for this class of compounds, and the characterization, nanomorphologies, and application of their se...

  8. Decorative motifs in the interior of the town house of the 19th century in Macedonia

    OpenAIRE

    Namicev, Petar; Namiceva, Ekaterina

    2015-01-01

    An integral part of the decoration of the house in Macedonia in the 19th century is, the application of certain stylized motifs in shaping the interior. Based upon the specific material (wood, plaster) gets a certain typology of decorative elements, with partial or full use of the wood or plaster in their representation in the interior. According to the style of decorative motifs include geometric processing, vegetable and zoomorphic decoration. Vegetabe and geometric decoration representing ...

  9. Defining and searching for structural motifs using DeepView/Swiss-PdbViewer

    OpenAIRE

    Johansson Maria U; Zoete Vincent; Michielin Olivier; Guex Nicolas

    2012-01-01

    Abstract Background Today, recognition and classification of sequence motifs and protein folds is a mature field, thanks to the availability of numerous comprehensive and easy to use software packages and web-based services. Recognition of structural motifs, by comparison, is less well developed and much less frequently used, possibly due to a lack of easily accessible and easy to use software. Results In this paper, we describe an extension of DeepView/Swiss-PdbViewer through which structura...

  10. Waddling Random Walk: Fast and Accurate Sampling of Motif Statistics in Large Graphs

    OpenAIRE

    Han, Guyue; Sethu, Harish

    2016-01-01

    The relative frequency of small subgraphs within a large graph, such as one representing an online social network, is of high interest to sociologists, computer scientists and marketeers alike. However, the computation of these network motif statistics via naive enumeration is infeasible for either its prohibitive computational costs or access restrictions on the full graph data. Methods to estimate the motif statistics based on random walks by sampling only a small fraction of the subgraphs ...

  11. Key Roles of Lewis Acid-base Pairs on ZnxZryOz in Direct Ethanol/Acetone to Isobutene Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Junming; Baylon, Rebecca A.; Liu, Changjun; Mei, Donghai; Martin, Kevin J.; Venkitasubramanian, Padmesh; Wang, Yong

    2016-01-20

    The effects of surface acidity on the cascade ethanol-to-isobutene conversion were studied using ZnxZryOz catalysts. The ethanol-to-isobutene reaction was found to be limited by the secondary reaction of the key intermediate, acetone, namely the acetone-to-isobutene reaction. Although the catalysts with coexisting Brønsted acidity could catalyze the rate-limiting acetone-to-isobutene reaction, the presence of Brønsted acidity is also detrimental. First, secondary isobutene isomerization is favored, producing a mixture of butene isomers. Second, undesired polymerization and coke formation prevail, leading to rapid catalyst deactivation. Most importantly, both steady-state and kinetic reaction studies as well as FTIR analysis of adsorbed acetone-d6 and D2O unambiguously showed that a highly active and selective nature of balanced Lewis acid-base pairs was masked by the coexisting Brønsted acidity in the aldolization and self-deoxygenation of acetone to isobutene. As a result, ZnxZryOz catalysts with only Lewis acid-base pairs were discovered, on which nearly a theoretical selectivity to isobutene (~88.9%) was successfully achieved, which has never been reported before. Moreover, the absence of Brønsted acidity in such ZnxZryOz catalysts also eliminates the side isobutene isomerization and undesired polymerization/coke reactions, resulting in the production of high purity isobutene with significantly improved catalyst stability (< 2% activity loss after 200 h time-on-stream). This work not only demonstrates a balanced Lewis acid-base pair for the highly active and selective cascade ethanol-to-isobutene reaction, but also sheds light on the rational design of selective and robust acid-base catalyst for C-C coupling via aldolization reaction.

  12. Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites

    Directory of Open Access Journals (Sweden)

    Lim Carmay

    2007-03-01

    Full Text Available Abstract Background For many metalloproteins, sequence motifs characteristic of metal-binding sites have not been found or are so short that they would not be expected to be metal-specific. Striking examples of such metalloproteins are those containing Mg2+, one of the most versatile metal cofactors in cellular biochemistry. Even when Mg2+-proteins share insufficient sequence homology to identify Mg2+-specific sequence motifs, they may still share similarity in the Mg2+-binding site structure. However, no structural motifs characteristic of Mg2+-binding sites have been reported. Thus, our aims are (i to develop a general method for discovering structural patterns/motifs characteristic of ligand-binding sites, given the 3D protein structures, and (ii to apply it to Mg2+-proteins sharing 2+-structural motifs are identified as recurring structural patterns. Results The structural alphabet-based motif discovery method has revealed the structural preference of Mg2+-binding sites for certain local/secondary structures: compared to all residues in the Mg2+-proteins, both first and second-shell Mg2+-ligands prefer loops to helices. Even when the Mg2+-proteins share no significant sequence homology, some of them share a similar Mg2+-binding site structure: 4 Mg2+-structural motifs, comprising 21% of the binding sites, were found. In particular, one of the Mg2+-structural motifs found maps to a specific functional group, namely, hydrolases. Furthermore, 2 of the motifs were not found in non metalloproteins or in Ca2+-binding proteins. The structural motifs discovered thus capture some essential biochemical and/or evolutionary properties, and hence may be useful for discovering proteins where Mg2+ plays an important biological role. Conclusion The structural motif discovery method presented herein is general and can be applied to any set of proteins with known 3D structures. This new method is timely considering the increasing number of structures for

  13. Importance of a single base pair for discrimination between intron-containing and intronless alleles by endonuclease I-BmoI.

    Science.gov (United States)

    Edgell, David R; Stanger, Matthew J; Belfort, Marlene

    2003-05-27

    Homing endonucleases initiate mobility of their host group I introns by binding to and cleaving lengthy recognition sequences that are typically centered on the intron insertion site (IS) of intronless alleles. Because the intron interrupts the endonucleases' recognition sequence, intron-containing alleles are immune to cleavage by their own endonuclease. I-TevI and I-BmoI are related GIY-YIG endonucleases that bind a homologous stretch of thymidylate synthase (TS)-encoding DNA but use different strategies to distinguish intronless from intron-containing substrates. I-TevI discriminates between substrates at the level of DNA binding, as its recognition sequence is centered on the intron IS. I-BmoI, in contrast, possesses a very asymmetric recognition sequence with respect to the intron IS, binds both intron-containing and intronless TS-encoding substrates, but efficiently cleaves only intronless substrate. Here, we show that I-BmoI is extremely tolerant of multiple substitutions around its cleavage sites and has a low specific activity. However, a single G-C base pair, at position -2 of a 39-base pair recognition sequence, is a major determinant for cleavage efficiency and distinguishes intronless from intron-containing alleles. Strikingly, this G-C base pair is universally conserved in phylogenetically diverse TS-coding sequences; this finding suggests that I-BmoI has evolved exquisite cleavage requirements to maximize the potential to spread to variant intronless alleles, while minimizing cleavage at its own intron-containing allele. PMID:12781137

  14. Effect of LNA- and OMeN-modified oligonucleotide probes on the stability and discrimination of mismatched base pairs of duplexes

    Indian Academy of Sciences (India)

    Ying Yan; Jing Yan; Xianyu Piao; Tianbiao Zhang; Yifu Guan

    2012-06-01

    Locked nucleic acid (LNA) and 2′--methyl nucleotide (OMeN) are the most extensively studied nucleotide analogues. Although both LNA and OMeN are characterized by the C3′-endo sugar pucker conformation, which is dominant in A-form DNA and RNA nucleotides, they demonstrate different binding behaviours. Previous studies have focused attention on their properties of duplex stabilities, hybridization kinetics and resistance against nuclease digestion; however, their ability to discriminate mismatched hybridizations has been explored much less. In this study, LNA- and OMeN-modified oligonucleotide probes have been prepared and their effects on the DNA duplex stability have been examined: LNA modifications can enhance the duplex stability, whereas OMeN modifications reduce the duplex stability. Next, we studied how the LNA:DNA and OMeN:DNA mismatches reduced the duplex stability. Melting temperature measurement showed that different LNA:DNA or OMeN:DNA mismatches indeed influence the duplex stability differently. LNA purines can discriminate LNA:DNA mismatches more effectively than LNA pyrimidines as well as DNA nucleotides. Furthermore, we designed five LNA- and five OMeN-modified oligonucleotide probes to simulate realistic situations where target–probe duplexes contain a complementary LNA:DNA or OMeN:DNA base pairs and a DNA:DNA mismatch simultaneously. The measured collective effect showed that the duplex stability was enhanced by the complementary LNA:DNA base pair but decreased by the DNA:DNA mismatch in a position-dependent manner regardless of the chemical identity and position of the complementary LNA:DNA base pair. On the other hand, the OMeN-modified probes also showed that the duplex stability was reduced by both the OMeN modification and the OMeN:DNA mismatch in a position-dependent manner.

  15. Triple helices formed at oligopyrimidine*oligopurine sequences with base pair inversions: effect of a triplex-specific ligand on stability and selectivity.

    OpenAIRE

    Kukreti, S; Sun, J S; Loakes, D; Brown, D M; Nguyen, C. H.; Bisagni, E.; Garestier, T; Helene, C

    1998-01-01

    Oligonucleotide-directed triple helix formation is mostly restricted to oligopyrimidine*oligopurine sequences of double helical DNA. An interruption of one or two pyrimidines in the oligopurine target strand leads to a strong triplex destabilisation. We have investigated the effect of nucleotide analogues introduced in the third strand at the site opposite the base pair inversion(s). We show that a 3-nitropyrrole derivative (M) discriminates G*C from C*G, A*T and T*A in the presence of a trip...

  16. Tn5supF, a 264-base-pair transposon derived from Tn5 for insertion mutagenesis and sequencing DNAs cloned in phage lambda.

    OpenAIRE

    Phadnis, S H; Huang, H V; Berg, D E

    1989-01-01

    We constructed a derivative of transposon Tn5 called Tn5supF for insertion mutagenesis and sequencing DNAs cloned in phage lambda. This element carries a supF amber-suppressor tRNA gene. Its insertion into lambda can be selected by plaque formation by using nonsuppressing (sup0) Escherichia coli for amber mutant lambda phage and sup0 dnaB-amber E. coli for nonamber lambda phage. Tn5supF is just 264 base pairs long. It transposes efficiently and inserts quasi-randomly into DNA targets. The uni...

  17. TrieAMD: a scalable and efficient apriori motif discovery approach.

    Science.gov (United States)

    Al-Turaiki, Isra; Badr, Ghada; Mathkour, Hassan

    2015-01-01

    Motif discovery is the problem of finding recurring patterns in biological sequences. It is one of the hardest and long-standing problems in bioinformatics. Apriori is a well-known data-mining algorithm for the discovery of frequent patterns in large datasets. In this paper, we apply the Apriori algorithm and use the Trie data structure to discover motifs. We propose several modifications so that we can adapt the classic Apriori to our problem. Experiments are conducted on Tompa's benchmark to investigate the performance of our proposed algorithm, the Trie-based Apriori Motif Discovery (TrieAMD). Results show that our algorithm outperforms all of the tested tools on real datasets for the average sensitivity measure, which means that our approach is able to discover more motifs. In terms of specificity, the performance of our algorithm is comparable to the other tools. The results also confirm both linear time and linear space scalability of the algorithm. PMID:26529905

  18. Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

    Science.gov (United States)

    Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-01-01

    Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

  19. The Motif of Meeting in Digital Education

    Science.gov (United States)

    Sheail, Philippa

    2015-01-01

    This article draws on theoretical work which considers the composition of meetings, in order to think about the form of the meeting in digital environments for higher education. To explore the motif of meeting, I undertake a "compositional interpretation" (Rose, 2012) of the default interface offered by "Collaborate", an…

  20. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoît

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  1. The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response.

    Science.gov (United States)

    Erill, Ivan; Campoy, Susana; Kılıç, Sefa; Barbé, Jordi

    2016-01-01

    The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division, and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls. PMID:27489856

  2. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

  3. Matched molecular pair-based data sets for computer-aided medicinal chemistry [v1; ref status: indexed, http://f1000r.es/2w9

    Directory of Open Access Journals (Sweden)

    Ye Hu

    2014-02-01

    Full Text Available Matched molecular pairs (MMPs are widely used in medicinal chemistry to study changes in compound properties including biological activity, which are associated with well-defined structural modifications. Herein we describe up-to-date versions of three MMP-based data sets that have originated from in-house research projects. These data sets include activity cliffs, structure-activity relationship (SAR transfer series, and second generation MMPs based upon retrosynthetic rules. The data sets have in common that they have been derived from compounds included in the latest release of the ChEMBL database for which high-confidence activity data are available. Thus, the activity data associated with MMP-based activity cliffs, SAR transfer series, and retrosynthetic MMPs cover the entire spectrum of current pharmaceutical targets. Our data sets are made freely available to the scientific community.

  4. R22(8 motifs in Aminopyrimidine sulfonate/carboxylate interactions: Crystal structures of pyrimethaminium benzenesulfonate monohydrate (2:2:1 and 2-amino-4,6-dimethylpyrimidinium sulfosalicylate dihydrate (4:2:2

    Directory of Open Access Journals (Sweden)

    Muthiah Packianathan

    2007-11-01

    Full Text Available Abstract Background Pyrimethamine [2,4-diamino-5-(p-chlorophenyl-6-ethylpyrimidine] is an antifolate drug used in anti-malarial chemotherapy. Pyrimidine and aminopyrimidine derivatives are biologically important compounds owing to their natural occurrence as components of nucleic acids. Results In the crystal structures of two organic salts, namely pyrimethaminium benzenesulfonate monohydrate 1 and 2-amino-4, 6-dimethylpyrimidinium 3-carboxy-4-hydroxy benzenesulfonate dihydrate 2, pyrimethamine (PMN and 2-amino-4,6-dimethylpyrimidine (AMPY are protonated at one of the nitrogens in the pyrimidine rings. In both the PMN and AMPY sulfonate complexes, the protonated pyrimidine rings are hydrogen bonded to the sulfonate groups, forming a hydrogen-bonded bimolecular ring motif with graph-set notation R22(8. The sulfonate group mimics the carboxylate anion's mode of association, which is more commonly seen when binding with 2-aminopyrimidines. In compound 1, the PMN moieties are centrosymmetrically paired through a complementary DADA array of hydrogen bonds. In compound 2, two types of bimolecular cyclic hydrogen bonded R22(8 motifs (one involving the carboxylate group and the other involving sulfonate group coexist. Furthermore, this compound is stabilized by intra and intermolecular O-H...O hydrogen bonds. Conclusion The crystal structures of pyrimethaminium benzenesulfonate monohydrate and 2-amino-4,6-dimethylpyrimidinium sulfosalicylate dihydrate have been investigated in detail. In compound 1, the R22(8 motif involving the sulfonate group is present. The role the sulfonic acid group plays in mimicking the carboxylate anions is thus evident. In compound 2, two types of bimolecular cyclic hydrogen bonded R22(8 motifs (one involving the carboxylate group and the other involving sulfonate group coexist. In both the compounds base pairing also occurs. Thus homo and hetero synthons are present.

  5. Key Roles of Lewis Acid-Base Pairs on ZnxZryOz in Direct Ethanol/Acetone to Isobutene Conversion.

    Science.gov (United States)

    Sun, Junming; Baylon, Rebecca A L; Liu, Changjun; Mei, Donghai; Martin, Kevin J; Venkitasubramanian, Padmesh; Wang, Yong

    2016-01-20

    The effects of surface acidity on the cascade ethanol-to-isobutene conversion were studied using ZnxZryOz catalysts. The ethanol-to-isobutene reaction was found to be limited by the secondary reaction of the key intermediate, acetone, namely the acetone-to-isobutene reaction. Although the catalysts with coexisting Brønsted acidity could catalyze the rate-limiting acetone-to-isobutene reaction, the presence of Brønsted acidity is also detrimental. First, secondary isobutene isomerization is favored, producing a mixture of butene isomers. Second, undesired polymerization and coke formation prevail, leading to rapid catalyst deactivation. Most importantly, both steady-state and kinetic reaction studies as well as FTIR analysis of adsorbed acetone-d6 and D2O unambiguously showed that a highly active and selective nature of balanced Lewis acid-base pairs was masked by the coexisting Brønsted acidity in the aldolization and self-deoxygenation of acetone to isobutene. As a result, ZnxZryOz catalysts with only Lewis acid-base pairs were discovered, on which nearly a theoretical selectivity to isobutene (∼ 88.9%) was successfully achieved, which has never been reported before. Moreover, the absence of Brønsted acidity in such ZnxZryOz catalysts also eliminates the side isobutene isomerization and undesired polymerization/coke reactions, resulting in the production of high purity isobutene with significantly improved catalyst stability (catalyst for C-C coupling via aldolization reaction. PMID:26624526

  6. Crystallization and preliminary X-ray diffraction analysis of the Bacillus subtilis replication termination protein in complex with the 37-base-pair TerI-binding site

    International Nuclear Information System (INIS)

    A preparation of replication terminator protein (RTP) of B. subtilis and a 37-base-pair TerI sequence (comprising two binding sites for RTP) has been purified and crystallized. The replication terminator protein (RTP) of Bacillus subtilis binds to specific DNA sequences that halt the progression of the replisome in a polar manner. These terminator complexes flank a defined region of the chromosome into which they allow replication forks to enter but not exit. Forcing the fusion of replication forks in a specific zone is thought to allow the coordination of post-replicative processes. The functional terminator complex comprises two homodimers each of 29 kDa bound to overlapping binding sites. A preparation of RTP and a 37-base-pair TerI sequence (comprising two binding sites for RTP) has been purified and crystallized. A data set to 3.9 Å resolution with 97.0% completeness and an Rsym of 12% was collected from a single flash-cooled crystal using synchrotron radiation. The diffraction data are consistent with space group P622, with unit-cell parameters a = b = 118.8, c = 142.6 Å

  7. The effect of the glycosylation position on the base pairing and supramolecular structure of the 5‧-deoxyribosyl Janus-type AT nucleosides

    Science.gov (United States)

    Zhou, Xinglong; Liu, Jiang; Guo, Xiurong; Meng, Liying; Chu, Liangyin; Chen, Qianming; Zhao, Hang; He, Yang

    2015-11-01

    The intrinsic structural diversity of the nucleosides is one of the essential properties for their wide participation in myriads of chemical or biochemical processes. Two unique regio-isomeric Janus-type AT nucleosides with the 5‧-deoxyribose attached on N1 or N3 position has been synthesized through Vorbrueggen or transglycosylation reactions. These two isomers display different supramolecular morphologies in solution state from their N8 glycosylated counterpart. The underneath structural details of the N3 glycosylated isomer were revealed by the single-crystal X-ray analysis. In addition to a novel base pair pattern was identified which is entirely different from the reverse Watson-Crick base pair adopted by its N8 isomer, an interesting water-filled columnar nanotuble-like structure was also found in its solid state. This study not only enriches the structural varieties of AT Janus-type nucleosides, but also provides specific information concerning the effect of the sugar glycosylation position on the properties of these new type of pyrimido[4,5-d]pyrimidine nucleosides.

  8. Variations in screening outcome among pairs of screening radiologists at non-blinded double reading of screening mammograms: a population-based study

    NARCIS (Netherlands)

    Klompenhouwer, E.G.; Duijm, L.E.M.; Voogd, A.C.; Heeten, GJ. den; Nederend, J.; Jansen, F.H.M.; Broeders, M.J.

    2014-01-01

    OBJECTIVES: Substantial inter-observer variability in screening mammography interpretation has been reported at single reading. However, screening results of pairs of screening radiologists have not yet been published. We determined variations in screening performances among pairs of screening radio

  9. 基于CyClus3D聚类算法的PPI网络模体研究%Research on PPI Network Motif Based on CyClus3D Clustering Algorithm

    Institute of Scientific and Technical Information of China (English)

    浦恩禄; 张孟娇; 张俊鹏

    2015-01-01

    为了研究蛋白质间的相互作用关系,基于CyClus3D聚类算法对人类蛋白质参考数据库(HPRD)、人类相互作用组资源(HIR)和生物相互作用数据集存储库所构成的整合型蛋白质-蛋白质相互作用网络(BioGRID)进行网络模体挖掘,然后对网络模体所构成的子网络进行基因本体生物过程(GO)和基因组京都百科全书信号通道(KEGG)富集分析.实验结果表明:网络模体挖掘简化了蛋白质-蛋白质相互作用网络分析,并且能够集中分析关键性的蛋白质.%To study the interactions between proteins, the 3D spectral clustering algorithm in Cytoscape(CyClus3D)is applied to identify the network motifs of integrated protein-protein interaction(PPI)networks, including Human Protein Reference Database (HPRD), Human Interactome Resource (HIR), and Biological General Repository for Interaction Datasets (BioGRID) databases. Then, enrichment analysis of GO (Gene Ontology) biological process and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways in the sub-networks formed by network motifs is conducted. The results show that network motif could simplifythe analysis of PPI networks, and could focus on analyzing key proteins.

  10. Analysis and Simulation of the Simplified Aircraft-Based Paired Approach Concept With the ALAS Alerting Algorithm in Conjunction With Echelon and Offset Strategies

    Science.gov (United States)

    Torres-Pomales, Wilfredo; Madden, Michael M.; Butler, Rickey W.; Perry, Raleigh B.

    2014-01-01

    This report presents analytical and simulation results of an investigation into proposed operational concepts for closely spaced parallel runways, including the Simplified Aircraft-based Paired Approach (SAPA) with alerting and an escape maneuver, MITRE?s echelon spacing and no escape maneuver, and a hybrid concept aimed at lowering the visibility minima. We found that the SAPA procedure can be used at 950 ft separations or higher with next-generation avionics and that 1150 ft separations or higher is feasible with current-rule compliant ADS-B OUT. An additional 50 ft reduction in runway separation for the SAPA procedure is possible if different glideslopes are used. For the echelon concept we determined that current generation aircraft cannot conduct paired approaches on parallel paths using echelon spacing on runways less than 1400 ft apart and next-generation aircraft will not be able to conduct paired approach on runways less than 1050 ft apart. The hybrid concept added alerting and an escape maneuver starting 1 NM from the threshold when flying the echelon concept. This combination was found to be effective, but the probability of a collision can be seriously impacted if the turn component of the escape maneuver has to be disengaged near the ground (e.g. 300 ft or below) due to airport buildings and surrounding terrain. We also found that stabilizing the approach path in the straight-in segment was only possible if the merge point was at least 1.5 to 2 NM from the threshold unless the total system error can be sufficiently constrained on the offset path and final turn.

  11. GPUmotif: an ultra-fast and energy-efficient motif analysis program using graphics processing units.

    Directory of Open Access Journals (Sweden)

    Pooya Zandevakili

    Full Text Available Computational detection of TF binding patterns has become an indispensable tool in functional genomics research. With the rapid advance of new sequencing technologies, large amounts of protein-DNA interaction data have been produced. Analyzing this data can provide substantial insight into the mechanisms of transcriptional regulation. However, the massive amount of sequence data presents daunting challenges. In our previous work, we have developed a novel algorithm called Hybrid Motif Sampler (HMS that enables more scalable and accurate motif analysis. Despite much improvement, HMS is still time-consuming due to the requirement to calculate matching probabilities position-by-position. Using the NVIDIA CUDA toolkit, we developed a graphics processing unit (GPU-accelerated motif analysis program named GPUmotif. We proposed a "fragmentation" technique to hide data transfer time between memories. Performance comparison studies showed that commonly-used model-based motif scan and de novo motif finding procedures such as HMS can be dramatically accelerated when running GPUmotif on NVIDIA graphics cards. As a result, energy consumption can also be greatly reduced when running motif analysis using GPUmotif. The GPUmotif program is freely available at http://sourceforge.net/projects/gpumotif/

  12. Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances.

    Science.gov (United States)

    Kim, Jaebum; Cunningham, Ryan; James, Brian; Wyder, Stefan; Gibson, Joshua D; Niehuis, Oliver; Zdobnov, Evgeny M; Robertson, Hugh M; Robinson, Gene E; Werren, John H; Sinha, Saurabh

    2010-01-01

    We address the problem of finding statistically significant associations between cis-regulatory motifs and functional gene sets, in order to understand the biological roles of transcription factors. We develop a computational framework for this task, whose features include a new statistical score for motif scanning, the use of different scores for predicting targets of different motifs, and new ways to deal with redundancies among significant motif-function associations. This framework is applied to the recently sequenced genome of the jewel wasp, Nasonia vitripennis, making use of the existing knowledge of motifs and gene annotations in another insect genome, that of the fruitfly. The framework uses cross-species comparison to improve the specificity of its predictions, and does so without relying upon non-coding sequence alignment. It is therefore well suited for comparative genomics across large evolutionary divergences, where existing alignment-based methods are not applicable. We also apply the framework to find motifs associated with socially regulated gene sets in the honeybee, Apis mellifera, using comparisons with Nasonia, a solitary species, to identify honeybee-specific associations. PMID:20126523

  13. Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances.

    Directory of Open Access Journals (Sweden)

    Jaebum Kim

    2010-01-01

    Full Text Available We address the problem of finding statistically significant associations between cis-regulatory motifs and functional gene sets, in order to understand the biological roles of transcription factors. We develop a computational framework for this task, whose features include a new statistical score for motif scanning, the use of different scores for predicting targets of different motifs, and new ways to deal with redundancies among significant motif-function associations. This framework is applied to the recently sequenced genome of the jewel wasp, Nasonia vitripennis, making use of the existing knowledge of motifs and gene annotations in another insect genome, that of the fruitfly. The framework uses cross-species comparison to improve the specificity of its predictions, and does so without relying upon non-coding sequence alignment. It is therefore well suited for comparative genomics across large evolutionary divergences, where existing alignment-based methods are not applicable. We also apply the framework to find motifs associated with socially regulated gene sets in the honeybee, Apis mellifera, using comparisons with Nasonia, a solitary species, to identify honeybee-specific associations.

  14. Pipeline for the Analysis of ChIP-seq Data and New Motif Ranking Procedure

    KAUST Repository

    Ashoor, Haitham

    2011-06-01

    This thesis presents a computational methodology for ab-initio identification of transcription factor binding sites based on ChIP-seq data. This method consists of three main steps, namely ChIP-seq data processing, motif discovery and models selection. A novel method for ranking the models of motifs identified in this process is proposed. This method combines multiple factors in order to rank the provided candidate motifs. It combines the model coverage of the ChIP-seq fragments that contain motifs from which that model is built, the suitable background data made up of shuffled ChIP-seq fragments, and the p-value that resulted from evaluating the model on actual and background data. Two ChIP-seq datasets retrieved from ENCODE project are used to evaluate and demonstrate the ability of the method to predict correct TFBSs with high precision. The first dataset relates to neuron-restrictive silencer factor, NRSF, while the second one corresponds to growth-associated binding protein, GABP. The pipeline system shows high precision prediction for both datasets, as in both cases the top ranked motif closely resembles the known motifs for the respective transcription factors.

  15. Cooperative interactions between paired domain and homeodomain.

    Science.gov (United States)

    Jun, S; Desplan, C

    1996-09-01

    The Pax proteins are a family of transcriptional regulators involved in many developmental processes in all higher eukaryotes. They are characterized by the presence of a paired domain (PD), a bipartite DNA binding domain composed of two helix-turn-helix (HTH) motifs,the PAI and RED domains. The PD is also often associated with a homeodomain (HD) which is itself able to form homo- and hetero-dimers on DNA. Many of these proteins therefore contain three HTH motifs each able to recognize DNA. However, all PDs recognize highly related DNA sequences, and most HDs also recognize almost identical sites. We show here that different Pax proteins use multiple combinations of their HTHs to recognize several types of target sites. For instance, the Drosophila Paired protein can bind, in vitro, exclusively through its PAI domain, or through a dimer of its HD, or through cooperative interaction between PAI domain and HD. However, prd function in vivo requires the synergistic action of both the PAI domain and the HD. Pax proteins with only a PD appear to require both PAI and RED domains, while a Pax-6 isoform and a new Pax protein, Lune, may rely on the RED domain and HD. We propose a model by which Pax proteins recognize different target genes in vivo through various combinations of their DNA binding domains, thus expanding their recognition repertoire. PMID:8787739

  16. Determination of h2JNN and h1JHN coupling constants across Watson-Crick base pairs in the Antennapedia homeodomain-DNA complex using TROSY

    International Nuclear Information System (INIS)

    This paper describes NMR measurements of 15N-15N and 1H-15N scalar couplings across hydrogen bonds in Watson-Crick base pairs, h2JNN and h1JHN, in a 17 kDa Antennapedia homeodomain-DNA complex. A new NMR experiment is introduced which relies on zero-quantum coherence-based transverse relaxation-optimized spectroscopy (ZQ-TROSY) and enables measurements of h1JHN couplings in larger molecules. The h2JNN and h1JHN couplings open a new avenue for comparative studies of DNA duplexes and other forms of nucleic acids free in solution and in complexes with proteins, drugs or possibly other classes of compounds

  17. Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli.

    Science.gov (United States)

    Sharma, Virag; Prère, Marie-Françoise; Canal, Isabelle; Firth, Andrew E; Atkins, John F; Baranov, Pavel V; Fayet, Olivier

    2014-06-01

    Programmed ribosomal -1 frameshifting is a non-standard decoding process occurring when ribosomes encounter a signal embedded in the mRNA of certain eukaryotic and prokaryotic genes. This signal has a mandatory component, the frameshift motif: it is either a Z_ZZN tetramer or a X_XXZ_ZZN heptamer (where ZZZ and XXX are three identical nucleotides) allowing cognate or near-cognate repairing to the -1 frame of the A site or A and P sites tRNAs. Depending on the signal, the frameshifting frequency can vary over a wide range, from less than 1% to more than 50%. The present study combines experimental and bioinformatics approaches to carry out (i) a systematic analysis of the frameshift propensity of all possible motifs (16 Z_ZZN tetramers and 64 X_XXZ_ZZN heptamers) in Escherichia coli and (ii) the identification of genes potentially using this mode of expression amongst 36 Enterobacteriaceae genomes. While motif efficiency varies widely, a major distinctive rule of bacterial -1 frameshifting is that the most efficient motifs are those allowing cognate re-pairing of the A site tRNA from ZZN to ZZZ. The outcome of the genomic search is a set of 69 gene clusters, 59 of which constitute new candidates for functional utilization of -1 frameshifting. PMID:24875478

  18. Do short, frequent DNA sequence motifs mould the epigenome?

    Science.gov (United States)

    Quante, Timo; Bird, Adrian

    2016-04-01

    'Epigenome' refers to the panoply of chemical modifications borne by DNA and its associated proteins that locally affect genome function. Epigenomic patterns are thought to be determined by external constraints resulting from development, disease and the environment, but DNA sequence is also a potential influence. We propose that domains of relatively uniform DNA base composition may modulate the epigenome through cell type-specific proteins that recognize short, frequent sequence motifs. Differential recruitment of epigenomic modifiers may adjust gene expression in multigene blocks as an alternative to tuning the activity of each gene separately, thus simplifying gene expression programming. PMID:26837845

  19. Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0

    Directory of Open Access Journals (Sweden)

    Mahadevan Padmanabhan

    2010-02-01

    Full Text Available Abstract Background The growing whole genome sequence databases necessitate the development of user-friendly software tools to mine these data. Web-based tools are particularly useful to wet-bench biologists as they enable platform-independent analysis of sequence data, without having to perform complex programming tasks and software compiling. Findings GeneOrder4.0 is a web-based "on-the-fly" synteny and gene order analysis tool for comparative bacterial genomics (ca. 8 Mb. It enables the visualization of synteny by plotting protein similarity scores between two genomes and it also provides visual annotation of "hypothetical" proteins from older archived genomes based on more recent annotations. Conclusions The web-based software tool GeneOrder4.0 is a user-friendly application that has been updated to allow the rapid analysis of synteny and gene order in large bacterial genomes. It is developed with the wet-bench researcher in mind.

  20. The frustrated brain: from dynamics on motifs to communities and networks.

    Science.gov (United States)

    Gollo, Leonardo L; Breakspear, Michael

    2014-10-01

    Cognitive function depends on an adaptive balance between flexible dynamics and integrative processes in distributed cortical networks. Patterns of zero-lag synchrony likely underpin numerous perceptual and cognitive functions. Synchronization fulfils integration by reducing entropy, while adaptive function mandates that a broad variety of stable states be readily accessible. Here, we elucidate two complementary influences on patterns of zero-lag synchrony that derive from basic properties of brain networks. First, mutually coupled pairs of neuronal subsystems-resonance pairs-promote stable zero-lag synchrony among the small motifs in which they are embedded, and whose effects can propagate along connected chains. Second, frustrated closed-loop motifs disrupt synchronous dynamics, enabling metastable configurations of zero-lag synchrony to coexist. We document these two complementary influences in small motifs and illustrate how these effects underpin stable versus metastable phase-synchronization patterns in prototypical modular networks and in large-scale cortical networks of the macaque (CoCoMac). We find that the variability of synchronization patterns depends on the inter-node time delay, increases with the network size and is maximized for intermediate coupling strengths. We hypothesize that the dialectic influences of resonance versus frustration may form a dynamic substrate for flexible neuronal integration, an essential platform across diverse cognitive processes. PMID:25180310

  1. Multilayer motif analysis of brain networks

    OpenAIRE

    Battiston, Federico; Nicosia, Vincenzo; Chavez, Mario; Latora, Vito

    2016-01-01

    In the last decade network science has shed new light on the anatomical connectivity and on correlations in the activity of different areas of the human brain. The study of brain networks has made possible in fact to detect the central areas of a neural system, and to identify its building blocks by looking at overabundant small subgraphs, known as motifs. However, network analysis of the brain has so far mainly focused on structural and functional networks as separate entities. The recently ...

  2. Identification of imine reductase-specific sequence motifs.

    Science.gov (United States)

    Fademrecht, Silvia; Scheller, Philipp N; Nestl, Bettina M; Hauer, Bernhard; Pleiss, Jürgen

    2016-05-01

    Chiral amines are valuable building blocks for the production of a variety of pharmaceuticals, agrochemicals and other specialty chemicals. Only recently, imine reductases (IREDs) were discovered which catalyze the stereoselective reduction of imines to chiral amines. Although several IREDs were biochemically characterized in the last few years, knowledge of the reaction mechanism and the molecular basis of substrate specificity and stereoselectivity is limited. To gain further insights into the sequence-function relationships, the Imine Reductase Engineering Database (www.IRED.BioCatNet.de) was established and a systematic analysis of 530 putative IREDs was performed. A standard numbering scheme based on R-IRED-Sk was introduced to facilitate the identification and communication of structurally equivalent positions in different proteins. A conservation analysis revealed a highly conserved cofactor binding region and a predominantly hydrophobic substrate binding cleft. Two IRED-specific motifs were identified, the cofactor binding motif GLGxMGx5 [ATS]x4 Gx4 [VIL]WNR[TS]x2 [KR] and the active site motif Gx[DE]x[GDA]x[APS]x3 {K}x[ASL]x[LMVIAG]. Our results indicate a preference toward NADPH for all IREDs and explain why, despite their sequence similarity to β-hydroxyacid dehydrogenases (β-HADs), no conversion of β-hydroxyacids has been observed. Superfamily-specific conservations were investigated to explore the molecular basis of their stereopreference. Based on our analysis and previous experimental results on IRED mutants, an exclusive role of standard position 187 for stereoselectivity is excluded. Alternatively, two standard positions 139 and 194 were identified which are superfamily-specifically conserved and differ in R- and S-selective enzymes. Proteins 2016; 84:600-610. © 2016 Wiley Periodicals, Inc. PMID:26857686

  3. Multilayer motif analysis of brain networks

    CERN Document Server

    Battiston, Federico; Chavez, Mario; Latora, Vito

    2016-01-01

    In the last decade network science has shed new light on the anatomical connectivity and on correlations in the activity of different areas of the human brain. The study of brain networks has made possible in fact to detect the central areas of a neural system, and to identify its building blocks by looking at overabundant small subgraphs, known as motifs. However, network analysis of the brain has so far mainly focused on structural and functional networks as separate entities. The recently developed mathematical framework of multi-layer networks allows to perform a multiplex analysis of the human brain where the structural and functional layers are considered at the same time. In this work we describe how to classify subgraphs in multiplex networks, and we extend motif analysis to networks with many layers. We then extract multi-layer motifs in brain networks of healthy subjects by considering networks with two layers, respectively obtained from diffusion and functional magnetic resonance imaging. Results i...

  4. Dynamic motifs in socio-economic networks

    Science.gov (United States)

    Zhang, Xin; Shao, Shuai; Stanley, H. Eugene; Havlin, Shlomo

    2014-12-01

    Socio-economic networks are of central importance in economic life. We develop a method of identifying and studying motifs in socio-economic networks by focusing on “dynamic motifs,” i.e., evolutionary connection patterns that, because of “node acquaintances” in the network, occur much more frequently than random patterns. We examine two evolving bi-partite networks: i) the world-wide commercial ship chartering market and ii) the ship build-to-order market. We find similar dynamic motifs in both bipartite networks, even though they describe different economic activities. We also find that “influence” and “persistence” are strong factors in the interaction behavior of organizations. When two companies are doing business with the same customer, it is highly probable that another customer who currently only has business relationship with one of these two companies, will become customer of the second in the future. This is the effect of influence. Persistence means that companies with close business ties to customers tend to maintain their relationships over a long period of time.

  5. Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Hanke, S.; Hinsby, A. M.; Friis, Carsten; Brunak, Søren; Mann, M.; Blom, Nikolaj

    Advances in mass spectrometry-based proteomics have yielded a substantial mapping of the tyrosine phosphoproteome and thus provided an important step toward a systematic analysis of intracellular signaling networks in higher eukaryotes. In this study we decomposed an uncharacterized proteomics data...... and validated as a binding motif for the SH2 domain-containing inositol phosphatase SHIP2. Our decomposition of the in vivo Tyr(P) proteome furthermore suggests that two-thirds of the Tyr(P) sites mediate interaction, whereas the remaining third govern processes such as enzyme activation and nucleic...

  6. Dynamics of network motifs in genetic regulatory networks

    Institute of Scientific and Technical Information of China (English)

    Li Ying; Liu Zeng-Rong; Zhang Jian-Bao

    2007-01-01

    Network motifs hold a very important status in genetic regulatory networks. This paper aims to analyse the dynamical property of the network motifs in genetic regulatory networks. The main result we obtained is that the dynamical property of a single motif is very simple with only an asymptotically stable equilibrium point, but the combination of several motifs can make more complicated dynamical properties emerge such as limit cycles. The above-mentioned result shows that network motif is a stable substructure in genetic regulatory networks while their combinations make the genetic regulatory network more complicated.

  7. Iterated combination-based paired permutation tests to determine shape effects of chemotherapy in patients with esophageal cancer.

    Science.gov (United States)

    Alfieri, Rita; Bonnini, Stefano; Brombin, Chiara; Castoro, Carlo; Salmaso, Luigi

    2016-04-01

    The nonparametric combination of dependent permutation tests method is a useful general tool when a testing problem can be broken down into a set of different k > 1 partial tests. These partial tests, after adjustment of p-values to control for multiplicity, can be marginally analyzed, but jointly considered they can provide information on an overall hypothesis, which might represent the true goal of the testing problem. On the one hand, independence among the partial tests is usually an unrealistic assumption; on the other, even when the underlying dependence relations are known quite often they are difficult to cope with properly. Therefore this combination must be achieved nonparametrically, by implicitly taking into account the dependence structure of tests without explicitly describing it. An important property of the tests based on nonparametric combination methodology, when the number of response variables is high compared to the sample sizes, consists in the finite sample consistency. A practical problem involves choosing the most suitable combining function for each specific testing problem given that the final result can be affected by this crucial choice. The purpose of this article is to present an nonparametric combination solution based on the iterated combination of partial tests, evaluate its power behavior using a Monte Carlo simulation study and apply it to a real medical problem, namely the evaluation of the effects of chemotherapy on the shape of esophageal tumors. R code has been implemented to carry out the analyses. PMID:23070597

  8. Application of a model based on a pair of Laplace transforms for standard low-energy X-ray beams spectral reconstruction

    International Nuclear Information System (INIS)

    The direct measurement of the spectrum of an X-ray beam by some spectroscopic method is relatively difficult and expensive. Spectra can be alternatively derived by an indirect method from measurements of transmission curve of the X-ray beam and the use of Laplace transforms. The objective of this work was the application of an indirect method that use a spectral model based on a pair of Laplace transforms to reconstruct experimental published spectra of standard low energy X-ray beams at radiation protection level and determine the mean photon energy from the reconstructed spectra for radiation quality specification. The spectral model was applied using calculated transmission curves and the reconstructed spectra provided a coarse approximation to experimental data. Even though, the mean photon energy of the X-ray beams determined from these reconstructed spectra present a satisfactory result showing the value of the analysis of transmission curves for the X-ray beam quality specification. (author)

  9. QM/MM Lineshape Simulation of the Hydrogen-bonded Uracil NH Stretching Vibration of the Adenine:Uracil Base Pair in CDCl$_3$

    CERN Document Server

    Yan, Yun-an; Kühn, Oliver

    2008-01-01

    A hybrid Car-Parrinello QM/MM molecular dynamics simulation has been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. The resulting trajectory is analyzed putting emphasis on the N-H$...$N Hydrogen bond geometry. Using an empirical correlation between the $\\NN$-distance and the fundamental NH-stretching frequency, the time-dependence of this energy gap along the trajectory is obtained. From the gap-correlation function we determine the infrared absorption spectrum using lineshape theory in combination with a multimode oscillator model. The obtained average transition frequency and the width of the spectrum is in reasonable agreement with recent experimental data.

  10. ET-Motif: Solving the Exact (l, d)-Planted Motif Problem Using Error Tree Structure.

    Science.gov (United States)

    Al-Okaily, Anas; Huang, Chun-Hsi

    2016-07-01

    Motif finding is an important and a challenging problem in many biological applications such as discovering promoters, enhancers, locus control regions, transcription factors, and more. The (l, d)-planted motif search, PMS, is one of several variations of the problem. In this problem, there are n given sequences over alphabets of size [Formula: see text], each of length m, and two given integers l and d. The problem is to find a motif m of length l, where in each sequence there is at least an l-mer at a Hamming distance of [Formula: see text] of m. In this article, we propose ET-Motif, an algorithm that can solve the PMS problem in [Formula: see text] time and [Formula: see text] space. The time bound can be further reduced by a factor of m with [Formula: see text] space. In case the suffix tree that is built for the input sequences is balanced, the problem can be solved in [Formula: see text] time and [Formula: see text] space. Similarly, the time bound can be reduced by a factor of m using [Formula: see text] space. Moreover, the variations of the problem, namely the edit distance PMS and edited PMS (Quorum), can be solved using ET-Motif with simple modifications but upper bands of space and time. For edit distance PMS, the time and space bounds will be increased by [Formula: see text], while for edited PMS the increase will be of [Formula: see text] in the time bound. PMID:27152692

  11. Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

    Energy Technology Data Exchange (ETDEWEB)

    Riplinger, Christoph; Pinski, Peter; Becker, Ute; Neese, Frank, E-mail: frank.neese@cec.mpg.de, E-mail: evaleev@vt.edu [Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr (Germany); Valeev, Edward F., E-mail: frank.neese@cec.mpg.de, E-mail: evaleev@vt.edu [Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061 (United States)

    2016-01-14

    Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate

  12. Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

    International Nuclear Information System (INIS)

    Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate

  13. Sparse maps--A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory.

    Science.gov (United States)

    Riplinger, Christoph; Pinski, Peter; Becker, Ute; Valeev, Edward F; Neese, Frank

    2016-01-14

    Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate

  14. Cyanine-based probe\\tag-peptide pair for fluorescence protein imaging and fluorescence protein imaging methods

    Science.gov (United States)

    Mayer-Cumblidge, M. Uljana; Cao, Haishi

    2010-08-17

    A molecular probe comprises two arsenic atoms and at least one cyanine based moiety. A method of producing a molecular probe includes providing a molecule having a first formula, treating the molecule with HgOAc, and subsequently transmetallizing with AsCl.sub.3. The As is liganded to ethanedithiol to produce a probe having a second formula. A method of labeling a peptide includes providing a peptide comprising a tag sequence and contacting the peptide with a biarsenical molecular probe. A complex is formed comprising the tag sequence and the molecular probe. A method of studying a peptide includes providing a mixture containing a peptide comprising a peptide tag sequence, adding a biarsenical probe to the mixture, and monitoring the fluorescence of the mixture.

  15. Implementation of FFT by using MATLAB: SIMULINK on Xilinx Virtex - 4 FPGAs: Performance of a Paired Transform Based FFT

    Directory of Open Access Journals (Sweden)

    Ranganadh Narayanam

    2013-06-01

    Full Text Available Discrete Fourier Transform is principalmathematical method for the frequency analysisand is having wide applications in Engineering andSciences. Because the DFT is so ubiquitous, fastmethods for computing DFT have been studiedextensively, and continuous to be an activeresearch.The way of splitting the DFT gives outvarious fast algorithms.In this paper, we presentthe implementation of two fast algorithms for theDFT for evaluating their performance.One of themis the popular radix-2Cooley-Tukey fast Fouriertransform algorithm (FFT [1] and the other one isthe Grigoryan FFT based on the splitting by thepaired transform [2].We evaluate the performanceof these algorithms by implementing them on theXilinx Virtex-4 FPGAs [3], by developing our ownFFT processor architectures.Finally we show thatthe Grigoryan FFT is working faster than Cooley-Tukey FFT, consequently it is useful for highersampling rates. Operating at higher sampling ratesis a challenge in DSP applications.

  16. Unique TTC repeat base pair loss mutation in cases of pure neural leprosy: A survival strategy of Mycobacterium leprae?

    Directory of Open Access Journals (Sweden)

    Abhishek De

    2015-01-01

    Full Text Available Background: Genomic reduction helps obligate intracellular microbes to survive difficult host niches. Adaptation of Mycobacterium leprae in cases of pure neural leprosy (PNL in the intracellular niche of peripheral nerves can be associated with some gene loss. Recently, a stable but variable number of tandem repefzats (TTC have been reported in strains of M. leprae. FolP and rpoB genes are the two common mutation sites which deal with the susceptibility of the bacteria to drugs. Aim: We attempted to find if genomic reduction of M. leprae in context of these TTC repeats or mutations in folP1 and rpoB can be the reason for the restriction of M. leprae in the nerves in PNL. Materials and Methods: DNA extracts taken from fine needle aspiration of affected nerves of 24 PNL cases were studied for tandem repeats with 21TTC primer in multiplex-PCR. Mutations were also studied by PCR Amplification of SRDR (Sulphone Resistance Determining Region of the folP1 and multiple primer PCR amplification refractory mutation system (MARS of the rpoB. Results: Of the 24 PNL, only 1 patient showed mutation in the rpoB gene and none in the folp1 gene. Studying the mutation in TTC region of the M. leprae gene we found that all the cases have a loss of a few bases in the sequence. Conclusion: We can conclude that there is consistent loss in the bases in the TTC region in all cases of pure neural Hansen and we postulate that it may be an adaptive response of the bacteria to survive host niche resulting in its restriction to peripheral nerves.

  17. CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design.

    Science.gov (United States)

    Zhang, Shaoqiang; Chen, Yong

    2016-01-01

    A set of conserved binding sites recognized by a transcription factor is called a motif, which can be found by many applications of comparative genomics for identifying over-represented segments. Moreover, when numerous putative motifs are predicted from a collection of genome-wide data, their similarity data can be represented as a large graph, where these motifs are connected to one another. However, an efficient clustering algorithm is desired for clustering the motifs that belong to the same groups and separating the motifs that belong to different groups, or even deleting an amount of spurious ones. In this work, a new motif clustering algorithm, CLIMP, is proposed by using maximal cliques and sped up by parallelizing its program. When a synthetic motif dataset from the database JASPAR, a set of putative motifs from a phylogenetic foot-printing dataset, and a set of putative motifs from a ChIP dataset are used to compare the performances of CLIMP and two other high-performance algorithms, the results demonstrate that CLIMP mostly outperforms the two algorithms on the three datasets for motif clustering, so that it can be a useful complement of the clustering procedures in some genome-wide motif prediction pipelines. CLIMP is available at http://sqzhang.cn/climp.html. PMID:27487245

  18. No tradeoff between versatility and robustness in gene circuit motifs

    Science.gov (United States)

    Payne, Joshua L.

    2016-05-01

    Circuit motifs are small directed subgraphs that appear in real-world networks significantly more often than in randomized networks. In the Boolean model of gene circuits, most motifs are realized by multiple circuit genotypes. Each of a motif's constituent circuit genotypes may have one or more functions, which are embodied in the expression patterns the circuit forms in response to specific initial conditions. Recent enumeration of a space of nearly 17 million three-gene circuit genotypes revealed that all circuit motifs have more than one function, with the number of functions per motif ranging from 12 to nearly 30,000. This indicates that some motifs are more functionally versatile than others. However, the individual circuit genotypes that constitute each motif are less robust to mutation if they have many functions, hinting that functionally versatile motifs may be less robust to mutation than motifs with few functions. Here, I explore the relationship between versatility and robustness in circuit motifs, demonstrating that functionally versatile motifs are robust to mutation despite the inherent tradeoff between versatility and robustness at the level of an individual circuit genotype.

  19. Context-dependent splicing regulation: Exon definition, co-occurring motif pairs and tissue specificity

    OpenAIRE

    Ke, Shengdong; CHASIN, LAWRENCE A.

    2011-01-01

    Splicing is a crucial process in gene expression in higher organisms because: (1) most vertebrate genes contain introns; and (2) alternative splicing is primarily responsible for increasing proteomic complexity and functional diversity. Intron definition, the coordination across an intron, is a mandatory step in the splicing process. However, exon definition, the coordination across an exon, is also thought to be required for the splicing of most vertebrate exons. Recent investigations of exo...

  20. Assessing the Exceptionality of Coloured Motifs in Networks

    Directory of Open Access Journals (Sweden)

    Lacroix Vincent

    2009-01-01

    Full Text Available Various methods have been recently employed to characterise the structure of biological networks. In particular, the concept of network motif and the related one of coloured motif have proven useful to model the notion of a functional/evolutionary building block. However, algorithms that enumerate all the motifs of a network may produce a very large output, and methods to decide which motifs should be selected for downstream analysis are needed. A widely used method is to assess if the motif is exceptional, that is, over- or under-represented with respect to a null hypothesis. Much effort has been put in the last thirty years to derive -values for the frequencies of topological motifs, that is, fixed subgraphs. They rely either on (compound Poisson and Gaussian approximations for the motif count distribution in Erdös-Rényi random graphs or on simulations in other models. We focus on a different definition of graph motifs that corresponds to coloured motifs. A coloured motif is a connected subgraph with fixed vertex colours but unspecified topology. Our work is the first analytical attempt to assess the exceptionality of coloured motifs in networks without any simulation. We first establish analytical formulae for the mean and the variance of the count of a coloured motif in an Erdös-Rényi random graph model. Using simulations under this model, we further show that a Pólya-Aeppli distribution better approximates the distribution of the motif count compared to Gaussian or Poisson distributions. The Pólya-Aeppli distribution, and more generally the compound Poisson distributions, are indeed well designed to model counts of clumping events. Altogether, these results enable to derive a -value for a coloured motif, without spending time on simulations.