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Sample records for au-rich signature motif

  1. Evolutionary conservation of the AU-rich 3' untranslated region of messenger RNA.

    OpenAIRE

    Asson-Batres, M A; Spurgeon, S L; Diaz, J.; DeLoughery, T G; Bagby, G C

    1994-01-01

    AU-rich sequence motifs (specifically sequences containing reiterations of AUUUA) are found in the 3' untranslated region of mammalian mRNAs encoding cytokines, adhesion molecules, and protooncogenes. Because these AU-rich elements (3'AURE) have been observed to reduce the stability and translational efficiency of transcripts that contain them, and because many of these transcripts accumulate in cells exposed to inflammatory stimuli, we reasoned that mRNAs with 3'AURE may be...

  2. Structural relationships in the lysozyme superfamily: significant evidence for glycoside hydrolase signature motifs.

    Directory of Open Access Journals (Sweden)

    Alexandre Wohlkönig

    Full Text Available BACKGROUND: Chitin is a polysaccharide that forms the hard, outer shell of arthropods and the cell walls of fungi and some algae. Peptidoglycan is a polymer of sugars and amino acids constituting the cell walls of most bacteria. Enzymes that are able to hydrolyze these cell membrane polymers generally play important roles for protecting plants and animals against infection with insects and pathogens. A particular group of such glycoside hydrolase enzymes share some common features in their three-dimensional structure and in their molecular mechanism, forming the lysozyme superfamily. RESULTS: Besides having a similar fold, all known catalytic domains of glycoside hydrolase proteins of lysozyme superfamily (families and subfamilies GH19, GH22, GH23, GH24 and GH46 share in common two structural elements: the central helix of the all-α domain, which invariably contains the catalytic glutamate residue acting as general-acid catalyst, and a β-hairpin pointed towards the substrate binding cleft. The invariant β-hairpin structure is interestingly found to display the highest amino acid conservation in aligned sequences of a given family, thereby allowing to define signature motifs for each GH family. Most of such signature motifs are found to have promising performances for searching sequence databases. Our structural analysis further indicates that the GH motifs participate in enzymatic catalysis essentially by containing the catalytic water positioning residue of inverting mechanism. CONCLUSIONS: The seven families and subfamilies of the lysozyme superfamily all have in common a β-hairpin structure which displays a family-specific sequence motif. These GH β-hairpin motifs contain potentially important residues for the catalytic activity, thereby suggesting the participation of the GH motif to catalysis and also revealing a common catalytic scheme utilized by enzymes of the lysozyme superfamily.

  3. Requirement for asparagine in the aquaporin NPA sequence signature motifs for cation exclusion

    DEFF Research Database (Denmark)

    Wree, Dorothea; Wu, Binghua; Zeuthen, Thomas;

    2011-01-01

    Two highly conserved NPA motifs are a hallmark of the aquaporin (AQP) family. The NPA triplets form N-terminal helix capping structures with the Asn side chains located in the centre of the water or solute-conducting channel, and are considered to play an important role in AQP selectivity. Althou...

  4. Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori HtrA.

    Science.gov (United States)

    Schmidt, Thomas P; Perna, Anna M; Fugmann, Tim; Böhm, Manja; Jan Hiss; Haller, Sarah; Götz, Camilla; Tegtmeyer, Nicole; Hoy, Benjamin; Rau, Tilman T; Neri, Dario; Backert, Steffen; Schneider, Gisbert; Wessler, Silja

    2016-01-01

    The cell adhesion protein and tumour suppressor E-cadherin exhibits important functions in the prevention of gastric cancer. As a class-I carcinogen, Helicobacter pylori (H. pylori) has developed a unique strategy to interfere with E-cadherin functions. In previous studies, we have demonstrated that H. pylori secretes the protease high temperature requirement A (HtrA) which cleaves off the E-cadherin ectodomain (NTF) on epithelial cells. This opens cell-to-cell junctions, allowing bacterial transmigration across the polarised epithelium. Here, we investigated the molecular mechanism of the HtrA-E-cadherin interaction and identified E-cadherin cleavage sites for HtrA. Mass-spectrometry-based proteomics and Edman degradation revealed three signature motifs containing the [VITA]-[VITA]-x-x-D-[DN] sequence pattern, which were preferentially cleaved by HtrA. Based on these sites, we developed a substrate-derived peptide inhibitor that selectively bound and inhibited HtrA, thereby blocking transmigration of H. pylori. The discovery of HtrA-targeted signature sites might further explain why we detected a stable 90 kDa NTF fragment during H. pylori infection, but also additional E-cadherin fragments ranging from 105 kDa to 48 kDa in in vitro cleavage experiments. In conclusion, HtrA targets E-cadherin signature sites that are accessible in in vitro reactions, but might be partially masked on epithelial cells through functional homophilic E-cadherin interactions. PMID:26983597

  5. Evolution of the Twist Subfamily Vertebrate Proteins: Discovery of a Signature Motif and Origin of the Twist1 Glycine-Rich Motifs in the Amino-Terminus Disordered Domain.

    Science.gov (United States)

    Rodriguez, Yacidzohara; Gonzalez-Mendez, Ricardo R; Cadilla, Carmen L

    2016-01-01

    Twist proteins belong to the basic helix-loop-helix (bHLH) family of multifunctional transcriptional factors. These factors are known to use domains other than the common bHLH in protein-protein interactions. There has been much work characterizing the bHLH domain and the C-terminus in protein-protein interactions but despite a few attempts more focus is needed at the N-terminus. Since the region of highest diversity in Twist proteins is the N-terminus, we analyzed the conservation of this region in different vertebrate Twist proteins and study the sequence differences between Twist1 and Twist2 with emphasis on the glycine-rich regions found in Twist1. We found a highly conserved sequence motif in all Twist1 (SSSPVSPADDSLSNSEEE) and Twist2 (SSSPVSPVDSLGTSEEE) mammalian species with unknown function. Through sequence comparison we demonstrate that the Twist protein family ancestor was "Twist2-like" and the two glycine-rich regions found in Twist1 sequences were acquired late in evolution, apparently not at the same time. The second glycine-rich region started developing first in the fish vertebrate group, while the first glycine region arose afterwards within the reptiles. Disordered domain and secondary structure predictions showed that the amino acid sequence and disorder feature found at the N-terminus is highly evolutionary conserved and could be a functional site that interacts with other proteins. Detailed examination of the glycine-rich regions in the N-terminus of Twist1 demonstrate that the first region is completely aliphatic while the second region contains some polar residues that could be subject to post-translational modification. Phylogenetic and sequence space analysis showed that the Twist1 subfamily is the result of a gene duplication during Twist2 vertebrate fish evolution, and has undergone more evolutionary drift than Twist2. We identified a new signature motif that is characteristic of each Twist paralog and identified important residues within

  6. TTP and BRF proteins nucleate processing body formation to silence mRNAs with AU-rich elements

    OpenAIRE

    Franks, Tobias M.; Lykke-Andersen, Jens

    2007-01-01

    In mammalian cells, mRNAs with AU-rich elements (AREs) are targeted for translational silencing and rapid degradation. Here we present evidence that in human cells the proteins Tristetraprolin (TTP) and BRF-1 deliver ARE-mRNAs to processing bodies (PBs), cytoplasmic assemblies of mRNAs, and associated factors that promote translational silencing and mRNA decay. First, depletion of endogenous TTP and BRF proteins, or overexpression of dominant-negative mutant TTP proteins, impairs the localiza...

  7. AU-Rich-Element-Dependent Translation Repression Requires the Cooperation of Tristetraprolin and RCK/P54

    OpenAIRE

    Qi, Mei-Yan; Wang, Zhi-Zhang; Zhang, Zhuo; SHAO, QIN; Zeng, An; Li, Xiang-Qi; Li, Wen-Qing; Wang, Chen; Tian, Fu-Ju; Li, Qing; ZOU, Jun; Qin, Yong-Wen; Brewer, Gary; Huang, Shuang; Jing, Qing

    2012-01-01

    AU-rich elements (AREs), residing in the 3′ untranslated region (UTR) of many labile mRNAs, are important cis-acting elements that modulate the stability of these mRNAs by collaborating with trans-acting factors such as tristetraprolin (TTP). AREs also regulate translation, but the underlying mechanism is not fully understood. Here we examined the function and mechanism of TTP in ARE-mRNA translation. Through a luciferase-based reporter system, we used knockdown, overexpression, and tethering...

  8. The p53 target Wig-1 regulates p53 mRNA stability through an AU-rich element

    DEFF Research Database (Denmark)

    Vilborg, Anna; Glahder, Jacob-Andreas Harald; Wilhelm, Margareta T;

    2009-01-01

    The p53 target gene Wig-1 encodes a double-stranded-RNA-binding zinc finger protein. We show here that Wig-1 binds to p53 mRNA and stabilizes it through an AU-rich element (ARE) in the 3' UTR of the p53 mRNA. This effect is mirrored by enhanced p53 protein levels in both unstressed cells and cells...... exposed to p53-activating stress agents. Thus, the p53 target Wig-1 is a previously undescribed ARE-regulating protein that acts as a positive feedback regulator of p53, with implications both for the steady-state levels of p53 and for the p53 stress response. Our data reveal a previously undescribed link...... between the tumor suppressor p53 and posttranscriptional gene regulation via AREs in mRNA....

  9. Characterization of Butyrate response factor 2 and study of its role in AU-rich element-mediated mRNA decay

    OpenAIRE

    Kulkarni, Meeta Girish

    2012-01-01

    AU-rich element-mediated mRNA decay (AMD) is a prominent mode of mRNA degradation in the cell considering 10-15 % of mRNA in the cells include an AU-rich element (ARE) in their 3’ UTR. These mRNAs code for proteins involved in important cellular processes, namely, growth and maintenance, development, transcription, inflammation, apoptosis, etc. AMD is majorly promoted by the TTP family of proteins consisting of TTP, BRF1, and BRF2, which bind to the AREs in the 3’UTR of mRNAs and accelerate t...

  10. Chaperone Hsp27 modulates AUF1 proteolysis and AU-rich element-mediated mRNA degradation.

    Science.gov (United States)

    Knapinska, Anna M; Gratacós, Frances M; Krause, Christopher D; Hernandez, Kristina; Jensen, Amber G; Bradley, Jacquelyn J; Wu, Xiangyue; Pestka, Sidney; Brewer, Gary

    2011-04-01

    AUF1 is an AU-rich element (ARE)-binding protein that recruits translation initiation factors, molecular chaperones, and mRNA degradation enzymes to the ARE for mRNA destruction. We recently found chaperone Hsp27 to be an AUF1-associated ARE-binding protein required for tumor necrosis factor alpha (TNF-α) mRNA degradation in monocytes. Hsp27 is a multifunctional protein that participates in ubiquitination of proteins for their degradation by proteasomes. A variety of extracellular stimuli promote Hsp27 phosphorylation on three serine residues--Ser(15), Ser(78), and Ser(82)-by a number of kinases, including the mitogen-activated protein (MAP) pathway kinases p38 and MK2. Activating either kinase stabilizes ARE mRNAs. Likewise, ectopic expression of phosphomimetic mutant forms of Hsp27 stabilizes reporter ARE mRNAs. Here, we continued to examine the contributions of Hsp27 to mRNA degradation. As AUF1 is ubiquitinated and degraded by proteasomes, we addressed the hypothesis that Hsp27 phosphorylation controls AUF1 levels to modulate ARE mRNA degradation. Indeed, selected phosphomimetic mutants of Hsp27 promote proteolysis of AUF1 in a proteasome-dependent fashion and render ARE mRNAs more stable. Our results suggest that the p38 MAP kinase (MAPK)-MK2-Hsp27 signaling axis may target AUF1 destruction by proteasomes, thereby promoting ARE mRNA stabilization. PMID:21245386

  11. Tristetraprolin and Its Family Members Can Promote the Cell-Free Deadenylation of AU-Rich Element-Containing mRNAs by Poly(A) Ribonuclease

    OpenAIRE

    Lai, Wi S.; Kennington, Elizabeth A; Blackshear, Perry J.

    2003-01-01

    Eukaryotic mRNA stability can be influenced by AU-rich elements (AREs) within mRNA primary sequences. Tristetraprolin (TTP) is a CCCH tandem zinc finger protein that binds to ARE-containing transcripts and destabilizes them, apparently by first promoting the removal of their poly(A) tails. We developed a cell-free system in which TTP and its related proteins stimulated the deadenylation of ARE-containing, polyadenylated transcripts. Transcript deadenylation was not stimulated when a mutant TT...

  12. 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...

  13. SL1 trans-splicing specified by AU-rich synthetic RNA inserted at the 5' end of Caenorhabditis elegans pre-mRNA.

    OpenAIRE

    Conrad, R; Lea, K; Blumenthal, T

    1995-01-01

    In Caenorhabditis elegans, pre-mRNAs of many genes are trans-spliced to one of two spliced leaders, SL1 or SL2. Some of those that receive exclusively SL1 have been characterized as having at their 5' ends outrons, AU-rich sequences similar to introns followed by conventional 3' splice sites. Comparison of outrons from many different SL1-specific C. elegans genes has not revealed the presence of any consensus sequence that might encode SL1-specificity. In order to determine what parameters in...

  14. Tristetraprolin Recruits Eukaryotic Initiation Factor 4E2 To Repress Translation of AU-Rich Element-Containing mRNAs

    OpenAIRE

    Tao, Xianzun; Gao, Guangxia

    2015-01-01

    Tristetraprolin (TTP) regulates the expression of AU-rich element-containing mRNAs through promoting the degradation and repressing the translation of target mRNA. While the mechanism for promoting target mRNA degradation has been extensively studied, the mechanism underlying translational repression is not well established. Here, we show that TTP recruits eukaryotic initiation factor 4E2 (eIF4E2) to repress target mRNA translation. TTP interacted with eIF4E2 but not with eIF4E. Overexpressio...

  15. The RNA Binding Zinc Finger Protein Tristetraprolin Regulates AU-Rich mRNAs Involved in Breast Cancer-Related Processes

    OpenAIRE

    Al-Souhibani, Norah; Al-Ahmadi, Wijdan; Hesketh, John E.; Blackshear, Perry J.; Khabar, Khalid S.A.

    2010-01-01

    Tristetraprolin (TTP or ZFP36) is a tandem CCCH zinc finger RNA binding protein that regulates the stability of certain AU-rich mRNAs. Recent work suggests that TTP is deficient in cancer cells when compared to normal cell types. Here we found that TTP expression was lower in invasive breast cancer cells (MDA-MB-231) compared to normal breast cell lines, MCF12A and MCF-10. TTP targets were probed using a novel approach by expressing the C124R zinc finger TTP mutant that act as dominant negati...

  16. Nutritional Control of mRNA Stability Is Mediated by a Conserved AU-rich Element That Binds the Cytoplasmic Shuttling Protein HuR*

    OpenAIRE

    Yaman, Ibrahim; Fernandez, James; Sarkar, Bedabrata; Schneider, Robert J.; Snider, Martin D.; Nagy, Laura E.; Hatzoglou, Maria

    2002-01-01

    The cationic amino acid transporter, Cat-1, is a high affinity transporter of the essential amino acids, arginine and lysine. Expression of the cat-1 gene increases during nutritional stress as part of the adaptive response to starvation. Amino acid limitation induces coordinate increases in stability and translation of the cat-1 mRNA, at a time when global protein synthesis decreases. It is shown here that increased cat-1 mRNA stability requires an 11 nucleotide AU-rich element within the di...

  17. The AU-rich element mRNA decay-promoting activity of BRF1 is regulated by mitogen-activated protein kinase-activated protein kinase 2

    OpenAIRE

    Maitra, Sushmit; Chou, Chu-Fang; Luber, Christian A.; Lee, Kyung-Yeol; Mann, Matthias; Chen, Ching-Yi

    2008-01-01

    Regulated mRNA decay is a highly important process for the tight control of gene expression. Inherently unstable mRNAs contain AU-rich elements (AREs) in the 3′ untranslated regions that direct rapid mRNA decay by interaction with decay-promoting ARE-binding proteins (ARE-BPs). The decay of ARE-containing mRNAs is regulated by signaling pathways that are believed to directly target ARE-BPs. Here, we show that BRF1 involved in ARE-mediated mRNA decay (AMD) is phosphorylated by MAPK-activated p...

  18. Signatures of RNA binding proteins globally coupled to effective microRNA target sites

    DEFF Research Database (Denmark)

    Jacobsen, Anders; Wen, Jiayu; Marks, Debora S;

    2010-01-01

    in 3' untranslated regions (UTRs) correlate with expression changes following transfection of small RNAs. The most significantly overrepresented motifs in down-regulated mRNAs are two novel U-rich motifs (URMs), UUUUAAA and UUUGUUU, recently discovered as binding sites for the ELAVL4 (also known as...... HuD) RNA-BP. Surprisingly, the most significantly overrepresented motif in up-regulated mRNAs is the heptanucleotide AU-rich element (ARE), UAUUUAU, which is known to affect mRNA stability via at least 20 different RNA-BPs. We show that destabilization mediated by the transfected miRNA is generally...

  19. The association of Alu repeats with the generation of potential AU-rich elements (ARE at 3' untranslated regions.

    Directory of Open Access Journals (Sweden)

    Bhak Jonghwa

    2004-12-01

    Full Text Available Abstract Background A significant portion (about 8% in the human genome of mammalian mRNA sequences contains AU (Adenine and Uracil rich elements or AREs at their 3' untranslated regions (UTR. These mRNA sequences are usually stable. However, an increasing number of observations have been made of unstable species, possibly depending on certain elements such as Alu repeats. ARE motifs are repeats of the tetramer AUUU and a monomer A at the end of the repeats ((AUUUnA. The importance of AREs in biology is that they make certain mRNA unstable. Proto-oncogene, such as c-fos, c-myc, and c-jun in humans, are associated with AREs. Although it has been known that the increased number of ARE motifs caused the decrease of the half-life of mRNA containing ARE repeats, the exact mechanism is as of yet unknown. We analyzed the occurrences of AREs and Alu and propose a possible mechanism for how human mRNA could acquire and keep AREs at its 3' UTR originating from Alu repeats. Results Interspersed in the human genome, Alu repeats occupy 5% of the 3' UTR of mRNA sequences. Alu has poly-adenine (poly-A regions at its end, which lead to poly-thymine (poly-T regions at the end of its complementary Alu. It has been found that AREs are present at the poly-T regions. From the 3' UTR of the NCBI's reference mRNA sequence database, we found nearly 40% (38.5% of ARE (Class I were associated with Alu sequences (Table 1 within one mismatch allowance in ARE sequences. Other ARE classes had statistically significant associations as well. This is far from a random occurrence given their limited quantity. At each ARE class, random distribution was simulated 1,000 times, and it was shown that there is a special relationship between ARE patterns and the Alu repeats. Table 1 Defined ARE classes. (Symbol marks are used in this study instead of full sequences. Symbol ARE sequence Class I (AUUU5A AUUUAUUUAUUUAUUUAUUUA Class II (AUUU4A AUUUAUUUAUUUAUUUA Class III U(AUUU3AU

  20. Deletion of AU-rich elements within the Bcl2 3'UTR reduces protein expression and B cell survival in vivo.

    Directory of Open Access Journals (Sweden)

    Manuel D Díaz-Muñoz

    Full Text Available Post-transcriptional mRNA regulation by RNA binding proteins (RBPs associated with AU-rich elements (AREs present in the 3' untranslated region (3'UTR of specific mRNAs modulates transcript stability and translation in eukaryotic cells. Here we have functionally characterised the importance of the AREs present within the Bcl2 3'UTR in order to maintain Bcl2 expression. Gene targeting deletion of 300 nucleotides of the Bcl2 3'UTR rich in AREs diminishes Bcl2 mRNA stability and protein levels in primary B cells, decreasing cell lifespan. Generation of chimeric mice indicates that Bcl2-ARE∆/∆ B cells have an intrinsic competitive disadvantage compared to wild type cells. Biochemical assays and predictions using a bioinformatics approach show that several RBPs bind to the Bcl2 AREs, including AUF1 and HuR proteins. Altogether, association of RBPs to Bcl2 AREs contributes to Bcl2 protein expression by stabilizing Bcl2 mRNA and promotes B cell maintenance.

  1. 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

  2. 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.

  3. 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...

  4. 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...

  5. Crystal Structure of the N-Terminal RNA Recognition Motif of mRNA Decay Regulator AUF1

    Directory of Open Access Journals (Sweden)

    Young Jun Choi

    2016-01-01

    Full Text Available AU-rich element binding/degradation factor 1 (AUF1 plays a role in destabilizing mRNAs by forming complexes with AU-rich elements (ARE in the 3′-untranslated regions. Multiple AUF1-ARE complexes regulate the translation of encoded products related to the cell cycle, apoptosis, and inflammation. AUF1 contains two tandem RNA recognition motifs (RRM and a Gln- (Q- rich domain in their C-terminal region. To observe how the two RRMs are involved in recognizing ARE, we obtained the AUF1-p37 protein covering the two RRMs. However, only N-terminal RRM (RRM1 was crystallized and its structure was determined at 1.7 Å resolution. It appears that the RRM1 and RRM2 separated before crystallization. To demonstrate which factors affect the separate RRM1-2, we performed limited proteolysis using trypsin. The results indicated that the intact proteins were cleaved by unknown proteases that were associated with them prior to crystallization. In comparison with each of the monomers, the conformations of the β2-β3 loops were highly variable. Furthermore, a comparison with the RRM1-2 structures of HuR and hnRNP A1 revealed that a dimer of RRM1 could be one of the possible conformations of RRM1-2. Our data may provide a guidance for further structural investigations of AUF1 tandem RRM repeat and its mode of ARE binding.

  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. 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....

  8. 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...

  9. 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

  10. 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...

  11. 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

  12. Tools and resources for identifying protein families, domains and motifs

    OpenAIRE

    Mulder, Nicola J.; Apweiler, Rolf

    2001-01-01

    With the large influx of raw sequence data from genome sequencing projects, there is a need for reliable automatic methods for protein sequence analysis and classification. The most useful tools use various methods for identifying motifs or domains found in previously characterized protein families. This article reviews the tools and resources available on the web for identifying signatures within proteins and discusses how they may be used in the analysis of new or unknown protein sequences.

  13. CERTIFICATELESS SIGNATURE AND BLIND SIGNATURE

    Institute of Scientific and Technical Information of China (English)

    Zhang Lei; Zhang Futai

    2008-01-01

    Certificateless public key cryptography is a new paradigm introduced by AI-Riyami and Paterson. It eliminates the need of the certificates in traditional public key cryptosystems and the key escrow problem in IDentity-based Public Key Cryptography (ID-PKC). Due to the advantages of the certificateless public key cryptography,a new efficient certificateless pairing-based signature scheme is presented,which has some advantages over previous constructions in computational cost. Based on this new signature scheme,a certificateless blind signature scheme is proposed. The security of our schemes is proven based on the hardness of computational Diffie-Hellman problem.

  14. A novel zinc-binding motif found in two ubiquitous deaminase families.

    Science.gov (United States)

    Reizer, J.; Buskirk, S.; Bairoch, A.; Reizer, A.; Saier, M. H.

    1994-01-01

    Two families of deaminases, one specific for cytidine, the other for deoxycytidylate, are shown to possess a novel zinc-binding motif, here designated ZBS. We have (1) identified the protein members of these 2 families, (2) carried out sequence analyses that allow specification of this zinc-binding motif, and (3) determined signature sequences that will allow identification of additional members of these families as their sequences become available. PMID:8061614

  15. Radiation signatures

    International Nuclear Information System (INIS)

    A new concept for modelling radiation risk is proposed. This concept is based on the proposal that the spectrum of molecular lesions, which we dub ''the radiation signature'', can be used to identify the quality of the causal radiation. If the proposal concerning radiation signatures can be established then, in principle, both prospective and retrospective risk determination can be assessed on an individual basis. A major goal of biophysical modelling is to relate physical events such as ionization, excitation, etc. to the production of radiation carcinogenesis. A description of the physical events is provided by track structure. The track structure is determined by radiation quality, and it can be considered to be the ''physical signature'' of the radiation. Unfortunately, the uniqueness characteristics of this signature are dissipated in biological systems in ∼10-9s. Nonetheless, it is our contention that this physical disturbance of the biological system eventuates later, at ∼100s, in molecular lesion spectra which also characterize the causal radiation. (author)

  16. 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.

  17. 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.

  18. Searching for protein signatures using a multilevel alphabet.

    Science.gov (United States)

    Hod, Ronit; Kohen, Refael; Mandel-Gutfreund, Yael

    2013-06-01

    Short motifs are known to play diverse roles in proteins, such as in mediating the interactions with other molecules, binding to membranes, or conducting a specific biological function. Standard approaches currently employed to detect short motifs in proteins search for enrichment of amino acid motifs considering mostly the sequence information. Here, we presented a new approach to search for common motifs (protein signatures) which share both physicochemical and structural properties, looking simultaneously at different features. Our method takes as an input an amino acid sequence and translates it to a new alphabet that reflects its intrinsic structural and chemical properties. Using the MEME search algorithm, we identified the proteins signatures within subsets of protein which encompass common sequence and structural information. We demonstrated that we can detect enriched structural motifs, such as the amphipathic helix, from large datasets of linear sequences, as well as predicting common structural properties (such as disorder, surface accessibility, or secondary structures) of known functional-motifs. Finally, we applied the method to the yeast protein interactome and identified novel putative interacting motifs. We propose that our approach can be applied for de novo protein function prediction given either sequence or structural information. PMID:23386227

  19. 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 ...

  20. Predicting conserved protein motifs with Sub-HMMs

    Directory of Open Access Journals (Sweden)

    Girke Thomas

    2010-04-01

    Full Text Available Abstract Background Profile HMMs (hidden Markov models provide effective methods for modeling the conserved regions of protein families. A limitation of the resulting domain models is the difficulty to pinpoint their much shorter functional sub-features, such as catalytically relevant sequence motifs in enzymes or ligand binding signatures of receptor proteins. Results To identify these conserved motifs efficiently, we propose a method for extracting the most information-rich regions in protein families from their profile HMMs. The method was used here to predict a comprehensive set of sub-HMMs from the Pfam domain database. Cross-validations with the PROSITE and CSA databases confirmed the efficiency of the method in predicting most of the known functionally relevant motifs and residues. At the same time, 46,768 novel conserved regions could be predicted. The data set also allowed us to link at least 461 Pfam domains of known and unknown function by their common sub-HMMs. Finally, the sub-HMM method showed very promising results as an alternative search method for identifying proteins that share only short sequence similarities. Conclusions Sub-HMMs extend the application spectrum of profile HMMs to motif discovery. Their most interesting utility is the identification of the functionally relevant residues in proteins of known and unknown function. Additionally, sub-HMMs can be used for highly localized sequence similarity searches that focus on shorter conserved features rather than entire domains or global similarities. The motif data generated by this study is a valuable knowledge resource for characterizing protein functions in the future.

  1. 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...

  2. 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

  3. Identification of group specific motifs in Beta-lactamase family of proteins

    Directory of Open Access Journals (Sweden)

    Saxena Akansha

    2009-12-01

    Full Text Available Abstract Background Beta-lactamases are one of the most serious threats to public health. In order to combat this threat we need to study the molecular and functional diversity of these enzymes and identify signatures specific to these enzymes. These signatures will enable us to develop inhibitors and diagnostic probes specific to lactamases. The existing classification of beta-lactamases was developed nearly 30 years ago when few lactamases were available. DLact database contain more than 2000 beta-lactamase, which can be used to study the molecular diversity and to identify signatures specific to this family. Methods A set of 2020 beta-lactamase proteins available in the DLact database http://59.160.102.202/DLact were classified using graph-based clustering of Best Bi-Directional Hits. Non-redundant (> 90 percent identical protein sequences from each group were aligned using T-Coffee and annotated using information available in literature. Motifs specific to each group were predicted using PRATT program. Results The graph-based classification of beta-lactamase proteins resulted in the formation of six groups (Four major groups containing 191, 726, 774 and 73 proteins while two minor groups containing 50 and 8 proteins. Based on the information available in literature, we found that each of the four major groups correspond to the four classes proposed by Ambler. The two minor groups were novel and do not contain molecular signatures of beta-lactamase proteins reported in literature. The group-specific motifs showed high sensitivity (> 70% and very high specificity (> 90%. The motifs from three groups (corresponding to class A, C and D had a high level of conservation at DNA as well as protein level whereas the motifs from the fourth group (corresponding to class B showed conservation at only protein level. Conclusion The graph-based classification of beta-lactamase proteins corresponds with the classification proposed by Ambler, thus there is

  4. 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/.

  5. 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...

  6. 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.

  7. 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

  8. Novel motifs distinguish multiple homologues of Polycomb in vertebrates: expansion and diversification of the epigenetic toolkit

    Directory of Open Access Journals (Sweden)

    Senthilkumar Ramamoorthy

    2009-11-01

    Full Text Available Abstract Background Polycomb group (PcG proteins maintain expression pattern of genes set early during development. Although originally isolated as regulators of homeotic genes, PcG members play a key role in epigenetic mechanism that maintains the expression state of a large number of genes. Polycomb (PC is conserved during evolution and while invertebrates have one PC gene, vertebrates have five or more homologues. It remains unclear if different vertebrate PC homologues have distinct or overlapping functions. We have identified and compared the sequence of PC homologues in various organisms to analyze similarities and differences that shaped the evolutionary history of this key regulatory protein. Results All PC homologues have an N-terminal chromodomain and a C-terminal Polycomb Repressor box. We searched the protein and genome sequence database of various organisms for these signatures and identified ~100 PC homologues. Comparative analysis of these sequences led to the identification of a novel insect specific motif and several novel and signature motifs in the vertebrate homologue: two in CBX2 (Cx2.1 and Cx2.2, four in CBX4 (Cx4.1, Cx4.2, Cx4.3 and Cx4.4, three in CBX6 (Cx6.1, Cx6.2 and Cx6.3 and one in CBX8 (Cx8.1. Additionally, adjacent to the chromodomain, all the vertebrate homologues have a DNA binding motif - AT-Hook in case of CBX2, which was known earlier, and 'AT-Hook Like' motif, from this study, in other PC homologues. Conclusion Our analysis shows that PC is an ancient gene dating back to pre bilaterian origin that has not only been conserved but has also expanded during the evolution of complexity. Unique motifs acquired by each homologue have been maintained for more than 500 millions years indicating their functional relevance in boosting the epigenetic 'tool kit'. We report the presence of a DNA interaction motif adjacent to chromodomain in all vertebrate PC homologues and suggest a three-way 'PC-histoneH3-DNA' interaction

  9. The crystal structure of the interleukin 21 receptor bound to interleukin 21 reveals that a sugar chain interacting with the WSXWS motif is an integral part of the interleukin 21 receptor

    DEFF Research Database (Denmark)

    Hamming, Ole Jensen; Kang, Lishan; Svensson, Anders; Karlsen, Jesper Lykkegaard; Rahbek-Nielsen, Henrik; Paludan, Søren Riis; Hjorth, Siv A; Bondensgaard, Kent; Hartmann, Rune

    2012-01-01

    the class I cytokine receptor signature motif (WSXWS). The exact role of this motif has not been determined yet, however, it has been implicated in diverse functions including ligand binding, receptor internalization, proper folding, and export as well as signal transduction. Furthermore, the WXXW is...

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Qualified Mobile Server Signature

    OpenAIRE

    Orthacker, Clemens; Centner, Martin; Kittl, Christian

    2010-01-01

    International audience A legal basis for the use of electronic signatures exists since the introduction of qualified electronic signatures in EU Directive 1999/ 93/EC. Although considered as key enablers for e-Government and e-Commerce, qualified electronic signatures are still not widely used. Introducing amobile component addresses most of the shortcomings of existing qualified signature approaches but poses certain difficulties in the security reasoning. The proposed server based mobile...

  15. Efficient Threshold Signature Scheme

    Directory of Open Access Journals (Sweden)

    Sattar J Aboud

    2012-01-01

    Full Text Available In this paper, we introduce a new threshold signature RSA-typed scheme. The proposed scheme has the characteristics of un-forgeable and robustness in random oracle model. Also, signature generation and verification is entirely non-interactive. In addition, the length of the entity signature participate is restricted by a steady times of the length of the RSA signature modulus. Also, the signing process of the proposed scheme is more efficient in terms of time complexity and interaction.

  16. 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

  17. 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...

  18. Quantum threshold group signature

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    In most situations, the signer is generally a single person. However, when the message is written on behalf of an organization, a valid message may require the approval or consent of several persons. Threshold signature is a solution to this problem. Generally speaking, as an authority which can be trusted by all members does not exist, a threshold signature scheme without a trusted party appears more attractive. Following some ideas of the classical Shamir’s threshold signature scheme, a quantum threshold group signature one is proposed. In the proposed scheme, only t or more of n persons in the group can generate the group signature and any t-1 or fewer ones cannot do that. In the verification phase, any t or more of n signature receivers can verify the message and any t-1 or fewer receivers cannot verify the validity of the signature.

  19. A Conserved GPG-Motif in the HIV-1 Nef Core Is Required for Principal Nef-Activities.

    Directory of Open Access Journals (Sweden)

    Marta Martínez-Bonet

    Full Text Available To find out new determinants required for Nef activity we performed a functional alanine scanning analysis along a discrete but highly conserved region at the core of HIV-1 Nef. We identified the GPG-motif, located at the 121-137 region of HIV-1 NL4.3 Nef, as a novel protein signature strictly required for the p56Lck dependent Nef-induced CD4-downregulation in T-cells. Since the Nef-GPG motif was dispensable for CD4-downregulation in HeLa-CD4 cells, Nef/AP-1 interaction and Nef-dependent effects on Tf-R trafficking, the observed effects on CD4 downregulation cannot be attributed to structure constraints or to alterations on general protein trafficking. Besides, we found that the GPG-motif was also required for Nef-dependent inhibition of ring actin re-organization upon TCR triggering and MHCI downregulation, suggesting that the GPG-motif could actively cooperate with the Nef PxxP motif for these HIV-1 Nef-related effects. Finally, we observed that the Nef-GPG motif was required for optimal infectivity of those viruses produced in T-cells. According to these findings, we propose the conserved GPG-motif in HIV-1 Nef as functional region required for HIV-1 infectivity and therefore with a potential interest for the interference of Nef activity during HIV-1 infection.

  20. 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

  1. 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....

  2. Uncertainty in hydrological signatures

    Science.gov (United States)

    Westerberg, I. K.; McMillan, H. K.

    2015-09-01

    Information about rainfall-runoff processes is essential for hydrological analyses, modelling and water-management applications. A hydrological, or diagnostic, signature quantifies such information from observed data as an index value. Signatures are widely used, e.g. for catchment classification, model calibration and change detection. Uncertainties in the observed data - including measurement inaccuracy and representativeness as well as errors relating to data management - propagate to the signature values and reduce their information content. Subjective choices in the calculation method are a further source of uncertainty. We review the uncertainties relevant to different signatures based on rainfall and flow data. We propose a generally applicable method to calculate these uncertainties based on Monte Carlo sampling and demonstrate it in two catchments for common signatures including rainfall-runoff thresholds, recession analysis and basic descriptive signatures of flow distribution and dynamics. Our intention is to contribute to awareness and knowledge of signature uncertainty, including typical sources, magnitude and methods for its assessment. We found that the uncertainties were often large (i.e. typical intervals of ±10-40 % relative uncertainty) and highly variable between signatures. There was greater uncertainty in signatures that use high-frequency responses, small data subsets, or subsets prone to measurement errors. There was lower uncertainty in signatures that use spatial or temporal averages. Some signatures were sensitive to particular uncertainty types such as rating-curve form. We found that signatures can be designed to be robust to some uncertainty sources. Signature uncertainties of the magnitudes we found have the potential to change the conclusions of hydrological and ecohydrological analyses, such as cross-catchment comparisons or inferences about dominant processes.

  3. 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...

  4. 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...

  5. 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

  6. 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

  7. Blind Collective Signature Protocol

    Directory of Open Access Journals (Sweden)

    Nikolay A. Moldovyan

    2011-06-01

    Full Text Available Using the digital signature (DS scheme specified by Belarusian DS standard there are designed the collective and blind collective DS protocols. Signature formation is performed simultaneously by all of the assigned signers, therefore the proposed protocols can be used also as protocols for simultaneous signing a contract. The proposed blind collective DS protocol represents a particular implementation of the blind multisignature schemes that is a novel type of the signature schemes. The proposed protocols are the first implementations of the multisignature schemes based on Belarusian signature standard.

  8. Unconditionally Secure Quantum Signatures

    Directory of Open Access Journals (Sweden)

    Ryan Amiri

    2015-08-01

    Full Text Available Signature schemes, proposed in 1976 by Diffie and Hellman, have become ubiquitous across modern communications. They allow for the exchange of messages from one sender to multiple recipients, with the guarantees that messages cannot be forged or tampered with and that messages also can be forwarded from one recipient to another without compromising their validity. Signatures are different from, but no less important than encryption, which ensures the privacy of a message. Commonly used signature protocols—signatures based on the Rivest–Adleman–Shamir (RSA algorithm, the digital signature algorithm (DSA, and the elliptic curve digital signature algorithm (ECDSA—are only computationally secure, similar to public key encryption methods. In fact, since these rely on the difficulty of finding discrete logarithms or factoring large primes, it is known that they will become completely insecure with the emergence of quantum computers. We may therefore see a shift towards signature protocols that will remain secure even in a post-quantum world. Ideally, such schemes would provide unconditional or information-theoretic security. In this paper, we aim to provide an accessible and comprehensive review of existing unconditionally securesecure signature schemes for signing classical messages, with a focus on unconditionally secure quantum signature schemes.

  9. 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

  10. 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...

  11. 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.

  12. 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.

  13. 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.

  14. Machine Fault Signature Analysis

    Directory of Open Access Journals (Sweden)

    K. B. Mulchandani

    2008-03-01

    Full Text Available The objective of this paper is to present recent developments in the field of machine fault signature analysis with particular regard to vibration analysis. The different types of faults that can be identified from the vibration signature analysis are, for example, gear fault, rolling contact bearing fault, journal bearing fault, flexible coupling faults, and electrical machine fault. It is not the intention of the authors to attempt to provide a detailed coverage of all the faults while detailed consideration is given to the subject of the rolling element bearing fault signature analysis.

  15. Are there molecular signatures?

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, W.P.

    1995-10-01

    This report describes molecular signatures and mutational spectrum analysis. The mutation spectrum is defined as the type and location of DNA base change. There are currently about five well documented cases. Mutations and radon-associated tumors are discussed.

  16. Advanced Missile Signature Center

    Data.gov (United States)

    Federal Laboratory Consortium — The Advanced Missile Signature Center (AMSC) is a national facility supporting the Missile Defense Agency (MDA) and other DoD programs and customers with analysis,...

  17. THE ELECTRONIC SIGNATURE

    OpenAIRE

    Voiculescu Madalina Irena; Gramada Dragu Argentina

    2009-01-01

    Article refers to significance and the digital signature in electronic commerce. Internet and electronic commerce open up many new opportunities for the consumer, yet, the security (or perceived lack of security) of exchanging personal and financial data

  18. 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…

  19. 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.

  20. Meteor signature interpretation

    Energy Technology Data Exchange (ETDEWEB)

    Canavan, G.H.

    1997-01-01

    Meteor signatures contain information about the constituents of space debris and present potential false alarms to early warnings systems. Better models could both extract the maximum scientific information possible and reduce their danger. Accurate predictions can be produced by models of modest complexity, which can be inverted to predict the sizes, compositions, and trajectories of object from their signatures for most objects of interest and concern.

  1. Stateless Transitive Signature Schemes

    Institute of Scientific and Technical Information of China (English)

    MA Chun-guang; CAI Man-chun; YANG Yi-xian

    2004-01-01

    A new practical method is introduced to transform the stateful transitive signature scheme to stateless one without the loss of security. According to the approach, two concrete stateless transitive signature schemes based on Factoring and RSA are presented respectively. Under the assumption of the hardness of factoring and one-more- RSA-inversion problem, both two schemes are secure under the adaptive chosen-message attacks in random oracle model.

  2. Machine Fault Signature Analysis

    OpenAIRE

    Mulchandani, K. B.; A.K. Wadhwani; Pratesh Jayaswal

    2008-01-01

    The objective of this paper is to present recent developments in the field of machine fault signature analysis with particular regard to vibration analysis. The different types of faults that can be identified from the vibration signature analysis are, for example, gear fault, rolling contact bearing fault, journal bearing fault, flexible coupling faults, and electrical machine fault. It is not the intention of the authors to attempt to provide a detailed coverage of all the faults while deta...

  3. Accumulation of extracellular proteins bearing unique proline-rich motifs in intercellular spaces of the legume nodule parenchyma.

    Science.gov (United States)

    Sherrier, D J; Taylor, G S; Silverstein, K A T; Gonzales, M B; VandenBosch, K A

    2005-04-01

    Nodulins encoding repetitive proline-rich cell wall proteins (PRPs) are induced during early interactions with rhizobia, suggesting a massive restructuring of the plant extracellular matrix during infection and nodulation. However, the proteins corresponding to these gene products have not been isolated or characterized, nor have cell wall localizations been confirmed. Posttranslational modifications, conformation, and interactions with other wall polymers are difficult to predict on the basis of only the deduced amino acid sequence of PRPs. PsENOD2 is expressed in nodule parenchyma tissue during nodule organogenesis and encodes a protein with distinctive PRP motifs that are rich in glutamate and basic amino acids. A database search for the ENOD2 signature motifs indicates that similar proteins may have a limited phylogenetic distribution, as they are presently only known from legumes. To determine the ultrastructural location of the proteins, antibodies were raised against unique motifs from the predicted ENOD2 sequence. The antibodies recognized nodule-specific proteins in pea (Pisum sativum), with a major band detected at 110 kDa, representing a subset of PRPs from nodules. The protein was detected specifically in organelles of the secretory pathway and intercellular spaces in the nodule parenchyma, but it was not abundant in primary walls. Similar proteins with an analogous distribution were detected in soybean (Glycine max). The use of polyclonal antibodies raised against signature motifs of extracellular matrix proteins thus appears to be an effective strategy to identify and isolate specific structural proteins for functional analysis. PMID:15868212

  4. Peri-Implantation Lethality in Mice Lacking the Sm Motif-Containing Protein Lsm4

    OpenAIRE

    Hirsch, Emilio; Oohashi, Toshitaka; Ahmad, Marianne; Stamm, Stefan; Fässler, Reinhard

    2000-01-01

    Small nuclear ribonucleoproteins (snRNPs) are particles present only in eukaryotic cells. They are involved in a large variety of RNA maturation processes, most notably in pre-mRNA splicing. Several of the proteins typically found in snRNPs contain a sequence signature, the Sm domain, conserved from yeast to mammals. By using a promoter trap strategy to target actively transcribed loci in murine embryonic stem cells, a new murine gene encoding an Sm motif-containing protein was identified. Da...

  5. 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).

  6. 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).

  7. Mitochondrial and Y chromosome haplotype motifs as diagnostic markers of Jewish ancestry: a reconsideration

    Science.gov (United States)

    Tofanelli, Sergio; Taglioli, Luca; Bertoncini, Stefania; Francalacci, Paolo; Klyosov, Anatole; Pagani, Luca

    2014-01-01

    Several authors have proposed haplotype motifs based on site variants at the mitochondrial genome (mtDNA) and the non-recombining portion of the Y chromosome (NRY) to trace the genealogies of Jewish people. Here, we analyzed their main approaches and test the feasibility of adopting motifs as ancestry markers through construction of a large database of mtDNA and NRY haplotypes from public genetic genealogical repositories. We verified the reliability of Jewish ancestry prediction based on the Cohen and Levite Modal Haplotypes in their “classical” 6 STR marker format or in the “extended” 12 STR format, as well as four founder mtDNA lineages (HVS-I segments) accounting for about 40% of the current population of Ashkenazi Jews. For this purpose we compared haplotype composition in individuals of self-reported Jewish ancestry with the rest of European, African or Middle Eastern samples, to test for non-random association of ethno-geographic groups and haplotypes. Overall, NRY and mtDNA based motifs, previously reported to differentiate between groups, were found to be more represented in Jewish compared to non-Jewish groups. However, this seems to stem from common ancestors of Jewish lineages being rather recent respect to ancestors of non-Jewish lineages with the same “haplotype signatures.” Moreover, the polyphyly of haplotypes which contain the proposed motifs and the misuse of constant mutation rates heavily affected previous attempts to correctly dating the origin of common ancestries. Accordingly, our results stress the limitations of using the above haplotype motifs as reliable Jewish ancestry predictors and show its inadequacy for forensic or genealogical purposes. PMID:25431579

  8. Functionally specified protein signatures distinctive for each of the different blue copper proteins

    Directory of Open Access Journals (Sweden)

    Anishetty Sharmila

    2004-09-01

    Full Text Available Abstract Background Proteins having similar functions from different sources can be identified by the occurrence in their sequences, a conserved cluster of amino acids referred to as pattern, motif, signature or fingerprint. The wide usage of protein sequence analysis in par with the growth of databases signifies the importance of using patterns or signatures to retrieve out related sequences. Blue copper proteins are found in the electron transport chain of prokaryotes and eukaryotes. The signatures already existing in the databases like the type 1 copper blue, multiple copper oxidase, cyt b/b6, photosystem 1 psaA&B, psaG&K, and reiske iron sulphur protein are not specified signatures for blue copper proteins as the name itself suggests. Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. This work describes the signatures designed based on the copper metal binding motifs in blue copper proteins. The common feature in all blue copper proteins is a trigonal planar arrangement of two nitrogen ligands [each from histidine] and one sulphur containing thiolate ligand [from cysteine], with strong interactions between the copper center and these ligands. Results Sequences that share such conserved motifs are crucial to the structure or function of the protein and this could provide a signature of family membership. The blue copper proteins chosen for the study were plantacyanin, plastocyanin, cucumber basic protein, stellacyanin, dicyanin, umecyanin, uclacyanin, cusacyanin, rusticyanin, sulfocyanin, halocyanin, azurin, pseudoazurin, amicyanin and nitrite reductase which were identified in both eukaryotes and prokaryotes. ClustalW analysis of the protein sequences of each of the blue copper proteins was the basis for designing protein signatures or peptides. The protein signatures and peptides identified in this study were designed involving the active site region involving the amino acids

  9. 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...

  10. Actions for signature change

    CERN Document Server

    Embacher, F

    1995-01-01

    This is a contribution on the controversy about junction conditions for classical signature change. The central issue in this debate is whether the extrinsic curvature on slices near the hypersurface of signature change has to be continuous ({\\it weak} signature change) or to vanish ({\\it strong} signature change). Led by a Lagrangian point of view, we write down eight candidate action functionals S_1,...S_8 as possible generalizations of general relativity and investigate to what extent each of these defines a sensible variational problem, and which junction condition is implied. Four of the actions involve an integration over the total manifold. A particular subtlety arises from the precise definition of the Einstein-Hilbert Lagrangian density |g|^{1/2} R[g]. The other four actions are constructed as sums of integrals over singe-signature domains. The result is that {\\it both} types of junction conditions occur in different models, i.e. are based on different first principles, none of which can be claimed t...

  11. 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 ...

  12. 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 ...

  13. 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...

  14. Practical quantum digital signature

    Science.gov (United States)

    Yin, Hua-Lei; Fu, Yao; Chen, Zeng-Bing

    2016-03-01

    Guaranteeing nonrepudiation, unforgeability as well as transferability of a signature is one of the most vital safeguards in today's e-commerce era. Based on fundamental laws of quantum physics, quantum digital signature (QDS) aims to provide information-theoretic security for this cryptographic task. However, up to date, the previously proposed QDS protocols are impractical due to various challenging problems and most importantly, the requirement of authenticated (secure) quantum channels between participants. Here, we present the first quantum digital signature protocol that removes the assumption of authenticated quantum channels while remaining secure against the collective attacks. Besides, our QDS protocol can be practically implemented over more than 100 km under current mature technology as used in quantum key distribution.

  15. 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...

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. Aperiodic logarithmic signatures

    CERN Document Server

    Baumeister, Barbara

    2011-01-01

    In this paper we propose a method to construct logarithmic signatures which are not amalgamated transversal and further do not even have a periodic block. The latter property was crucial for the successful attack on the system MST3 by Blackburn et al. [1]. The idea for our construction is based on the theory in Szab\\'o's book about group factorizations [12].

  2. The dark energy signature

    International Nuclear Information System (INIS)

    Though the concept of a dark energy driven accelerating universe was introduced by the author in 1997, to date dark energy itself, as described below has remained a paradigm. We quickly review these and find a second cosmological signature of the 1997 model, consistent with latest observations. (author)

  3. UV missile plume signatures

    NARCIS (Netherlands)

    Neele, F.P.; Schleijpen, H.M.A.

    2002-01-01

    As a result of the deployment of UV missile warning systems, recent years have seen an increasing interest in threat assessment in the UV band. Unfortunately, due to the different nature of the physical processes that are needed to describe a missile signature in the UV, available codes for the IR c

  4. 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.

  5. 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...

  6. 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.

  7. A PRACTICAL PROXY SIGNATURE SCHEME

    Directory of Open Access Journals (Sweden)

    Sattar Aboud

    2012-01-01

    Full Text Available A proxy signature scheme is a variation of the ordinary digital signature scheme which enables a proxy signer to generate signatures on behalf of an original signer. In this paper, we present two efficient types of proxy signature scheme. The first one is the proxy signature for warrant partial delegation combines an advantage of two well known warrant partial delegation schemes. This proposed proxy signature scheme is based on the difficulty of solving the discrete logarithm problem. The second proposed scheme is based on threshold delegation the proxy signer power to sign the message is share. We claim that the proposed proxy signature schemes meet the security requirements and more practical than the existing proxy signature schemes.

  8. Acidic/IQ Motif Regulator of Calmodulin*

    OpenAIRE

    Putkey, John A.; Waxham, M. Neal; Gaertner, Tara R.; Brewer, Kari J.; Goldsmith, Michael; Kubota, Yoshihisa; Kleerekoper, Quinn K.

    2007-01-01

    The small IQ motif proteins PEP-19 (62 amino acids) and RC3 (78 amino acids) greatly accelerate the rates of Ca2+ binding to sites III and IV in the C-domain of calmodulin (CaM). We show here that PEP-19 decreases the degree of cooperativity of Ca2+ binding to sites III and IV, and we present a model showing that this could increase Ca2+ binding rate constants. Comparative sequence analysis showed that residues 28 to 58 from PEP-19 are conserved in other proteins. This region includes the IQ ...

  9. Two Improved Digital Signature Schemes

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In this paper, two improved digital signature schemes are presented based on the design of directed signaturescheme [3]. The peculiarity of the system is that only if the scheme is specific recipient, the signature is authenticated.Since the scheme adds the screen of some information parameters, the difficulty of deciphered keys and the security ofdigital signature system are increased.

  10. 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

  11. A combinatorial optimization approach for diverse motif finding applications

    Directory of Open Access Journals (Sweden)

    Singh Mona

    2006-08-01

    Full Text Available Abstract Background Discovering approximately repeated patterns, or motifs, in biological sequences is an important and widely-studied problem in computational molecular biology. Most frequently, motif finding applications arise when identifying shared regulatory signals within DNA sequences or shared functional and structural elements within protein sequences. Due to the diversity of contexts in which motif finding is applied, several variations of the problem are commonly studied. Results We introduce a versatile combinatorial optimization framework for motif finding that couples graph pruning techniques with a novel integer linear programming formulation. Our approach is flexible and robust enough to model several variants of the motif finding problem, including those incorporating substitution matrices and phylogenetic distances. Additionally, we give an approach for determining statistical significance of uncovered motifs. In testing on numerous DNA and protein datasets, we demonstrate that our approach typically identifies statistically significant motifs corresponding to either known motifs or other motifs of high conservation. Moreover, in most cases, our approach finds provably optimal solutions to the underlying optimization problem. Conclusion Our results demonstrate that a combined graph theoretic and mathematical programming approach can be the basis for effective and powerful techniques for diverse motif finding applications.

  12. 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.

  13. Cross-disciplinary detection and analysis of network motifs.

    Science.gov (United States)

    Tran, Ngoc Tam L; DeLuccia, Luke; McDonald, Aidan F; Huang, Chun-Hsi

    2015-01-01

    The detection of network motifs has recently become an important part of network analysis across all disciplines. In this work, we detected and analyzed network motifs from undirected and directed networks of several different disciplines, including biological network, social network, ecological network, as well as other networks such as airlines, power grid, and co-purchase of political books networks. Our analysis revealed that undirected networks are similar at the basic three and four nodes, while the analysis of directed networks revealed the distinction between networks of different disciplines. The study showed that larger motifs contained the three-node motif as a subgraph. Topological analysis revealed that similar networks have similar small motifs, but as the motif size increases, differences arise. Pearson correlation coefficient showed strong positive relationship between some undirected networks but inverse relationship between some directed networks. The study suggests that the three-node motif is a building block of larger motifs. It also suggests that undirected networks share similar low-level structures. Moreover, similar networks share similar small motifs, but larger motifs define the unique structure of individuals. Pearson correlation coefficient suggests that protein structure networks, dolphin social network, and co-authorships in network science belong to a superfamily. In addition, yeast protein-protein interaction network, primary school contact network, Zachary's karate club network, and co-purchase of political books network can be classified into a superfamily. PMID:25983553

  14. 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.

  15. Network Motifs: Simple Building Blocks of Complex Networks

    Science.gov (United States)

    Milo, R.; Shen-Orr, S.; Itzkovitz, S.; Kashtan, N.; Chklovskii, D.; Alon, U.

    2002-10-01

    Complex networks are studied across many fields of science. To uncover their structural design principles, we defined ``network motifs,'' patterns of interconnections occurring in complex networks at numbers that are significantly higher than those in randomized networks. We found such motifs in networks from biochemistry, neurobiology, ecology, and engineering. The motifs shared by ecological food webs were distinct from the motifs shared by the genetic networks of Escherichia coli and Saccharomyces cerevisiae or from those found in the World Wide Web. Similar motifs were found in networks that perform information processing, even though they describe elements as different as biomolecules within a cell and synaptic connections between neurons in Caenorhabditis elegans. Motifs may thus define universal classes of networks. This approach may uncover the basic building blocks of most networks.

  16. Meisetz and the birth of the KRAB motif.

    Science.gov (United States)

    Birtle, Zoë; Ponting, Chris P

    2006-12-01

    The largest family of transcription factors in mammals is of Cys(2)His(2) zinc finger-proteins, each with an NH(2)-terminal KRAB motif. Extensive expansions of this family have occurred in separate mammalian lineages, with approximately 400 such genes known in the human genome. Despite their widespread occurrence, the evolutionary provenance of the KRAB motif is unclear since previously it has not been found outside of the tetrapod vertebrates. Here, we show that homologues of the histone methyltransferase Meisetz are present within the sea urchin (Strongylocentrotus purpuratus) genome. Sea urchin and mammalian Meisetz sequences each contain an N-terminal KRAB motif, which thereby establishes an early origin of the KRAB motif prior to the divergence of echinoderm and chordate lineages. Finally, we present evidence that KRAB motifs derive from a novel family of KRI (KRAB Interior) motifs that were present in the last common ancestor of animals, plants and fungi. PMID:17032681

  17. 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.

  18. 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...

  19. Sequence motif discovery with computational genome-wide analysis

    OpenAIRE

    Akashi, Hirofumi; Aoki, Fumio; Toyota, Minoru; Maruyama, Reo; Sasaki, Yasushi; Mita, Hiroaki; Tokura, Hajime; Imai, Kohzoh; Tatsumi, Haruyuki

    2006-01-01

    As a result of the human genome project and advancements in DNA sequencing technology, we can utilize a huge amount of nucleotide sequence data and can search DNA sequence motifs in whole human genome. However, searching motifs with the naked eye is an enormous task and searching throughout the whole genome is absolutely impossible. Therefore, we have developed a computational genome-wide analyzing system for detecting DNA sequence motifs with biological significance. We used a multi-parallel...

  20. AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments.

    Science.gov (United States)

    Dao, Phuong; Hoinka, Jan; Takahashi, Mayumi; Zhou, Jiehua; Ho, Michelle; Wang, Yijie; Costa, Fabrizio; Rossi, John J; Backofen, Rolf; Burnett, John; Przytycka, Teresa M

    2016-07-01

    Aptamers, short RNA or DNA molecules that bind distinct targets with high affinity and specificity, can be identified using high-throughput systematic evolution of ligands by exponential enrichment (HT-SELEX), but scalable analytic tools for understanding sequence-function relationships from diverse HT-SELEX data are not available. Here we present AptaTRACE, a computational approach that leverages the experimental design of the HT-SELEX protocol, RNA secondary structure, and the potential presence of many secondary motifs to identify sequence-structure motifs that show a signature of selection. We apply AptaTRACE to identify nine motifs in C-C chemokine receptor type 7 targeted by aptamers in an in vitro cell-SELEX experiment. We experimentally validate two aptamers whose binding required both sequence and structural features. AptaTRACE can identify low-abundance motifs, and we show through simulations that, because of this, it could lower HT-SELEX cost and time by reducing the number of selection cycles required. PMID:27467247

  1. 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 ...

  2. On Constructing Certificateless Proxy Signature from Certificateless Signature

    Institute of Scientific and Technical Information of China (English)

    WAN Zhong-mei; LAI Xue-jia; WENG Jian; HONG Xuan; LONG Yu; JIA Wei-wei

    2008-01-01

    In proxy signature schemes,an original signer A delegates its signing capability to a proxy signer B,in such a way that B can sign message on behalf of A.The recipient of the final message verifies at the same time that B computes the signature and that A has delegated its signing capability to B.Recently many identity-based (ID-based) proxy signature schemes have been proposed,however,the problem of key escrow is inherent in this setting.Certificateless cryptography can overcome the key escrow problem.In this paper,we present a general security model for certificateless proxy signature scheme.Then,we give a method to construct a secure certificateless proxy scheme from a secure certificateless signature scheme,and prove that the security of the construction can be reduced to the security of the original certificateless signature scheme.

  3. Motif-role-fingerprints: the building-blocks of motifs, clustering-coefficients and transitivities in directed networks.

    Directory of Open Access Journals (Sweden)

    Mark D McDonnell

    Full Text Available Complex networks are frequently characterized by metrics for which particular subgraphs are counted. One statistic from this category, which we refer to as motif-role fingerprints, differs from global subgraph counts in that the number of subgraphs in which each node participates is counted. As with global subgraph counts, it can be important to distinguish between motif-role fingerprints that are 'structural' (induced subgraphs and 'functional' (partial subgraphs. Here we show mathematically that a vector of all functional motif-role fingerprints can readily be obtained from an arbitrary directed adjacency matrix, and then converted to structural motif-role fingerprints by multiplying that vector by a specific invertible conversion matrix. This result demonstrates that a unique structural motif-role fingerprint exists for any given functional motif-role fingerprint. We demonstrate a similar result for the cases of functional and structural motif-fingerprints without node roles, and global subgraph counts that form the basis of standard motif analysis. We also explicitly highlight that motif-role fingerprints are elemental to several popular metrics for quantifying the subgraph structure of directed complex networks, including motif distributions, directed clustering coefficient, and transitivity. The relationships between each of these metrics and motif-role fingerprints also suggest new subtypes of directed clustering coefficients and transitivities. Our results have potential utility in analyzing directed synaptic networks constructed from neuronal connectome data, such as in terms of centrality. Other potential applications include anomaly detection in networks, identification of similar networks and identification of similar nodes within networks. Matlab code for calculating all stated metrics following calculation of functional motif-role fingerprints is provided as S1 Matlab File.

  4. Signatures of nonthermal melting

    Directory of Open Access Journals (Sweden)

    Tobias Zier

    2015-09-01

    Full Text Available Intense ultrashort laser pulses can melt crystals in less than a picosecond but, in spite of over thirty years of active research, for many materials it is not known to what extent thermal and nonthermal microscopic processes cause this ultrafast phenomenon. Here, we perform ab-initio molecular-dynamics simulations of silicon on a laser-excited potential-energy surface, exclusively revealing nonthermal signatures of laser-induced melting. From our simulated atomic trajectories, we compute the decay of five structure factors and the time-dependent structure function. We demonstrate how these quantities provide criteria to distinguish predominantly nonthermal from thermal melting.

  5. The signature package on Witt spaces, II. Higher signatures

    CERN Document Server

    Albin, Pierre; Mazzeo, Rafe; Piazza, Paolo

    2009-01-01

    This is a sequel to the paper "The signature package on Witt spaces, I. Index classes" by the same authors. In the first part we investigated, via a parametrix construction, the regularity properties of the signature operator on a stratified Witt pseudomanifold, proving, in particular, that one can define a K-homology signature class. We also established the existence of an analytic index class for the signature operator twisted by a C^*_r\\Gamma Mischenko bundle and proved that the K-homology signature class is mapped to the signature index class by the assembly map. In this paper we continue our study, showing that the signature index class is invariant under rational Witt bordisms and stratified homotopies. We are also able to identify this analytic class with the topological analogue of the Mischenko symmetric signature recently defined by Banagl. Finally, we define Witt-Novikov higher signatures and show that our analytic results imply a purely topological theorem, namely that the Witt-Novikov higher sign...

  6. 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

  7. Application of a case–control study design to investigate genotypic signatures of HIV-1 transmission

    OpenAIRE

    Mota Talia M; Murray John M; Center Rob J; Purcell Damian F J; McCaw James M

    2012-01-01

    Abstract Background The characterization of HIV-1 transmission strains may inform the design of an effective vaccine. Shorter variable loops with fewer predicted glycosites have been suggested as signatures enriched in envelope sequences derived during acute HIV-1 infection. Specifically, a transmission-linked lack of glycosites within the V1 and V2 loops of gp120 provides greater access to an α4β7 binding motif, which promotes the establishment of infection. Also, a histidine at position 12 ...

  8. The MHC motif viewer: a visualization tool for MHC binding motifs

    DEFF Research Database (Denmark)

    Rapin, Nicolas; 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....

  9. Signatures of AGN feedback

    Science.gov (United States)

    Wylezalek, D.; Zakamska, N.

    2016-06-01

    Feedback from active galactic nuclei (AGN) is widely considered to be the main driver in regulating the growth of massive galaxies. It operates by either heating or driving the gas that would otherwise be available for star formation out of the galaxy, preventing further increase in stellar mass. Observational proof for this scenario has, however, been hard to come by. We have assembled a large sample of 133 radio-quiet type-2 and red AGN at 0.1importantly, we find a negative correlation between W_{90} and sSFR in the AGN hosts with the highest star formation rates, i.e., with the highest gas content. This relationship implies that AGN with strong outflow signatures are hosted in galaxies that are more `quenched' considering their stellar mass than galaxies with weaker outflow signatures. This correlation is only seen in AGN host galaxies with SFR >100 M_{⊙} yr^{-1} where presumably the coupling of the AGN-driven wind to the gas is strongest. This observation is consistent with the AGN having a net suppression, or `negative' impact, through feedback on the galaxies' star formation history.

  10. Clustering signatures classify directed networks

    Science.gov (United States)

    Ahnert, S. E.; Fink, T. M. A.

    2008-09-01

    We use a clustering signature, based on a recently introduced generalization of the clustering coefficient to directed networks, to analyze 16 directed real-world networks of five different types: social networks, genetic transcription networks, word adjacency networks, food webs, and electric circuits. We show that these five classes of networks are cleanly separated in the space of clustering signatures due to the statistical properties of their local neighborhoods, demonstrating the usefulness of clustering signatures as a classifier of directed networks.

  11. Indicators and signatures

    International Nuclear Information System (INIS)

    Full text: The goal of this presentation is to give an idea of the methodology used to deal with proliferation problems. It can be useful for chemical, biological, balistical proliferation. Here, we underline nuclear proliferation scenarios. Nevertheless, the overall approach is also similar to activities related to terrorism. Everyone knows that to strengthen the NPT/IAEA safeguards and similar treaties verification protocols, the organisations in charge need to build strong capabilities to assess known situations and also to prepare themselves to unknown, or undeclared events and activities. To accomplish this, to collect, analyze, build ad hoc knowledge, organisations have to select the information, to manage the enormous amount of available data. Rather recently, the emergence of new crisis has confirmed the central and vital role that information processing plays at each levels of the international or national non-proliferation community. It is why looking for indicators and signatures is so important, to focus on pertinent information, that could mean something from a nuclear proliferation perspective. This allows people dealing with nuclear proliferation not to be overwhelmed by tons of paper or G bites of memory. A strong need for expertise. Identifying, select and following indicators or looking for signatures is not an easy task. It requires strong expertise. From the development and maintenance of its nuclear deterrence, France acquired expertise in the design, production of fissile material, manufacture and testing of nuclear weapons. There is also in France a long history of nuclear achievements, with small or large scale facilities, both in civilian and military fields; each step of the nuclear fuel cycle can be very precisely described. French nuclear technical assessment relies on Commissariat a l'Energie Atomique (CEA, i.e. Atomic Energy Commission). Since 1958, CEA laboratories are in charge of nuclear civilian and military applications. Other

  12. Discovering large network motifs from a complex biological network

    International Nuclear Information System (INIS)

    Graph structures representing relationships between entries have been studied in statistical analysis, and the results of these studies have been applied to biological networks, whose nodes and edges represent proteins and the relationships between them, respectively. Most of the studies have focused on only graph structures such as scale-free properties and cliques, but the relationships between nodes are also important features since most of the proteins perform their functions by connecting to other proteins. In order to determine such relationships, the problem of network motif discovery has been addressed; network motifs are frequently appearing graph structures in a given graph. However, the methods for network motif discovery are highly restrictive for the application to biological network because they can only be used to find small network motifs or they do not consider noise and uncertainty in observations. In this study, we introduce a new index to measure network motifs called AR index and develop a novel algorithm called ARIANA for finding large motifs even when the network has noise. Experiments using a synthetic network verify that our method can find better network motifs than an existing algorithm. By applying ARIANA to a real complex biological network, we find network motifs associated with regulations of start time of cell functions and generation of cell energies and discover that the cell cycle proteins can be categorized into two different groups.

  13. The phenomenon of astral motifs on late mediaeval tombstones

    Science.gov (United States)

    Mijatović, V.; Ninković, S.; Vemić, D.

    2003-10-01

    The authors study astral motifs present on some mediaeval tombstones found in present-day Serbia and Montenegro and in the neighbouring countries (especially in Bosnia and Herzegovina). The authors discern some important astral motifs, explain them and present a short review concerning their frequency.

  14. 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)

  15. Role of GxxxG Motifs in Transmembrane Domain Interactions.

    Science.gov (United States)

    Teese, Mark G; Langosch, Dieter

    2015-08-25

    Transmembrane (TM) helices of integral membrane proteins can facilitate strong and specific noncovalent protein-protein interactions. Mutagenesis and structural analyses have revealed numerous examples in which the interaction between TM helices of single-pass membrane proteins is dependent on a GxxxG or (small)xxx(small) motif. It is therefore tempting to use the presence of these simple motifs as an indicator of TM helix interactions. In this Current Topic review, we point out that these motifs are quite common, with more than 50% of single-pass TM domains containing a (small)xxx(small) motif. However, the actual interaction strength of motif-containing helices depends strongly on sequence context and membrane properties. In addition, recent studies have revealed several GxxxG-containing TM domains that interact via alternative interfaces involving hydrophobic, polar, aromatic, or even ionizable residues that do not form recognizable motifs. In multipass membrane proteins, GxxxG motifs can be important for protein folding, and not just oligomerization. Our current knowledge thus suggests that the presence of a GxxxG motif alone is a weak predictor of protein dimerization in the membrane. PMID:26244771

  16. 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

  17. 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

  18. Expressiveness considerations of XML signatures

    DEFF Research Database (Denmark)

    Jensen, Meiko; Meyer, Christopher

    2011-01-01

    more and more challenging. In this paper, we investigate this issue, describing how an attacker can still interfere with Web Services communication even in the presence of XML Signatures. Additionally, we discuss the interrelation of XML Signatures and XML Encryption, focussing on their security......XML Signatures are used to protect XML-based Web Service communication against a broad range of attacks related to man-in-the-middle scenarios. However, due to the complexity of the Web Services specification landscape, the task of applying XML Signatures in a robust and reliable manner becomes...

  19. Guanine nucleotide dissociation inhibitor activity of the triple GoLoco motif protein G18: alanine-to-aspartate mutation restores function to an inactive second GoLoco motif.

    Science.gov (United States)

    Kimple, Randall J; Willard, Francis S; Hains, Melinda D; Jones, Miller B; Nweke, Gift K; Siderovski, David P

    2004-03-15

    GoLoco ('Galpha(i/o)-Loco' interaction) motif proteins have recently been identified as novel GDIs (guanine nucleotide dissociation inhibitors) for heterotrimeric G-protein alpha subunits. G18 is a member of the mammalian GoLoco-motif gene family and was uncovered by analyses of human and mouse genomes for anonymous open-reading frames. The encoded G18 polypeptide is predicted to contain three 19-amino-acid GoLoco motifs, which have been shown in other proteins to bind Galpha subunits and inhibit spontaneous nucleotide release. However, the G18 protein has thus far not been characterized biochemically. Here, we have cloned and expressed the G18 protein and assessed its ability to act as a GDI. G18 is capable of simultaneously binding more than one Galpha(i1) subunit. In binding assays with the non-hydrolysable GTP analogue guanosine 5'-[gamma-thio]triphosphate, G18 exhibits GDI activity, slowing the exchange of GDP for GTP by Galpha(i1). Only the first and third GoLoco motifs within G18 are capable of interacting with Galpha subunits, and these bind with low micromolar affinity only to Galpha(i1) in the GDP-bound form, and not to Galpha(o), Galpha(q), Galpha(s) or Galpha12. Mutation of Ala-121 to aspartate in the inactive second GoLoco motif of G18, to restore the signature acidic-glutamine-arginine tripeptide that forms critical contacts with Galpha and its bound nucleotide [Kimple, Kimple, Betts, Sondek and Siderovski (2002) Nature (London) 416, 878-881], results in gain-of-function with respect to Galpha binding and GDI activity. PMID:14656218

  20. Dynamic Motifs of Strategies in Prisoner's Dilemma Games

    CERN Document Server

    Kim, Young Jin; Jeong, Seon-Young; Son, Seung-Woo

    2014-01-01

    We investigate the win-lose relations between strategies of iterated prisoner's dilemma games by using a directed network concept to display the replicator dynamics results. In the giant strongly-connected component of the win/lose network, we find win-lose circulations similar to rock-paper-scissors and analyze the fixed point and its stability. Applying the network motif concept, we introduce dynamic motifs, which describe the population dynamics relations among the three strategies. Through exact enumeration, we find 22 dynamic motifs and display their phase portraits. Visualization using directed networks and motif analysis is a useful method to make complex dynamic behavior simple in order to understand it more intuitively. Dynamic motifs can be building blocks for dynamic behavior among strategies when they are applied to other types of games.

  1. 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.

  2. 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.

  3. PROXY BLIND SIGNATURE BASED ON ECDLP

    Directory of Open Access Journals (Sweden)

    SATARUPA PRADHAN,

    2011-03-01

    Full Text Available Proxy blind signature combines the properties of both proxy signature and blind signature. In a proxy signature scheme, a signer delegates his signing power to a proxy, who signs a message on behalf of the original signer. In a blind signature scheme, the signer cannot link the relationship between the blind message and the signature of the chosen message. Therefore, it is very suitable for electronic commerceapplication. In this paper, a proxy blind signature scheme based on ECDLP (Elliptic Curve Discrete Logarithm Problem has been proposed, which satisfy the security properties of both the blind signature and the proxy signature. Analysis shows that our scheme is secure and efficient.

  4. Signatures de l'invisible

    CERN Multimedia

    CERN Press Office. Geneva

    2000-01-01

    "Signatures of the Invisible" is an unique collaboration between contemporary artists and contemporary physicists which has the potential to help redefine the relationship between science and art. "Signatures of the Invisible" is jointly organised by the London Institute - the world's largest college of art and design and CERN*, the world's leading particle physics laboratory. 12 leading visual artists:

  5. MISAE: a new approach for regulatory motif extraction.

    Science.gov (United States)

    Sun, Zhaohui; Yang, Jingyi; Deogun, Jitender S

    2004-01-01

    The recognition of regulatory motifs of co-regulated genes is essential for understanding the regulatory mechanisms. However, the automatic extraction of regulatory motifs from a given data set of the upstream non-coding DNA sequences of a family of co-regulated genes is difficult because regulatory motifs are often subtle and inexact. This problem is further complicated by the corruption of the data sets. In this paper, a new approach called Mismatch-allowed Probabilistic Suffix Tree Motif Extraction (MISAE) is proposed. It combines the mismatch-allowed probabilistic suffix tree that is a probabilistic model and local prediction for the extraction of regulatory motifs. The proposed approach is tested on 15 co-regulated gene families and compares favorably with other state-of-the-art approaches. Moreover, MISAE performs well on "corrupted" data sets. It is able to extract the motif from a "corrupted" data set with less than one fourth of the sequences containing the real motif. PMID:16448011

  6. BlockLogo: visualization of peptide and sequence motif conservation.

    Science.gov (United States)

    Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian; Sun, Jing; Schönbach, Christian; Reinherz, Ellis L; Zhang, Guang Lan; Brusic, Vladimir

    2013-12-31

    BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, selection of motif positions, type of sequence, and output format definition. The output has BlockLogo along with the sequence logo, and a table of motif frequencies. We deployed BlockLogo as an online application and have demonstrated its utility through examples that show visualization of T-cell epitopes and B-cell epitopes (both continuous and discontinuous). Our additional example shows a visualization and analysis of structural motifs that determine the specificity of peptide binding to HLA-DR molecules. The BlockLogo server also employs selected experimentally validated prediction algorithms to enable on-the-fly prediction of MHC binding affinity to 15 common HLA class I and class II alleles as well as visual analysis of discontinuous epitopes from multiple sequence alignments. It enables the visualization and analysis of structural and functional motifs that are usually described as regular expressions. It provides a compact view of discontinuous motifs composed of distant positions within biological sequences. BlockLogo is available at: http://research4.dfci.harvard.edu/cvc/blocklogo/ and http://met-hilab.bu.edu/blocklogo/. PMID:24001880

  7. 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.

  8. 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

  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. Coherent feedforward transcriptional regulatory motifs enhance drug resistance

    Science.gov (United States)

    Charlebois, Daniel A.; Balázsi, Gábor; Kærn, Mads

    2014-05-01

    Fluctuations in gene expression give identical cells access to a spectrum of phenotypes that can serve as a transient, nongenetic basis for natural selection by temporarily increasing drug resistance. In this study, we demonstrate using mathematical modeling and simulation that certain gene regulatory network motifs, specifically coherent feedforward loop motifs, can facilitate the development of nongenetic resistance by increasing cell-to-cell variability and the time scale at which beneficial phenotypic states can be maintained. Our results highlight how regulatory network motifs enabling transient, nongenetic inheritance play an important role in defining reproductive fitness in adverse environments and provide a selective advantage subject to evolutionary pressure.

  11. A Novel Alignment-Free Method for Comparing Transcription Factor Binding Site Motifs

    OpenAIRE

    Minli Xu; Zhengchang Su

    2010-01-01

    BACKGROUND: Transcription factor binding site (TFBS) motifs can be accurately represented by position frequency matrices (PFM) or other equivalent forms. We often need to compare TFBS motifs using their PFMs in order to search for similar motifs in a motif database, or cluster motifs according to their binding preference. The majority of current methods for motif comparison involve a similarity metric for column-to-column comparison and a method to find the optimal position alignment between ...

  12. UTSig: A Persian Offline Signature Dataset

    OpenAIRE

    Soleimani, Amir; Fouladi, Kazim; Araabi, Babak N.

    2016-01-01

    The crucial role of datasets in signature verification systems has motivated researchers to collect signature samples. However, with regard to the distinct characteristics of Persian signature, existing offline signature datasets cannot be used in Persian systems. This paper presents a new and public Persian offline signature dataset, UTSig, which consists of 8280 images from 115 classes that each class has 27 genuine, 3 opposite-hand signatures of the genuine signer, and 42 skilled forgeries...

  13. On the signature of LINCOS

    Science.gov (United States)

    Ollongren, Alexander

    2010-12-01

    Suppose the international SETI effort yields the discovery of some signal of evidently non-natural origin. Could it contain linguistic information formulated in some kind of Lingua Cosmica? One way to get insight into this matter is to consider what specific (bio) linguistic signature( s) could be attached to a cosmic language for interstellar communication—designed by humans or an alien society having reached a level of intelligence (and technology) comparable to or surpassing ours. For this purpose, we consider in the present paper the logico-linguistic system LINCOS for ( A)CETI, developed during a number of years by the author in several papers and a monograph [1]. The system has a two-fold signature, which distinguishes it significantly from natural languages. In fact abstract and concrete signatures can be distinguished. That an abstract kind occurs is due to the manner in which abstractions of reality are represented in LINCOS-texts. They can take compound forms because the system is multi-expressive—partly due to the availability of inductive (recursive) entities. On the other hand, the concrete signature of LINCOS is related to the distribution of delimiters and predefined tokens in texts. Assigning measures to concrete signatures will be discussed elsewhere. The present contribution concentrates on the abstract signature of the language. At the same time, it is realized that an alien Lingua Cosmica might, but not necessarily needs to have this kind of signatures.

  14. Paradigm Signature S8

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    不说不知道,Paradigm在北美市场可是占用率位居前列的品牌,而且产品在世界各地获奖连连.足以证明他的成功。但风光的背后,肯定离不开默默的耕耘。Paradigm工厂就在加拿大,全世界销售的Paradigm产品都出自这个地广人稀、资源丰富、风景优美的北美绿洲。Paradigm的产品线甚广,SignatureS8是其中的现役旗舰。和很多旗舰产品动不动就要价数十万的品牌相比,这个Paradigm的产品定位可是务实得多,

  15. Statistical clumped isotope signatures.

    Science.gov (United States)

    Röckmann, T; Popa, M E; Krol, M C; Hofmann, M E G

    2016-01-01

    High precision measurements of molecules containing more than one heavy isotope may provide novel constraints on element cycles in nature. These so-called clumped isotope signatures are reported relative to the random (stochastic) distribution of heavy isotopes over all available isotopocules of a molecule, which is the conventional reference. When multiple indistinguishable atoms of the same element are present in a molecule, this reference is calculated from the bulk (≈average) isotopic composition of the involved atoms. We show here that this referencing convention leads to apparent negative clumped isotope anomalies (anti-clumping) when the indistinguishable atoms originate from isotopically different populations. Such statistical clumped isotope anomalies must occur in any system where two or more indistinguishable atoms of the same element, but with different isotopic composition, combine in a molecule. The size of the anti-clumping signal is closely related to the difference of the initial isotope ratios of the indistinguishable atoms that have combined. Therefore, a measured statistical clumped isotope anomaly, relative to an expected (e.g. thermodynamical) clumped isotope composition, may allow assessment of the heterogeneity of the isotopic pools of atoms that are the substrate for formation of molecules. PMID:27535168

  16. Secure mediated certificateless signature scheme

    Institute of Scientific and Technical Information of China (English)

    YANG Chen; MA Wen-ping; WANG Xin-mei

    2007-01-01

    Ju et al proposed a certificateless signature scheme with instantaneous revocation by introducing security mediator (SEM) mechanism. This article presents a detailed cryptoanalysis of this scheme and shows that, in their proposed scheme, once a valid signature has been produced, the signer can recover his private key information and the instantaneous revocation property will be damaged. Furthermore, an improved mediated signature scheme, which can eliminate these disadvantages, is proposed, and security proof of the improved scheme under elliptic curve factorization problem (ECFP) assumption and bilinear computational diffie-hellman problem (BCDH) assumption is also proposed.

  17. Review article: The mountain motif in the plot of Matthew

    Directory of Open Access Journals (Sweden)

    Gert J. Volschenk

    2010-02-01

    Full Text Available This article reviewed T.L. Donaldson’s book, Jesus on the mountain: A study in Matthean theology, published in 1985 by JSOT Press, Sheffield, and focused on the mountain motif in the structure and plot of the Gospel of Matthew, in addition to the work of Donaldson on the mountain motif as a literary motif and as theological symbol. The mountain is a primary theological setting for Jesus’ ministry and thus is an important setting, serving as one of the literary devices by which Matthew structured and progressed his narrative. The Zion theological and eschatological significance and Second Temple Judaism serve as the historical and theological background for the mountain motif. The last mountain setting (Mt 28:16–20 is the culmination of the three theological themes in the plot of Matthew, namely Christology, ecclesiology and salvation history.

  18. BayesMD: flexible biological modeling for motif discovery

    DEFF Research Database (Denmark)

    Tang, Man-Hung Eric; Krogh, Anders; Winther, Ole

    2008-01-01

    and the marginal probabilities can be used directly to assess the significance of the findings. The framework is benchmarked against other methods on a number of real and artificial data sets. The accompanying prediction server, documentation, software, models and data are available from http://bayesmd.binf.ku.dk/.......We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained...... sampling results are achieved using the advanced sampling method parallel tempering. In a post-analysis step candidate motifs with high marginal probability are found by searching among those motifs that contain sites that occur frequently. Thereby, maximum a posteriori inference for the motifs is avoided...

  19. Automatic Network Fingerprinting through Single-Node Motifs

    CERN Document Server

    Echtermeyer, Christoph; Rodrigues, Francisco A; Kaiser, Marcus; 10.1371/journal.pone.0015765

    2011-01-01

    Complex networks have been characterised by their specific connectivity patterns (network motifs), but their building blocks can also be identified and described by node-motifs---a combination of local network features. One technique to identify single node-motifs has been presented by Costa et al. (L. D. F. Costa, F. A. Rodrigues, C. C. Hilgetag, and M. Kaiser, Europhys. Lett., 87, 1, 2009). Here, we first suggest improvements to the method including how its parameters can be determined automatically. Such automatic routines make high-throughput studies of many networks feasible. Second, the new routines are validated in different network-series. Third, we provide an example of how the method can be used to analyse network time-series. In conclusion, we provide a robust method for systematically discovering and classifying characteristic nodes of a network. In contrast to classical motif analysis, our approach can identify individual components (here: nodes) that are specific to a network. Such special nodes...

  20. BlockLogo: Visualization of peptide and sequence motif conservation

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian;

    2013-01-01

    , selection of motif positions, type of sequence, and output format definition. The output has BlockLogo along with the sequence logo, and a table of motif frequencies. We deployed BlockLogo as an online application and have demonstrated its utility through examples that show visualization of T-cell epitopes...... and B-cell epitopes (both continuous and discontinuous). Our additional example shows a visualization and analysis of structural motifs that determine the specificity of peptide binding to HLA-DR molecules. The BlockLogo server also employs selected experimentally validated prediction algorithms to...... enable on-the-fly prediction of MHC binding affinity to 15 common HLA class I and class II alleles as well as visual analysis of discontinuous epitopes from multiple sequence alignments. It enables the visualization and analysis of structural and functional motifs that are usually described as regular...

  1. Robust and Adaptive MicroRNA-Mediated Incoherent Feedforward Motifs

    Science.gov (United States)

    Xu, Feng-Dan; Liu, Zeng-Rong; Zhang, Zhi-Yong; Shen, Jian-Wei

    2009-02-01

    We integrate transcriptional and post-transcriptional regulation into microRNA-mediated incoherent feedforward motifs and analyse their dynamical behaviour and functions. The analysis show that the behaviour of the system is almost uninfluenced by the varying input in certain ranges and by introducing of delay and noise. The results indicate that microRNA-mediated incoherent feedforward motifs greatly enhance the robustness of gene regulation.

  2. Cross-Disciplinary Detection and Analysis of Network Motifs

    OpenAIRE

    Ngoc Tam L. Tran; Luke DeLuccia; McDonald, Aidan F; Chun-Hsi Huang

    2015-01-01

    The detection of network motifs has recently become an important part of network analysis across all disciplines. In this work, we detected and analyzed network motifs from undirected and directed networks of several different disciplines, including biological network, social network, ecological network, as well as other networks such as airlines, power grid, and co-purchase of political books networks. Our analysis revealed that undirected networks are similar at the basic three and four nod...

  3. Mining Tertiary Structural Motifs for Assessment of Designability

    OpenAIRE

    Zhang, Jian; Grigoryan, Gevorg

    2013-01-01

    The observation of a limited secondary-structural alphabet in native proteins, with significant sequence preferences, has profoundly influenced the fields of protein design and structure prediction (Simons et al., 1997; Verschueren et al., 2011). In the era of structural genomics, as the size of the structural dataset continues to grow rapidly, it is becoming possible to extend this analysis to tertiary structural motifs and their sequences. For a hypothetical tertiary motif, the rate of its ...

  4. Temporal Analysis of Motif Mixtures using Dirichlet Processes

    OpenAIRE

    Emonet, Rémi; Varadarajan, J.; Odobez, Jean-Marc

    2014-01-01

    International audience In this paper, we present a new model for unsupervised discovery of recurrent temporal patterns (or motifs) in time series (or documents). The model is designed to handle the difficult case of multivariate time series obtained from a mixture of activities, that is, our observations are caused by the superposition of multiple phenomena occurring concurrently and with no synchronization. The model uses nonparametric Bayesian methods to describe both the motifs and thei...

  5. Robust and Adaptive MicroRNA-Mediated Incoherent Feedforward Motifs

    Institute of Scientific and Technical Information of China (English)

    XU Feng-Dan; LIU Zeng-Rong; ZHANG Zhi-Yong; SHEN Jian-Wei

    2009-01-01

    We integrate transcriptional and post-transcriptional regulation into microRNA-mediated incoherent feedforward motifs and analyse their dynamical behaviour and functions. The analysis show that the behaviour of the system is almost uninfluenced by the varying input in certain ranges and by introducing of delay and noise. The results indicate that microRNA-mediated incoherent feedforward motifs greatly enhance the robustness of gene regulation.

  6. Triplex-induced recombination and repair in the pyrimidine motif

    OpenAIRE

    Kalish, Jennifer M.; Seidman, Michael M.; Weeks, Daniel L.; Glazer, Peter M.

    2005-01-01

    Triplex-forming oligonucleotides (TFOs) bind DNA in a sequence-specific manner at polypurine/polypyrimidine sites and mediate targeted genome modification. Triplexes are formed by either pyrimidine TFOs, which bind parallel to the purine strand of the duplex (pyrimidine, parallel motif), or purine TFOs, which bind in an anti-parallel orientation (purine, anti-parallel motif). Both purine and pyrimidine TFOs, when linked to psoralen, have been shown to direct psoralen adduct formation in cells...

  7. Robust and Adaptive MicroRNA-Mediated Incoherent Feedforward Motifs

    International Nuclear Information System (INIS)

    We integrate transcriptional and post-transcriptional regulation into microRNA-mediated incoherent feedforward motifs and analyse their dynamical behaviour and functions. The analysis show that the behaviour of the system is almost uninfluenced by the varying input in certain ranges and by introducing of delay and noise. The results indicate that microRNA-mediated incoherent feedforward motifs greatly enhance the robustness of gene regulation

  8. Interpretation of Konya Seljuk Carpet Motifs in Exlibrises

    OpenAIRE

    SÜRMELİ, Kader

    2013-01-01

    Traditional Turkish carpets’ technical characteristics with strong motifs and knotting technique, have been its greatest support in regular and continuing development which carry on to survive today. The discovery of Gordes - Turkish knotting technique was born from the need of a nomadic tribe to find a thicker and warmer floor material. Located in Konya, the center of the Anatolian Seljuks, Seljuk carpets with their rich color tones and motifs were the ones where this technique was applied ...

  9. Motif depletion in bacteriophages infecting hosts with CRISPR systems

    OpenAIRE

    Kupczok, Anne; Bollback, Jonathan P

    2014-01-01

    Background CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pre...

  10. Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs

    OpenAIRE

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

    2011-01-01

    Proper subcellular localization is critical for proteins to perform their roles in cellular functions. Proteins are transported by different cellular sorting pathways, some of which take a protein through several intermediate locations until reaching its final destination. The pathway a protein is transported through is determined by carrier proteins that bind to specific sequence motifs. In this article, we present a new method that integrates protein interaction and sequence motif data to m...

  11. Initial Semantics for Strengthened Signatures

    CERN Document Server

    Hirschowitz, André; 10.4204/EPTCS.77.5

    2012-01-01

    We give a new general definition of arity, yielding the companion notions of signature and associated syntax. This setting is modular in the sense requested by Ghani and Uustalu: merging two extensions of syntax corresponds to building an amalgamated sum. These signatures are too general in the sense that we are not able to prove the existence of an associated syntax in this general context. So we have to select arities and signatures for which there exists the desired initial monad. For this, we follow a track opened by Matthes and Uustalu: we introduce a notion of strengthened arity and prove that the corresponding signatures have initial semantics (i.e. associated syntax). Our strengthened arities admit colimits, which allows the treatment of the \\lambda-calculus with explicit substitution.

  12. Initial Semantics for Strengthened Signatures

    Directory of Open Access Journals (Sweden)

    André Hirschowitz

    2012-02-01

    Full Text Available We give a new general definition of arity, yielding the companion notions of signature and associated syntax. This setting is modular in the sense requested by Ghani and Uustalu: merging two extensions of syntax corresponds to building an amalgamated sum. These signatures are too general in the sense that we are not able to prove the existence of an associated syntax in this general context. So we have to select arities and signatures for which there exists the desired initial monad. For this, we follow a track opened by Matthes and Uustalu: we introduce a notion of strengthened arity and prove that the corresponding signatures have initial semantics (i.e. associated syntax. Our strengthened arities admit colimits, which allows the treatment of the λ-calculus with explicit substitution.

  13. Equiangular Frames and Signature Sets

    OpenAIRE

    Singh, Preeti

    2009-01-01

    We will present a relation between real equiangular frames and certain special sets in groups which we call signature sets and show that many equiangular frames arise in this manner. Then we will define quasi-signature sets and will examine equiangular frames associated to these subsets of groups. We will extend these results to complex equiangular frames where the inner product between any pair of vectors is a common multiple of a cube root of unity and exhibit equiangular frames that arise ...

  14. Object Recognition Using Spatiotemporal Signatures

    OpenAIRE

    James V Stone

    1998-01-01

    The sequence of images generated by motion between observer and object specifies a spatiotemporal signature for that object. Evidence is presented that such spatiotemporal signatures are used in object recognition. Subjects learned novel, three-dimensional, rotating objects from image sequences in a continuous recognition task. During learning, the temporal order of images of a given object was constant. During testing, the order of images in each sequence was reversed, relative to its order ...

  15. An arbitrated quantum signature scheme

    CERN Document Server

    Zeng, G; Zeng, Guihua; Keitel, Christoph H.

    2002-01-01

    The general principle for a quantum signature scheme is proposed and investigated based on ideas from classical signature schemes and quantum cryptography. The suggested algorithm is implemented by a symmetrical quantum key cryptosystem and Greenberger-Horne-Zeilinger (GHZ) triplet states and relies on the availability of an arbitrator. We can guarantee the unconditional security of the algorithm, mostly due to the correlation of the GHZ triplet states and the use of quantum one-time pads.

  16. Contract Signature Using Quantum Information

    CERN Document Server

    De Sousa, P B M; Ramos, Rubens Viana; Sousa, Paulo Benicio Melo de

    2006-01-01

    This paper describes how to perform contract signature in a fair way using quantum information. The protocol proposed permits two partners, users of a communication network, to exchange their signatures with non-repudiation. For this, we assume that there is a trustable arbitrator, responsible for the authentication of the signers and that performs a central task in a quantum teleportation protocol of the XOR function between two classical bits.

  17. Visual identification by signature tracking

    OpenAIRE

    Munich, Mario E.; Perona, Pietro

    2003-01-01

    We propose a new camera-based biometric: visual signature identification. We discuss the importance of the parameterization of the signatures in order to achieve good classification results, independently of variations in the position of the camera with respect to the writing surface. We show that affine arc-length parameterization performs better than conventional time and Euclidean arc-length ones. We find that the system verification performance is better than 4 percent error on skilled fo...

  18. Assessing the effects of symmetry on motif discovery and modeling.

    Directory of Open Access Journals (Sweden)

    Lala M Motlhabi

    Full Text Available BACKGROUND: Identifying the DNA binding sites for transcription factors is a key task in modeling the gene regulatory network of a cell. Predicting DNA binding sites computationally suffers from high false positives and false negatives due to various contributing factors, including the inaccurate models for transcription factor specificity. One source of inaccuracy in the specificity models is the assumption of asymmetry for symmetric models. METHODOLOGY/PRINCIPAL FINDINGS: Using simulation studies, so that the correct binding site model is known and various parameters of the process can be systematically controlled, we test different motif finding algorithms on both symmetric and asymmetric binding site data. We show that if the true binding site is asymmetric the results are unambiguous and the asymmetric model is clearly superior to the symmetric model. But if the true binding specificity is symmetric commonly used methods can infer, incorrectly, that the motif is asymmetric. The resulting inaccurate motifs lead to lower sensitivity and specificity than would the correct, symmetric models. We also show how the correct model can be obtained by the use of appropriate measures of statistical significance. CONCLUSIONS/SIGNIFICANCE: This study demonstrates that the most commonly used motif-finding approaches usually model symmetric motifs incorrectly, which leads to higher than necessary false prediction errors. It also demonstrates how alternative motif-finding methods can correct the problem, providing more accurate motif models and reducing the errors. Furthermore, it provides criteria for determining whether a symmetric or asymmetric model is the most appropriate for any experimental dataset.

  19. In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs

    Directory of Open Access Journals (Sweden)

    Zheng Haixia

    2008-08-01

    Full Text Available Abstract Background Noncoding RNAs (ncRNAs play important roles in a variety of cellular processes. Characterizing the transcriptional activity of ncRNA promoters is therefore a critical step toward understanding the complex cellular roles of ncRNAs. Results Here we present an in vivo transcriptional analysis of three C. elegans ncRNA upstream motifs (UM1-3. Transcriptional activity of all three motifs has been demonstrated, and mutational analysis revealed differential contributions of different parts of each motif. We showed that upstream motif 1 (UM1 can drive the expression of green fluorescent protein (GFP, and utilized this for detailed analysis of temporal and spatial expression patterns of 5 SL2 RNAs. Upstream motifs 2 and 3 do not drive GFP expression, and termination at consecutive T runs suggests transcription by RNA polymerase III. The UM2 sequence resembles the tRNA promoter, and is actually embedded within its own short-lived, primary transcript. This is a structure which is also found at a few plant and yeast loci, and may indicate an evolutionarily very old dicistronic transcription pattern in which a tRNA serves as a promoter for an adjacent snoRNA. Conclusion The study has demonstrated that the three upstream motifs UM1-3 have promoter activity. The UM1 sequence can drive expression of GFP, which allows for the use of UM1::GFP fusion constructs to study temporal-spatial expression patterns of UM1 ncRNA loci. The UM1 loci appear to act in concert with other upstream sequences, whereas the transcriptional activities of the UM2 and UM3 are confined to the motifs themselves.

  20. SIGNATURE: A workbench for gene expression signature analysis

    Directory of Open Access Journals (Sweden)

    Chang Jeffrey T

    2011-11-01

    Full Text Available Abstract Background The biological phenotype of a cell, such as a characteristic visual image or behavior, reflects activities derived from the expression of collections of genes. As such, an ability to measure the expression of these genes provides an opportunity to develop more precise and varied sets of phenotypes. However, to use this approach requires computational methods that are difficult to implement and apply, and thus there is a critical need for intelligent software tools that can reduce the technical burden of the analysis. Tools for gene expression analyses are unusually difficult to implement in a user-friendly way because their application requires a combination of biological data curation, statistical computational methods, and database expertise. Results We have developed SIGNATURE, a web-based resource that simplifies gene expression signature analysis by providing software, data, and protocols to perform the analysis successfully. This resource uses Bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures, all carried out within a GenePattern web interface for easy use and access. Conclusions SIGNATURE is available for public use at http://genepattern.genome.duke.edu/signature/.

  1. Quantum messages with signatures forgeable in arbitrated quantum signature schemes

    Science.gov (United States)

    Kim, Taewan; Choi, Jeong Woon; Jho, Nam-Su; Lee, Soojoon

    2015-02-01

    Even though a method to perfectly sign quantum messages has not been known, the arbitrated quantum signature scheme has been considered as one of the good candidates. However, its forgery problem has been an obstacle to the scheme becoming a successful method. In this paper, we consider one situation, which is slightly different from the forgery problem, that we use to check whether at least one quantum message with signature can be forged in a given scheme, although all the messages cannot be forged. If there are only a finite number of forgeable quantum messages in the scheme, then the scheme can be secured against the forgery attack by not sending forgeable quantum messages, and so our situation does not directly imply that we check whether the scheme is secure against the attack. However, if users run a given scheme without any consideration of forgeable quantum messages, then a sender might transmit such forgeable messages to a receiver and in such a case an attacker can forge the messages if the attacker knows them. Thus it is important and necessary to look into forgeable quantum messages. We show here that there always exists such a forgeable quantum message-signature pair for every known scheme with quantum encryption and rotation, and numerically show that there are no forgeable quantum message-signature pairs that exist in an arbitrated quantum signature scheme.

  2. Structural and functional studies of a phosphatidic acid-binding antifungal plant defensin MtDef4: Identification of an RGFRRR motif governing fungal cell entry

    Energy Technology Data Exchange (ETDEWEB)

    Sagaram, Uma S.; El-Mounadi, Kaoutar; Buchko, Garry W.; Berg, Howard R.; Kaur, Jagdeep; Pandurangi, Raghoottama; Smith, Thomas J.; Shah, Dilip

    2013-12-04

    A highly conserved plant defensin MtDef4 potently inhibits the growth of a filamentous fungus Fusarium graminearum. MtDef4 is internalized by cells of F. graminearum. To determine its mechanism of fungal cell entry and antifungal action, NMR solution structure of MtDef4 has been determined. The analysis of its structure has revealed a positively charged patch on the surface of the protein consisting of arginine residues in its γ-core signature, a major determinant of the antifungal activity of MtDef4. Here, we report functional analysis of the RGFRRR motif of the γ-core signature of MtDef4. The replacement of RGFRRR to AAAARR or to RGFRAA not only abolishes fungal cell entry but also results in loss of the antifungal activity of MtDef4. MtDef4 binds strongly to phosphatidic acid (PA), a precursor for the biosynthesis of membrane phospholipids and a signaling lipid known to recruit cytosolic proteins to membranes. Mutations of RGFRRR which abolish fungal cell entry of MtDef4 also impair its binding to PA. Our results suggest that RGFRRR motif is a translocation signal for entry of MtDef4 into fungal cells and that this positively charged motif likely mediates interaction of this defensin with PA as part of its antifungal action.

  3. Mining tertiary structural motifs for assessment of designability.

    Science.gov (United States)

    Zhang, Jian; Grigoryan, Gevorg

    2013-01-01

    The observation of a limited secondary-structural alphabet in native proteins, with significant sequence preferences, has profoundly influenced the fields of protein design and structure prediction (Simons, Kooperberg, Huang, & Baker, 1997; Verschueren et al., 2011). In the era of structural genomics, as the size of the structural dataset continues to grow rapidly, it is becoming possible to extend this analysis to tertiary structural motifs and their sequences. For a hypothetical tertiary motif, the rate of its utilization in natural proteins may be used to assess its designability-the ease with which the motif can be realized with natural amino acids. This requires a structural similarity search methodology, which rather than looking for global topological agreement (more appropriate for categorization of full proteins or domains), identifies detailed geometric matches. In this chapter, we introduce such a method, called MaDCaT, and demonstrate its use by assessing the designability landscapes of two tertiary structural motifs. We also show that such analysis can establish structure/sequence links by providing the sequence constraints necessary to encode designable motifs. As logical extension of their secondary-structure counterparts, tertiary structural preferences will likely prove extremely useful in de novo protein design and structure prediction. PMID:23422424

  4. Signature molecular descriptor : advanced applications.

    Energy Technology Data Exchange (ETDEWEB)

    Visco, Donald Patrick, Jr. (Tennessee Technological University, Cookeville, TN)

    2010-04-01

    In this work we report on the development of the Signature Molecular Descriptor (or Signature) for use in the solution of inverse design problems as well as in highthroughput screening applications. The ultimate goal of using Signature is to identify novel and non-intuitive chemical structures with optimal predicted properties for a given application. We demonstrate this in three studies: green solvent design, glucocorticoid receptor ligand design and the design of inhibitors for Factor XIa. In many areas of engineering, compounds are designed and/or modified in incremental ways which rely upon heuristics or institutional knowledge. Often multiple experiments are performed and the optimal compound is identified in this brute-force fashion. Perhaps a traditional chemical scaffold is identified and movement of a substituent group around a ring constitutes the whole of the design process. Also notably, a chemical being evaluated in one area might demonstrate properties very attractive in another area and serendipity was the mechanism for solution. In contrast to such approaches, computer-aided molecular design (CAMD) looks to encompass both experimental and heuristic-based knowledge into a strategy that will design a molecule on a computer to meet a given target. Depending on the algorithm employed, the molecule which is designed might be quite novel (re: no CAS registration number) and/or non-intuitive relative to what is known about the problem at hand. While CAMD is a fairly recent strategy (dating to the early 1980s), it contains a variety of bottlenecks and limitations which have prevented the technique from garnering more attention in the academic, governmental and industrial institutions. A main reason for this is how the molecules are described in the computer. This step can control how models are developed for the properties of interest on a given problem as well as how to go from an output of the algorithm to an actual chemical structure. This report

  5. 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...

  6. 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...

  7. Robustness to noise in synchronization of network motifs: Experimental results

    Science.gov (United States)

    Buscarino, Arturo; Fortuna, Luigi; Frasca, Mattia; Iachello, Marco; Pham, Viet-Thanh

    2012-12-01

    In this work, we experimentally investigate the robustness to noise of synchronization in all the four-nodes network motifs. The experimental setup consists of four Chua's circuits diffusively coupled in order to implement the six different undirected network motifs that can be obtained with four nodes. In this experimental setup, synchronization in the presence of noise injected in one of the network nodes is investigated and network motifs are compared in terms of the synchronization error obtained. The analysis has been then extended to some selected case studies of networks with five and six nodes. Numerical simulations have been also performed and results in agreement with experiments have been obtained. A correlation between node degree and robustness to noise has been found also in these networks.

  8. How pathogens use linear motifs to perturb host cell networks

    KAUST Repository

    Via, Allegra

    2015-01-01

    Molecular mimicry is one of the powerful stratagems that pathogens employ to colonise their hosts and take advantage of host cell functions to guarantee their replication and dissemination. In particular, several viruses have evolved the ability to interact with host cell components through protein short linear motifs (SLiMs) that mimic host SLiMs, thus facilitating their internalisation and the manipulation of a wide range of cellular networks. Here we present convincing evidence from the literature that motif mimicry also represents an effective, widespread hijacking strategy in prokaryotic and eukaryotic parasites. Further insights into host motif mimicry would be of great help in the elucidation of the molecular mechanisms behind host cell invasion and the development of anti-infective therapeutic strategies.

  9. Graph Analytics for Signature Discovery

    Energy Technology Data Exchange (ETDEWEB)

    Hogan, Emilie A.; Johnson, John R.; Halappanavar, Mahantesh; Lo, Chaomei

    2013-06-01

    Within large amounts of seemingly unstructured data it can be diffcult to find signatures of events. In our work we transform unstructured data into a graph representation. By doing this we expose underlying structure in the data and can take advantage of existing graph analytics capabilities, as well as develop new capabilities. Currently we focus on applications in cybersecurity and communication domains. Within cybersecurity we aim to find signatures for perpetrators using the pass-the-hash attack, and in communications we look for emails or phone calls going up or down a chain of command. In both of these areas, and in many others, the signature we look for is a path with certain temporal properties. In this paper we discuss our methodology for finding these temporal paths within large graphs.

  10. 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

  11. Selection against spurious promoter motifs correlates withtranslational efficiency across bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Froula, Jeffrey L.; Francino, M. Pilar

    2007-05-01

    Because binding of RNAP to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of DNA motifs capable of RNAP-binding across the genome. Here we analyze the distribution of the -10 promoter motifs that bind the {sigma}{sup 70} subunit of RNAP in 42 bacterial genomes. We show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequences while eliminating them from the nonfunctional and, in most cases, from the protein coding regions. In some genomes, however, -10 sites are over-represented in the coding sequences; these sites could induce pauses effecting regulatory roles throughout the length of a transcriptional unit. For nonfunctional sequences, the extent of motif under-representation varies across genomes in a manner that broadly correlates with the number of tRNA genes, a good indicator of translational speed and growth rate. This suggests that minimizing the time invested in gene transcription is an important selective pressure against spurious binding. However, selection against spurious binding is detectable in the reduced genomes of host-restricted bacteria that grow at slow rates, indicating that components of efficiency other than speed may also be important. Minimizing the number of RNAP molecules per cell required for transcription, and the corresponding energetic expense, may be most relevant in slow growers. These results indicate that genome-level properties affecting the efficiency of transcription and translation can respond in an integrated manner to optimize gene expression. The detection of selection against promoter motifs in nonfunctional regions also implies that no sequence may evolve free of selective constraints, at least in the relatively small and unstructured genomes of bacteria.

  12. Equiangular Frames and Signature Sets

    CERN Document Server

    Singh, Preeti

    2009-01-01

    We will present a relation between real equiangular frames and certain special sets in groups which we call signature sets and show that many equiangular frames arise in this manner. Then we will define quasi-signature sets and will examine equiangular frames associated to these subsets of groups. We will extend these results to complex equiangular frames where the inner product between any pair of vectors is a common multiple of a cube root of unity and exhibit equiangular frames that arise from groups in this manner.

  13. A Signature Scheme with Non-Repudiation

    Institute of Scientific and Technical Information of China (English)

    XIN Xiangjun; GUO Xiaoli; XIAO Guozhen

    2006-01-01

    Based on the Schnorr signature scheme, a new signature scheme with non-repudiation is proposed. In this scheme, only the signer and the designated receiver can verify the signature signed by the signer, and if necessary, both the signer and the designated receiver can prove and show the validity of the signature signed by the signer. The proof of the validity of the signature is noninteractive and transferable. To verify and prove the validity of the signature, the signer and the nominated receiver needn't store extra information besides the signature. At the same time, neither the signer nor the designated receiver can deny a valid signature signed. Then, there is no repudiation in this new signature scheme. According to the security analysis of this scheme, it is found the proposed scheme is secure against existential forgery on adaptive chosen message attack.

  14. Some results on more flexible versions of Graph Motif

    CERN Document Server

    Rizzi, Romeo

    2012-01-01

    The problems studied in this paper originate from Graph Motif, a problem introduced in 2006 in the context of biological networks. Informally speaking, it consists in deciding if a multiset of colors occurs in a connected subgraph of a vertex-colored graph. Due to the high rate of noise in the biological data, more flexible definitions of the problem have been outlined. We present in this paper two inapproximability results for two different optimization variants of Graph Motif. We also study another definition of the problem, when the connectivity constraint is replaced by modularity. While the problem stays NP-complete, it allows algorithms in FPT for biologically relevant parameterizations.

  15. 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.

  16. Galaxy interactions : The HI signature

    NARCIS (Netherlands)

    Sancisi, R; Barnes, JE; Sanders, DB

    1999-01-01

    HI observations are an excellent tool for investigating tidal interactions. Ongoing major and minor interactions which can lead to traumatic mergers or to accretion and the triggering of star formation, show distinct HI signatures. Interactions and mergers in the recent past can also be recognized i

  17. Disaster relief through composite signatures

    Science.gov (United States)

    Hawley, Chadwick T.; Hyde, Brian; Carpenter, Tom; Nichols, Steve

    2012-06-01

    A composite signature is a group of signatures that are related in such a way to more completely or further define a target or operational endeavor at a higher fidelity. This paper builds on previous work developing innovative composite signatures associated with civil disasters, including physical, chemical and pattern/behavioral. For the composite signature approach to be successful it requires effective data fusion and visualization. This plays a key role in both preparedness and the response and recovery which are critical to saving lives. Visualization tools enhance the overall understanding of the crisis by pulling together and analyzing the data, and providing a clear and complete analysis of the information to the organizations/agencies dependant on it for a successful operation. An example of this, Freedom Web, is an easy-to-use data visualization and collaboration solution for use in homeland security, emergency preparedness, situational awareness, and event management. The solution provides a nationwide common operating picture for all levels of government through a web based, map interface. The tool was designed to be utilized by non-geospatial experts and is easily tailored to the specific needs of the users. Consisting of standard COTS and open source databases and a web server, users can view, edit, share, and highlight information easily and quickly through a standard internet browser.

  18. How curved membranes recruit amphipathic helices and protein anchoring motifs

    DEFF Research Database (Denmark)

    Hatzakis, Nikos; Bhatia, Vikram Kjøller; Larsen, Jannik;

    2009-01-01

    : membrane-anchored proteins. The fact that unrelated structural motifs such as alpha-helices and alkyl chains sense MC led us to propose that MC sensing is a generic property of curved membranes rather than a property of the anchoring molecules. We therefore anticipate that MC will promote the...... redistribution of proteins that are anchored in membranes through other types of hydrophobic moieties....

  19. An Interaction between the Walker A and D-loop Motifs Is Critical to ATP Hydrolysis and Cooperativity in Bacteriophage T4 Rad50*

    OpenAIRE

    De la Rosa, Metzere Bierlein; Nelson, Scott W.

    2011-01-01

    The ATP binding cassette (ABC) proteins make up a large superfamily with members coming from all kingdoms. The functional form of the ABC protein nucleotide binding domain (NBD) is dimeric with ATP binding sites shared between subunits. The NBD is defined by six motifs: the Walker A, Q-loop, Signature, Walker-B, D-loop, and H-loop. The D-loop contains a conserved aspartate whose function is not clear but has been proposed to be involved in cross-talk between ATP binding sites. Structures of v...

  20. Elliptic Curve Blind Digital Signature Schemes

    Institute of Scientific and Technical Information of China (English)

    YOULin; YANGYixian; WENQiaoyan

    2003-01-01

    Blind signature schemes are important cryptographic protocols in guaranteeing the privacy or anonymity of the users.Three new blind signature schemes and their corresponding generalizations are pro-posed. Moreover, their securities are simply analyzed.

  1. Blind Signature Scheme Based on Chebyshev Polynomials

    Directory of Open Access Journals (Sweden)

    Maheswara Rao Valluri

    2011-12-01

    Full Text Available A blind signature scheme is a cryptographic protocol to obtain a valid signature for a message from a signer such that signer’s view of the protocol can’t be linked to the resulting message signature pair. This paper presents blind signature scheme using Chebyshev polynomials. The security of the given scheme depends upon the intractability of the integer factorization problem and discrete logarithms ofChebyshev polynomials.

  2. Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori HtrA

    OpenAIRE

    Schmidt, Thomas P.; Perna, Anna M.; Tim Fugmann; Manja Böhm; Jan Hiss; Sarah Haller; Camilla Götz; Nicole Tegtmeyer; Benjamin Hoy; Rau, Tilman T; Dario Neri; Steffen Backert; Gisbert Schneider; Silja Wessler

    2016-01-01

    The cell adhesion protein and tumour suppressor E-cadherin exhibits important functions in the prevention of gastric cancer. As a class-I carcinogen, Helicobacter pylori (H. pylori) has developed a unique strategy to interfere with E-cadherin functions. In previous studies, we have demonstrated that H. pylori secretes the protease high temperature requirement A (HtrA) which cleaves off the E-cadherin ectodomain (NTF) on epithelial cells. This opens cell-to-cell junctions, allowing bacterial t...

  3. Motivated Proteins: A web application for studying small three-dimensional protein motifs

    Directory of Open Access Journals (Sweden)

    Milner-White E James

    2009-02-01

    Full Text Available Abstract Background Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are αβ-motifs, asx-motifs, asx-turns, β-bulges, β-bulge loops, β-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns. We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. Description The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (XHTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. Conclusion Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema.

  4. Composite motifs integrating multiple protein structures increase sensitivity for function prediction.

    Science.gov (United States)

    Chen, Brian Y; Bryant, Drew H; Cruess, Amanda E; Bylund, Joseph H; Fofanov, Viacheslav Y; Kristensen, David M; Kimmel, Marek; Lichtarge, Olivier; Kavraki, Lydia E

    2007-01-01

    The study of disease often hinges on the biological function of proteins, but determining protein function is a difficult experimental process. To minimize duplicated effort, algorithms for function prediction seek characteristics indicative of possible protein function. One approach is to identify substructural matches of geometric and chemical similarity between motifs representing known active sites and target protein structures with unknown function. In earlier work, statistically significant matches of certain effective motifs have identified functionally related active sites. Effective motifs must be carefully designed to maintain similarity to functionally related sites (sensitivity) and avoid incidental similarities to functionally unrelated protein geometry (specificity). Existing motif design techniques use the geometry of a single protein structure. Poor selection of this structure can limit motif effectiveness if the selected functional site lacks similarity to functionally related sites. To address this problem, this paper presents composite motifs, which combine structures of functionally related active sites to potentially increase sensitivity. Our experimentation compares the effectiveness of composite motifs with simple motifs designed from single protein structures. On six distinct families of functionally related proteins, leave-one-out testing showed that composite motifs had sensitivity comparable to the most sensitive of all simple motifs and specificity comparable to the average simple motif. On our data set, we observed that composite motifs simultaneously capture variations in active site conformation, diminish the problem of selecting motif structures, and enable the fusion of protein structures from diverse data sources. PMID:17951837

  5. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

    DEFF Research Database (Denmark)

    Stark, Alexander; Lin, Michael F; Kheradpour, Pouya;

    2007-01-01

    Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional...... element shows characteristic patterns of change, or 'evolutionary signatures', dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop......-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict...

  6. Polarization signatures of airborne particulates

    Science.gov (United States)

    Raman, Prashant; Fuller, Kirk A.; Gregory, Don A.

    2013-07-01

    Exploratory research has been conducted with the aim of completely determining the polarization signatures of selected particulates as a function of wavelength. This may lead to a better understanding of the interaction between electromagnetic radiation and such materials, perhaps leading to the point detection of bio-aerosols present in the atmosphere. To this end, a polarimeter capable of measuring the complete Mueller matrix of highly scattering samples in transmission and reflection (with good spectral resolution from 300 to 1100 nm) has been developed. The polarization properties of Bacillus subtilis (surrogate for anthrax spore) are compared to ambient particulate matter species such as pollen, dust, and soot. Differentiating features in the polarization signatures of these samples have been identified, thus demonstrating the potential applicability of this technique for the detection of bio-aerosol in the ambient atmosphere.

  7. Robust RSA for Digital Signature

    OpenAIRE

    Virendra Kumar; Puran Krishen Koul

    2011-01-01

    The RSA cryptosystem is currently used in a wide variety of products, platforms, and industries around the world. It is found in many commercial software products and is planned to be in many more. In hardware, the RSA algorithm can be found in secure telephones, on ethernet network cards, and on smart cards.It offers encryption and digital signatures (authentication). In this paper we will illustrate the application and problem associated with RSA Algorithm.

  8. Quantum signatures of Chimera states

    OpenAIRE

    Bastidas, V. M.; Omelchenko, I.; ZAKHAROVA, A.; Schöll, E.; Brandes, T.

    2015-01-01

    Chimera states are complex spatiotemporal patterns in networks of identical oscillators, characterized by the coexistence of synchronized and desynchronized dynamics. Here we propose to extend the phenomenon of chimera states to the quantum regime, and uncover intriguing quantum signatures of these states. We calculate the quantum fluctuations about semiclassical trajectories and demonstrate that chimera states in the quantum regime can be characterized by bosonic squeezing, weighted quantum ...

  9. Nonlinear control of magnetic signatures

    Science.gov (United States)

    Niemoczynski, Bogdan

    Magnetic properties of ferrite structures are known to cause fluctuations in Earth's magnetic field around the object. These fluctuations are known as the object's magnetic signature and are unique based on the object's geometry and material. It is a common practice to neutralize magnetic signatures periodically after certain time intervals, however there is a growing interest to develop real time degaussing systems for various applications. Development of real time degaussing system is a challenging problem because of magnetic hysteresis and difficulties in measurement or estimation of near-field flux data. The goal of this research is to develop a real time feedback control system that can be used to minimize magnetic signatures for ferrite structures. Experimental work on controlling the magnetic signature of a cylindrical steel shell structure with a magnetic disturbance provided evidence that the control process substantially increased the interior magnetic flux. This means near field estimation using interior sensor data is likely to be inaccurate. Follow up numerical work for rectangular and cylindrical cross sections investigated variations in shell wall flux density under a variety of ambient excitation and applied disturbances. Results showed magnetic disturbances could corrupt interior sensor data and magnetic shielding due to the shell walls makes the interior very sensitive to noise. The magnetic flux inside the shell wall showed little variation due to inner disturbances and its high base value makes it less susceptible to noise. This research proceeds to describe a nonlinear controller to use the shell wall data as an input. A nonlinear plant model of magnetics is developed using a constant tau to represent domain rotation lag and a gain function k to describe the magnetic hysteresis curve for the shell wall. The model is justified by producing hysteresis curves for multiple materials, matching experimental data using a particle swarm algorithm, and

  10. Robust RSA for Digital Signature

    Directory of Open Access Journals (Sweden)

    Virendra Kumar

    2011-11-01

    Full Text Available The RSA cryptosystem is currently used in a wide variety of products, platforms, and industries around the world. It is found in many commercial software products and is planned to be in many more. In hardware, the RSA algorithm can be found in secure telephones, on ethernet network cards, and on smart cards.It offers encryption and digital signatures (authentication. In this paper we will illustrate the application and problem associated with RSA Algorithm.

  11. Selection signatures in Shetland ponies.

    Science.gov (United States)

    Frischknecht, M; Flury, C; Leeb, T; Rieder, S; Neuditschko, M

    2016-06-01

    Shetland ponies were selected for numerous traits including small stature, strength, hardiness and longevity. Despite the different selection criteria, Shetland ponies are well known for their small stature. We performed a selection signature analysis including genome-wide SNPs of 75 Shetland ponies and 76 large-sized horses. Based upon this dataset, we identified a selection signature on equine chromosome (ECA) 1 between 103.8 Mb and 108.5 Mb. A total of 33 annotated genes are located within this interval including the IGF1R gene at 104.2 Mb and the ADAMTS17 gene at 105.4 Mb. These two genes are well known to have a major impact on body height in numerous species including humans. Homozygosity mapping in the Shetland ponies identified a region with increased homozygosity between 107.4 Mb and 108.5 Mb. None of the annotated genes in this region have so far been associated with height. Thus, we cannot exclude the possibility that the identified selection signature on ECA1 is associated with some trait other than height, for which Shetland ponies were selected. PMID:26857482

  12. Signature Inversion in Odd-odd Nuclei

    Institute of Scientific and Technical Information of China (English)

    LIU Min-liang; ZHANG Yu-hu; ZHOU Xiao-hong; GUO Ying-xiang; LEI Xiang-guo; GUO Wen-tao

    2009-01-01

    Signature inversion in odd-odd nuclei is investigated by using a proton and a neutron coupling to the coherent state of the core.Two parameters are employed in the Hamiltonian to set the energy scales of rotation,neutron-proton coupling and their competition.Typical level staggering is extracted from the calculated level energies.The calculation can approximately reproduce experimental signature inversion.Signature inversion is attributed to the rotational motion and neutronproton residual interaction having reversed signature splitting rules.It is found signature inversion can appear at axially symmetric shape and high-K band.

  13. Infrared signature studies of aerospace vehicles

    Science.gov (United States)

    Mahulikar, Shripad P.; Sonawane, Hemant R.; Arvind Rao, G.

    2007-10-01

    Infrared (IR) emissions from aircraft are used to detect, track, and lock-on to the target. MAN Portable Air Defence Systems (MANPADS) have emerged as a major cause of aircraft and helicopter loss. Therefore, IR signature studies are important to counter this threat for survivability enhancement, and are an important aspect of stealth technology. This paper reviews contemporary developments in this discipline, with particular emphasis on IR signature prediction from aerospace vehicles. The role of atmosphere in IR signature analysis, and relation between IR signature level and target susceptibility are illustrated. Also, IR signature suppression systems and countermeasure techniques are discussed, to highlight their effectiveness and implications in terms of penalties.

  14. A New Signature Scheme with Shared Verification

    Institute of Scientific and Technical Information of China (English)

    JIA Xiao-yun; LUO Shou-shan; YUAN Chao-wei

    2006-01-01

    With expanding user demands, digital signature techniques are also being expanded greatly, from single signature and single verification techniques to techniques supporting multi-users. This paper presents a new digital signature scheme vith shared verification based on the fiat-shamir signature scheme. This scheme is suitable not only for digital signatures of one public key, but also for situations where multiple public keys are required. In addition, the scheme can resist all kinds of collusion, making it more practicable and safer. Additionally it is more efficient than other schemes.

  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. 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...

  17. Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances

    OpenAIRE

    Jaebum Kim; Ryan Cunningham; Brian James; Stefan Wyder; Gibson, Joshua D.; Oliver Niehuis; Zdobnov, Evgeny M.; Hugh M Robertson; Robinson, Gene E.; Werren, John H; Saurabh Sinha

    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 app...

  18. Selection against spurious promoter motifs correlates with translational efficiency across bacteria

    OpenAIRE

    Froula, Jeffrey L.; M. Pilar Francino

    2008-01-01

    Because binding of RNAP to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of DNA motifs capable of RNAP-binding across the genome. Here we analyze the distribution of the -10 promoter motifs that bind the sigma(70) subunit of RNAP in 42 bacterial genomes. We show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory s...

  19. Provably secure robust threshold partial blind signature

    Institute of Scientific and Technical Information of China (English)

    CAO Zhenfu; ZHU Haojin; LU Rongxing

    2006-01-01

    Threshold digital signature and blind signature are playing important roles in cryptography as well as in practical applications such as e-cash and e-voting systems.Over the past few years, many cryptographic researchers have made considerable headway in this field. However, to our knowledge, most of existing threshold blind signature schemes are based on the discrete logarithm problem. In this paper, we propose a new robust threshold partial blind signature scheme based on improved RSA cryptosystem.This scheme is the first threshold partial blind signature scheme based on factoring, and the robustness of threshold partial blind signature is also introduced. Moreover, in practical application, the proposed scheme will be especially suitable for blind signature-based voting systems with multiple administrators and secure electronic cash systems to prevent their abuse.

  20. A new quantum blind signature with unlinkability

    Science.gov (United States)

    Shi, Wei-Min; Zhang, Jian-Biao; Zhou, Yi-Hua; Yang, Yu-Guang

    2015-08-01

    Recently, some quantum blind signature protocols have been proposed. However, the previous schemes cannot satisfy the unlinkability requirement. To overcome the drawback of unlinkability in the previous schemes, we propose a new quantum blind signature based on Bell states with the help of an authentic party. In this paper, we provide a method to inject a randomizing factor into a message when it is signed by the signer and then get rid of the blind factor from the blinded signature when it is verified by the verifier. Even when the message owner publishes the message-signature pair, the signer cannot identify the association between the message-signature pair and the blind signature he generated. Therefore, our scheme really realizes unlinkability property. At last, analysis results show that this scheme satisfies the basis security requirements of a weak signature such as no-counterfeiting, no-disavowing, blindness and traceability, and our total efficiency is not less than the previous schemes.

  1. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

    LENUS (Irish Health Repository)

    Casey, Fergal

    2011-08-22

    Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

  2. 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

  3. 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...

  4. Nephila clavipes Flagelliform Silk-like GGX Motifs Contribute to Extensibility and Spacer Motifs Contribute to Strength in Synthetic Spider Silk Fibers

    OpenAIRE

    Adrianos, Sherry L.; Teulé, Florence; Hinman, Michael B.; Jones, Justin A.; Weber, Warner S.; Yarger, Jeffery L.; Lewis, Randolph V.

    2013-01-01

    Flagelliform spider silk is the most extensible silk fiber produced by orb weaver spiders, though not as strong as the dragline silk of the spider. The motifs found in the core of the Nephila clavipes flagelliform Flag protein are: GGX, spacer, and GPGGX. Flag does not contain the polyalanine motif known to provide the strength of dragline silk. To investigate the source of flagelliform fiber strength, four recombinant proteins were produced containing variations of the three core motifs of t...

  5. Nature-inspired design of motif-specific antibody scaffolds

    OpenAIRE

    Koerber, James T.; Thomsen, Nathan D.; Hannigan, Brett T.; DeGrado, William F.; Wells, James A.

    2013-01-01

    Aberrant changes in post-translational modifications (PTMs) such as phosphorylation underlie a majority of human diseases. However, detection and quantification of PTMs for diagnostic or biomarker applications often requires monoclonal PTM-specific antibodies, which are challenging to generate using traditional antibody-generation platforms. Here we outline a general strategy for producing synthetic PTM-specific antibodies by engineering a motif-specific ‘hot spot’ into an antibody scaffold. ...

  6. Defense-Inducing Volatiles: In Search of the Active Motif

    OpenAIRE

    Heil, Martin; Lion, Ulrich; Boland, Wilhelm

    2008-01-01

    Herbivore-induced volatile organic compounds (VOCs) are widely appreciated as an indirect defense mechanism since carnivorous arthropods use VOCs as cues for host localization and then attack herbivores. Another function of VOCs is plant–plant signaling. That VOCs elicit defensive responses in neighboring plants has been reported from various species, and different compounds have been found to be active. In order to search for a structural motif that characterizes active VOCs, we used lima be...

  7. 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.

  8. Exon silencing by UAGG motifs in response to neuronal excitation.

    Directory of Open Access Journals (Sweden)

    Ping An

    2007-02-01

    Full Text Available Alternative pre-mRNA splicing plays fundamental roles in neurons by generating functional diversity in proteins associated with the communication and connectivity of the synapse. The CI cassette of the NMDA R1 receptor is one of a variety of exons that show an increase in exon skipping in response to cell excitation, but the molecular nature of this splicing responsiveness is not yet understood. Here we investigate the molecular basis for the induced changes in splicing of the CI cassette exon in primary rat cortical cultures in response to KCl-induced depolarization using an expression assay with a tight neuron-specific readout. In this system, exon silencing in response to neuronal excitation was mediated by multiple UAGG-type silencing motifs, and transfer of the motifs to a constitutive exon conferred a similar responsiveness by gain of function. Biochemical analysis of protein binding to UAGG motifs in extracts prepared from treated and mock-treated cortical cultures showed an increase in nuclear hnRNP A1-RNA binding activity in parallel with excitation. Evidence for the role of the NMDA receptor and calcium signaling in the induced splicing response was shown by the use of specific antagonists, as well as cell-permeable inhibitors of signaling pathways. Finally, a wider role for exon-skipping responsiveness is shown to involve additional exons with UAGG-related silencing motifs, and transcripts involved in synaptic functions. These results suggest that, at the post-transcriptional level, excitable exons such as the CI cassette may be involved in strategies by which neurons mount adaptive responses to hyperstimulation.

  9. Tricksters Trot to America: Areal Distribution of Folklore Motifs

    OpenAIRE

    Yuri Berezkin

    2010-01-01

    The folklore Trickster is usually considered a universally known combination of features intrinsic to human nature. However, there are strong anomalies in the areal distribution of such a figure. Sub-Saharan Africa, North America (except for the Arctic), Northeast Asia and South American Chaco not only are the preferred zones of tricksters’ activity but also share some peculiar trickster motifs unknown in most of the other regions. The range of animals which play the role of tricksters is als...

  10. The ADAMTS (A Disintegrin and Metalloproteinase with Thrombospondin motifs) family

    OpenAIRE

    Kelwick, Richard; Desanlis, Ines; Wheeler, Grant N.; Edwards, Dylan R

    2015-01-01

    The ADAMTS (A Disintegrin and Metalloproteinase with Thrombospondin motifs) enzymes are secreted, multi-domain matrix-associated zinc metalloendopeptidases that have diverse roles in tissue morphogenesis and patho-physiological remodeling, in inflammation and in vascular biology. The human family includes 19 members that can be sub-grouped on the basis of their known substrates, namely the aggrecanases or proteoglycanases (ADAMTS1, 4, 5, 8, 9, 15 and 20), the procollagen N-propeptidases (ADAM...

  11. 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

  12. Interlinking motifs and entropy landscapes of statistically interacting particles

    Directory of Open Access Journals (Sweden)

    P. Lu

    2012-03-01

    Full Text Available The s=1/2 Ising chain with uniform nearest-neighbor and next-nearest-neighbor coupling is used to construct a system of floating particles characterized by motifs of up to six consecutive local spins. The spin couplings cause the assembly of particles which, in turn, remain free of interaction energies even at high density. All microstates are configurations of particles from one of three different sets, excited from pseudo-vacua associated with ground states of periodicities one, two, and four. The motifs of particles and elements of pseudo-vacuum interlink in two shared site variables. The statistical interaction between particles is encoded in a generalized Pauli principle, describing how the placement of one particle modifies the options for placing further particles. In the statistical mechanical analysis arbitrary energies can be assigned to all particle species. The entropy is a function of the particle populations. The statistical interaction specifications are transparently built into that expression. The energies and structures of the particles alone govern the ordering at low temperature. Under special circumstances the particles can be replaced by more fundamental particles with shorter motifs that interlink in only one shared site variable. Structures emerge from interactions on two levels: particles with shapes from coupled spins and long-range ordering tendencies from statistically interacting particles with shapes.

  13. 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.

  14. Insertion of tetracysteine motifs into dopamine transporter extracellular domains.

    Directory of Open Access Journals (Sweden)

    Deanna M Navaroli

    Full Text Available The neuronal dopamine transporter (DAT is a major determinant of extracellular dopamine (DA levels and is the primary target for a variety of addictive and therapeutic psychoactive drugs. DAT is acutely regulated by protein kinase C (PKC activation and amphetamine exposure, both of which modulate DAT surface expression by endocytic trafficking. In order to use live imaging approaches to study DAT endocytosis, methods are needed to exclusively label the DAT surface pool. The use of membrane impermeant, sulfonated biarsenic dyes holds potential as one such approach, and requires introduction of an extracellular tetracysteine motif (tetraCys; CCPGCC to facilitate dye binding. In the current study, we took advantage of intrinsic proline-glycine (Pro-Gly dipeptides encoded in predicted DAT extracellular domains to introduce tetraCys motifs into DAT extracellular loops 2, 3, and 4. [(3H]DA uptake studies, surface biotinylation and fluorescence microscopy in PC12 cells indicate that tetraCys insertion into the DAT second extracellular loop results in a functional transporter that maintains PKC-mediated downregulation. Introduction of tetraCys into extracellular loops 3 and 4 yielded DATs with severely compromised function that failed to mature and traffic to the cell surface. This is the first demonstration of successful introduction of a tetracysteine motif into a DAT extracellular domain, and may hold promise for use of biarsenic dyes in live DAT imaging studies.

  15. 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

  16. GxxxG motifs hold the TIM23 complex together.

    Science.gov (United States)

    Demishtein-Zohary, Keren; Marom, Milit; Neupert, Walter; Mokranjac, Dejana; Azem, Abdussalam

    2015-06-01

    Approximately 99% of the mitochondrial proteome is nucleus-encoded, synthesized in the cytosol, and subsequently imported into and sorted to the correct compartment in the organelle. The translocase of the inner mitochondrial membrane 23 (TIM23) complex is the major protein translocase of the inner membrane, and is responsible for translocation of proteins across the inner membrane and their insertion into the inner membrane. Tim23 is the central component of the complex that forms the import channel. A high-resolution structure of the import channel is still missing, and structural elements important for its function are unknown. In the present study, we analyzed the importance of the highly abundant GxxxG motifs in the transmembrane segments of Tim23 for the structural integrity of the TIM23 complex. Of 10 glycines present in the GxxxG motifs in the first, second and third transmembrane segments of Tim23, mutations of three of them in transmembrane segments 1 and 2 resulted in a lethal phenotype, and mutations of three others in a temperature-sensitive phenotype. The remaining four caused no obvious growth phenotype. Importantly, none of the mutations impaired the import and membrane integration of Tim23 precursor into mitochondria. However, the severity of growth impairment correlated with the destabilization of the TIM23 complex. We conclude that the GxxxG motifs found in the first and second transmembrane segments of Tim23 are necessary for the structural integrity of the TIM23 complex. PMID:25765297

  17. 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

  18. 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...

  19. 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.

  20. Genetic signatures of heroin addiction

    Science.gov (United States)

    Chen, Shaw-Ji; Liao, Ding-Lieh; Shen, Tsu-Wang; Yang, Hsin-Chou; Chen, Kuang-Chi; Chen, Chia-Hsiang

    2016-01-01

    Abstract Heroin addiction is a complex psychiatric disorder with a chronic course and a high relapse rate, which results from the interaction between genetic and environmental factors. Heroin addiction has a substantial heritability in its etiology; hence, identification of individuals with a high genetic propensity to heroin addiction may help prevent the occurrence and relapse of heroin addiction and its complications. The study aimed to identify a small set of genetic signatures that may reliably predict the individuals with a high genetic propensity to heroin addiction. We first measured the transcript level of 13 genes (RASA1, PRKCB, PDK1, JUN, CEBPG, CD74, CEBPB, AUTS2, ENO2, IMPDH2, HAT1, MBD1, and RGS3) in lymphoblastoid cell lines in a sample of 124 male heroin addicts and 124 male control subjects using real-time quantitative PCR. Seven genes (PRKCB, PDK1, JUN, CEBPG, CEBPB, ENO2, and HAT1) showed significant differential expression between the 2 groups. Further analysis using 3 statistical methods including logistic regression analysis, support vector machine learning analysis, and a computer software BIASLESS revealed that a set of 4 genes (JUN, CEBPB, PRKCB, ENO2, or CEBPG) could predict the diagnosis of heroin addiction with the accuracy rate around 85% in our dataset. Our findings support the idea that it is possible to identify genetic signatures of heroin addiction using a small set of expressed genes. However, the study can only be considered as a proof-of-concept study. As the establishment of lymphoblastoid cell line is a laborious and lengthy process, it would be more practical in clinical settings to identify genetic signatures for heroin addiction directly from peripheral blood cells in the future study. PMID:27495086

  1. Infrared signatures for remote sensing

    International Nuclear Information System (INIS)

    PNL's capabilities for infrared and near-infrared spectroscopy include tunable-diode-laser (TDL) systems covering 300--3,000 cm-1 at 2 laser. PNL also has a beam expansion source with a 12-cm slit, which provides a 3-m effective path for gases at ∼10 K, giving a Doppler width of typically 10 MHz; and long-path static gas cells (to 100 m). In applying this equipment to signatures work, the authors emphasize the importance of high spectral resolution for detecting and identifying atmospheric interferences; for identifying the optimum analytical frequencies; for deriving, by spectroscopic analysis, the molecular parameters needed for modeling; and for obtaining data on species and/or bands that are not in existing databases. As an example of such spectroscopy, the authors have assigned and analyzed the C-Cl stretching region of CCl4 at 770--800 cm-1. This is an important potential signature species whose IR absorption has remained puzzling because of the natural isotopic mix, extensive hot-band structure, and a Fermi resonance involving a nearby combination band. Instrument development projects include the IR sniffer, a small high-sensitivity, high-discrimination (Doppler-limited) device for fence-line or downwind monitoring that is effective even in regions of atmospheric absorption; preliminary work has achieved sensitivities at the low-ppb level. Other work covers trace species detection with TDLs, and FM-modulated CO2 laser LIDAR. The authors are planning a field experiment to interrogate the Hanford tank farm for signature species from Rattlesnake Mountain, a standoff of ca. 15 km, to be accompanied by simultaneous ground-truthing at the tanks

  2. Saturation Physics: Probes and Signatures

    International Nuclear Information System (INIS)

    A hadron wavefunction at high energy contains many gluons which carry a small fraction x of the valence quark energy. At fixed impact parameters as one increases the hadron energy, the gluon occupation number in the wavefunction eventually saturates and becomes of order of 1/αs, the maximum allowed by QCD. The resulting hadron state at high energy is then called a Color Glass Condensate (CGC). Signatures and predictions of the formalism are reviewed and compared with the experimental data at RHIC.

  3. Quantum signatures of chimera states

    Science.gov (United States)

    Bastidas, V. M.; Omelchenko, I.; Zakharova, A.; Schöll, E.; Brandes, T.

    2015-12-01

    Chimera states are complex spatiotemporal patterns in networks of identical oscillators, characterized by the coexistence of synchronized and desynchronized dynamics. Here we propose to extend the phenomenon of chimera states to the quantum regime, and uncover intriguing quantum signatures of these states. We calculate the quantum fluctuations about semiclassical trajectories and demonstrate that chimera states in the quantum regime can be characterized by bosonic squeezing, weighted quantum correlations, and measures of mutual information. Our findings reveal the relation of chimera states to quantum information theory, and give promising directions for experimental realization of chimera states in quantum systems.

  4. Quantum broadcasting multiple blind signature with constant size

    Science.gov (United States)

    Xiao, Min; Li, Zhenli

    2016-06-01

    Using quantum homomorphic signature in quantum network, we propose a quantum broadcasting multiple blind signature scheme. Different from classical signature and current quantum signature schemes, the multi-signature proposed in our scheme is not generated by simply putting the individual signatures together, but by aggregating the individual signatures based on homomorphic property. Therefore, the size of the multi-signature is constant. Furthermore, based on a wide range of investigation for the security of existing quantum signature protocols, our protocol is designed to resist possible forgery attacks against signature and message from the various attack sources and disavowal attacks from participants.

  5. A Novel Alignment-Free Method for Comparing Transcription Factor Binding Site Motifs

    Science.gov (United States)

    Xu, Minli; Su, Zhengchang

    2010-01-01

    Background Transcription factor binding site (TFBS) motifs can be accurately represented by position frequency matrices (PFM) or other equivalent forms. We often need to compare TFBS motifs using their PFMs in order to search for similar motifs in a motif database, or cluster motifs according to their binding preference. The majority of current methods for motif comparison involve a similarity metric for column-to-column comparison and a method to find the optimal position alignment between the two compared motifs. In some applications, alignment-free methods might be preferred; however, few such methods with high accuracy have been described. Methodology/Principal Findings Here we describe a novel alignment-free method for quantifying the similarity of motifs using their PFMs by converting PFMs into k-mer vectors. The motifs could then be compared by measuring the similarity among their corresponding k-mer vectors. Conclusions/Significance We demonstrate that our method in general achieves similar performance or outperforms the existing methods for clustering motifs according to their binding preference and identifying similar motifs of transcription factors of the same family. PMID:20098703

  6. A novel alignment-free method for comparing transcription factor binding site motifs.

    Directory of Open Access Journals (Sweden)

    Minli Xu

    Full Text Available BACKGROUND: Transcription factor binding site (TFBS motifs can be accurately represented by position frequency matrices (PFM or other equivalent forms. We often need to compare TFBS motifs using their PFMs in order to search for similar motifs in a motif database, or cluster motifs according to their binding preference. The majority of current methods for motif comparison involve a similarity metric for column-to-column comparison and a method to find the optimal position alignment between the two compared motifs. In some applications, alignment-free methods might be preferred; however, few such methods with high accuracy have been described. METHODOLOGY/PRINCIPAL FINDINGS: Here we describe a novel alignment-free method for quantifying the similarity of motifs using their PFMs by converting PFMs into k-mer vectors. The motifs could then be compared by measuring the similarity among their corresponding k-mer vectors. CONCLUSIONS/SIGNIFICANCE: We demonstrate that our method in general achieves similar performance or outperforms the existing methods for clustering motifs according to their binding preference and identifying similar motifs of transcription factors of the same family.

  7. 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...

  8. Signature splitting in 135Pr

    International Nuclear Information System (INIS)

    In-beam spectroscopic study of 135Pr was made using 91 MeV 120Sn(19F,4n) reaction. A strong negative parity proton band based on the h/sub 11/2-/ 1/2[550] configuration with α = -1/2 was observed. Possibly α = +1/2 unfavored band is observed. Also two positive parity proton bands are observed most likely based on the g/sub 7/2+/ 5/2[413] configurations with α = +-1/2. In all cases (except for the (π,α) = (-,+1/2) band) the backbending is caused by alignment of two h/sub 11/2-/ 9/2[514] quasi-neutrons. For the strongly decoupled π(-) bands the observed signature splitting decreases with increasing rotational frequency. The signature splitting of the positive parity bands increases with rotational frequency and then inverts above the backbending. This is interpreted to be caused by the quasi-neutrons, which drive the γ-deformation to the negative values. 18 refs., 6 figs

  9. Collider Signatures of Goldstone Bosons

    CERN Document Server

    Cheung, Kingman; Yuan, Tzu-Chiang

    2014-01-01

    Recently Weinberg suggested that Goldstone bosons arising from the spontaneous breakdown of some global hidden symmetries can interact weakly in the early Universe and account for a fraction of the effective number of neutrino species N_{eff}, which has been reported persistently 2\\sigma away from its expected value of three. In this work, we study in some details a number of experimental constraints on this interesting idea based on the simplest possibility of a global U(1), as studied by Weinberg. We work out the decay branching ratios of the associated light scalar field \\sigma and suggest a possible collider signature at the Large Hadron Collider (LHC). In some corners of the parameter space, the scalar field \\sigma can decay into a pair of pions with a branching ratio of order 10% while the rest is mostly a pair of Goldstone bosons. The collider signature would be gluon fusion into the standard model Higgs boson gg -> H followed by H -> \\sigma \\sigma -> (\\pi\\pi) (\\alpha\\alpha) where \\alpha is the Goldsto...

  10. Update on PIN or Signature

    Science.gov (United States)

    Matyas, Vashek

    We promised a year back some data on the experiment that we ran with chip and PIN. If you recall, it was the first phase that we reported on here last year, where we used the University bookstore, and two PIN pads, one with very solid privacy shielding, the other one without any. We ran 17 people through the first one, 15 people through the second one, and we also had the students do, about half of them forging the signature, half of them signing their own signature, on the back of the card that is used for purchasing books, or whatever.We had a second phase of the experiment, after long negotiations, and very complicated logistics, with a supermarket in Brno where we were able to do anything that we wanted through the experiment for five hours on the floor, with only the supermarket manager, the head of security, and the camera operators knowing about the experiment. So the shop assistants, the ground floor security, everybody basically on the floor, did not know about the experiment. That was one of the reasons why the supermarket, or management, agreed to take part, they wanted to control their own internal security procedures.

  11. Theoretical Characterizaiton of Visual Signatures

    Science.gov (United States)

    Kashinski, D. O.; Chase, G. M.; di Nallo, O. E.; Scales, A. N.; Vanderley, D. L.; Byrd, E. F. C.

    2015-05-01

    We are investigating the accuracy of theoretical models used to predict the visible, ultraviolet, and infrared spectra, as well as other properties, of product materials ejected from the muzzle of currently fielded systems. Recent advances in solid propellants has made the management of muzzle signature (flash) a principle issue in weapons development across the calibers. A priori prediction of the electromagnetic spectra of formulations will allow researchers to tailor blends that yield desired signatures and determine spectrographic detection ranges. Quantum chemistry methods at various levels of sophistication have been employed to optimize molecular geometries, compute unscaled vibrational frequencies, and determine the optical spectra of specific gas-phase species. Electronic excitations are being computed using Time Dependent Density Functional Theory (TD-DFT). A full statistical analysis and reliability assessment of computational results is currently underway. A comparison of theoretical results to experimental values found in the literature is used to assess any affects of functional choice and basis set on calculation accuracy. The status of this work will be presented at the conference. Work supported by the ARL, DoD HPCMP, and USMA.

  12. Narrow terahertz attenuation signatures in Bacillus thuringiensis.

    Science.gov (United States)

    Zhang, Weidong; Brown, Elliott R; Viveros, Leamon; Burris, Kellie P; Stewart, C Neal

    2014-10-01

    Terahertz absorption signatures from culture-cultivated Bacillus thuringiensis were measured with a THz photomixing spectrometer operating from 400 to 1200 GHz. We observe two distinct signatures centered at ∼955 and 1015 GHz, and attribute them to the optically coupled particle vibrational resonance (surface phonon-polariton) of Bacillus spores. This demonstrates the potential of the THz attenuation signatures as "fingerprints" for label-free biomolecular detection. PMID:23821459

  13. Cryptoschemes Based on New Signature Formation Mechanism

    Directory of Open Access Journals (Sweden)

    A.A.Moldovyan

    2006-12-01

    Full Text Available Several variants of new digital signature schemes (DSS based on the discrete logarithm and factorization problems have been proposed. Considered DSS are characterized in that a novel mechanism of the signature generation is used, in which two parameters of the (k,S or (R,S signature are defined after solving a system of two congruences. In the case of composite modulus additional restrictions conditions have been introduced for selection of the public key.

  14. Mediated Certificateless Signature without Random Oracles

    Directory of Open Access Journals (Sweden)

    Minghui Zheng

    2011-08-01

    Full Text Available It is worthwhile challenges to deal with the key escrow problem and key revocation in identity-based signatures. We first introduce the notion of security-mediated certificateless signature scheme and proves the scheme in the standard model. The mediated certificateless public key cryptography not only provides a fast revocation with fine granularity but also overcomes the key escrow property which exists in ID-based signature. The scheme is provably secure without random oracles.

  15. AN INSPECTION ON OFFLINE SIGNATURE AUTHENTICATION

    OpenAIRE

    Sapna Agrawal; Neelmani Verma

    2015-01-01

    In the era of emergent technology, security is that the foremost anxiety to avoid replicas and counterfeits. There are diverse Biometric systems that enable in personal identification, amongst those verification systems, one system is Signature Verification System. Signatures are substantiated discrimination on-line and offline systems. Every human being has their own writing style and hence their signature is used in the financial domain for identity verification. So it is necess...

  16. Short Signatures from Difficulty of Factorization Problem

    Directory of Open Access Journals (Sweden)

    Nikolay A. Moldovyan

    2009-01-01

    Full Text Available New ways are proposed to design short signature schemes based on difficulty of factorizing a composite number n that is a product of two large secret primes. The paper presents digital signature schemes in which the signature represents a pair of numbers (k,g and its length is reduced to 320~bits providing security of the RSA cryptosystem with 1024-bit modulus.

  17. Institute of Geophysics, Planetary Physics, and Signatures

    Data.gov (United States)

    Federal Laboratory Consortium — The Institute of Geophysics, Planetary Physics, and Signatures at Los Alamos National Laboratory is committed to promoting and supporting high quality, cutting-edge...

  18. On reliable discovery of molecular signatures

    Directory of Open Access Journals (Sweden)

    Björkegren Johan

    2009-01-01

    Full Text Available Abstract Background Molecular signatures are sets of genes, proteins, genetic variants or other variables that can be used as markers for a particular phenotype. Reliable signature discovery methods could yield valuable insight into cell biology and mechanisms of human disease. However, it is currently not clear how to control error rates such as the false discovery rate (FDR in signature discovery. Moreover, signatures for cancer gene expression have been shown to be unstable, that is, difficult to replicate in independent studies, casting doubts on their reliability. Results We demonstrate that with modern prediction methods, signatures that yield accurate predictions may still have a high FDR. Further, we show that even signatures with low FDR may fail to replicate in independent studies due to limited statistical power. Thus, neither stability nor predictive accuracy are relevant when FDR control is the primary goal. We therefore develop a general statistical hypothesis testing framework that for the first time provides FDR control for signature discovery. Our method is demonstrated to be correct in simulation studies. When applied to five cancer data sets, the method was able to discover molecular signatures with 5% FDR in three cases, while two data sets yielded no significant findings. Conclusion Our approach enables reliable discovery of molecular signatures from genome-wide data with current sample sizes. The statistical framework developed herein is potentially applicable to a wide range of prediction problems in bioinformatics.

  19. 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

  20. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  1. Tricksters Trot to America: Areal Distribution of Folklore Motifs

    Directory of Open Access Journals (Sweden)

    Yuri Berezkin

    2010-12-01

    Full Text Available The folklore Trickster is usually considered a universally known combination of features intrinsic to human nature. However, there are strong anomalies in the areal distribution of such a figure. Sub-Saharan Africa, North America (except for the Arctic, Northeast Asia and South American Chaco not only are the preferred zones of tricksters’ activity but also share some peculiar trickster motifs unknown in most of the other regions. The range of animals which play the role of tricksters is also restricted and not always easily explained, E.g. the Hare and Spider, known in both Africa and North America, are neither “mediators” between life and death (suggested by C. Lévi-Strauss for Coyote nor “really tricky” (“materialistic” hypothesis of M. Harris. The set of trickster motifs and the zoo- or anthropomorphic impersonations of the Trickster are independentvariables. The same episodes are easily linked to different tricksters while every trickster usually attracts episodes characteristic of a particular region. Though the original emergence of Trickster as a mental construct can indeed be rooted in human psychology (and where else?, the distribution of tricksters in folklore is discretionary and depends of many uncertain, i.e. chance, factors. The wide spread or lack of tricksters in certain cultural areas hardly reflect any fundamental differences in the psychology of inhabitants of these regions. The study of trickster motifs, just as of any other folklore motifs, helps us reconstruct possible historic links between populations. The African – North American links remain enigmatic (independent emergence is possible but slight historicallinks cannot be completely excluded but the parallels between (Western and Northeast Siberian – North American tricksters are almost certainly due to former cultural ties across Northern Asia. Another interesting case is the proliferation of tricksters with different zoomorphic and other identities

  2. 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

  3. Motif Discovery in Tissue-Specific Regulatory Sequences Using Directed Information

    Directory of Open Access Journals (Sweden)

    James Douglas Engel

    2007-12-01

    Full Text Available Motif discovery for the identification of functional regulatory elements underlying gene expression is a challenging problem. Sequence inspection often leads to discovery of novel motifs (including transcription factor sites with previously uncharacterized function in gene expression. Coupled with the complexity underlying tissue-specific gene expression, there are several motifs that are putatively responsible for expression in a certain cell type. This has important implications in understanding fundamental biological processes such as development and disease progression. In this work, we present an approach to the identification of motifs (not necessarily transcription factor sites and examine its application to some questions in current bioinformatics research. These motifs are seen to discriminate tissue-specific gene promoter or regulatory regions from those that are not tissue-specific. There are two main contributions of this work. Firstly, we propose the use of directed information for such classification constrained motif discovery, and then use the selected features with a support vector machine (SVM classifier to find the tissue specificity of any sequence of interest. Such analysis yields several novel interesting motifs that merit further experimental characterization. Furthermore, this approach leads to a principled framework for the prospective examination of any chosen motif to be discriminatory motif for a group of coexpressed/coregulated genes, thereby integrating sequence and expression perspectives. We hypothesize that the discovery of these motifs would enable the large-scale investigation for the tissue-specific regulatory role of any conserved sequence element identified from genome-wide studies.

  4. Motif Discovery in Tissue-Specific Regulatory Sequences Using Directed Information

    Directory of Open Access Journals (Sweden)

    States David

    2007-01-01

    Full Text Available Motif discovery for the identification of functional regulatory elements underlying gene expression is a challenging problem. Sequence inspection often leads to discovery of novel motifs (including transcription factor sites with previously uncharacterized function in gene expression. Coupled with the complexity underlying tissue-specific gene expression, there are several motifs that are putatively responsible for expression in a certain cell type. This has important implications in understanding fundamental biological processes such as development and disease progression. In this work, we present an approach to the identification of motifs (not necessarily transcription factor sites and examine its application to some questions in current bioinformatics research. These motifs are seen to discriminate tissue-specific gene promoter or regulatory regions from those that are not tissue-specific. There are two main contributions of this work. Firstly, we propose the use of directed information for such classification constrained motif discovery, and then use the selected features with a support vector machine (SVM classifier to find the tissue specificity of any sequence of interest. Such analysis yields several novel interesting motifs that merit further experimental characterization. Furthermore, this approach leads to a principled framework for the prospective examination of any chosen motif to be discriminatory motif for a group of coexpressed/coregulated genes, thereby integrating sequence and expression perspectives. We hypothesize that the discovery of these motifs would enable the large-scale investigation for the tissue-specific regulatory role of any conserved sequence element identified from genome-wide studies.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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...

  10. 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

  11. The Origin of Motif Families in Food Webs

    CERN Document Server

    Klaise, Janis

    2016-01-01

    Food webs have been found to exhibit remarkable motif profiles, patterns in the relative prevalences of all possible three-species sub-graphs, and this has been related to ecosystem properties such as stability and robustness. Analysing 46 food webs of various kinds, we find that most food webs fall into one of two distinct motif families. The separation between the families is well predicted by a global measure of hierarchical order in directed networks - trophic coherence. We find that trophic coherence is also a good predictor for the extent of omnivory, defined as the tendency of species to feed on multiple trophic levels. We compare our results to a network assembly model that admits tunable trophic coherence via a single free parameter. The model is able to generate food webs in either of the two families by varying this parameter, and correctly classifies almost all the food webs in our database. This establishes a link between global order and local preying patterns in food webs.

  12. Proline Rich Motifs as Drug Targets in Immune Mediated Disorders

    Directory of Open Access Journals (Sweden)

    Mythily Srinivasan

    2012-01-01

    Full Text Available The current version of the human immunome network consists of nearly 1400 interactions involving approximately 600 proteins. Intermolecular interactions mediated by proline-rich motifs (PRMs are observed in many facets of the immune response. The proline-rich regions are known to preferentially adopt a polyproline type II helical conformation, an extended structure that facilitates transient intermolecular interactions such as signal transduction, antigen recognition, cell-cell communication and cytoskeletal organization. The propensity of both the side chain and the backbone carbonyls of the polyproline type II helix to participate in the interface interaction makes it an excellent recognition motif. An advantage of such distinct chemical features is that the interactions can be discriminatory even in the absence of high affinities. Indeed, the immune response is mediated by well-orchestrated low-affinity short-duration intermolecular interactions. The proline-rich regions are predominantly localized in the solvent-exposed regions such as the loops, intrinsically disordered regions, or between domains that constitute the intermolecular interface. Peptide mimics of the PRM have been suggested as potential antagonists of intermolecular interactions. In this paper, we discuss novel PRM-mediated interactions in the human immunome that potentially serve as attractive targets for immunomodulation and drug development for inflammatory and autoimmune pathologies.

  13. Graph animals, subgraph sampling and motif search in large networks

    CERN Document Server

    Baskerville, Kim; Paczuski, Maya

    2007-01-01

    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 et al., 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 super-exponential). 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 TAP high throughput 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 anti-motifs (Z-scores <-10) when the null model is the...

  14. A motif for reversible nitric oxide interactions in metalloenzymes.

    Science.gov (United States)

    Zhang, Shiyu; Melzer, Marie M; Sen, S Nermin; Çelebi-Ölçüm, Nihan; Warren, Timothy H

    2016-07-01

    Nitric oxide (NO) participates in numerous biological processes, such as signalling in the respiratory system and vasodilation in the cardiovascular system. Many metal-mediated processes involve direct reaction of NO to form a metal-nitrosyl (M-NO), as occurs at the Fe(2+) centres of soluble guanylate cyclase or cytochrome c oxidase. However, some copper electron-transfer proteins that bear a type 1 Cu site (His2Cu-Cys) reversibly bind NO by an unknown motif. Here, we use model complexes of type 1 Cu sites based on tris(pyrazolyl)borate copper thiolates [Cu(II)]-SR to unravel the factors involved in NO reactivity. Addition of NO provides the fully characterized S-nitrosothiol adduct [Cu(I)](κ(1)-N(O)SR), which reversibly loses NO on purging with an inert gas. Computational analysis outlines a low-barrier pathway for the capture and release of NO. These findings suggest a new motif for reversible binding of NO at bioinorganic metal centres that can interconvert NO and RSNO molecular signals at copper sites. PMID:27325092

  15. Debit card competition: signature versus pin

    OpenAIRE

    Victor Lubasi

    2005-01-01

    This article explores costs and benefits of two types of debit card authorization methods—signature and PIN (personal identification number)—for merchants, consumers, and financial institutions. It also considers competition between signature- and PIN-based debit cards in the United States and looks at Canada's predominant usage of PIN-based debit cards.

  16. A Dark Matter Signature for Condensed Neutrinos

    OpenAIRE

    Morley, P. D.; Buettner, D. J.

    2016-01-01

    We derive the signature for condensed neutrino objects (CNOs) as the primary source of Dark Matter. Restricting our source data to minimize systematic errors, we find that by just using weak lensing data and Sunyaev-Zel'dovich data, that there may be a weak CNO signature.

  17. Does Social Work Have a Signature Pedagogy?

    Science.gov (United States)

    Earls Larrison, Tara; Korr, Wynne S.

    2013-01-01

    This article contributes to discourse on signature pedagogy by reconceptualizing how our pedagogies are understood and defined for social work education. We critique the view that field education is social work's signature pedagogy and consider what pedagogies are distinct about the teaching and learning of social work. Using Shulman's…

  18. Analysis of signature wrapping attacks and countermeasures

    DEFF Research Database (Denmark)

    Gajek, Sebastian; Jensen, Meiko; Liao, Lijun;

    2009-01-01

    In recent research it turned out that Boolean verification, of digital signatures in the context of WSSecurity, is likely to fail: If parts of a SOAP message, are signed and the signature verification applied to, the whole document returns true, then nevertheless the, document may have been signi......, that this solution is both efficient and secure. © 2009 IEEE....

  19. Redactable signatures for signed CDA Documents.

    Science.gov (United States)

    Wu, Zhen-Yu; Hsueh, Chih-Wen; Tsai, Cheng-Yu; Lai, Feipei; Lee, Hung-Chang; Chung, Yufang

    2012-06-01

    The Clinical Document Architecture, introduced by Health Level Seven, is a XML-based standard intending to specify the encoding, structure, and semantics of clinical documents for exchange. Since the clinical document is in XML form, its authenticity and integrity could be guaranteed by the use of the XML signature published by W3C. While a clinical document wants to conceal some personal or private information, the document needs to be redacted. It makes the signed signature of the original clinical document not be verified. The redactable signature is thus proposed to enable verification for the redacted document. Only a little research does the implementation of the redactable signature, and there still not exists an appropriate scheme for the clinical document. This paper will investigate the existing web-technologies and find a compact and applicable model to implement a suitable redactable signature for the clinical document viewer. PMID:21181244

  20. Robust Threshold Guillou-Quisquater Signature Scheme

    Institute of Scientific and Technical Information of China (English)

    WANG Hong; ZHANG Zhen-feng; FENG Deng-guo

    2005-01-01

    The deficiencies of the first threshold GuillouQuisquater signature scheme presented by Li-San Liu, ChengKang Chu and Wen-Guey Tzeng are analysised at first, and then a new threshold Guillou-Quisquater signature scheme is presented. The new scheme is unforgeable and robust against any adaptive adversary if the base Guillou-Quisquater signature scheme is unforgeable under the chosen message attack and computing the discrete logarithm modulo a prime is hard.This scheme can also achieve optimal resilience. However,the new scheme does not need the assumption that N is the product of two safe primes. The basic signature scheme underlying the new scheme is exactly Guillou-Quisquater signature scheme, and the additional strong computation assumption introduced by the first threshold Guillou-Quisquater scheme is weaken.

  1. An ECC-Based Blind Signature Scheme

    Directory of Open Access Journals (Sweden)

    Fuh-Gwo Jeng

    2010-08-01

    Full Text Available Cryptography is increasingly applied to the E-commerce world, especially to the untraceable payment system and the electronic voting system. Protocols for these systems strongly require the anonymous digital signature property, and thus a blind signature strategy is the answer to it. Chaum stated that every blind signature protocol should hold two fundamental properties, blindness and intractableness. All blind signature schemes proposed previously almost are based on the integer factorization problems, discrete logarithm problems, or the quadratic residues, which are shown by Lee et al. that none of the schemes is able to meet the two fundamental properties above. Therefore, an ECC-based blind signature scheme that possesses both the above properties is proposed in this paper.

  2. DIGITAL SIGNATURE IN THE WAY OF LAW

    Directory of Open Access Journals (Sweden)

    Ruya Samlı

    2013-01-01

    Full Text Available Signature can be defined as a person’s name or special signs that he/she writes when he/she wants to indicate he/she wrote or confirm that writing. A person signs many times in his/her life. A person’s signature that is used for thousands of times for many things from formal documents to exams has importance for that person. Especially, signing in legal operations is an operation that can build important results. If a person’s signature is imitated by another person, he/she can become beholden, donate his/her whole wealth, commits offences or do some judicial operations. Today, because many operations can be done with digital environments and internet, signature operation that provides identity validation must also be carried to digital environment. In this paper digital signature concept that is approved for this reason and its situation in international areas and Turkish laws are investigated.

  3. Signatures of mutational processes in human cancer

    Science.gov (United States)

    Alexandrov, Ludmil B.; Nik-Zainal, Serena; Wedge, David C.; Aparicio, Samuel A.J.R.; Behjati, Sam; Biankin, Andrew V.; Bignell, Graham R.; Bolli, Niccolo; Borg, Ake; Børresen-Dale, Anne-Lise; Boyault, Sandrine; Burkhardt, Birgit; Butler, Adam P.; Caldas, Carlos; Davies, Helen R.; Desmedt, Christine; Eils, Roland; Eyfjörd, Jórunn Erla; Foekens, John A.; Greaves, Mel; Hosoda, Fumie; Hutter, Barbara; Ilicic, Tomislav; Imbeaud, Sandrine; Imielinsk, Marcin; Jäger, Natalie; Jones, David T.W.; Jones, David; Knappskog, Stian; Kool, Marcel; Lakhani, Sunil R.; López-Otín, Carlos; Martin, Sancha; Munshi, Nikhil C.; Nakamura, Hiromi; Northcott, Paul A.; Pajic, Marina; Papaemmanuil, Elli; Paradiso, Angelo; Pearson, John V.; Puente, Xose S.; Raine, Keiran; Ramakrishna, Manasa; Richardson, Andrea L.; Richter, Julia; Rosenstiel, Philip; Schlesner, Matthias; Schumacher, Ton N.; Span, Paul N.; Teague, Jon W.; Totoki, Yasushi; Tutt, Andrew N.J.; Valdés-Mas, Rafael; van Buuren, Marit M.; van ’t Veer, Laura; Vincent-Salomon, Anne; Waddell, Nicola; Yates, Lucy R.; Zucman-Rossi, Jessica; Futreal, P. Andrew; McDermott, Ultan; Lichter, Peter; Meyerson, Matthew; Grimmond, Sean M.; Siebert, Reiner; Campo, Elías; Shibata, Tatsuhiro; Pfister, Stefan M.; Campbell, Peter J.; Stratton, Michael R.

    2013-01-01

    All cancers are caused by somatic mutations. However, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here, we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, kataegis, is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer with potential implications for understanding of cancer etiology, prevention and therapy. PMID:23945592

  4. An Approach to Shorten Digital Signature Length

    Directory of Open Access Journals (Sweden)

    Nikolay A. Moldovyan

    2006-12-01

    Full Text Available A new method is proposed to design short signature schemes based on difficulty of factorizing a composite number n=qr, where q and r are two large primes. Using the method new digital signature schemes (DSS with the 320-bit and 240-bit signature size are developed. The characteristic feature of the 240-bit signature DSS is the use of "three-level" verification equation. The (k,g signature corresponds to the H hash value and represents a pair of natural numbers having the size of 80 and 160~bits, respectively. The δ modulus is a prime number. The public key is the triple (α,β,p , where p=2n+1 is prime, β is the q order element modulo p,α is the γ order element modulo q. The private key is represented by the pair of two prime numbers (q, γ.

  5. Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections.

    Directory of Open Access Journals (Sweden)

    S Gnanakaran

    2011-09-01

    Full Text Available Here we have identified HIV-1 B clade Envelope (Env amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. To accomplish this, we compared thousands of sequences derived by single genome amplification from several hundred individuals that were sampled either early in infection or were chronically infected. Samples were divided at the outset into hypothesis-forming and validation sets, and we used phylogenetically corrected statistical strategies to identify signatures, systematically scanning all of Env. Signatures included single amino acids, glycosylation motifs, and multi-site patterns based on functional or structural groupings of amino acids. We identified signatures near the CCR5 co-receptor-binding region, near the CD4 binding site, and in the signal peptide and cytoplasmic domain, which may influence Env expression and processing. Two signatures patterns associated with transmission were particularly interesting. The first was the most statistically robust signature, located in position 12 in the signal peptide. The second was the loss of an N-linked glycosylation site at positions 413-415; the presence of this site has been recently found to be associated with escape from potent and broad neutralizing antibodies, consistent with enabling a common pathway for immune escape during chronic infection. Its recurrent loss in early infection suggests it may impact fitness at the time of transmission or during early viral expansion. The signature patterns we identified implicate Env expression levels in selection at viral transmission or in early expansion, and suggest that immune evasion patterns that recur in many individuals during chronic infection when antibodies are present can be selected against when the infection is being established prior to the adaptive immune response.

  6. Over-represented localized sequence motifs in ribosomal protein gene promoters of basal metazoans.

    Science.gov (United States)

    Perina, Drago; Korolija, Marina; Roller, Maša; Harcet, Matija; Jeličić, Branka; Mikoč, Andreja; Cetković, Helena

    2011-07-01

    Equimolecular presence of ribosomal proteins (RPs) in the cell is needed for ribosome assembly and is achieved by synchronized expression of ribosomal protein genes (RPGs) with promoters of similar strengths. Over-represented motifs of RPG promoter regions are identified as targets for specific transcription factors. Unlike RPs, those motifs are not conserved between mammals, drosophila, and yeast. We analyzed RPGs proximal promoter regions of three basal metazoans with sequenced genomes: sponge, cnidarian, and placozoan and found common features, such as 5'-terminal oligopyrimidine tracts and TATA-boxes. Furthermore, we identified over-represented motifs, some of which displayed the highest similarity to motifs abundant in human RPG promoters and not present in Drosophila or yeast. Our results indicate that humans over-represented motifs, as well as corresponding domains of transcription factors, were established very early in metazoan evolution. The fast evolving nature of RPGs regulatory network leads to formation of other, lineage specific, over-represented motifs. PMID:21457775

  7. Dissecting the chemical interactions and substrate structural signatures governing RNA polymerase II trigger loop closure by synthetic nucleic acid analogues

    DEFF Research Database (Denmark)

    Xu, Liang; Butler, Kyle Vincent; Chong, Jenny; Wengel, Jesper; Kool, Eric T; Wang, Dong

    2014-01-01

    The trigger loop (TL) of RNA polymerase II (Pol II) is a conserved structural motif that is crucial for Pol II catalytic activity and transcriptional fidelity. The TL remains in an inactive open conformation when the mismatched substrate is bound. In contrast, TL switches from an inactive open...... remains elusive. Here we employed synthetic nucleotide analogues as 'chemical mutation' tools coupling with α-amanitin transcription inhibition assay to systematically dissect the key chemical interactions and structural signatures governing the substrate-coupled TL closure in Saccharomyces cerevisiae Pol...

  8. SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data

    OpenAIRE

    DING, JUN; Hu, Haiyan; Li, Xiaoman

    2013-01-01

    The identification of transcription factor binding motifs is important for the study of gene transcriptional regulation. The chromatin immunoprecipitation (ChIP), followed by massive parallel sequencing (ChIP-seq) experiments, provides an unprecedented opportunity to discover binding motifs. Computational methods have been developed to identify motifs from ChIP-seq data, while at the same time encountering several problems. For example, existing methods are often not scalable to the large num...

  9. Phosphopeptide interactions with BRCA1 BRCT domains: More than just a motif

    OpenAIRE

    Wu, Qian; Jubb, Harry; Blundell, Tom L.

    2015-01-01

    BRCA1 BRCT domains function as phosphoprotein-binding modules for recognition of the phosphory-lated protein-sequence motif pSXXF. While the motif interaction interface provides strong anchor points for binding, protein regions outside the motif have recently been found to be important for binding affinity. In this review, we compare the available structural data for BRCA1 BRCT domains in complex with phosphopeptides in order to gain a more complete understanding of the interaction betw...

  10. An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance

    OpenAIRE

    Vinga Susana; Casimiro Ana C; Freitas Ana T; Oliveira Arlindo L

    2008-01-01

    Abstract Background Motif finding algorithms have developed in their ability to use computationally efficient methods to detect patterns in biological sequences. However the posterior classification of the output still suffers from some limitations, which makes it difficult to assess the biological significance of the motifs found. Previous work has highlighted the existence of positional bias of motifs in the DNA sequences, which might indicate not only that the pattern is important, but als...

  11. Vampirism today : the change of the vampire motif from the gothic novel to today's fantasy literature

    OpenAIRE

    2009-01-01

    This thesis examins the change of the vampire motif throughout time. How have vampires and their clichés changed and why? Starting with a brief examination of the 'classical' litarary vampire, I mainly focus on contemporary fantasy literature by discussing recent works of vampire fiction. The adaptation of the vampire motif in role-playing games will as well be discussed as the effects the vampire film had on the motif.

  12. 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...

  13. 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...

  14. 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...

  15. Belief-propagation algorithm and the Ising model on networks with arbitrary distributions of motifs

    OpenAIRE

    Yoon, S; Goltsev, A. V.; Dorogovtsev, S. N.; Mendes, J. F. F.

    2011-01-01

    We generalize the belief-propagation algorithm to sparse random networks with arbitrary distributions of motifs (triangles, loops, etc.). Each vertex in these networks belongs to a given set of motifs (generalization of the configuration model). These networks can be treated as sparse uncorrelated hypergraphs in which hyperedges represent motifs. Here a hypergraph is a generalization of a graph, where a hyperedge can connect any number of vertices. These uncorrelated hypergraphs are tree-like...

  16. 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.

  17. Transition from winnerless competition to synchronization in time-delayed neuronal motifs

    Science.gov (United States)

    Zhang, X.; Li, P. J.; Wu, F. P.; Wu, W. J.; Jiang, M.; Chen, L.; Qi, G. X.; Huang, H. B.

    2012-03-01

    The dynamics of brain functional motifs are studied. It is shown that different rhythms can occur in the motifs when time delay is taken into account. These rhythms include synchronization, winnerless competition (WLC) and "two plus one" (TPO). The main discovery is that the transition from WLC to synchronization can be induced simply by time delay. It is also concluded that some medium time delay is needed to achieve WLC in the realistic case. The motifs composed of heterogeneous neurons are also considered.

  18. 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

  19. Maximizing biomarker discovery by minimizing gene signatures

    Directory of Open Access Journals (Sweden)

    Chang Chang

    2011-12-01

    Full Text Available Abstract Background The use of gene signatures can potentially be of considerable value in the field of clinical diagnosis. However, gene signatures defined with different methods can be quite various even when applied the same disease and the same endpoint. Previous studies have shown that the correct selection of subsets of genes from microarray data is key for the accurate classification of disease phenotypes, and a number of methods have been proposed for the purpose. However, these methods refine the subsets by only considering each single feature, and they do not confirm the association between the genes identified in each gene signature and the phenotype of the disease. We proposed an innovative new method termed Minimize Feature's Size (MFS based on multiple level similarity analyses and association between the genes and disease for breast cancer endpoints by comparing classifier models generated from the second phase of MicroArray Quality Control (MAQC-II, trying to develop effective meta-analysis strategies to transform the MAQC-II signatures into a robust and reliable set of biomarker for clinical applications. Results We analyzed the similarity of the multiple gene signatures in an endpoint and between the two endpoints of breast cancer at probe and gene levels, the results indicate that disease-related genes can be preferably selected as the components of gene signature, and that the gene signatures for the two endpoints could be interchangeable. The minimized signatures were built at probe level by using MFS for each endpoint. By applying the approach, we generated a much smaller set of gene signature with the similar predictive power compared with those gene signatures from MAQC-II. Conclusions Our results indicate that gene signatures of both large and small sizes could perform equally well in clinical applications. Besides, consistency and biological significances can be detected among different gene signatures, reflecting the

  20. Multifractal signatures of infectious diseases.

    Science.gov (United States)

    Holdsworth, Amber M; Kevlahan, Nicholas K-R; Earn, David J D

    2012-09-01

    Incidence of infection time-series data for the childhood diseases measles, chicken pox, rubella and whooping cough are described in the language of multifractals. We explore the potential of using the wavelet transform maximum modulus (WTMM) method to characterize the multiscale structure of the observed time series and of simulated data generated by the stochastic susceptible-exposed-infectious-recovered (SEIR) epidemic model. The singularity spectra of the observed time series suggest that each disease is characterized by a unique multifractal signature, which distinguishes that particular disease from the others. The wavelet scaling functions confirm that the time series of measles, rubella and whooping cough are clearly multifractal, while chicken pox has a more monofractal structure in time. The stochastic SEIR epidemic model is unable to reproduce the qualitative singularity structure of the reported incidence data: it is too smooth and does not appear to have a multifractal singularity structure. The precise reasons for the failure of the SEIR epidemic model to reproduce the correct multiscale structure of the reported incidence data remain unclear. PMID:22442094

  1. Sequential dynamics in the motif of excitatory coupled elements

    Science.gov (United States)

    Korotkov, Alexander G.; Kazakov, Alexey O.; Osipov, Grigory V.

    2015-11-01

    In this article a new model of motif (small ensemble) of neuron-like elements is proposed. It is built with the use of the generalized Lotka-Volterra model with excitatory couplings. The main motivation for this work comes from the problems of neuroscience where excitatory couplings are proved to be the predominant type of interaction between neurons of the brain. In this paper it is shown that there are two modes depending on the type of coupling between the elements: the mode with a stable heteroclinic cycle and the mode with a stable limit cycle. Our second goal is to examine the chaotic dynamics of the generalized three-dimensional Lotka-Volterra model.

  2. μXRF analysis of decoration motifs on Majolica pottery

    International Nuclear Information System (INIS)

    μXRF analysis of decoration motifs on Majolica pottery in fragments corresponding to several Majolica types was carried out using an spectrometer comprising a low power Mo X-ray tube and a elliptic-shape concentration lens with a 60 um spot. Both surface scanning and spot measurements were carried a out, allowing the qualitative identification of the inorganic pigments used for the surface painting decoration and the quantitative analysis of the main glaze composition. The absence of interference signal arising from the excitation on the underlying paste when analysing thin-lead glazing was evaluated, allowing ensuring the suitable of the analytical procedures. A distinction was found between different types of majolica by the composition of the lead tin glaze enamel and by the presence of other elements in the blue, black and orange decoration

  3. RNA Sociology: Group Behavioral Motifs of RNA Consortia

    Directory of Open Access Journals (Sweden)

    Guenther Witzany

    2014-11-01

    Full Text Available RNA sociology investigates the behavioral motifs of RNA consortia from the social science perspective. Besides the self-folding of RNAs into single stem loop structures, group building of such stem loops results in a variety of essential agents that are highly active in regulatory processes in cellular and non-cellular life. RNA stem loop self-folding and group building do not depend solely on sequence syntax; more important are their contextual (functional needs. Also, evolutionary processes seem to occur through RNA stem loop consortia that may act as a complement. This means the whole entity functions only if all participating parts are coordinated, although the complementary building parts originally evolved for different functions. If complementary groups, such as rRNAs and tRNAs, are placed together in selective pressure contexts, new evolutionary features may emerge. Evolution initiated by competent agents in natural genome editing clearly contrasts with statistical error replication narratives.

  4. Study on online community user motif using web usage mining

    Science.gov (United States)

    Alphy, Meera; Sharma, Ajay

    2016-04-01

    The Web usage mining is the application of data mining, which is used to extract useful information from the online community. The World Wide Web contains at least 4.73 billion pages according to Indexed Web and it contains at least 228.52 million pages according Dutch Indexed web on 6th august 2015, Thursday. It’s difficult to get needed data from these billions of web pages in World Wide Web. Here is the importance of web usage mining. Personalizing the search engine helps the web user to identify the most used data in an easy way. It reduces the time consumption; automatic site search and automatic restore the useful sites. This study represents the old techniques to latest techniques used in pattern discovery and analysis in web usage mining from 1996 to 2015. Analyzing user motif helps in the improvement of business, e-commerce, personalisation and improvement of websites.

  5. Viroid Intercellular Trafficking: RNA Motifs, Cellular Factors and Broad Impacts

    Directory of Open Access Journals (Sweden)

    Ryuta Takeda

    2009-09-01

    Full Text Available Viroids are noncoding RNAs that infect plants. In order to establish systemic infection, these RNAs must traffic from an initially infected host cell into neighboring cells and ultimately throughout a whole plant. Recent studies have identified structural motifs in a viroid that are required for trafficking, enabling further studies on the mechanisms of their function. Some cellular proteins interact with viroids in vivo and may play a role in viroid trafficking, which can now be directly tested by using a virus-induced gene silencing system that functions efficiently in plant species from which these factors were identified. This review discusses these recent advances, unanswered questions and the use of viroid infection as an highly productive model to elucidate mechanisms of RNA trafficking that is of broad biological significance.

  6. Ecosystem engineers and geomorphological signatures in landscapes

    Science.gov (United States)

    Jones, Clive G.

    2012-07-01

    Biogeomorphologists study the roles of biota in landscape formation and decay. Ecologists interested in ecosystem engineering study environmental change caused by biota and the consequences for the engineer, other organisms, and ecological processes. The interface is geomorphological change, an interface both are aware of but study somewhat independently and differently. Interaction and integration among the two fields is the goal of this special issue. Here I take an ecological perspective of geomorphological change caused by ecosystem engineers in patches within landscapes that I hope can help facilitate this goal. I ask the following general questions: When will an ecosystem engineering species create a geomorphological signature in a landscape? What, in qualitative terms, is such a signature? How can the signature be estimated and how long will it last? What engineer attributes and ecological factors will determine signature change? What creates complications? How do the answers inform whether or not life leaves a geomorphological signature? To attempt answers, I develop a provisional, general theory of ecosystem engineering signatures that draws on and integrates a geomorphological foundation of balance between formation and decay; landscape patch dynamics; a general framework for ecosystem engineering; and empirical studies. I treat a landscape engineering signature as the balance of rates of formation (F) and rates of decay (D) across patches whose ratio value (F/D) can be transformed (> 1), intermediate (1) or untransformed (leaves a geomorphological signature, using this to contrast my approach with biogeomorphology, and asking what a hypothetical analysis of signature patterns across many engineer species/landscape combinations might imply for the interface of ecology and biogeomorphology.

  7. Reduction of a Ship's Magnetic Field Signatures

    CERN Document Server

    Holmes, John

    2008-01-01

    Decreasing the magnetic field signature of a naval vessel will reduce its susceptibility to detonating naval influence mines and the probability of a submarine being detected by underwater barriers and maritime patrol aircraft. Both passive and active techniques for reducing the magnetic signatures produced by a vessel's ferromagnetism, roll-induced eddy currents, corrosion-related sources, and stray fields are presented. Mathematical models of simple hull shapes are used to predict the levels of signature reduction that might be achieved through the use of alternate construction materials. Al

  8. DIGITAL SIGNATURE IN THE WAY OF LAW

    OpenAIRE

    Ruya Samlı

    2013-01-01

    Signature can be defined as a person’s name or special signs that he/she writes when he/she wants to indicate he/she wrote or confirm that writing. A person signs many times in his/her life. A person’s signature that is used for thousands of times for many things from formal documents to exams has importance for that person. Especially, signing in legal operations is an operation that can build important results. If a person’s signature is imitated by another person, he/she can be...

  9. Arbitrated quantum signature with an untrusted arbitrator

    Science.gov (United States)

    Yang, Yu-Guang; Zhou, Zheng; Teng, Yi-Wei; Wen, Qiao-Yan

    2011-02-01

    In an arbitrated signature scheme, all communications involve a so called arbitrator who has access to the contents of the messages. The security of most arbitrated signature schemes depends heavily on the trustworthiness of the arbitrators. In this paper we show how to construct an arbitrated quantum signature protocol of classical messages with an untrusted arbitrator. Its security is analyzed and it is proved to be secure even if the arbitrator is compromised. In addition, the proposed protocol does not require a direct quantum link between any two communicating users, which is an appealing advantage in the implementation of a practical quantum distributed communication network.

  10. Improved Quantum Signature Scheme with Weak Arbitrator

    Science.gov (United States)

    Su, Qi; Li, Wen-Min

    2013-09-01

    In this paper, we find a man-in-the-middle attack on the quantum signature scheme with a weak arbitrator (Luo et al., Int. J. Theor. Phys., 51:2135, 2012). In that scheme, the authors proposed a quantum signature based on quantum one way function which contains both verifying the signer phase and verifying the signed message phase. However, after our analysis we will show that Eve can adopt different strategies in respective phases to forge the signature without being detected. Then we present an improved scheme to increase the security.

  11. Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

    Directory of Open Access Journals (Sweden)

    Vassilev Boris

    2010-04-01

    Full Text Available Abstract Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94% appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1 a dimer interface motif found in voltage-gated chloride channels, (2 a proton transfer motif found in heme-copper oxidases, and (3 a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

  12. An Improved Proxy Multi-Signature, Multi-Proxy Signature and Multi-Proxy Multi-Signature Scheme

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    2011-08-01

    Full Text Available Zhou’s proxy multi-signature scheme was a safe and effective scheme, but this scheme was not safety enough. In this work, security analysis was given to the scheme and results showed that the scheme was very easy aggressed by the forgery attack. The paper proposed that any attacker can sign some certain unauthorized messages after the attacker knows a valid signature, and any original signer ally with his proxy signer can forge any unauthorized messages. Then, the paper gave two kinds of inside attacks and outside attacks to the scheme correspondingly. Finally this paper proposed a new improved proxy multi-signature, multi-proxy signature and multi-proxy multi-signature schemes which based on the difficulty of the discrete logarithm problem (DLP. With verifying all the signers’ public keys, the improved schemes can resist lots of outsider attack and insider attack. The validity of the new scheme can be verified, and they are secure signature schemes.

  13. Isotopic signatures by bulk analyses

    International Nuclear Information System (INIS)

    Los Alamos National Laboratory has developed a series of measurement techniques for identification of nuclear signatures by analyzing bulk samples. Two specific applications for isotopic fingerprinting to identify the origin of anthropogenic radioactivity in bulk samples are presented. The first example is the analyses of environmental samples collected in the US Arctic to determine the impact of dumping of radionuclides in this polar region. Analyses of sediment and biota samples indicate that for the areas sampled the anthropogenic radionuclide content of sediments was predominantly the result of the deposition of global fallout. The anthropogenic radionuclide concentrations in fish, birds and mammals were very low. It can be surmised that marine food chains are presently not significantly affected. The second example is isotopic fingerprinting of water and sediment samples from the Rocky Flats Facility (RFP). The largest source of anthropogenic radioactivity presently affecting surface-waters at RFP is the sediments that are currently residing in the holding ponds. One gram of sediment from a holding pond contains approximately 50 times more plutonium than 1 liter of water from the pond. Essentially 100% of the uranium in Ponds A-1 and A-2 originated as depleted uranium. The largest source of radioactivity in the terminal Ponds A-4, B-5 and C-2 was naturally occurring uranium and its decay product radium. The uranium concentrations in the waters collected from the terminal ponds contained 0.05% or less of the interim standard calculated derived concentration guide for uranium in waters available to the public. All of the radioactivity observed in soil, sediment and water samples collected at RFP was naturally occurring, the result of processes at RFP or the result of global fallout. No extraneous anthropogenic alpha, beta or gamma activities were detected. The plutonium concentrations in Pond C-2 appear to vary seasonally

  14. ACCRETING CIRCUMPLANETARY DISKS: OBSERVATIONAL SIGNATURES

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Zhaohuan, E-mail: zhzhu@astro.princeton.edu [Department of Astrophysical Sciences, 4 Ivy Lane, Peyton Hall, Princeton University, Princeton, NJ 08544 (United States)

    2015-01-20

    I calculate the spectral energy distributions of accreting circumplanetary disks using atmospheric radiative transfer models. Circumplanetary disks only accreting at 10{sup –10} M {sub ☉} yr{sup –1} around a 1 M{sub J} planet can be brighter than the planet itself. A moderately accreting circumplanetary disk ( M-dot ∼10{sup −8} M{sub ⊙} yr{sup −1}; enough to form a 10 M{sub J} planet within 1 Myr) around a 1 M{sub J} planet has a maximum temperature of ∼2000 K, and at near-infrared wavelengths (J, H, K bands), this disk is as bright as a late-M-type brown dwarf or a 10 M{sub J} planet with a ''hot start''. To use direct imaging to find the accretion disks around low-mass planets (e.g., 1 M{sub J} ) and distinguish them from brown dwarfs or hot high-mass planets, it is crucial to obtain photometry at mid-infrared bands (L', M, N bands) because the emission from circumplanetary disks falls off more slowly toward longer wavelengths than those of brown dwarfs or planets. If young planets have strong magnetic fields (≳100 G), fields may truncate slowly accreting circumplanetary disks ( M-dot ≲10{sup −9} M{sub ⊙} yr{sup −1}) and lead to magnetospheric accretion, which can provide additional accretion signatures, such as UV/optical excess from the accretion shock and line emission.

  15. Signature Region of Interest using Auto cropping

    CERN Document Server

    Al-Mahadeen, Bassam; AlTarawneh, Islam H

    2010-01-01

    A new approach for signature region of interest pre-processing was presented. It used new auto cropping preparation on the basis of the image content, where the intensity value of pixel is the source of cropping. This approach provides both the possibility of improving the performance of security systems based on signature images, and also the ability to use only the region of interest of the used image to suit layout design of biometric systems. Underlying the approach is a novel segmentation method which identifies the exact region of foreground of signature for feature extraction usage. Evaluation results of this approach shows encouraging prospects by eliminating the need for false region isolating, reduces the time cost associated with signature false points detection, and addresses enhancement issues. A further contribution of this paper is an automated cropping stage in bio-secure based systems.

  16. 5 CFR 850.106 - Electronic signatures.

    Science.gov (United States)

    2010-01-01

    ... 850.106 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL SERVICE REGULATIONS... patterns, and voice recognition; (2) Cryptographic control methods, including— (i) Shared symmetric key cryptography; (ii) Public/private key (asymmetric) cryptography, also known as digital signatures; (3)...

  17. Threshold Ring Signature Scheme Based on TPM

    Institute of Scientific and Technical Information of China (English)

    Gong Bei; Jiang Wei; Lin Li; Li Yu; Zhang Xing

    2012-01-01

    The conventional ring signature schemes cannot address the scenario where the rank of members of the ring needs to be distinguished, for example, in electronically commerce application. To solve this problem, we presented a Trusted Platform Module (TPM)-based threshold ring signature schen. Employing a reliable secret Share Distribution Center (SDC), the proposed approach can authenticate the TPM-based identity rank of members of the ring but not track a specific member's identity. A subset including t members with the same identity rank is built. With the signing cooperation of t members of the subset, the ring signature based on Chinese remainder theorem is generated. We proved the anonymity and unforgeability of the proposed scheme and compared it with the threshold ring signature based on Lagrange interpolation polynomial. Our scheme is relatively simpler to calculate.

  18. Probabilistic Model for Dynamic Signature Verification System

    Directory of Open Access Journals (Sweden)

    Chai Tong Yuen

    2011-11-01

    Full Text Available This study has proposed the algorithm for signature verification system using dynamic parameters of the signature: pen pressure, velocity and position. The system is proposed to read, analyze and verify the signatures from the SUSig online database. Firstly, the testing and reference samples will have to be normalized, re-sampled and smoothed through pre-processing stage. In verification stage, the difference between reference and testing signatures will be calculated based on the proposed thresholded standard deviation method. A probabilistic acceptance model has been designed to enhance the performance of the verification system. The proposed algorithm has reported False Rejection Rate (FRR of 14.8% and False Acceptance Rate (FAR of 2.64%. Meanwhile, the classification rate of the system is around 97%.

  19. Electronic Signatures for Public Procurement across Europe

    Science.gov (United States)

    Ølnes, Jon; Andresen, Anette; Arbia, Stefano; Ernst, Markus; Hagen, Martin; Klein, Stephan; Manca, Giovanni; Rossi, Adriano; Schipplick, Frank; Tatti, Daniele; Wessolowski, Gesa; Windheuser, Jan

    The PEPPOL (Pan-European Public Procurement On-Line) project is a large scale pilot under the CIP programme of the EU, exploring electronic public procurement in a unified European market. An important element is interoperability of electronic signatures across borders, identified today as a major obstacle to cross-border procurement. PEPPOL will address use of signatures in procurement processes, in particular tendering but also post-award processes like orders and invoices. Signature policies, i.e. quality requirements and requirements on information captured in the signing process, will be developed. This as well as technical interoperability of e-signatures across Europe will finally be piloted in demonstrators starting late 2009 or early 2010.

  20. Secure quantum signatures using insecure quantum channels

    Science.gov (United States)

    Amiri, Ryan; Wallden, Petros; Kent, Adrian; Andersson, Erika

    2016-03-01

    Digital signatures are widely used in modern communication to guarantee authenticity and transferability of messages. The security of currently used classical schemes relies on computational assumptions. We present a quantum signature scheme that does not require trusted quantum channels. We prove that it is unconditionally secure against the most general coherent attacks, and show that it requires the transmission of significantly fewer quantum states than previous schemes. We also show that the quantum channel noise threshold for our scheme is less strict than for distilling a secure key using quantum key distribution. This shows that "direct" quantum signature schemes can be preferable to signature schemes relying on secret shared keys generated using quantum key distribution.

  1. Construction of a Three-Dimensional Motif Dictionary for Protein Structural Data Mining

    Science.gov (United States)

    Hiroaki, Kato; Tadokoro, Tetsuo; Miyata, Hiroyuki; Chikamatsu, Shin-Ichi; Takahashi, Yoshimasa; Abe, Hidetsugu

    With the rapidly increasing number of proteins of which three-dimensional (3D) structures are known, the protein structure database is one of the key elements in many attempts being made to derive the knowledge of structure-function relationships of proteins. In this work, the authors have developed a software tool to assist in constructing the 3D protein motif dictionary that is closely related to the PROSITE sequence motif database. In the PROSITE, a structural feature called motif is described by a sequence pattern of amino acid residues with the regular expression defined in the database. The present system allows us to automatically find the related sites for all the 3D protein structures taken from a protein structure database such as the Protein Data Bank (PDB), and to make a dictionary of the 3D motifs related to the PROSITE sequence motif patterns. A computational trial was carried out for a subset of the PDB's structure data file. The structural feature analysis resulted with the tool showed that there are many different 3D motif patterns but having a particular PROSITE sequence pattern. For this reason, the authors also tried to classify the 3D motif patterns into several groups on the basis of distance similarity matrix, and to determine a representative pattern for each group in preparing the dictionary. The usefulness of the additional approach for preparing the 3D motif dictionary is also discussed with an illustrative example.

  2. 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

  3. Dynamic consequences of mutating the typical HPGG motif of apocytochrome b5 revealed by computer simulation

    Institute of Scientific and Technical Information of China (English)

    Ying Wu Lin; Tian Lei Ying; Li Fu Liao

    2009-01-01

    Apecytochrome b5 with a typical heme-binding motif of HPGC,and its variants with mutated motifs,GPGG,GPGH,HVGG,and HPGP,have been subjected to molecular dynamics simulation.Comparison of the dynamic consequences has revealed the crucial role of HPGG in assembling the heme group of cytochrome b5 and in modulating protein structure,property and function.

  4. MOMFER: A Search Engine of Thompson's Motif-Index of Folk Literature

    NARCIS (Netherlands)

    Karsdorp, F.; Meulen, M. van der; Meder, Th.; Bosch, A.P.J. van den

    2015-01-01

    More than fifty years after the first edition of Thompson's seminal Motif-Indexof Folk Literature, we present an online search engine tailored to fully disclose the index digitally. This search engine, called MOMFER, greatly enhances the searchability of the Motif-Index and provides exciting new way

  5. Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

    Directory of Open Access Journals (Sweden)

    Down Thomas A

    2010-09-01

    Full Text Available Abstract Background DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predicted TFBS" but the large majority of these are proven by chromatin immunoprecipitation and high throughput sequencing (ChIP-seq not to be biological transcription factor binding sites ("empirical TFBS". We hypothesize that DNA methylation at conserved consensus motifs prevents promiscuous or disorderly transcription factor binding. Results Using genome-wide methylation maps of the human heart and sperm, we found that all conserved consensus motifs as well as the subset of those that reside outside CpG islands have an aggregate profile of hyper-methylation. In contrast, empirical TFBS with conserved consensus motifs have a profile of hypo-methylation. 40% of empirical TFBS with conserved consensus motifs resided in CpG islands whereas only 7% of all conserved consensus motifs were in CpG islands. Finally we further identified a minority subset of TF whose profiles are either hypo-methylated or neutral at their respective conserved consensus motifs implicating that these TF may be responsible for establishing or maintaining an un-methylated DNA state, or whose binding is not regulated by DNA methylation. Conclusions Our analysis supports the hypothesis that at least for a subset of TF, empirical binding to conserved consensus motifs genome-wide may be controlled by DNA methylation.

  6. Genome adaptations of a tripartite motif protein for retroviral defense in cattle and sheep

    Science.gov (United States)

    Tripartite motif (TRIM) genes encode proteins composed of RING, B-box, and coiled coil motif domains. Primate TRIM5' has been shown to be a primary determinant of retroviral host cell range restriction in primates. TRIM5 restriction was originally thought to be a primate-specific defense mechanism...

  7. Electronic Seal Stamping Based on Group Signature

    OpenAIRE

    Girija Srikanth

    2011-01-01

    This paper describes a new electronic official seal stamping based on Group Signature, USB Key. Bill/Contract in E-commerce must be seal stamped to gain tamper proof and non-repudiation. The seal stamping control is designed based on the certificate-based public key. This technique is more efficient for generating and verifying individual/group signatures in terms of computational efforts and communication costs. Web page electronic seal-stamping system is implemented which has been adopted b...

  8. Persistence of social signatures in human communication

    OpenAIRE

    Saramäki, Jari; Leicht, E. A.; López, Eduardo; Roberts, Sam G. B.; Reed-Tsochas, Felix; Robin I M Dunbar

    2014-01-01

    We combine cell phone data with survey responses to show that a person’s social signature, as we call the pattern of their interactions with different friends and family members, is remarkably robust. People focus a high proportion of their communication efforts on a small number of individuals, and this behavior persists even when there are changes in the identity of the individuals involved. Although social signatures vary between individuals, a given individual appears to retain a specific...

  9. Mutations in the K+ channel signature sequence.

    OpenAIRE

    Heginbotham, L; Lu, Z; Abramson, T; MacKinnon, R

    1994-01-01

    Potassium channels share a highly conserved stretch of eight amino acids, a K+ channel signature sequence. The conserved sequence falls within the previously defined P-region of voltage-activated K+ channels. In this study we investigate the effect of mutations in the signature sequence of the Shaker channel on K+ selectivity determined under bi-ionic conditions. Nonconservative substitutions of two threonine residues and the tyrosine residue leave selectivity intact. In contrast, mutations a...

  10. Damping signatures in future neutrino oscillation experiments

    OpenAIRE

    Blennow, Mattias; Ohlsson, Tommy; Winter, Walter

    2005-01-01

    We discuss the phenomenology of damping signatures in the neutrino oscillation probabilities, where either the oscillating terms or the probabilities can be damped. This approach is a possibility for tests of damping effects in future neutrino oscillation experiments, where we mainly focus on reactor and long-baseline experiments. We extensively motivate different damping signatures due to small corrections by neutrino decoherence, neutrino decay, oscillations into sterile neutrinos, or other...

  11. Prediction of soil effects on GPR signatures

    OpenAIRE

    Rhebergen, J.B.; Lensen, H.A.; Wijk, C.V. van; Hendrickx, J.M.H.; Dam, R.; Borchers, B.

    2004-01-01

    In previous work we have shown that GPR signatures are affected by soil texture and soil water content. In this contribution we will use a three dimensional electromagnetic model and a hydrological soil model to explore in more detail the relationships between GPR signatures, soil physical conditions and GPR detection performance. First, we will use the HYDRUS2D hydrological model to calculate a soil water content distribution around a land-mine. This model has been verified against measured ...

  12. Computing negentropy based signatures for texture recognition

    OpenAIRE

    Daniela COLTUC; Laurentiu FRANGU; Ana-Elena LUNGU

    2007-01-01

    The proposed method aims to provide a new tool for texture recognition. For this purpose, a set of texture samples are decomposed by using the FastICA algorithm and characterized by a negentropy based signature. In order to do recognition, the texture signatures are compared by means of Minkowski distance. The recognition rates, computed for a set of 320 texture samples, show a medium recognition accuracy and the method may be further improved.

  13. SS-IDS: Statistical Signature Based IDS

    OpenAIRE

    Gupta, Payas; Raïssi, Chedy; Dray, Gérard; Poncelet, Pascal; Brissaud, Johan

    2009-01-01

    Security of web servers has become a sensitive subject today. Prediction of normal and abnormal request is problematic due to large number of false alarms in many anomaly based Intrusion Detection Systems(IDS). SS-IDS derives automatical ly the parameter profiles from the analyzed data thereby generating the Statistical Signatures. Statistical Signatures are based on modeling of normal requests and their distribution value without explicit intervention. Several attributes are used to calculate...

  14. Kinematics of Signature Writing in Healthy Aging*

    OpenAIRE

    Caligiuri, Michael P.; Kim, Chi; Landy, Kelly M.

    2014-01-01

    Forensic document examiners (FDE) called upon to distinguish a genuine from a forged signature of an elderly person are often required to consider the question of age-related deterioration and whether the available exemplars reliably capture the natural effects of aging of the original writer. An understanding of the statistical relationship between advanced age and handwriting movements can reduce the uncertainty that may exist in an examiner’s approach to questioned signatures formed by eld...

  15. 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

  16. 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

  17. 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.

  18. RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes.

    Science.gov (United States)

    Contreras-Moreira, Bruno; Castro-Mondragon, Jaime A; Rioualen, Claire; Cantalapiedra, Carlos P; van Helden, Jacques

    2016-01-01

    The plant-dedicated mirror of the Regulatory Sequence Analysis Tools (RSAT, http://plants.rsat.eu ) offers specialized options for researchers dealing with plant transcriptional regulation. The website contains whole-sequenced genomes from species regularly updated from Ensembl Plants and other sources (currently 40), and supports an array of tasks frequently required for the analysis of regulatory sequences, such as retrieving upstream sequences, motif discovery, motif comparison, and pattern matching. RSAT::Plants also integrates the footprintDB collection of DNA motifs. This protocol explains step-by-step how to discover DNA motifs in regulatory regions of clusters of co-expressed genes in plants. It also explains how to empirically control the significance of the result, and how to associate the discovered motifs with putative binding factors. PMID:27557774

  19. 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

  20. Bioinformatics Study of Cancer-Related Mutations within p53 Phosphorylation Site Motifs

    Directory of Open Access Journals (Sweden)

    Xiaona Ji

    2014-07-01

    Full Text Available p53 protein has about thirty phosphorylation sites located at the N- and C-termini and in the core domain. The phosphorylation sites are relatively less mutated than other residues in p53. To understand why and how p53 phosphorylation sites are rarely mutated in human cancer, using a bioinformatics approaches, we examined the phosphorylation site and its nearby flanking residues, focusing on the consensus phosphorylation motif pattern, amino-acid correlations within the phosphorylation motifs, the propensity of structural disorder of the phosphorylation motifs, and cancer mutations observed within the phosphorylation motifs. Many p53 phosphorylation sites are targets for several kinases. The phosphorylation sites match 17 consensus sequence motifs out of the 29 classified. In addition to proline, which is common in kinase specificity-determining sites, we found high propensity of acidic residues to be adjacent to phosphorylation sites. Analysis of human cancer mutations in the phosphorylation motifs revealed that motifs with adjacent acidic residues generally have fewer mutations, in contrast to phosphorylation sites near proline residues. p53 phosphorylation motifs are mostly disordered. However, human cancer mutations within phosphorylation motifs tend to decrease the disorder propensity. Our results suggest that combination of acidic residues Asp and Glu with phosphorylation sites provide charge redundancy which may safe guard against loss-of-function mutations, and that the natively disordered nature of p53 phosphorylation motifs may help reduce mutational damage. Our results further suggest that engineering acidic amino acids adjacent to potential phosphorylation sites could be a p53 gene therapy strategy.

  1. MMW, IR, and SAM signature collection

    Science.gov (United States)

    Reichstetter, Fred; Ward, Mary E.

    2002-08-01

    During the development of smart weapon's seeker/sensors, it is imperative to collect high quality signatures of the targets the system is intended to engage. These signatures are used to support algorithm development so the system can find and engage the targets of interest in the specific kill area on the target. Englin AFB FL is the AF development center for munitions; and in support of the development effort, the 46th Test Wing (46 TW) has initiated significant improvements in collection capabilities for signatures in the MMW, Infrared and Seismic, Acoustic and Magnetic (SAM) spectrum. Additionally, the Joint Munitions Test and Evaluation program office maintains a fleet of foreign ground vehicle targets used for such signature collection including items such as tanks, SCUD missile launchers, air defense units such as SA-06, SA-8, SA-13, and associated ground support trucks and general purpose vehicles. The major test facility includes a 300 ft tower used for mounting the instrumentation suite that currently includes, 10, 35 and 94 GHz MMW and 2-5(mu) and 8-12(mu) IR instrumentation systems. This facility has undergone major improvements in terms of background signature reduction, construction of a high bay building to house the turntable on which the targets are mounted, and an additional in- ground stationary turntable primarily for IR signature collection. Our experience using this facility to collect signatures for the smart weapons development community has confirmed a significant improvement in quality and efficiency. The need for the stationary turntable signature collection capability was driven by the requirements of the IR community who are interested in collecting signatures in clutter. This tends to be contrary to the MMW community that desires minimum background clutter. The resulting location, adjacent to the MMW tower, allows variations in the type and amount of clutter background that could be incorporated and also provides maximum utilization of

  2. A Formal Model for the Security of Proxy Signature Schemes

    Institute of Scientific and Technical Information of China (English)

    GU Chun-xiang; ZHU Yue-fei; ZHANG Ya-juan

    2005-01-01

    This paper provides theoretical foundations for the secure proxy signature primitive. We present a formal model for the security of proxy signature schemes, which defines the capabilities of the adversary and the security goals to capture which mean for a proxy signature scheme to be secure. Then, we present an example of proxy signature scheme that can be proven secure in the standard model.

  3. The genomic signature of human rhinoviruses A, B and C.

    Science.gov (United States)

    Megremis, Spyridon; Demetriou, Philippos; Makrinioti, Heidi; Manoussaki, Alkistis E; Papadopoulos, Nikolaos G

    2012-01-01

    Human rhinoviruses are single stranded positive sense RNA viruses that are presented in more than 50% of acute upper respiratory tract infections. Despite extensive studies on the genetic diversity of the virus, little is known about the forces driving it. In order to explain this diversity, many research groups have focused on protein sequence requirements for viable, functional and transmissible virus but have missed out an important aspect of viral evolution such as the genomic ontology of the virus. This study presents for the first time the genomic signature of 111 fully sequenced HRV strains from all three groups HRV-A, HRV-B and HRV-C. We observed an HRV genome tendency to eliminate CpG and UpA dinucleotides, coupling with over-representation of UpG and CpA. We propose a specific mechanism which describes how rapid changes in the HRV genomic sequence can take place under the strict control of conservation of the polypeptide backbone. Moreover, the distribution of the observed under- and over-represented dinucleotides along the HRV genome is presented. Distance matrice tables based on CpG and UpA odds ratios were constructed and viewed as heatmaps and distance trees. None of the suppressions can be attributed to codon usage or in RNA secondary structure requirements. Since viral recognition is dependent on RNA motifs rich in CpG and UpA, it is possible that the overall described genome evolution mechanism acts in order to protect the virus from host recognition. PMID:23028561

  4. The signature sequence of voltage-gated potassium channels projects into the external vestibule.

    Science.gov (United States)

    Aiyar, J; Rizzi, J P; Gutman, G A; Chandy, K G

    1996-12-01

    A highly conserved motif, GYGD, contributes to the formation of the ion selectivity filter in voltage-gated K+ channels and is thought to interact with the scorpion toxin residue, Lys27. By probing the pore of the Kv1.3 channel with synthetic kaliotoxin-Lys27 mutants, each containing a non-natural lysine analog of a different length, and using mutant cycle analysis, we determined the spatial locations of Tyr400 and Asp402 in the GYGD motif, relative to His404 located at the base of the outer vestibule. Our data indicate that the terminal amines of the shorter Lys27 analogs lie close to His404 and to Asp402, while Lys27 itself interacts with Tyr400. Based on these data, we developed a molecular model of this region of the channel. The junction between the outer vestibule and the pore is defined by a ring ( approximately 8-9-A diameter) formed from alternating Asp402 and His404 residues. Tyr400 lies 4-6 A deeper into the pore, and its interaction with kaliotoxin-Lys27 is in competition with K+ ions. Studies with dimeric Kv1.3 constructs suggest that two Tyr400 residues in the tetramer are sufficient to bind K+ ions. Thus, at least part of the K+ channel signature sequence extends into a shallow trough at the center of a wide external vestibule. PMID:8940091

  5. Fusion of Multiple Matchers using SVM for Offline Signature Identification

    CERN Document Server

    Kisku, Dakshina Ranjan; Sing, Jamuna Kanta

    2010-01-01

    This paper uses Support Vector Machines (SVM) to fuse multiple classifiers for an offline signature system. From the signature images, global and local features are extracted and the signatures are verified with the help of Gaussian empirical rule, Euclidean and Mahalanobis distance based classifiers. SVM is used to fuse matching scores of these matchers. Finally, recognition of query signatures is done by comparing it with all signatures of the database. The proposed system is tested on a signature database contains 5400 offline signatures of 600 individuals and the results are found to be promising.

  6. Untraceable partially blind signature based on DLOG problem

    Institute of Scientific and Technical Information of China (English)

    HUANG Zheng(黄征); CHEN Ke-fei(陈克非); KOU Wei-dong(寇卫东)

    2004-01-01

    This paper proposes a new untraceable Partially Blind Signature scheme which is a cross between the traditional signature scheme and the blind signature scheme. In this proposed scheme, the message M that the signer signed can be divided into two parts. The first part can be known to the signer (like that in the traditional signature scheme) while the other part cannot be known to the signer (like that in the blind signature scheme). After having signed M, the signer cannot determine if he has made the signature of M except through the part that he knows. We draw ideas from Brands' "Restricted Blind Signature" to solve the Untraceable Partially Blind Signature problem. Our scheme is a probabilistic signature scheme and the security of our Untraceable Partially Blind Signature scheme relies on the difficulty of computing discrete logarithm.

  7. Untraceable partially blind signature based on DLOG problem.

    Science.gov (United States)

    Huang, Zheng; Chen, Ke-fei; Kou, Wei-dong

    2004-01-01

    This paper proposes a new untraceable Partially Blind Signature scheme which is a cross between the traditional signature scheme and the blind signature scheme. In this proposed scheme, the message M that the signer signed can be divided into two parts. The first part can be known to the signer (like that in the traditional signature scheme) while the other part cannot be known to the signer (like that in the blind signature scheme). After having signed M, the signer cannot determine if he has made the signature of M except through the part that he knows. We draw ideas from Brands' "Restricted Blind Signature" to solve the Untraceable Partially Blind Signature problem. Our scheme is a probabilistic signature scheme and the security of our Untraceable Partially Blind Signature scheme relies on the difficulty of computing discrete logarithm. PMID:14663850

  8. On ULF Signatures of Lightning Discharges

    Science.gov (United States)

    Bösinger, T.; Shalimov, S. L.

    2008-06-01

    Recent works on magnetic signatures due to distant lightning discharges are reviewed. Emphasis is laid on magnetic signatures in the ULF range (in the old definition from less than 1 mHz up to 1 Hz), that is in the frequency range below the Schumann resonance. These signatures are known to be of importance for the excitation of the ionospheric Alfvén resonator (IAR) which works only at night time conditions. This emphasizes the difference between night and day time ULF signatures of lightning. The IAR forms a link between the atmosphere and magnetosphere. Similarities and differences of this link in the VLF (Trimpi effect) and ULF range are worked out. A search for a unique signature of sprite-associated positive cloud-to-ground (+CG) lightning discharges ended with a negative result. In this context, however, a new model of lightning-associated induced mesospheric currents was built. Depending on mesospheric condition it can produce magnetic signatures in the entire frequency range from VLF, ELF to ULF. In the latter case it can explain signatures known as the Ultra Slow Tail of +CG lightning discharges. A current problem on the magnetic background noise intensity has been solved by taking more seriously the contribution of +CG lightning discharges to the overall background noise. Their low occurrence rate is more than compensated by their large and long lasting continuing currents. By superposed epoch analysis it could be shown that the ULF response to -CG is one to two orders smaller that in case of +CG with similar peak current values of the return stroke.

  9. Does Twitter trigger bursts in signature collections?

    Directory of Open Access Journals (Sweden)

    Rui Yamaguchi

    Full Text Available INTRODUCTION: The quantification of social media impacts on societal and political events is a difficult undertaking. The Japanese Society of Oriental Medicine started a signature-collecting campaign to oppose a medical policy of the Government Revitalization Unit to exclude a traditional Japanese medicine, "Kampo," from the public insurance system. The signature count showed a series of aberrant bursts from November 26 to 29, 2009. In the same interval, the number of messages on Twitter including the keywords "Signature" and "Kampo," increased abruptly. Moreover, the number of messages on an Internet forum that discussed the policy and called for signatures showed a train of spikes. METHODS AND FINDINGS: In order to estimate the contributions of social media, we developed a statistical model with state-space modeling framework that distinguishes the contributions of multiple social media in time-series of collected public opinions. We applied the model to the time-series of signature counts of the campaign and quantified contributions of two social media, i.e., Twitter and an Internet forum, by the estimation. We found that a considerable portion (78% of the signatures was affected from either of the social media throughout the campaign and the Twitter effect (26% was smaller than the Forum effect (52% in total, although Twitter probably triggered the initial two bursts of signatures. Comparisons of the estimated profiles of the both effects suggested distinctions between the social media in terms of sustainable impact of messages or tweets. Twitter shows messages on various topics on a time-line; newer messages push out older ones. Twitter may diminish the impact of messages that are tweeted intermittently. CONCLUSIONS: The quantification of social media impacts is beneficial to better understand people's tendency and may promote developing strategies to engage public opinions effectively. Our proposed method is a promising tool to explore

  10. Motif mediated protein-protein interactions as drug targets.

    Science.gov (United States)

    Corbi-Verge, Carles; Kim, Philip M

    2016-01-01

    Protein-protein interactions (PPI) are involved in virtually every cellular process and thus represent an attractive target for therapeutic interventions. A significant number of protein interactions are frequently formed between globular domains and short linear peptide motifs (DMI). Targeting these DMIs has proven challenging and classical approaches to inhibiting such interactions with small molecules have had limited success. However, recent new approaches have led to the discovery of potent inhibitors, some of them, such as Obatoclax, ABT-199, AEG-40826 and SAH-p53-8 are likely to become approved drugs. These novel inhibitors belong to a wide range of different molecule classes, ranging from small molecules to peptidomimetics and biologicals. This article reviews the main reasons for limited success in targeting PPIs, discusses how successful approaches overcome these obstacles to discovery promising inhibitors for human protein double minute 2 (HDM2), B-cell lymphoma 2 (Bcl-2), X-linked inhibitor of apoptosis protein (XIAP), and provides a summary of the promising approaches currently in development that indicate the future potential of PPI inhibitors in drug discovery. PMID:26936767

  11. The bridge: suggestions about the meaning of a pictorial motif

    Directory of Open Access Journals (Sweden)

    Omar Calabrese

    2011-12-01

    Full Text Available Developing research begun at the Warburg Institute in 1983, this paper reflects on the construction of meaning in a work of art, through the analysis of the bridge’s function in painting. It tries to reply to some objections the author received there from Gombrich, about the chance of finding a stable content in the configuration of the bridge. Hence, the study reconsiders the concept of ‘motif’ applied to this structure. In a semiotic perspective a motif is partially independent as regards to a single textual organization, because it has a mobile and migrant feature. However, it is also partially flexible as it depends upon the same organization. The inquiry shows that bridge’s internal structure corresponds to the category of a ‘junction’, with two opposite items, ‘conjunction’ and ‘disjunction’. The development of this theoretical object can be carried out also by figures that are not ‘bridges’, in the natural sense of the word. Furthermore, its meaning does not depend upon the number of examples we can find but only upon their relevance for constructing a ‘grammar of cases’. Differently from the traditional iconographical approach, but also from panofskian iconology, the analysis moves not only towards the simple or complex content of a figure but also towards its description.

  12. 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.

  13. Sulfur-induced structural motifs on copper and gold surfaces

    Science.gov (United States)

    Walen, Holly

    The interaction of sulfur with copper and gold surfaces plays a fundamental role in important phenomena that include coarsening of surface nanostructures, and self-assembly of alkanethiols. Here, we identify and analyze unique sulfur-induced structural motifs observed on the low-index surfaces of these two metals. We seek out these structures in an effort to better understand the fundamental interactions between these metals and sulfur that lends to the stability and favorability of metal-sulfur complexes vs. chemisorbed atomic sulfur. We choose very specific conditions: very low temperature (5 K), and very low sulfur coverage (≤ 0.1 monolayer). In this region of temperature-coverage space, which has not been examined previously for these adsorbate-metal systems, the effects of individual interactions between metals and sulfur are most apparent and can be assessed extensively with the aid of theory and modeling. Furthermore, at this temperature diffusion is minimal and relatively-mobile species can be isolated, and at low coverage the structures observed are not consumed by an extended reconstruction. The primary experimental technique is scanning tunneling microscopy (STM). The experimental observations presented here---made under identical conditions---together with extensive DFT analyses, allow comparisons and insights into factors that favor the existence of metal-sulfur complexes, vs. chemisorbed atomic sulfur, on metal terraces. We believe this data will be instrumental in better understanding the complex phenomena occurring between the surfaces of coinage metals and sulfur.

  14. Network motifs that stabilize the hybrid epithelial/mesenchymal phenotype

    Science.gov (United States)

    Jolly, Mohit Kumar; Jia, Dongya; Tripathi, Satyendra; Hanash, Samir; Mani, Sendurai; Ben-Jacob, Eshel; Levine, Herbert

    Epithelial to Mesenchymal Transition (EMT) and its reverse - MET - are hallmarks of cancer metastasis. While transitioning between E and M phenotypes, cells can also attain a hybrid epithelial/mesenchymal (E/M) phenotype that enables collective cell migration as a cluster of Circulating Tumor Cells (CTCs). These clusters can form 50-times more tumors than individually migrating CTCs, underlining their importance in metastasis. However, this hybrid E/M phenotype has been hypothesized to be only a transient one that is attained en route EMT. Here, via mathematically modeling, we identify certain `phenotypic stability factors' that couple with the core three-way decision-making circuit (miR-200/ZEB) and can maintain or stabilize the hybrid E/M phenotype. Further, we show experimentally that this phenotype can be maintained stably at a single-cell level, and knockdown of these factors impairs collective cell migration. We also show that these factors enable the association of hybrid E/M with high stemness or tumor-initiating potential. Finally, based on these factors, we deduce specific network motifs that can maintain the E/M phenotype. Our framework can be used to elucidate the effect of other players in regulating cellular plasticity during metastasis. This work was supported by NSF PHY-1427654 (Center for Theoretical Biological Physics) and the CPRIT Scholar in Cancer Research of the State of Texas at Rice University.

  15. Tyrosine motifs are required for prestin basolateral membrane targeting

    Directory of Open Access Journals (Sweden)

    Yifan Zhang

    2015-01-01

    Full Text Available Prestin is targeted to the lateral wall of outer hair cells (OHCs where its electromotility is critical for cochlear amplification. Using MDCK cells as a model system for polarized epithelial sorting, we demonstrate that prestin uses tyrosine residues, in a YXXΦ motif, to target the basolateral surface. Both Y520 and Y667 are important for basolateral targeting of prestin. Mutation of these residues to glutamine or alanine resulted in retention within the Golgi and delayed egress from the Golgi in Y667Q. Basolateral targeting is restored upon mutation to phenylalanine suggesting the importance of a phenol ring in the tyrosine side chain. We also demonstrate that prestin targeting to the basolateral surface is dependent on AP1B (μ1B, and that prestin uses transferrin containing early endosomes in its passage from the Golgi to the basolateral plasma membrane. The presence of AP1B (μ1B in OHCs, and parallels between prestin targeting to the basolateral surface of OHCs and polarized epithelial cells suggest that outer hair cells resemble polarized epithelia rather than neurons in this important phenotypic measure.

  16. Characteristics of Constrained Handwritten Signatures: An Experimental Investigation

    OpenAIRE

    Donato, Impedovo; Pirlo, Giuseppe; Rizzi, Fabrizio

    2015-01-01

    Handwritten signatures are considered one of the most useful biometric traits for personal verification. In the networked society, in which a multitude of different devices can be used for signature acquisition, specific research is still needed to determine the extent to which features of an input signature depend on the characteristics of the signature apposition process. In this paper an experimental investigation was carried out on constrained signatures, which were acquired using writing...

  17. 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

  18. Recurrent motifs as resonant attractor states in the narrative field: a testable model of archetype.

    Science.gov (United States)

    Goodwyn, Erik

    2013-06-01

    At the most basic level, archetypes represented Jung's attempt to explain the phenomenon of recurrent myths and folktale motifs (Jung 1956, 1959, para. 99). But the archetype remains controversial as an explanation of recurrent motifs, as the existence of recurrent motifs does not prove that archetypes exist. Thus, the challenge for contemporary archetype theory is not merely to demonstrate that recurrent motifs exist, since that is not disputed, but to demonstrate that archetypes exist and cause recurrent motifs. The present paper proposes a new model which is unlike others in that it postulates how the archetype creates resonant motifs. This model necessarily clarifies and adapts some of Jung's seminal ideas on archetype in order to provide a working framework grounded in contemporary practice and methodologies. For the first time, a model of archetype is proposed that can be validated on empirical, rather than theoretical grounds. This is achieved by linking the archetype to the hard data of recurrent motifs rather than academic trends in other fields. PMID:23750942

  19. MODA: an efficient algorithm for network motif discovery in biological networks.

    Science.gov (United States)

    Omidi, Saeed; Schreiber, Falk; Masoudi-Nejad, Ali

    2009-10-01

    In recent years, interest has been growing in the study of complex networks. Since Erdös and Rényi (1960) proposed their random graph model about 50 years ago, many researchers have investigated and shaped this field. Many indicators have been proposed to assess the global features of networks. Recently, an active research area has developed in studying local features named motifs as the building blocks of networks. Unfortunately, network motif discovery is a computationally hard problem and finding rather large motifs (larger than 8 nodes) by means of current algorithms is impractical as it demands too much computational effort. In this paper, we present a new algorithm (MODA) that incorporates techniques such as a pattern growth approach for extracting larger motifs efficiently. We have tested our algorithm and found it able to identify larger motifs with more than 8 nodes more efficiently than most of the current state-of-the-art motif discovery algorithms. While most of the algorithms rely on induced subgraphs as motifs of the networks, MODA is able to extract both induced and non-induced subgraphs simultaneously. The MODA source code is freely available at: http://LBB.ut.ac.ir/Download/LBBsoft/MODA/ PMID:20154426

  20. 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.

  1. Trend Motif: A Graph Mining Approach for Analysis of Dynamic Complex Networks

    Energy Technology Data Exchange (ETDEWEB)

    Jin, R; McCallen, S; Almaas, E

    2007-05-28

    Complex networks have been used successfully in scientific disciplines ranging from sociology to microbiology to describe systems of interacting units. Until recently, studies of complex networks have mainly focused on their network topology. However, in many real world applications, the edges and vertices have associated attributes that are frequently represented as vertex or edge weights. Furthermore, these weights are often not static, instead changing with time and forming a time series. Hence, to fully understand the dynamics of the complex network, we have to consider both network topology and related time series data. In this work, we propose a motif mining approach to identify trend motifs for such purposes. Simply stated, a trend motif describes a recurring subgraph where each of its vertices or edges displays similar dynamics over a userdefined period. Given this, each trend motif occurrence can help reveal significant events in a complex system; frequent trend motifs may aid in uncovering dynamic rules of change for the system, and the distribution of trend motifs may characterize the global dynamics of the system. Here, we have developed efficient mining algorithms to extract trend motifs. Our experimental validation using three disparate empirical datasets, ranging from the stock market, world trade, to a protein interaction network, has demonstrated the efficiency and effectiveness of our approach.

  2. 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

  3. Cytokine signature profiles in acquired aplastic anemia and myelodysplastic syndromes

    OpenAIRE

    Feng, Xingmin; Scheinberg, Phillip; Wu, Colin O.; Samsel, Leigh; Nunez, Olga; Prince, Courtney; Ganetzky, Rebecca D.; McCoy, J. Philip; Maciejewski, Jaroslaw P.; Young, Neal S.

    2010-01-01

    Although aplastic anemia and myelodysplasia have been extensively investigated, little is known about their circulating cytokine patterns. We compared plasma soluble cytokines in 33 aplastic anemia, 57 myelodysplasia patients, and 48 healthy controls. High levels of thrombopoietin and granulocyte colony-stimulating factor, with low levels of CD40 ligand, chemokine (C-X-C motif) ligand 5, chemokine (C-C motif) ligand 5, chemokine (C-X-C motif) ligand 11, epidermal growth factor, vascular endot...

  4. The signature package on Witt spaces

    CERN Document Server

    Albin, Pierre; Mazzeo, Rafe; Piazza, Paolo

    2011-01-01

    In this paper we prove a variety of results about the signature operator on Witt spaces. First, we give a parametrix construction for the signature operator on any compact, oriented, stratified pseudomanifold X which satisfies the Witt condition. This construction, which is inductive over the `depth' of the singularity, is then used to show that the signature operator is essentially self-adjoint and has discrete spectrum of finite multiplicity, so that its index -- the analytic signature of X -- is well-defined. This provides an alternate approach to some well-known results due to Cheeger. We then prove some new results. By coupling this parametrix construction to a C*_r\\Gamma-Mishchenko bundle associated to any Galois covering of X with covering group \\Gamma, we prove analogues of the same analytic results, from which it follows that one may define an analytic signature index class as an element of the K-theory of C*_r\\Gamma. We go on to establish in this setting and for this class the full range of conclusi...

  5. Observational signatures of binary supermassive black holes

    International Nuclear Information System (INIS)

    Observations indicate that most massive galaxies contain a supermassive black hole, and theoretical studies suggest that when such galaxies have a major merger, the central black holes will form a binary and eventually coalesce. Here we discuss two spectral signatures of such binaries that may help distinguish them from ordinary active galactic nuclei. These signatures are expected when the mass ratio between the holes is not extreme and the system is fed by a circumbinary disk. One such signature is a notch in the thermal continuum that has been predicted by other authors; we point out that it should be accompanied by a spectral revival at shorter wavelengths and also discuss its dependence on binary properties such as mass, mass ratio, and separation. In particular, we note that the wavelength λ n at which the notch occurs depends on these three parameters in such a way as to make the number of systems displaying these notches ∝λn16/3; longer wavelength searches are therefore strongly favored. A second signature, first discussed here, is hard X-ray emission with a Wien-like spectrum at a characteristic temperature ∼100 keV produced by Compton cooling of the shock generated when streams from the circumbinary disk hit the accretion disks around the individual black holes. We investigate the observability of both signatures. The hard X-ray signal may be particularly valuable as it can provide an indicator of black hole merger a few decades in advance of the event.

  6. Aliasing Errours in Parallel Signature Analyzers

    Institute of Scientific and Technical Information of China (English)

    闵应骅; YashwantK.Malaiya

    1990-01-01

    A Linear Feedback Shift Register(LFSR)can be used to compress test response data as a Signature Analyzer(SA).Parallel Signature Analyzers(PSAs)implemented as multiple input LFSRs are faster and require less hardware overhead than Serial Signature Analyzers(SSAs) for compacting test response data for Built-In Self-Test(BIST)in IC of boare-testing environments.However,the SAs are prone to aliasing errors because of some specific types of error patterns.An alias is a faulty output signature that is identical to the fault-free signature.A penetrating analysis of detecting capability of SAs depends strongly on mathematical manipulations,instead of being aware of some special cases of examples.In addition,the analysis should not be restricted to a particular structure of LFSR,but be appropriate for various structures of LFSRs.This paper presents necessary and sufficient conditions for aliasing errors based on a complete mathematical description of various types of SAs.An LFSR reconfiguration scheme is suggested which will prevent any aliasing double errors.Such a prevention cannot be obtained by any extension of an LFSR.

  7. Calculated NWIS signatures for enriched uranium metal

    International Nuclear Information System (INIS)

    Nuclear Weapons Identification System (NWIS) signatures have been calculated using a Monte Carlo transport code for measurement configurations of a 252Cf source, detectors, and a uranium metal casting. NWIS signatures consist of a wide variety of time-and frequency-analysis signatures such as the time distribution of neutrons after californium fission, the time distribution of counts in a detector after a previous count, the number of times n pulses occur in a time interval, and various frequency-analysis signatures, such as auto-power and cross-power spectral densities, coherences, and a ratio of spectral densities. This ratio is independent of detection efficiency. The analysis presented here, using the MCNP-DSP code, evaluates the applicability of this method for measurement of the 235U content of 19-kg castings of depleted uranium and uranium with enrichments of 20, 40, 60, 80, 90, and 93.2 wt % 235U. The dependence of the wide variety of NWIS signatures on 235U content and possible configurations of a measurement system are presented. These preliminary calculations indicate short measurement times. Additional calculations are being performed to optimize the source-detector-moderator-casting configuration for the shortest measurement time. Although the NWIS method was developed for nuclear weapons identification, the development of a small processor now allows it to be also applied in a practical way to subcriticality measurements, nuclear fuel process monitoring and qualitative nondestructive assay of special nuclear material

  8. Identification of a putative nuclear export signal motif in human NANOG homeobox domain

    International Nuclear Information System (INIS)

    Highlights: ► We found the putative nuclear export signal motif within human NANOG homeodomain. ► Leucine-rich residues are important for human NANOG homeodomain nuclear export. ► CRM1-specific inhibitor LMB blocked the potent human NANOG NES-mediated nuclear export. -- Abstract: NANOG is a homeobox-containing transcription factor that plays an important role in pluripotent stem cells and tumorigenic cells. To understand how nuclear localization of human NANOG is regulated, the NANOG sequence was examined and a leucine-rich nuclear export signal (NES) motif (125MQELSNILNL134) was found in the homeodomain (HD). To functionally validate the putative NES motif, deletion and site-directed mutants were fused to an EGFP expression vector and transfected into COS-7 cells, and the localization of the proteins was examined. While hNANOG HD exclusively localized to the nucleus, a mutant with both NLSs deleted and only the putative NES motif contained (hNANOG HD-ΔNLSs) was predominantly cytoplasmic, as observed by nucleo/cytoplasmic fractionation and Western blot analysis as well as confocal microscopy. Furthermore, site-directed mutagenesis of the putative NES motif in a partial hNANOG HD only containing either one of the two NLS motifs led to localization in the nucleus, suggesting that the NES motif may play a functional role in nuclear export. Furthermore, CRM1-specific nuclear export inhibitor LMB blocked the hNANOG potent NES-mediated export, suggesting that the leucine-rich motif may function in CRM1-mediated nuclear export of hNANOG. Collectively, a NES motif is present in the hNANOG HD and may be functionally involved in CRM1-mediated nuclear export pathway.

  9. 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.

  10. 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

  11. Miz-1 activates gene expression via a novel consensus DNA binding motif.

    Directory of Open Access Journals (Sweden)

    Bonnie L Barrilleaux

    Full Text Available The transcription factor Miz-1 can either activate or repress gene expression in concert with binding partners including the Myc oncoprotein. The genomic binding of Miz-1 includes both core promoters and more distal sites, but the preferred DNA binding motif of Miz-1 has been unclear. We used a high-throughput in vitro technique, Bind-n-Seq, to identify two Miz-1 consensus DNA binding motif sequences--ATCGGTAATC and ATCGAT (Mizm1 and Mizm2--bound by full-length Miz-1 and its zinc finger domain, respectively. We validated these sequences directly as high affinity Miz-1 binding motifs. Competition assays using mutant probes indicated that the binding affinity of Miz-1 for Mizm1 and Mizm2 is highly sequence-specific. Miz-1 strongly activates gene expression through the motifs in a Myc-independent manner. MEME-ChIP analysis of Miz-1 ChIP-seq data in two different cell types reveals a long motif with a central core sequence highly similar to the Mizm1 motif identified by Bind-n-Seq, validating the in vivo relevance of the findings. Miz-1 ChIP-seq peaks containing the long motif are predominantly located outside of proximal promoter regions, in contrast to peaks without the motif, which are highly concentrated within 1.5 kb of the nearest transcription start site. Overall, our results indicate that Miz-1 may be directed in vivo to the novel motif sequences we have identified, where it can recruit its specific binding partners to control gene expression and ultimately regulate cell fate.

  12. 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...

  13. An examination of quantitative methods for Forensic Signature Analysis and the admissibility of signature verification system as legal evidence.

    OpenAIRE

    Chatzisterkotis, Thomas

    2015-01-01

    The experiments described in this thesis deal with handwriting characteristics which are involved in the production of forged and genuine signatures and complexity of signatures. The objectives of this study were (1) to provide sufficient details on which of the signature characteristics are easier to forge, (2) to investigate the capabilities of the signature complexity formula given by Found et al. based on a different signature database provided by University of Kent. This database includes ...

  14. ELM 2016--data update and new functionality of the eukaryotic linear motif resource.

    Science.gov (United States)

    Dinkel, Holger; Van Roey, Kim; Michael, Sushama; Kumar, Manjeet; Uyar, Bora; Altenberg, Brigitte; Milchevskaya, Vladislava; Schneider, Melanie; Kühn, Helen; Behrendt, Annika; Dahl, Sophie Luise; Damerell, Victoria; Diebel, Sandra; Kalman, Sara; Klein, Steffen; Knudsen, Arne C; Mäder, Christina; Merrill, Sabina; Staudt, Angelina; Thiel, Vera; Welti, Lukas; Davey, Norman E; Diella, Francesca; Gibson, Toby J

    2016-01-01

    The Eukaryotic Linear Motif (ELM) resource (http://elm.eu.org) is a manually curated database of short linear motifs (SLiMs). In this update, we present the latest additions to this resource, along with more improvements to the web interface. ELM 2016 contains more than 240 different motif classes with over 2700 experimentally validated instances, manually curated from more than 2400 scientific publications. In addition, more data have been made available as individually searchable pages and are downloadable in various formats. PMID:26615199

  15. 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...

  16. Stochastic Resonance in Neuronal Network Motifs with Ornstein-Uhlenbeck Colored Noise

    Directory of Open Access Journals (Sweden)

    Xuyang Lou

    2014-01-01

    Full Text Available We consider here the effect of the Ornstein-Uhlenbeck colored noise on the stochastic resonance of the feed-forward-loop (FFL network motif. The FFL motif is modeled through the FitzHugh-Nagumo neuron model as well as the chemical coupling. Our results show that the noise intensity and the correlation time of the noise process serve as the control parameters, which have great impacts on the stochastic dynamics of the FFL motif. We find that, with a proper choice of noise intensities and the correlation time of the noise process, the signal-to-noise ratio (SNR can display more than one peak.

  17. FTZ-Factor1 and Fushi tarazu interact via conserved nuclear receptor and coactivator motifs

    OpenAIRE

    Schwartz, Carol J.E.; Sampson, Heidi M.; Hlousek, Daniela; Percival-Smith, Anthony; Copeland, John W.R.; Simmonds, Andrew J.; Krause, Henry M.

    2001-01-01

    To activate transcription, most nuclear receptor proteins require coactivators that bind to their ligand-binding domains (LBDs). The Drosophila FTZ-Factor1 (FTZ-F1) protein is a conserved member of the nuclear receptor superfamily, but was previously thought to lack an AF2 motif, a motif that is required for ligand and coactivator binding. Here we show that FTZ-F1 does have an AF2 motif and that it is required to bind a coactivator, the homeodomain-containing protein Fushi tarazu (FTZ). We al...

  18. Capping motifs stabilize the leucine-rich repeat protein PP32 and rigidify adjacent repeats

    OpenAIRE

    Dao, Thuy P; Majumdar, Ananya; Barrick, Doug

    2014-01-01

    Capping motifs are found to flank most β-strand-containing repeat proteins. To better understand the roles of these capping motifs in organizing structure and stability, we carried out folding and solution NMR studies on the leucine-rich repeat (LRR) domain of PP32, which is composed of five tandem LRR, capped by α-helical and β-hairpin motifs on the N- and C-termini. We were able to purify PP32 constructs lacking either cap and containing destabilizing substitutions. Removing the C-cap resul...

  19. 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

  20. Negative in vitro selection identifies the rRNA recognition motif for ErmE methyltransferase

    DEFF Research Database (Denmark)

    Nielsen, A K; Douthwaite, S; Vester, B

    1999-01-01

    the adjacent single-stranded region around A2058. An RNA transcript of 72 nt that displays this motif functions as an efficient substrate for the ErmE methyltransferase. Pools of degenerate RNAs were formed by doping 34-nt positions that extend over and beyond the putative Erm recognition motif within...... contained substitutions at single sites, and these are confined to 12 nucleotide positions. These nucleotides, corresponding to A2051-A2060, C2611, and A2614 in 23S rRNA, presumably comprise the RNA recognition motif for ErmE methyltransferase. The structure formed by these nucleotides is highly conserved...

  1. Explosives Detection: Exploitation of the Physical Signatures

    Science.gov (United States)

    Atkinson, David

    2010-10-01

    Explosives based terrorism is an ongoing threat that is evolving with respect to implementation, configuration and materials used. There are a variety of devices designed to detect explosive devices, however, each technology has limitations and operational constraints. A full understanding of the signatures available for detection coupled with the array of detection choices can be used to develop a conceptual model of an explosives screening operation. Physics based sensors provide a robust approach to explosives detection, typically through the identification of anomalies, and are currently used for screening in airports around the world. The next generation of detectors for explosives detection will need to be more sensitive and selective, as well as integrate seamlessly with devices focused on chemical signatures. An appreciation for the details of the physical signature exploitation in cluttered environments with time, space, and privacy constraints is necessary for effective explosives screening of people, luggage, cargo, and vehicles.

  2. A Methodology for Calculating Radiation Signatures

    Energy Technology Data Exchange (ETDEWEB)

    Klasky, Marc Louis [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wilcox, Trevor [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Bathke, Charles G. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); James, Michael R. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-05-01

    A rigorous formalism is presented for calculating radiation signatures from both Special Nuclear Material (SNM) as well as radiological sources. The use of MCNP6 in conjunction with CINDER/ORIGEN is described to allow for the determination of both neutron and photon leakages from objects of interest. In addition, a description of the use of MCNP6 to properly model the background neutron and photon sources is also presented. Examinations of the physics issues encountered in the modeling are investigated so as to allow for guidance in the user discerning the relevant physics to incorporate into general radiation signature calculations. Furthermore, examples are provided to assist in delineating the pertinent physics that must be accounted for. Finally, examples of detector modeling utilizing MCNP are provided along with a discussion on the generation of Receiver Operating Curves, which are the suggested means by which to determine detectability radiation signatures emanating from objects.

  3. Animal Models of Interferon Signature Positive Lupus.

    Science.gov (United States)

    Zhuang, Haoyang; Szeto, Christopher; Han, Shuhong; Yang, Lijun; Reeves, Westley H

    2015-01-01

    Human lupus is strongly associated with a gene expression signature characterized by over-expression of Type I interferon-regulated genes. A strong interferon signature generally is not seen in the standard mouse models of lupus, despite considerable evidence for the involvement of toll-like receptor-driven interferon production. In contrast, pristane-induced lupus exhibits a prominent TLR7-dependent interferon signature. Importantly, genetic disorders with dysregulated interferon production in both human beings and mice cause severe autoinflammatory diseases but not the typical manifestations of lupus, suggesting that interferon over-production is insufficient to cause systemic lupus erythematosus itself. Single-gene models in mice suggest that lupus-like disease may result from abnormalities in B-cell activation and the clearance of dead cells. Pristane may mimic human systemic lupus erythematosus by causing synergistic abnormalities in interferon production along with defective clearance of apoptotic cells and over-active B-cell signaling. PMID:26097482

  4. Geometry of Killing spinors in neutral signature

    CERN Document Server

    Klemm, Dietmar

    2015-01-01

    We classify the supersymmetric solutions of minimal $N=2$ gauged supergravity in four dimensions with neutral signature. They are distinguished according to the sign of the cosmological constant and whether the vector field constructed as a bilinear of the Killing spinor is null or non-null. In neutral signature the bilinear vector field can be spacelike, which is a new feature not arising in Lorentzian signature. In the $\\Lambda0$ non-null case, the manifold is a fibration over a Lorentzian Gauduchon-Tod base space. Finally, in the $\\Lambda>0$ null class, the metric is contained in the Kundt family, and it turns out that the holonomy is reduced to ${\\rm Sim}(1)\\times{\\rm Sim}(1)$. There appear no self-dual solutions in the null class for either sign of the cosmological constant.

  5. Fluorescent taggants with temporally coded signatures.

    Science.gov (United States)

    Wang, Siyang; Vyas, Raul; Dwyer, Chris

    2016-07-11

    In this paper, resonance energy transfer (RET) networks between chromophores are used to implement fluorescent taggants with temporally coded signatures. Because the temporal signature of such a fluorescent taggant is a phase-type distribution defined by the geometry of its RET network, the taggant design is not constrained by resolvable dyes and has a significantly larger coding capacity than spectrally or lifetime coded fluorescent taggants. Meanwhile, the detection process becomes highly efficient when the signatures are coded in the time domain. The taggant identification method is based on the multinomial distribution of detected photons and Maximum Likelihood Estimation, which guarantees high accuracy even with only a few hundred photons and also applies to a mixture of taggants in multiplex detection. Therefore, these temporally coded fluorescent taggants have great potential for both in situ and Lidar applications. PMID:27410827

  6. Cryptanalysis of the arbitrated quantum signature protocols

    CERN Document Server

    Gao, Fei; Guo, Fen-Zhuo; Wen, Qiao-Yan

    2011-01-01

    As a new model for signing quantum message, arbitrated quantum signature (AQS) has recently received a lot of attention. In this paper we study the cryptanalysis of previous AQS protocols from the aspects of forgery and disavowal. We show that in these protocols the receiver Bob can realize existential forgery of the sender's signature under known message attack. Bob can even achieve universal forgery when the protocols are used to sign a classical message. Furthermore, the sender Alice can successfully disavow any of her signatures by simple attack. The attack strategies are described in detail and some discussions about the potential improvements of the protocols are given. Finally we also present several interesting topics in future study on AQS protocols.

  7. Temporal shape analysis via the spectral signature.

    Science.gov (United States)

    Bernardis, Elena; Konukoglu, Ender; Ou, Yangming; Metaxas, Dimitris N; Desjardins, Benoit; Pohl, Kilian M

    2012-01-01

    In this paper, we adapt spectral signatures for capturing morphological changes over time. Advanced techniques for capturing temporal shape changes frequently rely on first registering the sequence of shapes and then analyzing the corresponding set of high dimensional deformation maps. Instead, we propose a simple encoding motivated by the observation that small shape deformations lead to minor refinements in the spectral signature composed of the eigenvalues of the Laplace operator. The proposed encoding does not require registration, since spectral signatures are invariant to pose changes. We apply our representation to the shapes of the ventricles extracted from 22 cine MR scans of healthy controls and Tetralogy of Fallot patients. We then measure the accuracy score of our encoding by training a linear classifier, which outperforms the same classifier based on volumetric measurements. PMID:23286031

  8. Trace element ink spiking for signature authentication

    International Nuclear Information System (INIS)

    Signature authentication is a critical question in forensic document examination. Last years the evolution of personal computers made signature copying a quite easy task, so the development of new ways for signature authentication is crucial. In the present work a commercial ink was spiked with many trace elements in various concentrations. Inorganic and organometallic ink soluble compounds were used as spiking agents, whilst ink retained its initial properties. The spiked inks were used for paper writing and the documents were analyzed by a non destructive method, the energy dispersive X-ray fluorescence. The thin target model was proved right for quantitative analysis and a very good linear relationship of the intensity (X-ray signal) against concentration was estimated for all used elements. Intensity ratios between different elements in the same ink gave very stable results, independent on the writing alterations. The impact of time both to written document and prepared inks was also investigated. (author)

  9. Elongated polyproline motifs facilitate enamel evolution through matrix subunit compaction.

    Directory of Open Access Journals (Sweden)

    Tianquan Jin

    2009-12-01

    Full Text Available Vertebrate body designs rely on hydroxyapatite as the principal mineral component of relatively light-weight, articulated endoskeletons and sophisticated tooth-bearing jaws, facilitating rapid movement and efficient predation. Biological mineralization and skeletal growth are frequently accomplished through proteins containing polyproline repeat elements. Through their well-defined yet mobile and flexible structure polyproline-rich proteins control mineral shape and contribute many other biological functions including Alzheimer's amyloid aggregation and prolamine plant storage. In the present study we have hypothesized that polyproline repeat proteins exert their control over biological events such as mineral growth, plaque aggregation, or viscous adhesion by altering the length of their central repeat domain, resulting in dramatic changes in supramolecular assembly dimensions. In order to test our hypothesis, we have used the vertebrate mineralization protein amelogenin as an exemplar and determined the biological effect of the four-fold increased polyproline tandem repeat length in the amphibian/mammalian transition. To study the effect of polyproline repeat length on matrix assembly, protein structure, and apatite crystal growth, we have measured supramolecular assembly dimensions in various vertebrates using atomic force microscopy, tested the effect of protein assemblies on crystal growth by electron microscopy, generated a transgenic mouse model to examine the effect of an abbreviated polyproline sequence on crystal growth, and determined the structure of polyproline repeat elements using 3D NMR. Our study shows that an increase in PXX/PXQ tandem repeat motif length results (i in a compaction of protein matrix subunit dimensions, (ii reduced conformational variability, (iii an increase in polyproline II helices, and (iv promotion of apatite crystal length. Together, these findings establish a direct relationship between polyproline tandem

  10. The ADAMTS (A Disintegrin and Metalloproteinase with Thrombospondin motifs) family.

    Science.gov (United States)

    Kelwick, Richard; Desanlis, Ines; Wheeler, Grant N; Edwards, Dylan R

    2015-01-01

    The ADAMTS (A Disintegrin and Metalloproteinase with Thrombospondin motifs) enzymes are secreted, multi-domain matrix-associated zinc metalloendopeptidases that have diverse roles in tissue morphogenesis and patho-physiological remodeling, in inflammation and in vascular biology. The human family includes 19 members that can be sub-grouped on the basis of their known substrates, namely the aggrecanases or proteoglycanases (ADAMTS1, 4, 5, 8, 9, 15 and 20), the procollagen N-propeptidases (ADAMTS2, 3 and 14), the cartilage oligomeric matrix protein-cleaving enzymes (ADAMTS7 and 12), the von-Willebrand Factor proteinase (ADAMTS13) and a group of orphan enzymes (ADAMTS6, 10, 16, 17, 18 and 19). Control of the structure and function of the extracellular matrix (ECM) is a central theme of the biology of the ADAMTS, as exemplified by the actions of the procollagen-N-propeptidases in collagen fibril assembly and of the aggrecanases in the cleavage or modification of ECM proteoglycans. Defects in certain family members give rise to inherited genetic disorders, while the aberrant expression or function of others is associated with arthritis, cancer and cardiovascular disease. In particular, ADAMTS4 and 5 have emerged as therapeutic targets in arthritis. Multiple ADAMTSs from different sub-groupings exert either positive or negative effects on tumorigenesis and metastasis, with both metalloproteinase-dependent and -independent actions known to occur. The basic ADAMTS structure comprises a metalloproteinase catalytic domain and a carboxy-terminal ancillary domain, the latter determining substrate specificity and the localization of the protease and its interaction partners; ancillary domains probably also have independent biological functions. Focusing primarily on the aggrecanases and proteoglycanases, this review provides a perspective on the evolution of the ADAMTS family, their links with developmental and disease mechanisms, and key questions for the future. PMID:26025392

  11. Peripheral blood signatures of lead exposure.

    Directory of Open Access Journals (Sweden)

    Heather G LaBreche

    Full Text Available BACKGROUND: Current evidence indicates that even low-level lead (Pb exposure can have detrimental effects, especially in children. We tested the hypothesis that Pb exposure alters gene expression patterns in peripheral blood cells and that these changes reflect dose-specific alterations in the activity of particular pathways. METHODOLOGY/PRINCIPAL FINDING: Using Affymetrix Mouse Genome 430 2.0 arrays, we examined gene expression changes in the peripheral blood of female Balb/c mice following exposure to per os lead acetate trihydrate or plain drinking water for two weeks and after a two-week recovery period. Data sets were RMA-normalized and dose-specific signatures were generated using established methods of supervised classification and binary regression. Pathway activity was analyzed using the ScoreSignatures module from GenePattern. CONCLUSIONS/SIGNIFICANCE: The low-level Pb signature was 93% sensitive and 100% specific in classifying samples a leave-one-out crossvalidation. The high-level Pb signature demonstrated 100% sensitivity and specificity in the leave-one-out crossvalidation. These two signatures exhibited dose-specificity in their ability to predict Pb exposure and had little overlap in terms of constituent genes. The signatures also seemed to reflect current levels of Pb exposure rather than past exposure. Finally, the two doses showed differential activation of cellular pathways. Low-level Pb exposure increased activity of the interferon-gamma pathway, whereas high-level Pb exposure increased activity of the E2F1 pathway.

  12. Self-Similarity Limits of Genomic Signatures

    CERN Document Server

    Wu, Z B

    2002-01-01

    It is shown that metric representation of DNA sequences is one-to-one. By using the metric representation method, suppression of nucleotide strings in the DNA sequences is determined. For a DNA sequence, an optimal string length to display genomic signature in chaos game representation is obtained by eliminating effects of the finite sequence. The optical string length is further shown as a self- similarity limit in computing information dimension. By using the method, self-similarity limits of bacteria complete genomic signatures are further determined.

  13. Electronic Seal Stamping Based on Group Signature

    Directory of Open Access Journals (Sweden)

    Girija Srikanth

    2011-05-01

    Full Text Available This paper describes a new electronic official seal stamping based on Group Signature, USB Key. Bill/Contract in E-commerce must be seal stamped to gain tamper proof and non-repudiation. The seal stamping control is designed based on the certificate-based public key. This technique is more efficient for generating and verifying individual/group signatures in terms of computational efforts and communication costs. Web page electronic seal-stamping system is implemented which has been adopted by CNBAB platform since Mar., 2008

  14. Transient aspects of stream interface signatures

    Energy Technology Data Exchange (ETDEWEB)

    Crooker, N.U.; Shodhan, S. [Boston Univ., MA (United States). Center for Space Physics; Forsyth, R.J. [Imperial Coll., London (United Kingdom). Blackett Lab.; Burton, M.E. [Jet Propulsion Lab., Pasadena, CA (United States); Gosling, J.T. [Los Alamos National Lab., NM (United States); Fitzenreiter, R.J.; Lepping, R.P. [NASA Goddard Space Flight Center, Greenbelt, MD (United States). Lab. for Extraterrestrial Physics

    1999-06-01

    Although stream interfaces are steady-state, corotating boundaries between slow and fast solar wind, their signatures are sometimes associated with transient features. Here the authors illustrate two modes of association: interfaces trailing interplanetary coronal mass ejections (ICMEs) at 1 AU and interfaces within ICMEs in the range 4--5 AU. The former are readily understood as boundaries between transient slow wind and steady-state fast wind, where the ICMEs add variability to the interface signatures. The latter are puzzling and may be related to evolution of interfaces.

  15. LHC Signatures Of Scalar Dark Energy

    CERN Document Server

    Brax, Philippe; Englert, Christoph; Spannowsky, Michael

    2016-01-01

    Scalar dark energy fields that couple to the Standard Model can give rise to observable signatures at the LHC. In this work we show that $t\\bar t+$missing energy and mono-jet searches are suitable probes in the limit where the dark energy scalar is stable on collider distances. We discuss the prospects of distinguishing the dark energy character of new physics signals from dark matter signatures and the possibility of probing the self-interactions of the dark energy sector.

  16. Security problem on arbitrated quantum signature schemes

    CERN Document Server

    Choi, Jeong Woon; Hong, Dowon

    2011-01-01

    Until now, there have been developed many arbitrated quantum signature schemes implemented with a help of a trusted third party. In order to guarantee the unconditional security, most of them take advantage of the optimal quantum one-time encryption method based on Pauli operators. However, we in this paper point out that the previous schemes only provides a security against total break and actually show that there exists a simple existential forgery attack to validly modify the transmitted pair of message and signature. In addition, we also provide a simple method to recover the security against the proposed attack.

  17. Plasma signatures of radial field power dropouts

    International Nuclear Information System (INIS)

    A class of small scale structures, with a near-radial magnetic field and a drop in magnetic field fluctuation power, have recently been identified in the polar solar wind. An earlier study of 24 events, each lasting for 6 hours or more, identified no clear plasma signature. In an extension of that work, radial intervals lasting for 4 hours or more (89 in total), have been used to search for a statistically significant plasma signature. It was found that, despite considerable variations between intervals, there was a small but significant drop, on average, in plasma temperature, density and β during these events. copyright 1999 American Institute of Physics

  18. Plasma Signatures of Radial Field Power Dropouts

    International Nuclear Information System (INIS)

    A class of small scale structures, with a near-radial magnetic field and a drop in magnetic field fluctuation power, have recently been identified in the polar solar wind. An earlier study of 24 events, each lasting for 6 hours or more, identified no clear plasma signature. In an extension of that work, radial intervals lasting for 4 hours or more (89 in total), have been used to search for a statistically significant plasma signature. It was found that, despite considerable variations between intervals, there was a small but significant drop, on average, in plasma temperature, density and β during these events

  19. Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Joshi NV

    2009-01-01

    Full Text Available Abstract Background Regulation of gene expression in Plasmodium falciparum (Pf remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS; this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

  20. Threshold Signature Scheme Based on Discrete Logarithm and Quadratic Residue

    Institute of Scientific and Technical Information of China (English)

    FEI Ru-chun; WANG Li-na

    2004-01-01

    Digital signature scheme is a very important research field in computer security and modern cryptography.A(k,n) threshold digital signature scheme is proposed by integrating digital signature scheme with Shamir secret sharing scheme.It can realize group-oriented digital signature, and its security is based on the difficulty in computing discrete logarithm and quadratic residue on some special conditions.In this scheme, effective digital signature can not be generated by any k-1 or fewer legal users, or only by signature executive.In addition, this scheme can identify any legal user who presents incorrect partial digital signature to disrupt correct signature, or any illegal user who forges digital signature.A method of extending this scheme to an Abelian group such as elliptical curve group is also discussed.The extended scheme can provide rapider computing speed and stronger security in the case of using shorter key.

  1. Correlating overrepresented upstream motifs to gene expression a computational approach to regulatory element discovery in eukaryotes

    CERN Document Server

    Caselle, M; Provero, P

    2002-01-01

    Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: If this level is significantly higher or lower than the average taken over the whole genome, then the overerpresented motif shared by the genes in the set is likely to play a role in their regulation. The method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA microarray experiment, in which expression levels for virtually all the genes were measured during the diauxic shift from fermentation to respiration. Several known motifs were correctly identified, and a new candidate regulat...

  2. 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

  3. An intracellular motif of GLUT4 regulates fusion of GLUT4-containing vesicles

    Directory of Open Access Journals (Sweden)

    Welsh Gavin I

    2008-05-01

    Full Text Available Abstract Background Insulin stimulates glucose uptake by adipocytes through increasing translocation of the glucose transporter GLUT4 from an intracellular compartment to the plasma membrane. Fusion of GLUT4-containing vesicles at the cell surface is thought to involve phospholipase D activity, generating the signalling lipid phosphatidic acid, although the mechanism of action is not yet clear. Results Here we report the identification of a putative phosphatidic acid-binding motif in a GLUT4 intracellular loop. Mutation of this motif causes a decrease in the insulin-induced exposure of GLUT4 at the cell surface of 3T3-L1 adipocytes via an effect on vesicle fusion. Conclusion The potential phosphatidic acid-binding motif identified in this study is unique to GLUT4 among the sugar transporters, therefore this motif may provide a unique mechanism for regulating insulin-induced translocation by phospholipase D signalling.

  4. Rice bZIP protein, REB, interacts with GCN4 motif in promoter of Waxy gene

    Institute of Scientific and Technical Information of China (English)

    CHENG; Shijun; (程世军); WANG; Zongyang(王宗阳); HONG; Mengmin(洪孟民)

    2002-01-01

    A bifactorial endosperm box (EB), which contains an endosperm motif (EM) and a GCN4 motif, was found in rice Wx promoter. EB was found in 5′ upstream region of many seed storage protein genes accounting for these genes expression exclusive in endosperm among various cereals. Many reports demonstrated that the bZIP transcription activators isolated from wheat, barley and maize, etc. regulate the gene expression through binding to the GCN4 motif. In this research, we showed that GCN4 sequence could be recognized by nuclear proteins extracted from immature rice seeds. Furthermore, a rice bZIP protein, REB was isolated by using PCR method and REB fusion protein was expressed in E. coli. The results of gel shift analysis showed that REB could recognize and bind to the GCN4 motif in the Wx gene in addition to binding to the target sequence in the promoter of α-globulin.

  5. Application of a case–control study design to investigate genotypic signatures of HIV-1 transmission

    Directory of Open Access Journals (Sweden)

    Mota Talia M

    2012-06-01

    Full Text Available Abstract Background The characterization of HIV-1 transmission strains may inform the design of an effective vaccine. Shorter variable loops with fewer predicted glycosites have been suggested as signatures enriched in envelope sequences derived during acute HIV-1 infection. Specifically, a transmission-linked lack of glycosites within the V1 and V2 loops of gp120 provides greater access to an α4β7 binding motif, which promotes the establishment of infection. Also, a histidine at position 12 in the leader sequence of Env has been described as a transmission signature that is selected against during chronic infection. The purpose of this study is to measure the association of the presence of an α4β7 binding motif, the number of N-linked glycosites, the length of the variable loops, and the prevalence of histidine at position 12 with HIV-1 transmission. A case–control study design was used to measure the prevalence of these variables between subtype B and C transmission sequences and frequency-matched randomly-selected sequences derived from chronically infected controls. Results Subtype B transmission strains had shorter V3 regions than chronic strains (p = 0.031; subtype C transmission strains had shorter V1 loops than chronic strains (p = 0.047; subtype B transmission strains had more V3 loop glycosites (p = 0.024 than chronic strains. Further investigation showed that these statistically significant results were unlikely to be biologically meaningful. Also, there was no difference observed in the prevalence of a histidine at position 12 among transmission strains and controls of either subtype. Conclusions Although a genetic bottleneck is observed after HIV-1 transmission, our results indicate that summary characteristics of Env hypothesised to be important in transmission are not divergent between transmission and chronic strains of either subtype. The success of a transmission strain to initiate infection may be a random

  6. A New Batch Verifying Scheme for Identifying Illegal Signatures

    Institute of Scientific and Technical Information of China (English)

    Adrian Atanasiu

    2013-01-01

    The concept of batch verifying multiple digital signatures is to find a method by which multiple digital signatures can be verified simultaneously in a lower time complexity than separately verifying all the signatures.In this article,we analyze the complexity of the batch verifying schemes defined by Li,Hwang and Chen in 2010,and propose a new batch verifying multiple digital signature scheme,in two variants:one for RSA-by completing the Harn's schema with an identifying illegal signatures algorithm,and the other adapted for a modified Elliptic Curve Digital Signature Algorithm protocol.

  7. A group signature scheme based on quantum teleportation

    Energy Technology Data Exchange (ETDEWEB)

    Wen Xiaojun; Tian Yuan; Ji Liping; Niu Xiamu, E-mail: wxjun36@gmail.co [Information Countermeasure Technique Research Institute, Harbin Institute of Technology, Harbin 150001 (China)

    2010-05-01

    In this paper, we present a group signature scheme using quantum teleportation. Different from classical group signature and current quantum signature schemes, which could only deliver either group signature or unconditional security, our scheme guarantees both by adopting quantum key preparation, quantum encryption algorithm and quantum teleportation. Security analysis proved that our scheme has the characteristics of group signature, non-counterfeit, non-disavowal, blindness and traceability. Our quantum group signature scheme has a foreseeable application in the e-payment system, e-government, e-business, etc.

  8. Feasibility analysis of two identity- based proxy ring signature schemes

    Institute of Scientific and Technical Information of China (English)

    Wang Huaqun; Zhang Lijun; Zhao Junxi

    2007-01-01

    Recently , proxy ring signature schemes have been shown to be useful in various applications , such as electronic polling, electronic payment, etc. Although many proxy ring signature schemes have been proposed, there are only two identity- based proxy ring signature schemes have been proposed until now, I.e., Cheng's scheme and Lang's scheme. It's unlucky that the two identity- based proxy ring signature schemes are unfeasible . This paper points out the reasons why the two identity- based proxy ring signature schemes are unfeasible. In order to design feasible and efficient identity-based proxy ring signature schemes from bilinear pairings , we have to search for other methods .

  9. A group signature scheme based on quantum teleportation

    International Nuclear Information System (INIS)

    In this paper, we present a group signature scheme using quantum teleportation. Different from classical group signature and current quantum signature schemes, which could only deliver either group signature or unconditional security, our scheme guarantees both by adopting quantum key preparation, quantum encryption algorithm and quantum teleportation. Security analysis proved that our scheme has the characteristics of group signature, non-counterfeit, non-disavowal, blindness and traceability. Our quantum group signature scheme has a foreseeable application in the e-payment system, e-government, e-business, etc.

  10. Effect of the DEF motif on phosphorylation of peptide substrates by ERK

    OpenAIRE

    Fernandes, Neychelle; Allbritton, Nancy L.

    2009-01-01

    MAP kinase ERK maintains specificity by binding to docking sites such as the DEF domain or D domain. It was previously shown that appending peptides derived from D domains to a substrate peptide increased apparent efficiency of peptide phosphorylation while preserving its apparent specificity for ERK. Here we determine the effect of the DEF motif on efficiency and specificity of peptide phosphorylation by ERK. The DEF motif modulated the apparent affinity of the peptide for ERK while the subs...

  11. A Nucleotide Binding Motif in Hepatitis C Virus (HCV) NS4B Mediates HCV RNA Replication

    OpenAIRE

    Einav, Shirit; Elazar, Menashe; Danieli, Tsafi; Glenn, Jeffrey S.

    2004-01-01

    Hepatitis C virus (HCV) is a major cause of viral hepatitis. There is no effective therapy for most patients. We have identified a nucleotide binding motif (NBM) in one of the virus's nonstructural proteins, NS4B. This structural motif binds and hydrolyzes GTP and is conserved across HCV isolates. Genetically disrupting the NBM impairs GTP binding and hydrolysis and dramatically inhibits HCV RNA replication. These results have exciting implications for the HCV life cycle and novel antiviral s...

  12. An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases.

    Science.gov (United States)

    Bailey, T L; Baker, M E; Elkan, C P

    1997-05-01

    MEME (Multiple Expectation-maximization for Motif Elicitation) is a unique new software tool that uses artificial intelligence techniques to discover motifs shared by a set of protein sequences in a fully automated manner. This paper is the first detailed study of the use of MEME to analyse a large, biologically relevant set of sequences, and to evaluate the sensitivity and accuracy of MEME in identifying structurally important motifs. For this purpose, we chose the short-chain alcohol dehydrogenase superfamily because it is large and phylogenetically diverse, providing a test of how well MEME can work on sequences with low amino acid similarity. Moreover, this dataset contains enzymes of biological importance, and because several enzymes have known X-ray crystallographic structures, we can test the usefulness of MEME for structural analysis. The first six motifs from MEME map onto structurally important alpha-helices and beta-strands on Streptomyces hydrogenans 20beta-hydroxysteroid dehydrogenase. We also describe MAST (Motif Alignment Search Tool), which conveniently uses output from MEME for searching databases such as SWISS-PROT and Genpept. MAST provides statistical measures that permit a rigorous evaluation of the significance of database searches with individual motifs or groups of motifs. A database search of Genpept90 by MAST with the log-odds matrix of the first six motifs obtained from MEME yields a bimodal output, demonstrating the selectivity of MAST. We show for the first time, using primary sequence analysis, that bacterial sugar epimerases are homologs of short-chain dehydrogenases. MEME and MAST will be increasingly useful as genome sequencing provides large datasets of phylogenetically divergent sequences of biomedical interest. PMID:9366496

  13. REVIEW THE JEWELERY OF TURKMEN WOMEN BY EMPHASIZING ON THE CONCEPTS OF MOTIFS IN CULTURE

    OpenAIRE

    Noruzi, Hossein; Kermani, Iman Zakariai

    2015-01-01

    One way to understand the culture of the people is to recognize used concepts in arts and especially their artifacts. These concepts represent in appearances and motifs of these relics. Turkmen are tribes who have used several designs in decorating their arts and crafts. Turkmen women jewelry is considered as remarkable art of this tribe and it not only includes special visual properties but also drawings with broad concepts. The aim of this study is to recognize motifs and the used concepts ...

  14. 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...

  15. 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 ...

  16. 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

  17. 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...

  18. 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 ...

  19. Extraction of Protein Sequence Motif Information using PSO K-Means

    OpenAIRE

    Gowri, R.; Rathipriya, R.

    2015-01-01

    The main objective of the paper is to find the motif information.The functionalities of the proteins are ideally found from their motif information which is extracted using various techniques like clustering with k-means, hybrid k-means, self-organising maps, etc., in the literature. In this work protein sequence information is extracted using optimised k-means algorithm. The particle swarm optimisation technique is one of the frequently used optimisation method. In the current work the PSO k...

  20. A Nucleotide Binding Motif in Hepatitis C Virus (HCV) NS4B Mediates HCV RNA Replication

    Science.gov (United States)

    Einav, Shirit; Elazar, Menashe; Danieli, Tsafi; Glenn, Jeffrey S.

    2004-01-01

    Hepatitis C virus (HCV) is a major cause of viral hepatitis. There is no effective therapy for most patients. We have identified a nucleotide binding motif (NBM) in one of the virus's nonstructural proteins, NS4B. This structural motif binds and hydrolyzes GTP and is conserved across HCV isolates. Genetically disrupting the NBM impairs GTP binding and hydrolysis and dramatically inhibits HCV RNA replication. These results have exciting implications for the HCV life cycle and novel antiviral strategies. PMID:15452248

  1. Signatures of black holes at the LHC

    OpenAIRE

    Cavaglia, Marco; Godang, Romulus; Cremaldi, Lucien M.; Summers, Donald J.

    2007-01-01

    Signatures of black hole events at CERN's Large Hadron Collider are discussed. Event simulations are carried out with the Fortran Monte Carlo generator CATFISH. Inelasticity effects, exact field emissivities, color and charge conservation, corrections to semiclassical black hole evaporation, gravitational energy loss at formation and possibility of a black hole remnant are included in the analysis.

  2. New particles and their experimental signatures

    International Nuclear Information System (INIS)

    This report summarizes work done by our theoretical working group on exotic particles before, during and since the Lausanne meeting. We discuss the motivations, rates and experimental signatures for new physics and new particles in the 1 TeV mass range. (orig./HSI)

  3. Molecular signatures of thyroid follicular neoplasia

    DEFF Research Database (Denmark)

    Helweg-Larsen, Rehannah Holga Andrea; Rossing, Maria; Henao, Ricardo;

    2010-01-01

    The molecular pathways leading to thyroid follicular neoplasia are incompletely understood, and the diagnosis of follicular tumors is a clinical challenge. To provide leads to the pathogenesis and diagnosis of the tumors, we examined the global transcriptome signatures of follicular thyroid...

  4. Exploring Signature Pedagogies in Undergraduate Leadership Education

    Science.gov (United States)

    Jenkins, Daniel M.

    2012-01-01

    This research explores the instructional strategies most frequently used by leadership educators who teach academic credit-bearing undergraduate leadership studies courses through a national survey and identifies signature pedagogies within the leadership discipline. Findings from this study suggest that class discussion--whether in the form of…

  5. SUSY with ATLAS Leptonic Signatures, Coannihilation Region

    CERN Document Server

    Comune, G

    2004-01-01

    In this work we present an initial study on how leptonic signatures can be used at ATLAS to constrain SUSY particle masses combinations for the first time in the so called "coannihilation region''. The analysis is carried out in the framework of mSUGRA constrained SUSY model using fast detector simulation and reconstruction exploiting an invariant mass endpoint technique.

  6. An Arbitrated Quantum Signature with Bell States

    Science.gov (United States)

    Liu, Feng; Qin, Su-Juan; Huang, Wei

    2014-05-01

    Entanglement is the main resource in quantum communication. The main aims of the arbitrated quantum signature (AQS) scheme are to present an application of the entanglement in cryptology and to prove the possibility of the quantum signature. More specifically, the main function of quantum entangled states in the existing AQS schemes is to assist the signatory to transfer quantum states to the receiver. However, teleportation and the Leung quantum one-time pad (L-QOTP) algorithm are not enough to design a secure AQS scheme. For example, Pauli operations commute or anticommute with each other, which makes the implementation of attacks easily from the aspects of forgery and disavowal. To conquer this shortcoming, we construct an improved AQS scheme using a new QOTP algorithm. This scheme has three advantages: it randomly uses the Hadamard operation in the new QOTP to resist attacks by using the anticommutativity of nontrivial Pauli operators and it preserves almost all merits in the existing AQS schemes; even in the process of handling disputes, no party has chance to change the message and its signature without being discovered; the receiver can verify the integrity of the signature and discover the disavow of the signatory even in the last step of verification.

  7. Quantum Signature Scheme with Weak Arbitrator

    Science.gov (United States)

    Luo, Ming-Xing; Chen, Xiu-Bo; Yun, Deng; Yang, Yi-Xian

    2012-07-01

    In this paper, we propose one quantum signature scheme with a weak arbitrator to sign classical messages. This scheme can preserve the merits in the original arbitrated scheme with some entanglement resources, and provide a higher efficiency in transmission and reduction the complexity of implementation. The arbitrator is costless and only involved in the disagreement case.

  8. The Pedagogic Signature of Special Needs Education

    Science.gov (United States)

    Weiß, Sabine; Kollmannsberger, Markus; Lerche, Thomas; Oubaid, Viktor; Kiel, Ewald

    2014-01-01

    The goal of the following study is to identify a pedagogic signature, according to LS Shulman, for working with students who have special educational needs. Special educational needs are defined as significant limitations in personal development and learning which require particular educational measures beyond regular education. The development of…

  9. 76 FR 30542 - Adult Signature Services

    Science.gov (United States)

    2011-05-26

    ... Signature labels are located in the Intelligent Mail Package Barcode Specification and the addendum to Publication 91, Addendum for Intelligent Mail Package Barcode (IMpb) and 3-digit Service Type Code, available... Intelligent Mail package barcode. * * * * * 3.0 Certified Mail * * * * * 3.2 Basic Information * * * * *...

  10. Detection of signature volatiles for cariogenic microorganisms.

    Science.gov (United States)

    Hertel, M; Preissner, R; Gillissen, B; Schmidt-Westhausen, A M; Paris, S; Preissner, S

    2016-02-01

    The development of a breath test by the identification of volatile organic compounds (VOCs) emitted by cariogenic bacteria is a promising approach for caries risk assessment and early caries detection. The aim of the present study was to investigate the volatile profiles of three major cariogenic bacteria and to assess whether the obtained signatures were species-specific. Therefore, the headspaces above cultures of Streptococcus mutans, Lactobacillus salivarius and Propionibacterium acidifaciens were analysed after 24 and 48 h of cultivation using gas chromatography and mass spectrometry. A volatile database was queried for the obtained VOC profiles. Sixty-four compounds were detected within the analysed culture headspaces and were absent (36) or at least only present in minor amounts (28) in the control headspace. For S. mutans 18, for L. salivarius three and for P. acidifaciens five compounds were found to be unique signature VOCs. Database matching revealed that the identified signatures of all bacteria were unique. Furthermore, 13 of the 64 detected substances have not been previously reported to be emitted by bacteria or fungi. Specific VOC signatures were found in all the investigated bacteria cultures. The obtained results encourage further research to investigate the transferability to in vivo conditions towards the development of a breath test. PMID:26610336

  11. Fully polarimetric analysis of weather radar signatures

    OpenAIRE

    Galletti, Michele; Bebbington, David; Chandra, Madhukar; Börner, Thomas

    2008-01-01

    In this work the concept of depolarization response, namely the degree of polarization as a function of transmit polarization state, is investigated. Application examples are shown in the field of radar meteorology, namely for hydrometeor identification with fully polarimetric weather radar signatures. Data are from POLDIRAD, DLR research weather radar.

  12. 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

  13. 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/

  14. Discriminative motif discovery via simulated evolution and random under-sampling.

    Directory of Open Access Journals (Sweden)

    Tao Song

    Full Text Available Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

  15. 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

  16. 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.

  17. 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.

  18. Identification of disease-specific motifs in the antibody specificity repertoire via next-generation sequencing.

    Science.gov (United States)

    Pantazes, Robert J; Reifert, Jack; Bozekowski, Joel; Ibsen, Kelly N; Murray, Joseph A; Daugherty, Patrick S

    2016-01-01

    Disease-specific antibodies can serve as highly effective biomarkers but have been identified for only a relatively small number of autoimmune diseases. A method was developed to identify disease-specific binding motifs through integration of bacterial display peptide library screening, next-generation sequencing (NGS) and computational analysis. Antibody specificity repertoires were determined by identifying bound peptide library members for each specimen using cell sorting and performing NGS. A computational algorithm, termed Identifying Motifs Using Next- generation sequencing Experiments (IMUNE), was developed and applied to discover disease- and healthy control-specific motifs. IMUNE performs comprehensive pattern searches, identifies patterns statistically enriched in the disease or control groups and clusters the patterns to generate motifs. Using celiac disease sera as a discovery set, IMUNE identified a consensus motif (QPEQPF[PS]E) with high diagnostic sensitivity and specificity in a validation sera set, in addition to novel motifs. Peptide display and sequencing (Display-Seq) coupled with IMUNE analysis may thus be useful to characterize antibody repertoires and identify disease-specific antibody epitopes and biomarkers. PMID:27481573

  19. Identification of disease-specific motifs in the antibody specificity repertoire via next-generation sequencing

    Science.gov (United States)

    Pantazes, Robert J.; Reifert, Jack; Bozekowski, Joel; Ibsen, Kelly N.; Murray, Joseph A.; Daugherty, Patrick S.

    2016-01-01

    Disease-specific antibodies can serve as highly effective biomarkers but have been identified for only a relatively small number of autoimmune diseases. A method was developed to identify disease-specific binding motifs through integration of bacterial display peptide library screening, next-generation sequencing (NGS) and computational analysis. Antibody specificity repertoires were determined by identifying bound peptide library members for each specimen using cell sorting and performing NGS. A computational algorithm, termed Identifying Motifs Using Next- generation sequencing Experiments (IMUNE), was developed and applied to discover disease- and healthy control-specific motifs. IMUNE performs comprehensive pattern searches, identifies patterns statistically enriched in the disease or control groups and clusters the patterns to generate motifs. Using celiac disease sera as a discovery set, IMUNE identified a consensus motif (QPEQPF[PS]E) with high diagnostic sensitivity and specificity in a validation sera set, in addition to novel motifs. Peptide display and sequencing (Display-Seq) coupled with IMUNE analysis may thus be useful to characterize antibody repertoires and identify disease-specific antibody epitopes and biomarkers. PMID:27481573

  20. Comparison of metagenomic samples using sequence signatures

    Directory of Open Access Journals (Sweden)

    Jiang Bai

    2012-12-01

    Full Text Available Abstract Background Sequence signatures, as defined by the frequencies of k-tuples (or k-mers, k-grams, have been used extensively to compare genomic sequences of individual organisms, to identify cis-regulatory modules, and to study the evolution of regulatory sequences. Recently many next-generation sequencing (NGS read data sets of metagenomic samples from a variety of different environments have been generated. The assembly of these reads can be difficult and analysis methods based on mapping reads to genes or pathways are also restricted by the availability and completeness of existing databases. Sequence-signature-based methods, however, do not need the complete genomes or existing databases and thus, can potentially be very useful for the comparison of metagenomic samples using NGS read data. Still, the applications of sequence signature methods for the comparison of metagenomic samples have not been well studied. Results We studied several dissimilarity measures, including d2, d2* and d2S recently developed from our group, a measure (hereinafter noted as Hao used in CVTree developed from Hao’s group (Qi et al., 2004, measures based on relative di-, tri-, and tetra-nucleotide frequencies as in Willner et al. (2009, as well as standard lp measures between the frequency vectors, for the comparison of metagenomic samples using sequence signatures. We compared their performance using a series of extensive simulations and three real next-generation sequencing (NGS metagenomic datasets: 39 fecal samples from 33 mammalian host species, 56 marine samples across the world, and 13 fecal samples from human individuals. Results showed that the dissimilarity measure d2S can achieve superior performance when comparing metagenomic samples by clustering them into different groups as well as recovering environmental gradients affecting microbial samples. New insights into the environmental factors affecting microbial compositions in metagenomic samples

  1. Observational signatures of binary supermassive black holes

    Energy Technology Data Exchange (ETDEWEB)

    Roedig, Constanze; Krolik, Julian H. [Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218 (United States); Miller, M. Coleman [Department of Astronomy and Joint Space-Science Institute, University of Maryland, College Park, MD 20742 (United States)

    2014-04-20

    Observations indicate that most massive galaxies contain a supermassive black hole, and theoretical studies suggest that when such galaxies have a major merger, the central black holes will form a binary and eventually coalesce. Here we discuss two spectral signatures of such binaries that may help distinguish them from ordinary active galactic nuclei. These signatures are expected when the mass ratio between the holes is not extreme and the system is fed by a circumbinary disk. One such signature is a notch in the thermal continuum that has been predicted by other authors; we point out that it should be accompanied by a spectral revival at shorter wavelengths and also discuss its dependence on binary properties such as mass, mass ratio, and separation. In particular, we note that the wavelength λ {sub n} at which the notch occurs depends on these three parameters in such a way as to make the number of systems displaying these notches ∝λ{sub n}{sup 16/3}; longer wavelength searches are therefore strongly favored. A second signature, first discussed here, is hard X-ray emission with a Wien-like spectrum at a characteristic temperature ∼100 keV produced by Compton cooling of the shock generated when streams from the circumbinary disk hit the accretion disks around the individual black holes. We investigate the observability of both signatures. The hard X-ray signal may be particularly valuable as it can provide an indicator of black hole merger a few decades in advance of the event.

  2. A new threshold proxy signature scheme from bilinear pairings

    Institute of Scientific and Technical Information of China (English)

    QIAN Haifeng; CAO Zhenfu; XUE Qingshui

    2004-01-01

    Based on the GDH signature (short signature scheme) a probabilistic signature scheme is proposed in this paper with security proof. Then a new threshold proxy signature from bilinear pairings is proposed as well by using the new probabilistic signature scheme and the properties of the Gap Diffie-Hellman (GDH) group (where the Computational Diffie-Hellman problem is hard but the Decisional Diffie-Hellman problem is easy to solve). Our constructions are based on the recently proposed GDH signature scheme of Bonel et al.'s article. Bilinear pairings could be built from Weil pairing or Tate pairing. So most our constructions would be simpler, but still with high security. The proposed threshold proxy signature is the first one which is built from bilinear pairings. At the end of this paper security and performance of the threshold proxy signature scheme is also analyzed.

  3. A New Proxy Blind Signature Scheme based on ECDLP

    Directory of Open Access Journals (Sweden)

    Daniyal M Alghazzawi

    2011-05-01

    Full Text Available A proxy blind signature scheme is a special form of blind signature which allows a designated person called proxy signer to sign on behalf of two or more original signers without knowing the content of the message or document. It combines the advantages of proxy signature, blind signature and multi-signature scheme and satisfies the security properties of both proxy and blind signature scheme. Most of the exiting proxy blind signature schemes were developed based on the mathematical hard problems integer factorization (IFP and simple discrete logarithm (DLP which take sub-exponential time to solve. This paper describes an secure simple proxy blind signature scheme based on Elliptic Curve Discrete Logarithm Problem (ECDLP takes fully-exponential time. This can be implemented in low power and small processor mobile devices such as smart card, PDA etc. Here also we describes implementation issues of various scalar multiplication for ECDLP.

  4. OFFLINE HANDWRITTEN SIGNATURE IDENTIFICATION USING ADAPTIVE WINDOW POSITIONING TECHNIQUES

    Directory of Open Access Journals (Sweden)

    Ghazali Sulong

    2014-10-01

    Full Text Available The paper presents to address this challenge, we have proposed the use of Adaptive Window Positioning technique which focuses on not just the meaning of the handwritten signature but also on the individuality of the writer. This innovative technique divides the handwritten signature into 13 small windows of size nxn (13x13. This size should be large enough to contain ample information about the style of the author and small enough to ensure a good identification performance. The process was tested with a GPDS datasetcontaining 4870 signature samples from 90 different writers by comparing the robust features of the test signature with that of the user’s signature using an appropriate classifier. Experimental results reveal that adaptive window positioning technique proved to be the efficient and reliable method for accurate signature feature extraction for the identification of offline handwritten signatures .The contribution of this technique can be used to detect signatures signed under emotional duress.

  5. An Immune Clonal Selection Algorithm for Synthetic Signature Generation

    OpenAIRE

    2014-01-01

    The collection of signature data for system development and evaluation generally requires significant time and effort. To overcome this problem, this paper proposes a detector generation based clonal selection algorithm for synthetic signature set generation. The goal of synthetic signature generation is to improve the performance of signature verification by providing more training samples. Our method uses the clonal selection algorithm to maintain the diversity of the overall set and avoid ...

  6. Enhancing the Security of He-Kiesler Signature Schemes

    Institute of Scientific and Technical Information of China (English)

    李春辉; 陈一宏

    2003-01-01

    Although the He-Kiesler signature is said to be proposed based on the discrete logarithm problem and the factorization problem, it has been proved that the signature is not as secure as it was stated to be. A new signature scheme is here proposed based on the discrete logarithm problem and the factorization problem to enhance the security of the He-Kiesler signature.

  7. Verifiable (t, n) Threshold Signature Scheme Based on Elliptic Curve

    Institute of Scientific and Technical Information of China (English)

    WANG Hua-qun; ZHAO Jun-xi; ZHANG Li-jun

    2005-01-01

    Based on the difficulty of solving the ECDLP (elliptic curve discrete logarithm problem) on the finite field,we present a (t, n) threshold signature scheme and a verifiable key agreement scheme without trusted party. Applying a modified elliptic curve signature equation, we get a more efficient signature scheme than the existing ECDSA (elliptic curve digital signature algorithm) from the computability and security view. Our scheme has a shorter key, faster computation, and better security.

  8. 17 CFR 201.65 - Identity and signature.

    Science.gov (United States)

    2010-04-01

    ... 17 Commodity and Securities Exchanges 2 2010-04-01 2010-04-01 false Identity and signature. 201.65... of 1934 § 201.65 Identity and signature. Applications pursuant to this subpart may omit the identity, mailing address, and signature of the applicant; provided, that such identity, mailing address...

  9. Acoustic Signature Monitoring and Management of Naval Platforms

    NARCIS (Netherlands)

    Basten, T.G.H.; Jong, C.A.F. de; Graafland, F.; Hof, J. van 't

    2015-01-01

    Acoustic signatures make naval platforms susceptible to detection by threat sensors. The variable operational conditions and lifespan of a platform cause variations in the acoustic signature. To deal with these variations, a real time signature monitoring capability is being developed, with advisory

  10. Radar micro-doppler signatures processing and applications

    CERN Document Server

    Chen, Victor C; Miceli, William J

    2014-01-01

    Radar Micro-Doppler Signatures: Processing and applications concentrates on the processing and application of radar micro-Doppler signatures in real world situations, providing readers with a good working knowledge on a variety of applications of radar micro-Doppler signatures.

  11. A Recursive Definition of the Holographic Standard Signature

    OpenAIRE

    Bradley, William F.

    2009-01-01

    We provide a recursive description of the signatures realizable on the standard basis by a holographic algorithm. The description allows us to prove tight bounds on the size of planar matchgates and efficiently test for standard signatures. Over finite fields, it allows us to count the number of n-bit standard signatures and calculate their expected sparsity.

  12. APOCALYPTIC MOTIFS IN THE CYCLE OF STORIES BY M.A. BULGAKOV «NOTES OF A YOUNG DOCTOR»

    Directory of Open Access Journals (Sweden)

    Evgeniy Igorevich Erokhov

    2015-10-01

    Full Text Available The motif analysis of a cycle of stories by M.A. Bulgakov «Notes of a Young Doctor» from the point of view of their apocalyptic problematics was first performed in this article. To identify apocalyptic motifs the method of motif analysis, developed by B.M. Gasparov, was used which will also help to prove the interpenetration of motifs in the cycle of stories. The result of the research work is the identification of apocalyptic motifs which are manifested in the experiences of the main character and the events taking place around him and passing through the prism of physician’s perception of the world. Our identified motifs show that the stories in the cycle are united not only thematically and with the help of the image of the main character, but with the help of the motifs which reflect interpenetration of apocalyptic motifs in the stories of one cycle. There are the following apocalyptic motifs in the cycle of stories by Bulgakov: diseases, darkness (as part of the landscape, resurrection from the dead and beast. They all belong to the biblical type which is allocated on the basis of the associative bond of these motifs with the biblical texts.

  13. How to find a leucine in a haystack? Structure, ligand recognition and regulation of leucine-aspartic acid (LD) motifs

    KAUST Repository

    Alam, Tanvir

    2014-05-29

    LD motifs (leucine-aspartic acidmotifs) are short helical protein-protein interaction motifs that have emerged as key players in connecting cell adhesion with cell motility and survival. LD motifs are required for embryogenesis, wound healing and the evolution of multicellularity. LD motifs also play roles in disease, such as in cancer metastasis or viral infection. First described in the paxillin family of scaffolding proteins, LD motifs and similar acidic LXXLL interaction motifs have been discovered in several other proteins, whereas 16 proteins have been reported to contain LDBDs (LD motif-binding domains). Collectively, structural and functional analyses have revealed a surprising multivalency in LD motif interactions and a wide diversity in LDBD architectures. In the present review, we summarize the molecular basis for function, regulation and selectivity of LD motif interactions that has emerged from more than a decade of research. This overview highlights the intricate multi-level regulation and the inherently noisy and heterogeneous nature of signalling through short protein-protein interaction motifs. © 2014 Biochemical Society.

  14. Disparate requirements for the Walker A and B ATPase motifs ofhuman RAD51D in homologous recombination

    Energy Technology Data Exchange (ETDEWEB)

    Wiese, Claudia; Hinz, John M.; Tebbs, Robert S.; Nham, Peter B.; Urbin, Salustra S.; Collins, David W.; Thompson, Larry H.; Schild, David

    2006-04-21

    In vertebrates, homologous recombinational repair (HRR) requires RAD51 and five RAD51 paralogs (XRCC2, XRCC3, RAD51B, RAD51C, and RAD51D) that all contain conserved Walker A and B ATPase motifs. In human RAD51D we examined the requirement for these motifs in interactions with XRCC2 and RAD51C, and for survival of cells in response to DNA interstrand crosslinks. Ectopic expression of wild type human RAD51D or mutants having a non-functional A or B motif was used to test for complementation of a rad51d knockout hamster CHO cell line. Although A-motif mutants complement very efficiently, B-motif mutants do not. Consistent with these results, experiments using the yeast two- and three-hybrid systems show that the interactions between RAD51D and its XRCC2 and RAD51C partners also require a functional RAD51D B motif, but not motif A. Similarly, hamster Xrcc2 is unable to bind to the non-complementing human RAD51D B-motif mutants in co-immunoprecipitation assays. We conclude that a functional Walker B motif, but not A motif, is necessary for RAD51D's interactions with other paralogs and for efficient HRR. We present a model in which ATPase sites are formed in a bipartite manner between RAD51D and other RAD51 paralogs.

  15. The Geometry of Plasticity-Induced Sensitization in Isoinhibitory Rate Motifs.

    Science.gov (United States)

    Kumar, Gautam; Ching, ShiNung

    2016-09-01

    A well-known phenomenon in sensory perception is desensitization, wherein behavioral responses to persistent stimuli become attenuated over time. In this letter, our focus is on studying mechanisms through which desensitization may be mediated at the network level and, specifically, how sensitivity changes arise as a function of long-term plasticity. Our principal object of study is a generic isoinhibitory motif: a small excitatory-inhibitory network with recurrent inhibition. Such a motif is of interest due to its overrepresentation in laminar sensory network architectures. Here, we introduce a sensitivity analysis derived from control theory in which we characterize the fixed-energy reachable set of the motif. This set describes the regions of the phase-space that are more easily (in terms of stimulus energy) accessed, thus providing a holistic assessment of sensitivity. We specifically focus on how the geometry of this set changes due to repetitive application of a persistent stimulus. We find that for certain motif dynamics, this geometry contracts along the stimulus orientation while expanding in orthogonal directions. In other words, the motif not only desensitizes to the persistent input, but heightens its responsiveness (sensitizes) to those that are orthogonal. We develop a perturbation analysis that links this sensitization to both plasticity-induced changes in synaptic weights and the intrinsic dynamics of the network, highlighting that the effect is not purely due to weight-dependent disinhibition. Instead, this effect depends on the relative neuronal time constants and the consequent stimulus-induced drift that arises in the motif phase-space. For tightly distributed (but random) parameter ranges, sensitization is quite generic and manifests in larger recurrent E-I networks within which the motif is embedded. PMID:27391684

  16. Lipid motif of a bacterial antigen mediates immune responses via TLR2 signaling.

    Directory of Open Access Journals (Sweden)

    Amit A Lugade

    Full Text Available The cross-talk between the innate and the adaptive immune system is facilitated by the initial interaction of antigen with dendritic cells. As DCs express a large array of TLRs, evidence has accumulated that engagement of these molecules contributes to the activation of adaptive immunity. We have evaluated the immunostimulatory role of the highly-conserved outer membrane lipoprotein P6 from non-typeable Haemophilus influenzae (NTHI to determine whether the presence of the lipid motif plays a critical role on its immunogenicity. We undertook a systematic analysis of the role that the lipid motif plays in the activation of DCs and the subsequent stimulation of antigen-specific T and B cells. To facilitate our studies, recombinant P6 protein that lacked the lipid motif was generated. Mice immunized with non-lipidated rP6 were unable to elicit high titers of anti-P6 Ig. Expression of the lipid motif on P6 was also required for proliferation and cytokine secretion by antigen-specific T cells. Upregulation of T cell costimulatory molecules was abrogated in DCs exposed to non-lipidated rP6 and in TLR2(-/- DCs exposed to native P6, thereby resulting in diminished adaptive immune responses. Absence of either the lipid motif on the antigen or TLR2 expression resulted in diminished cytokine production from stimulated DCs. Collectively, our data suggest that the lipid motif of the lipoprotein antigen is essential for triggering TLR2 signaling and effective stimulation of APCs. Our studies establish the pivotal role of a bacterial lipid motif on activating both innate and adaptive immune responses to an otherwise poorly immunogenic protein antigen.

  17. An Analysis of Multi-type Relational Interactions in FMA Using Graph Motifs with Disjointness Constraints

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Guo Qiang; Luo, Lingyun; Ogbuji, Chime; Joslyn, Cliff A.; Mejino, Jose; Sahoo, Satya S.

    2012-11-24

    The interaction of multiple types of relationships among anatomical classes in the Foundational Model of Anatomy (FMA) can provide inferred information valuable for quality assurance. This paper introduces a method called Motif Checking (MOCH) to study the effects of such multi-relation type interactions. MOCH represents patterns of multitype interaction as small labeled sub-graph motifs, whose nodes represent class variables, and labeled edges represent relational types. By representing FMA as an RDF graph and motifs as SPARQL queries, fragments of FMA are automatically obtained as auditing candidates. Leveraging the scalability and reconfigurability of Semantic Web Technology (OWL, RDF and SPARQL) and Virtuoso, we performed exhaustive analyses of three 2-node motifs, resulting in 638 matching FMA configurations; twelve 3-node motifs, resulting in 202,960 configurations. Using the Principal Ideal Explorer (PIE) methodology as an extension of MOCH, we were able to identify 755 root nodes with 4,100 respective descendants with opposing antonyms in their class names for arbitrary-length motifs. With possible disjointness implied by antonyms, we performed manual inspection of a subset of the resulting FMA fragments and tracked down a source of abnormal inferred conclusions (captured by the motifs), coming from a gender-neutral class being modeled as a part of gender-specific class, such as “Urinary system” is a part of “Female human body.” Our results demonstrate that MOCH and PIE provide a unique source of valuable information for quality assurance. Since our approach is general, it is applicable to any ontological system with an OWL representation.

  18. Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes

    Directory of Open Access Journals (Sweden)

    Kistler Corby

    2010-03-01

    Full Text Available Abstract Background Fusarium graminearum (Fg, a major fungal pathogen of cultivated cereals, is responsible for billions of dollars in agriculture losses. There is a growing interest in understanding the transcriptional regulation of this organism, especially the regulation of genes underlying its pathogenicity. The generation of whole genome sequence assemblies for Fg and three closely related Fusarium species provides a unique opportunity for such a study. Results Applying comparative genomics approaches, we developed a computational pipeline to systematically discover evolutionarily conserved regulatory motifs in the promoter, downstream and the intronic regions of Fg genes, based on the multiple alignments of sequenced Fusarium genomes. Using this method, we discovered 73 candidate regulatory motifs in the promoter regions. Nearly 30% of these motifs are highly enriched in promoter regions of Fg genes that are associated with a specific functional category. Through comparison to Saccharomyces cerevisiae (Sc and Schizosaccharomyces pombe (Sp, we observed conservation of transcription factors (TFs, their binding sites and the target genes regulated by these TFs related to pathways known to respond to stress conditions or phosphate metabolism. In addition, this study revealed 69 and 39 conserved motifs in the downstream regions and the intronic regions, respectively, of Fg genes. The top intronic motif is the splice donor site. For the downstream regions, we noticed an intriguing absence of the mammalian and Sc poly-adenylation signals among the list of conserved motifs. Conclusion This study provides the first comprehensive list of candidate regulatory motifs in Fg, and underscores the power of comparative genomics in revealing functional elements among related genomes. The conservation of regulatory pathways among the Fusarium genomes and the two yeast species reveals their functional significance, and provides new insights in their

  19. Hole-transfer induced energy transfer in perylene diimide dyads with a donor-spacer-acceptor motif.

    Science.gov (United States)

    Kölle, Patrick; Pugliesi, Igor; Langhals, Heinz; Wilcken, Roland; Esterbauer, Andreas J; de Vivie-Riedle, Regina; Riedle, Eberhard

    2015-10-14

    We investigate the photoinduced dynamics of perylene diimide dyads based on a donor-spacer-acceptor motif with polyyne spacers of varying length by pump-probe spectroscopy, time resolved fluorescence, chemical variation and quantum chemistry. While the dyads with pyridine based polyyne spacers undergo energy transfer with near-unity quantum efficiency, in the dyads with phenyl based polyyne spacers the energy transfer efficiency drops below 50%. This suggests the presence of a competing electron transfer process from the spacer to the energy donor as the excitation sink. Transient absorption spectra, however, reveal that the spacer actually mediates the energy transfer dynamics. The ground state bleach features of the polyyne spacers appear due to the electron transfer decay with the same time constant present in the rise of the ground state bleach and stimulated emission of the perylene energy acceptor. Although the electron transfer process initially quenches the fluorescence of the donor it does not inhibit energy transfer to the perylene energy acceptor. The transient signatures reveal that electron and energy transfer processes are sequential and indicate that the donor-spacer electron transfer state itself is responsible for the energy transfer. Through the introduction of a Dexter blocker unit into the spacer we can clearly exclude any through bond Dexter-type energy transfer. Ab initio calculations on the donor-spacer and the donor-spacer-acceptor systems reveal the existence of a bright charge transfer state that is close in energy to the locally excited state of the acceptor. Multipole-multipole interactions between the bright charge transfer state and the acceptor state enable the energy transfer. We term this mechanism coupled hole-transfer FRET. These dyads represent a first example that shows how electron transfer can be connected to energy transfer for use in novel photovoltaic and optoelectronic devices. PMID:26347443

  20. Decoding a signature-based model of transcription cofactor recruitment dictated by cardinal cis-regulatory elements in proximal promoter regions.

    Directory of Open Access Journals (Sweden)

    Christopher Benner

    2013-11-01

    Full Text Available Genome-wide maps of DNase I hypersensitive sites (DHSs reveal that most human promoters contain perpetually active cis-regulatory elements between -150 bp and +50 bp (-150/+50 bp relative to the transcription start site (TSS. Transcription factors (TFs recruit cofactors (chromatin remodelers, histone/protein-modifying enzymes, and scaffold proteins to these elements in order to organize the local chromatin structure and coordinate the balance of post-translational modifications nearby, contributing to the overall regulation of transcription. However, the rules of TF-mediated cofactor recruitment to the -150/+50 bp promoter regions remain poorly understood. Here, we provide evidence for a general model in which a series of cis-regulatory elements (here termed 'cardinal' motifs prefer acting individually, rather than in fixed combinations, within the -150/+50 bp regions to recruit TFs that dictate cofactor signatures distinctive of specific promoter subsets. Subsequently, human promoters can be subclassified based on the presence of cardinal elements and their associated cofactor signatures. In this study, furthermore, we have focused on promoters containing the nuclear respiratory factor 1 (NRF1 motif as the cardinal cis-regulatory element and have identified the pervasive association of NRF1 with the cofactor lysine-specific demethylase 1 (LSD1/KDM1A. This signature might be distinctive of promoters regulating nuclear-encoded mitochondrial and other particular genes in at least some cells. Together, we propose that decoding a signature-based, expanded model of control at proximal promoter regions should lead to a better understanding of coordinated regulation of gene transcription.

  1. Observational Signatures of Self-Destructive Civilisations

    CERN Document Server

    Stevens, Adam; O'Malley-James, Jack

    2015-01-01

    We address the possibility that intelligent civilisations that destroy themselves could present signatures observable by humanity. Placing limits on the number of self-destroyed civilisations in the Milky Way has strong implications for the final three terms in Drake's Equation, and would allow us to identify which classes of solution to Fermi's Paradox fit with the evidence (or lack thereof). Using the Earth as an example, we consider a variety of scenarios in which humans could extinguish their own technological civilisation. Each scenario presents some form of observable signature that could be probed by astronomical campaigns to detect and characterise extrasolar planetary systems. Some observables are unlikely to be detected at interstellar distances, but some scenarios are likely to produce significant changes in atmospheric composition that could be detected serendipitously with next-generation telescopes. In some cases, the timing of the observation would prove crucial to detection, as the decay of si...

  2. Photostatistics Reconstruction via Loop Detector Signatures

    CERN Document Server

    Webb, J G; 10.1364/OE.17.011799

    2009-01-01

    Photon-number resolving detectors are a fundamental building-block of optical quantum information processing protocols. A loop detector, combined with appropriate statistical processing, can be used to convert a binary on/off photon counter into a photon-number-resolving detector. Here we describe the idea of a signature of photon-counts, which may be used to more robustly reconstruct the photon number distribution of a quantum state. The methodology is applied experimentally in a 9-port loop detector operating at a telecommunications wavelength and compared directly to the approach whereby only the number of photon-counts is used to reconstruct the input distribution. The signature approach is shown to be more robust against calibration errors, exhibit reduced statistical uncertainty, and reduced reliance on a-priori assumptions about the input state.

  3. Universally Composable Proactive Threshold RSA Signature

    Institute of Scientific and Technical Information of China (English)

    HONG Xuan; CHEN Ke-fei; LONG Yu

    2008-01-01

    Recently some efforts were made towards capturing the security requirements within the composable security framework.This modeling has some significant advantages in designing and analyzing complex systems.The threshold signature was discussed and a definition was given based on the universal composability framework,which is proved to be equivalent to the standard security definition.Furthermore,a simple,efficient and proactive threshold RSA signature protocol was presented.It is proved to be correct,consistent and unforgeable relative to the environment that at most t-1 parties are corrupted in each proactive stage.It is also secure under the universal composability framework.It is a UC based security and is proved to be equivalent to the standard security.

  4. Cryptanalysis to a Certificateless Threshold Signature Scheme

    Directory of Open Access Journals (Sweden)

    Wenjie Yang

    2012-10-01

    Full Text Available Certificateless public key cryptography is a new paradigm with two interesting features. On one hand, it keeps the certificate free property of identity-based public key cryptography (ID-PKC, while on the other hand, it gets rid of the inherent key escrow problem of ID-PKC. These two distinctive features make certificateless threshold signature schemes more applicable in practice as it removes the cost of transmitting and verifying the public key certificates of the participants who are involved in signing, and yet without the fear of key escrow. In this paper, we analyze the security of an existing certificateless threshold signature (CLTHS scheme recently proposed by Zhong et al.[26]. We show it is insure by demonstrating its three security drawbacks. Especially, we present a kind of public key replacement attack against it. Our attack reveals that it is subject to universal forgeries of type I adversaries

  5. Infrared signature evolution of a CUBI

    Science.gov (United States)

    van Iersel, M.; van Eijk, A. M. J.; Veerman, H. E. T.; Benoist, K. W.; Cohen, L. H.

    2015-09-01

    A CUBI, a simple geometric metal test-object, is placed in an outdoor environment to monitor the infrared signature. The (daily) temperature evolution of the individual facets is monitored as function of environmental parameters, such as solar irradiance and ambient temperature. This provides insight in the parameters that have the strongest effects on the thermal signature of the CUBI. The CUBI is also imaged by infrared cameras and these recordings are used to estimate the temperature of the CUBI. The recorded images are also used to provide insight in the amount of air turbulence generated by the radiance of the hot CUBI facets. The amount of turbulence is compared with the ambient turbulence as calculated by standard bulk theories.

  6. Preparing for a (RSA Digital Signature

    Directory of Open Access Journals (Sweden)

    Dragan Vidakovic

    2013-03-01

    Full Text Available Many people know the general story about RSA and large (probably prime numbers, without having an idea of how to perform arithmetic operations with the numbers of thousands of bits. Even if they want to develop their own tool for a digital signature, they give up because they think that special hardware-software offers are required for that. In this paper we want to show that even by using a very simple console application, the tools for signature can be developed. Those tools are not as powerful and functional as the products of renowned companies, but they are sufficient to stimulate the interest in cryptography (and the coding of known algorithms is the best way for that, and that is our overriding and permanent goal[3].

  7. Definite signature conformal holonomy: a complete classification

    OpenAIRE

    Armstrong, Stuart

    2005-01-01

    This paper aims to classify the holonomy of the conformal Tractor connection, and relate these holonomies to the geometry of the underlying manifold. The conformally Einstein case is dealt with through the construction of metric cones, whose Riemmanian holonomy is the same as the Tractor holonomy of the underlying manifold. Direct calculations in the Ricci-flat case and an important decomposition theorem complete the classification for definitive signature.

  8. Signatures versus histograms: Definitions, distances and algorithms

    OpenAIRE

    Serratosa, Francesc; Sanfeliu, Alberto

    2006-01-01

    The aim of this paper is to present a new method to compare histograms. The main advantage is that there is an important time-complexity reduction respect the methods presented before. This reduction is statistically and analytically demonstrated in the paper. The distances between histograms that we present are defined on a structure called signature, which is a lossless representation of histograms. Moreover, the type of the elements of the sets that the histograms represent are ordinal, no...

  9. Cosmological signatures of time-asymmetric gravity

    OpenAIRE

    Cortês, Marina; Liddle, Andrew R; Smolin, Lee

    2016-01-01

    We develop the model proposed by Cort\\^es, Gomes & Smolin, to predict cosmological signatures of time-asymmetric extensions of general relativity they proposed recently. Within this class of models the equation of motion of chiral fermions is modified by a torsion term. This term leads to a dispersion law for neutrinos that associates a new time-varying energy with each particle. We find a new neutrino contribution to the Friedmann equation resulting from the torsion term in the Ashtekar conn...

  10. Conductance and noise signatures of Majorana backscattering

    OpenAIRE

    Chung, Suk Bum; Qi, Xiao-Liang; Maciejko, Joseph; Zhang, Shou-Cheng

    2010-01-01

    We propose a conductance measurement to detect the backscattering of chiral Majorana edge states. Because normal and Andreev processes have equal probability for backscattering of a single chiral Majorana edge state, there is qualitative difference from backscattering of a chiral Dirac edge state, giving rise to half-integer Hall conductivity and decoupling of fluctuation in incoming and outgoing modes. The latter can be detected through thermal noise measurement. These experimental signature...

  11. Quantum Gravity signatures in the Unruh effect

    OpenAIRE

    Alkofer, Natalia; D'Odorico, Giulio; Saueressig, Frank; Versteegen, Fleur

    2016-01-01

    We study quantum gravity signatures emerging from phenomenologically motivated multiscale models, spectral actions, and Causal Set Theory within the detector approach to the Unruh effect. We show that while the Unruh temperature is unaffected, Lorentz-invariant corrections to the two-point function leave a characteristic fingerprint in the induced emission rate of the accelerated detector. Generically, quantum gravity models exhibiting dynamical dimensional reduction exhibit a suppression of ...

  12. Observational Signatures of Self-Destructive Civilisations

    OpenAIRE

    Stevens, Adam; Forgan, Duncan; O'Malley-James, Jack

    2015-01-01

    We address the possibility that intelligent civilisations that destroy themselves could present signatures observable by humanity. Placing limits on the number of self-destroyed civilisations in the Milky Way has strong implications for the final three terms in Drake's Equation, and would allow us to identify which classes of solution to Fermi's Paradox fit with the evidence (or lack thereof). Using the Earth as an example, we consider a variety of scenarios in which humans could extinguish t...

  13. Constraining blazar physics with polarization signatures

    Science.gov (United States)

    Zhang, Haocheng; Boettcher, Markus; Li, Hui

    2016-01-01

    Blazars are active galactic nuclei whose jets are directed very close to our line of sight. They emit nonthermal-dominated emission from radio to gamma-rays, with the radio to optical emissions known to be polarized. Both radiation and polarization signatures can be strongly variable. Observations have shown that sometimes strong multiwavelength flares are accompanied by drastic polarization variations, indicating active participation of the magnetic field during flares. We have developed a 3D multi-zone time-dependent polarization-dependent radiation transfer code, which enables us to study the spectral and polarization signatures of blazar flares simultaneously. By combining this code with a Fokker-Planck nonthermal particle evolution scheme, we are able to derive simultaneous fits to time-dependent spectra, multiwavelength light curves, and time-dependent optical polarization signatures of a well-known multiwavelength flare with 180 degree polarization angle swing of the blazar 3C279. Our work shows that with detailed consideration of light travel time effects, the apparently symmetric time-dependent radiation and polarization signatures can be naturally explained by a straight, helically symmetric jet pervaded by a helical magnetic field, without the need of any asymmetric structures. Also our model suggests that the excess in the nonthermal particles during flares can originate from magnetic reconnection events, initiated by a shock propagating through the emission region. Additionally, the magnetic field should generally revert to its initial topology after the flare. We conclude that such shock-initiated magnetic reconnection event in an emission environment with relatively strong magnetic energy can be the driver of multiwavelength flares with polarization angle swings. Future statistics on such observations will constrain general features of such events, while magneto-hydrodynamic simulations will provide physical scenarios for the magnetic field evolution

  14. Signatures of homoclinic motion in quantum chaos

    OpenAIRE

    Wisniacki, D. A.; Vergini, E.; Benito, R. M.; Borondo, F.

    2004-01-01

    Homoclinic motion plays a key role in the organization of classical chaos in Hamiltonian systems. In this Letter, we show that it also imprints a clear signature in the corresponding quantum spectra. By numerically studying the fluctuations of the widths of wavefunctions localized along periodic orbits we reveal the existence of an oscillatory behavior, that is explained solely in terms of the primary homoclinic motion. Furthermore, our results indicate that it survives the semiclassical limit.

  15. New Certificateless Blind Ring Signature Scheme

    Directory of Open Access Journals (Sweden)

    Hua Sun

    2013-07-01

    Full Text Available A new certificateless blind ring signature scheme was proposed in this paper. The scheme could not only avoid the problem of certificate management of public key certificate cryptography, but also overcome the inherent key-escrow problem of identity-based public key cryptography. In the last, by using bilinear pairing technique, it was proved that this scheme satisfied the security of existential unforgeability, blindness and unconditional anonymity.

  16. Infra-sound Signature of Lightning

    Science.gov (United States)

    Arechiga, R. O.; Badillo, E.; Johnson, J.; Edens, H. E.; Rison, W.; Thomas, R. J.

    2012-12-01

    We have analyzed thunder from over 200 lightning flashes to determine which part of thunder comes from the gas dynamic expansion of portions of the rapidly heated lightning channel and which from electrostatic field changes. Thunder signals were recorded by a ~1500 m network of 3 to 4 4-element microphone deployed in the Magdalena mountains of New Mexico in the summers of 2011 and 2012. The higher frequency infra-sound and audio-range portion of thunder is thought to come from the gas dynamic expansion, and the electrostatic mechanism gives rise to a signature infra-sound pulse peaked at a few Hz. More than 50 signature infra-sound pulses were observed in different portions of the thunder signal, with no preference towards the beginning or the end of the signal. Detection of the signature pulse occurs sometimes only for one array and sometimes for several arrays, which agrees with the theory that the pulse is highly directional (i.e., the recordings have to be in a specific position with respect to the cloud generating the pulse to be able to detect it). The detection of these pulses under quiet wind conditions by different acoustic arrays corroborates the electrostatic mechanism originally proposed by Wilson [1920], further studied by Dessler [1973] and Few [1985], observed by Bohannon [1983] and Balachandran [1979, 1983], and recently analyzed by Pasko [2009]. Pasko employed a model to explain the electrostatic-to-acoustic energy conversion and the initial compression waves in observed infrasonic pulses, which agrees with the observations we have made. We present thunder samples that exhibit signature infra-sound pulses at different times and acoustic source reconstruction to demonstrate the beaming effect.

  17. V1R promoters are well conserved and exhibit common putative regulatory motifs

    Directory of Open Access Journals (Sweden)

    Lane Robert P

    2007-07-01

    Full Text Available Abstract Background The mouse vomeronasal organ (VNO processes chemosensory information, including pheromone signals that influence reproductive behaviors. The sensory neurons of the VNO express two types of chemosensory receptors, V1R and V2R. There are ~165 V1R genes in the mouse genome that have been classified into ~12 divergent subfamilies. Each sensory neuron of the apical compartment of the VNO transcribes only one of the repertoire of V1R genes. A model for mutually exclusive V1R transcription in these cells has been proposed in which each V1R gene might compete stochastically for a single transcriptional complex. This model predicts that the large repertoire of divergent V1R genes in the mouse genome contains common regulatory elements. In this study, we have characterized V1R promoter regions by comparative genomics and by mapping transcription start sites. Results We find that transcription is initiated from ~1 kb promoter regions that are well conserved within V1R subfamilies. While cross-subfamily homology is not evident by traditional methods, we developed a heuristic motif-searching tool, LogoAlign, and applied this tool to identify motifs shared within the promoters of all V1R genes. Our motif-searching tool exhibits rapid convergence to a relatively small number of non-redundant solutions (97% convergence. We also find that the best motifs contain significantly more information than those identified in controls, and that these motifs are more likely to be found in the immediate vicinity of transcription start sites than elsewhere in gene blocks. The best motifs occur near transcription start sites of ~90% of all V1R genes and across all of the divergent subfamilies. Therefore, these motifs are candidate binding sites for transcription factors involved in V1R co-regulation. Conclusion Our analyses show that V1R subfamilies have broad and well conserved promoter regions from which transcription is initiated. Results from a new

  18. Spectroscopic characterization of nitroaromatic landmine signature explosives

    Science.gov (United States)

    Hernandez-Rivera, Samuel P.; Manrique-Bastidas, Cesar A.; Blanco, Alejandro; Primera, Oliva M.; Pacheco, Leonardo C.; Castillo-Chara, Jairo; Castro, Miguel E.; Mina, Nairmen

    2004-09-01

    TNT and DNT are important explosives used as base charges of landmines and other explosive devices. They are often combined with RDX in specific explosive formulations. Their detection in vapor phase as well as in soil in contact with the explosives is important in landmine detection technology. The spectroscopic signatures of nitroaromatic compounds in neat forms: crystals, droplets, and recrystallized samples were determined by Raman Microspectroscopy (RS), Fourier Transform Infrared Microscopy (FTIR) and Fiber Optics Coupled - Fourier Transform Infrared Spectroscopy (FOC-FTIR) using a grazing angle (GA) probe. TNT exhibits a series of characteristic bands: vibrational signatures, which allow its detection in soil. The spectroscopic signature of neat TNT is dominated by strong bands about 1380 and 2970 cm-1. The intensity and position of these bands were found remarkably different in soil samples spiked with TNT. The 1380 cm-1 band is split into a number of bands in that region. The 2970 cm-1 band is reduced in intensity and new bands are observed about 2880 cm-1. The results are consistent with a different chemical environment of TNT in soil as compared to neat TNT. Interactions were found to be dependent on the physical source of the explosive. In the case of DNT-sand interactions, shifts in vibrational frequencies of the explosives as well as the substrates were found.

  19. New particles and their experimental signatures

    International Nuclear Information System (INIS)

    This report summarizes work done by our theoretical working group on exotic particles before, during and since the Lausanne meeting. We discuss the motivations, rates and experimental signatures for new physics and new particles in the 1 TeV mass range. Section 2 reviews some of the motivations for expecting new physics in this range. Of particular interest is the physics of gauge symmetry breaking. In section 3 we discuss the rates and experimental signatures of new particles predicted by theoretical models of gauge symmetry breaking, notably the Higgs boson supersymmetry and technicolour. Among the signatures we discuss are multiple Wsup(+-) and/or Z0 events (for the Higgs), missing transverse energy (for supersymmetry) and multiple anti tt events (for the Higgs and technicolour). We provide many examples of final state differential distributions in rapidity and Psub(T), particularly for Higgses and for supersymmetry. We also analyse some physics backgrounds to the new particle production processes which interest us. Examples include W+W-, Z0Z0, W(anti tt) and (anti tt) production as backgrounds to Higgs production. However, we do not consider in detail non-physics backgrounds such as the jet fluctuation background to missing energy signals for supersymmetry production. Section 4 summarizes our preliminary conclusions on the observability at a high energy hadron collider of the new particles studied in this report. (orig./HSI)

  20. Online Signature Verification Using Fourier Descriptors

    Science.gov (United States)

    Yanikoglu, Berrin; Kholmatov, Alisher

    2009-12-01

    We present a novel online signature verification system based on the Fast Fourier Transform. The advantage of using the Fourier domain is the ability to compactly represent an online signature using a fixed number of coefficients. The fixed-length representation leads to fast matching algorithms and is essential in certain applications. The challenge on the other hand is to find the right preprocessing steps and matching algorithm for this representation. We report on the effectiveness of the proposed method, along with the effects of individual preprocessing and normalization steps, based on comprehensive tests over two public signature databases. We also propose to use the pen-up duration information in identifying forgeries. The best results obtained on the SUSIG-Visual subcorpus and the MCYT-100 database are 6.2% and 12.1% error rate on skilled forgeries, respectively. The fusion of the proposed system with our state-of-the-art Dynamic Time Warping (DTW) system lowers the error rate of the DTW system by up to about 25%. While the current error rates are higher than state-of-the-art results for these databases, as an approach using global features, the system possesses many advantages. Considering also the suggested improvements, the FFT system shows promise both as a stand-alone system and especially in combination with approaches that are based on local features.

  1. Radiation-induced cathodoluminescent signatures in calcite

    International Nuclear Information System (INIS)

    At ambient temperatures, a permanent change due to neutron irradiation has been identified in the luminescent properties of the common mineral calcite. Calcite is one of many ubiquitous minerals that are known to exhibit luminescence under electron bombardment, a process known as cathodoluminescence (CL). The UV–Visible spectra of individual calcite grains were measured with CL spectroscopy before and after neutron irradiation. Exposure to neutrons causes additional crystal lattice defects (beyond those naturally-occurring) that leave a permanent, readily-measurable CL signature in the 515 nm region of the spectrum. Dose response results following irradiation have been measured and a spectroscopic signature is described that increases proportionately to neutron dose. The CL measurements are complicated by a dependence on the orientation relative to direction of excitation. When taken into account, the total dose to the crystal can be estimated, and possibly even the direction of the neutron source can be determined. This signature could potentially be developed into a nuclear forensics tool to help identify locations where special nuclear materials have been stored.

  2. Lower Bounds on Signatures from Symmetric Primitives

    CERN Document Server

    Barak, Boaz

    2008-01-01

    We show that every construction of one-time signature schemes from a random oracle achieves black-box security at most $2^{(1+o(1))q}$, where $q$ is the total number of oracle queries asked by the key generation, signing, and verification algorithms. That is, any such scheme can be broken with probability close to 1 by a (computationally unbounded) adversary making $2^{(1+o(1))q}$ queries to the oracle. This is tight up to a constant factor in the number of queries, since a simple modification of Lamport's one-time signatures (Lamport '79) achieves $2^{(0.812-o(1))q}$ black-box security using $q$ queries to the oracle. \\Bnote{standard def of signature scheme is for any size message, so there's no need to talk about $n$ in the abstract.} Our result extends (with a loss of a constant factor in the number of queries) also to the random permutation and ideal-cipher oracles. Since the symmetric primitives (e.g. block ciphers, hash functions, and message authentication codes) can be constructed by a constant number...

  3. SIGNATURES OF LONG-LIVED SPIRAL PATTERNS

    Energy Technology Data Exchange (ETDEWEB)

    Martinez-Garcia, Eric E. [Instituto Nacional de Astrofisica, Optica y Electronica (INAOE), Aptdo. Postal 51 y 216, 72000 Puebla, Pue. (Mexico); Gonzalez-Lopezlira, Rosa A., E-mail: ericmartinez@inaoep.mx, E-mail: martinez@astro.unam.mx, E-mail: r.gonzalez@crya.unam.mx [Centro de Radioastronomia y Astrofisica, UNAM, Campus Morelia, Michoacan, C.P. 58089 (Mexico)

    2013-03-10

    Azimuthal age/color gradients across spiral arms are a signature of long-lived spirals. From a sample of 19 normal (or weakly barred) spirals where we have previously found azimuthal age/color gradient candidates, 13 objects were further selected if a two-armed grand-design pattern survived in a surface density stellar mass map. Mass maps were obtained from optical and near-infrared imaging, by comparison with a Monte Carlo library of stellar population synthesis models that allowed us to obtain the mass-to-light ratio in the J band, (M/L){sub J}, as a function of (g - i) versus (i - J) color. The selected spirals were analyzed with Fourier methods in search of other signatures of long-lived modes related to the gradients, such as the gradient divergence toward corotation, and the behavior of the phase angle of the two-armed spiral in different wavebands, as expected from theory. The results show additional signatures of long-lived spirals in at least 50% of the objects.

  4. EEVD motif of heat shock cognate protein 70 contributes to bacterial uptake by trophoblast giant cells

    Directory of Open Access Journals (Sweden)

    Kim Suk

    2009-12-01

    Full Text Available Abstract Background The uptake of abortion-inducing pathogens by trophoblast giant (TG cells is a key event in infectious abortion. However, little is known about phagocytic functions of TG cells against the pathogens. Here we show that heat shock cognate protein 70 (Hsc70 contributes to bacterial uptake by TG cells and the EEVD motif of Hsc70 plays an important role in this. Methods Brucella abortus and Listeria monocytogenes were used as the bacterial antigen in this study. Recombinant proteins containing tetratricopeptide repeat (TPR domains were constructed and confirmation of the binding capacity to Hsc70 was assessed by ELISA. The recombinant TPR proteins were used for investigation of the effect of TPR proteins on bacterial uptake by TG cells and on pregnancy in mice. Results The monoclonal antibody that inhibits bacterial uptake by TG cells reacted with the EEVD motif of Hsc70. Bacterial TPR proteins bound to the C-terminal of Hsc70 through its EEVD motif and this binding inhibited bacterial uptake by TG cells. Infectious abortion was also prevented by blocking the EEVD motif of Hsc70. Conclusions Our results demonstrate that surface located Hsc70 on TG cells mediates the uptake of pathogenic bacteria and proteins containing the TPR domain inhibit the function of Hsc70 by binding to its EEVD motif. These molecules may be useful in the development of methods for preventing infectious abortion.

  5. Duplication and Divergence Effect on Network Motifs in Undirected Bio-Molecular Networks.

    Science.gov (United States)

    Pei Wang; Jinhu Lu; Xinghuo Yu; Zengrong Liu

    2015-06-01

    Duplication and divergence are two basic evolutionary mechanisms of bio-molecular networks. Real-world bio-molecular networks and their statistical characteristics can be well mimicked by artificial algorithms based on the two mechanisms. Bio-molecular networks consist of network motifs, which act as building blocks of large-scale networks. A fundamental question is how network motifs are evolved from long time evolution and natural selection. By considering the effect of various duplication and divergence strategies, we find that the underlying duplication scheme of the real-world undirected bio-molecular networks would rather follow the anti-preference strategy than the random one. The anti-preference duplication mechanism and the dimerization processes can lead to the formation of various motifs, and robustly conserve proper quantities of motifs in the artificial networks as that in the real-world ones. Furthermore, the anti-preference mechanism and edge deletion divergence can robustly preserve the sparsity of the networks. The investigations reveal the possible evolutionary mechanisms of network motifs in real-world bio-molecular networks, and have potential implications in the design, synthesis and reengineering of biological networks for biomedical purpose. PMID:25203993

  6. Stochastic resonance in feedforward-loop neuronal network motifs in astrocyte field.

    Science.gov (United States)

    Liu, Ying; Li, Chunguang

    2013-10-21

    Elucidating the underlying dynamical properties of neuronal network motifs, statistically significant patterns of interconnections, is essential to understand the dynamics of the whole networks. Besides, the brain is intrinsically noisy. Various noise-induced dynamical behaviors, in particular, the stochastic resonance (SR), have been found in both neuronal systems and neuronal network motifs. However, the effect of astrocytes, active partners in neuronal signal processing, has not yet received much attention. In this paper, we study the effect of astrocytes on the stochastic behaviors of the typical triple-neuron feedforward-loop (FFL) neuronal network motifs. The neurons are described by the Hodgkin-Huxley model, while the astrocytes are modeled by extending the Li-Rinzel model to a two-dimensional field with the effect of diffusion. The mutual neuron-astrocyte interactions are established correspondingly. Simulation results indicate that the stochastic behaviors of the FFL motifs show bell-shaped dependence on the intensities of both noise and astrocyte-neuron coupling. Moreover, in the presence of astrocytes, the performance of the FFL motifs on weak signal transmission in both noisy and noise-free environments can be significantly improved. From this point of view, the astrocytes can be regarded as a possible internal source of "noise", which assist the neurons in signal processing. PMID:23871712

  7. Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif

    International Nuclear Information System (INIS)

    The DNA i-motif is a quadruplex structure formed in tandem cytosine-rich sequences in slightly acidic conditions. Besides being considered as a building block of DNA nano-devices, it may also play potential roles in regulating chromosome stability and gene transcriptions. The stability of i-motif is crucial for these functions. In this work, we investigated the mechanical stability of a single i-motif formed in the human telomeric sequence 5'-(CCCTAA)3CCC, which revealed a novel pH and loading rate-dependent bimodal unfolding force distribution. Although the cause of the bimodal unfolding force species is not clear, we proposed a phenomenological model involving a direct unfolding favored at lower loading rate or higher pH value, which is subject to competition with another unfolding pathway through a mechanically stable intermediate state whose nature is yet to be determined. Overall, the unique mechano—chemical responses of i-motif-provide a new perspective to its stability, which may be useful to guide designing new i-motif-based DNA mechanical nano-devices

  8. Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

    Science.gov (United States)

    Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

    2016-04-01

    The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

  9. A Simple Decision Rule for Recognition of Poly(A) Tail Signal Motifs in Human Genome

    KAUST Repository

    Eisha, Hassan Abou

    2015-05-12

    Background is the numerous attempts were made to predict motifs in genomic sequences that correspond to poly (A) tail signals. Vast portion of this effort has been directed to a plethora of nonlinear classification methods. Even when such approaches yield good discriminant results, identifying dominant features of regulatory mechanisms nevertheless remains a challenge. In this work, we look at decision rules that may help identifying such features. Findings are we present a simple decision rule for classification of candidate poly (A) tail signal motifs in human genomic sequence obtained by evaluating features during the construction of gradient boosted trees. We found that values of a single feature based on the frequency of adenine in the genomic sequence surrounding candidate signal and the number of consecutive adenine molecules in a well-defined region immediately following the motif displays good discriminative potential in classification of poly (A) tail motifs for samples covered by the rule. Conclusions is the resulting simple rule can be used as an efficient filter in construction of more complex poly(A) tail motifs classification algorithms.

  10. Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Kim Man-Sun

    2012-05-01

    Full Text Available Abstract Background Network motifs provided a “conceptual tool” for understanding the functional principles of biological networks, but such motifs have primarily been used to consider static network structures. Static networks, however, cannot be used to reveal time- and region-specific traits of biological systems. To overcome this limitation, we proposed the concept of a “spatiotemporal network motif,” a spatiotemporal sequence of network motifs of sub-networks which are active only at specific time points and body parts. Results On the basis of this concept, we analyzed the developmental gene regulatory network of the Drosophila melanogaster embryo. We identified spatiotemporal network motifs and investigated their distribution pattern in time and space. As a result, we found how key developmental processes are temporally and spatially regulated by the gene network. In particular, we found that nested feedback loops appeared frequently throughout the entire developmental process. From mathematical simulations, we found that mutual inhibition in the nested feedback loops contributes to the formation of spatial expression patterns. Conclusions Taken together, the proposed concept and the simulations can be used to unravel the design principle of developmental gene regulatory networks.

  11. FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web.

    Science.gov (United States)

    Shapiro, Jessica; Brutlag, Douglas

    2004-07-01

    The FoldMiner web server (http://foldminer.stanford.edu/) provides remote access to methods for protein structure alignment and unsupervised motif discovery. FoldMiner is unique among such algorithms in that it improves both the motif definition and the sensitivity of a structural similarity search by combining the search and motif discovery methods and using information from each process to enhance the other. In a typical run, a query structure is aligned to all structures in one of several databases of single domain targets in order to identify its structural neighbors and to discover a motif that is the basis for the similarity among the query and statistically significant targets. This process is fully automated, but options for manual refinement of the results are available as well. The server uses the Chime plugin and customized controls to allow for visualization of the motif and of structural superpositions. In addition, we provide an interface to the LOCK 2 algorithm for rapid alignments of a query structure to smaller numbers of user-specified targets. PMID:15215444

  12. DXD Motif-Dependent and -Independent Effects of the Chlamydia trachomatis Cytotoxin CT166

    Directory of Open Access Journals (Sweden)

    Miriam Bothe

    2015-02-01

    Full Text Available The Gram-negative, intracellular bacterium Chlamydia trachomatis causes acute and chronic urogenital tract infection, potentially leading to infertility and ectopic pregnancy. The only partially characterized cytotoxin CT166 of serovar D exhibits a DXD motif, which is important for the enzymatic activity of many bacterial and mammalian type A glycosyltransferases, leading to the hypothesis that CT166 possess glycosyltransferase activity. CT166-expressing HeLa cells exhibit actin reorganization, including cell rounding, which has been attributed to the inhibition of the Rho-GTPases Rac/Cdc42. Exploiting the glycosylation-sensitive Ras(27H5 antibody, we here show that CT166 induces an epitope change in Ras, resulting in inhibited ERK and PI3K signaling and delayed cell cycle progression. Consistent with the hypothesis that these effects strictly depend on the DXD motif, CT166 with the mutated DXD motif causes neither Ras-ERK inhibition nor delayed cell cycle progression. In contrast, CT166 with the mutated DXD motif is still capable of inhibiting cell migration, suggesting that CT166 with the mutated DXD motif cannot be regarded as inactive in any case. Taken together, CT166 affects various fundamental cellular processes, strongly suggesting its importance for the intracellular survival of chlamydia.

  13. Importance of NPA motifs in the expression and function of water channel aquaporin-1

    Institute of Scientific and Technical Information of China (English)

    JIANG Yong; MA TongHui

    2007-01-01

    The asparagine-proline-alanine sequences (NPA motifs) are highly conserved in aquaporin water channel family. Crystallographic studies of AQP1 structure demonstrated that the two NPA motifs are in the narrow central constriction of the channel, serving to bind water molecules for selective and efficient water passage. To investigate the importance of the two NPA motifs in the structure, function and biogenesis of aquaporin water channels, we generated AQP1 mutations with NPA1 deletion, NPA2 deletion and NPA1,2 double deletion. The coding sequences of the three mutated cDNAs were subcloned into the mammalian expression vector pcDNA3.1 to form expression plasmids. We established stably transfected CHO cell lines expressing these AQP1 mutants. Immunofluorescence indicated that all the three mutated AQP1 proteins are expressed normally on the plasma membrane of stably transfected CHO cells, suggesting that deletion of NPA motifs does not influence the expression and intracellular processing of AQP1. Functional analysis demonstrated that NPA1 or NPA2 deletion reduced AQP1 water permeability by 49.6% and 46.7%, respectively, while NPA1,2 double deletion had little effect on AQP1 water permeability. These results provide evidence that NPA motifs are important for water per-meation but not essential for the expression, intracellular processing and the basic structure of AQP1 water channel.

  14. Dragon polya spotter: Predictor of poly(A) motifs within human genomic DNA sequences

    KAUST Repository

    Kalkatawi, Manal Matoq Saeed

    2011-11-15

    Motivation: Recognition of poly(A) signals in mRNA is relatively straightforward due to the presence of easily recognizable polyadenylic acid tail. However, the task of identifying poly(A) motifs in the primary genomic DNA sequence that correspond to poly(A) signals in mRNA is a far more challenging problem. Recognition of poly(A) signals is important for better gene annotation and understanding of the gene regulation mechanisms. In this work, we present one such poly(A) motif prediction method based on properties of human genomic DNA sequence surrounding a poly(A) motif. These properties include thermodynamic, physico-chemical and statistical characteristics. For predictions, we developed Artificial Neural Network and Random Forest models. These models are trained to recognize 12 most common poly(A) motifs in human DNA. Our predictors are available as a free web-based tool accessible at http://cbrc.kaust.edu.sa/dps. Compared with other reported predictors, our models achieve higher sensitivity and specificity and furthermore provide a consistent level of accuracy for 12 poly(A) motif variants. The Author(s) 2011. Published by Oxford University Press. All rights reserved.

  15. 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

  16. qPMS9: An Efficient Algorithm for Quorum Planted Motif Search

    Science.gov (United States)

    Nicolae, Marius; Rajasekaran, Sanguthevar

    2015-01-01

    Discovering patterns in biological sequences is a crucial problem. For example, the identification of patterns in DNA sequences has resulted in the determination of open reading frames, identification of gene promoter elements, intron/exon splicing sites, and SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have led to domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, discovery of short functional motifs, etc. In this paper we focus on the identification of an important class of patterns, namely, motifs. We study the (l, d) motif search problem or Planted Motif Search (PMS). PMS receives as input n strings and two integers l and d. It returns all sequences M of length l that occur in each input string, where each occurrence differs from M in at most d positions. Another formulation is quorum PMS (qPMS), where the motif appears in at least q% of the strings. We introduce qPMS9, a parallel exact qPMS algorithm that offers significant runtime improvements on DNA and protein datasets. qPMS9 solves the challenging DNA (l, d)-instances (28, 12) and (30, 13). The source code is available at https://code.google.com/p/qpms9/.

  17. Identification of helix capping and {beta}-turn motifs from NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2012-03-15

    We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and {sup 13}C{sup {beta}} chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of {beta}-turns: I, II, I Prime , II Prime and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and {beta}-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7-0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

  18. Cyclostationary signature design for common control channel of cognitive radio

    Institute of Scientific and Technical Information of China (English)

    QI Yuan; PENG Tao; WANG Wen-bo; LUO Shi-feng

    2009-01-01

    Embedding specific signatures in transmitted signals for identifying common control channels of cognitive radio are addressed in research laboratories because availability of the spectrum occupied by the common control channel might change in time. A novel solution to embed a unique cyclostationary signature for the common control channel of cognitive radio is proposed in this article. Based on linear periodically time-variant transformation (LPTV) model, the cyclic autocorrelation expression of the proposed signature is derived, which characterizes its cyclostationarity. Analysis of the cyclostationary signature is presented considering effects of additive white Gaussian noise(AWGN)and multiplath channels. Simulation results illustrating the reliability of signatures are given.

  19. Identity-Based Verifiably Encrypted Signatures without Random Oracles

    Science.gov (United States)

    Zhang, Lei; Wu, Qianhong; Qin, Bo

    Fair exchange protocol plays an important role in electronic commerce in the case of exchanging digital contracts. Verifiably encrypted signatures provide an optimistic solution to these scenarios with an off-line trusted third party. In this paper, we propose an identity-based verifiably encrypted signature scheme. The scheme is non-interactive to generate verifiably encrypted signatures and the resulting encrypted signature consists of only four group elements. Based on the computational Diffie-Hellman assumption, our scheme is proven secure without using random oracles. To the best of our knowledge, this is the first identity-based verifiably encrypted signature scheme provably secure in the standard model.

  20. A NEW EFFICIENT ID-BASED PROXY BLIND SIGNATURE SCHEME

    Institute of Scientific and Technical Information of China (English)

    Ming Yang; Wang Yumin

    2008-01-01

    In a proxy blind signature scheme, the proxy signer is allowed to generate a blind signature on behalf of the original signer. The proxy blind signature scheme is useful in several applications such as e-voting, e-payment, etc. Recently, Zheng, et al. presented an IDentity (ID)-based proxy blind signature. In this paper, a new efficient ID-based proxy blind signature scheme from bilinear pairings is proposed, which can satisfy the security properties of both the proxy signatures and the blind signature schemes. Analysis of the scheme efficiency shows that the new scheme is more efficient than Zheng, et al.'s scheme. The proposed scheme is more practical in the real world.