WorldWideScience

Sample records for graph-set motif c2

  1. The conserved basic residues and the charged amino acid residues at the α-helix of the zinc finger motif regulate the nuclear transport activity of triple C2H2 zinc finger proteins

    Science.gov (United States)

    Lin, Chih-Ying

    2018-01-01

    Zinc finger (ZF) motifs on proteins are frequently recognized as a structure for DNA binding. Accumulated reports indicate that ZF motifs contain nuclear localization signal (NLS) to facilitate the transport of ZF proteins into nucleus. We investigated the critical factors that facilitate the nuclear transport of triple C2H2 ZF proteins. Three conserved basic residues (hot spots) were identified among the ZF sequences of triple C2H2 ZF proteins that reportedly have NLS function. Additional basic residues can be found on the α-helix of the ZFs. Using the ZF domain (ZFD) of Egr-1 as a template, various mutants were constructed and expressed in cells. The nuclear transport activity of various mutants was estimated by analyzing the proportion of protein localized in the nucleus. Mutation at any hot spot of the Egr-1 ZFs reduced the nuclear transport activity. Changes of the basic residues at the α-helical region of the second ZF (ZF2) of the Egr-1 ZFD abolished the NLS activity. However, this activity can be restored by substituting the acidic residues at the homologous positions of ZF1 or ZF3 with basic residues. The restored activity dropped again when the hot spots at ZF1 or the basic residues in the α-helix of ZF3 were mutated. The variations in nuclear transport activity are linked directly to the binding activity of the ZF proteins with importins. This study was extended to other triple C2H2 ZF proteins. SP1 and KLF families, similar to Egr-1, have charged amino acid residues at the second (α2) and the third (α3) positions of the α-helix. Replacing the amino acids at α2 and α3 with acidic residues reduced the NLS activity of the SP1 and KLF6 ZFD. The reduced activity can be restored by substituting the α3 with histidine at any SP1 and KLF6 ZFD. The results show again the interchangeable role of ZFs and charge residues in the α-helix in regulating the NLS activity of triple C2H2 ZF proteins. PMID:29381770

  2. Cryptanalysis of C2

    DEFF Research Database (Denmark)

    Borghoff, Julia; Knudsen, Lars Ramkilde; Leander, Gregor

    2009-01-01

    We present several attacks on the block cipher C2, which is used for encrypting DVD Audio discs and Secure Digital cards. C2 has a 56 bit key and a secret 8 to 8 bit S-box. We show that if the attacker is allowed to choose the key, the S-box can be recovered in 2^24 C2 encryptions. Attacking the 56...... bit key for a known S-box can be done in complexity 2^48. Finally, a C2 implementation with a 8 to 8 bit secret S-box (equivalent to 2048 secret bits) and a 56 bit secret key can be attacked in 2^53.5 C2 encryptions on average....

  3. C2 Agility

    DEFF Research Database (Denmark)

    Mitchell, Dr. William; Alberts, David S.; Bernier, Francois

    of improving C2 Agility with empirical evidence obtained from a set of retrospective case studies and simulation-based experiments. Further, it identified next steps toward practical implementation in NATO operations and priorities for increasing the rigor and practicality of methods for measuring...... and improving C2 Agility. The 21st century military mission space is large and complex, characterized by extreme uncertainty, and exposed to increased public and media scrutiny. In addition to the high intensity combat operations traditionally associated with the military, potential missions include a wide...

  4. CompariMotif: quick and easy comparisons of sequence motifs.

    Science.gov (United States)

    Edwards, Richard J; Davey, Norman E; Shields, Denis C

    2008-05-15

    CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/

  5. MHC motif viewer

    DEFF Research Database (Denmark)

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

    2008-01-01

    . 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....... A special viewing feature, MHC fight, allows for display of the specificity of two different MHC molecules side by side. We show how the web server can be used to discover and display surprising similarities as well as differences between MHC molecules within and between different species. The MHC motif...

  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.

  7. Motif enrichment tool.

    Science.gov (United States)

    Blatti, Charles; Sinha, Saurabh

    2014-07-01

    The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. The C2HDM revisited

    Science.gov (United States)

    Fontes, Duarte; Mühlleitner, Margarete; Romão, Jorge C.; Santos, Rui; Silva, João P.; Wittbrodt, Jonas

    2018-02-01

    The complex two-Higgs doublet model is one of the simplest ways to extend the scalar sector of the Standard Model to include a new source of CP-violation. The model has been used as a benchmark model to search for CP-violation at the LHC and as a possible explanation for the matter-antimatter asymmetry of the Universe. In this work, we re-analyse in full detail the softly broken ℤ 2 symmetric complex two-Higgs doublet model (C2HDM). We provide the code C2HDM_HDECAY implementing the C2HDM in the well-known HDECAY program which calculates the decay widths including the state-of-the-art higher order QCD corrections and the relevant off-shell decays. Using C2HDM_HDECAY together with the most relevant theoretical and experimental constraints, including electric dipole moments (EDMs), we review the parameter space of the model and discuss its phenomenology. In particular, we find cases where large CP-odd couplings to fermions are still allowed and provide benchmark points for these scenarios. We examine the prospects of discovering CP-violation at the LHC and show how theoretically motivated measures of CP-violation correlate with observables.

  9. MotifMark: Finding regulatory motifs in DNA sequences.

    Science.gov (United States)

    Hassanzadeh, Hamid Reza; Kolhe, Pushkar; Isbell, Charles L; Wang, May D

    2017-07-01

    The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.

  10. Transfinite C2 interpolant over triangles

    International Nuclear Information System (INIS)

    Alfeld, P.; Barnhill, R.E.

    1984-01-01

    A transfinite C 2 interpolant on a general triangle is created. The required data are essentially C 2 , no compatibility conditions arise, and the precision set includes all polynomials of degree less than or equal to eight. The symbol manipulation language REDUCE is used to derive the scheme. The scheme is discretized to two different finite dimensional C 2 interpolants in an appendix

  11. Motif signatures of transcribed enhancers

    KAUST Repository

    Kleftogiannis, Dimitrios

    2017-09-14

    In mammalian cells, transcribed enhancers (TrEn) play important roles in the initiation of gene expression and maintenance of gene expression levels in spatiotemporal manner. One of the most challenging questions in biology today is how the genomic characteristics of enhancers relate to enhancer activities. This is particularly critical, as several recent studies have linked enhancer sequence motifs to specific functional roles. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers genomic code in a more systematic way. To address this problem, we developed a novel computational method, TELS, aimed at identifying predictive cell type/tissue specific motif signatures. We used TELS to compile a comprehensive catalog of motif signatures for all known TrEn identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that distinct cell type/tissue specific motif signatures characterize TrEn. These signatures allow discriminating successfully a) TrEn from random controls, proxy of non-enhancer activity, and b) cell type/tissue specific TrEn from enhancers expressed and transcribed in different cell types/tissues. TELS codes and datasets are publicly available at http://www.cbrc.kaust.edu.sa/TELS.

  12. Kopi dan Kakao dalam Kreasi Motif Batik Khas Jember

    Directory of Open Access Journals (Sweden)

    Irfa'ina Rohana Salma

    2015-06-01

    Full Text Available ABSTRAK Batik Jember selama ini identik dengan motif daun tembakau. Visualisasi daun tembakau dalam motif Batik Jember cukup lemah, yaitu kurang berkarakter karena motif yang muncul adalah seperti gambar daun pada umumnya. Oleh karena itu perlu diciptakan desain motif batik khas Jember yang sumber inspirasinya digali dari kekayaan alam lainnya dari Jember yang mempunyai bentuk spesifik dan karakteristik sehingga identitas motif bisa didapatkan dengan lebih kuat. Hasil alam khas Jember tersebut adalah kopi dan kakao. Tujuan penciptaan seni ini adalah untuk menghasilkan motif batik  baru yang mempunyai ciri khas Jember. Metode yang digunakan yaitu pengumpulan data, pengamatan mendalam terhadap objek penciptaan, pengkajian sumber inspirasi, pembuatan desain motif, dan perwujudan menjadi batik. Dari penciptaan seni ini berhasil dikreasikan 6 (enam motif batik yaitu: (1 Motif Uwoh Kopi; (2 Motif Godong Kopi;  (3 Motif Ceplok Kakao; (4 Motif Kakao Raja; (5 Motif Kakao Biru; dan (6 Motif Wiji Mukti. Berdasarkan hasil penilaian “Selera Estetika” diketahui bahwa motif yang paling banyak disukai adalah Motif Uwoh Kopi dan Motif Kakao Raja. Kata kunci: Motif Woh Kopi, Motif Godong Kopi, Motif Ceplok Kakao, Motif Kakao Raja, Motif Kakao Biru, Motif Wiji Mukti ABSTRACTBatik Jember is synonymous with tobacco leaf motif. Tobacco leaf shape is quite weak in the visual appearance characterized as that motif emerges like a picture of leaves in general. Therefore, it is necessary to create a distinctive design motif extracted from other natural resources of Jember that have specific shapes and characteristics that can be obtained as the stronger motif identity. The typical natural resources from Jember are coffee and cocoa. The purpose of the creation of this art is to produce the unique, creative and innovative batik and have specific characteristics of Jember. The method used are data collection, observation of the object, reviewing inspiration sources

  13. Statistical tests to compare motif count exceptionalities

    Directory of Open Access Journals (Sweden)

    Vandewalle Vincent

    2007-03-01

    Full Text Available Abstract Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.

  14. Exploitation of Web Technologies for C2

    National Research Council Canada - National Science Library

    Gardner, Sheldon; Callihan, Hubert D; Balash, John A; Saverino, Michael A

    1999-01-01

    .... They address some major issues related to the use and relevance of these technologies for C2 such as Scalability, Multi-Site Collaboration, Software Migration, Legacy Integration, Obsolescence, and Extensibility. Web links to sites containing further information are provided.

  15. BayesMotif: de novo protein sorting motif discovery from impure datasets.

    Science.gov (United States)

    Hu, Jianjun; Zhang, Fan

    2010-01-18

    Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms. We formulated the protein sorting motif discovery problem as a classification problem and proposed a Bayesian classifier based algorithm (BayesMotif) for de novo identification of a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions. A false positive removal procedure is developed to iteratively remove sequences that are unlikely to contain true motifs so that the algorithm can identify motifs from impure input sequences. Experiments on both implanted motif datasets and real-world datasets showed that the enhanced BayesMotif algorithm can identify anchored sorting motifs from pure or impure protein sequence dataset. It also shows that the false positive removal procedure can help to identify true motifs even when there is only 20% of the input sequences containing true motif instances. We proposed BayesMotif, a novel Bayesian classification based algorithm for de novo discovery of a special category of anchored protein sorting motifs from impure datasets. Compared to conventional motif discovery algorithms such as MEME, our algorithm can find less-conserved motifs with short highly conserved anchors. Our algorithm also has the advantage of easy incorporation of additional meta-sequence features such as hydrophobicity or charge of the motifs which may help to overcome the limitations of

  16. Fitness for synchronization of network motifs

    DEFF Research Database (Denmark)

    Vega, Y.M.; Vázquez-Prada, M.; Pacheco, A.F.

    2004-01-01

    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....

  17. Compact toroid injection into C-2U

    Science.gov (United States)

    Roche, Thomas; Gota, H.; Garate, E.; Asai, T.; Matsumoto, T.; Sekiguchi, J.; Putvinski, S.; Allfrey, I.; Beall, M.; Cordero, M.; Granstedt, E.; Kinley, J.; Morehouse, M.; Sheftman, D.; Valentine, T.; Waggoner, W.; the TAE Team

    2015-11-01

    Sustainment of an advanced neutral beam-driven FRC for a period in excess of 5 ms is the primary goal of the C-2U machine at Tri Alpha Energy. In addition, a criteria for long-term global sustainment of any magnetically confined fusion reactor is particle refueling. To this end, a magnetized coaxial plasma-gun has been developed. Compact toroids (CT) are to be injected perpendicular to the axial magnetic field of C-2U. To simulate this environment, an experimental test-stand has been constructed. A transverse magnetic field of B ~ 1 kG is established (comparable to the C-2U axial field) and CTs are fired across it. As a minimal requirement, the CT must have energy density greater than that of the magnetic field it is to penetrate, i.e., 1/2 ρv2 >=B2 / 2μ0 . This criteria is easily met and indeed the CTs traverse the test-stand field. A preliminary experiment on C-2U shows the CT also capable of penetrating into FRC plasmas and refueling is observed resulting in a 20 - 30% increase in total particle number per single-pulsed CT injection. Results from test-stand and C-2U experiments will be presented.

  18. Molecular Evolutionary Constraints that Determine the Avirulence State of Clostridium botulinum C2 Toxin.

    Science.gov (United States)

    Prisilla, A; Prathiviraj, R; Chellapandi, P

    2017-04-01

    Clostridium botulinum (group-III) is an anaerobic bacterium producing C2 toxin along with botulinum neurotoxins. C2 toxin is belonged to binary toxin A family in bacterial ADP-ribosylation superfamily. A structural and functional diversity of binary toxin A family was inferred from different evolutionary constraints to determine the avirulence state of C2 toxin. Evolutionary genetic analyses revealed evidence of C2 toxin cluster evolution through horizontal gene transfer from the phage or plasmid origins, site-specific insertion by gene divergence, and homologous recombination event. It has also described that residue in conserved NAD-binding core, family-specific domain structure, and functional motifs found to predetermine its virulence state. Any mutational changes in these residues destabilized its structure-function relationship. Avirulent mutants of C2 toxin were screened and selected from a crucial site required for catalytic function of C2I and pore-forming function of C2II. We found coevolved amino acid pairs contributing an essential role in stabilization of its local structural environment. Avirulent toxins selected in this study were evaluated by detecting evolutionary constraints in stability of protein backbone structure, folding and conformational dynamic space, and antigenic peptides. We found 4 avirulent mutants of C2I and 5 mutants of C2II showing more stability in their local structural environment and backbone structure with rapid fold rate, and low conformational flexibility at mutated sites. Since, evolutionary constraints-free mutants with lack of catalytic and pore-forming function suggested as potential immunogenic candidates for treating C. botulinum infected poultry and veterinary animals. Single amino acid substitution in C2 toxin thus provides a major importance to understand its structure-function link, not only of a molecule but also of the pathogenesis.

  19. A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.

    Science.gov (United States)

    Tran, Ngoc Tam L; Huang, Chun-Hsi

    2014-02-20

    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 that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data.

  20. MSDmotif: exploring protein sites and motifs

    Directory of Open Access Journals (Sweden)

    Henrick Kim

    2008-07-01

    Full Text Available Abstract Background Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. Results We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS protocol. An additional entry point facilitates XML requests with XML responses. Conclusion MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.

  1. Temporal motifs in time-dependent networks

    International Nuclear Information System (INIS)

    Kovanen, Lauri; Karsai, Márton; 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 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

  2. Motif discovery in ranked lists of sequences

    DEFF Research Database (Denmark)

    Nielsen, Morten Muhlig; Tataru, Paula; Madsen, Tobias

    2016-01-01

    Motif analysis has long been an important method to characterize biological functionality and the current growth of sequencing-based genomics experiments further extends its potential. These diverse experiments often generate sequence lists ranked by some functional property. There is therefore...... advantage of the regular expression feature, including enrichments for combinations of different microRNA seed sites. The method is implemented and made publicly available as an R package and supports high parallelization on multi-core machinery....... a growing need for motif analysis methods that can exploit this coupled data structure and be tailored for specific biological questions. Here, we present an exploratory motif analysis tool, Regmex (REGular expression Motif EXplorer), which offers several methods to evaluate the correlation of motifs...

  3. New C2 synchondrosal fracture classification system

    Energy Technology Data Exchange (ETDEWEB)

    Rusin, Jerome A.; Ruess, Lynne [Department of Radiology, Nationwide Children' s Hospital, Columbus, OH (United States); The Ohio State University College of Medicine and Public Health, Columbus, OH (United States); Daulton, Robert S. [Department of Radiology, Nationwide Children' s Hospital, Columbus, OH (United States)

    2015-06-15

    Excessive cervical flexion-extension accompanying mild to severe impact injuries can lead to C2 synchondrosal fractures in young children. To characterize and classify C2 synchondrosal fracture patterns. We retrospectively reviewed imaging and medical records of children who were treated for cervical spine fractures at our institution between 1995 and 2014. We reviewed all fractures involving the five central C2 synchondroses with regard to patient demographics, mechanism of injury, fracture pattern, associated fractures and other injuries, treatment plans and outcome. Fourteen children had fractures involving the central C2 synchondroses. There were nine boys and five girls, all younger than 6 years. We found four distinct fracture patterns. Eleven complete fractures were further divided into four subtypes (a, b, c and d) based on degree of anterior displacement of the odontoid segment and presence of distraction. Nine of these 11 children had fractures through both odontoneural synchondroses and the odontocentral synchondrosis; one had fractures involving both neurocentral synchondroses and the odontoneural synchondrosis; one had fractures through bilateral odontoneural and bilateral neurocentral synchondroses. Three children had incomplete fractures, defined as a fracture through a single odontoneural synchondrosis with or without partial extension into either the odontocentral or the adjacent neurocentral synchondroses. All complete fractures were displaced or angulated. Four had associated spinal cord injury, including two contusions (subtype c fractures) and two fatal transections (subtype d fractures). Most children were treated with primary halo stabilization. Subtype c fractures required surgical fixation. We describe four patterns of central C2 synchondrosal fractures, including two unique patterns that have not been reported. We propose a classification system to distinguish these fractures and aid in treatment planning. (orig.)

  4. MotifNet: a web-server for network motif analysis.

    Science.gov (United States)

    Smoly, Ilan Y; Lerman, Eugene; Ziv-Ukelson, Michal; Yeger-Lotem, Esti

    2017-06-15

    Network motifs are small topological patterns that recur in a network significantly more often than expected by chance. Their identification emerged as a powerful approach for uncovering the design principles underlying complex networks. However, available tools for network motif analysis typically require download and execution of computationally intensive software on a local computer. We present MotifNet, the first open-access web-server for network motif analysis. MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes. The output motifs are presented graphically and the user can interactively filter them by their significance, number of instances, node and edge labels, and node identities, and view their instances. MotifNet also allows the user to distinguish between motifs that are centered on specific nodes and motifs that recur in distinct parts of the network. MotifNet is freely available at http://netbio.bgu.ac.il/motifnet . The website was implemented using ReactJs and supports all major browsers. The server interface was implemented in Python with data stored on a MySQL database. estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  5. The Rest of the C2 Iceberg

    Science.gov (United States)

    2014-08-01

    Iceberg Feature ones—another documented cognitive bias that is largely subconscious . A final opportunity lost by not having a forward geographic presence...leading to a subtle bias towards the tip-of-the-iceberg systems that most individuals have more famil- iarity with from their tactical backgrounds...as soon as possible to maintain career viability in a system biased more towards tactical achievement. Acknowledge That the Heart of Operational C2 Is

  6. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

    Science.gov (United States)

    Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

    2013-01-01

    The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

  7. Hunting Motifs in Situla Art

    Directory of Open Access Journals (Sweden)

    Andrej Preložnik

    2013-07-01

    Full Text Available Situla art developed as an echo of the toreutic style which had spread from the Near East through the Phoenicians, Greeks and Etruscans as far as the Veneti, Raeti, Histri, and their eastern neighbours in the region of Dolenjska (Lower Carniola. An Early Iron Age phenomenon (c. 600—300 BC, it rep- resents the major and most arresting form of the contemporary visual arts in an area stretching from the foot of the Apennines in the south to the Drava and Sava rivers in the east. Indeed, individual pieces have found their way across the Alpine passes and all the way north to the Danube. In the world and art of the situlae, a prominent role is accorded to ani- mals. They are displayed in numerous representations of human activities on artefacts crafted in the classic situla style – that is, between the late 6th  and early 5th centuries BC – as passive participants (e.g. in pageants or in harness or as an active element of the situla narrative. The most typical example of the latter is the hunting scene. Today we know at least four objects decorat- ed exclusively with hunting themes, and a number of situlae and other larger vessels where hunting scenes are embedded in composite narratives. All this suggests a popularity unparallelled by any other genre. Clearly recognisable are various hunting techniques and weapons, each associated with a particu- lar type of game (Fig. 1. The chase of a stag with javelin, horse and hound is depicted on the long- familiar and repeatedly published fibula of Zagorje (Fig. 2. It displays a hound mauling the stag’s back and a hunter on horseback pursuing a hind, her neck already pierced by the javelin. To judge by the (so far unnoticed shaft end un- der the stag’s muzzle, the hunter would have been brandishing a second jave- lin as well, like the warrior of the Vače fibula or the rider of the Nesactium situla, presumably himself a hunter. Many parallels to his motif are known from Greece, Etruria, and

  8. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed; Mansour, Essam; Kalnis, Panos

    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

  9. Deciphering functional glycosaminoglycan motifs in development.

    Science.gov (United States)

    Townley, Robert A; Bülow, Hannes E

    2018-03-23

    Glycosaminoglycans (GAGs) such as heparan sulfate, chondroitin/dermatan sulfate, and keratan sulfate are linear glycans, which when attached to protein backbones form proteoglycans. GAGs are essential components of the extracellular space in metazoans. Extensive modifications of the glycans such as sulfation, deacetylation and epimerization create structural GAG motifs. These motifs regulate protein-protein interactions and are thereby repsonsible for many of the essential functions of GAGs. This review focusses on recent genetic approaches to characterize GAG motifs and their function in defined signaling pathways during development. We discuss a coding approach for GAGs that would enable computational analyses of GAG sequences such as alignments and the computation of position weight matrices to describe GAG motifs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Bayesian centroid estimation for motif discovery.

    Science.gov (United States)

    Carvalho, Luis

    2013-01-01

    Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

  11. Bayesian centroid estimation for motif discovery.

    Directory of Open Access Journals (Sweden)

    Luis Carvalho

    Full Text Available Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

  12. C2 Lithium Campaign Power Balance

    Science.gov (United States)

    Trask, Erik; Deng, Bihe; Douglass, Jon; Garate, Eusebio; Gupta, Deepak; Gupta, Sangeeta; Tuszewski, Michel; TAE Team

    2014-10-01

    Several key changes have lead to record performance of the Tri Alpha Energy's (TAE) C2 Field Reversed Configuration (FRC) device. Wall conditioning changes from titanium to lithium have decreased radiative losses, while changes in the magnetic field of the SOL and jet have substantially increased energy confinement times. An overview of 0D power flows and timescales will be presented demonstrating that ions behave classically, that anomalous electron losses have been substantially reduced, and that plasma sustainment will require modest increases in heating power. These observations will be quantitatively analyzed as well as compared with both theoretical modeling of the TAE transport and numerical simulations (Q2D).

  13. Command and Control (C2) Agility (Agilite du commandement et du controle (C2))

    Science.gov (United States)

    2014-10-01

    Theoretical v. Calculated C2 Approach Positions maps each C2 Approach into a three- dimensional space (right) with colours and orientation similar to the...218-230. [10] Curran, P.J. and Hussong, A.M. (2009). “Integrative Data Analysis: The Simultaneous Analysis of Multiple Data Sets”, Psychological ...of attack including psychological , physical and Cyber. The Endeavour Space complexity was high initially, but less so towards the end of the campaign

  14. Overview of C-2U FRC Experimental Program and Plans for C-2W

    Science.gov (United States)

    Gota, H.; Binderbauer, M. W.; Tajima, T.; Putvinski, S.; Tuszewski, M.; Dettrick, S.; Korepanov, S.; Smirnov, A.; Thompson, M. C.; Yang, X.; Cappello, M.; Ivanov, A. A.; TAE Team

    2016-10-01

    Tri Alpha Energy's experimental program has been focused on a demonstration of reliable field-reversed configuration (FRC) formation and sustainment, driven by fast ions via high-power neutral-beam (NB) injection. The world's largest compact-toroid experimental devices, C-2 and C-2U, have successfully produced a well-stabilized, sustainable FRC plasma state with NB injection (input power, PNB 10 + MW; 15 keV hydrogen) and end-on coaxial plasma guns. Remarkable improvements in confinement and stability of FRC plasmas have led to further improved fast-ion build up; thereby, an advanced beam-driven FRC state has been produced and sustained for up to 5 + ms (longer than all characteristic system time scales), only limited by hardware and electric supply constraints such as NB and plasma-gun power supplies. To further improve the FRC performance the C-2U device is being replaced by C-2W featuring higher injected NB power, longer pulse duration as well as enhanced edge-biasing systems and substantially upgraded divertors. Main C-2U experimental results and key features of C-2W will be presented. Tri Alpha Energy, Inc.

  15. Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

    Science.gov (United States)

    Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

    2012-01-01

    To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

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

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Hoof, Ilka; Lund, Ole

    2010-01-01

    is 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...

  17. Analisis Unsur Matematika pada Motif Sulam Usus

    Directory of Open Access Journals (Sweden)

    Fredi Ganda Putra

    2017-12-01

    Full Text Available Based on interviews with researchers sources said that the beginning of the intestine embroidery is an art of genuine crafts. Called the intestine embroidery because this technique is a technique of combining a strand of cloth resembling the intestine formed according to the pattern by means of embroidered using a thread. Intestinal embroidery techniques were originally used to create a cover of the women's customary wardrobe of Lampung or often referred to as bebe. But not many people in Lampung, especially people who live in Lampung are still many who do not know and recognize the intestine embroidery because most only know tapis only characteristic of Lampung, besides that there are other cultural results that is embroidered intestine. There are still many who do not know that the intestine motif there is a knowledge of mathematics. The researcher's problem formulation is whether there are mathematical elements contained in the intestine embroidery motif based on the concept of geometry. The purpose of this study is to determine whether there are elements of mathematics contained in the intestine motif based on the concept of geometry. Subjects in this study consisted of 4 people obtained by purposive sampling technique. From the results of data analysis conducted by using descriptive analysis and discussion as follows: (1 Intestinal embroidery motif contains the meaning of mathematics and culture or often called Etnomatematika. On the meaning of culture there is a link between the embroidery intestine with a culture that has been there before as the existence of cultural linkage between Hindu belief Buddhism and there are similarities of motifs and decorative patterns contained in the motif embroidery intestine with ornamental variety in Indonesia. (2 The relationship between the intestine with mathematical motifs there are elements of mathematics such as geometry elements in the form of geometry of dimension one and dimension two, and the

  18. Armadillo motifs involved in vesicular transport.

    Directory of Open Access Journals (Sweden)

    Harald Striegl

    Full Text Available Armadillo (ARM repeat proteins function in various cellular processes including vesicular transport and membrane tethering. They contain an imperfect repeating sequence motif that forms a conserved three-dimensional structure. Recently, structural and functional insight into tethering mediated by the ARM-repeat protein p115 has been provided. Here we describe the p115 ARM-motifs for reasons of clarity and nomenclature and show that both sequence and structure are highly conserved among ARM-repeat proteins. We argue that there is no need to invoke repeat types other than ARM repeats for a proper description of the structure of the p115 globular head region. Additionally, we propose to define a new subfamily of ARM-like proteins and show lack of evidence that the ARM motifs found in p115 are present in other long coiled-coil tethering factors of the golgin family.

  19. Direct AUC optimization of regulatory motifs.

    Science.gov (United States)

    Zhu, Lin; Zhang, Hong-Bo; Huang, De-Shuang

    2017-07-15

    The discovery of transcription factor binding site (TFBS) motifs is essential for untangling the complex mechanism of genetic variation under different developmental and environmental conditions. Among the huge amount of computational approaches for de novo identification of TFBS motifs, discriminative motif learning (DML) methods have been proven to be promising for harnessing the discovery power of accumulated huge amount of high-throughput binding data. However, they have to sacrifice accuracy for speed and could fail to fully utilize the information of the input sequences. We propose a novel algorithm called CDAUC for optimizing DML-learned motifs based on the area under the receiver-operating characteristic curve (AUC) criterion, which has been widely used in the literature to evaluate the significance of extracted motifs. We show that when the considered AUC loss function is optimized in a coordinate-wise manner, the cost function of each resultant sub-problem is a piece-wise constant function, whose optimal value can be found exactly and efficiently. Further, a key step of each iteration of CDAUC can be efficiently solved as a computational geometry problem. Experimental results on real world high-throughput datasets illustrate that CDAUC outperforms competing methods for refining DML motifs, while being one order of magnitude faster. Meanwhile, preliminary results also show that CDAUC may also be useful for improving the interpretability of convolutional kernels generated by the emerging deep learning approaches for predicting TF sequences specificities. CDAUC is available at: https://drive.google.com/drive/folders/0BxOW5MtIZbJjNFpCeHlBVWJHeW8 . dshuang@tongji.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  20. Exploring Effects of C2 Warfare on C2 Ability in a Simulated Environment

    Science.gov (United States)

    2011-06-01

    Principal Axis Factoring, Oblimin rotation with Kaiser Normalization) included all prerequisites, but not the total value of C2 ability ( KMO = .84...Mission intent had the lowest value in this factor, a separate factor analysis was conducted on this factor ( KMO = .75; Bartlett’s test of

  1. Atmospheric studies of C2 white dwarfs

    Science.gov (United States)

    Swanson, Steven Roger

    Model atmosphere and line formation calculations for the delta nu = + 1 Swan bands of the C2 molecule are presented for seven white dwarfs and are compared to high resolution optical spectra. Limits on the C-12 to C-13 ratio are computed for highly pressure broadened lines and are used to analyze the observed spectra for any sign of absorption by the (C-12)(C-13) molecule. The metal abundances in cool white dwarf atmospheres and the usefulness of the determination of the C-12 to C-13 ratio are discussed. The line center shift and the pressure broadening are used to determine a value for the van der Waals interaction constant, C6. This is done using a detailed line modelling program which explicitly includes approximately 2000 rotational transition lines within the vibrational bands, in conjunction with atmospheric models calculated by the LUCIFER atmosphere modelling program. The isotopic shift of the vibrational and rotational lines is also included in the model to compare the detectability of various C-12 to C-13 ratios. The line models fit the observed spectra with varying degrees of accuracy. One star, WD0548-001, shows an unusually small pressure shift and broadening for the high pressures that the atmospheric model predicts. The results show that only in the hottest stars with the least pressure broadened lines in this study can the isotopic effect be seen. With the data available, the best limit on the C-12 to C-13 ratio is a minimum of 40 for WD0856 + 331. The models show that even for very high signal to noise data, the isotopic shift in the Swan bands in very cool white dwarfs would be difficult to separate from the pressure broadening effects. It is shown that the isotopic ratio is high enough to rule out the possibility that the carbon is a relic from previous CNO burning.

  2. Atmospheric studies of C2 white dwarfs

    International Nuclear Information System (INIS)

    Swanson, S.R.

    1989-01-01

    Model atmosphere and line formation calculations for the delta nu = + 1 Swan bands of the C2 molecule are presented for seven white dwarfs and are compared to high resolution optical spectra. Limits on the C-12 to C-13 ratio are computed for highly pressure broadened lines and are used to analyze the observed spectra for any sign of absorption by the (C-12)(C-13) molecule. The metal abundances in cool white dwarf atmospheres and the usefulness of the determination of the C-12 to C-13 ratio are discussed. The line center shift and the pressure broadening are used to determine a value for the van der Waals interaction constant, C6. This is done using a detailed line modelling program which explicitly includes approximately 2000 rotational transition lines within the vibrational bands, in conjunction with atmospheric models calculated by the LUCIFER atmosphere modelling program. The isotopic shift of the vibrational and rotational lines is also included in the model to compare the detectability of various C-12 to C-13 ratios. The line models fit the observed spectra with varying degrees of accuracy. One star, WD0548-001, shows an unusually small pressure shift and broadening for the high pressures that the atmospheric model predicts. The results show that only in the hottest stars with the least pressure broadened lines in this study can the isotopic effect be seen. With the data available, the best limit on the C-12 to C-13 ratio is a minimum of 40 for WD0856 + 331. The models show that even for very high signal to noise data, the isotopic shift in the Swan bands in very cool white dwarfs would be difficult to separate from the pressure broadening effects. It is shown that the isotopic ratio is high enough to rule out the possibility that the carbon is a relic from previous CNO burning

  3. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit; Bajic, Vladimir B.; Kaushik, Dinesh

    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.

  4. 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).

  5. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-01-01

    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. DNA motif elucidation using belief propagation.

    Science.gov (United States)

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-09-01

    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.

  7. 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).

  8. CombiMotif: A new algorithm for network motifs discovery in protein-protein interaction networks

    Science.gov (United States)

    Luo, Jiawei; Li, Guanghui; Song, Dan; Liang, Cheng

    2014-12-01

    Discovering motifs in protein-protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.

  9. A Study of Operationally Relevant C2 Knowledge Management

    National Research Council Canada - National Science Library

    Petrov, Plamen

    2003-01-01

    .... The empirical phase of the project was designed to compare the performance of C2 personnel using an advanced information/knowledge management software environment to C2 personnel using a currently...

  10. Annotating RNA motifs in sequences and alignments.

    Science.gov (United States)

    Gardner, Paul P; Eldai, Hisham

    2015-01-01

    RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterize RNA motifs, which are critical components of many RNA structure-function relationships. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterized RNAs. Moreover, we introduce a new profile-based database of RNA motifs--RMfam--and illustrate some applications for investigating the evolution and functional characterization of RNA. All the data and scripts associated with this work are available from: https://github.com/ppgardne/RMfam. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. 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.

  12. Large-scale discovery of promoter motifs in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Thomas A Down

    2007-01-01

    Full Text Available A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.

  13. The structure of C2b, a fragment of complement component C2 produced during C3 convertase formation

    Energy Technology Data Exchange (ETDEWEB)

    Krishnan, Vengadesan [Center for Biophysical Sciences and Engineering, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294 (United States); Xu, Yuanyuan [Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294 (United States); Macon, Kevin [Center for Biophysical Sciences and Engineering, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294 (United States); Volanakis, John E. [Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 (United States); Narayana, Sthanam V. L., E-mail: narayana@uab.edu [Center for Biophysical Sciences and Engineering, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294 (United States)

    2009-03-01

    The crystal structure of C2b has been determined at 1.8 Å resolution, which reveals the arrangement of its three complement control protein (CCP) modules. A model for complement component C2 is presented and its conformational changes during the C3-convertase formation are also discussed. The second component of complement (C2) is a multi-domain serine protease that provides catalytic activity for the C3 and C5 convertases of the classical and lectin pathways of human complement. The formation of these convertases requires the Mg{sup 2+}-dependent binding of C2 to C4b and the subsequent cleavage of C2 by C1s or MASP2, respectively. The crystal structure of full-length C2 is not yet available, although the structure of its C-terminal catalytic segment C2a has been determined. The crystal structure of the N-terminal segment C2b of C2 determined to 1.8 Å resolution presented here reveals the arrangement of its three CCP domains. The domains are arranged differently compared with most other CCP-domain assemblies, but their arrangement is similar to that found in the Ba part of the full-length factor B structure. The crystal structures of C2a, C2b and full-length factor B are used to generate a model for C2 and a discussion of the domain association and possible interactions with C4b during formation of the C4b–C2 complex is presented. The results of this study also suggest that upon cleavage by C1s, C2a domains undergo conformational rotation while bound to C4b and the released C2b domains may remain folded together similar to as observed in the intact protein.

  14. The structure of C2b, a fragment of complement component C2 produced during C3 convertase formation

    International Nuclear Information System (INIS)

    Krishnan, Vengadesan; Xu, Yuanyuan; Macon, Kevin; Volanakis, John E.; Narayana, Sthanam V. L.

    2009-01-01

    The crystal structure of C2b has been determined at 1.8 Å resolution, which reveals the arrangement of its three complement control protein (CCP) modules. A model for complement component C2 is presented and its conformational changes during the C3-convertase formation are also discussed. The second component of complement (C2) is a multi-domain serine protease that provides catalytic activity for the C3 and C5 convertases of the classical and lectin pathways of human complement. The formation of these convertases requires the Mg 2+ -dependent binding of C2 to C4b and the subsequent cleavage of C2 by C1s or MASP2, respectively. The crystal structure of full-length C2 is not yet available, although the structure of its C-terminal catalytic segment C2a has been determined. The crystal structure of the N-terminal segment C2b of C2 determined to 1.8 Å resolution presented here reveals the arrangement of its three CCP domains. The domains are arranged differently compared with most other CCP-domain assemblies, but their arrangement is similar to that found in the Ba part of the full-length factor B structure. The crystal structures of C2a, C2b and full-length factor B are used to generate a model for C2 and a discussion of the domain association and possible interactions with C4b during formation of the C4b–C2 complex is presented. The results of this study also suggest that upon cleavage by C1s, C2a domains undergo conformational rotation while bound to C4b and the released C2b domains may remain folded together similar to as observed in the intact protein

  15. CONTEMPORARY USAGE OF TRADITIONAL TURKISH MOTIFS IN PRODUCT DESIGNS

    Directory of Open Access Journals (Sweden)

    Tulay Gumuser

    2012-12-01

    Full Text Available The aim of this study is to identify the traditional Turkish motifs and its relations among present industrial designs. Traditional Turkish motifs played a very important role in 16th century onwards. The arts of the Ottoman Empire were used because of their symbolic meanings and unique styles. When we examine these motifs we encounter; Tiger Stripe, Three Spot (Çintemani, Rumi, Hatayi, Penç, Cloud, Crescent, Star, Crown, Hyacinth, Tulip and Carnation motifs. Nowadays, Turkish designers have begun to use these traditional Turkish motifs in their designs so as to create differences and awareness in the world design. The examples of these industrial designs, using the Turkish motifs, have survived and have Ottoman heritage and historical value. In this study, the Turkish motifs will be examined along with their focus on contemporary Turkish industrial designs used today.

  16. Aplikasi Ornamen Khas Maluku untuk Pengembangan Desain Motif Batik

    Directory of Open Access Journals (Sweden)

    Masiswo Masiswo

    2016-04-01

    Full Text Available ABSTRAKMaluku memiliki banyak ragam hias budaya warisan nilai leluhur berupa ornamen etnis yang merupakan kesenian dan keterampilan kerajinan. Hasil warisan tersebut sampai saat ini masih lestari hidup serta dapat dinikmati sebagai konsumsi rohani yang memuaskan manusia. Berkaitan dengan keberlangsungan nilai-nilai tradisi etnis yang berwujud pada ornamen-ornamen daerah Maluku, maka dikembangkan untuk kebutuhan manusia berupa motif batik pada kain. Pengembangan ornamen ini lebih menekankan pada representasi akan bentuk-bentuk ornamen yang diterapkan pada kerajinan batik berupa motif khas Maluku. Pengembangan alternatif desain motif batik dibuat tiga variasi yang bersumber dari ornamen khas Maluku dibuat prototipe produknya dan diuji ketahanan luntur warnanya. Hasil uji ketahanan luntur warna terhadap gosokan basah dari tiga prototipe produk berpredikat baik sekali terdapat pada “Motif Siwa” dan predikat baik pada motif “Siwa Talang” dan motif “Matahari Siwa Talang”.Kata kunci: desain, Maluku, motif batik, ornamenABSTRACTMaluku has much decorative ancestral cultural heritage value in the form of ornament ethnic arts and crafts skills. The result of the legacy is still sustainable living can be enjoyed as well as satisfying spiritual human consumption.Related to the sustainability of traditional values in the form of ethnic ornaments Maluku, it was developed for human needs in the form of batik cloth . The development of these ornaments will be more emphasis on the representation forms of ornamentation that is applied to a batik motif Maluku. Development of alternative design motif made three variations. The development of three alternative design motifs derived from the Maluku ornaments made and tested a prototype product color fastness. The test results of color fastness to wet rubbing of the three prototypes are excellent products predicated on the "Motif Siwa" and a good rating on the motif "Siwa Talang" and motif "Matahari Siwa

  17. Identity and functions of CxxC-derived motifs.

    Science.gov (United States)

    Fomenko, Dmitri E; Gladyshev, Vadim N

    2003-09-30

    Two cysteines separated by two other residues (the CxxC motif) are employed by many redox proteins for formation, isomerization, and reduction of disulfide bonds and for other redox functions. The place of the C-terminal cysteine in this motif may be occupied by serine (the CxxS motif), modifying the functional repertoire of redox proteins. Here we found that the CxxC motif may also give rise to a motif, in which the C-terminal cysteine is replaced with threonine (the CxxT motif). Moreover, in contrast to a view that the N-terminal cysteine in the CxxC motif always serves as a nucleophilic attacking group, this residue could also be replaced with threonine (the TxxC motif), serine (the SxxC motif), or other residues. In each of these CxxC-derived motifs, the presence of a downstream alpha-helix was strongly favored. A search for conserved CxxC-derived motif/helix patterns in four complete genomes representing bacteria, archaea, and eukaryotes identified known redox proteins and suggested possible redox functions for several additional proteins. Catalytic sites in peroxiredoxins were major representatives of the TxxC motif, whereas those in glutathione peroxidases represented the CxxT motif. Structural assessments indicated that threonines in these enzymes could stabilize catalytic thiolates, suggesting revisions to previously proposed catalytic triads. Each of the CxxC-derived motifs was also observed in natural selenium-containing proteins, in which selenocysteine was present in place of a catalytic cysteine.

  18. Scientific and Graphic Design Foundations for C2

    Science.gov (United States)

    2007-06-01

    the elements in the composition. This section presents a summary of the concepts in graphic design layout, typography , color, and data graphics ...document for ease of use 4 Graphic Design • Layout – Literally the aesthetic of the display design • Typography – Serif versus san serif – Font sizes...12th ICCRTS “Adapting C2 to the 21st Century” Title: Scientific and graphic design foundations for C2 Topics: C2 Concepts, Theory and

  19. 26 CFR 1.1402(c)-2 - Public office.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 12 2010-04-01 2010-04-01 false Public office. 1.1402(c)-2 Section 1.1402(c)-2...) INCOME TAXES Tax on Self-Employment Income § 1.1402(c)-2 Public office. (a) In general—(1) General rule... public office does not constitute a trade or business. (2) Fee basis public officials—(i) In general. If...

  20. UKIRAN KERAWANG ACEH GAYO SEBAGAI INSPIRASI PENCIPTAAN MOTIF BATIK KHAS GAYO

    Directory of Open Access Journals (Sweden)

    Irfa ina Rohana Salma

    2016-12-01

    Full Text Available ABSTRAK Industri batik mulai berkembang di Gayo, tetapi belum memiliki motif batik khas daerah. Oleh karena itu perlu diciptakan motif batik khas Gayo, dengan mengambil inspirasi dari ukiran yang terdapat pada rumah tradisional yang biasa disebut ukiran kerawang Gayo. Tujuan penciptaan seni ini adalah untuk menciptakan motif batik yang memiliki ciri khas Gayo. Metode yang digunakan yaitu eksplorasi ide, perancangan, dan perwujudan menjadi motif batik. Dalam kegiatan ini telah diciptakan enam motif batik khas Gayo yaitu: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif Gayo Lurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. Hasil uji kesukaan terhadap motif kepada lima puluh responden menunjukkan bahwa Motif Ceplok Gayo paling banyak dipilih oleh responden yaitu sebesar 19%, sedangkan Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo Lurus 15% dan Motif Gayo Tegak 14%. Rata-rata motif yang dihasilkan mendapatkan apresiasi yang baik dari responden, sehingga semua motif layak diproduksi sebagai batik khas Gayo.Kata kunci: batik Gayo, Motif Ceplok Gayo, Motif Parang Gayo.ABSTRACTBatik industry began to develop in Gayo, but have not had a typical batik motif itself. Therefore, it is necessary to create batik motifs of Gayo, by taking inspiration from the carvings found in traditional houses commonly called kerawang Gayo. The purpose of this art is to create motifs those have a Gayo characteristic. The method used are the idea exploration, design, and motifs embodiment. In this activity has created six Gayo batik motifs, namely: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif GayoLurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. The test results fondness of the motives to fifty respondents indicated that the Motif Ceplok Gayo most preferred by respondents ie 19%, while Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo

  1. 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.

  2. Structural motifs of pre-nucleation clusters.

    Science.gov (United States)

    Zhang, Y; Türkmen, I R; Wassermann, B; Erko, A; Rühl, E

    2013-10-07

    Structural motifs of pre-nucleation clusters prepared in single, optically levitated supersaturated aqueous aerosol microparticles containing CaBr2 as a model system are reported. Cluster formation is identified by means of X-ray absorption in the Br K-edge regime. The salt concentration beyond the saturation point is varied by controlling the humidity in the ambient atmosphere surrounding the 15-30 μm microdroplets. This leads to the formation of metastable supersaturated liquid particles. Distinct spectral shifts in near-edge spectra as a function of salt concentration are observed, in which the energy position of the Br K-edge is red-shifted by up to 7.1 ± 0.4 eV if the dilute solution is compared to the solid. The K-edge positions of supersaturated solutions are found between these limits. The changes in electronic structure are rationalized in terms of the formation of pre-nucleation clusters. This assumption is verified by spectral simulations using first-principle density functional theory and molecular dynamics calculations, in which structural motifs are considered, explaining the experimental results. These consist of solvated CaBr2 moieties, rather than building blocks forming calcium bromide hexahydrates, the crystal system that is formed by drying aqueous CaBr2 solutions.

  3. POWRS: position-sensitive motif discovery.

    Directory of Open Access Journals (Sweden)

    Ian W Davis

    Full Text Available Transcription factors and the short, often degenerate DNA sequences they recognize are central regulators of gene expression, but their regulatory code is challenging to dissect experimentally. Thus, computational approaches have long been used to identify putative regulatory elements from the patterns in promoter sequences. Here we present a new algorithm "POWRS" (POsition-sensitive WoRd Set for identifying regulatory sequence motifs, specifically developed to address two common shortcomings of existing algorithms. First, POWRS uses the position-specific enrichment of regulatory elements near transcription start sites to significantly increase sensitivity, while providing new information about the preferred localization of those elements. Second, POWRS forgoes position weight matrices for a discrete motif representation that appears more resistant to over-generalization. We apply this algorithm to discover sequences related to constitutive, high-level gene expression in the model plant Arabidopsis thaliana, and then experimentally validate the importance of those elements by systematically mutating two endogenous promoters and measuring the effect on gene expression levels. This provides a foundation for future efforts to rationally engineer gene expression in plants, a problem of great importance in developing biotech crop varieties.BSD-licensed Python code at http://grassrootsbio.com/papers/powrs/.

  4. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Science.gov (United States)

    Oliveira, Graziele Pereira; Andrade, Ana Cláudia dos Santos Pereira; Rodrigues, Rodrigo Araújo Lima; Arantes, Thalita Souza; Boratto, Paulo Victor Miranda; Silva, Ludmila Karen dos Santos; Dornas, Fábio Pio; Trindade, Giliane de Souza; Drumond, Betânia Paiva; La Scola, Bernard; Kroon, Erna Geessien; Abrahão, Jônatas Santos

    2017-01-01

    For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations. PMID:28117683

  5. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    Graziele Pereira Oliveira

    2017-01-01

    Full Text Available For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV, raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’ that could be evolved gradually by nucleotides’ gain and loss and point mutations.

  6. C2H observations toward the Orion Bar

    NARCIS (Netherlands)

    Nagy, Z.; Ossenkopf, V.; Van der Tak, F. F. S.; Faure, A.; Makai, Z.; Bergin, E. A.

    Context. The ethynyl radical (C2H) is one of the first radicals to be detected in the interstellar medium. Its higher rotational transitions have recently become available with the Herschel Space Observatory. Aims: We aim to constrain the physical parameters of the C2H emitting gas toward the Orion

  7. Progressively unstable c2 spondylolysis requiring spinal fusion: case report.

    Science.gov (United States)

    Nishimura, Yusuke; Ellis, Michael John; Anderson, Jennifer; Hara, Masahito; Natsume, Atsushi; Ginsberg, Howard Joeseph

    2014-01-01

    Cervical spondylolysis is a rare condition defined as a corticated cleft at the pars interarticularis in the cervical spine. This is the case of C2 spondylolysis demonstrating progressive significant instability, which was successfully treated by anterior cervical discectomy and fusion (ACDF) with cervical anterior plate. We describe a 20-year-old female with C2 spondylolysis presenting with progressive worsening of neck pain associated with progressive instability at the C2/3 segment. The progression of instability was well-documented on flexion-extension cervical spine x-rays. She was successfully treated by C2/3 ACDF with anterior cervical plate. Her preoperative significant neck pain resolved immediately after the surgical intervention. She was completely free from neurological symptoms at 1-year postoperative follow-up. We also review the literature and discuss 24 reported cases with C2 spondylolysis. When planning treatment, we should make sure to differentiate this pathology from acute traumatic fracture, which is a hangman's fracture. Assessment of C2/3 instability associated with neurological deficits is extremely important to consider management properly. C2/3 ACDF with cervical plate is biomechanically viable, less invasive, and provides adequate surgical stabilization for unstable C2 spondylolysis.

  8. Parole, Sintagmatik, dan Paradigmatik Motif Batik Mega Mendung

    Directory of Open Access Journals (Sweden)

    Rudi - Nababan

    2012-04-01

    Full Text Available ABSTRACT   Discussing traditional batik is related a lot to the organization system of fine arts element ac- companying it, either the pattern of the motif or the technique of the making. In this case, the motif of Mega Mendung Cirebon certainly has patterns and rules which are traditionally different from the other motifs in other areas. Through  semiotics analysis especially with Saussure and Pierce concept, it can be traced that batik with Cirebon motif, in this case Mega Mendung motif, has parole and langue system, as unique fine arts language in batik, and structure of visual syntagmatic and paradigmatic. In the context of batik motif as fine arts language, it is surely related to sign system as symbol and icon.       Keywords: visual semiotic, Cirebon’s batik.

  9. Tunable Robust pacs-MOFs: a Platform for Systematic Enhancement of the C2H2 Uptake and C2H2/C2H4 Separation Performance.

    Science.gov (United States)

    Chen, Di-Ming; Sun, Chun-Xiao; Zhang, Nan-Nan; Si, Huan-Huan; Liu, Chun-Sen; Du, Miao

    2018-03-05

    As a modulatable class of porous crystalline materials, metal-organic frameworks (MOFs) have gained intensive research attention in the domain of gas storage and separation. In this study, we report on the synthesis and gas adsorption properties of two robust MOFs with the general formula [Co 3 (μ 3 -OH)(cpt) 3 Co 3 (μ 3 -OH)(L) 3 (H 2 O) 9 ](NO 3 ) 4 (guests) n [L = 3-amino-1,2,4-triazole (1) and 3,5-diamino-1,2,4-triazole (2); Hcpt = 4-(4-carboxyphenyl)-1,2,4-triazole], which show the same pacs topology. Both MOFs are isostructural to each other and show MIL-88-type frameworks whose pore spaces are partitioned by different functionlized trinuclear 1,2,4-triazolate-based clusters. The similar framework components with different amounts of functional groups make them an ideal platform to permit a systematic gas sorption/separation study to evaluate the effects of distinctive parameters on the C 2 H 2 uptake and separation performance. Because of the presence of additional amido groups, the MOF 2 equipped with a datz-based cluster (Hdatz = 3,5-diamino-1,2,4-triazole) shows a much improved C 2 H 2 uptake capacity and separation performance over that of the MOF 1 equipped with atz-based clusters (Hatz = 3-amino-1,2,4-triazole), although the surface area of the MOF 1 is almost twice than that of the MOF 2. Moreover, the high density of open metal sites, abundant free amido groups, and charged framework give the MOF 2 an excellent C 2 H 2 separation performance, with ideal adsorbed solution theory selectivity values reaching up to 11.5 and 13 for C 2 H 2 /C 2 H 4 (1:99) and C 2 H 2 /CO 2 (50:50) at 298 K and 1 bar, showing potential for use in natural gas purification.

  10. Fourier spectroscopy of the 12C2, 13C2, and 12C13C (0-0) swan bands

    International Nuclear Information System (INIS)

    Amiot, C.

    1983-01-01

    The (0-0) band of the C 2 Swan electronic system d 3 Pi/sub g/→a 3 Pi/sub u/ has been recorded by Fourier spectroscopy. The three isotopes species 12 C 2 , 13 C 2 , and 12 C 13 C were investigated. The observed wavenumbers were reduced to molecular parameters using a nonlinear least-square fitting procedure. Well-known perturbations at N' = 47 and N' = 51 again observed in the e 12 C 2 d 3 Pi/sub g/ (v = 0) level. Perturbations of the same kind are present in the 13 C 2 spectrum at N' = 34 and N' = 44,48,52. The 12 C 13 C spectrum exhibits in the observed spectral range a unique perturbation for N' = 41

  11. 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.

  12. Rekayasa Pengembangan Desain Motif Batik Khas Melayu

    Directory of Open Access Journals (Sweden)

    Eustasia Sri Murwati

    2016-04-01

    Full Text Available ABSTRAKPengembangan desain batik melalui rancang bangun perekayasaan desain menurut ragam hias Melayu meliputi pengembangan motif dan proses, termasuk pemilihan komposisi warna. Proses yang sering dilakukan yaitu proses celup, penghilangan lilin dan celup warna tumpangan atau proses colet, celup, penghilangan lilin atau celup kemudian penghilangan lilin yang disebut Batik Kelengan. Setiap pulau di Indonesia mempunyai ciri khas budaya dan kesenian yang dikenal dengan corak/ragam hias khas daerah, juga ornamen yang diminati oleh masyarakat dari daerah tersebut atau dari daerah lain. Kondisi demikian mendorong pertumbuhan industri kerajinan yang memanfaatkan unsur–unsur seni. Adapun motif yang diperoleh adalah: Ayam Berlaga, Bungo Matahari, Kuntum Bersanding, Lancang Kuning, Encong Kerinci, Durian Pecah, Bungo Bintang, Bungo Pauh Kecil, Riang-riang, Bungo Nagaro. Pengembangan desain tersebut dipilih 3 produk terbaik yang dinilai oleh 5 penilai yang ahli di bidang desain batik, yaitu motif Durian Pecah, Ayam Berlaga, dan Bungo Matahari. Rancang bangun diversifikasi desain dengan memanfaatkan unsur–unsur seni dan ketrampilan etnis Melayu yaitu pemilihan ragam hias dan motif batik Melayu untuk diterapkan ke bahan sandang dengan komposisi warna yang menarik, sehingga produk memenuhi selera konsumen. Memperbaiki keberagaman batik dengan meningkatkan desain produk antara lain menuangkan ragam hias Melayu ke dalam proses batik yang menggunakan berbagai macam warna sehingga komposisi warna memadai. Diperoleh hasil produk batik dengan ragam hias Melayu yang berkualitas dan komposisi warna yang sesuai dengan karakter ragam hias Melayu. Rancang bangun desain produk untuk mendapatkan formulasi desain serta kelayakan prosesnya dengan penekanan pada teknologi akrab lingkungan dilaksanakan dengan alternatif pendekatan yaitu penciptaan desain bentuk baru.Kata kunci: desain, batik, rancang bangun, ragam hias, MelayuABSTRACTDevelopment of batik design through

  13. Transnationalism as a motif in family stories.

    Science.gov (United States)

    Stone, Elizabeth; Gomez, Erica; Hotzoglou, Despina; Lipnitsky, Jane Y

    2005-12-01

    Family stories have long been recognized as a vehicle for assessing components of a family's emotional and social life, including the degree to which an immigrant family has been willing to assimilate. Transnationalism, defined as living in one or more cultures and maintaining connections to both, is now increasingly common. A qualitative study of family stories in the family of those who appear completely "American" suggests that an affiliation with one's home country is nevertheless detectable in the stories via motifs such as (1) positively connotated home remedies, (2) continuing denigration of home country "enemies," (3) extensive knowledge of the home country history and politics, (4) praise of endogamy and negative assessment of exogamy, (5) superiority of home country to America, and (6) beauty of home country. Furthermore, an awareness of which model--assimilationist or transnational--governs a family's experience may help clarify a clinician's understanding of a family's strengths, vulnerabilities, and mode of framing their cultural experiences.

  14. Voltage-sensing phosphatase modulation by a C2 domain

    Directory of Open Access Journals (Sweden)

    Paul M. Castle

    2015-04-01

    Full Text Available The voltage-sensing phosphatase (VSP is the first example of an enzyme controlled by changes in membrane potential. VSP has four distinct regions: the transmembrane voltage-sensing domain (VSD, the inter-domain linker, the cytosolic catalytic domain and the C2 domain. The VSD transmits the changes in membrane potential through the inter-domain linker activating the catalytic domain which then dephosphorylates phosphatidylinositol phosphate lipids. The role of the C2, however, has not been established. In this study, we explore two possible roles for the C2: catalysis and membrane-binding. The Ci-VSP crystal structures show that the C2 residue Y522 lines the active site suggesting a contribution to catalysis. When we mutated Y522 to phenylalanine, we found a shift in the voltage dependence of activity. This suggests hydrogen bonding as a mechanism of action. Going one step further, when we deleted the entire C2 domain, we found voltage-dependent enzyme activity was no longer detectable. This result clearly indicates the entire C2 is necessary for catalysis as well as for modulating activity. As C2s are known membrane-binding domains, we tested whether the VSP C2 interacts with the membrane. We probed a cluster of four positively charged residues lining the top of the C2 and suggested by previous studies to interact with phosphatidylinositol 4,5-bisphosphate (PI(4,5P2 (Kalli et al., 2014. Neutralizing those positive charges significantly shifted the voltage dependence of activity to higher voltages. We tested membrane binding by depleting PI(4,5P2 from the membrane using the 5HT2C receptor and found that the VSD motions as measured by voltage clamp fluorometry were not changed. These results suggest that if the C2 domain interacts with the membrane to influence VSP function it may not occur exclusively through PI(4,5P2. Together, this data advances our understanding of the VSP C2 by demonstrating a necessary and critical role for the C2 domain in

  15. Voltage-sensing phosphatase modulation by a C2 domain.

    Science.gov (United States)

    Castle, Paul M; Zolman, Kevin D; Kohout, Susy C

    2015-01-01

    The voltage-sensing phosphatase (VSP) is the first example of an enzyme controlled by changes in membrane potential. VSP has four distinct regions: the transmembrane voltage-sensing domain (VSD), the inter-domain linker, the cytosolic catalytic domain, and the C2 domain. The VSD transmits the changes in membrane potential through the inter-domain linker activating the catalytic domain which then dephosphorylates phosphatidylinositol phosphate (PIP) lipids. The role of the C2, however, has not been established. In this study, we explore two possible roles for the C2: catalysis and membrane-binding. The Ci-VSP crystal structures show that the C2 residue Y522 lines the active site suggesting a contribution to catalysis. When we mutated Y522 to phenylalanine, we found a shift in the voltage dependence of activity. This suggests hydrogen bonding as a mechanism of action. Going one step further, when we deleted the entire C2 domain, we found voltage-dependent enzyme activity was no longer detectable. This result clearly indicates the entire C2 is necessary for catalysis as well as for modulating activity. As C2s are known membrane-binding domains, we tested whether the VSP C2 interacts with the membrane. We probed a cluster of four positively charged residues lining the top of the C2 and suggested by previous studies to interact with phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] (Kalli et al., 2014). Neutralizing those positive charges significantly shifted the voltage dependence of activity to higher voltages. We tested membrane binding by depleting PI(4,5)P2 from the membrane using the 5HT2C receptor and found that the VSD motions as measured by voltage clamp fluorometry (VCF) were not changed. These results suggest that if the C2 domain interacts with the membrane to influence VSP function it may not occur exclusively through PI(4,5)P2. Together, this data advances our understanding of the VSP C2 by demonstrating a necessary and critical role for the C2 domain in

  16. Irradiation damages in Ti3SiC2

    International Nuclear Information System (INIS)

    Nappe, J.C.; Grosseau, Ph.; Guilhot, B.; Audubert, F.; Beauvy, M.

    2007-01-01

    Carbides, by their remarkable properties, are considered as possible materials (fuel cans) in reactor of generation IV. Among those studied, Ti 3 SiC 2 is particularly considered because it joins both the ceramics and metals properties. Nevertheless, its behaviour under irradiation is not known. Characterizations have been carried out on samples irradiated at 75 MeV krypton ions. They have revealed that TiO 2 (formed at the surface of Ti 3 SiC 2 ) is pulverized by the irradiation and that the crystal lattice of Ti 3 SiC 2 dilates with c. (O.M.)

  17. 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.

    2008-01-01

    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......(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified...

  18. The limits of de novo DNA motif discovery.

    Directory of Open Access Journals (Sweden)

    David Simcha

    Full Text Available A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of

  19. DNA motif alignment by evolving a population of Markov chains.

    Science.gov (United States)

    Bi, Chengpeng

    2009-01-30

    Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

  20. Spondylolysis of C-2 in 2 athletically active individuals.

    Science.gov (United States)

    Gottfried, Oren N; Parker, Scott L; Omeis, Ibrahim; Bydon, Ali; Gokaslan, Ziya L; Wolinsky, Jean-Paul

    2010-07-01

    Cervical spondylolysis is an uncommon disorder involving a cleft at the pars interarticularis. It is most often found at the C-6 level, and clinical presentations have included incidental radiographic findings, neck pain, and rarely neurological compromise. Although subaxial cervical spondylolysis has been described in 150 patients, defects at the C-2 pedicles are rare. The authors present 2 new cases of C-2 spondylolysis in athletically active young persons who did not demonstrate instability or neurological deficits, were able to remain active, and are being managed conservatively with serial examinations and imaging. They also discuss the results of 22 previously reported cases of C-2 spondylolysis. Based on the literature and their own experience, the authors conclude that most patients with C-2 spondylolysis remain neurologically intact, maintain stability despite the bony defect, and can be managed conservatively. Surgery is reserved for patients who demonstrate severe instability or spinal cord compromise due to stenosis.

  1. Assessing local structure motifs using order parameters for motif recognition, interstitial identification, and diffusion path characterization

    Science.gov (United States)

    Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav; Haranczyk, Maciej

    2017-11-01

    Structure-property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal closed packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

  2. Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization

    Directory of Open Access Journals (Sweden)

    Nils E. R. Zimmermann

    2017-11-01

    Full Text Available Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP database (61,422 compounds for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

  3. C2 Rising: A Historical View of Our Critical Advantage

    Science.gov (United States)

    2014-08-01

    of six.11 In 1937 Tukhachevskii even conceptualized these C2 functions performed in the air, where a bird’s-eye view would offer maximum awareness to...terminology. • F1, orient shooters: increase shooter/sensor SA and threat warn- ing by providing SA. Battle management and ISR fusion tasks in this...this era seem to stumble upon the need for high-functioning C2 systems. Carrier war rooms, nuclear reactor control rooms, the National Military

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

    KAUST Repository

    Lee, Iljoon; Patil, Sachin; Fhayli, Karim; Alsaiari, Shahad K.; Khashab, Niveen M.

    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

  5. The identification of functional motifs in temporal gene expression analysis

    Directory of Open Access Journals (Sweden)

    Michael G. Surette

    2005-01-01

    Full Text Available The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.

  6. RNA recognition motif (RRM)-containing proteins in Bombyx mori

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... Recognition Motif (RRM), sometimes referred to as. RNP1, is one of the first identified domains for RNA interaction. RRM is very common ..... Apart from the RRM motif, eIF3-S9 has a Trp-Asp. (WD) repeat domain, Poly (A) ...

  7. BlockLogo: Visualization of peptide and sequence motif conservation

    DEFF Research Database (Denmark)

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

    2013-01-01

    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, se...

  8. Fingerprint motifs of phytases | Fan | African Journal of Biotechnology

    African Journals Online (AJOL)

    Among the total of potential 173 phytases gained in 11 plant genomes through MAST, PAPhys are the major phytases, and HAPhys are the minor, and other phytase groups are not found in planta. Keywords: Phytase, fingerprint motif, multiple EM for motif elicitation (MEME), MAST African Journal of Biotechnology Vol.

  9. Identification of sequence motifs significantly associated with antisense activity

    Directory of Open Access Journals (Sweden)

    Peek Andrew S

    2007-06-01

    Full Text Available Abstract Background Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the model to be efficient we must know what properties do not associate significantly and can be omitted from the model. This paper will discuss the results of a randomization procedure to find motifs that associate significantly with either high or low antisense suppression activity, analysis of their properties, as well as the results of support vector machine modelling using these significant motifs as features. Results We discovered 155 motifs that associate significantly with high antisense suppression activity and 202 motifs that associate significantly with low suppression activity. The motifs range in length from 2 to 5 bases, contain several motifs that have been previously discovered as associating highly with antisense activity, and have thermodynamic properties consistent with previous work associating thermodynamic properties of sequences with their antisense activity. Statistical analysis revealed no correlation between a motif's position within an antisense sequence and that sequences antisense activity. Also, many significant motifs existed as subwords of other significant motifs. Support vector regression experiments indicated that the feature set of significant motifs increased correlation compared to all possible motifs as well as several subsets of the significant motifs. Conclusion The thermodynamic properties of the significantly associated motifs support existing data correlating the thermodynamic properties of the antisense oligonucleotide with antisense efficiency, reinforcing our hypothesis that antisense suppression is strongly associated with probe/target thermodynamics, as there are no enzymatic

  10. 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.

  11. The upgrade of the Thomson scattering system for measurement on the C-2/C-2U devices

    Energy Technology Data Exchange (ETDEWEB)

    Zhai, K.; Schindler, T.; Kinley, J.; Deng, B.; Thompson, M. C. [Tri Alpha Energy, Inc., P.O. Box 7010, Rancho Santa Margarita, California 92688 (United States)

    2016-11-15

    The C-2/C-2U Thomson scattering system has been substantially upgraded during the latter phase of C-2/C-2U program. A Rayleigh channel has been added to each of the three polychromators of the C-2/C-2U Thomson scattering system. Onsite spectral calibration has been applied to avoid the issue of different channel responses at different spots on the photomultiplier tube surface. With the added Rayleigh channel, the absolute intensity response of the system is calibrated with Rayleigh scattering in argon gas from 0.1 to 4 Torr, where the Rayleigh scattering signal is comparable to the Thomson scattering signal at electron densities from 1 × 10{sup 13} to 4 × 10{sup 14} cm{sup −3}. A new signal processing algorithm, using a maximum likelihood method and including detailed analysis of different noise contributions within the system, has been developed to obtain electron temperature and density profiles. The system setup, spectral and intensity calibration procedure and its outcome, data analysis, and the results of electron temperature/density profile measurements will be presented.

  12. High pressure oxidation of C2H4/NO mixtures

    DEFF Research Database (Denmark)

    Giménez-López, J.; Alzueta, M.U.; Rasmussen, C.T.

    2011-01-01

    An experimental and kinetic modeling study of the interaction between C2H4 and NO has been performed under flow reactor conditions in the intermediate temperature range (600–900K), high pressure (60bar), and for stoichiometries ranging from reducing to oxidizing conditions. The main reaction...... pathways of the C2H4/O2/NOx conversion, the capacity of C2H4 to remove NO, and the influence of the presence of NOx on the C2H4 oxidation are analyzed. Compared to the C2H4/O2 system, the presence of NOx shifts the onset of reaction 75–150K to lower temperatures. The mechanism of sensitization involves...... the reaction HOCH2CH2OO+NO→CH2OH+CH2O+NO2, which pushes a complex system of partial equilibria towards products. This is a confirmation of the findings of Doughty et al. [3] for a similar system at atmospheric pressure. Under reducing conditions and temperatures above 700K, a significant fraction of the NOx...

  13. Motif statistics and spike correlations in neuronal networks

    International Nuclear Information System (INIS)

    Hu, Yu; Shea-Brown, Eric; Trousdale, James; Josić, Krešimir

    2013-01-01

    Motifs are patterns of subgraphs of complex networks. We studied the impact of such patterns of connectivity on the level of correlated, or synchronized, spiking activity among pairs of cells in a recurrent network of integrate and fire neurons. For a range of network architectures, we find that the pairwise correlation coefficients, averaged across the network, can be closely approximated using only three statistics of network connectivity. These are the overall network connection probability and the frequencies of two second order motifs: diverging motifs, in which one cell provides input to two others, and chain motifs, in which two cells are connected via a third intermediary cell. Specifically, the prevalence of diverging and chain motifs tends to increase correlation. Our method is based on linear response theory, which enables us to express spiking statistics using linear algebra, and a resumming technique, which extrapolates from second order motifs to predict the overall effect of coupling on network correlation. Our motif-based results seek to isolate the effect of network architecture perturbatively from a known network state. (paper)

  14. 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.

  15. Triadic motifs in the dependence networks of virtual societies

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-01

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  16. RNA motif search with data-driven element ordering.

    Science.gov (United States)

    Rampášek, Ladislav; Jimenez, Randi M; Lupták, Andrej; Vinař, Tomáš; Brejová, Broňa

    2016-05-18

    In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .

  17. Triadic motifs in the dependence networks of virtual societies.

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-10

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  18. 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

  19. Functional analysis of a novel KRAB/C2H2 zinc finger protein Mipu1

    International Nuclear Information System (INIS)

    Jiang, Lei; Tang, Daolin; Wang, Kangkai; Zhang, Huali; Yuan, Can; Duan, Dayue; Xiao, Xianzhong

    2007-01-01

    A novel rat gene, Mipu1, encodes a 608 amino acid protein with an amino-terminal KRAB domain and 14 carboxyl-terminal C 2 H 2 zinc finger motifs. Mipu1 is localized to the nucleus through its KRAB domain or the linker adjacent to its zinc finger region. Using the GST-Mipu1 bound to glutathione-Sepharose beads, a consensus putative DNA binding site (5'-TGTCTTATCGAA-3') was extracted from a random oligonucleotide library. EMSA and target detection assay showed that the probe containing the putative site can bind to purified GST-Mipu1 fusion protein. The oligonucleotide containing the putative site was inserted into the pGL3-promotor vector to produce a reporter construct. The expression of reporter gene was repressed by overexpression of Mipu1 in a dose-dependent manner. Mutation analysis of the consensus sequence indicated that the repression mediated by Mipu1 is sequence-dependent. These results suggest that Mipu1 is a nuclear protein, which functions as a transcriptional repressor

  20. Solution Structure of a Novel C2-Symmetrical Bifunctional Bicyclic Inhibitor Based on SFTI-1

    International Nuclear Information System (INIS)

    Jaulent, Agnes M.; Brauer, Arnd B. E.; Matthews, Stephen J.; Leatherbarrow, Robin J.

    2005-01-01

    A novel bifunctional bicyclic inhibitor has been created that combines features both from the Bowman-Birk inhibitor (BBI) proteins, which have two distinct inhibitory sites, and from sunflower trypsin inhibitor-1 (SFTI-1), which has a compact bicyclic structure. The inhibitor was designed by fusing together a pair of reactive loops based on a sequence derived from SFTI-1 to create a backbone-cyclized disulfide-bridged 16-mer peptide. This peptide has two symmetrically spaced trypsin binding sites. Its synthesis and biological activity have been reported in a previous communication [Jaulent and Leatherbarrow, 2004, PEDS 17, 681]. In the present study we have examined the three-dimensional structure of the molecule. We find that the new inhibitor, which has a symmetrical 8-mer half-cystine CTKSIPP'I' motif repeated through a C 2 symmetry axis also shows a complete symmetry in its three-dimensional structure. Each of the two loops adopts the expected canonical conformation common to all BBIs as well as SFTI-1. We also find that the inhibitor displays a strong and unique structural identity, with a notable lack of minor conformational isomers that characterise most reactive site loop mimics examined to date as well as SFTI-1. This suggests that the presence of the additional cyclic loop acts to restrict conformational mobility and that the deliberate introduction of cyclic symmetry may offer a general route to locking the conformation of β-hairpin structures

  1. Myosin-1A Targets to Microvilli Using Multiple Membrane Binding Motifs in the Tail Homology 1 (TH1) Domain*

    Science.gov (United States)

    Mazerik, Jessica N.; Tyska, Matthew J.

    2012-01-01

    One of the most abundant components of the enterocyte brush border is the actin-based monomeric motor, myosin-1a (Myo1a). Within brush border microvilli, Myo1a carries out a number of critical functions at the interface between membrane and actin cytoskeleton. Proper physiological function of Myo1a depends on its ability to bind to microvillar membrane, an interaction mediated by a C-terminal tail homology 1 (TH1) domain. However, little is known about the mechanistic details of the Myo1a-TH1/membrane interaction. Structure-function analysis of Myo1a-TH1 targeting in epithelial cells revealed that an N-terminal motif conserved among class I myosins and a C-terminal motif unique to Myo1a-TH1 are both required for steady state microvillar enrichment. Purified Myo1a bound to liposomes composed of phosphatidylserine and phosphoinositol 4,5-bisphosphate, with moderate affinity in a charge-dependent manner. Additionally, peptides of the N- and C-terminal regions required for targeting were able to compete with Myo1a for binding to highly charged liposomes in vitro. Single molecule total internal reflection fluorescence microscopy showed that these motifs are also necessary for slowing the membrane detachment rate in cells. Finally, Myo1a-TH1 co-localized with both lactadherin-C2 (a phosphatidylserine-binding protein) and PLCδ1-PH (a phosphoinositol 4,5-bisphosphate-binding protein) in microvilli, but only lactaderin-C2 expression reduced brush border targeting of Myo1a-TH1. Together, our results suggest that Myo1a targeting to microvilli is driven by membrane binding potential that is distributed throughout TH1 rather than localized to a single motif. These data highlight the diversity of mechanisms that enable different class I myosins to target membranes in distinct biological contexts. PMID:22367206

  2. Targeting functional motifs of a protein family

    Science.gov (United States)

    Bhadola, Pradeep; Deo, Nivedita

    2016-10-01

    The structural organization of a protein family is investigated by devising a method based on the random matrix theory (RMT), which uses the physiochemical properties of the amino acid with multiple sequence alignment. A graphical method to represent protein sequences using physiochemical properties is devised that gives a fast, easy, and informative way of comparing the evolutionary distances between protein sequences. A correlation matrix associated with each property is calculated, where the noise reduction and information filtering is done using RMT involving an ensemble of Wishart matrices. The analysis of the eigenvalue statistics of the correlation matrix for the β -lactamase family shows the universal features as observed in the Gaussian orthogonal ensemble (GOE). The property-based approach captures the short- as well as the long-range correlation (approximately following GOE) between the eigenvalues, whereas the previous approach (treating amino acids as characters) gives the usual short-range correlations, while the long-range correlations are the same as that of an uncorrelated series. The distribution of the eigenvector components for the eigenvalues outside the bulk (RMT bound) deviates significantly from RMT observations and contains important information about the system. The information content of each eigenvector of the correlation matrix is quantified by introducing an entropic estimate, which shows that for the β -lactamase family the smallest eigenvectors (low eigenmodes) are highly localized as well as informative. These small eigenvectors when processed gives clusters involving positions that have well-defined biological and structural importance matching with experiments. The approach is crucial for the recognition of structural motifs as shown in β -lactamase (and other families) and selectively identifies the important positions for targets to deactivate (activate) the enzymatic actions.

  3. ROMANIAN FOLKLORE MOTIFS IN FASHION DESIGN

    Directory of Open Access Journals (Sweden)

    MOCENCO Alexandra

    2014-05-01

    Full Text Available The traditional Romanian costume such as the entire popular art (architecture, woodcarvins, pottery etc. was born and lasted in our country since ancient times. Closely related to human existence, the traditional costume reflected over the years as reflected nowadays, the mentality and artistic conception of the people. Today the traditional Romanian costume became an inspiration source to the wholesale fashion production industry designers, both Romanian and international. Although the contemporary designers are working in accordance with a vision, using a wide area of styles, methods and current technology, they usually return to traditional techniques and ethnic folklore motifs, which converts and resize them, integrating them in their contemporary space. Adrian Oianu is a very appreciated Romanian designer who launched two collections inspired by his native’s country traditional costumes: “Suflecata pan’ la brau” (“Turned up ‘til the belt” and “Bucurie” (“Joy”. Dorin Negrau had as inspiration for his “Lost” collection the traditional costume from the Bihor region. Yves Saint Laurent had a collection inspired by the Romanian traditional flax blouses called “La blouse roumaine”. The paper presents the traditional Romanian values throw fashion collections. The research activity will create innovative concepts to support the garment industry in order to develop their own brand and to bring the design activities in Romania at an international level. The research was conducted during the initial stage of a project, financed through national founds, consisting in a documentary study on ethnographic characteristics of the popular costume from different regions of the country.

  4. Shape Preserving Interpolation Using C2 Rational Cubic Spline

    Directory of Open Access Journals (Sweden)

    Samsul Ariffin Abdul Karim

    2016-01-01

    Full Text Available This paper discusses the construction of new C2 rational cubic spline interpolant with cubic numerator and quadratic denominator. The idea has been extended to shape preserving interpolation for positive data using the constructed rational cubic spline interpolation. The rational cubic spline has three parameters αi, βi, and γi. The sufficient conditions for the positivity are derived on one parameter γi while the other two parameters αi and βi are free parameters that can be used to change the final shape of the resulting interpolating curves. This will enable the user to produce many varieties of the positive interpolating curves. Cubic spline interpolation with C2 continuity is not able to preserve the shape of the positive data. Notably our scheme is easy to use and does not require knots insertion and C2 continuity can be achieved by solving tridiagonal systems of linear equations for the unknown first derivatives di, i=1,…,n-1. Comparisons with existing schemes also have been done in detail. From all presented numerical results the new C2 rational cubic spline gives very smooth interpolating curves compared to some established rational cubic schemes. An error analysis when the function to be interpolated is ft∈C3t0,tn is also investigated in detail.

  5. C2-Agents and Low-level BML

    NARCIS (Netherlands)

    Alstad, A.; Mevassvik, O.M.; Nielsen, M.N.; Løvlid, R.A.; Henderson, H.C.; Jansen, R.E.J.; Reus, N.M. de

    2013-01-01

    TNO (The Netherlands) and FFI (Norway) are cooperating in extending a COTS Computer Generated Forces (CGF) tool with a Coalition Battle Management Language (C-BML) interface for executing C-BML orders and issuing reports. Due to the lack of satisfactory models for command and control (C2)/combat

  6. Canonical realizations of B2 approximately C2 Lie algebras

    International Nuclear Information System (INIS)

    Iosifescu, M.; Scutaru, H.

    1982-12-01

    Canonical realizations associated to subrepresentations of ad x ad, for B 2 apppoximately C 2 semisimple Lie algebras, have been determined. An algebraic foundation has been obtained for the constraints satisfied by the dinamical variables of the classical limit of the generalized Helium problem. (authors)

  7. Interstellar C2, CH, and CN in translucent molecular clouds

    NARCIS (Netherlands)

    Dishoeck, van E.F.; Black, J.H.

    1989-01-01

    Optical absorption-line techniques have been applied to the study of a number of translucent molecular clouds in which the total column densities are large enough that substantial molecular abundances can be maintained. Results are presented for a survey of absorption lines of interstellar C2, CH,

  8. Does Δm = ΔErest/c2?

    International Nuclear Information System (INIS)

    Redzic, Dragan V

    2006-01-01

    We point out a logical possibility, based on special relativity, that the validity of Einstein's 1905 generalization, Δm = ΔE rest /c 2 , might depend on how the energy of a body is defined in special relativity. The analysis is another illustration of the importance of Ockham's razor in special relativity

  9. 26 CFR 1.663(c)-2 - Rules of administration.

    Science.gov (United States)

    2010-04-01

    ... calculate its distributable net income based upon its portion of gross income that is includible in... among the separate shares in the same proportion as section 643(b) income from the same source would be....663(c)-2 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX...

  10. Fluorescent vibration-rotation excitation of cometary C2

    NARCIS (Netherlands)

    Gredel, R.; Dishoeck, van E.F.; Black, J.H.

    1989-01-01

    The statistical equilibrium equations that determine the population densities of the energy levels in cometary C2 molecules due to fluorescent excitation are examined in detail. The adopted model and molecular parameters are discussed, and a theoretical estimate is made of the two intercombination

  11. Why is the Bond Multiplicity in C2 so Elusive?

    Czech Academy of Sciences Publication Activity Database

    Cooper, D.L.; Penotti, F.E.; Ponec, Robert

    2015-01-01

    Roč. 1053, SI (2015), s. 189-194 ISSN 2210-271X Institutional support: RVO:67985858 Keywords : bond multiplicity in C2 * spin correlation matrices * full GVB and spin-coupled Subject RIV: CC - Organic Chemistry Impact factor: 1.403, year: 2015

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

    Directory of Open Access Journals (Sweden)

    Gert J. Volschenk

    2010-09-01

    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.

  13. Methods and statistics for combining motif match scores.

    Science.gov (United States)

    Bailey, T L; Gribskov, M

    1998-01-01

    Position-specific scoring matrices are useful for representing and searching for protein sequence motifs. A sequence family can often be described by a group of one or more motifs, and an effective search must combine the scores for matching a sequence to each of the motifs in the group. We describe three methods for combining match scores and estimating the statistical significance of the combined scores and evaluate the search quality (classification accuracy) and the accuracy of the estimate of statistical significance of each. The three methods are: 1) sum of scores, 2) sum of reduced variates, 3) product of score p-values. We show that method 3) is superior to the other two methods in both regards, and that combining motif scores indeed gives better search accuracy. The MAST sequence homology search algorithm utilizing the product of p-values scoring method is available for interactive use and downloading at URL http:/(/)www.sdsc.edu/MEME.

  14. DNA regulatory motif selection based on support vector machine ...

    African Journals Online (AJOL)

    ... machine (SVM) and its application in microarray experiment of Kashin-Beck disease. ... speed and amount of the corresponding mRNA in gene replication process. ... and revealed that some motifs may be related to the immune reactions.

  15. Sequence stratigraphy of the Nukumaruan stratotype (Pliocene-Pleistocene, c. 2.08-1.63 Ma), Wanganui Basin, New Zealand

    International Nuclear Information System (INIS)

    Abbott, S.T.; Naish, T.R.; Carter, R.M.; Pillans, B.J.

    2005-01-01

    Late Pliocene to Early Pleistocene (c. 2.08-1.63 Ma) strata exposed in coastal cliffs along Nukumaru and Ototoka beaches near Wanganui, between the top of the Nukumaru Limestone and the base of the Butlers Shell Conglomerate, comprise 11 depositional sequences of a total thickness of c. 86 m. The sequences consist predominantly of siliciclastic shoreline facies. Non-marine facies (including palaeosols), and a variety of shallow-marine shellbed facies, are also represented. Patterns in facies composition and sequence architecture reveal three sequence motifs (Maxwell, Nukumaru, and Birdgrove) that represent progressively increasing maximum palaeowater depths within a broadly basin-margin palaeogeographic setting. The sequence motif changes systematically up section and records a lower order tectonic influence on accommodation that has modulated the stacking patterns of individual sequences. Correlation of the sequences with oxygen isotope stages 77-57 is achieved using the basin-wide Ototoka tephra, and indicates that the sequences accumulated in response to obliquity driven (41 k.y. duration) glacio-eustatic sea-level oscillations. Correlation of the Nukumaru coast sequences with other sections along basin strike, and the global oxygen isotope record indicates that (i) 500 k.y. (δ 18 O stages MIS 56-34) is missing at the unconformity between the Nukumaruan and overlying Castlecliffian stratotypes on the Wanganui coast, and (ii) the Pliocene-Pleistocene boundary lies within sequence NC7 at the base of the Lower Maxwell Formation. (author). 52 refs., 15 figs., 2 tabs

  16. BEAM web server: a tool for structural RNA motif discovery.

    Science.gov (United States)

    Pietrosanto, Marco; Adinolfi, Marta; Casula, Riccardo; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2018-03-15

    RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. marco.pietrosanto@uniroma2.it. Supplementary data are available at Bioinformatics online.

  17. Characterizing Motif Dynamics of Electric Brain Activity Using Symbolic Analysis

    Directory of Open Access Journals (Sweden)

    Massimiliano Zanin

    2014-10-01

    Full Text Available Motifs are small recurring circuits of interactions which constitute the backbone of networked systems. Characterizing motif dynamics is therefore key to understanding the functioning of such systems. Here we propose a method to define and quantify the temporal variability and time scales of electroencephalogram (EEG motifs of resting brain activity. Given a triplet of EEG sensors, links between them are calculated by means of linear correlation; each pattern of links (i.e., each motif is then associated to a symbol, and its appearance frequency is analyzed by means of Shannon entropy. Our results show that each motif becomes observable with different coupling thresholds and evolves at its own time scale, with fronto-temporal sensors emerging at high thresholds and changing at fast time scales, and parietal ones at low thresholds and changing at slower rates. Finally, while motif dynamics differed across individuals, for each subject, it showed robustness across experimental conditions, indicating that it could represent an individual dynamical signature.

  18. Efficient motif finding algorithms for large-alphabet inputs

    Directory of Open Access Journals (Sweden)

    Pavlovic Vladimir

    2010-10-01

    Full Text Available Abstract Background We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. Results The proposed algorithm (1 improves search efficiency compared to existing algorithms, and (2 scales well with the size of alphabet. On a synthetic planted DNA motif finding problem our algorithm is over 10× more efficient than MITRA, PMSPrune, and RISOTTO for long motifs. Improvements are orders of magnitude higher in the same setting with large alphabets. On benchmark TF-binding site problems (FNP, CRP, LexA we observed reduction in running time of over 12×, with high detection accuracy. The algorithm was also successful in rapidly identifying protein motifs in Lipocalin, Zinc metallopeptidase, and supersecondary structure motifs for Cadherin and Immunoglobin families. Conclusions Our algorithm reduces computational complexity of the current motif finding algorithms and demonstrate strong running time improvements over existing exact algorithms, especially in important and difficult cases of large-alphabet sequences.

  19. Discovering Motifs in Biological Sequences Using the Micron Automata Processor.

    Science.gov (United States)

    Roy, Indranil; Aluru, Srinivas

    2016-01-01

    Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the (l, d) motif search problem of identifying one or more motifs of length l present in at least q of the n given sequences, with each occurrence differing from the motif in at most d substitutions. The problem is known to be NP-complete, and the largest solved instance reported to date is (26,11). We propose a novel algorithm for the (l,d) motif search problem using streaming execution over a large set of non-deterministic finite automata (NFA). This solution is designed to take advantage of the micron automata processor, a new technology close to deployment that can simultaneously execute multiple NFA in parallel. We demonstrate the capability for solving much larger instances of the (l, d) motif search problem using the resources available within a single automata processor board, by estimating run-times for problem instances (39,18) and (40,17). The paper serves as a useful guide to solving problems using this new accelerator technology.

  20. An experimental test of a fundamental food web motif.

    Science.gov (United States)

    Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia

    2010-06-07

    Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.

  1. PISMA: A Visual Representation of Motif Distribution in DNA Sequences

    Directory of Open Access Journals (Sweden)

    Rogelio Alcántara-Silva

    2017-03-01

    Full Text Available Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. Results: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. Availability and Implementation: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf .

  2. Command and Control Rapid Prototyping Continuum (C2RPC): The Framework for Achieving a New C2 Strategy

    Science.gov (United States)

    2011-06-01

    Sync Matrix Assessing J/ADOCS (Fires) TBMCS (ATO) Executing Monitoring (SA) C2 Strategy Objectives • Provide Expanded Mission Management...Computers, and Intelligence T&E Test and Evaluation PMW150 Program Warfare Office Command and Control TBMCS Theater Battle Management Core System POR

  3. Online Trading C2C Operators Fight for Number One

    Institute of Scientific and Technical Information of China (English)

    DAVID HENDRICKSON

    2006-01-01

    @@ Whether shopping casually or searching for some obscure, hard to find item, more and more Chinese are logging online and turning to customer-to-customer (C2C) network operators for their trading needs rather than bother with the hassles of conventional buying and selling. Proof is in the numbers. A leading technology, new media, and telecom watchdog, Analysys International reports that China's C2C market users more than doubled in 2005 to 37.87 million, while the sector's total transaction value increased from 4.16 billion yuan in 2004, to 13.9billion yuan (US$1.74 billion). Supplanted by a web surfing pool of 100 million and counting, they are trends that Analysys and other industry groups expect will continue in China for some time, fundamentally transforming how the country's independent traders do business.

  4. Cervical myelography via C1/C2 lateral puncture

    International Nuclear Information System (INIS)

    Grange, B.

    1981-01-01

    The use of the water soluble, tri-iodinated contrast medium, metrizamide, in cervical myelography via C1/C2 lateral puncture is described. Details of the tomographic apparatus and the technique employed are given. The advantages of water soluble myelography using metrizamide are overwhelming due to its miscibility with CSF, improved anatomical demonstration, radiographic visualisation and diagnostic accuracy and advantageous pharmacological properties with reduced toxicity. This technique provided successful diagnoses in a series of 104 patients. (U.K.)

  5. TECRA: C2 Application of Adaptive Automation Theory

    Science.gov (United States)

    2010-03-01

    1 TECRA: C2 Application of Adaptive Automation Theory Ewart J. de Visser 1,2 , Melanie LeGoullon 1 , Don Horvath 1 , Gershon Weltman 1 , Amos...this second trip served to inform a modified version of Klein , Calderwood, and MacGregor’s [7] Critical Decision Method Cognitive Task Analysis (CTA...NSN:1550-01-538-9256, EIC:ICB, January 9. [7] Klein , G. A., Calderwood, R., & MacGregor, D. (1989). Critical decision method for eliciting

  6. Boundary states in c=-2 logarithmic conformal field theory

    International Nuclear Information System (INIS)

    Bredthauer, Andreas; Flohr, Michael

    2002-01-01

    Starting from first principles, a constructive method is presented to obtain boundary states in conformal field theory. It is demonstrated that this method is well suited to compute the boundary states of logarithmic conformal field theories. By studying the logarithmic conformal field theory with central charge c=-2 in detail, we show that our method leads to consistent results. In particular, it allows to define boundary states corresponding to both, indecomposable representations as well as their irreducible subrepresentations

  7. C2R2: Training Students To Build Coastal Resilience

    Science.gov (United States)

    Ferraro, C.; Kopp, R. E.; Jordan, R.; Gong, J.; Andrews, C.; Auermuller, L. M.; Herb, J.; McDonnell, J. D.; Bond, S.

    2017-12-01

    In the United States, about 23 million people live within 6 meters of sea level. In many parts of the country, sea-level rise between 1960 and 2010 has already led to a 2-5-fold increase in the rate of `nuisance' flooding. On top of rising seas, intensifying hurricanes and more frequent extremes of heat, humidity and precipitation pose additional risks to coastal societies, economies and ecosystems. Addressing risks posed by changing climate conditions in coastal areas demands innovative strategies that intersect multiple disciplines including engineering, ecology, communication, climate science, and community planning. To be usable, it also requires engaging coastal stakeholders in the development of research questions, the assessment of implications of research for planning and policy, and the communication of research results. Yet traditional, disciplinary programs are poorly configured to train the workforce needed to assess coastal climate risk and to develop and deploy integrated strategies for increasing coastal climate resilience. Coastal Climate Risk & Resilience (C2R2) is an NSF Research Traineeship (NRT) working to prepare the workforce that will build coastal resilience in the face of climate risks. Through its trainee and certificate programs, C2R2 works with graduate students at Rutgers University from multiple disciplines to better integrate all the elements of coastal systems and to communicate effectively with coastal stakeholders. C2R2 students will acquire the knowledge and practical skills needed to become leading researchers and practitioners tackling the critical challenges of coastal resilience.

  8. Interstellar C2 molecules in a Taurus dark cloud

    International Nuclear Information System (INIS)

    Hobbs, L.M.; Black, J.H.; van Dishoeck, E.F.

    1983-01-01

    Five relatively strong interstellar absorption lines of the 2--0) Phillips band of C 2 near lambda8760 are detected in the spectrum of HD 29647, a late B star which lies behind a substantial part of the Taurus molecular cloud complex about 20triangle-solid from TMC-1. In combination with newly determined oscillator strengths, the observations yield a column density N(C 2 )roughly-equal9 x 10 13 cm -2 , which is comparable to those of widely distributed molecules like CH and H 2 O. Theoreticl models of the observed C 2 rotational level populations indicate a kinetic temperature T = 14 +8 /sub -/ 5 K and a mean density n 3 cm -3 . A narrow, anomalous strong, stellar Mn II line yields for HD 29647 a project rotational velocity v sin i -1 and is explained by previous identifications HD 29647 as a Hg-Mn peculiar star. Similar spectra of ν Cyg and omicron And give an upper limit W/sub lambda/ 2 lines in the 2--0) band, toward both stars

  9. Verification of the MOTIF code version 3.0

    International Nuclear Information System (INIS)

    Chan, T.; Guvanasen, V.; Nakka, B.W.; Reid, J.A.K.; Scheier, N.W.; Stanchell, F.W.

    1996-12-01

    As part of the Canadian Nuclear Fuel Waste Management Program (CNFWMP), AECL has developed a three-dimensional finite-element code, MOTIF (Model Of Transport In Fractured/ porous media), for detailed modelling of groundwater flow, heat transport and solute transport in a fractured rock mass. The code solves the transient and steady-state equations of groundwater flow, solute (including one-species radionuclide) transport, and heat transport in variably saturated fractured/porous media. The initial development was completed in 1985 (Guvanasen 1985) and version 3.0 was completed in 1986. This version is documented in detail in Guvanasen and Chan (in preparation). This report describes a series of fourteen verification cases which has been used to test the numerical solution techniques and coding of MOTIF, as well as demonstrate some of the MOTIF analysis capabilities. For each case the MOTIF solution has been compared with a corresponding analytical or independently developed alternate numerical solution. Several of the verification cases were included in Level 1 of the International Hydrologic Code Intercomparison Project (HYDROCOIN). The MOTIF results for these cases were also described in the HYDROCOIN Secretariat's compilation and comparison of results submitted by the various project teams (Swedish Nuclear Power Inspectorate 1988). It is evident from the graphical comparisons presented that the MOTIF solutions for the fourteen verification cases are generally in excellent agreement with known analytical or numerical solutions obtained from independent sources. This series of verification studies has established the ability of the MOTIF finite-element code to accurately model the groundwater flow and solute and heat transport phenomena for which it is intended. (author). 20 refs., 14 tabs., 32 figs

  10. Mechanisms of zero-lag synchronization in cortical motifs.

    Directory of Open Access Journals (Sweden)

    Leonardo L Gollo

    2014-04-01

    Full Text Available Zero-lag synchronization between distant cortical areas has been observed in a diversity of experimental data sets and between many different regions of the brain. Several computational mechanisms have been proposed to account for such isochronous synchronization in the presence of long conduction delays: Of these, the phenomenon of "dynamical relaying"--a mechanism that relies on a specific network motif--has proven to be the most robust with respect to parameter mismatch and system noise. Surprisingly, despite a contrary belief in the community, the common driving motif is an unreliable means of establishing zero-lag synchrony. Although dynamical relaying has been validated in empirical and computational studies, the deeper dynamical mechanisms and comparison to dynamics on other motifs is lacking. By systematically comparing synchronization on a variety of small motifs, we establish that the presence of a single reciprocally connected pair--a "resonance pair"--plays a crucial role in disambiguating those motifs that foster zero-lag synchrony in the presence of conduction delays (such as dynamical relaying from those that do not (such as the common driving triad. Remarkably, minor structural changes to the common driving motif that incorporate a reciprocal pair recover robust zero-lag synchrony. The findings are observed in computational models of spiking neurons, populations of spiking neurons and neural mass models, and arise whether the oscillatory systems are periodic, chaotic, noise-free or driven by stochastic inputs. The influence of the resonance pair is also robust to parameter mismatch and asymmetrical time delays amongst the elements of the motif. We call this manner of facilitating zero-lag synchrony resonance-induced synchronization, outline the conditions for its occurrence, and propose that it may be a general mechanism to promote zero-lag synchrony in the brain.

  11. Phyloproteomic Analysis of 11780 Six-Residue-Long Motifs Occurrences

    Directory of Open Access Journals (Sweden)

    O. V. Galzitskaya

    2015-01-01

    Full Text Available How is it possible to find good traits for phylogenetic reconstructions? Here, we present a new phyloproteomic criterion that is an occurrence of simple motifs which can be imprints of evolution history. We studied the occurrences of 11780 six-residue-long motifs consisting of two randomly located amino acids in 97 eukaryotic and 25 bacterial proteomes. For all eukaryotic proteomes, with the exception of the Amoebozoa, Stramenopiles, and Diplomonadida kingdoms, the number of proteins containing the motifs from the first group (one of the two amino acids occurs once at the terminal position made about 20%; in the case of motifs from the second (one of two amino acids occurs one time within the pattern and third (the two amino acids occur randomly groups, 30% and 50%, respectively. For bacterial proteomes, this relationship was 10%, 27%, and 63%, respectively. The matrices of correlation coefficients between numbers of proteins where a motif from the set of 11780 motifs appears at least once in 9 kingdoms and 5 phyla of bacteria were calculated. Among the correlation coefficients for eukaryotic proteomes, the correlation between the animal and fungi kingdoms (0.62 is higher than between fungi and plants (0.54. Our study provides support that animals and fungi are sibling kingdoms. Comparison of the frequencies of six-residue-long motifs in different proteomes allows obtaining phylogenetic relationships based on similarities between these frequencies: the Diplomonadida kingdoms are more close to Bacteria than to Eukaryota; Stramenopiles and Amoebozoa are more close to each other than to other kingdoms of Eukaryota.

  12. The rate of the reaction between C2H and C2H2 at interstellar temperatures

    Science.gov (United States)

    Herbst, E.; Woon, D. E.

    1997-01-01

    The reaction between the radical C2H and the stable hydrocarbon C2H2 is one of the simplest neutral-neutral hydrocarbon reactions in chemical models of dense interstellar clouds and carbon-rich circumstellar shells. Although known to be rapid at temperatures > or = 300 K, the reaction has yet to be studied at lower temperatures. We present here ab initio calculations of the potential surface for this reaction and dynamical calculations to determine its rate at low temperature. Despite a small potential barrier in the exit channel, the calculated rate is large, showing that this reaction and, most probably, more complex analogs contribute to the formation of complex organic molecules in low-temperature sources.

  13. Channel formation by the binding component of Clostridium botulinum C2 toxin: glutamate 307 of C2II affects channel properties in vitro and pH-dependent C2I translocation in vivo.

    Science.gov (United States)

    Blöcker, Dagmar; Bachmeyer, Christoph; Benz, Roland; Aktories, Klaus; Barth, Holger

    2003-05-13

    The binding component (C2II) of the binary Clostridium botulinum C2 toxin mediates transport of the actin ADP-ribosylating enzyme component (C2I) into the cytosol of target cells. C2II (80 kDa) is activated by trypsin cleavage, and proteolytically activated C2II (60 kDa) oligomerizes to heptamers in solution. Activated C2II forms channels in lipid bilayer membranes which are highly cation selective and voltage-gated. A role for this channel in C2I translocation across the cell membrane into the cytosol is discussed. Amino acid residues 303-331 of C2II contain a conserved pattern of alternating hydrophobic and hydrophilic residues, which likely facilitates membrane insertion and channel formation by creating two antiparallel beta-strands. Some of the residues are in strategic positions within the putative C2II channel, in particular, glutamate 307 (E307) localized in its center and glycine 316 (G316) localized on the trans side of the membrane. Here, single-lysine substitutions of these amino acids and the double mutant E307K/G316K of C2II were analyzed in vivo and in artificial lipid bilayer experiments. The pH dependence of C2I transport across cellular membranes was altered, and a pH of properties of C2II were substantially changed by the mutations, as evidenced by reduced cation selectivity. Interestingly, the voltage dependence of wild-type C2II was completely lost for the E307K mutant, which means that E307 is responsible for voltage gating. Chloroquine blocked the E307K mutant channel and intoxication of Vero cells by mutant C2II and C2I, indicating that chloroquine binding does not involve E307. Overall, the voltage gating and cation selectivity of the C2II channel do not play an important role in translocation of C2I into the cytosol.

  14. Binding properties of SUMO-interacting motifs (SIMs) in yeast.

    Science.gov (United States)

    Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

    2015-03-01

    Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

  15. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements

    OpenAIRE

    Huang, Hsi-Yuan; Chien, Chia-Hung; Jen, Kuan-Hua; Huang, Hsien-Da

    2006-01-01

    Numerous regulatory structural motifs have been identified as playing essential roles in transcriptional and post-transcriptional regulation of gene expression. RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (i) motifs in mRNA 5′-untra...

  16. The primary structure of L37--a rat ribosomal protein with a zinc finger-like motif.

    Science.gov (United States)

    Chan, Y L; Paz, V; Olvera, J; Wool, I G

    1993-04-30

    The amino acid sequence of the rat 60S ribosomal subunit protein L37 was deduced from the sequence of nucleotides in a recombinant cDNA. Ribosomal protein L37 has 96 amino acids, the NH2-terminal methionine is removed after translation of the mRNA, and has a molecular weight of 10,939. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 13 or 14 copies of the L37 gene. The mRNA for the protein is about 500 nucleotides in length. Rat L37 is related to Saccharomyces cerevisiae ribosomal protein YL35 and to Caenorhabditis elegans L37. We have identified in the data base a DNA sequence that encodes the chicken homolog of rat L37.

  17. Robotic Range Clearance Competition (R2C2)

    Science.gov (United States)

    2011-10-01

    MON TUE MAP MAP VEG automated vegetation clearance, automated Aug 10 Aug 11 WED THU Med VEG ia and Visitor D MAP ay Aug 12 FRI SURF...competitors will not be penalized if they enter this area. For the competition we will add an additional Pan , Tilt, Zoom (PTZ) Camera that will be...Johnston’s Corner –Gas Station Restaurant: Pizza, Fired Chicken , Subs 550 W Whalen St., Guernsey, WY 82214 (307) 836-3155 R2C2 Competitor Information

  18. Development of Compact Toroid Injector for C-2 FRCs

    Science.gov (United States)

    Matsumoto, Tadafumi; Sekiguchi, Junichi; Asai, Tomohiko; Gota, Hiroshi; Garate, Eusebio; Allfrey, Ian; Valentine, Travis; Smith, Brett; Morehouse, Mark; TAE Team

    2014-10-01

    Collaborative research project with Tri Alpha Energy has been started and we have developed a new compact toroid (CT) injector for the C-2 device, mainly for fueling field-reversed configurations (FRCs). The CT is formed by a magnetized coaxial plasma-gun (MCPG), which consists of coaxial cylinder electrodes; a spheromak-like plasma is generated by discharge and pushed out from the gun by Lorentz force. The inner diameter of outer electrode is 83.1 mm and the outer diameter of inner electrode is 54.0 mm. The surface of the inner electrode is coated with tungsten in order to reduce impurities coming out from the electrode. The bias coil is mounted inside of the inner electrode. We have recently conducted test experiments and achieved a supersonic CT translation speed of up to ~100 km/s. Other typical plasma parameters are as follows: electron density ~ 5 × 1021 m-3, electron temperature ~ 40 eV, and the number of particles ~0.5-1.0 × 1019. The CT injector is now planned to be installed on C-2 and the first CT injection experiment will be conducted in the near future. The detailed MCPG design as well as the test experimental results will be presented.

  19. Characterization of the C-2W Plasma Guns

    Science.gov (United States)

    Dubois, Ami; Sokolov, Vladimir; Korepanov, Sergey; Osin, Dima; Player, Gabriel; TAE Team

    2017-10-01

    Previous use of coaxial arc discharge plasma guns on the C-2U device exhibited great success in plasma stabilization and improved confinement. On the C-2W experiment, arc discharge plasma guns will again be used to facilitate the electrical connection between the plasma core and the divertor electrodes in order to maintain the electrode edge biasing and induce E x B shear to control plasma rotation. Each plasma gun contains an internal solenoid used to shape the plasma stream. Characterization of electron density (ne) , electron temperature (Te) , floating potential (Vf) , and total plasma flux in an arc discharge lasting 6 ms without the internal solenoid are presented. A Langmuir probe located 27 cm axially outside of the plasma gun anode measures a bell-like radial ne profile with peak ne 1018 m-3 and Te 2 - 10 eV. Observed spectral lines of impurity ions provide an estimate of Te, and Balmer series line ratios of the main ion component are used to evaluate ne at both the probe location and near the plasma gun anode. A calorimeter measures the plasma flux to be constant and equivalent to 1 kA.

  20. Microendoscopic excision of C2 osteoid osteoma: a technical report.

    Science.gov (United States)

    Kulkarni, Arvind G; Dhruv, Abhilash N; Bassi, Anupreet J

    2013-09-01

    Case report and description of technique. To describe a microendoscopic posterior approach for excision of an osteoid osteoma of C2. Microendoscopic techniques are widely used in the management of degenerative disorders of the spine. This is the first report of their use in the management of an osteoid osteoma via the posterior approach. A 12-year-old-boy presented with left-sided neck pain of 3-month duration. Investigations revealed an osteoid osteoma of C2 lamina-lateral mass complex. The patient underwent a posterior microendoscopic excision using 18-mm diameter METRx system (Medtronic Sofamor Danek, Memphis, TN) of tubular retractors. A postoperative computed tomographic scan was done and preoperative and postoperative visual analogue scale and Neck Disability Index were evaluated. The patient was periodically followed up for 1 year. The postoperative computed tomographic scan revealed complete excision of the tumor. The visual analogue scale score for neck pain improved from 3/5 (preoperative) to 0/5 (postoperative) and Neck Disability Index from 33.33 (preoperative) to 0 (postoperative) at 1-year follow-up. Microendoscopic techniques can be extended to excise lesions of the spine. It is a safe procedure in experienced hands. The advantages are minimal morbidity, minimal postoperative pain and discomfort, less analgesic dependence, and better cosmesis. The authors recommend this technique for accessible lesions involving the spine.

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

    KAUST Repository

    Via, Allegra; Uyar, Bora; Brun, Christine; Zanzoni, Andreas

    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.

  2. Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.

    Science.gov (United States)

    Michael, Sushama; Travé, Gilles; Ramu, Chenna; Chica, Claudia; Gibson, Toby J

    2008-02-15

    KEN-box-mediated target selection is one of the mechanisms used in the proteasomal destruction of mitotic cell cycle proteins via the APC/C complex. While annotating the Eukaryotic Linear Motif resource (ELM, http://elm.eu.org/), we found that KEN motifs were significantly enriched in human protein entries with cell cycle keywords in the UniProt/Swiss-Prot database-implying that KEN-boxes might be more common than reported. Matches to short linear motifs in protein database searches are not, per se, significant. KEN-box enrichment with cell cycle Gene Ontology terms suggests that collectively these motifs are functional but does not prove that any given instance is so. Candidates were surveyed for native disorder prediction using GlobPlot and IUPred and for motif conservation in homologues. Among >25 strong new candidates, the most notable are human HIPK2, CHFR, CDC27, Dab2, Upf2, kinesin Eg5, DNA Topoisomerase 1 and yeast Cdc5 and Swi5. A similar number of weaker candidates were present. These proteins have yet to be tested for APC/C targeted destruction, providing potential new avenues of research.

  3. 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.

  4. Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants

    Directory of Open Access Journals (Sweden)

    Ahmad A. Malik

    2017-05-01

    Full Text Available Dehydrins, a large family of abiotic stress proteins, are defined by the presence of a mostly conserved motif known as the K-segment, and may also contain two other conserved motifs known as the Y-segment and S-segment. Using the dehydrin literature, we developed a sequence motif definition of the K-segment, which we used to create a large dataset of dehydrin sequences by searching the Pfam00257 dehydrin dataset and the Phytozome 10 sequences of vascular plants. A comprehensive analysis of these sequences reveals that lysine residues are highly conserved in the K-segment, while the amino acid type is often conserved at other positions. Despite the Y-segment name, the central tyrosine is somewhat conserved, but can be substituted with two other small aromatic amino acids (phenylalanine or histidine. The S-segment contains a series of serine residues, but in some proteins is also preceded by a conserved LHR sequence. In many dehydrins containing all three of these motifs the S-segment is linked to the K-segment by a GXGGRRKK motif (where X can be any amino acid, suggesting a functional linkage between these two motifs. An analysis of the sequences shows that the dehydrin architecture and several biochemical properties (isoelectric point, molecular mass, and hydrophobicity score are dependent on each other, and that some dehydrin architectures are overexpressed during certain abiotic stress, suggesting that they may be optimized for a specific abiotic stress while others are involved in all forms of dehydration stress (drought, cold, and salinity.

  5. BayesMD: flexible biological modeling for motif discovery

    DEFF Research Database (Denmark)

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

    2008-01-01

    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 on trans......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...

  6. Superdiffusive motion of membrane-targeting C2 domains

    Science.gov (United States)

    Campagnola, Grace; Nepal, Kanti; Schroder, Bryce W.; Peersen, Olve B.; Krapf, Diego

    2015-12-01

    Membrane-targeting domains play crucial roles in the recruitment of signalling molecules to the plasma membrane. For most peripheral proteins, the protein-to-membrane interaction is transient. After proteins dissociate from the membrane they have been observed to rebind following brief excursions in the bulk solution. Such membrane hops can have broad implications for the efficiency of reactions on membranes. We study the diffusion of membrane-targeting C2 domains using single-molecule tracking in supported lipid bilayers. The ensemble-averaged mean square displacement (MSD) exhibits superdiffusive behaviour. However, traditional time-averaged MSD analysis of individual trajectories remains linear and does not reveal superdiffusion. Our observations are explained in terms of bulk excursions that introduce jumps with a heavy-tail distribution. These hopping events allow proteins to explore large areas in a short time. The experimental results are shown to be consistent with analytical models of bulk-mediated diffusion and numerical simulations.

  7. Fluorescent vibration-rotation excitation of cometary C2

    International Nuclear Information System (INIS)

    Gredel, R.; Van Dishoeck, E.F.; Black, J.H.

    1989-01-01

    The statistical equilibrium equations that determine the population densities of the energy levels in cometary C2 molecules due to fluorescent excitation are examined in detail. The adopted model and molecular parameters are discussed, and a theoretical estimate is made of the two intercombination transition moments. From the theoretical population densities in the various rotational levels, flux ratios and synthetic emission profiles are calculated as functions of the a 3Pi(u) - X 1Sigma(g)+ and the c 3Sigma(u)+ - X 3Sigma(g)+ intercombination transition moments. The influence of each of these two transitions separately on the vibrational and rotational excitation temperatures is investigated. The observed emission spectra of the (0,0) Swan band in Comet Halley are presented and compared to the synthetic profiles. 70 references

  8. Fluorescent vibration-rotation excitation of cometary C2

    Science.gov (United States)

    Gredel, Roland; Van Dishoeck, Ewine F.; Black, John H.

    1989-01-01

    The statistical equilibrium equations that determine the population densities of the energy levels in cometary C2 molecules due to fluorescent excitation are examined in detail. The adopted model and molecular parameters are discussed, and a theoretical estimate is made of the two intercombination transition moments. From the theoretical population densities in the various rotational levels, flux ratios and synthetic emission profiles are calculated as functions of the a 3Pi(u) - X 1Sigma(g)+ and the c 3Sigma(u)+ - X 3Sigma(g)+ intercombination transition moments. The influence of each of these two transitions separately on the vibrational and rotational excitation temperatures is investigated. The observed emission spectra of the (0,0) Swan band in Comet Halley are presented and compared to the synthetic profiles.

  9. Electronically excited C 2 from laser photodissociated C 60

    Science.gov (United States)

    Arepalli, S.; Scott, C. D.; Nikolaev, P.; Smalley, R. E.

    2000-03-01

    Spectral and transient emission measurements are made of radiation from products of laser excitation of buckminsterfullerene (C 60) vapor diluted in argon at 973 K. The principal radiation is from the Swan band system of C 2 and, at early times, also from a black-body continuum. Transient measurements indicate two characteristic periods of decay 2 and 50 μs long, with characteristic decay times of ˜0.3 and 5 μs, respectively. The first period is thought to be associated with decomposition and radiative cooling of C 60 molecules or nano-sized carbon particles and the second period continues with decomposition products of laser excited C 60, C 58, C 56, etc.

  10. 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.

  11. Synthesis of [2-13C, 2-14C] 2-aminoethanol, [1-13C, 1-14C] 2-chloroethylamine, N,N'-bis([1-13C, 1-14C] 2-chloroethyl)-N-nitrosourea(BCNU) and N-([1-13C, 1-14C] 2-chloroethyl)-N-nitrosourea(CNU)

    International Nuclear Information System (INIS)

    Narayan, R.; Chang, C-j.

    1982-01-01

    [2- 13 C, 2- 14 C]2-Aminoethanol hydrochloride was prepared in good yield from Na*CN in a two step sequence by first converting the Na*CN to OHCH 2 *CN and then reducing the nitrile directly with a solution of borane-tetrahydrofuran complex. The reaction procedure was simple and the pure product could be obtained readily. Using this specifically labelled precursor, the synthesis of [1- 13 C, 1- 14 C]2-chloroethylamine hydrochloride, N-([1- 13 C, 1- 14 C]2-chloroethyl)-N-nitrosourea(CNU) and N,N'-bis([1- 13 C, 1- 14 C]2-chloroethyl)-N-nitrosourea(BCNU) in good yield without isotope scrambling was also reported. (author)

  12. Formation and early hydration characteristics of C2.75B1.25A3$ in binary system of C2.75B1.25A3$-C2S

    Directory of Open Access Journals (Sweden)

    Wang, Shoude

    2016-09-01

    Full Text Available C2.75B1.25A3$ (2.75CaO•1.25BaO• 3Al2O3• SO3 is one of the important minerals and it govern-directly the early-strength of belite-barium calcium sulphoaluminate cement. In this paper a binary system C2.75B1.25A3$-C2S is selected to investigate the formation of C2.75B1.25A3$. In the range of 1100 °C–1200 °C, the earlier formed C2S hinders the formation of C2.75B1.25A3$. On the contrary, when the temperature is in the range of 1200 °C–1350 °C, the initially formed C2S could provide a surface for the nucleation of C2.75B1.25A3$ and cut down the potential barrier (?Gk* for the heterogeneous nucleation of C2.75B1.25A3$, which contributes to its formation. Moreover, at 1350 °C, the large amount of previously formed C2S benefits the extent of formation of C2.75B1.25A3$. The possible reason was that it could prevent sulfur evaporation. In early hydration age, AFm and AFt originating from C2.75B1.25A3$ hydration are found within 2 h and 12 h under 95% RH at 1 °C, respectively, whereas C2S is unhydrated at this moment.En el cemento de sulfoaluminato de calcio y bario, el C2.75B1.25A3$ (2.75CaO•1.25BaO• 3Al2 O3• SO3 es una de las principales fases, y regula directamente la resistencia inicial del cemento. En este trabajo, se ha seleccionado el sistema binario C2.75B1.25A3$-C2S para investigar la formación de C2.75B1.25A3$. En el rango de 1100 °C-1200 °C, el C2S formado anteriormente impide la formación de C2.75B1.25A3$, mientras que cuando la temperatura está entre 1200 °C-1350 °C, el C2S proporcionaría una superficie de nucleación de C2.75B1.25A3$ reduciendo la barrera de potencial (?Gk* para la nucleación heterogénea de C2.75B1.25A3$, lo que contribuye a su formación. Además, a 1350 °C, la gran cantidad de C2S formado beneficia la formación de C2.75B1.25A3$, ya que podía prevenir la evaporación del azufre. En las primeras etapas de la hidratación (entre 2 y 12h y 95% HR a 1 ºC se pueden encontrar AFM y AFt

  13. SSTRAP: A computational model for genomic motif discovery ...

    African Journals Online (AJOL)

    Computational methods can potentially provide high-quality prediction of biological molecules such as DNA binding sites and Transcription factors and therefore reduce the time needed for experimental verification and challenges associated with experimental methods. These biological molecules or motifs have significant ...

  14. Identification of a Baeyer-Villiger monooxygenase sequence motif

    NARCIS (Netherlands)

    Fraaije, MW; Kamerbeek, NM; van Berkel, WJH; Janssen, DB; Kamerbeek, Nanne M.; Berkel, Willem J.H. van

    2002-01-01

    Baeyer-Villiger monooxygenases (BVMOs) form a distinct class of flavoproteins that catalyze the insertion of an oxygen atom in a C-C bond using dioxygen and NAD(P)H. Using newly characterized BVMO sequences, we have uncovered a BVMO-identifying sequence motif: FXGXXXRXXXW(P/D). Studies with

  15. Linear motif atlas for phosphorylation-dependent signaling

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Jensen, LJ; Diella, F

    2008-01-01

    bind to them remains a challenge. NetPhorest is an atlas of consensus sequence motifs that covers 179 kinases and 104 phosphorylation-dependent binding domains [Src homology 2 (SH2), phosphotyrosine binding (PTB), BRCA1 C-terminal (BRCT), WW, and 14-3-3]. The atlas reveals new aspects of signaling...

  16. [Cover motifs of the Tidsskrift. A 14-year cavalcade].

    Science.gov (United States)

    Nylenna, M

    1998-12-10

    In 1985 the Journal of the Norwegian Medical Association changed its cover policy, moving the table of contents inside the Journal and introducing cover illustrations. This article provides an analysis of all cover illustrations published over this 14-year period, 420 covers in all. There is a great variation in cover motifs and designs and a development towards more general motifs. The initial emphasis on historical and medical aspects is now less pronounced, while the use of works of art and nature motifs has increased, and the cover now more often has a direct bearing on the specific contents of the issue. Professor of medical history Oivind Larsen has photographed two thirds of the covers and contributed 95% of the inside essay-style reflections on the cover motif. Over the years, he has expanded the role of the historian of medicine disseminating knowledge to include that of the raconteur with a personal tone of voice. The Journal's covers are now one of its most characteristic features, emblematic of the Journal's ambition of standing for quality and timelessness vis-à-vis the news media, and of its aim of bridging the gap between medicine and the humanities.

  17. Perspektif Psikologi Humanistik Abraham Maslow dalam Meninjau Motif Pelaku Pembunuhan

    OpenAIRE

    Nurwatie, Azrina; Fauzia, Rahmi; Akbar, Sukma Noor

    2014-01-01

    Fokus penelitian ini diarahkan pada motif pelaku pembunuhan dengan meninjaunya melalui perspektif psikologi humanistik Abraham Maslow. Subyek dalam penelitian ini berjumlah dua orang narapidana yang berada di Lapas Kelas IIA Anak Martapura dengan kasus pembunuhan. Metode penelitian yang digunakan dalam penelitian ini adalah metode penelitian kualitatif. Teknik pengumpulan data melalui wawancara, observasi, dokumentasi,dan pemeriksaan psikologis (tes grafis). Berdasarkan hasil analisis data da...

  18. Motifs in triadic random graphs based on Steiner triple systems

    Science.gov (United States)

    Winkler, Marco; Reichardt, Jörg

    2013-08-01

    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 subnetwork patterns, i.e., the so-called motifs, has attracted much attention. It has been hypothesized that 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 graph models (ERGMs) to define 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 obstacle, we use Steiner triple systems (STSs). These are partitions of sets of nodes into pair-disjoint triads, which thus can be specified independently. Combining the concepts of ERGMs and STSs, we suggest generative models capable of generating ensembles of networks with nontrivial triadic Z-score profiles. Further, we discover inevitable correlations between the abundance of triad patterns, which occur solely for statistical reasons and need to be taken into account when discussing the functional implications of motif statistics. Moreover, we calculate the degree distributions of our triadic random graphs analytically.

  19. Genetic analysis of beta1 integrin "activation motifs" in mice

    DEFF Research Database (Denmark)

    Czuchra, Aleksandra; Meyer, Hannelore; Legate, Kyle R

    2006-01-01

    -null phenotype in vivo. Surprisingly, neither the substitution of the tyrosines with phenylalanine nor the aspartic acid with alanine resulted in an obvious defect. These data suggest that the NPXY motifs of the beta1 integrin tail are essential for beta1 integrin function, whereas tyrosine phosphorylation...

  20. Insights into the motif preference of APOBEC3 enzymes.

    Directory of Open Access Journals (Sweden)

    Diako Ebrahimi

    Full Text Available We used a multivariate data analysis approach to identify motifs associated with HIV hypermutation by different APOBEC3 enzymes. The analysis showed that APOBEC3G targets G mainly within GG, TG, TGG, GGG, TGGG and also GGGT. The G nucleotides flanked by a C at the 3' end (in +1 and +2 positions were indicated as disfavoured targets by APOBEC3G. The G nucleotides within GGGG were found to be targeted at a frequency much less than what is expected. We found that the infrequent G-to-A mutation within GGGG is not limited to the inaccessibility, to APOBEC3, of poly Gs in the central and 3'polypurine tracts (PPTs which remain double stranded during the HIV reverse transcription. GGGG motifs outside the PPTs were also disfavoured. The motifs GGAG and GAGG were also found to be disfavoured targets for APOBEC3. The motif-dependent mutation of G within the HIV genome by members of the APOBEC3 family other than APOBEC3G was limited to GA→AA changes. The results did not show evidence of other types of context dependent G-to-A changes in the HIV genome.

  1. Sequence alignment reveals possible MAPK docking motifs on HIV proteins.

    Directory of Open Access Journals (Sweden)

    Perry Evans

    Full Text Available Over the course of HIV infection, virus replication is facilitated by the phosphorylation of HIV proteins by human ERK1 and ERK2 mitogen-activated protein kinases (MAPKs. MAPKs are known to phosphorylate their substrates by first binding with them at a docking site. Docking site interactions could be viable drug targets because the sequences guiding them are more specific than phosphorylation consensus sites. In this study we use multiple bioinformatics tools to discover candidate MAPK docking site motifs on HIV proteins known to be phosphorylated by MAPKs, and we discuss the possibility of targeting docking sites with drugs. Using sequence alignments of HIV proteins of different subtypes, we show that MAPK docking patterns previously described for human proteins appear on the HIV matrix, Tat, and Vif proteins in a strain dependent manner, but are absent from HIV Rev and appear on all HIV Nef strains. We revise the regular expressions of previously annotated MAPK docking patterns in order to provide a subtype independent motif that annotates all HIV proteins. One revision is based on a documented human variant of one of the substrate docking motifs, and the other reduces the number of required basic amino acids in the standard docking motifs from two to one. The proposed patterns are shown to be consistent with in silico docking between ERK1 and the HIV matrix protein. The motif usage on HIV proteins is sufficiently different from human proteins in amino acid sequence similarity to allow for HIV specific targeting using small-molecule drugs.

  2. The role of C2-C7 and O-C2 angle in the development of dysphagia after cervical spine surgery.

    Science.gov (United States)

    Tian, Wei; Yu, Jie

    2013-06-01

    Dysphagia is a known complication of cervical surgery and may be prolonged or occasionally serious. A previous study showed that dysphagia after occipitocervical fusion was caused by oropharyngeal stenosis resulting from O-C2 (upper cervical lordosis) fixation in a flexed position. However, there have been few reports analyzing the association between the C2-C7 angle (middle-lower cervical lordosis) and postoperative dysphagia. The aim of this study was to analyze the relationship between cervical lordosis and the development of dysphagia after anterior and posterior cervical spine surgery (AC and PC). Three hundred fifty-four patients were reviewed in this retrospective clinical study, including 172 patients who underwent the AC procedure and 182 patients who had the PC procedure between June 2007 and May 2010. The presence and duration of postoperative dysphagia were recorded via face-to-face questioning or telephone interview performed at least 1 year after the procedure. Plain cervical radiographs before and after surgery were collected. The O-C2 angle and the C2-C7 angle were measured. Changes in the O-C2 angle and the C2-C7 angle were defined as dO-C2 angle = postoperative O-C2 angle - preoperative O-C2 angle and dC2-C7 angle = postoperative C2-C7 angle - preoperative C2-C7 angle. The association between postoperative dysphagia with dO-C2 angle and dC2-C7 angle was studied. Results showed that 12.8 % of AC and 9.4 % of PC patients reported dysphagia after cervical surgery. The dC2-C7 angle has considerable impact on postoperative dysphagia. When the dC2-C7 angle is greater than 5°, the chance of developing postoperative dysphagia is significantly greater. The dO-C2 angle, age, gender, BMI, operative time, blood loss, procedure type, revision surgery, most cephalic operative level, and number of operative levels did not significantly influence the incidence of postoperative dysphagia. No relationship was found between the dC2-C7 angle and the degree of

  3. Clostridial Binary Toxins: Iota and C2 Family Portraits

    Science.gov (United States)

    Stiles, Bradley G.; Wigelsworth, Darran J.; Popoff, Michel R.; Barth, Holger

    2011-01-01

    There are many pathogenic Clostridium species with diverse virulence factors that include protein toxins. Some of these bacteria, such as C. botulinum, C. difficile, C. perfringens, and C. spiroforme, cause enteric problems in animals as well as humans. These often fatal diseases can partly be attributed to binary protein toxins that follow a classic AB paradigm. Within a targeted cell, all clostridial binary toxins destroy filamentous actin via mono-ADP-ribosylation of globular actin by the A component. However, much less is known about B component binding to cell-surface receptors. These toxins share sequence homology amongst themselves and with those produced by another Gram-positive, spore-forming bacterium also commonly associated with soil and disease: Bacillus anthracis. This review focuses upon the iota and C2 families of clostridial binary toxins and includes: (1) basics of the bacterial source; (2) toxin biochemistry; (3) sophisticated cellular uptake machinery; and (4) host–cell responses following toxin-mediated disruption of the cytoskeleton. In summary, these protein toxins aid diverse enteric species within the genus Clostridium. PMID:22919577

  4. Fusion proton diagnostic for the C-2 field reversed configurationa)

    Science.gov (United States)

    Magee, R. M.; Clary, R.; Korepanov, S.; Smirnov, A.; Garate, E.; Knapp, K.; Tkachev, A.

    2014-11-01

    Measurements of the flux of fusion products from high temperature plasmas provide valuable insights into the ion energy distribution, as the fusion reaction rate is a very sensitive function of ion energy. In C-2, where field reversed configuration plasmas are formed by the collision of two compact toroids and partially sustained by high power neutral beam injection [M. Binderbauer et al., Phys. Rev. Lett. 105, 045003 (2010); M. Tuszewski et al., Phys. Rev. Lett. 108, 255008 (2012)], measurements of DD fusion neutron flux are used to diagnose ion temperature and study fast ion confinement and dynamics. In this paper, we will describe the development of a new 3 MeV proton detector that will complement existing neutron detectors. The detector is a large area (50 cm2), partially depleted, ion implanted silicon diode operated in a pulse counting regime. While the scintillator-based neutron detectors allow for high time resolution measurements (˜100 kHz), they have no spatial or energy resolution. The proton detector will provide 10 cm spatial resolution, allowing us to determine if the axial distribution of fast ions is consistent with classical fast ion theory or whether anomalous scattering mechanisms are active. We will describe in detail the diagnostic design and present initial data from a neutral beam test chamber.

  5. C-2-C market relations and word of mouth

    Directory of Open Access Journals (Sweden)

    Grubor Aleksandar

    2015-01-01

    Full Text Available Most market research focuses on business-to-business and business- to-consumer interactions to explain the structure and dynamics of the market. Meanwhile, negligible effort has been invested in researching consumer-to-consumer interaction and its impact on companies’ behaviour and purchase decision-making, which determines business performance. The greatest challenge for marketers at the beginning of the 21st century is this third relationship dimension, consumer-to-consumer interaction: how consumers influence each other’s attitudes, expectations, perceptions, preferences, satisfaction, loyalty, and purchasing decisions, and, importantly, the possibility of incorporating consumers into businesses’ marketing programmes. Despite the existence of a multitude of media and different forms of communication between businesses and the market, such as newspapers, periodicals, billboards, television etc., a considerable portion of information is communicated to consumers informally, mostly in the form of word-of-mouth. The information received by consumers through this communication form - from family and similar individuals -is very often accepted as more reliable and certain than information transmitted through formal communication channels. What is often neglected when studying the phenomenon of word-of-mouth communication is the fact that its efficiency and effect also depend on the type and character of the interaction between the consumers themselves. This paper aims to investigate the extent to which the nature of customer to-customer (C2C interaction influences the effect of word-of-mouth communication.

  6. Convergent evolution and mimicry of protein linear motifs in host-pathogen interactions.

    Science.gov (United States)

    Chemes, Lucía Beatriz; de Prat-Gay, Gonzalo; Sánchez, Ignacio Enrique

    2015-06-01

    Pathogen linear motif mimics are highly evolvable elements that facilitate rewiring of host protein interaction networks. Host linear motifs and pathogen mimics differ in sequence, leading to thermodynamic and structural differences in the resulting protein-protein interactions. Moreover, the functional output of a mimic depends on the motif and domain repertoire of the pathogen protein. Regulatory evolution mediated by linear motifs can be understood by measuring evolutionary rates, quantifying positive and negative selection and performing phylogenetic reconstructions of linear motif natural history. Convergent evolution of linear motif mimics is widespread among unrelated proteins from viral, prokaryotic and eukaryotic pathogens and can also take place within individual protein phylogenies. Statistics, biochemistry and laboratory models of infection link pathogen linear motifs to phenotypic traits such as tropism, virulence and oncogenicity. In vitro evolution experiments and analysis of natural sequences suggest that changes in linear motif composition underlie pathogen adaptation to a changing environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

    KAUST Repository

    Alam, Tanvir; Alazmi, Meshari; Naser, Rayan Mohammad Mahmoud; Huser, Franceline; Momin, Afaque Ahmad Imtiyaz; Walkiewicz, Katarzyna Wiktoria; Canlas, Christian; Huser, Raphaë l; Ali, Amal J.; Merzaban, Jasmeen; Bajic, Vladimir B.; Gao, Xin; Arold, Stefan T.

    2018-01-01

    and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter

  8. Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome

    Directory of Open Access Journals (Sweden)

    Böhm Siegfried

    2004-07-01

    Full Text Available Background The classical C2H2 zinc finger domain is involved in a wide range of functions and can bind to DNA, RNA and proteins. The comparison of zinc finger proteins in several eukaryotes has shown that there is a lot of lineage specific diversification and expansion. Although the number of characterized plant proteins that carry the classical C2H2 zinc finger motifs is growing, a systematic classification and analysis of a plant genome zinc finger gene set is lacking. Results We found through in silico analysis 176 zinc finger proteins in Arabidopsis thaliana that hence constitute the most abundant family of putative transcriptional regulators in this plant. Only a minority of 33 A. thaliana zinc finger proteins are conserved in other eukaryotes. In contrast, the majority of these proteins (81% are plant specific. They are derived from extensive duplication events and form expanded families. We assigned the proteins to different subgroups and families and focused specifically on the two largest and evolutionarily youngest families (A1 and C1 that are suggested to be primarily involved in transcriptional regulation. The newly defined family A1 (24 members comprises proteins with tandemly arranged zinc finger domains. Family C1 (64 members, earlier described as the EPF-family in Petunia, comprises proteins with one isolated or two to five dispersed fingers and a mostly invariant QALGGH motif in the zinc finger helices. Based on the amino acid pattern in these helices we could describe five different signature sequences prevalent in C1 zinc finger domains. We also found a number of non-finger domains that are conserved in these families. Conclusions Our analysis of the few evolutionarily conserved zinc finger proteins of A. thaliana suggests that most of them could be involved in ancient biological processes like RNA metabolism and chromatin-remodeling. In contrast, the majority of the unique A. thaliana zinc finger proteins are known or

  9. Bioenergetic Profile Experiment using C2C12 Myoblast Cells

    Science.gov (United States)

    Nicholls, David G.; Darley-Usmar, Victor M.; Wu, Min; Jensen, Per Bo; Rogers, George W.; Ferrick, David A.

    2010-01-01

    The ability to measure cellular metabolism and understand mitochondrial dysfunction, has enabled scientists worldwide to advance their research in understanding the role of mitochondrial function in obesity, diabetes, aging, cancer, cardiovascular function and safety toxicity. Cellular metabolism is the process of substrate uptake, such as oxygen, glucose, fatty acids, and glutamine, and subsequent energy conversion through a series of enzymatically controlled oxidation and reduction reactions. These intracellular biochemical reactions result in the production of ATP, the release of heat and chemical byproducts, such as lactate and CO2 into the extracellular environment. Valuable insight into the physiological state of cells, and the alteration of the state of those cells, can be gained through measuring the rate of oxygen consumed by the cells, an indicator of mitochondrial respiration - the Oxygen Consumption Rate - or OCR. Cells also generate ATP through glycolysis, i.e.: the conversion of glucose to lactate, independent of oxygen. In cultured wells, lactate is the primary source of protons. Measuring the lactic acid produced indirectly via protons released into the extracellular medium surrounding the cells, which causes acidification of the medium provides the Extra-Cellular Acidification Rate - or ECAR. In this experiment, C2C12 myoblast cells are seeded at a given density in Seahorse cell culture plates. The basal oxygen consumption (OCR) and extracellular acidification (ECAR) rates are measured to establish baseline rates. The cells are then metabolically perturbed by three additions of different compounds (in succession) that shift the bioenergetic profile of the cell. This assay is derived from a classic experiment to assess mitochondria and serves as a framework with which to build more complex experiments aimed at understanding both physiologic and pathophysiologic function of mitochondria and to predict the ability of cells to respond to stress and

  10. Finding a Leucine in a Haystack: Searching the Proteome for ambigous Leucine-Aspartic Acid motifs

    KAUST Repository

    Arold, Stefan T.

    2016-01-01

    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.

  11. DMINDA: an integrated web server for DNA motif identification and analyses.

    Science.gov (United States)

    Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

    2014-07-01

    DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. 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.

  13. Gene regulatory and signaling networks exhibit distinct topological distributions of motifs

    Science.gov (United States)

    Ferreira, Gustavo Rodrigues; Nakaya, Helder Imoto; Costa, Luciano da Fontoura

    2018-04-01

    The biological processes of cellular decision making and differentiation involve a plethora of signaling pathways and gene regulatory circuits. These networks in turn exhibit a multitude of motifs playing crucial parts in regulating network activity. Here we compare the topological placement of motifs in gene regulatory and signaling networks and observe that it suggests different evolutionary strategies in motif distribution for distinct cellular subnetworks.

  14. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

    Science.gov (United States)

    Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

    2011-06-20

    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. 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. 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.

  15. 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

  16. Core signalling motif displaying multistability through multi-state enzymes

    DEFF Research Database (Denmark)

    Feng, Song; Saez Cornellana, Meritxell; Wiuf, Carsten Henrik

    2016-01-01

    Bistability, and more generally multistability, is a key system dynamics feature enabling decision-making and memory in cells. Deciphering the molecular determinants of multistability is thus crucial for a better understanding of cellular pathways and their (re)engineering in synthetic biology....... Here, we show that a key motif found predominantly in eukaryotic signalling systems, namely a futile signalling cycle, can display bistability when featuring a two-state kinase. We provide necessary and sufficient mathematical conditions on the kinetic parameters of this motif that guarantee...... the existence of multiple steady states. These conditions foster the intuition that bistability arises as a consequence of competition between the two states of the kinase. Extending from this result, we find that increasing the number of kinase states linearly translates into an increase in the number...

  17. Factoring local sequence composition in motif significance analysis.

    Science.gov (United States)

    Ng, Patrick; Keich, Uri

    2008-01-01

    We recently introduced a biologically realistic and reliable significance analysis of the output of a popular class of motif finders. In this paper we further improve our significance analysis by incorporating local base composition information. Relying on realistic biological data simulation, as well as on FDR analysis applied to real data, we show that our method is significantly better than the increasingly popular practice of using the normal approximation to estimate the significance of a finder's output. Finally we turn to leveraging our reliable significance analysis to improve the actual motif finding task. Specifically, endowing a variant of the Gibbs Sampler with our improved significance analysis we demonstrate that de novo finders can perform better than has been perceived. Significantly, our new variant outperforms all the finders reviewed in a recently published comprehensive analysis of the Harbison genome-wide binding location data. Interestingly, many of these finders incorporate additional information such as nucleosome positioning and the significance of binding data.

  18. Theoretical characterizations of novel C2H5O+ reactions

    Science.gov (United States)

    Hudson, Charles E.; McAdoo, David J.

    2004-03-01

    Assorted reactions of C2H5O+ isomers are characterized by theory, including tracing their courses by means of intrinsic reaction coordinate computations. We establish that CH3CH=OH+ eliminates methane by transferring H from oxygen to a methyl hydrogen and then to the CC bond to produce CHO++CH4. This adds to the limited knowledge of the involvement of hypervalent structures in the reactions of cations in the gas phase. Second, we characterized the course of CH3CH=OH+-->H3O++HC[triple bond; length as m-dash]CH. In this dissociation, H first migrates from the methyl to the oxygen to give O-protonated vinyl alcohol, a stable intermediate. Then the H2O swings outward to over the middle of the CC bond while one of the two hydrogens on the non-O-bearing carbon revolves to between the oxygen and the two carbons, leading to formation of a [H3O+ HC[triple bond; length as m-dash]CH] complex. This complex contains sufficient energy to dissociate its partners because a high barrier is crossed in its formation. Third, we found that methane elimination from CH3O+=CH2 involves stretching of the CH3---O bond and then rotation of the methyl so that a methyl hydrogen is pointed directly toward the oxygen. This reaction is completed by further rotation of the methyl to abstract a methylene hydrogen to the opposite side of the methyl from that initially bonded to oxygen. This clearly establishes that this dissociation takes place through an ion-neutral complex. Each of the reaction coordinates for the three preceding reactions traverses a novel bonding stage involving H, evidence that such are not unusual in gas phase ion chemistry. Finally, we showed that in the rearrangement CH3O+=CH2-->CH2=O+CH3, before Ht is transferred CH2 rotates around the C=C bond from being in the skeletal plane to being perpendicular to it, and Ht remains in the skeletal plane throughout its transfer. This pathway appears to balance avoiding an orbital symmetry-forbidden suprafacial transition state with

  19. Neoanalysis, Orality, and Intertextuality: An Examination of Homeric Motif Transference

    Directory of Open Access Journals (Sweden)

    Jonathan Burgess

    2006-03-01

    Full Text Available In Homeric studies scholars have speculated on the influence of (non-surviving preHomeric material on the Iliad. This article expands this line of argument from an oralist perspective, with reference to modern intertextual theory. It concludes that preHomeric and nonHomeric motifs from oral traditions were transferred into the epic poem, creating an intertextually allusive poetics that would have been recognizable to an early Greek audience informed of mythological traditions.

  20. Motif Subscriber Menonton Channel YouTube Raditya Dika

    OpenAIRE

    Mellyaningsih, Adinda

    2016-01-01

    Penelitian ini dilakukan untuk mengetahui motif para subscriber dalam menonton channelYouTube Raditya Dika. Raditya Dika merupakan YouTuber Indonesia dengan jumlah subscriber terbanyak dan merupakan orang pertama di Indonesia yang mendapatkan penghargaan Certifies Award oleh YouTube. Peneliti menggunakan teori Uses and Gratification dengan empat indikator, yaitu hiburan dan relaksasi, hubungan antar pribadi, mencari informasi, dan persahabatan. Metode dalam penelitian ini adalah online survei...

  1. Perception Enhancement using Visual Attributes in Sequence Motif Visualization

    OpenAIRE

    Oon, Yin; Lee, Nung; Kok, Wei

    2016-01-01

    Sequence logo is a well-accepted scientific method to visualize the conservation characteristics of biological sequence motifs. Previous studies found that using sequence logo graphical representation for scientific evidence reports or arguments could seriously cause biases and misinterpretation by users. This study investigates on the visual attributes performance of a sequence logo in helping users to perceive and interpret the information based on preattentive theories and Gestalt principl...

  2. 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.

  3. Multiple TPR motifs characterize the Fanconi anemia FANCG protein.

    Science.gov (United States)

    Blom, Eric; van de Vrugt, Henri J; de Vries, Yne; de Winter, Johan P; Arwert, Fré; Joenje, Hans

    2004-01-05

    The genome protection pathway that is defective in patients with Fanconi anemia (FA) is controlled by at least eight genes, including BRCA2. A key step in the pathway involves the monoubiquitylation of FANCD2, which critically depends on a multi-subunit nuclear 'core complex' of at least six FANC proteins (FANCA, -C, -E, -F, -G, and -L). Except for FANCL, which has WD40 repeats and a RING finger domain, no significant domain structure has so far been recognized in any of the core complex proteins. By using a homology search strategy comparing the human FANCG protein sequence with its ortholog sequences in Oryzias latipes (Japanese rice fish) and Danio rerio (zebrafish) we identified at least seven tetratricopeptide repeat motifs (TPRs) covering a major part of this protein. TPRs are degenerate 34-amino acid repeat motifs which function as scaffolds mediating protein-protein interactions, often found in multiprotein complexes. In four out of five TPR motifs tested (TPR1, -2, -5, and -6), targeted missense mutagenesis disrupting the motifs at the critical position 8 of each TPR caused complete or partial loss of FANCG function. Loss of function was evident from failure of the mutant proteins to complement the cellular FA phenotype in FA-G lymphoblasts, which was correlated with loss of binding to FANCA. Although the TPR4 mutant fully complemented the cells, it showed a reduced interaction with FANCA, suggesting that this TPR may also be of functional importance. The recognition of FANCG as a typical TPR protein predicts this protein to play a key role in the assembly and/or stabilization of the nuclear FA protein core complex.

  4. Efficient sequential and parallel algorithms for planted motif search.

    Science.gov (United States)

    Nicolae, Marius; Rajasekaran, Sanguthevar

    2014-01-31

    Motif searching is an important step in the detection of rare events occurring in a set of DNA or protein sequences. One formulation of the problem is known as (l,d)-motif search or Planted Motif Search (PMS). In PMS we are given two integers l and d and n biological sequences. We want to find all sequences of length l that appear in each of the input sequences with at most d mismatches. The PMS problem is NP-complete. PMS algorithms are typically evaluated on certain instances considered challenging. Despite ample research in the area, a considerable performance gap exists because many state of the art algorithms have large runtimes even for moderately challenging instances. This paper presents a fast exact parallel PMS algorithm called PMS8. PMS8 is the first algorithm to solve the challenging (l,d) instances (25,10) and (26,11). PMS8 is also efficient on instances with larger l and d such as (50,21). We include a comparison of PMS8 with several state of the art algorithms on multiple problem instances. This paper also presents necessary and sufficient conditions for 3 l-mers to have a common d-neighbor. The program is freely available at http://engr.uconn.edu/~man09004/PMS8/. We present PMS8, an efficient exact algorithm for Planted Motif Search. PMS8 introduces novel ideas for generating common neighborhoods. We have also implemented a parallel version for this algorithm. PMS8 can solve instances not solved by any previous algorithms.

  5. Aplikasi Ornamen Khas Maluku untuk Pengembangan Desain Motif Batik

    OpenAIRE

    Masiswo Masiswo; Vivin Atika

    2016-01-01

    ABSTRAKMaluku memiliki banyak ragam hias budaya warisan nilai leluhur berupa ornamen etnis yang merupakan kesenian dan keterampilan kerajinan. Hasil warisan tersebut sampai saat ini masih lestari hidup serta dapat dinikmati sebagai konsumsi rohani yang memuaskan manusia. Berkaitan dengan keberlangsungan nilai-nilai tradisi etnis yang berwujud pada ornamen-ornamen daerah Maluku, maka dikembangkan untuk kebutuhan manusia berupa motif batik pada kain. Pengembangan ornamen ini lebih menekankan pa...

  6. ROMANIAN TRADITIONAL MOTIF ELEMENT OF MODERNITY IN CLOTHING

    Directory of Open Access Journals (Sweden)

    ŞUTEU Marius Darius

    2017-05-01

    Full Text Available In this paper are presented the phases for improving from an aesthetic point of view a clothing item, the T-shirt for women using software design patterns, computerised graphics and textile different modern technologies including: industrial embroidery, digital printing, sublimation. In the first phase a documentation was prepared in the University of Oradea and traditional motif was selected from a collection comprising a number of Romanian traditional motifs from different parts of the country and were reintepreted and stylized whilst preserving the symbolism and color range specified to the area. For the styling phase was used CorelDraw vector graphics program that allows changing the shape, size and color of the drawings without affecting the identity of the pattern. The embroidery was done using BERNINA Embroidery Software Designer Plus Software. This software allows you to export the model to any domestic or industrial embroidery machine regardless of brand. Finally we observed the resistance of the printed and embroided model to various: elasticity, resistance to abrasion and a sensory analysis on the preservation of color. After testing we noticed the imprint resistance applied to the fabric, resulting in a quality that makes possible to keep the Romanian traditional motif from generation to generation.

  7. 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.

  8. Codon based co-occurrence network motifs in human mitochondria

    Directory of Open Access Journals (Sweden)

    Pramod Shinde

    2017-10-01

    Full Text Available The nucleotide polymorphism in human mitochondrial genome (mtDNA tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, we constructed genome-wide nucleotide co-occurrence networks using a massive data consisting of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns between codon and non-codon positions. It was interesting to report a different evolution of Asian genomes than those of the rest which is divulged by network motifs. We found evidence that mtDNA undergoes substantial amounts of adaptive evolution, a finding which was supported by a number of previous studies. The dominance of higher order motifs indicated the importance of long-range nucleotide co-occurrence in genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analyses manifested that codon position co-evolution is very well conserved across human sub-populations and independently maintained within human sub-populations implying the selective role of evolutionary processes on codon position co-evolution. Ergo, this study provided a framework to investigate cooperative genomic interactions which are critical in underlying complex mitochondrial evolution.

  9. Organofluorine chemistry: synthesis and conformation of vicinal fluoromethylene motifs.

    Science.gov (United States)

    O'Hagan, David

    2012-04-20

    The C-F bond is the most polar bond in organic chemistry, and thus the bond has a relatively large dipole moment with a significant -ve charge density on the fluorine atom and correspondingly a +ve charge density on carbon. The electrostatic nature of the bond renders it the strongest one in organic chemistry. However, the fluorine atom itself is nonpolarizable, and thus, despite the charge localization on fluorine, it is a poor hydrogen-bonding acceptor. These properties of the C-F bond make it attractive in the design of nonviscous but polar organic compounds, with a polarity limited to influencing the intramolecular nature of the molecule and less so intermolecular interactions with the immediate environment. In this Perspective, the synthesis of aliphatic chains carrying multivicinal fluoromethylene motifs is described. It emerges that the dipoles of adjacent C-F bonds orientate relative to each other, and thus, individual diastereoisomers display different backbone carbon chain conformations. These conformational preferences recognize the influence of the well-known gauche effect associated with 1,2-difluoroethane but extend to considering 1,3-fluorine-fluorine dipolar repulsions. The synthesis of carbon chains carrying two, three, four, five, and six vicinal fluoromethylene motifs is described, with an emphasis on our own research contributions. These motifs obey almost predictable conformational behavior, and they emerge as candidates for inclusion in the design of performance organic molecules. © 2012 American Chemical Society

  10. iFORM: Incorporating Find Occurrence of Regulatory Motifs.

    Science.gov (United States)

    Ren, Chao; Chen, Hebing; Yang, Bite; Liu, Feng; Ouyang, Zhangyi; Bo, Xiaochen; Shu, Wenjie

    2016-01-01

    Accurately identifying the binding sites of transcription factors (TFs) is crucial to understanding the mechanisms of transcriptional regulation and human disease. We present incorporating Find Occurrence of Regulatory Motifs (iFORM), an easy-to-use and efficient tool for scanning DNA sequences with TF motifs described as position weight matrices (PWMs). Both performance assessment with a receiver operating characteristic (ROC) curve and a correlation-based approach demonstrated that iFORM achieves higher accuracy and sensitivity by integrating five classical motif discovery programs using Fisher's combined probability test. We have used iFORM to provide accurate results on a variety of data in the ENCODE Project and the NIH Roadmap Epigenomics Project, and the tool has demonstrated its utility in further elucidating individual roles of functional elements. Both the source and binary codes for iFORM can be freely accessed at https://github.com/wenjiegroup/iFORM. The identified TF binding sites across human cell and tissue types using iFORM have been deposited in the Gene Expression Omnibus under the accession ID GSE53962.

  11. THE MOTIF OF THE PRODIGAL SON IN IVAN TURGENEV'S NOVELS

    Directory of Open Access Journals (Sweden)

    Valentina Ivanovna Gabdullina

    2013-11-01

    Full Text Available The author questions the perception of Ivan Turgenev as a “non- Christian writer” and studies the problem of the prodigal son motif functioning in a series of his novels. In his novels, Turgenev pictured different phases of the archetypal story, originating from the Gospel parable of the prodigal son. In the novel Rudin he depicted the phase of spiritual wanderings of the hero who had lost touch with his native land — Russia. In his next novels (Home of the Gentry, Fathers and Sons and Smoke, after leading his hero in circles and sending him back to his paternal home, Turgenev reconstructs the model of human behavior, represented in the parable, thereby recognizing the immutability of the idea formalized in the Gospel. The motif of the return to Russian land gets its completion in Turgenev's last novel Virgin Soil, in which the author paradoxically connects the Westernist idea with the Gospel imperative. Solomin, the son of a deacon, sent by his wise father out to Europe “to get education”, studies in England, masters the European knowledge and returns back “to his native land” to establish his own business in inland Russia. Thus, a series of Turgenev's novels, in which he portrayed different phases of social life, are interlinked with the motif of the prodigal son, who is represented by novels' main characters.

  12. The city as a motif in Slovene youth literature

    Directory of Open Access Journals (Sweden)

    Milena Mileva Blažić

    2003-01-01

    Full Text Available The article presents the city as motif of Slovenian youth literature in four different periods, beginning in the first period of original Slovenian youth literature in the second half of the 19th century, second period in the first half of the 20th century, third period in the second half of the 20th century and after 1950, when significant books were produced in the field of short modern stories, emphasising on picture books and realistic narrative prose, and the fourth period after 1990. A discernable shift can be observed in the thirties of the 20th century, during the times of socialist realism. The most significant change occurred after 1960, when massive migration from rural to urban environments caused by industrialisation began. The motif of urban environment especially marked modern realistic narrative, coined problematic narrative after 1990, with its focus on issues of growing up in such environments. The city as motif or theme doesn’t appear only in realistic narrative, but since the early 20th century also in fantastic narrative, thus it dichotomically presents the image of real world in Slovenian youth realistic narrative.

  13. TOPDOM: database of conservatively located domains and motifs in proteins.

    Science.gov (United States)

    Varga, Julia; Dobson, László; Tusnády, Gábor E

    2016-09-01

    The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in α-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins. TOPDOM database is available at http://topdom.enzim.hu The webpage utilizes the common Apache, PHP5 and MySQL software to provide the user interface for accessing and searching the database. The database itself is generated on a high performance computer. tusnady.gabor@ttk.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  14. CRISPR-RT: A web service for designing CRISPR-C2c2 crRNA with improved target specificity

    OpenAIRE

    Zhu, Houxiang; Richmond, Emily; Liang, Chun

    2017-01-01

    CRISPR-Cas systems have been successfully applied in genome editing. Recently, the CRISPR-C2c2 system has been reported as a tool for RNA editing. Here we describe CRISPR-RT (CRISPR RNA-Targeting), the first web service to help biologists design the crRNA with improved target specificity for the CRISPR-C2c2 system. CRISPR-RT allows users to set up a wide range of parameters, making it highly flexible for current and future research in CRISPR-based RNA editing. CRISPR-RT covers major model org...

  15. Disruption of Fyn SH3 domain interaction with a proline-rich motif in liver kinase B1 results in activation of AMP-activated protein kinase.

    Directory of Open Access Journals (Sweden)

    Eijiro Yamada

    Full Text Available Fyn-deficient mice display increased AMP-activated Protein Kinase (AMPK activity as a result of Fyn-dependent regulation of Liver Kinase B1 (LKB1 in skeletal muscle. Mutation of Fyn-specific tyrosine sites in LKB1 results in LKB1 export into the cytoplasm and increased AMPK activation site phosphorylation. This study characterizes the structural elements responsible for the physical interaction between Fyn and LKB1. Effects of point mutations in the Fyn SH2/SH3 domains and in the LKB1 proline-rich motif on 1 Fyn and LKB1 binding, 2 LKB1 subcellular localization and 3 AMPK phosphorylation were investigated in C2C12 muscle cells. Additionally, novel LKB1 proline-rich motif mimicking cell permeable peptides were generated to disrupt Fyn/LKB1 binding and investigate the consequences on AMPK activity in both C2C12 cells and mouse skeletal muscle. Mutation of either Fyn SH3 domain or the proline-rich motif of LKB1 resulted in the disruption of Fyn/LKB1 binding, re-localization of 70% of LKB1 signal in the cytoplasm and a 2-fold increase in AMPK phosphorylation. In vivo disruption of the Fyn/LKB1 interaction using LKB1 proline-rich motif mimicking cell permeable peptides recapitulated Fyn pharmacological inhibition. We have pinpointed the structural elements within Fyn and LKB1 that are responsible for their binding, demonstrating the functionality of this interaction in regulating AMPK activity.

  16. Comparative Shock-Tube Study of Autoignition and Plasma-Assisted Ignition of C2-Hydrocarbons

    Science.gov (United States)

    Kosarev, Ilya; Kindysheva, Svetlana; Plastinin, Eugeny; Aleksandrov, Nikolay; Starikovskiy, Andrey

    2015-09-01

    The dynamics of pulsed picosecond and nanosecond discharge development in liquid water, ethanol and hexane Using a shock tube with a discharge cell, ignition delay time was measured in a lean (φ = 0.5) C2H6:O2:Ar mixture and in lean (φ = 0.5) and stoichiometric C2H4:O2:Ar mixtures with a high-voltage nanosecond discharge and without it. The measured results were compared with the measurements made previously with the same setup for C2H6-, C2H5OH- and C2H2-containing mixtures. It was shown that the effect of plasma on ignition is almost the same for C2H6, C2H4 and C2H5OH. The reduction in time is smaller for C2H2, the fuel that is well ignited even without the discharge. Autoignition delay time was independent of the stoichiometric ratio for C2H6 and C2H4, whereas this time in stoichiometric C2H2- and C2H5OH-containing mixtures was noticeably shorter than that in the lean mixtures. Ignition after the discharge was not affected by a change in the stoichiometric ratio for C2H2 and C2H4, whereas the plasma-assisted ignition delay time for C2H6 and C2H5OH decreased as the equivalence ratio changed from 1 to 0.5. Ignition delay time was calculated in C2-hydrocarbon-containing mixtures under study by simulating separately discharge and ignition processes. Good agreement was obtained between new measurements and calculated ignition delay times.

  17. Crankshafts: using simple, flat C2h-symmetric molecules to direct the assembly of chiral 2D nanopatterns.

    Science.gov (United States)

    Zhou, Hui; Wuest, James D

    2013-06-18

    Linear D2h-symmetric bisisophthalic acids 1 and 2 and related substances have well-defined flattened structures, high affinities for graphite, and strong abilities to engage in specific intermolecular interactions. Their adsorption produces characteristic nanopatterns that reveal how 2D molecular organization can be controlled by reliable interadsorbate interactions such as hydrogen bonds when properly oriented by molecular geometry. In addition, the behavior of these compounds shows how large-scale organization can be obstructed by programming molecules to associate strongly according to competing motifs that have similar stability and can coexist smoothly without creating significant defects. Analogous new bisisophthalic acids 3a and 4a have similar associative properties, and their unique C2h-symmetric crankshaft geometry gives them the added ability to probe the poorly understood effect of chirality on molecular organization. Their adsorption shows how nanopatterns composed predictably of a single enantiomer can be obtained by depositing molecules that can respect established rules of association only by accepting neighbors of the same configuration. In addition, an analysis of the adsorption of crankshaft compounds 3a and 4a and their derivatives by STM reveals directly on the molecular level how kinetics and thermodynamics compete to control the crystallization of chiral compounds. In such ways, detailed studies of the adsorption of properly designed compounds on surfaces are proving to be a powerful way to discover and test rules that broadly govern molecular organization in both 2D and 3D.

  18. 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

    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...... 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...

  19. Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks.

    Science.gov (United States)

    Gorochowski, Thomas E; Grierson, Claire S; di Bernardo, Mario

    2018-03-01

    Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli . Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution.

  20. On the sintering behaviour of steel bonded TiC-Cr3C2 and TiC-Cr3C2-WC mixed carbides

    International Nuclear Information System (INIS)

    Stojanov, L.G.; Exner, H.E.

    1978-01-01

    Powder mixtures of TiC+Cr 3 C 2 and TiC+Cr 3 C 2 + WC were hot pressed to nearly full density. The lattice parameter of the resulting cubic mixed crystal decreases linearly with increasing additions of Cr 3 C 2 and (Cr 3 C 2 +WC 1:1). Microhardness increases with Cr 3 C 2 content up to 20 wt.%. By addition of WC, microhardness is increased further and reaches a maximum value of approx. 38 000 MN/m 2 for 20 wt.% Cr 3 C 2 and 20 wt.% WC. From these solid solutions powder compositions of Ferro-TiC type were produced by milling with 55 wt.% Fe and 0.4 wt.% C. The sintering behaviour of these powders was studied in a vacuum dilatometer. The pronounced increase of shrinkage by Cr 3 C 2 and higher amounts of Cr 3 C 2 +WC dissolved in TiC previous to binder phase melting is attributed to the increased solubility of the carbide in solid iron. Presintering at 700 0 C in hydrogen has a negative influence on sintering activity and requires much higher temperatures for complete densification during subsequent vacuum sintering. (orig.) [de

  1. Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif

    Directory of Open Access Journals (Sweden)

    Launey Thomas

    2011-06-01

    Full Text Available Abstract Background The interactions between PDZ (PSD-95, Dlg, ZO-1 domains and PDZ-binding motifs play central roles in signal transductions within cells. Proteins with PDZ domains bind to PDZ-binding motifs almost exclusively when the motifs are located at the carboxyl (C- terminal ends of their binding partners. However, it remains little explored whether PDZ-binding motifs show any preferential location at the C-terminal ends of proteins, at genome-level. Results Here, we examined the distribution of the type-I (x-x-S/T-x-I/L/V or type-II (x-x-V-x-I/V PDZ-binding motifs in proteins encoded in the genomes of five different species (human, mouse, zebrafish, fruit fly and nematode. We first established that these PDZ-binding motifs are indeed preferentially present at their C-terminal ends. Moreover, we found specific amino acid (AA bias for the 'x' positions in the motifs at the C-terminal ends. In general, hydrophilic AAs were favored. Our genomics-based findings confirm and largely extend the results of previous interaction-based studies, allowing us to propose refined consensus sequences for all of the examined PDZ-binding motifs. An ontological analysis revealed that the refined motifs are functionally relevant since a large fraction of the proteins bearing the motif appear to be involved in signal transduction. Furthermore, co-precipitation experiments confirmed two new protein interactions predicted by our genomics-based approach. Finally, we show that influenza virus pathogenicity can be correlated with PDZ-binding motif, with high-virulence viral proteins bearing a refined PDZ-binding motif. Conclusions Our refined definition of PDZ-binding motifs should provide important clues for identifying functional PDZ-binding motifs and proteins involved in signal transduction.

  2. Trp[superscript 2313]-His[superscript 2315] of Factor VIII C2 Domain Is Involved in Membrane Binding Structure of a Complex Between the C[subscript 2] Domain and an Inhibitor of Membrane Binding

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhuo; Lin, Lin; Yuan, Cai; Nicolaes, Gerry A.F.; Chen, Liqing; Meehan, Edward J.; Furie, Bruce; Furie, Barbara; Huang, Mingdong (Harvard-Med); (UAH); (Maastricht); (Chinese Aca. Sci.)

    2010-11-03

    Factor VIII (FVIII) plays a critical role in blood coagulation by forming the tenase complex with factor IXa and calcium ions on a membrane surface containing negatively charged phospholipids. The tenase complex activates factor X during blood coagulation. The carboxyl-terminal C2 domain of FVIII is the main membrane-binding and von Willebrand factor-binding region of the protein. Mutations of FVIII cause hemophilia A, whereas elevation of FVIII activity is a risk factor for thromboembolic diseases. The C2 domain-membrane interaction has been proposed as a target of intervention for regulation of blood coagulation. A number of molecules that interrupt FVIII or factor V (FV) binding to cell membranes have been identified through high throughput screening or structure-based design. We report crystal structures of the FVIII C2 domain under three new crystallization conditions, and a high resolution (1.15 {angstrom}) crystal structure of the FVIII C2 domain bound to a small molecular inhibitor. The latter structure shows that the inhibitor binds to the surface of an exposed {beta}-strand of the C2 domain, Trp{sup 2313}-His{sup 2315}. This result indicates that the Trp{sup 2313}-His{sup 2315} segment is an important constituent of the membrane-binding motif and provides a model to understand the molecular mechanism of the C2 domain membrane interaction.

  3. 26 CFR 1.860C-2 - Determination of REMIC taxable income or net loss.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 9 2010-04-01 2010-04-01 false Determination of REMIC taxable income or net loss. 1.860C-2 Section 1.860C-2 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES Real Estate Investment Trusts § 1.860C-2 Determination of...

  4. 18 CFR 1c.2 - Prohibition of electric energy market manipulation.

    Science.gov (United States)

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Prohibition of electric energy market manipulation. 1c.2 Section 1c.2 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY GENERAL RULES PROHIBITION OF ENERGY MARKET MANIPULATION § 1c.2...

  5. 17 CFR 270.3c-2 - Definition of beneficial ownership in small business investment companies.

    Science.gov (United States)

    2010-04-01

    ... 1940 § 270.3c-2 Definition of beneficial ownership in small business investment companies. For the... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Definition of beneficial ownership in small business investment companies. 270.3c-2 Section 270.3c-2 Commodity and Securities...

  6. 26 CFR 1.381(c)(2)-1 - Earnings and profits.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 4 2010-04-01 2010-04-01 false Earnings and profits. 1.381(c)(2)-1 Section 1.381(c)(2)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES Insolvency Reorganizations § 1.381(c)(2)-1 Earnings and profits. (a) In...

  7. Amino acid residues involved in membrane insertion and pore formation of Clostridium botulinum C2 toxin.

    Science.gov (United States)

    Lang, Alexander E; Neumeyer, Tobias; Sun, Jianjun; Collier, R John; Benz, Roland; Aktories, Klaus

    2008-08-12

    The actin-ADP-ribosylating Clostridium botulinum C2 toxin consists of the enzymatic component C2I and the binding component C2II. C2II forms heptameric channels involved in translocation of the enzymatic component into the target cell. On the basis of the heptameric toxin channel, we studied functional consequences of mutagenesis of amino acid residues probably lining the lumen of the toxin channel. Substitution of glutamate-399 of C2II with alanine blocked channel formation and cytotoxicity of the holotoxin. Although cytotoxicity and rounding up of cells by C2I were completely blocked by exchange of phenylalanine-428 with alanine, the mutation increased potassium conductance caused by C2II in artificial membranes by about 2-3-fold over that of wild-type toxin. In contrast to its effects on single-channel potassium conductance in artificial membranes, the F428A mutation delayed the kinetics of pore formation in lipid vesicles and inhibited the activity of C2II in promoting (86)Rb (+) release from preloaded intact cells after pH shift of the medium. Moreover, F428A C2II exhibited delayed and diminished formation of C2II aggregates at low pH, indicating major changes of the biophysical properties of the toxin. The data indicate that phenylalanine-428 of C2II plays a major role in conformational changes occurring during pore formation of the binding component of C2II.

  8. Experimental studies of collisions of excited Li(4p) atoms with C2H4, C2H6, C3H8 and theoretical interpretation of the Li-C2H4 system

    International Nuclear Information System (INIS)

    Semmineh, Natenael; Bililign, Solomon; Hagebaum-Reignier, Denis; Jeung, Gwang-Hi

    2009-01-01

    Collisions of excited Li(4p) states with C 2 H 4 , C 2 H 6 and C 3 H 8 are studied experimentally using far-wing scattering state spectroscopy techniques. High-level ab initio quantum mechanical studies of the Li-C 2 H 4 system are conducted to explain the results of the experiment for this system. The recent and present works indicate that knowledge of the internal structure of the perturber (C 2 H 4 , C 2 H 6 and C 3 H 8 ) is essential to fully understand the interaction between the metal and the hydrocarbon molecules. The ab initio calculation shows that the Li(4d) (with little probability under the experimental conditions) and the Li(4p) can be formed directly through the laser pumping. It also shows that the Li(4s) and Li(3d) states can be formed through an electronic diabatic coupling involving a radiationless process. However, the Li(3p), Li(3s) and Li(2p) states can only be formed through a secondary diabatic coupling which is a much less probable process than the primary one. The calculation limited to two C 2v sections of the potential energy surfaces (PESs) shows peculiar multi-state crossings that we have never seen in other lithium complexes we studied

  9. Sequence-based classification using discriminatory motif feature selection.

    Directory of Open Access Journals (Sweden)

    Hao Xiong

    Full Text Available Most existing methods for sequence-based classification use exhaustive feature generation, employing, for example, all k-mer patterns. The motivation behind such (enumerative approaches is to minimize the potential for overlooking important features. However, there are shortcomings to this strategy. First, practical constraints limit the scope of exhaustive feature generation to patterns of length ≤ k, such that potentially important, longer (> k predictors are not considered. Second, features so generated exhibit strong dependencies, which can complicate understanding of derived classification rules. Third, and most importantly, numerous irrelevant features are created. These concerns can compromise prediction and interpretation. While remedies have been proposed, they tend to be problem-specific and not broadly applicable. Here, we develop a generally applicable methodology, and an attendant software pipeline, that is predicated on discriminatory motif finding. In addition to the traditional training and validation partitions, our framework entails a third level of data partitioning, a discovery partition. A discriminatory motif finder is used on sequences and associated class labels in the discovery partition to yield a (small set of features. These features are then used as inputs to a classifier in the training partition. Finally, performance assessment occurs on the validation partition. Important attributes of our approach are its modularity (any discriminatory motif finder and any classifier can be deployed and its universality (all data, including sequences that are unaligned and/or of unequal length, can be accommodated. We illustrate our approach on two nucleosome occupancy datasets and a protein solubility dataset, previously analyzed using enumerative feature generation. Our method achieves excellent performance results, with and without optimization of classifier tuning parameters. A Python pipeline implementing the approach is

  10. 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

  11. Indonesian Traditional Toys and the Development of Batik Motifs

    Directory of Open Access Journals (Sweden)

    Bagus Indrayana

    2016-06-01

    Full Text Available There is a wide array of traditional toys in Indonesia. In the past, traditional toys played an important role for skill and creativity development of children. Today, the position of traditional toys in the society is displaced by toys from large-scale manufacturers. Given the critical role of traditional toys for children’s motoric and social development, there is a need to develop media that can be used to promote these traditional products and strengthen their position in the public. We propose to use Batik as a way to effectively disseminate and promote traditional toys to the general public. Apart from this, using traditional toys to create new Batik motifs can have an economic value for the producers of Batik, promote Indonesian products and enrich the Indonesian Batik. This study aims to explore the variety of traditional toys, mainly from Klaten and Magelang, in the Central Java province of Indonesia, and use them as the basis for the development of Batik motif creation. This study used Trilogi Keseimbangan (or Harmony Trilogy aesthetic theory analytical approach that explains the creation of craft consists of the following phases: exploration, design, and materialization. The creation method in this study adopts Tiga Tahap Enam Langkah (Three Phases, Six Steps method offered in the theory. The finding in the field found that the traditional toys material used in Klaten and Magelang, mostly made from waste wood, plywood, and zinc. The manufacturing process is done manually by two or three craftsmen using a simple technology. The traditional toys are designed by the artisans mostly, although there may be designs from the clients. In addition, we also found that the traditional toys have never been used as a Batik motif. The traditional toys Batik motif presented in this work is researcher’s design. For the purposes of this study, we first research the variety of traditional toys available in the market today in Indonesia. We look

  12. Dimensionality of social networks using motifs and eigenvalues.

    Directory of Open Access Journals (Sweden)

    Anthony Bonato

    Full Text Available We consider the dimensionality of social networks, and develop experiments aimed at predicting that dimension. We find that a social network model with nodes and links sampled from an m-dimensional metric space with power-law distributed influence regions best fits samples from real-world networks when m scales logarithmically with the number of nodes of the network. This supports a logarithmic dimension hypothesis, and we provide evidence with two different social networks, Facebook and LinkedIn. Further, we employ two different methods for confirming the hypothesis: the first uses the distribution of motif counts, and the second exploits the eigenvalue distribution.

  13. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

    Science.gov (United States)

    Castro-Mondragon, Jaime Abraham; Jaeger, Sébastien; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

    2017-07-27

    Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures

    Directory of Open Access Journals (Sweden)

    Hamed Bostan

    2012-01-01

    Full Text Available Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.

  15. 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.

  16. 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.

  17. A cluster of Enterovirus 71 subgenogroup C2 in a nursery school, Italy, 2014.

    Science.gov (United States)

    Medici, Maria Cristina; Tummolo, Fabio; Arcangeletti, Maria Cristina; De Conto, Flora; Chezzi, Carlo; Dodi, Icilio; Calderaro, Adriana

    2016-10-01

    During October 2014, enterovirus (EV) RNA was detected in the stools of four children attending the same class in a nursery school, and hospitalized with mild febrile and vomiting disease in Parma, Italy. Upon sequencing, the viruses were characterized as EV71 subgenogroup C2. Phylogenetic analysis of the four EV71 C2 viruses allowed the distinction of a diverging lineage within subgenogroup C2, containing the Italian EV71 C2 strains and viruses detected in France in 2013. The identification of an outbreak of EV71 C2 in Italy extended information on the geographic diffusion and clinical relevance of these viruses in Europe.

  18. The C2 domain of PKCalpha is a Ca2+ -dependent PtdIns(4,5)P2 sensing domain: a new insight into an old pathway.

    Science.gov (United States)

    Sánchez-Bautista, Sonia; Marín-Vicente, Consuelo; Gómez-Fernández, Juan C; Corbalán-García, Senena

    2006-10-06

    The C2 domain is a targeting domain that responds to intracellular Ca2+ signals in classical protein kinases (PKCs) and mediates the translocation of its host protein to membranes. Recent studies have revealed a new motif in the C2 domain, named the lysine-rich cluster, that interacts with acidic phospholipids. The purpose of this work was to characterize the molecular mechanism by which PtdIns(4,5)P2 specifically interacts with this motif. Using a combination of isothermal titration calorimetry, fluorescence resonance energy transfer and time-lapse confocal microscopy, we show here that Ca2+ specifically binds to the Ca2+ -binding region, facilitating PtdIns(4,5)P2 access to the lysine-rich cluster. The magnitude of PtdIns(4,5)P2 binding is greater than in the case of other polyphosphate phosphatidylinositols. Very importantly, the residues involved in PtdIns(4,5)P2 binding are essential for the plasma membrane localization of PKCalpha when RBL-2H3 cells are stimulated through their IgE receptors. Additionally, CFP-PH and CFP-C1 domains were used as bioprobes to demonstrate the co-existence of PtdIns(4,5)P2 and diacylglycerol in the plasma membrane, and it was shown that although a fraction of PtdIns(4,5)P2 is hydrolyzed to generate diacylglycerol and IP3, an important amount still remains in the membrane where it is available to activate PKCalpha. These findings entail revision of the currently accepted model of PKCalpha recruitment to the membrane and its activation.

  19. Romanian traditional motif - element of modernity in clothing

    Science.gov (United States)

    Doble, L.; Stan, O.; Suteu, M. D.; Albu, A.; Bohm, G.; Tsatsarou-Michalaki, A.; Gialinou, E.

    2017-10-01

    In this paper are presented the phases for improving from an aesthetic point of view a clothing item, the jacket respectively, with a straight cut for women using software design patterns, computerised graphics and textile different modern technologies including: industrial embroidery, digital printing, sublimation. In the first phase a documentation was prepared in the Ethnographic Museum of Transylvania from Cluj Napoca where more traditional motifs were selected specific to Transylvania etnographic region and were reintepreted and stylized whilst preserving the symbolism and color range specified to the area. For the styling phase was used CorelDraw vector graphics program that allows changing the shape, size and color of the drawings without affecting the identity of the pattern. In the patterns design phase Gemini CAD software was used and for the modeling and model development Optitex software was used. The part for garnishing the model was performed using Embrodery machine software reproducing the stylized motif identically. In order to obtain a significantly improved aesthetic look and an added artistic value the pattern chosen for the jacket was done using a combination of modern textile technologies. This has allowed the realization of a particular texture on the surface of the designed product, demonstrating that traditional patterns can be reintepreted in modern clothing

  20. THE MOTIF OF THE SECOND COMING IN RUSSIAN FANTASTIC FICTION

    Directory of Open Access Journals (Sweden)

    Tatyana I. Khoruzhenko

    2017-06-01

    Full Text Available The motif of the Second Coming of Christ takes a special place in Russian fantastic fiction at the turn of the millennium. In the recent decades allusions to the Gospel topic appears in increasing frequency in the genre of fantasy. The aim of the given article was to analyze the peculiarities of the depiction of the subject of Advent in Russian fantastic fiction. As the basis for the research the novels of Y. Voznesenskaya, N. Perumov, V. Khlumov, S. Lukyanenko and T. Ustimenko are of particular interest. The Advent motif appears in the story line of each of the novels in question. Though, the attitude of the authors to the image of the Savior and his second coming to the world fluctuates: from a respectful expectation (Y. Voznesenskaya, T. Ustimenko, S. Lukyanenko to the depiction of the Savior as a monster (N. Perumov. The possibility of an ambivalent interpretation of the Savior is the eloquent evidence of desacralization of this image. The profaning of the sacred is one of the tendencies of the modern popular culture. The genre of fantastic fiction, as a product of mass culture, has caught this trend quite precisely.

  1. Regulation of amyloid precursor protein processing by its KFERQ motif.

    Science.gov (United States)

    Park, Ji-Seon; Kim, Dong-Hou; Yoon, Seung-Yong

    2016-06-01

    Understanding of trafficking, processing, and degradation mechanisms of amyloid precursor protein (APP) is important because APP can be processed to produce β-amyloid (Aβ), a key pathogenic molecule in Alzheimer's disease (AD). Here, we found that APP contains KFERQ motif at its C-terminus, a consensus sequence for chaperone-mediated autophagy (CMA) or microautophagy which are another types of autophagy for degradation of pathogenic molecules in neurodegenerative diseases. Deletion of KFERQ in APP increased C-terminal fragments (CTFs) and secreted N-terminal fragments of APP and kept it away from lysosomes. KFERQ deletion did not abolish the interaction of APP or its cleaved products with heat shock cognate protein 70 (Hsc70), a protein necessary for CMA or microautophagy. These findings suggest that KFERQ motif is important for normal processing and degradation of APP to preclude the accumulation of APP-CTFs although it may not be important for CMA or microautophagy. [BMB Reports 2016; 49(6): 337-342].

  2. Network motif frequency vectors reveal evolving metabolic network organisation.

    Science.gov (United States)

    Pearcy, Nicole; Crofts, Jonathan J; Chuzhanova, Nadia

    2015-01-01

    At the systems level many organisms of interest may be described by their patterns of interaction, and as such, are perhaps best characterised via network or graph models. Metabolic networks, in particular, are fundamental to the proper functioning of many important biological processes, and thus, have been widely studied over the past decade or so. Such investigations have revealed a number of shared topological features, such as a short characteristic path-length, large clustering coefficient and hierarchical modular structure. However, the extent to which evolutionary and functional properties of metabolism manifest via this underlying network architecture remains unclear. In this paper, we employ a novel graph embedding technique, based upon low-order network motifs, to compare metabolic network structure for 383 bacterial species categorised according to a number of biological features. In particular, we introduce a new global significance score which enables us to quantify important evolutionary relationships that exist between organisms and their physical environments. Using this new approach, we demonstrate a number of significant correlations between environmental factors, such as growth conditions and habitat variability, and network motif structure, providing evidence that organism adaptability leads to increased complexities in the resultant metabolic networks.

  3. Bulk Kosterlitz-Thouless Type Molecular Superconductor β″-(BEDT-TTF)2[(H2O)(NH4)2Cr(C2O4)3]·18-crown-6.

    Science.gov (United States)

    Martin, Lee; Lopez, Jordan R; Akutsu, Hiroki; Nakazawa, Yasuhiro; Imajo, Shusaku

    2017-11-20

    A new molecular superconductor, β″-(BEDT-TTF) 2 [(H 2 O)(NH 4 ) 2 Cr(C 2 O 4 ) 3 ]·18-crown-6, has been synthesized from the organic donor molecule BEDT-TTF with the anion Cr(C 2 O 4 ) 3 3- . The crystal structure consists of conducting organic layers of BEDT-TTF molecules which adopt the β″ packing motif (layer A), layers of NH 4 + and Λ-Cr(C 2 O 4 ) 3 3- (layer B), layers of (H 2 O)(NH 4 )18-crown-6 (layer C), and layers of NH 4 + and Δ-Cr(C 2 O 4 ) 3 3- (layer D) which produce a superstructure with a repeating pattern of ABCDABCDA. As a result of this packing arrangement, this is the 2D superconductor with the widest gap between conducting layers where only a single donor packing motif is present (β″). Superconducting critical temperatures at ambient pressure observed by electrical transport and magnetic measurements are 4.0-4.9 and 2.5 K, respectively. The strong 2D nature of this system, the broad transition to T zero at 1.8K, and the transition of α of V ∝ I α from 1 to 3 on I-V curves strongly suggest that the superconducting transition is very close to a Kosterlitz-Thouless transition. The magnetic field dependence of the superconducting critical temperature parallel to the conducting plane gives an upper critical field μ 0 H c2∥ > 8 T, which is over the calculated Pauli-Clogston limit for this material.

  4. Expression, purification, crystallization and preliminary X-ray analysis of conjugated polyketone reductase C2 (CPR-C2) from Candida parapsilosis IFO 0708.

    Science.gov (United States)

    Yamamura, Akihiro; Maruoka, Shintaro; Ohtsuka, Jun; Miyakawa, Takuya; Nagata, Koji; Kataoka, Michihiko; Kitamura, Nahoko; Shimizu, Sakayu; Tanokura, Masaru

    2009-11-01

    Conjugated polyketone reductase C2 (CPR-C2) from Candida parapsilosis IFO 0708 is a member of the NADPH-dependent aldo-keto reductase (AKR) superfamily and catalyzes the stereospecific reduction of ketopantoyl lactone to d-pantoyl lactone. A diffraction-quality crystal of recombinant CPR-C2 was obtained by the sitting-drop vapour-diffusion method using PEG 3350 as the precipitant. The crystal diffracted X-rays to 1.7 angstrom resolution on beamline NW12A of the Photon Factory-Advanced Ring (Tsukuba, Japan). The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 55.02, b = 68.30, c = 68.93 angstrom. The Matthews coefficient (V(M) = 1.76 angstrom(3) Da(-1)) indicated that the crystal contained one CPR-C2 molecule per asymmetric unit.

  5. Proliferation and skeletal myotube formation capability of C2C12 and H9c2 cells on isotropic and anisotropic electrospun nanofibrous PHB scaffolds

    International Nuclear Information System (INIS)

    Ricotti, Leonardo; Genchi, Giada G; Menciassi, Arianna; Polini, Alessandro; Iandolo, Donata; Pisignano, Dario; Ciofani, Gianni; Mattoli, Virgilio; Vazão, Helena; Ferreira, Lino

    2012-01-01

    This study aims at investigating the behavior in terms of the proliferation and skeletal muscle differentiation capability of two myoblastic cell lines, C2C12 and H9c2, on both isotropic and anisotropic electrospun nanofibrous poly(hydroxybutyrate) (PHB) scaffolds, as well as on PHB films and polystyrene controls. After a careful characterization of the matrices in terms of surface morphology, surface roughness and mechanical properties, the proliferation rate and the capability of the two cell lines to form skeletal myotubes were evaluated. Genetic analyses were also performed in order to assess the differentiation level of the cells on the different substrates. We demonstrated that the aligned nanofibrous mesh decreases the proliferation activity and provides a higher differentiative stimulus. We also clarified how the nanofibrous substrate influences myotube formation, and quantified a series of myotube-related parameters for both C2C12 and H9c2 cells. (paper)

  6. Anion induced conformational preference of Cα NN motif residues in functional proteins.

    Science.gov (United States)

    Patra, Piya; Ghosh, Mahua; Banerjee, Raja; Chakrabarti, Jaydeb

    2017-12-01

    Among different ligand binding motifs, anion binding C α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion. © 2017 Wiley Periodicals, Inc.

  7. The central subgroup of the nonabelian tensor square of Bieberbach group of dimension three with point group C2 × C2

    Science.gov (United States)

    Ladi, Nor Fadzilah Abdul; Masri, Rohaidah; Idrus, Nor'ashiqin Mohd; Ting, Tan Yee

    2017-05-01

    Bieberbach groups are crystallographic groups. By computing the central subgroup of the nonabelian tensor square of a group, the properties of the group can be determined. In this paper, the central subgroup of the nonabelian tensor square of one Bieberbach group of dimension three with point group C2 × C2 is computed. In order to compute the ∇ (S3 (3)), the derived subgroup and the abelianization of the group are first constructed.

  8. χ_{c1} and χ_{c2} Resonance Parameters with the Decays χ_{c1,c2}→J/ψμ^{+}μ^{-}.

    Science.gov (United States)

    Aaij, R; Adeva, B; Adinolfi, M; Ajaltouni, Z; Akar, S; Albrecht, J; Alessio, F; Alexander, M; Alfonso Albero, A; Ali, S; Alkhazov, G; Alvarez Cartelle, P; Alves, A A; Amato, S; Amerio, S; Amhis, Y; An, L; Anderlini, L; Andreassi, G; Andreotti, M; Andrews, J E; Appleby, R B; Archilli, F; d'Argent, P; Arnau Romeu, J; Artamonov, A; Artuso, M; Aslanides, E; Atzeni, M; Auriemma, G; Baalouch, M; Babuschkin, I; Bachmann, S; Back, J J; Badalov, A; Baesso, C; Baker, S; Balagura, V; Baldini, W; Baranov, A; Barlow, R J; Barschel, C; Barsuk, S; Barter, W; Baryshnikov, F; Batozskaya, V; Battista, V; Bay, A; Beaucourt, L; Beddow, J; Bedeschi, F; Bediaga, I; Beiter, A; Bel, L J; Beliy, N; Bellee, V; Belloli, N; Belous, K; Belyaev, I; Ben-Haim, E; Bencivenni, G; Benson, S; Beranek, S; Berezhnoy, A; Bernet, R; Berninghoff, D; Bertholet, E; Bertolin, A; Betancourt, C; Betti, F; Bettler, M-O; van Beuzekom, M; Bezshyiko, Ia; Bifani, S; Billoir, P; Birnkraut, A; Bizzeti, A; Bjørn, M; Blake, T; Blanc, F; Blusk, S; Bocci, V; Boettcher, T; Bondar, A; Bondar, N; Bordyuzhin, I; Borghi, S; Borisyak, M; Borsato, M; Bossu, F; Boubdir, M; Bowcock, T J V; Bowen, E; Bozzi, C; Braun, S; Britton, T; Brodzicka, J; Brundu, D; Buchanan, E; Burr, C; Bursche, A; Buytaert, J; Byczynski, W; Cadeddu, S; Cai, H; Calabrese, R; Calladine, R; Calvi, M; Calvo Gomez, M; Camboni, A; Campana, P; Campora Perez, D H; Capriotti, L; Carbone, A; Carboni, G; Cardinale, R; Cardini, A; Carniti, P; Carson, L; Carvalho Akiba, K; Casse, G; Cassina, L; Cattaneo, M; Cavallero, G; Cenci, R; Chamont, D; Chapman, M G; Charles, M; Charpentier, Ph; Chatzikonstantinidis, G; Chefdeville, M; Chen, S; Cheung, S F; Chitic, S-G; Chobanova, V; Chrzaszcz, M; Chubykin, A; Ciambrone, P; Cid Vidal, X; Ciezarek, G; Clarke, P E L; Clemencic, M; Cliff, H V; Closier, J; Cogan, J; Cogneras, E; Cogoni, V; Cojocariu, L; Collins, P; Colombo, T; Comerma-Montells, A; Contu, A; Cook, A; Coombs, G; Coquereau, S; Corti, G; Corvo, M; Costa Sobral, C M; Couturier, B; Cowan, G A; Craik, D C; Crocombe, A; Cruz Torres, M; Currie, R; D'Ambrosio, C; Da Cunha Marinho, F; Dall'Occo, E; Dalseno, J; Davis, A; De Aguiar Francisco, O; De Capua, S; De Cian, M; De Miranda, J M; De Paula, L; De Serio, M; De Simone, P; Dean, C T; Decamp, D; Del Buono, L; Dembinski, H-P; Demmer, M; Dendek, A; Derkach, D; Deschamps, O; Dettori, F; Dey, B; Di Canto, A; Di Nezza, P; Dijkstra, H; Dordei, F; Dorigo, M; Dosil Suárez, A; Douglas, L; Dovbnya, A; Dreimanis, K; Dufour, L; Dujany, G; Durante, P; Dzhelyadin, R; Dziewiecki, M; Dziurda, A; Dzyuba, A; Easo, S; Ebert, M; Egede, U; Egorychev, V; Eidelman, S; Eisenhardt, S; Eitschberger, U; Ekelhof, R; Eklund, L; Ely, S; Esen, S; Evans, H M; Evans, T; Falabella, A; Farley, N; Farry, S; Fazzini, D; Federici, L; Ferguson, D; Fernandez, G; Fernandez Declara, P; Fernandez Prieto, A; Ferrari, F; Ferreira Rodrigues, F; Ferro-Luzzi, M; Filippov, S; Fini, R A; Fiorini, M; Firlej, M; Fitzpatrick, C; Fiutowski, T; Fleuret, F; Fohl, K; Fontana, M; Fontanelli, F; Forshaw, D C; Forty, R; Franco Lima, V; Frank, M; Frei, C; Fu, J; Funk, W; Furfaro, E; Färber, C; Gabriel, E; Gallas Torreira, A; Galli, D; Gallorini, S; Gambetta, S; Gandelman, M; Gandini, P; Gao, Y; Garcia Martin, L M; García Pardiñas, J; Garra Tico, J; Garrido, L; Garsed, P J; Gascon, D; Gaspar, C; Gavardi, L; Gazzoni, G; Gerick, D; Gersabeck, E; Gersabeck, M; Gershon, T; Ghez, Ph; Gianì, S; Gibson, V; Girard, O G; Giubega, L; Gizdov, K; Gligorov, V V; Golubkov, D; Golutvin, A; Gomes, A; Gorelov, I V; Gotti, C; Govorkova, E; Grabowski, J P; Graciani Diaz, R; Granado Cardoso, L A; Graugés, E; Graverini, E; Graziani, G; Grecu, A; Greim, R; Griffith, P; Grillo, L; Gruber, L; Gruberg Cazon, B R; Grünberg, O; Gushchin, E; Guz, Yu; Gys, T; Göbel, C; Hadavizadeh, T; Hadjivasiliou, C; Haefeli, G; Haen, C; Haines, S C; Hamilton, B; Han, X; Hancock, T H; Hansmann-Menzemer, S; Harnew, N; Harnew, S T; Hasse, C; Hatch, M; He, J; Hecker, M; Heinicke, K; Heister, A; Hennessy, K; Henrard, P; Henry, L; van Herwijnen, E; Heß, M; Hicheur, A; Hill, D; Hombach, C; Hopchev, P H; Hu, W; Huard, Z C; Hulsbergen, W; Humair, T; Hushchyn, M; Hutchcroft, D; Ibis, P; Idzik, M; Ilten, P; Jacobsson, R; Jalocha, J; Jans, E; Jawahery, A; Jiang, F; John, M; Johnson, D; Jones, C R; Joram, C; Jost, B; Jurik, N; Kandybei, S; Karacson, M; Kariuki, J M; Karodia, S; Kazeev, N; Kecke, M; Keizer, F; Kelsey, M; Kenzie, M; Ketel, T; Khairullin, E; Khanji, B; Khurewathanakul, C; Kirn, T; Klaver, S; Klimaszewski, K; Klimkovich, T; Koliiev, S; Kolpin, M; Kopecna, R; Koppenburg, P; Kosmyntseva, A; Kotriakhova, S; Kozeiha, M; Kravchuk, L; Kreps, M; Kress, F; Krokovny, P; Kruse, F; Krzemien, W; Kucewicz, W; Kucharczyk, M; Kudryavtsev, V; Kuonen, A K; Kvaratskheliya, T; Lacarrere, D; Lafferty, G; Lai, A; Lanfranchi, G; Langenbruch, C; Latham, T; Lazzeroni, C; Le Gac, R; Leflat, A; Lefrançois, J; Lefèvre, R; Lemaitre, F; Lemos Cid, E; Leroy, O; Lesiak, T; Leverington, B; Li, P-R; Li, T; Li, Y; Li, Z; Likhomanenko, T; Lindner, R; Lionetto, F; Lisovskyi, V; Liu, X; Loh, D; Loi, A; Longstaff, I; Lopes, J H; Lucchesi, D; Luchinsky, A; Lucio Martinez, M; Luo, H; Lupato, A; Luppi, E; Lupton, O; Lusiani, A; Lyu, X; Machefert, F; Maciuc, F; Macko, V; Mackowiak, P; Maddrell-Mander, S; Maev, O; Maguire, K; Maisuzenko, D; Majewski, M W; Malde, S; Malecki, B; Malinin, A; Maltsev, T; Manca, G; Mancinelli, G; Marangotto, D; Maratas, J; Marchand, J F; Marconi, U; Marin Benito, C; Marinangeli, M; Marino, P; Marks, J; Martellotti, G; Martin, M; Martinelli, M; Martinez Santos, D; Martinez Vidal, F; Massacrier, L M; Massafferri, A; Matev, R; Mathad, A; Mathe, Z; Matteuzzi, C; Mauri, A; Maurice, E; Maurin, B; Mazurov, A; McCann, M; McNab, A; McNulty, R; Mead, J V; Meadows, B; Meaux, C; Meier, F; Meinert, N; Melnychuk, D; Merk, M; Merli, A; Michielin, E; Milanes, D A; Millard, E; Minard, M-N; Minzoni, L; Mitzel, D S; Mogini, A; Molina Rodriguez, J; Mombächer, T; Monroy, I A; Monteil, S; Morandin, M; Morello, M J; Morgunova, O; Moron, J; Morris, A B; Mountain, R; Muheim, F; Mulder, M; Müller, D; Müller, J; Müller, K; Müller, V; Naik, P; Nakada, T; Nandakumar, R; Nandi, A; Nasteva, I; Needham, M; Neri, N; Neubert, S; Neufeld, N; Neuner, M; Nguyen, T D; Nguyen-Mau, C; Nieswand, S; Niet, R; Nikitin, N; Nikodem, T; Nogay, A; O'Hanlon, D P; Oblakowska-Mucha, A; Obraztsov, V; Ogilvy, S; Oldeman, R; Onderwater, C J G; Ossowska, A; Otalora Goicochea, J M; Owen, P; Oyanguren, A; Pais, P R; Palano, A; Palutan, M; Papanestis, A; Pappagallo, M; Pappalardo, L L; Parker, W; Parkes, C; Passaleva, G; Pastore, A; Patel, M; Patrignani, C; Pearce, A; Pellegrino, A; Penso, G; Pepe Altarelli, M; Perazzini, S; Perret, P; Pescatore, L; Petridis, K; Petrolini, A; Petrov, A; Petruzzo, M; Picatoste Olloqui, E; Pietrzyk, B; Pikies, M; Pinci, D; Pisani, F; Pistone, A; Piucci, A; Placinta, V; Playfer, S; Plo Casasus, M; Polci, F; Poli Lener, M; Poluektov, A; Polyakov, I; Polycarpo, E; Pomery, G J; Ponce, S; Popov, A; Popov, D; Poslavskii, S; Potterat, C; Price, E; Prisciandaro, J; Prouve, C; Pugatch, V; Puig Navarro, A; Pullen, H; Punzi, G; Qian, W; Quagliani, R; Quintana, B; Rachwal, B; Rademacker, J H; Rama, M; Ramos Pernas, M; Rangel, M S; Raniuk, I; Ratnikov, F; Raven, G; Ravonel Salzgeber, M; Reboud, M; Redi, F; Reichert, S; Dos Reis, A C; Remon Alepuz, C; Renaudin, V; Ricciardi, S; Richards, S; Rihl, M; Rinnert, K; Rives Molina, V; Robbe, P; Robert, A; Rodrigues, A B; Rodrigues, E; Rodriguez Lopez, J A; Rogozhnikov, A; Roiser, S; Rollings, A; Romanovskiy, V; Romero Vidal, A; Ronayne, J W; Rotondo, M; Rudolph, M S; Ruf, T; Ruiz Valls, P; Ruiz Vidal, J; Saborido Silva, J J; Sadykhov, E; Sagidova, N; Saitta, B; Salustino Guimaraes, V; Sanchez Mayordomo, C; Sanmartin Sedes, B; Santacesaria, R; Santamarina Rios, C; Santimaria, M; Santovetti, E; Sarpis, G; Sarti, A; Satriano, C; Satta, A; Saunders, D M; Savrina, D; Schael, S; Schellenberg, M; Schiller, M; Schindler, H; Schmelling, M; Schmelzer, T; Schmidt, B; Schneider, O; Schopper, A; Schreiner, H F; Schubiger, M; Schune, M-H; Schwemmer, R; Sciascia, B; Sciubba, A; Semennikov, A; Sepulveda, E S; Sergi, A; Serra, N; Serrano, J; Sestini, L; Seyfert, P; Shapkin, M; Shapoval, I; Shcheglov, Y; Shears, T; Shekhtman, L; Shevchenko, V; Siddi, B G; Silva Coutinho, R; Silva de Oliveira, L; Simi, G; Simone, S; Sirendi, M; Skidmore, N; Skwarnicki, T; Smith, E; Smith, I T; Smith, J; Smith, M; Soares Lavra, L; Sokoloff, M D; Soler, F J P; Souza De Paula, B; Spaan, B; Spradlin, P; Sridharan, S; Stagni, F; Stahl, M; Stahl, S; Stefko, P; Stefkova, S; Steinkamp, O; Stemmle, S; Stenyakin, O; Stepanova, M; Stevens, H; Stone, S; Storaci, B; Stracka, S; Stramaglia, M E; Straticiuc, M; Straumann, U; Sun, J; Sun, L; Sutcliffe, W; Swientek, K; Syropoulos, V; Szumlak, T; Szymanski, M; T'Jampens, S; Tayduganov, A; Tekampe, T; Tellarini, G; Teubert, F; Thomas, E; van Tilburg, J; Tilley, M J; Tisserand, V; Tobin, M; Tolk, S; Tomassetti, L; Tonelli, D; Toriello, F; Tourinho Jadallah Aoude, R; Tournefier, E; Traill, M; Tran, M T; Tresch, M; Trisovic, A; Tsaregorodtsev, A; Tsopelas, P; Tully, A; Tuning, N; Ukleja, A; Usachov, A; Ustyuzhanin, A; Uwer, U; Vacca, C; Vagner, A; Vagnoni, V; Valassi, A; Valat, S; Valenti, G; Vazquez Gomez, R; Vazquez Regueiro, P; Vecchi, S; van Veghel, M; Velthuis, J J; Veltri, M; Veneziano, G; Venkateswaran, A; Verlage, T A; Vernet, M; Vesterinen, M; Viana Barbosa, J V; Viaud, B; Vieira, D; Vieites Diaz, M; Viemann, H; Vilasis-Cardona, X; Vitti, M; Volkov, V; Vollhardt, A; Voneki, B; Vorobyev, A; Vorobyev, V; Voß, C; de Vries, J A; Vázquez Sierra, C; Waldi, R; Wallace, C; Wallace, R; Walsh, J; Wang, J; Ward, D R; Wark, H M; Watson, N K; Websdale, D; Weiden, A; Weisser, C; Whitehead, M; Wicht, J; Wilkinson, G; Wilkinson, M; Williams, M; Williams, M P; Williams, M; Williams, T; Wilson, F F; Wimberley, J; Winn, M; Wishahi, J; Wislicki, W; Witek, M; Wormser, G; Wotton, S A; Wraight, K; Wyllie, K; Xie, Y; Xu, M; Xu, Z; Yang, Z; Yang, Z; Yao, Y; Yin, H; Yu, J; Yuan, X; Yushchenko, O; Zarebski, K A; Zavertyaev, M; Zhang, L; Zhang, Y; Zhelezov, A; Zheng, Y; Zhu, X; Zhukov, V; Zonneveld, J B; Zucchelli, S

    2017-12-01

    The decays χ_{c1}→J/ψμ^{+}μ^{-} and χ_{c2}→J/ψμ^{+}μ^{-} are observed and used to study the resonance parameters of the χ_{c1} and χ_{c2} mesons. The masses of these states are measured to be m(χ_{c1})=3510.71±0.04(stat)±0.09(syst)  MeV and m(χ_{c2})=3556.10±0.06(stat)±0.11(syst)  MeV, where the knowledge of the momentum scale for charged particles dominates the systematic uncertainty. The momentum-scale uncertainties largely cancel in the mass difference m(χ_{c2})-m(χ_{c1})=45.39±0.07(stat)±0.03(syst)  MeV. The natural width of the χ_{c2} meson is measured to be Γ(χ_{c2})=2.10±0.20(stat)±0.02(syst)  MeV. These results are in good agreement with and have comparable precision to the current world averages.

  9. I-Ad-binding peptides derived from unrelated protein antigens share a common structural motif

    DEFF Research Database (Denmark)

    Sette, A; Buus, S; Colon, S

    1988-01-01

    on the I-Ad binding of the immunogenic peptide OVA 323-339. The results obtained demonstrated the very permissive nature of Ag-Ia interaction. We also showed that unrelated peptides that are good I-Ad binders share a common structural motif and speculated that recognition of such motifs could represent...... that I-Ad molecules recognize a large library of Ag by virtue of common structural motifs present in peptides derived from phylogenetically unrelated proteins....

  10. Lucky Motifs in Chinese Folk Art: Interpreting Paper-cut from Chinese Shaanxi

    OpenAIRE

    Xuxiao WANG

    2013-01-01

    Paper-cut is not simply a form of traditional Chinese folk art. Lucky motifs developed in paper-cut certainly acquired profound cultural connotations. As paper-cut is a time-honoured skill across the nation, interpreting those motifs requires cultural receptiveness and anthropological sensitivity. The author of this article analyzes examples of paper-cut from Northern Shaanxi, China, to identify the cohesive motifs and explore the auspiciousness of the specific concepts of Fu, Lu, Shou, Xi. T...

  11. Low-dimensional morphospace of topological motifs in human fMRI brain networks

    Directory of Open Access Journals (Sweden)

    Sarah E. Morgan

    2018-06-01

    Full Text Available We present a low-dimensional morphospace of fMRI brain networks, where axes are defined in a data-driven manner based on the network motifs. The morphospace allows us to identify the key variations in healthy fMRI networks in terms of their underlying motifs, and we observe that two principal components (PCs can account for 97% of the motif variability. The first PC of the motif distribution is correlated with efficiency and inversely correlated with transitivity. Hence this axis approximately conforms to the well-known economical small-world trade-off between integration and segregation in brain networks. Finally, we show that the economical clustering generative model proposed by Vértes et al. (2012 can approximately reproduce the motif morphospace of the real fMRI brain networks, in contrast to other generative models. Overall, the motif morphospace provides a powerful way to visualize the relationships between network properties and to investigate generative or constraining factors in the formation of complex human brain functional networks. Motifs have been described as the building blocks of complex networks. Meanwhile, a morphospace allows networks to be placed in a common space and can reveal the relationships between different network properties and elucidate the driving forces behind network topology. We combine the concepts of motifs and morphospaces to create the first motif morphospace of fMRI brain networks. Crucially, the morphospace axes are defined by the motifs, in a data-driven manner. We observe strong correlations between the networks’ positions in morphospace and their global topological properties, suggesting that motif morphospaces are a powerful way to capture the topology of networks in a low-dimensional space and to compare generative models of brain networks. Motif morphospaces could also be used to study other complex networks’ topologies.

  12. An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.

    Science.gov (United States)

    Liu, Bingqiang; Zhang, Hanyuan; Zhou, Chuan; Li, Guojun; Fennell, Anne; Wang, Guanghui; Kang, Yu; Liu, Qi; Ma, Qin

    2016-08-09

    Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif prediction. Here we present an integrative phylogenetic footprinting framework for accurate motif predictions in prokaryotic genomes (MP(3)). The framework includes a new orthologous data preparation procedure, an additional promoter scoring and pruning method and an integration of six existing motif finding algorithms as basic motif search engines. Specifically, we collected orthologous genes from available prokaryotic genomes and built the orthologous regulatory regions based on sequence similarity of promoter regions. This procedure made full use of the large-scale genomic data and taxonomy information and filtered out the promoters with limited contribution to produce a high quality orthologous promoter set. The promoter scoring and pruning is implemented through motif voting by a set of complementary predicting tools that mine as many motif candidates as possible and simultaneously eliminate the effect of random noise. We have applied the framework to Escherichia coli k12 genome and evaluated the prediction performance through comparison with seven existing programs. This evaluation was systematically carried out at the nucleotide and binding site level, and the results showed that MP(3) consistently outperformed other popular motif finding tools. We have integrated MP(3) into our motif identification and analysis server DMINDA, allowing users to efficiently identify and analyze motifs in 2,072 completely sequenced prokaryotic genomes. The performance evaluation indicated that MP(3) is effective for predicting regulatory motifs in prokaryotic genomes. Its application may enhance

  13. 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.

  14. Hybrid DNA i-motif: Aminoethylprolyl-PNA (pC5) enhance the stability of DNA (dC5) i-motif structure.

    Science.gov (United States)

    Gade, Chandrasekhar Reddy; Sharma, Nagendra K

    2017-12-15

    This report describes the synthesis of C-rich sequence, cytosine pentamer, of aep-PNA and its biophysical studies for the formation of hybrid DNA:aep-PNAi-motif structure with DNA cytosine pentamer (dC 5 ) under acidic pH conditions. Herein, the CD/UV/NMR/ESI-Mass studies strongly support the formation of stable hybrid DNA i-motif structure with aep-PNA even near acidic conditions. Hence aep-PNA C-rich sequence cytosine could be considered as potential DNA i-motif stabilizing agents in vivo conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Christian J. Michel

    2017-12-01

    Full Text Available A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C 3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X , using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X , in the complete genome of the yeast Saccharomyces cerevisiae. Several properties of X motifs are identified by basic statistics (at the frequency level, and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R . We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae. We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae, but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions. This property is true for all cardinalities of X motifs (from 4 to 20 and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non- X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together

  16. Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Michel, Christian J; Ngoune, Viviane Nguefack; Poch, Olivier; Ripp, Raymond; Thompson, Julie D

    2017-12-03

    A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading) frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X, using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X, in the complete genome of the yeast Saccharomyces cerevisiae . Several properties of X motifs are identified by basic statistics (at the frequency level), and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R. We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae . We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae , but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions). This property is true for all cardinalities of X motifs (from 4 to 20) and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non-X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together, represent the first

  17. Purification and functional motifs of the recombinant ATPase of orf virus.

    Science.gov (United States)

    Lin, Fong-Yuan; Chan, Kun-Wei; Wang, Chi-Young; Wong, Min-Liang; Hsu, Wei-Li

    2011-10-01

    Our previous study showed that the recombinant ATPase encoded by the A32L gene of orf virus displayed ATP hydrolysis activity as predicted from its amino acids sequence. This viral ATPase contains four known functional motifs (motifs I-IV) and a novel AYDG motif; they are essential for ATP hydrolysis reaction by binding ATP and magnesium ions. The motifs I and II correspond with the Walker A and B motifs of the typical ATPase, respectively. To examine the biochemical roles of these five conserved motifs, recombinant ATPases of five deletion mutants derived from the Taiping strain were expressed and purified. Their ATPase functions were assayed and compared with those of two wild type strains, Taiping and Nantou isolated in Taiwan. Our results showed that deletions at motifs I-III or IV exhibited lower activity than that of the wild type. Interestingly, deletion of AYDG motif decreased the ATPase activity more significantly than those of motifs I-IV deletions. Divalent ions such as magnesium and calcium were essential for ATPase activity. Moreover, our recombinant proteins of orf virus also demonstrated GTPase activity, though weaker than the original ATPase activity. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. Systematic comparison of the response properties of protein and RNA mediated gene regulatory motifs.

    Science.gov (United States)

    Iyengar, Bharat Ravi; Pillai, Beena; Venkatesh, K V; Gadgil, Chetan J

    2017-05-30

    We present a framework enabling the dissection of the effects of motif structure (feedback or feedforward), the nature of the controller (RNA or protein), and the regulation mode (transcriptional, post-transcriptional or translational) on the response to a step change in the input. We have used a common model framework for gene expression where both motif structures have an activating input and repressing regulator, with the same set of parameters, to enable a comparison of the responses. We studied the global sensitivity of the system properties, such as steady-state gain, overshoot, peak time, and peak duration, to parameters. We find that, in all motifs, overshoot correlated negatively whereas peak duration varied concavely with peak time. Differences in the other system properties were found to be mainly dependent on the nature of the controller rather than the motif structure. Protein mediated motifs showed a higher degree of adaptation i.e. a tendency to return to baseline levels; in particular, feedforward motifs exhibited perfect adaptation. RNA mediated motifs had a mild regulatory effect; they also exhibited a lower peaking tendency and mean overshoot. Protein mediated feedforward motifs showed higher overshoot and lower peak time compared to the corresponding feedback motifs.

  19. Structure and action of the binary C2 toxin from Clostridium botulinum.

    Science.gov (United States)

    Schleberger, Christian; Hochmann, Henrike; Barth, Holger; Aktories, Klaus; Schulz, Georg E

    2006-12-08

    C2 toxin from Clostridium botulinum is composed of the enzyme component C2-I, which ADP-ribosylates actin, and the binding and translocation component C2-II, responsible for the interaction with eukaryotic cell receptors and the following endocytosis. Three C2-I crystal structures at resolutions of up to 1.75 A are presented together with a crystal structure of C2-II at an appreciably lower resolution and a model of the prepore formed by fragment C2-IIa. The C2-I structure was determined at pH 3.0 and at pH 6.1. The structural differences are small, indicating that C2-I does not unfold, even at a pH value as low as 3.0. The ADP-ribosyl transferase activity of C2-I was determined for alpha and beta/gamma-actin and related to that of Iota toxin and of mutant S361R of C2-I that introduced the arginine observed in Iota toxin. The substantial activity differences between alpha and beta/gamma-actin cannot be explained by the protein structures currently available. The structure of the transport component C2-II at pH 4.3 was established by molecular replacement using a model of the protective antigen of anthrax toxin at pH 6.0. The C-terminal receptor-binding domain of C2-II could not be located but was present in the crystals. It may be mobile. The relative orientation and positions of the four other domains of C2-II do not differ much from those of the protective antigen, indicating that no large conformational changes occur between pH 4.3 and pH 6.0. A model of the C2-IIa prepore structure was constructed based on the corresponding assembly of the protective antigen. It revealed a surprisingly large number of asparagine residues lining the pore. The interaction between C2-I and C2-IIa and the translocation of C2-I into the target cell are discussed.

  20. Dynamics of C2 formation in laser-produced carbon plasma in helium environment

    International Nuclear Information System (INIS)

    Al-Shboul, K. F.; Harilal, S. S.; Hassanein, A.; Polek, M.

    2011-01-01

    We investigated the role of helium ambient gas on the dynamics of C 2 species formation in laser-produced carbon plasma. The plasma was produced by focusing 1064 nm pulses from an Nd:YAG laser onto a carbon target. The emission from the C 2 species was studied using optical emission spectroscopy, and spectrally resolved and integrated fast imaging. Our results indicate that the formation of C 2 in the plasma plume is strongly affected by the pressure of the He gas. In vacuum, the C 2 emission zone was located near the target and C 2 intensity oscillations were observed both in axial and radial directions with increasing the He pressure. The oscillations in C 2 intensity at higher pressures in the expanding plume could be caused by various formation zones of carbon dimers.

  1. Spectrometric study of the folding process of i-motif-forming DNA sequences upstream of the c-kit transcription initiation site

    International Nuclear Information System (INIS)

    Bucek, Pavel; Gargallo, Raimundo; Kudrev, Andrei

    2010-01-01

    The c-kit oncogene shows a cytosine-rich DNA region upstream of the transcription initiation site which forms an i-motif structure at slightly acidic pH values (Bucek et al. ). In the present study, the pH-induced formation of i-motif - forming sequences 5'-CCC CTC CCT CGC GCC CGC CCG-3' (ckitC1, native), 5'-CCC TTC CCT TGT GCC CGC CCG-3' (ckitC2) and 5'-CCCTT CCC TTTTT CCC T CCC T-3' (ckitC3) was studied by spectroscopic techniques, such as UV molecular absorption and circular dichroism (CD), in tandem with two multivariate data analysis methods, the hard modelling-based matrix method and the soft modelling-based MCR-ALS approach. Use of the hard chemical modelling enabled us to propose the equilibrium model, which describes spectral changes as functions of solution acidity. Additionally, the intrinsic protonation constant, K in , and the cooperativity parameters, ω c , and ω a , were calculated from the fitting procedure of the coupled CD and molecular absorption spectra. In the case of ckitC2 and ckitC3, the hard model correctly reproduced the spectral variations observed experimentally. The results indicated that folding was accompanied by a cooperative process, i.e. the enhancement of protonated structure stability upon protonation. In contrast, unfolding was accompanied by an anticooperative process. Finally, folding of the native sequence, ckitC1, seemed to follow a more complex mechanism.

  2. The synthesis of [2-13C]2-nitropropane at room temperature and at atmospheric pressure

    OpenAIRE

    Jacquemijns M; Zomer G

    1990-01-01

    In this report the synthesis of [2-13C]2-nitropropane at room temperature is described. [2-13C]Acetone was converted into the oxime with hydroxy hydrochloridelamine and sodium carbonate. Treatment with hypobromic acid resulted in 2-13C]2-bromo-2-nitropropane. Hydrogenation with sodium borohydride gave [2-13C]2-nitropropane in 14,3% overall yield.

  3. Kinetics of the reactions H+C2H4->C2H5, H+C2H5->2CH3 and CH3+C2H5->products studies by pulse radiolysis combined with infrared diode laser spectroscopy

    DEFF Research Database (Denmark)

    Sillesen, A.; Ratajczak, E.; Pagsberg, P.

    1993-01-01

    Formation of methyl radicals via the consecutive reactions H+C2H4+M-->C2H5+M (1) and H+C2H5-->CH3+CH3 (2a) was initiated by pulse radiolysis of 10-100 mbar H-2 in the presence of ethylene. The kinetics of CH3 Were studied by monitoring the transient infrared absorption at the Q(3, 3) line of the ...

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

    Energy Technology Data Exchange (ETDEWEB)

    Walen, Holly [Iowa State Univ., Ames, IA (United States)

    2016-01-01

    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. 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.

  5. 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.

  6. 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.

  7. μXRF analysis of decoration motifs on Majolica pottery

    International Nuclear Information System (INIS)

    Padilla Lavarez, Roman; Van Espen, Pierr M.; Janssens, K; Schalm, O.

    2001-01-01

    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

  8. Data of evolutionary structure change: 1BZ0C-2ZLWD [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1BZ0C-2ZLWD 1BZ0 2ZLW C D -VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPT...R VQLSGEEKAAVLALWDKVN--EEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSEL...index> 2ZLW D 2ZLWD

  9. Quantitation of the calcium and membrane binding properties of the C2 domains of dysferlin.

    Science.gov (United States)

    Abdullah, Nazish; Padmanarayana, Murugesh; Marty, Naomi J; Johnson, Colin P

    2014-01-21

    Dysferlin is a large membrane protein involved in calcium-triggered resealing of the sarcolemma after injury. Although it is generally accepted that dysferlin is Ca(2+) sensitive, the Ca(2+) binding properties of dysferlin have not been characterized. In this study, we report an analysis of the Ca(2+) and membrane binding properties of all seven C2 domains of dysferlin as well as a multi-C2 domain construct. Isothermal titration calorimetry measurements indicate that all seven dysferlin C2 domains interact with Ca(2+) with a wide range of binding affinities. The C2A and C2C domains were determined to be the most sensitive, with Kd values in the tens of micromolar, whereas the C2D domain was least sensitive, with a near millimolar Kd value. Mutagenesis of C2A demonstrates the requirement for negatively charged residues in the loop regions for divalent ion binding. Furthermore, dysferlin displayed significantly lower binding affinity for the divalent cations magnesium and strontium. Measurement of a multidomain construct indicates that the solution binding affinity does not change when C2 domains are linked. Finally, sedimentation assays suggest all seven C2 domains bind lipid membranes, and that Ca(2+) enhances but is not required for interaction. This report reveals for the first time, to our knowledge, that all dysferlin domains bind Ca(2+) albeit with varying affinity and stoichiometry. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  10. Measurement of two-photon production of the χc2

    International Nuclear Information System (INIS)

    Dominick, J.; Sanghera, S.; Shelkov, V.; Skwarnicki, T.; Stroynowski, R.; Volobouev, I.; Zadorozhny, P.; Artuso, M.; He, D.; Goldberg, M.; Horwitz, N.; Kennett, R.; Moneti, G.C.; Muheim, F.; Mukhin, Y.; Playfer, S.; Rozen, Y.; Stone, S.; Thulasidas, M.; Vasseur, G.; Zhu, G.; Bartelt, J.; Csorna, S.E.; Egyed, Z.; Jain, V.; Sheldon, P.; Akerib, D.S.; Barish, B.; Chadha, M.; Chan, S.; Cowen, D.F.; Eigen, G.; Miller, J.S.; O'Grady, C.; Urheim, J.; Weinstein, A.J.; Acosta, D.; Athanas, M.; Masek, G.; Paar, H.; Sivertz, M.; Bean, A.; Gronberg, J.; Kutschke, R.; Menary, S.; Morrison, R.J.; Nakanishi, S.; Nelson, H.N.; Nelson, T.K.; Richman, J.D.; Ryd, A.; Tajima, H.; Schmidt, D.; Sperka, D.; Witherell, M.S.; Procario, M.; Yang, S.; Balest, R.; Cho, K.; Daoudi, M.; Ford, W.T.; Johnson, D.R.; Lingel, K.; Lohner, M.; Rankin, P.; Smith, J.G.; Alexander, J.P.; Bebek, C.; Berkelman, K.; Besson, D.; Browder, T.E.; Cassel, D.G.; Cho, H.A.; Coffman, D.M.; Drell, P.S.; Ehrlich, R.; Galik, R.S.; Garcia-Sciveres, M.; Geiser, B.; Gittelman, B.; Gray, S.W.; Hartill, D.L.; Heltsley, B.K.; Jones, C.D.; Jones, S.L.; Kandaswamy, J.; Katayama, N.; Kim, P.C.; Kreinick, D.L.; Ludwig, G.S.; Masui, J.; Mevissen, J.; Mistry, N.B.; Ng, C.R.; Nordberg, E.; Ogg, M.; Patterson, J.R.; Peterson, D.; Riley, D.; Salman, S.; Sapper, M.; Worden, H.; Wuerthwein, F.; Avery, P.; Freyberger, A.; Rodriguez, J.; Stephens, R.; Yelton, J.; Cinabro, D.; Henderson, S.; Kinoshita, K.; Liu, T.; Saulnier, M.; Shen, F.; Wilson, R.; Yamamoto, H.; Ong, B.; Selen, M.; Sadoff, A.J.; Ammar, R.; Ball, S.; Baringer, P.; Coppage, D.; Copty, N.; Davis, R.; Hancock, N.; Kelly, M.; Kwak, N.; Lam, H.; Kubota, Y.; Lattery, M.; Nelson, J.K.; Patton, S.; Perticone, D.; Poling, R.; Savinov, V.; Schrenk, S.; Wang, R.; Alam, M.S.; Kim, I.J.; Nemati, B.; O'Neill, J.J.; Severini, H.; Sun, C.R.; Zoeller, M.M.; Crawford, G.; Daubenmeir, M.; Fulton, R.; Fujino, D.; Gan, K.K.; Honscheid, K.; Kagan, H.; Kass, R.; Lee, J.

    1994-01-01

    The CLEO II detector is used to search for the production of χ c2 states in two-photon interactions. We use the signature χ c2 →γJ/ψ→γl + l - with l=e,μ. Using 1.49 fb -1 of data taken with beam energies near 5.29 GeV, the two-photon width of the χ c2 is determined to be Γ(χ c2 →γγ)=1.08±0.30(stat)±0.26(syst) keV, in agreement with predictions from perturbative QCD

  11. Action Plan to Tackle an Aggressive Competitor in C2C Online Marketplace Business

    OpenAIRE

    Ruuska, Toni

    2015-01-01

    This Thesis focuses on business model innovation in consumer-to-consumer (C2C) online marketplace business. The C2C industry has constantly grown since the early days of the commercial Internet of the 1990’s into a global megatrend, evaluated worth hundreds of billions of Euros. Despite the world wide rise of the C2C industry, there is still relatively little literature available about the business models behind the successful C2C online marketplaces, making it an interesting research topic. ...

  12. Expression, purification, crystallization and preliminary X-ray analysis of conjugated polyketone reductase C2 (CPR-C2) from Candida parapsilosis IFO 0708

    International Nuclear Information System (INIS)

    Yamamura, Akihiro; Maruoka, Shintaro; Ohtsuka, Jun; Miyakawa, Takuya; Nagata, Koji; Kataoka, Michihiko; Kitamura, Nahoko; Shimizu, Sakayu; Tanokura, Masaru

    2009-01-01

    Conjugated polyketone reductase C2 from C. parapsilosis IFO 0708 was expressed, purified and crystallized by the sitting-drop vapour-diffusion method. The crystal belonged to space group P2 1 2 1 2 1 and diffracted X-rays to 1.7 Å resolution. Conjugated polyketone reductase C2 (CPR-C2) from Candida parapsilosis IFO 0708 is a member of the NADPH-dependent aldo-keto reductase (AKR) superfamily and catalyzes the stereospecific reduction of ketopantoyl lactone to d-pantoyl lactone. A diffraction-quality crystal of recombinant CPR-C2 was obtained by the sitting-drop vapour-diffusion method using PEG 3350 as the precipitant. The crystal diffracted X-rays to 1.7 Å resolution on beamline NW12A of the Photon Factory-Advanced Ring (Tsukuba, Japan). The crystal belonged to space group P2 1 2 1 2 1 , with unit-cell parameters a = 55.02, b = 68.30, c = 68.93 Å. The Matthews coefficient (V M = 1.76 Å 3 Da −1 ) indicated that the crystal contained one CPR-C2 molecule per asymmetric unit

  13. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin

    2015-01-01

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  14. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun

    2015-09-27

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  15. 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.

  16. ZNF322, a novel human C2H2 Krueppel-like zinc-finger protein, regulates transcriptional activation in MAPK signaling pathways

    International Nuclear Information System (INIS)

    Li Yongqing; Wang Yuequn; Zhang Caibo; Yuan Wuzhou; Wang Jun; Zhu Chuanbing; Chen Lei; Huang Wen; Zeng Weiqi; Wu Xiushan; Liu Mingyao

    2004-01-01

    Cardiac differentiation involves a cascade of coordinated gene expression that regulates cell proliferation and matrix protein formation in a defined temporal-spatial manner. The C 2 H 2 zinc finger-containing transcription factors have been implicated as critical regulators of multiple cardiac-expressed genes and are important for human heart development and diseases. Here we have identified and characterized a novel zinc-finger gene named ZNF322 using degenerated primers from a human embryo heart cDNA library. The gene contains four exons and spans 23.2 kb in chromosome 6p22.1 region, and transcribes a 2.7 kb mRNA that encodes a protein with 402 amino acid residues. The predicted protein contains 9 tandem C 2 H 2 -type zinc-finger motifs. Northern blot analysis shows that ZNF322 is expressed in every human tissue examined at adult stage and during embryonic developmental stages from 80 days to 24 weeks. When overexpressed in COS-7 cells, ZNF322-EGFP fusion protein is detected in the nucleus and cytoplasm. Reporter gene assays show that ZNF322 is a transcriptional activator. Furthermore, overexpression of ZNF322 in COS-7 cells activates the transcriptional activity of SRE and AP-1. Together, these results suggest that ZNF322 is a member of the zinc-finger transcription factor family and may act as a positive regulator in gene transcription mediated by the MAPK signaling pathways

  17. Cloning and characterization of a novel human zinc finger gene, hKid3, from a C2H2-ZNF enriched human embryonic cDNA library

    International Nuclear Information System (INIS)

    Gao Li; Sun Chong; Qiu Hongling; Liu Hui; Shao Huanjie; Wang Jun; Li Wenxin

    2004-01-01

    To investigate the zinc finger genes involved in human embryonic development, we constructed a C 2 H 2 -ZNF enriched human embryonic cDNA library, from which a novel human gene named hKid3 was identified. The hKid3 cDNA encodes a 554 amino acid protein with an amino-terminal KRAB domain and 11 carboxyl-terminal C 2 H 2 zinc finger motifs. Northern blot analysis indicates that two hKid3 transcripts of 6 and 8.5 kb express in human fetal brain and kidney. The 6 kb transcript can also be detected in human adult brain, heart, and skeletal muscle while the 8.5 kb transcript appears to be embryo-specific. GFP-fused hKid3 protein is localized to nuclei and the ZF domain is necessary and sufficient for nuclear localization. To explore the DNA-binding specificity of hKid3, an oligonucleotide library was selected by GST fusion protein of hKid3 ZF domain, and the consensus core sequence 5'-CCAC-3' was evaluated by competitive electrophoretic mobility shift assay. Moreover, The KRAB domain of hKid3 exhibits transcription repressor activity when tested in GAL4 fusion protein assay. These results indicate that hKid3 may function as a transcription repressor with regulated expression pattern during human development of brain and kidney

  18. Anatomical Variations of the Vertebral Artery in the Upper Cervical Spine: Clinical Relevance for Procedures Targeting the C1/C2 and C2/C3 Joints.

    Science.gov (United States)

    Elgueta, Maria Francisca; Ortiz Jimenez, Johanna; Wang, Nina Nan; Pérez Lara, Almudena; Chankowsky, Jeffrey; Charghi, Roshanak; Tran, De Q; Finlayson, Roderick J

    2018-05-01

    Accidental breach of the vertebral artery (VA) during the performance of cervical pain blocks can result in significant morbidity. Whereas anatomical variations have been described for the foraminal (V2) segment of the VA, those involving its V3 portion (between the C2 transverse process and dura) have not been investigated and may be of importance for procedures targeting the third occipital nerve or the lateral atlantoaxial joint. Five hundred computed tomography angiograms of the neck performed in patients older than 50 years for the management of cerebrovascular accident or cervical trauma (between January 2010 and May 2016) were retrospectively and independently reviewed by 2 neuroradiologists. Courses of the VA in relation to the lateral aspect of the C2/C3 joint and the posterior surface of the C1/C2 joint were examined. For the latter, any medial encroachment of the VA (or one of its branches) was noted. The presence of a VA loop between C1 and C2 and its distance from the upper border of the superior articular process (SAP) of C3 were also recorded. If the VA loop coursed posteriorly, its position in relation to 6 fields found on the lateral aspects of the articular pillars of C2 and C3 was tabulated. At the C1/C2 level, the VA coursed medially over the lateral quarter of the dorsal joint surface in 1% of subjects (0.6% and 0.4% on the left and right sides, respectively; P = 0.998). A VA loop originating between C1 and C2 was found to travel posteroinferiorly over the anterolateral aspect of the inferior articular pillar of C2 in 55.5% of patients on the left and 41.9% on the right side (P < 0.001), as well as over the SAP of C3 in 0.4% of subjects. When present in the quadrant immediately cephalad to the C3 SAP, VA loops coursed within 2.0 ± 1.5 and 3.3 ± 2.5 mm on the left and right sides, respectively, of its superior aspect (P < 0.001). The VA commonly travels adjacent to areas targeted by third occipital nerve procedures and more rarely over the

  19. Photoelectron Diffraction Imaging for C2H2 and C2H4 Chemisorbed on Si(100) Reveals a New Bonding Configuration

    International Nuclear Information System (INIS)

    Xu, S. H.; Keeffe, M.; Yang, Y.; Chen, C.; Yu, M.; Lapeyre, G. J.; Rotenberg, E.; Denlinger, J.; Yates, J. T. Jr.

    2000-01-01

    A new adsorption site for adsorbed acetylene on Si(100) is observed by photoelectron imaging based on the holographic principle. The diffraction effects in the carbon 1s angle-resolved photoemission are inverted (including the small-cone method) to obtain an image of the atom's neighboring carbon. The chemisorbed acetylene molecule is bonded to four silicon surface atoms. In contrast to the C 2 H 2 case, the image for adsorbed C 2 H 4 shows it bonded to two Si surface atoms. (c) 2000 The American Physical Society

  20. A leucine repeat motif in AbiA is required for resistance of Lactococcus lactis to phages representing three species.

    Science.gov (United States)

    Dinsmore, P K; O'Sullivan, D J; Klaenhammer, T R

    1998-05-28

    The abiA gene encodes an abortive bacteriophage infection mechanism that can protect Lactococcus species from infection by a variety of bacteriophages including three unrelated phage species. Five heptad leucine repeats suggestive of a leucine zipper motif were identified between residues 232 and 266 in the predicted amino acid sequence of the AbiA protein. The biological role of residues in the repeats was investigated by incorporating amino acid substitutions via site-directed mutagenesis. Each mutant was tested for phage resistance against three phages, phi 31, sk1, and c2, belonging to species P335, 936, and c2, respectively. The five residues that comprise the heptad repeats were designated L234, L242, A249, L256, and L263. Three single conservative mutations of leucine to valine in positions L235, L242, and L263 and a double mutation of two leucines (L235 and L242) to valines did not affect AbiA activity on any phages tested. Non-conservative single substitutions of charged amino acids for three of the leucines (L235, L242, and L256) virtually eliminated AbiA activity on all phages tested. Substitution of the alanine residue in the third repeat (A249) with a charged residue did not affect AbiA activity. Replacement of L242 with an alanine elimination phage resistance against phi 31, but partial resistance to sk1 and c2 remained. Two single proline substitutions for leucines L242 and L263 virtually eliminated AbiA activity against all phages, indicating that the predicted alpha-helical structure of this region is important. Mutations in an adjacent region of basic amino acids had various effects on phage resistance, suggesting that these basic residues are also important for AbiA activity. This directed mutagenesis analysis of AbiA indicated that the leucine repeat structure is essential for conferring phage resistance against three species of lactococcal bacteriophages.

  1. Wayward Warriors: The Viking Motif in Swedish and English Children's Literature

    Science.gov (United States)

    Sundmark, Björn

    2014-01-01

    In this article the Viking motif in children's literature is explored--from its roots in (adult) nationalist and antiquarian discourse, over pedagogical and historical texts for children, to the eventual diversification (or dissolution) of the motif into different genres and forms. The focus is on Swedish Viking narratives, but points of…

  2. Physical-chemical property based sequence motifs and methods regarding same

    Science.gov (United States)

    Braun, Werner [Friendswood, TX; Mathura, Venkatarajan S [Sarasota, FL; Schein, Catherine H [Friendswood, TX

    2008-09-09

    A data analysis system, program, and/or method, e.g., a data mining/data exploration method, using physical-chemical property motifs. For example, a sequence database may be searched for identifying segments thereof having physical-chemical properties similar to the physical-chemical property motifs.

  3. Gene Isolation Using Degenerate Primers Targeting Protein Motif: A Laboratory Exercise

    Science.gov (United States)

    Yeo, Brandon Pei Hui; Foong, Lian Chee; Tam, Sheh May; Lee, Vivian; Hwang, Siaw San

    2018-01-01

    Structures and functions of protein motifs are widely included in many biology-based course syllabi. However, little emphasis is placed to link this knowledge to applications in biotechnology to enhance the learning experience. Here, the conserved motifs of nucleotide binding site-leucine rich repeats (NBS-LRR) proteins, successfully used for the…

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

    NARCIS (Netherlands)

    Karsdorp, F.B.; van der Meulen, Marten; Meder, Theo; van den Bosch, Antal

    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

  5. Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network

    Directory of Open Access Journals (Sweden)

    Barabási Albert-László

    2004-01-01

    Full Text Available Abstract Background Transcriptional regulation of cellular functions is carried out through a complex network of interactions among transcription factors and the promoter regions of genes and operons regulated by them.To better understand the system-level function of such networks simplification of their architecture was previously achieved by identifying the motifs present in the network, which are small, overrepresented, topologically distinct regulatory interaction patterns (subgraphs. However, the interaction of such motifs with each other, and their form of integration into the full network has not been previously examined. Results By studying the transcriptional regulatory network of the bacterium, Escherichia coli, we demonstrate that the two previously identified motif types in the network (i.e., feed-forward loops and bi-fan motifs do not exist in isolation, but rather aggregate into homologous motif clusters that largely overlap with known biological functions. Moreover, these clusters further coalesce into a supercluster, thus establishing distinct topological hierarchies that show global statistical properties similar to the whole network. Targeted removal of motif links disintegrates the network into small, isolated clusters, while random disruptions of equal number of links do not cause such an effect. Conclusion Individual motifs aggregate into homologous motif clusters and a supercluster forming the backbone of the E. coli transcriptional regulatory network and play a central role in defining its global topological organization.

  6. High affinity recognition of a Phytophthora protein by Arabidopsis via an RGD motif

    NARCIS (Netherlands)

    Senchou, V.; Weide, R.L.; Carrasco, A.; Bouyssou, H.; Pont-Lezica, R.; Govers, F.; Canut, H.

    2004-01-01

    The RGD tripeptide sequence, a cell adhesion motif present in several extracellular matrix proteins of mammalians, is involved in numerous plant processes. In plant-pathogen interactions, the RGD motif is believed to reduce plant defence responses by disrupting adhesions between the cell wall and

  7. Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium

    Directory of Open Access Journals (Sweden)

    Lynch Michael

    2010-05-01

    Full Text Available Abstract Background In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa remains a virtually unexplored issue. Results By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Conclusions Our observations 1 shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2 are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3 reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

  8. Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.

    Science.gov (United States)

    Catania, Francesco; Lynch, Michael

    2010-05-04

    In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa) remains a virtually unexplored issue. By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Our observations 1) shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2) are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3) reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

  9. Mechanism for activation of the growth factor-activated AGC kinases by turn motif phosphorylation

    DEFF Research Database (Denmark)

    Hauge, Camilla; Antal, Torben L; Hirschberg, Daniel

    2007-01-01

    investigated the role of the third, so-called turn motif phosphate, also located in the tail, in the AGC kinases PKB, S6K, RSK, MSK, PRK and PKC. We report cooperative action of the HM phosphate and the turn motif phosphate, because it binds a phosphoSer/Thr-binding site above the glycine-rich loop within...

  10. Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

    KAUST Repository

    Alam, Tanvir

    2018-03-11

    Short Linear Motifs (SLiMs) contribute to almost every cellular function by connecting appropriate protein partners. Accurate prediction of SLiMs is difficult due to their shortness and sequence degeneracy. Leucine-aspartic acid (LD) motifs are SLiMs that link paxillin family proteins to factors controlling (cancer) cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. To enable a proteome-wide assessment of these motifs, we developed an active-learning based framework that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome identified a dozen proteins that contain LD motifs, all being involved in cell adhesion and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter-species comparison revealed a conserved LD signalling core, and reveals the emergence of species-specific adaptive connections, while maintaining a strong functional focus of the LD motif interactome. Collectively, our data elucidate the mechanisms underlying the origin and adaptation of an ancestral SLiM.

  11. A proposed vestigial translation initiation motif in VP1 of hepatitis A virus.

    Science.gov (United States)

    Kang, Jeong-Ah; Funkhouser, Ann W

    2002-07-01

    The internal ribosome entry site (IRES) of picornaviruses has a 3' polypyrimidine tract (PPT) 16-24 bases upstream of an AUG triplet (PPT/AUG motif). This motif is critical in determining the efficiency of cap-independent translation. HAV has a conserved PPT/AUG motif consisting of a nine base sequence (AGGUUUUUC) 23 bases upstream of the preferred AUG start codon. This HAV-specific PPT/AUG motif is repeated and conserved in VP1 of HAV, but not of other picornaviruses. We proposed that the PPT/AUG motif in the open reading frame initiated translation and/or had an impact on the life cycle of the virus. In vitro translation of mutant bicistronic mRNAs and growth in cell culture of mutant viruses provided no evidence that the VP1 PPT/AUG motif had any impact on either translation or growth. HAV differs from other picornaviruses in its inefficient growth in cell culture. Since the HAV-specific PPT/AUG motif is found in only 1 in 300,000 reported viral sequences outside the hepatovirus genus, this motif may be a vestigial translation initiation element and may have played a role in determining the unusual phenotype of HAV.

  12. 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.

  13. Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

    Science.gov (United States)

    Kinjo, Akira R.; Nakamura, Haruki

    2012-01-01

    Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

  14. Fast response dry-type artificial molecular muscles with [c2]daisy chains

    Science.gov (United States)

    Iwaso, Kazuhisa; Takashima, Yoshinori; Harada, Akira

    2016-06-01

    Hierarchically organized myosin and actin filaments found in biological systems exhibit contraction and expansion behaviours that produce work and force by consuming chemical energy. Inspired by these naturally occurring examples, we have developed photoresponsive wet- and dry-type molecular actuators built from rotaxane-based compounds known as [c2]daisy chains (specifically, [c2]AzoCD2 hydrogel and [c2]AzoCD2 xerogel). These actuators were prepared via polycondensation between four-armed poly(ethylene glycol) and a [c2]daisy chain based on α-cyclodextrin as the host component and azobenzene as a photoresponsive guest component. The light-induced actuation arises from the sliding motion of the [c2]daisy chain unit. Ultraviolet irradiation caused the gels to bend towards the light source. The response of the [c2]AzoCD2 xerogel, even under dry conditions, is very fast (7° every second), which is 10,800 times faster than the [c2]AzoCD2 hydrogel (7° every 3 h). In addition, the [c2]AzoCD2 xerogel was used as a crane arm to lift an object using ultraviolet irradiation to produce mechanical work.

  15. Electron Attachment to C2 Fluorocarbon Radicals at High Temperature (Postprint)

    Science.gov (United States)

    2016-01-28

    constant curve for C2F3. Figure 3 shows an extrap - olation of the electron attachment rate constant for C2F3 as a function of Tgas and Tel similar to...weight to the use of kinetic modeling to extrap - olate data taken over narrower ranges. ACKNOWLEDGMENTS The project was funded by the United States Air

  16. C-2 anterior plate-screw fixation: a quantitative anatomical and morphometric evaluation.

    Science.gov (United States)

    Senoglu, M; Ozbag, D; Gumusalan, Y

    2010-01-01

    Discectomy and inter-vertebral body fusion combined with the anterior plate-screw fixa tion is the common procedure in cervical spine surgery. But the anterior plate-screw fixation of the C2 spine has been the uncommon surgical procedure. In this study, we analyze the anatomy of the C2 body relevant to C2 anterior plate-screw fixation. Eighty-six dried C2 spines were evaluated directly for this study. Measurements were made on the C2 body width and midsagittal anteroposterior (AP) depth and the anteroposterior parasagittal depth 5 mm lateral to midline on the inferior endplates, in addition to on the middle body. Measurements also were made of anteroposterior parasagittal vertebral depth with both medial and lateral inclination of 10 degrees, with respect to the parasagittal plane of the vertebral body. The ideal maximum screw length and trajectory was found to be AP medial parasagittal depth of inferior surface of the C2 body [Right: 13.7 +/- 1.4 mm (11.0-17.9), Left: 13.6 +/- 1.5 mm (10.7-17.8)]. We report the measurements of the vertebral body of the C2. We think these measurements provide guidelines for operating on the anterior C2 spine, and enhance the confidence interval for the surgeon (Tab. 3, Fig. 1, Ref. 24).

  17. Evidence for multiple polytypes of semiconducting boron carbide (C2B10) from electronic structure

    International Nuclear Information System (INIS)

    Lunca-Popa, Petru; Brand, J I; Balaz, Snjezana; Rosa, Luis G; Boag, N M; Bai Mengjun; Robertson, B W; Dowben, P A

    2005-01-01

    Boron carbides fabricated via plasma enhanced chemical vapour deposition from different isomeric source compounds with the same C 2 B 10 H 12 closo-icosahedral structure result in materials with very different direct (optical) band gaps. This provides compelling evidence for the existence of multiple polytypes of C 2 B 10 boron carbide and is consistent with electron diffraction results

  18. Fragmentations and rearrangements of metastable [C2H5OS]+ ions

    NARCIS (Netherlands)

    de Vries, Marcel; Oudman, D; Weringa, WD

    1992-01-01

    Several [C2H5OS]+ ions with different structures were generated from the appropriate precursors and their metastable ion spectra were determined. Deuterium labelled analogues of some of the [C2H5OS]+ ions were used to elucidate the nature of the observed fragmentations and their mechanisms.

  19. State estimation approach for live aircraft engagement in a C2 simulation environment

    CSIR Research Space (South Africa)

    Duvenhage, A

    2007-01-01

    Full Text Available The increased use of simulations during live air defense exercises requires interoperability between different Command and Control (C2) systems and simulators. By accepting air picture or sensor tracks from each other, C2 systems and simulators can...

  20. Structural investigation of the ZnSe(001)-c(2×2) surface

    DEFF Research Database (Denmark)

    Weigand, W.; Müller, A.; Kilian, L.

    2003-01-01

    Zinc selenide is a model system for II-VI compound semiconductors. The geometric structure of the clean (001)-c(2x2) surface has recently been the subject of intense debate. We report here a surface x-ray-diffraction study on the ZnSe(001)-c(2x2) surface performed under ultrahigh vacuum using...

  1. The synthesis of [2-13C]2-nitropropane at room temperature and at atmospheric pressure

    NARCIS (Netherlands)

    Jacquemijns M; Zomer G

    1990-01-01

    In this report the synthesis of [2-13C]2-nitropropane at room temperature is described. [2-13C]Acetone was converted into the oxime with hydroxy hydrochloridelamine and sodium carbonate. Treatment with hypobromic acid resulted in 2-13C]2-bromo-2-nitropropane. Hydrogenation with sodium borohydride

  2. Sintering behaviour and mechanical properties of Cr3C2–NiCr ...

    Indian Academy of Sciences (India)

    fracture toughness. Keywords. Cermet; Cr3C2–NiCr; sintering; mechanical properties. ... et al investigated the mechanical properties of VC, Cr3C2 and NbC doped ..... Huang S G, Li L, Van der Biest O and Vleugels J 2008 J. Alloys. Compds.

  3. 77 FR 40928 - Self-Regulatory Organizations; C2 Options Exchange, Incorporated; Order Granting Approval of...

    Science.gov (United States)

    2012-07-11

    ... SECURITIES AND EXCHANGE COMMISSION [Release No. 34-67357; File No. SR-C2-2012-011] Self-Regulatory Organizations; C2 Options Exchange, Incorporated; Order Granting Approval of Proposed Rule Change To Implement a... and subsequently migrates to the DRF, the regulatory data for the portion of the day that the main...

  4. Higher-order multipole amplitude measurement in psi ' -> gamma chi(c2)

    NARCIS (Netherlands)

    Ablikim, M.; Achasov, M. N.; Alberto, D.; An, F. F.; An, Q.; An, Z. H.; Bai, J. Z.; Baldini, R.; Ban, Y.; Becker, J.; Berger, N.; Bertani, M.; Bian, J. M.; Boger, E.; Bondarenko, O.; Boyko, I.; Briere, R. A.; Bytev, V.; Cai, X.; Calcaterra, A. C.; Cao, G. F.; Chang, J. F.; Chelkov, G.; Chen, G.; Chen, H. S.; Chen, J. C.; Chen, M. L.; Chen, S. J.; Chen, Y.; Chen, Y. B.; Cheng, H. P.; Chu, Y. P.; Cronin-Hennessy, D.; Dai, H. L.; Dai, J. P.; Dedovich, D.; Deng, Z. Y.; Denysenko, I.; Destefanis, M.; Ding, Y.; Dong, L. Y.; Dong, M. Y.; Du, S. X.; Fang, J.; Fang, S. S.; Feng, C. Q.; Fu, C. D.; Fu, J. L.; Gao, Y.; Geng, C.; Goetzen, K.; Gong, W. X.; Greco, M.; Gu, M. H.; Gu, Y. T.; Guan, Y. H.; Guo, A. Q.; Guo, L. B.; Guo, Y. P.; Han, Y. L.; Hao, X. Q.; Harris, F. A.; He, K. L.; He, M.; He, Z. Y.; Heng, Y. K.; Hou, Z. L.; Hu, H. M.; Hu, J. F.; Hu, T.; Huang, B.; Huang, G. M.; Huang, J. S.; Huang, X. T.; Huang, Y. P.; Hussain, T.; Ji, C. S.; Ji, Q.; Ji, X. B.; Ji, X. L.; Jia, L. K.; Jiang, L. L.; Jiang, X. S.; Jiao, J. B.; Jiao, Z.; Jin, D. P.; Jin, S.; Jing, F. F.; Kalantar-Nayestanaki, N.; Kavatsyuk, M.; Kuehn, W.; Lai, W.; Lange, J. S.; Leung, J. K. C.; Li, C. H.; Li, Cheng; Li, Cui; Li, D. M.; Li, F.; Li, G.; Li, H. B.; Li, J. C.; Li, K.; Li, Lei; Li, N. B.; Li, Q. J.; Li, S. L.; Li, W. D.; Li, W. G.; Li, X. L.; Li, X. N.; Li, X. Q.; Li, X. R.; Li, Z. B.; Liang, H.; Liang, Y. F.; Liang, Y. T.; Liao, X. T.; Liu, B. J.; Liu, C. L.; Liu, C. X.; Liu, C. Y.; Liu, F. H.; Liu, Fang; Liu, Feng; Liu, H.; Liu, H. B.; Liu, H. H.; Liu, H. M.; Liu, H. W.; Liu, J. P.; Liu, K.; Liu, K.; Liu, K. Y.; Liu, Q.; Liu, S. B.; Liu, X.; Liu, X. H.; Liu, Y. B.; Liu, Y. W.; Liu, Yong; Liu, Z. A.; Liu, Zhiqiang; Liu, Zhiqing; Loehner, H.; Lu, G. R.; Lu, H. J.; Lu, J. G.; Lu, Q. W.; Lu, X. R.; Lu, Y. P.; Luo, C. L.; Luo, M. X.; Luo, T.; Luo, X. L.; Lv, M.; Ma, C. L.; Ma, F. C.; Ma, H. L.; Ma, Q. M.; Ma, S.; Ma, T.; Ma, X.; Ma, X. Y.; Maggiora, M.; Malik, Q. A.; Mao, H.; Mao, Y. J.; Mao, Z. P.; Messchendorp, J. G.; Min, J.; Min, T. J.; Mitchell, R. E.; Mo, X. H.; Muchnoi, N. Yu; Nefedov, Y.; Nikolaev, I. B.; Ning, Z.; Olsen, S. L.; Ouyang, Q.; Pacetti, S.; Park, J. W.; Pelizaeus, M.; Peters, K.; Ping, J. L.; Ping, R. G.; Poling, R.; Pun, C. S. J.; Qi, M.; Qian, S.; Qiao, C. F.; Qin, X. S.; Qiu, J. F.; Rashid, K. H.; Rong, G.; Ruan, X. D.; Sarantsev, A.; Schulze, J.; Shao, M.; Shen, C. P.; Shen, X. Y.; Sheng, H. Y.; Shepherd, M. R.; Song, X. Y.; Spataro, S.; Spruck, B.; Sun, D. H.; Sun, G. X.; Sun, J. F.; Sun, S. S.; Sun, X. D.; Sun, Y. J.; Sun, Y. Z.; Sun, Z. J.; Sun, Z. T.; Tang, C. J.; Tang, X.; Tian, H. L.; Toth, D.; Varner, G. S.; Wang, B.; Wang, B. Q.; Wang, K.; Wang, L. L.; Wang, L. S.; Wang, M.; Wang, P.; Wang, P. L.; Wang, Q.; Wang, Q. J.; Wang, S. G.; Wang, X. L.; Wang, Y. D.; Wang, Y. F.; Wang, Y. Q.; Wang, Z.; Wang, Z. G.; Wang, Z. Y.; Wei, D. H.; Wen, Q. G.; Wen, S. P.; Wiedner, U.; Wu, L. H.; Wu, N.; Wu, W.; Wu, Z.; Xiao, Z. J.; Xie, Y. G.; Xiu, Q. L.; Xu, G. F.; Xu, G. M.; Xu, H.; Xu, Q. J.; Xu, X. P.; Xu, Y.; Xu, Z. R.; Xu, Z. Z.; Xue, Z.; Yan, L.; Yan, W. B.; Yan, Y. H.; Yang, H. X.; Yang, T.; Yang, Y.; Yang, Y. X.; Ye, H.; Ye, M.; Ye, M. H.; Yu, B. X.; Yu, C. X.; Yu, S. P.; Yuan, C. Z.; Yuan, W. L.; Yuan, Y.; Zafar, A. A.; Zallo, A.; Zeng, Y.; Zhang, B. X.; Zhang, B. Y.; Zhang, C.; Zhang, C. C.; Zhang, D. H.; Zhang, H. H.; Zhang, H. Y.; Zhang, J.; Zhang, J. Q.; Zhang, J. W.; Zhang, J. Y.; Zhang, J. Z.; Zhang, L.; Zhang, S. H.; Zhang, T. R.; Zhang, X. J.; Zhang, X. Y.; Zhang, Y.; Zhang, Y. H.; Zhang, Y. S.; Zhang, Z. P.; Zhang, Z. Y.; Zhao, G.; Zhao, H. S.; Zhao, Jiawei; Zhao, Jingwei; Zhao, Lei; Zhao, Ling; Zhao, M. G.; Zhao, Q.; Zhao, S. J.; Zhao, T. C.; Zhao, X. H.; Zhao, Y. B.; Zhao, Z. G.; Zhao, Z. L.; Zhemchugov, A.; Zheng, B.; Zheng, J. P.; Zheng, Y. H.; Zheng, Z. P.; Zhong, B.; Zhong, J.; Zhong, L.; Zhou, L.; Zhou, X. K.; Zhou, X. R.; Zhu, C.; Zhu, K.; Zhu, K. J.; Zhu, S. H.; Zhu, X. L.; Zhu, X. W.; Zhu, Y. S.; Zhu, Z. A.; Zhuang, J.; Zou, B. S.; Zou, J. H.; Zuo, J. X.

    2011-01-01

    Using 106 x 10(6) psi' events collected with the BESIII detector at the BEPCII storage ring, the higher-order multipole amplitudes in the radiative transition psi' -> gamma chi(c2) -> gamma pi(+)pi(-)/gamma K+K- are measured. A fit to the chi(c2) production and decay angular distributions yields M2

  5. EXO70C2 is a key regulatory factor for optimal tip growth of pollen

    KAUST Repository

    Synek, Lukas; Vukasinovic, Nemanja; Kulich, Ivan; Hala, Michal; Aldorfova, Klara; Fendrych, Matyas; Zarsky, Viktor

    2017-01-01

    paralogs. Out of 23 Arabidopsis EXO70 isoforms, we analyzed seven isoforms expressed in pollen. Genetic and microscopic analyses of single mutants in EXO70A2, C1, C2, F1, H3, H5, and H6 genes revealed that only a loss-of-function EXO70C2 allele resulted

  6. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Science.gov (United States)

    Fauteux, François; Strömvik, Martina V

    2009-01-01

    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 of conserved motifs

  7. 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

  8. Probing the electronic structure and Au–C chemical bonding in AuC2− and AuC2 using high-resolution photoelectron spectroscopy

    International Nuclear Information System (INIS)

    León, Iker; Yang, Zheng; Wang, Lai-Sheng

    2014-01-01

    We report photoelectron spectroscopy (PES) and high-resolution PE imaging of AuC 2 − at a wide range of photon energies. The ground state of AuC 2 − is found to be linear (C ∞v , 1 Σ + ) with a …8π 4 4δ 4 17σ 2 9π 4 18σ 2 valence configuration. Detachments from all the five valence orbitals of the ground state of AuC 2 − are observed at 193 nm. High-resolution PE images are obtained in the energy range from 830 to 330 nm, revealing complicated vibronic structures from electron detachment of the 18σ, 9π, and 17σ orbitals. Detachment from the 18σ orbital results in the 2 Σ + ground state of neutral AuC 2 , which, however, is bent due to strong vibronic coupling with the nearby 2 Π state from detachment of a 9π electron. The 2 Σ + – 2 Π vibronic and spin-orbit coupling results in complicated vibronic structures for the 2 Σ + and 2 Π 3/2 states with extensive bending excitations. The electron affinity of AuC 2 is measured accurately to be 3.2192(7) eV with a ground state bending frequency of 195(6) cm −1 . The first excited state ( 2 A′) of AuC 2 , corresponding to the 2 Π 3/2 state at the linear geometry, is only 0.0021 eV above the ground state ( 2 A′) and has a bending frequency of 207(6) cm −1 . The 2 Π 1/2 state, 0.2291 eV above the ground state, is linear with little geometry change relative to the anion ground state. The detachment of the 17σ orbital also results in complicated vibronic structures, suggesting again a bent state due to possible vibronic coupling with the lower 2 Π state. The spectrum at 193 nm shows the presence of a minor species with less than 2% intensity relative to the ground state of AuC 2 − . High-resolution data of the minor species reveal several vibrational progressions in the Au–C stretching mode, which are assigned to be from the metastable 3 Π 2,1,0 spin-orbit excited states of AuC 2 − to the 2 Π 3/2,1/2 spin-orbit states of neutral AuC 2 . The spin-orbit splittings of the 3 Π and 2

  9. [Identification of C(2)M interacting proteins by yeast two-hybrid screening].

    Science.gov (United States)

    Yue, Shan-shan; Xia, Lai-xin

    2015-11-01

    The synaptonemal complex (SC) is a huge structure which assembles between the homologous chromosomes during meiotic prophase I. Drosophila germ cell-specific nucleoprotein C(2)M clustering at chromosomes can induce SC formation. To further study the molecular function and mechanism of C(2)M in meiosis, we constructed a bait vector for C(2)M and used the yeast two-hybrid system to identify C(2)M interacting proteins. Forty interacting proteins were obtained, including many DNA and histone binding proteins, ATP synthases and transcription factors. Gene silencing assays in Drosophila showed that two genes, wech and Psf1, may delay the disappearance of SC. These results indicate that Wech and Psf1 may form a complex with C(2)M to participate in the formation or stabilization of the SC complex.

  10. Effect of enhanced C2 growth chemistry on nanodiamond film deposition

    International Nuclear Information System (INIS)

    Teii, Kungen; Ikeda, Tomohiro

    2007-01-01

    A route to high-purity nanocrystalline diamond films from C 2 dimers and related mechanisms have been investigated by enhancing C 2 growth chemistry in Ar-rich microwave plasmas. Efficient C 2 production by direct dissociation from acetylene causes the micro- to nanocrystal transition with a low threshold Ar concentration of ∼70% and produces films of ∼20 nm grains with a distinct visible-Raman peak of diamond. C 2 grows nanodiamond on diamond surfaces but rarely initiates nucleation on foreign surfaces. The phase purity can be improved by increasing the dominance of nanodiamond growth from C 2 over nondiamond growth from CH x (x=0-3) and large radicals

  11. A Summary of Two Recent UAS Command and Control (C2) Communications Feasibility Studies

    Science.gov (United States)

    Ponchak, Denise S.; Auld, Elisabeth; Church, Gary; Henriksen, Stephen

    2016-01-01

    In Spring of 2015, the NextGen Institute conducted two UAS C2 Communications Feasibility Studies on behalf of the FAA UAS Integration Office to develop two limited UAS C2 operational examples, each involving low-altitude BLOS (Beyond Line of Sight) Line of Communication (LOC) UAS applications, as part of assessing the myriad practical UAS C2 deployment challenges associated with these approaches. The studies investigated the feasibility of "Point-to-Point" (PTP) and "Network" approaches to UAS C2 to better understand potential user needs and to explore evolutionary paths to establishing a nation-wide system for delivering UAS C2 communications. This paper will summarize the solicitation, approach and results of the two studies teams led by Aviation Management Associates, Inc. and Exelis Inc.

  12. Thermal Stability of Modified i-Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

    DEFF Research Database (Denmark)

    El-Sayed, Ahmed Ali; Pedersen, Erik B.; Khaireldin, Nahid Y.

    2016-01-01

    In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion of naphtha......In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion...... of naphthalimide (1H-benzo[de]isoquinoline-1,3(2H)-dione) as the intercalating nucleic acid. The stabilities of i-motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures (Tm) and circular dichroism spectra at different pH values and conditions (crowding...

  13. I-motif DNA structures are formed in the nuclei of human cells

    Science.gov (United States)

    Zeraati, Mahdi; Langley, David B.; Schofield, Peter; Moye, Aaron L.; Rouet, Romain; Hughes, William E.; Bryan, Tracy M.; Dinger, Marcel E.; Christ, Daniel

    2018-06-01

    Human genome function is underpinned by the primary storage of genetic information in canonical B-form DNA, with a second layer of DNA structure providing regulatory control. I-motif structures are thought to form in cytosine-rich regions of the genome and to have regulatory functions; however, in vivo evidence for the existence of such structures has so far remained elusive. Here we report the generation and characterization of an antibody fragment (iMab) that recognizes i-motif structures with high selectivity and affinity, enabling the detection of i-motifs in the nuclei of human cells. We demonstrate that the in vivo formation of such structures is cell-cycle and pH dependent. Furthermore, we provide evidence that i-motif structures are formed in regulatory regions of the human genome, including promoters and telomeric regions. Our results support the notion that i-motif structures provide key regulatory roles in the genome.

  14. EXO70C2 is a key regulatory factor for optimal tip growth of pollen

    KAUST Repository

    Synek, Lukas

    2017-03-30

    The exocyst, an eukaryotic tethering complex, co-regulates targeted exocytosis as an effector of small GTPases in polarized cell growth. In land plants, several exocyst subunits are encoded by double or triple paralogs, culminating in tens of EXO70 paralogs. Out of 23 Arabidopsis EXO70 isoforms, we analyzed seven isoforms expressed in pollen. Genetic and microscopic analyses of single mutants in EXO70A2, C1, C2, F1, H3, H5, and H6 genes revealed that only a loss-of-function EXO70C2 allele resulted in a significant male-specific transmission defect (segregation 40%:51%:9%) due to aberrant pollen tube growth. Mutant pollen tubes grown in vitro exhibited enhanced growth rate and a decreased thickness of the tip cell wall, causing tip bursts. However, exo70C2 pollen tubes could frequently recover and restart their speedy elongation, resulting in a repetitive stop-and-go growth dynamics. A pollen-specific depletion of the closest paralog, EXO70C1, using ami-RNA in the exo70C2 mutant background resulted in a complete pollen-specific transmission defect, suggesting redundant functions of EXO70C1 and EXO70C2. Both EXO70C1 and EXO70C2, GFP-tagged and expressed under their native promoters, localized in the cytoplasm of pollen grains, pollen tubes, and also root trichoblast cells. Expression of EXO70C2-GFP complemented aberrant growth of exo70C2 pollen tubes. The absent EXO70C2 interactions with core exocyst subunits in the yeast two-hybrid assay, cytoplasmic localization, and genetic effect suggest an unconventional EXO70 function possibly as a regulator of exocytosis outside the exocyst complex. In conclusion, EXO70C2 is a novel factor contributing to the regulation of optimal tip growth of Arabidopsis pollen tubes.

  15. MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.

    Science.gov (United States)

    Ozaki, Haruka; Iwasaki, Wataru

    2016-08-01

    As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory networks and evaluating mutations in cis-regulatory elements. Although chromatin immunoprecipitation sequencing (ChIP-seq) now provides abundant data on the genomic sequences to which a given TF binds, existing motif discovery methods are unable to directly answer whether a given TF can bind to a specific DNA-binding motif. Here, we report a method for clarifying the DNA-binding motif ambiguity, MOCCS. Given ChIP-Seq data of any TF, MOCCS comprehensively analyzes and describes every k-mer to which that TF binds. Analysis of simulated datasets revealed that MOCCS is applicable to various ChIP-Seq datasets, requiring only a few minutes per dataset. Application to the ENCODE ChIP-Seq datasets proved that MOCCS directly evaluates whether a given TF binds to each DNA-binding motif, even if known position weight matrix models do not provide sufficient information on DNA-binding motif ambiguity. Furthermore, users are not required to provide numerous parameters or background genomic sequence models that are typically unavailable. MOCCS is implemented in Perl and R and is freely available via https://github.com/yuifu/moccs. By complementing existing motif-discovery software, MOCCS will contribute to the basic understanding of how the genome controls diverse cellular processes via DNA-protein interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Expression, purification, crystallization and preliminary X-ray analysis of conjugated polyketone reductase C2 (CPR-C2) from Candida parapsilosis IFO 0708

    OpenAIRE

    Yamamura, Akihiro; Maruoka, Shintaro; Ohtsuka, Jun; Miyakawa, Takuya; Nagata, Koji; Kataoka, Michihiko; Kitamura, Nahoko; Shimizu, Sakayu; Tanokura, Masaru

    2009-01-01

    Conjugated polyketone reductase C2 from C. parapsilosis IFO 0708 was expressed, purified and crystallized by the sitting-drop vapour-diffusion method. The crystal belonged to space group P212121 and diffracted X-rays to 1.7 Å resolution.

  17. Evaluation report on CCTF Core-II reflood tests C2-AC1 (run 51) and C2-4 (run 62)

    International Nuclear Information System (INIS)

    Sugimoto, Jun; Iguchi, Tadashi; Murao, Yoshio

    1984-02-01

    A reflood test program has been conducted at Japan Atomic Energy Research Institute (JAERI) using large scale test facilities named Cylindrical Core Test Facility (CCTF) and Slab Core Test Facility (SCTF). The present report describes the effect of the initial clad temperature i.e., the initial stored energy on reflood phenomena observed in CCTF Core-II tests C2-ACl and C2-4. The peak clad temperatures of tests C2-ACl and C2-4 were 863 K and 1069 K, respectively at reflood initiation. With higher initial clad temperature, obtained were lower water accumulation in the core and upper plenum, and higher loop mass flow rate in an early reflood transient due to larger heat release of the stored energy in the core. Core inlet flow conditions were only affected shortly after the reflood initiation, causing the suppressed flooding rate and the larger U-tube flow oscillation between the core and the downcomer. In the core, with higher initial clad temperature, slower quench front propagation and higher turnaround temperature were observed. Responses to a higher initial clad temperature were similar to those observed in CCTF Core-I and FLECHT tests. Thus, the lower temperature rise with higher initial clad temperature was experimentally confirmed. The importance of higher flooding rate at initial period was analytically shown for further decreasing the temperature rise. (author)

  18. Direct measurements of rate constants for the reactions of CH3 radicals with C2H6, C2H4, and C2H2 at high temperatures.

    Science.gov (United States)

    Peukert, S L; Labbe, N J; Sivaramakrishnan, R; Michael, J V

    2013-10-10

    The shock tube technique has been used to study the reactions CH3 + C2H6 → C2H4 + CH4 + H (1), CH3 + C2H4 → Products + H (2), and CH3 + C2H2 → Products + H (3). Biacetyl, (CH3CO)2, was used as a clean high temperature thermal source for CH3-radicals for all the three reactions studied in this work. For reaction 1, the experiments span a T-range of 1153 K ≤ T ≤ 1297 K, at P ~ 0.4 bar. The experiments on reaction 2 cover a T-range of 1176 K ≤ T ≤ 1366 K, at P ~ 1.0 bar, and those on reaction 3 a T-range of 1127 K ≤ T ≤ 1346 K, at P ~ 1.0 bar. Reflected shock tube experiments performed on reactions 1-3, monitored the formation of H-atoms with H-atom Atomic Resonance Absorption Spectrometric (ARAS). Fits to the H-atom temporal profiles using an assembled kinetics model were used to make determinations for k1, k2, and k3. In the case of C2H6, the measurements of [H]-atoms were used to derive direct high-temperature rate constants, k1, that can be represented by the Arrhenius equation k1(T) = 5.41 × 10(-12) exp(-6043 K/T) cm(3) molecules(-1) s(-1) (1153 K ≤ T ≤ 1297 K) for the only bimolecular process that occurs, H-atom abstraction. TST calculations based on ab initio properties calculated at the CCSD(T)/CBS//M06-2X/cc-pVTZ level of theory show excellent agreement, within ±20%, of the measured rate constants. For the reaction of CH3 with C2H4, the present rate constant results, k2', refer to the sum of rate constants, k(2b) + k(2c), from two competing processes, addition-elimination, and the direct abstraction CH3 + C2H4 → C3H6 + H (2b) and CH3 + C2H4 → C2H2 + H + CH4 (2c). Experimental rate constants for k2' can be represented by the Arrhenius equation k2'(T) = 2.18 × 10(-10) exp(-11830 K/T) cm(3) molecules(-1) s(-1) (1176 K ≤ T ≤ 1366 K). The present results are in excellent agreement with recent theoretical predictions. The present study provides the only direct measurement for the high-temperature rate constants for these channels

  19. A Repeating Sulfated Galactan Motif Resuscitates Dormant Micrococcus luteus Bacteria.

    Science.gov (United States)

    Böttcher, Thomas; Szamosvári, Dávid; Clardy, Jon

    2018-07-01

    Only a small fraction of bacteria can autonomously initiate growth on agar plates. Nongrowing bacteria typically enter a metabolically inactive dormant state and require specific chemical trigger factors or signals to exit this state and to resume growth. Micrococcus luteus has become a model organism for this important yet poorly understood phenomenon. Only a few resuscitation signals have been described to date, and all of them are produced endogenously by bacterial species. We report the discovery of a novel type of resuscitation signal that allows M. luteus to grow on agar but not agarose plates. Fractionation of the agar polysaccharide complex and sulfation of agarose allowed us to identify the signal as highly sulfated saccharides found in agar or carrageenans. Purification of hydrolyzed κ-carrageenan ultimately led to the identification of the signal as a small fragment of a large linear polysaccharide, i.e., an oligosaccharide of five or more sugars with a repeating disaccharide motif containing d-galactose-4-sulfate (G4S) 1,4-linked to 3,6-anhydro-α-d-galactose (DA), G4S-(DA-G4S) n ≥2 IMPORTANCE Most environmental bacteria cannot initiate growth on agar plates, but they can flourish on the same plates once growth is initiated. While there are a number of names for and manifestations of this phenomenon, the underlying cause appears to be the requirement for a molecular signal indicating safe growing conditions. Micrococcus luteus has become a model organism for studying this growth initiation process, often called resuscitation, because of its apparent connection with the persistent or dormant form of Mycobacterium tuberculosis , an important human pathogen. In this report, we identify a highly sulfated saccharide from agar or carrageenans that robustly resuscitates dormant M. luteus on agarose plates. We identified and characterized the signal as a small repeating disaccharide motif. Our results indicate that signals inherent in or absent from the

  20. One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs.

    Science.gov (United States)

    Lock, Antonia; Forfar, Rachel; Weston, Cathryn; Bowsher, Leo; Upton, Graham J G; Reynolds, Christopher A; Ladds, Graham; Dixon, Ann M

    2014-12-01

    G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins and well-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the full-length protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conserved mechanism for assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs. Copyright © 2014. Published by Elsevier B.V.

  1. Hypovalency--a kinetic-energy density description of a 4c-2e bond.

    Science.gov (United States)

    Jacobsen, Heiko

    2009-06-07

    A bond descriptor based on the kinetic energy density, the localized-orbital locator (LOL), is used to characterize the nature of the chemical bond in electron deficient multi-center bonds. The boranes B(2)H(6), B(4)H(4), B(4)H(10), [B(6)H(6)](2-), and [B(6)H(7)](-) serve as prototypical examples of hypovalent 3c-2e and 4c-2e bonding. The kinetic energy density is derived from a set of Kohn-Sham orbitals obtained from pure density functional calculations (PBE/TZVP), and the topology of LOL is analyzed in terms of (3,-3) attractors (Gamma). The B-B-B and B-H-B 3c-2e, and the B-B-H-B 4c-2e bonding situations are defined by their own characteristic LOL profiles. The presence of one attractor in relation to the three or four atoms that are engaged in electron deficient bonding provides sufficient indication of the type of 3c-2e or 4c-2e bond present. For the 4c-2e bond in [B(6)H(7)](-) the LOL analysis is compared to results from an experimental QTAIM study.

  2. Synthesis and Electrochemical Properties of Two-Dimensional RGO/Ti3C2Tx Nanocomposites

    Directory of Open Access Journals (Sweden)

    Changjie Shen

    2018-01-01

    Full Text Available MXene is a new type of two-dimensional layered material. Herein, a GO/Ti3C2Tx nanocomposite was prepared by a simple liquid phase method, and the obtained GO/Ti3C2Tx was transformed into RGO/Ti3C2Tx under high temperature with Ar/H2. The prepared samples were characterized using X-ray diffraction (XRD, Raman measurement, scanning electron microscopy (SEM, energy disperse spectroscopy (EDS, and X-ray photoelectron spectroscopy (XPS. As an electrode material in lithium-ion batteries, the RGO/Ti3C2Tx nanocomposite exhibited an excellent electrochemical performance and an excellent rate performance. Compared to pure Ti3C2Tx, the nanocomposite had a better reversible capacity at different current densities and had no attenuation after 200 cycles, which is one time higher than pure Ti3C2Tx. The improvement in the specific capacity was due to the excellent electrical conductivity and the unique structure of RGO, in which a charge transfer bridge was built among the Ti3C2Tx flakes. Such a bridge shortened the transmission distance of the electrons and ions and effectively controlled the restacking of the laminated materials.

  3. Radioassays for quantitation of intact complement proteins C2 and B in human serum

    Energy Technology Data Exchange (ETDEWEB)

    Oglesby, T J; Ueda, A; Volanakis, J E

    1988-05-25

    Availability of polyclonal and monoclonal antibodies recognizing determinants on the major cleavage fragments of complement proteins C2 and B enabled development of sensitive radioassays which can be used to quantitate the intact proteins in human sera. Changes in C2 and B concentrations indicative of classical or alternative pathway activation, or both, were seen in normal serum after incubation with complement activators. The authors determined the normal range of C2 concentration to be 11-35 ..mu..g/ml in 32 healthy individuals, and that of protein B to be 74-286 ..mu..g/ml. Sera from patients with systemic lupus erythematosus (SLE), septic shock, infections, and following orthopedic surgery were then assayed. Mean protein B concentration was significantly higher in SLE sera and in the infected and post-operative sera, and the mean C2 concentration in the septic shock group was significantly lower than the mean of healthy individuals. Intact C2 was not detected in known C2-deficient individuals. These assays allow parallel quantitation of the structurally and functionally homologous proteins of the classical (C2) and alternative (B) pathways, which is of interest in patients with genetic and acquired hypocomplementemia. 22 refs.; 3 figs.

  4. β‐Taxilin participates in differentiation of C2C12 myoblasts into myotubes

    Energy Technology Data Exchange (ETDEWEB)

    Sakane, Hiroshi; Makiyama, Tomohiko; Nogami, Satoru; Horii, Yukimi [Department of Molecular and Cell Biology, Graduate school of Medicine, Dokkyo Medical University, 880 Kitakobayashi, Mibu-town, Tochigi 321-0293 (Japan); Akasaki, Kenji [Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University, Fukuyama, Hiroshima 729-0292 (Japan); Shirataki, Hiromichi, E-mail: hiro-sh@dokkyomed.ac.jp [Department of Molecular and Cell Biology, Graduate school of Medicine, Dokkyo Medical University, 880 Kitakobayashi, Mibu-town, Tochigi 321-0293 (Japan)

    2016-07-15

    Myogenesis is required for the development of skeletal muscle. Accumulating evidence indicates that the expression of several genes are upregulated during myogenesis and these genes play pivotal roles in myogenesis. However, the molecular mechanism underlying myogenesis is not fully understood. In this study, we found that β-taxilin, which is specifically expressed in the skeletal muscle and heart tissues, was progressively expressed during differentiation of C2C12 myoblasts into myotubes, prompting us to investigate the role of β-taxilin in myogenesis. In C2C12 cells, knockdown of β-taxilin impaired the fusion of myoblasts into myotubes, and decreased the diameter of myotubes. We also found that β-taxilin interacted with dysbindin, a coiled-coil-containing protein. Knockdown of dysbindin conversely promoted the fusion of myoblasts into myotubes and increased the diameter of myotubes in C2C12 cells. Furthermore, knockdown of dysbindin attenuated the inhibitory effect of β-taxilin depletion on myotube formation of C2C12 cells. These results demonstrate that β-taxilin participates in myogenesis through suppressing the function of dysbindin to inhibit the differentiation of C2C12 myoblasts into myotubes. - Highlights: • β‐Taxilin is progressively expressed during differentiation of C2C12 cell. • Knockdown of β-taxilin impaired C2C12 myotube formation. • β‐Taxilin interacted with dysbindin. • Knockdown of dysbindin promoted C2C12 myotube formation. • The function of β-taxilin in C2C12 myotube formation depends on dysbindin.

  5. Endocytosis‒Mediated Invasion and Pathogenicity of Streptococcus agalactiae in Rat Cardiomyocyte (H9C2).

    Science.gov (United States)

    Pooja, Sharma; Pushpanathan, Muthuirulan; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

    2015-01-01

    Streptococcus agalactiae infection causes high mortality in cardiovascular disease (CVD) patients, especially in case of setting prosthetic valve during cardiac surgery. However, the pathogenesis mechanism of S. agalactiae associate with CVD has not been well studied. Here, we have demonstrated the pathogenicity of S. agalactiae in rat cardiomyocytes (H9C2). Interestingly, both live and dead cells of S. agalactiae were uptaken by H9C2 cells. To further dissect the process of S. agalactiae internalization, we chemically inhibited discrete parts of cellular uptake system in H9C2 cells using genistein, chlorpromazine, nocodazole and cytochalasin B. Chemical inhibition of microtubule and actin formation by nocodazole and cytochalasin B impaired S. agalactiae internalization into H9C2 cells. Consistently, reverse‒ transcription PCR (RT‒PCR) and quantitative real time‒PCR (RT-qPCR) analyses also detected higher levels of transcripts for cytoskeleton forming genes, Acta1 and Tubb5 in S. agalactiae‒infected H9C2 cells, suggesting the requirement of functional cytoskeleton in pathogenesis. Host survival assay demonstrated that S. agalactiae internalization induced cytotoxicity in H9C2 cells. S. agalactiae cells grown with benzyl penicillin reduced its ability to internalize and induce cytotoxicity in H9C2 cells, which could be attributed with the removal of surface lipoteichoic acid (LTA) from S. agalactiae. Further, the LTA extracted from S. agalactiae also exhibited dose‒dependent cytotoxicity in H9C2 cells. Taken together, our data suggest that S. agalactiae cells internalized H9C2 cells through energy‒dependent endocytic processes and the LTA of S. agalactiae play major role in host cell internalization and cytotoxicity induction.

  6. Perkembangan Motif Sineas Film Indie dalam Menghadapi Industri Film Mainstream

    Directory of Open Access Journals (Sweden)

    Yoppy Ardiyono

    2016-03-01

    Full Text Available The research aims to review to review determine the effect and its impact raised by motive - a motive the ada in the hearts period travel time history of film short against cinematographer-filmmaker as principal especially filmmakers left path (indie. The used platform theory research hearts singer adopts from theory commodification media vincent mosco. Singer helped shift theory understanding the motive filmmakers working hearts differences fundamental basis of political pressure economic happens under with demands regime. The method used is descriptive qualitative research methods. Data collection techniques through observation of the environment of an independent film live and in-depth interviews with speakers including mr. Yang prayer orangutan direct contact 'with realm of research. Coupled with study to review the literature references adding insight research. And that was concluded change appears motif among indie film cinematographer it is true the situation is closely linked to the mainstream industry, konstilasi politics, and the orientation of capitalism. Necessary their one thing is clear and systematic regulation from the government to the future movement of currents sidestream (indie more with good operates professionally arranged, the air so that the contribution of indie cinema film land for progress can feels good to yourself indie filmmakers as well as those of its main industries.

  7. Crammed signaling motifs in the T-cell receptor.

    Science.gov (United States)

    Borroto, Aldo; Abia, David; Alarcón, Balbino

    2014-09-01

    Although the T cell antigen receptor (TCR) is long known to contain multiple signaling subunits (CD3γ, CD3δ, CD3ɛ and CD3ζ), their role in signal transduction is still not well understood. The presence of at least one immunoreceptor tyrosine-based activation motif (ITAM) in each CD3 subunit has led to the idea that the multiplication of such elements essentially serves to amplify signals. However, the evolutionary conservation of non-ITAM sequences suggests that each CD3 subunit is likely to have specific non-redundant roles at some stage of development or in mature T cell function. The CD3ɛ subunit is paradigmatic because in a relatively short cytoplasmic sequence (∼55 amino acids) it contains several docking sites for proteins involved in intracellular trafficking and signaling, proteins whose relevance in T cell activation is slowly starting to be revealed. In this review we will summarize our current knowledge on the signaling effectors that bind directly to the TCR and we will propose a hierarchy in their response to TCR triggering. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. DNA mutation motifs in the genes associated with inherited diseases.

    Directory of Open Access Journals (Sweden)

    Michal Růžička

    Full Text Available Mutations in human genes can be responsible for inherited genetic disorders and cancer. Mutations can arise due to environmental factors or spontaneously. It has been shown that certain DNA sequences are more prone to mutate. These sites are termed hotspots and exhibit a higher mutation frequency than expected by chance. In contrast, DNA sequences with lower mutation frequencies than expected by chance are termed coldspots. Mutation hotspots are usually derived from a mutation spectrum, which reflects particular population where an effect of a common ancestor plays a role. To detect coldspots/hotspots unaffected by population bias, we analysed the presence of germline mutations obtained from HGMD database in the 5-nucleotide segments repeatedly occurring in genes associated with common inherited disorders, in particular, the PAH, LDLR, CFTR, F8, and F9 genes. Statistically significant sequences (mutational motifs rarely associated with mutations (coldspots and frequently associated with mutations (hotspots exhibited characteristic sequence patterns, e.g. coldspots contained purine tract while hotspots showed alternating purine-pyrimidine bases, often with the presence of CpG dinucleotide. Using molecular dynamics simulations and free energy calculations, we analysed the global bending properties of two selected coldspots and two hotspots with a G/T mismatch. We observed that the coldspots were inherently more flexible than the hotspots. We assume that this property might be critical for effective mismatch repair as DNA with a mutation recognized by MutSα protein is noticeably bent.

  9. ARCHETYPES AND MYTHOLOGICAL MOTIFS: JOHN UPDIKE’S LEGACY REVISITED

    Directory of Open Access Journals (Sweden)

    Loreta Ulvydienė

    2018-04-01

    Full Text Available John Updike is widely considered to be one of the greatest, one of the most popular and sometimes most controversial writers concerned with the American small town and middle-class materialism. A lot of literary critics and researchers observe that Updike’s finest work came from his exploration of ordinary America and from his use of elegant prose, rich with metaphor, to portray the public and private feelings of Americans, their daily rounds of life. In addition, discussing Updike’s individual works a lot of literary critics and researchers have observed the writer’s attempts to re-write myth in “the mythical age”1 of the twentieth century. Naturally enough, as the return to myth is assumed to be a certain feature of the Modernist movement, half a century later since Updike’s famous novel Centaur was penned, it is indispensable to re-examine the writer’s fictional intentions in the usage of myth. More importantly, it is needful to determine whether we can see the mythic elements and realistic details as a continuum or as the contrasted opposites in his so called “historical chronicles”. Updike’s novels and stories are filled with mythological motifs and character archetypes. Thus, the study aims at revisiting John Updike’s creation considering mythological elements and archetypal images of his heroes alongside with heroic masculinity, war, terrorism and American perfectionism.

  10. Dystroglycan versatility in cell adhesion: a tale of multiple motifs

    Directory of Open Access Journals (Sweden)

    Winder Steve J

    2010-02-01

    Full Text Available Abstract Dystroglycan is a ubiquitously expressed heterodimeric adhesion receptor. The extracellular α-subunit makes connections with a number of laminin G domain ligands including laminins, agrin and perlecan in the extracellular matrix and the transmembrane β-subunit makes connections to the actin filament network via cytoskeletal linkers including dystrophin, utrophin, ezrin and plectin, depending on context. Originally discovered as part of the dystrophin glycoprotein complex of skeletal muscle, dystroglycan is an important adhesion molecule and signalling scaffold in a multitude of cell types and tissues and is involved in several diseases. Dystroglycan has emerged as a multifunctional adhesion platform with many interacting partners associating with its short unstructured cytoplasmic domain. Two particular hotspots are the cytoplasmic juxtamembrane region and at the very carboxy terminus of dystroglycan. Regions which between them have several overlapping functions: in the juxtamembrane region; a nuclear localisation signal, ezrin/radixin/moesin protein, rapsyn and ERK MAP Kinase binding function, and at the C terminus a regulatory tyrosine governing WW, SH2 and SH3 domain interactions. We will discuss the binding partners for these motifs and how their interactions and regulation can modulate the involvement of dystroglycan in a range of different adhesion structures and functions depending on context. Thus dystroglycan presents as a multifunctional scaffold involved in adhesion and adhesion-mediated signalling with its functions under exquisite spatio-temporal regulation.

  11. The Phenylpropanoid Pathway Is Controlled at Different Branches by a Set of R2R3-MYB C2 Repressors in Grapevine1

    Science.gov (United States)

    Cavallini, Erika; Matus, José Tomás; Finezzo, Laura; Zenoni, Sara; Loyola, Rodrigo; Guzzo, Flavia; Schlechter, Rudolf; Ageorges, Agnès; Arce-Johnson, Patricio

    2015-01-01

    Because of the vast range of functions that phenylpropanoids possess, their synthesis requires precise spatiotemporal coordination throughout plant development and in response to the environment. The accumulation of these secondary metabolites is transcriptionally controlled by positive and negative regulators from the MYB and basic helix-loop-helix protein families. We characterized four grapevine (Vitis vinifera) R2R3-MYB proteins from the C2 repressor motif clade, all of which harbor the ethylene response factor-associated amphiphilic repression domain but differ in the presence of an additional TLLLFR repression motif found in the strong flavonoid repressor Arabidopsis (Arabidopsis thaliana) AtMYBL2. Constitutive expression of VvMYB4a and VvMYB4b in petunia (Petunia hybrida) repressed general phenylpropanoid biosynthetic genes and selectively reduced the amount of small-weight phenolic compounds. Conversely, transgenic petunia lines expressing VvMYBC2-L1 and VvMYBC2-L3 showed a severe reduction in petal anthocyanins and seed proanthocyanidins together with a higher pH of crude petal extracts. The distinct function of these regulators was further confirmed by transient expression in tobacco (Nicotiana benthamiana) leaves and grapevine plantlets. Finally, VvMYBC2-L3 was ectopically expressed in grapevine hairy roots, showing a reduction in proanthocyanidin content together with the down-regulation of structural and regulatory genes of the flavonoid pathway as revealed by a transcriptomic analysis. The physiological role of these repressors was inferred by combining the results of the functional analyses and their expression patterns in grapevine during development and in response to ultraviolet B radiation. Our results indicate that VvMYB4a and VvMYB4b may play a key role in negatively regulating the synthesis of small-weight phenolic compounds, whereas VvMYBC2-L1 and VvMYBC2-L3 may additionally fine tune flavonoid levels, balancing the inductive effects of

  12. Argo_CUDA: Exhaustive GPU based approach for motif discovery in large DNA datasets.

    Science.gov (United States)

    Vishnevsky, Oleg V; Bocharnikov, Andrey V; Kolchanov, Nikolay A

    2018-02-01

    The development of chromatin immunoprecipitation sequencing (ChIP-seq) technology has revolutionized the genetic analysis of the basic mechanisms underlying transcription regulation and led to accumulation of information about a huge amount of DNA sequences. There are a lot of web services which are currently available for de novo motif discovery in datasets containing information about DNA/protein binding. An enormous motif diversity makes their finding challenging. In order to avoid the difficulties, researchers use different stochastic approaches. Unfortunately, the efficiency of the motif discovery programs dramatically declines with the query set size increase. This leads to the fact that only a fraction of top "peak" ChIP-Seq segments can be analyzed or the area of analysis should be narrowed. Thus, the motif discovery in massive datasets remains a challenging issue. Argo_Compute Unified Device Architecture (CUDA) web service is designed to process the massive DNA data. It is a program for the detection of degenerate oligonucleotide motifs of fixed length written in 15-letter IUPAC code. Argo_CUDA is a full-exhaustive approach based on the high-performance GPU technologies. Compared with the existing motif discovery web services, Argo_CUDA shows good prediction quality on simulated sets. The analysis of ChIP-Seq sequences revealed the motifs which correspond to known transcription factor binding sites.

  13. A Novel Protein Interaction between Nucleotide Binding Domain of Hsp70 and p53 Motif

    Directory of Open Access Journals (Sweden)

    Asita Elengoe

    2015-01-01

    Full Text Available Currently, protein interaction of Homo sapiens nucleotide binding domain (NBD of heat shock 70 kDa protein (PDB: 1HJO with p53 motif remains to be elucidated. The NBD-p53 motif complex enhances the p53 stabilization, thereby increasing the tumor suppression activity in cancer treatment. Therefore, we identified the interaction between NBD and p53 using STRING version 9.1 program. Then, we modeled the three-dimensional structure of p53 motif through homology modeling and determined the binding affinity and stability of NBD-p53 motif complex structure via molecular docking and dynamics (MD simulation. Human DNA binding domain of p53 motif (SCMGGMNR retrieved from UniProt (UniProtKB: P04637 was docked with the NBD protein, using the Autodock version 4.2 program. The binding energy and intermolecular energy for the NBD-p53 motif complex were −0.44 Kcal/mol and −9.90 Kcal/mol, respectively. Moreover, RMSD, RMSF, hydrogen bonds, salt bridge, and secondary structure analyses revealed that the NBD protein had a strong bond with p53 motif and the protein-ligand complex was stable. Thus, the current data would be highly encouraging for designing Hsp70 structure based drug in cancer therapy.

  14. Conserved binding of GCAC motifs by MEC-8, couch potato, and the RBPMS protein family

    Science.gov (United States)

    Soufari, Heddy

    2017-01-01

    Precise regulation of mRNA processing, translation, localization, and stability relies on specific interactions with RNA-binding proteins whose biological function and target preference are dictated by their preferred RNA motifs. The RBPMS family of RNA-binding proteins is defined by a conserved RNA recognition motif (RRM) domain found in metazoan RBPMS/Hermes and RBPMS2, Drosophila couch potato, and MEC-8 from Caenorhabditis elegans. In order to determine the parameters of RNA sequence recognition by the RBPMS family, we have first used the N-terminal domain from MEC-8 in binding assays and have demonstrated a preference for two GCAC motifs optimally separated by >6 nucleotides (nt). We have also determined the crystal structure of the dimeric N-terminal RRM domain from MEC-8 in the unbound form, and in complex with an oligonucleotide harboring two copies of the optimal GCAC motif. The atomic details reveal the molecular network that provides specificity to all four bases in the motif, including multiple hydrogen bonds to the initial guanine. Further studies with human RBPMS, as well as Drosophila couch potato, confirm a general preference for this double GCAC motif by other members of the protein family and the presence of this motif in known targets. PMID:28003515

  15. Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences

    Science.gov (United States)

    König, Sebastian L. B.; Huppert, Julian L.; Sigel, Roland K. O.; Evans, Amanda C.

    2013-01-01

    G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions. PMID:23771141

  16. 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/

  17. Comparative analysis of evolutionarily conserved motifs of epidermal growth factor receptor 2 (HER2) predicts novel potential therapeutic epitopes

    DEFF Research Database (Denmark)

    Deng, Xiaohong; Zheng, Xuxu; Yang, Huanming

    2014-01-01

    druggable epitopes/targets. We employed the PROSITE Scan to detect structurally conserved motifs and PRINTS to search for linearly conserved motifs of ECD HER2. We found that the epitopes recognized by trastuzumab and pertuzumab are located in the predicted conserved motifs of ECD HER2, supporting our...

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

    International Nuclear Information System (INIS)

    Park, Sung-Won; Do, Hyun-Jin; Huh, Sun-Hyung; Sung, Boreum; Uhm, Sang-Jun; Song, Hyuk; Kim, Nam-Hyung; Kim, Jae-Hwan

    2012-01-01

    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 ( 125 MQELSNILNL 134 ) 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.

  19. Felix Spectroscopy of Likely Astronomical Molecular Ions: HC_3O^+, C_2H_3CNH^+, and C_2H_5CNH^+

    Science.gov (United States)

    Thorwirth, Sven; Asvany, Oskar; Brünken, Sandra; Jusko, Pavol; Schlemmer, Stephan; Martin-Drumel, Marie-Aline; McCarthy, Michael C.

    2017-06-01

    Infrared signatures of three molecular ions of relevance to the interstellar medium and planetary atmospheres have been detected at the Free Electron Laser for Infrared eXperiments, FELIX, at Radboud University (Nijmegen, The Netherlands) in combination with the 4K FELion 22-pole ion trap facility. Mid-infrared vibrational modes of protonated tricarbon monoxide, HC_3O^+, protonated vinyl cyanide, C_2H_3CNH^+, and protonated ethyl cyanide, C_2H_5CNH^+, were detected using resonant photodissociation of the respective Ne-complexes by monitoring the depletion of their cluster mass signal as a function of wavenumber. The infrared fingerprints compare very favorably with results from high-level quantum-chemical calculations performed at the CCSD(T) level of theory.

  20. An Experimental and Theoretical Study on the Kinetic Isotope Effect of C2H6 and C2D6 Reaction with OH

    KAUST Repository

    Khaled, Fathi; Giri, Binod; Szőri, Milá n; Viskolcz, Bé la; Farooq, Aamir

    2015-01-01

    We report experimental and theoretical results for the deuterated kinetic isotope effect (DKIE) of the reaction of OH with ethane (C2H6) and deuterated ethane (C2D6). The reactions were investigated behind reflected shock waves over 800–1350 K by monitoring OH radicals near 306.69 nm using laser absorption. In addition, high level CCSD(T)/cc-pV(T,Q)Z//MP2/cc-pVTZ quantum chemical and statistical rate theory calculations were performed which agreed very well with the experimental findings. The results reported herein provide the first experimental evidence that DKIE for alkanes asymptotes to a value of 1.4 at high temperatures.

  1. Atmospheric chemistry of C2F5CHO: mechanism of the C2F5C(O)O-2+HO2 reaction

    DEFF Research Database (Denmark)

    Andersen, Mads Peter Sulbæk; Hurley, MD; Wallington, TJ

    2003-01-01

    in a yield of 76 +/- 4 The gas phase reaction of CnF2n+1C(O)O-2 with HO2 radicals offers a potential explanation for at least part of the observed environmental burden of fluorinated carboxylic acids, CnF2n+1C(O)OH. As part of this work an upper limit for the rate constant of reaction of Cl atorns with C2F5C......(O)OH at 296 K was determined; k(Cl + C2F5C(O)OH) 1 x 10(-11) cm(3) molecule(-1) s(-1). (C) 2003 Published by Elsevier B.V....

  2. An Experimental and Theoretical Study on the Kinetic Isotope Effect of C2H6 and C2D6 Reaction with OH

    KAUST Repository

    Khaled, Fathi

    2015-10-30

    We report experimental and theoretical results for the deuterated kinetic isotope effect (DKIE) of the reaction of OH with ethane (C2H6) and deuterated ethane (C2D6). The reactions were investigated behind reflected shock waves over 800–1350 K by monitoring OH radicals near 306.69 nm using laser absorption. In addition, high level CCSD(T)/cc-pV(T,Q)Z//MP2/cc-pVTZ quantum chemical and statistical rate theory calculations were performed which agreed very well with the experimental findings. The results reported herein provide the first experimental evidence that DKIE for alkanes asymptotes to a value of 1.4 at high temperatures.

  3. Work-Centered Design and Evaluation of a C2 Visualization Aid

    National Research Council Canada - National Science Library

    Roth, Emilie; Scott, Ronald; Kazmierczak, Tom; Whitaker, Randall; Stilson, Mona; Thomas-Meyers, Gina; Wampler, Jeffrey

    2006-01-01

    .... We have been developing and applying work-centered design and evaluation methodologies to design advanced visualization and support tools intended to more effectively support C2 cognitive and collaborative work...

  4. Data of evolutionary structure change: 1A00C-2ZLWD [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1A00C-2ZLWD 1A00 2ZLW C D -VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPT...SKYR VQLSGEEKAAVLALWDKVN--EEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEG---VHHLDNLKGTF...D> 0 2ZLW D 2ZLWD

  5. Data of evolutionary structure change: 1A01C-2ZLWD [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 1A01C-2ZLWD 1A01 2ZLW C D -VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPT...R VQLSGEEKAAVLALWDKVN--EEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSEL...0 2ZLW D 2ZLWD

  6. HCI Design Patterns for C2: A Vision for a DoD Design Reference Library

    National Research Council Canada - National Science Library

    Stanard, Terry; Wampler, Jeffrey L; Conrad, Kendall; Osga, Glenn

    2006-01-01

    .... However, NCO is a double edged sword for C2 centers. While it offers information sharing like never before, it creates new task demands of info management with the potential for warfighters to get lost in the sea of data...

  7. Possibility of gas sensor based on C_2_0 molecular devices

    International Nuclear Information System (INIS)

    Zhao, Wenkai; Yang, Chuanlu; Zou, Dongqing; Sun, Zhaopeng; Ji, Guomin

    2017-01-01

    We theoretically investigate the possibility of diatomic gas detection (NO, CO, O_2) by making use of the transport properties of the C_2_0 molecular junctions. The calculations are performed by using nonequilibrium Green's function (NEGF) formalism in combination with density functional theory (DFT). In this work, we systematically study the most stable adsorption structural configurations, adsorption energy, and the transport properties on C_2_0 molecular junctions with these diatomic gas molecules. It is found that NO and O_2 gas molecule can be detected selectively. We suggest its possibility of nanosensors for highly sensitive and selective based on C_2_0 molecular junction systems. - Highlights: • The most favorable adsorption site is investigated. • The mechanism of gas sensors is revealed. • NO and O_2 gas molecules can be detected by C_2_0 selectively.

  8. Fully-kinetic Ion Simulation of Global Electrostatic Turbulent Transport in C-2U

    Science.gov (United States)

    Fulton, Daniel; Lau, Calvin; Bao, Jian; Lin, Zhihong; Tajima, Toshiki; TAE Team

    2017-10-01

    Understanding the nature of particle and energy transport in field-reversed configuration (FRC) plasmas is a crucial step towards an FRC-based fusion reactor. The C-2U device at Tri Alpha Energy (TAE) achieved macroscopically stable plasmas and electron energy confinement time which scaled favorably with electron temperature. This success led to experimental and theoretical investigation of turbulence in C-2U, including gyrokinetic ion simulations with the Gyrokinetic Toroidal Code (GTC). A primary objective of TAE's new C-2W device is to explore transport scaling in an extended parameter regime. In concert with the C-2W experimental campaign, numerical efforts have also been extended in A New Code (ANC) to use fully-kinetic (FK) ions and a Vlasov-Poisson field solver. Global FK ion simulations are presented. Future code development is also discussed.

  9. An Analytical Model That Provides Insights into Various C2 Issues

    National Research Council Canada - National Science Library

    Taylor, James G; Neta, Beny; Shugart, Peter A

    2004-01-01

    .... A Lanchester-type model of force-on-force combat that reflects C2 architecture at the platform level is developed through a detailed analysis of the target-engagement cycle for a single typical firer...

  10. Septicemia caused by the gram-negative bacterium CDC IV c-2 in an immunocompromised human.

    OpenAIRE

    Dan, M; Berger, S A; Aderka, D; Levo, Y

    1986-01-01

    A 37-year-old man with plasma cell leukemia developed nonfatal septicemia caused by the gram-negative bacterium CDC IV c-2. Recovery followed appropriate treatment with antibiotics. The biochemical features of this organism are reviewed.

  11. Graphene-Based Patterning and Differentiation of C2C12 Myoblasts

    DEFF Research Database (Denmark)

    Bajaj, Piyush; Rivera, Jose A; Marchwiany, Daniel

    2014-01-01

    This study aims at generating highly aligned functional myotubes using graphene as the underlying scaffold. Graphene not only supports the growth of C2C12 muscle cells but also enhances its differentiation and leads to spontaneous patterning of myotubes....

  12. Infrared spectrum and compressibility of Ti3GeC2 to 51 GPa

    International Nuclear Information System (INIS)

    Manoun, Bouchaib; Yang, H.; Saxena, S.K.; Ganguly, A.; Barsoum, M.W.; El Bali, B.; Liu, Z.X.; Lachkar, M.

    2007-01-01

    Using a synchrotron radiation source and a diamond anvil cell, we measured the pressure dependence of the lattice parameters of a polycrystalline Ti 3 GeC 2 sample up to a pressure of 51 GPa. No phase transformations were observed. Like Ti 3 SiC 2 , and most other compounds belonging to the same family of ternary carbides and nitrides, the so-called MAX phases, the compressibility of Ti 3 GeC 2 along the c axis is greater than that along the a axis. The bulk modulus is 197 ± 4 GPa, with a pressure derivative of 3.4 ± 0.1. We also characterized Ti 3 GeC 2 by infrared spectroscopy; four of the five expected infrared modes were observed for this material

  13. Simulation-based Agent Support in a Synthetic Team-based C2 Task Environment

    National Research Council Canada - National Science Library

    Elliott, Linda R; Chaiken, Scott; Dalrymple, Mathieu; Petrov, Plamen; Stoyen, Alexander

    2000-01-01

    In our long-term program of research in command and control (C2) teamwork and performance, we have extensively analyzed the roles, responsibilities, and interdependencies of Airborne Warning and Control System (AWACS) Weapons Director (WD...

  14. COMPARATIVE STUDY TO FIND THE EFFECT OF MULLIGANS SNAG TECHNIQUE (C1-C2 VERSUS MAITLANDS TECHNIQUE (C1-C2 IN CERVICOGENIC HEADACHE AMONG INFORMATION TECHNOLOGY PROFESSIONALS

    Directory of Open Access Journals (Sweden)

    Neeti Christian

    2017-06-01

    Full Text Available Background: Headache is a common condition which physiotherapists have to deal with in clinical practice.Headaches which arise from the cervical spine are termed as Cervicogenic headaches (CGH, and these types of headaches are common form of a chronic and recurrent headache.The diagnostic criteria for CGH are outlined by the IHS (International Headache Society. The upper cervical joints, namely the occiput-C1 and C1-C2 segments are the most common origin of pain. Office and computer workers have the highest incidence of neck disorders than other occupations; the prevalence of neck disorders is above 50% among them. The purpose of this study is to find the effectiveness of Mulligan’s SNAG technique (C1-C2 and Maitland’s technique (C1-C2 in CGH and to compare these manual therapy techniques (Mulligan’s SNAG technique and Maitland’s technique with a control group. Methods: 30 subjects were selected for the study among them 23 subjects completed the study. The subjects were randomly allocated to 3 groups. The range of motion (ROM and severity of a headache were assessed pre and post intervention using FRT and HDI respectively. Result: The comparison revealed that SNAG group had a greater increase in cervical rotation (p<0.01 range than the Maitland’s technique and control groups. The mean value between pre-post differences shows a decrease in severity of a headache among all three groups. The significant difference between 3 groups was found through Tukey’s post hoc test using ANOVA method (Group A versus Group C; p<0.01 and Group B versus Group C; p<0.05. Conclusion: The present study suggested that C1-C2 SNAG technique showed statistically significant improvement in reducing headache and disability when compared to the Maitland’s mobilization technique among cervicogenic headache subjects

  15. Salt-bridge Swapping in the EXXERFXYY Motif of Proton Coupled Oligopeptide Transporters

    DEFF Research Database (Denmark)

    Aduri, Nanda G; Prabhala, Bala K; Ernst, Heidi A

    2015-01-01

    to as E1XXE2R), located on Helix I, in interactions with the proton. In this study we investigated the intracellular substrate accumulation by motif variants with all possible combinations of glutamate residues changed to glutamine and arginine changed to a tyrosine; the latter being a natural variant......-motif salt bridge, i.e. R-E2 to R-E1, which is consistent with previous structural studies. Molecular dynamics simulations of the motif variants E1XXE2R and E1XXQ2R support this mechanism. The simulations showed that upon changing conformation, arginine pushes Helix V, through interactions with the highly...

  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. Superconductivity in intercalated and substituted Y2Br2C2

    International Nuclear Information System (INIS)

    Baecker, M.; Simon, A.; Kremer, R.K.; Mattausch, H.J.; Dronskowski, R.; Rouxel, J.

    1996-01-01

    Layer compounds of the type Y 2 X 2 C 2 (X=Cl, Br, I) show superconductivity at temperatures between 2.3 and 11.2 K. The transition temperature is related to the tendency of conduction electrons toward pairwise localization in C 2 -π * states at the Fermi level, and changes with the concentration of valence electrons, which is varied by intercalation of Na. (orig.)

  18. Endocytosis‒Mediated Invasion and Pathogenicity of Streptococcus agalactiae in Rat Cardiomyocyte (H9C2)

    OpenAIRE

    Pooja, Sharma; Pushpanathan, Muthuirulan; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

    2015-01-01

    Streptococcus agalactiae infection causes high mortality in cardiovascular disease (CVD) patients, especially in case of setting prosthetic valve during cardiac surgery. However, the pathogenesis mechanism of S. agalactiae associate with CVD has not been well studied. Here, we have demonstrated the pathogenicity of S. agalactiae in rat cardiomyocytes (H9C2). Interestingly, both live and dead cells of S. agalactiae were uptaken by H9C2 cells. To further dissect the process of S. agalactiae int...

  19. The C2H3O+ chemi-ion acetyl cation or O-protonated ketene

    DEFF Research Database (Denmark)

    Egsgaard, H.; Carlsen, L.

    1995-01-01

    The C2H3O+ chemi-ion sampled from a premixed methane/oxygen flame has been demonstrated to be the acetyl cation based on ion-molecule reactions with isoprene and 1,3-dioxolane.......The C2H3O+ chemi-ion sampled from a premixed methane/oxygen flame has been demonstrated to be the acetyl cation based on ion-molecule reactions with isoprene and 1,3-dioxolane....

  20. Anomalous temperature dependence of H{sub c2} in BiSrCuO

    Energy Technology Data Exchange (ETDEWEB)

    Broto, J.M. [Service National Des Champs Magnetiques Pulses, 31077 Toulouse Cedex (France); Rakoto, H. [Service National Des Champs Magnetiques Pulses, 31077 Toulouse Cedex (France); Ousset, J.C. [Service National Des Champs Magnetiques Pulses, 31077 Toulouse Cedex (France); Coffe, G. [Service National Des Champs Magnetiques Pulses, 31077 Toulouse Cedex (France); Askenazy, S. [Service National Des Champs Magnetiques Pulses, 31077 Toulouse Cedex (France); Osofsky, M.S. [Naval Research Laboratory, Washington, DC 20375-5000 (United States); Soulen, R.J. Jr. [Naval Research Laboratory, Washington, DC 20375-5000 (United States); Wolf, S.A. [Naval Research Laboratory, Washington, DC 20375-5000 (United States); Pari, P. [Centre d`Etudes de Saclay, Service de Physique de l`Etat Condense, Laboratoire des Basses Temperatures, 91191 Gif-sur-Yvette (France); Bozovic, I. [Edward L. Ginzton Research Center, Varian Associates, Palo Alto, CA 94304-1025 (United States); Eckstein, J.N. [Edward L. Ginzton Research Center, Varian Associates, Palo Alto, CA 94304-1025 (United States); Virshup, G.F. [Edward L. Ginzton Research Center, Varian Associates, Palo Alto, CA 94304-1025 (United States)

    1995-05-01

    H{sub c2}(T) has been measured for thin BSCO films at temperatures down to 65 mK and pulsed fields up to 35 T. H{sub c2}(T) diverged anomalously as the temperature decreased: at the lowest temperature, it was five times that expected for a conventional superconductor. Although deviations from the conventional behavior have been observed in other superconductors, such strong divergence over such a large range of reduced temperature has not been seen before. (orig.).

  1. Minimum variance and variance of outgoing quality limit MDS-1(c1, c2) plans

    Science.gov (United States)

    Raju, C.; Vidya, R.

    2016-06-01

    In this article, the outgoing quality (OQ) and total inspection (TI) of multiple deferred state sampling plans MDS-1(c1,c2) are studied. It is assumed that the inspection is rejection rectification. Procedures for designing MDS-1(c1,c2) sampling plans with minimum variance of OQ and TI are developed. A procedure for obtaining a plan for a designated upper limit for the variance of the OQ (VOQL) is outlined.

  2. C2 subcutaneous stimulation for failed back surgery syndrome: a case report.

    Science.gov (United States)

    De Ridder, Dirk; Plazier, Mark; Menovsky, Tomas; Kamerling, Niels; Vanneste, Sven

    2013-01-01

    Failed back surgery syndrome (FBSS) is a term embracing a constellation of conditions that describes persistent or recurring low back pain, with or without sciatica following one or more spine surgeries. It has been shown in animals that electrical stimulation of the high cervical C2 area can suppress pain stimuli derived from the L5-S1 dermatome. It is unknown whether C2 electrical stimulation in humans can be used to treat pain derived from the L5-S1 area, and a case is reported in which subcutaneous C2 is applied to treat FBSS. A patient presents to the neuromodulation clinic because of FBSS (after three lumbar diskectomies) and noninvasive neuromodulation is performed consisting of transcutaneous electrical nerve stimulation (TENS) at C2. The C2 TENS stimulation is successful in improving pain. It induces paresthesias in the C2 dermatome above a certain amplitude threshold, but does not generate paresthesias in the pain area. However, the patient becomes allergic to the skin-applied TENS electrodes and therefore a new treatment strategy is discussed with the patient. A subcutaneous C2 electrode is inserted under local anesthesia, and attached to an external pulse generator. Three stimulation designs are tested: a classical tonic stimulation, consisting of 40 Hz stimulation, a placebo, and a burst stimulation, consisting of 40 Hz burst mode, with five spikes delivered at 500 Hz at 1000 μsec pulse width and 1000 μsec interspike interval. The patient's stimulation results demonstrate that burst mode is superior to placebo and tonic mode, and she receives a fully implanted C2 electrode connected to an internal pulse generator via an extension wire. The burst design is capable of both suppressing the least and worst pain effectively, and she has remained almost pain-free for over three years. © 2012 International Neuromodulation Society.

  3. Three C2 Models for Military Agility in the 21st Century

    DEFF Research Database (Denmark)

    Mitchell, Dr. William

    2012-01-01

    Briefet beskriver kort 3 Command &Control (C2) modeller som skulle føre til mere agile eller smidige militær organisationer der kan omstilles hurtig til at løse de gaver der nu må komme i den 21 århundrede. Alle 3 modeller er baseret på 4 C2 principper: Jointness; Intelligence; Cyber; og Speciel ...

  4. Measurements of H[sub c2](T) in Bi-Sr-Cu-O

    Energy Technology Data Exchange (ETDEWEB)

    Osofsky, M.S.; Soulen, R.J. Jr.; Wolf, S.A. (Naval Research Lab., Washington, DC (United States)); Broto, J.M.; Rakoto, H.; Ousset, J.C.; Coffe, G.; Askenazy, S. (Service National des Champs Magnetique Pulses, Toulouse (France)); Pari, P. (Laboratoire des Basses Temperatures, Gif-sur-Yvette (France)); Bozovic, I.; Eckstein, J.N.; Virshup, G.F. (Varian Associates, Palo Alto, CA (United States))

    1994-04-01

    H[sub c2](T) has been measured for thin BSCO films at temperatures down to 65 mK and pulsed fields up to 35 T. H[sub c2](T) diverged anomalously as the temperature decreased. At the lowest temperature, it was five times that expected for a conventional superconductor. This result cannot be explained by any conventional model which relies on magnetic ordering, local pairing mechanisms, or superlattice superconductivity. 51 refs., 3 figs.

  5. Analyzing C2 Structures and Self-Synchronization with Simple Computational Models

    Science.gov (United States)

    2011-06-01

    16th ICCRTS “Collective C2 in Multinational Civil-Military Operations” Analyzing C2 Structures and Self- Synchronization with Simple...Self- Synchronization with Simple Computational Models 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT...models. The Kuramoto Model, though with some serious limitations, provides a representation of information flow and self- synchronization in an

  6. Gating of human ClC-2 chloride channels and regulation by carboxy-terminal domains.

    Science.gov (United States)

    Garcia-Olivares, Jennie; Alekov, Alexi; Boroumand, Mohammad Reza; Begemann, Birgit; Hidalgo, Patricia; Fahlke, Christoph

    2008-11-15

    Eukaryotic ClC channels are dimeric proteins with each subunit forming an individual protopore. Single protopores are gated by a fast gate, whereas the slow gate is assumed to control both protopores through a cooperative movement of the two carboxy-terminal domains. We here study the role of the carboxy-terminal domain in modulating fast and slow gating of human ClC-2 channels, a ubiquitously expressed ClC-type chloride channel involved in transepithelial solute transport and in neuronal chloride homeostasis. Partial truncation of the carboxy-terminus abolishes function of ClC-2 by locking the channel in a closed position. However, unlike other isoforms, its complete removal preserves function of ClC-2. ClC-2 channels without the carboxy-terminus exhibit fast and slow gates that activate and deactivate significantly faster than in WT channels. In contrast to the prevalent view, a single carboxy-terminus suffices for normal slow gating, whereas both domains regulate fast gating of individual protopores. Our findings demonstrate that the carboxy-terminus is not strictly required for slow gating and that the cooperative gating resides in other regions of the channel protein. ClC-2 is expressed in neurons and believed to open at negative potentials and increased internal chloride concentrations after intense synaptic activity. We propose that the function of the ClC-2 carboxy-terminus is to slow down the time course of channel activation in order to stabilize neuronal excitability.

  7. A high-resolution photoelectron imaging and theoretical study of CP- and C2P.

    Science.gov (United States)

    Czekner, Joseph; Cheung, Ling Fung; Johnson, Eric L; Fortenberry, Ryan C; Wang, Lai-Sheng

    2018-01-28

    The discovery of interstellar anions has been a milestone in astrochemistry. In the search for new interstellar anions, CP - and C 2 P - are viable candidates since their corresponding neutrals have already been detected astronomically. However, scarce data exist for these negatively charged species. Here we report the electron affinities of CP and C 2 P along with the vibrational frequencies of their anions using high-resolution photoelectron imaging. These results along with previous spectroscopic data of the neutral species are used further to benchmark very accurate quartic force field quantum chemical methods that are applied to CP, CP - , C 2 P, and two electronic states of C 2 P - . The predicted electron affinities, vibrational frequencies, and rotational constants are in excellent agreement with the experimental data. The electron affinities of CP (2.8508 ± 0.0007 eV) and C 2 P (2.6328 ± 0.0006 eV) are measured accurately and found to be quite high, suggesting that the CP - and C 2 P - anions are thermodynamically stable and possibly observable. The current study suggests that the combination of high-resolution photoelectron imaging and quantum chemistry can be used to determine accurate molecular constants for exotic radical species of astronomical interest.

  8. Synthesis, extraction and electronic structure of Ce@C2n

    Science.gov (United States)

    Liu, Bing-Bing; Zou, Guang-Tian; Yang, Hai-Bin; Yu, San; Lu, Jin-Shan; Liu, Zi-Yang; Liu, Shu-Ying; Xu, Wen-Guo

    1997-11-01

    In view of the growing interest in endohedral lanthanide fullerenes, Ce, as a typical+ 4 oxidation state lanthanide element, has been systematically studied. The synthesis, extraction and electronic structure of Ce @ C2n are investigated. Soot containing Ce@C2n was synthesized in high yield by carbonizing CeO2-containing graphite rods and are back-burning the CeC2-enriched cathode deposit in a DC arc plasma apparatus. Ce@C2n dominated by Ce@C82, can be efficiently extracted from the insoluble part of the soot after toluene Soxhlet extraction by pyridine at high temperature and high pressure in a closed vessel. About 60% Ce@C2n(2n = 82, 80, 78, 76) and 35% Ce@C82 can be enriched in the pyridine extract. This fact is identified by desorption electron impact mass spectrometry (DEI MS). The electronic structure of Ce@C2n is analyzed by using X-ray photoemission spectroscopy (XPS) of pyridine-free film. It is suggested that the encapsulated Ce atom is in a charge state close to+ 3 and was effectively protected from reaction with water and oxygen by the enclosing fullerene cage. Unlike theoretical expectation, the electronic state of Ce@C82 is formally described as Ce+3@C3-82.

  9. Electronic Structure and Chemical Bond of Ti3SiC2 and Adding Al Element

    Institute of Scientific and Technical Information of China (English)

    MIN Xinmin; LU Ning; MEI Bingchu

    2006-01-01

    The relation among electronic structure, chemical bond and property of Ti3SiC2 and Al-doped was studied by density function and discrete variation (DFT-DVM) method. When Al element is added into Ti3SiC2, there is a less difference of ionic bond, which does not play a leading role to influent the properties. After adding Al, the covalent bond of Al and the near Ti becomes somewhat weaker, but the covalent bond of Al and the Si in the same layer is obviously stronger than that of Si and Si before adding. Therefore, in preparation of Ti3SiC2, adding a proper quantity of Al can promote the formation of Ti3SiC2. The density of state shows that there is a mixed conductor character in both of Ti3SiC2 and adding Al element. Ti3SiC2 is with more tendencies to form a semiconductor. The total density of state near Fermi lever after adding Al is larger than that before adding, so the electric conductivity may increase after adding Al.

  10. 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.

  11. Comparison of revision strategies for failed C2-posterior cervical pedicle screws: a biomechanical study.

    Science.gov (United States)

    Mayer, Michael; Zenner, Juliane; Bogner, Robert; Hitzl, Wolfgang; Figl, Markus; von Keudell, Arvind; Stephan, Daniel; Penzkofer, Rainer; Augat, Peter; Korn, Gundobert; Resch, Herbert; Koller, Heiko

    2013-01-01

    With increasing usage within challenging biomechanical constructs, failures of C2 posterior cervical pedicle screws (C2-pCPSs) will occur. The purpose of the study was therefore to investigate the biomechanical characteristics of two revision techniques after the failure of C2-pCPSs. Twelve human C2 vertebrae were tested in vitro in a biomechanical study to compare two strategies for revision screws after failure of C2-pCPSs. C2 pedicles were instrumented using unicortical 3.5-mm CPS bilaterally (Synapse/Synthes, Switzerland). Insertion accuracy was verified by fluoroscopy. C2 vertebrae were potted and fixed in an electromechanical testing machine with the screw axis coaxial to the pullout direction. Pullout testing was conducted with load and displacement data taken continuously. The peak load to failure was measured in newtons (N) and is reported as the pullout resistance (POR). After pullout, two revision strategies were tested in each vertebra. In Group-1, revision was performed with 4.0-mm C2-pCPSs. In Group-2, revision was performed with C2-pedicle bone-plastic combined with the use of a 4-mm C2-pCPSs. For the statistical analysis, the POR between screws was compared using absolute values (N) and the POR of the revision techniques normalized to that of the primary procedures (%). The POR of primary 3.5-mm CPSs was 1,140.5 ± 539.6 N for Group-1 and 1,007.7 ± 362.5 N for Group-2; the difference was not significant. In the revision setting, the POR in Group-1 was 705.8 ± 449.1 N, representing a reduction of 38.1 ± 32.9 % compared with that of primary screw fixation. For Group-2, the POR was 875.3 ± 367.9 N, representing a reduction of 13.1 ± 23.4 %. A statistical analysis showed a significantly higher POR for Group-2 compared with Group-1 (p = 0.02). Although the statistics showed a significantly reduced POR for both revision strategies compared with primary fixation (p plastic, the POR can be significantly increased compared with the use of only an

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

    Science.gov (United States)

    Heyward, Catherine A; Pettitt, Trevor R; Leney, Sophie E; Welsh, Gavin I; Tavaré, Jeremy M; Wakelam, Michael J O

    2008-05-20

    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. 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. 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.

  13. 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.

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

    KAUST Repository

    AbouEisha, Hassan M.; Chikalov, Igor; Moshkov, Mikhail; Jankovic, Boris R.

    2015-01-01

    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

  15. Lucky Motifs in Chinese Folk Art: Interpreting Paper-cut from Chinese Shaanxi

    Directory of Open Access Journals (Sweden)

    Xuxiao WANG

    2013-11-01

    Full Text Available Paper-cut is not simply a form of traditional Chinese folk art. Lucky motifs developed in paper-cut certainly acquired profound cultural connotations. As paper-cut is a time-honoured skill across the nation, interpreting those motifs requires cultural receptiveness and anthropological sensitivity. The author of this article analyzes examples of paper-cut from Northern Shaanxi, China, to identify the cohesive motifs and explore the auspiciousness of the specific concepts of Fu, Lu, Shou, Xi. The paper-cut of Northern Shaanxi is an ideal representative of the craft as a whole because of the relative stability of this region in history, in terms of both art and culture. Furthermore, its straightforward style provides a clear demonstration of motifs regarding folk understanding of expectations for life.

  16. Design of Fashion Accessories Using Akwa-Ocha Motifs and Symbols

    African Journals Online (AJOL)

    Nneka Umera-Okeke

    Nkpopu: holes. 16. Osikapa na ... accessories anchors in both social semiotics and archetypal theories. Social semiotics theory as ... the two earrings incorporate the Onwa (moon) motif in spherical shape and in black colour. They are held ...

  17. On the origin of distribution patterns of motifs in biological networks

    Directory of Open Access Journals (Sweden)

    Lesk Arthur M

    2008-08-01

    Full Text Available Abstract Background Inventories of small subgraphs in biological networks have identified commonly-recurring patterns, called motifs. The inference that these motifs have been selected for function rests on the idea that their occurrences are significantly more frequent than random. Results Our analysis of several large biological networks suggests, in contrast, that the frequencies of appearance of common subgraphs are similar in natural and corresponding random networks. Conclusion Indeed, certain topological features of biological networks give rise naturally to the common appearance of the motifs. We therefore question whether frequencies of occurrences are reasonable evidence that the structures of motifs have been selected for their functional contribution to the operation of networks.

  18. Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs.

    KAUST Repository

    Sayadi, Ahmed; Briganti, Leonardo; Tramontano, Anna; Via, Allegra

    2011-01-01

    The function of proteins is often mediated by short linear segments of their amino acid sequence, called Short Linear Motifs or SLiMs, the identification of which can provide important information about a protein function. However, the short length

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

    Science.gov (United States)

    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 also show that FTZ contains an AF2-interacting nuclear receptor box, the first to be found in a homeodomain protein. Both interaction motifs are shown to be necessary for physical interactions in vitro and for functional interactions in developing embryos. These unexpected findings have important implications for the conserved homologs of the two proteins. PMID:11157757

  20. Recent Advances in Layered Ti3 C2 Tx MXene for Electrochemical Energy Storage.

    Science.gov (United States)

    Xiong, Dongbin; Li, Xifei; Bai, Zhimin; Lu, Shigang

    2018-04-01

    Ti 3 C 2 T x , a typical representative among the emerging family of 2D layered transition metal carbides and/or nitrides referred to as MXenes, has exhibited multiple advantages including metallic conductivity, a plastic layer structure, small band gaps, and the hydrophilic nature of its functionalized surface. As a result, this 2D material is intensively investigated for application in the energy storage field. The composition, morphology and texture, surface chemistry, and structural configuration of Ti 3 C 2 T x directly influence its electrochemical performance, e.g., the use of a well-designed 2D Ti 3 C 2 T x as a rechargeable battery anode has significantly enhanced battery performance by providing more chemically active interfaces, shortened ion-diffusion lengths, and improved in-plane carrier/charge-transport kinetics. Some recent progresses of Ti 3 C 2 T x MXene are achieved in energy storage. This Review summarizes recent advances in the synthesis and electrochemical energy storage applications of Ti 3 C 2 T x MXene including supercapacitors, lithium-ion batteries, sodium-ion batteries, and lithium-sulfur batteries. The current opportunities and future challenges of Ti 3 C 2 T x MXene are addressed for energy-storage devices. This Review seeks to provide a rational and in-depth understanding of the relation between the electrochemical performance and the nanostructural/chemical composition of Ti 3 C 2 T x , which will promote the further development of 2D MXenes in energy-storage applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Chloroquine Analog Interaction with C2- and Iota-Toxin in Vitro and in Living Cells.

    Science.gov (United States)

    Kronhardt, Angelika; Beitzinger, Christoph; Barth, Holger; Benz, Roland

    2016-08-10

    C2-toxin from Clostridium botulinum and Iota-toxin from Clostridium perfringens belong both to the binary A-B-type of toxins consisting of two separately secreted components, an enzymatic subunit A and a binding component B that facilitates the entry of the corresponding enzymatic subunit into the target cells. The enzymatic subunits are in both cases actin ADP-ribosyltransferases that modify R177 of globular actin finally leading to cell death. Following their binding to host cells' receptors and internalization, the two binding components form heptameric channels in endosomal membranes which mediate the translocation of the enzymatic components Iota a and C2I from endosomes into the cytosol of the target cells. The binding components form ion-permeable channels in artificial and biological membranes. Chloroquine and related 4-aminoquinolines were able to block channel formation in vitro and intoxication of living cells. In this study, we extended our previous work to the use of different chloroquine analogs and demonstrate that positively charged aminoquinolinium salts are able to block channels formed in lipid bilayer membranes by the binding components of C2- and Iota-toxin. Similarly, these molecules protect cultured mammalian cells from intoxication with C2- and Iota-toxin. The aminoquinolinium salts did presumably not interfere with actin ADP-ribosylation or receptor binding but blocked the pores formed by C2IIa and Iota b in living cells and in vitro. The blocking efficiency of pores formed by Iota b and C2IIa by the chloroquine analogs showed interesting differences indicating structural variations between the types of protein-conducting nanochannels formed by Iota b and C2IIa.

  2. Adsorption, hydrogenation and dehydrogenation of C2H on a CoCu bimetallic layer

    Science.gov (United States)

    Wu, Donghai; Yuan, Jinyun; Yang, Baocheng; Chen, Houyang

    2018-05-01

    In this paper, adsorption, hydrogenation and dehydrogenation of C2H on a single atomic layer of bimetallic CoCu were investigated using first-principles calculations. The CoCu bimetallic layer is formed by Cu replacement of partial Co atoms on the top layer of a Co(111) surface. Our adsorption and reaction results showed those sites, which have stronger adsorption energy of C2H, possess higher reactivity. The bimetallic layer possesses higher reactivity than either of the pure monometallic layer. A mechanism of higher reactivity of the bimetallic layer is proposed and identified, i.e. in the bimetallic catalyst, the catalytic performance of one component is promoted by the second component, and in our work, the catalytic performance of Co atoms in the bimetallic layer are improved by introducing Cu atoms, lowing the activation barrier of the reaction of C2H. The bimetallic layer could tune adsorption and reaction of C2H by modulating the ratio of Co and Cu. Results of adsorption energies and adsorption configurations reveal that C2H prefers to be adsorbed in parallel on both the pure Co metallic and CoCu bimetallic layers, and Co atoms in subsurface which support the metallic or bimetallic layer have little effect on C2H adsorption. For hydrogenation reactions, the products greatly depend on the concentration and initial positions of hydrogen atoms, and the C2H hydrogenation forming acetylene is more favorable than forming vinylidene in both thermodynamics and kinetics. This study would provide fundamental guidance for hydrocarbon reactions on Co-based and/or Cu-based bimetallic surface chemistry and for development of new bimetallic catalysts.

  3. Diffusion of Ag, Au and Cs implants in MAX phase Ti3SiC2

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Weilin; Henager, Charles H.; Varga, Tamas; Jung, Hee Joon; Overman, Nicole R.; Zhang, Chonghong; Gou, Jie

    2015-05-16

    MAX phases (M: early transition metal; A: elements in group 13 or 14; X: C or N), such as titanium silicon carbide (Ti3SiC2), have a unique combination of both metallic and ceramic properties, which make them attractive for potential nuclear applications. Ti3SiC2 has been considered as a possible fuel cladding material. This study reports on the diffusivities of fission product surrogates (Ag and Cs) and a noble metal Au (with diffusion behavior similar to Ag) in this ternary compound at elevated temperatures, as well as in dual-phase nanocomposite of Ti3SiC2/3C-SiC and polycrystalline CVD 3C-SiC for behavior comparisons. Samples were implanted with Ag, Au or Cs ions and characterized with various methods, including x-ray diffraction, electron backscatter diffraction, energy dispersive x-ray spectroscopy, Rutherford backscattering spectrometry, helium ion microscopy, and transmission electron microscopy. The results show that in contrast to immobile Ag in 3C-SiC, there is a significant outward diffusion of Ag in Ti3SiC2 within the dual-phase nanocomposite during Ag ion implantation at 873 K. Similar behavior of Au in polycrystalline Ti3SiC2 was also observed. Cs out-diffusion and release from Ti3SiC2 occurred during post-implantation thermal annealing at 973 K. This study suggests caution and further studies in consideration of Ti3SiC2 as a fuel cladding material for advanced nuclear reactors operating at very high temperatures.

  4. Single-crystal study of the charge density wave metal LuNiC2

    Science.gov (United States)

    Steiner, S.; Michor, H.; Sologub, O.; Hinterleitner, B.; Höfenstock, F.; Waas, M.; Bauer, E.; Stöger, B.; Babizhetskyy, V.; Levytskyy, V.; Kotur, B.

    2018-05-01

    We report on single-crystal growth, single-crystal x-ray diffraction, physical properties, and density functional theory (DFT) electronic structure as well as Fermi surface calculations for two ternary carbides, LuCoC2 and LuNiC2. Electrical resistivity measurements reveal for LuNiC2 a charge density wave (CDW) transition at TCDW≃450 K and, for T >TCDW , a significant anisotropy of the electrical resistivity, which is lowest along the orthorhombic a axis. The analysis of x-ray superstructure reflections suggest a commensurate CDW state with a Peierls-type distortion of the Ni atom periodicity along the orthorhombic a axis. DFT calculations based on the CDW modulated monoclinic structure model of LuNiC2 as compared to results of the orthorhombic parent type reveal the formation of a partial CDW gap at the Fermi level which reduces the electronic density of states from N (EF)=1.03 states/eV f.u. without CDW to N (EF)=0.46 states/eV f.u. in the CDW state. The corresponding bare DFT Sommerfeld value of the latter, γDFTCDW=0.90 mJ/mol K2, reaches reasonable agreement with the experimental value γ =0.83 (5 ) mJ/mol K2 of LuNiC2. LuCoC2 displays a simple metallic behavior with neither CDW ordering nor superconductivity above 0.4 K. Its experimental Sommerfeld coefficient, γ =5.9 (1) mJ/mol K2, is in realistic correspondence with the calculated, bare Sommerfeld coefficient, γDFT=3.82 mJ/mol K2, of orthorhombic LuCoC2.

  5. The Verrucomicrobia LexA-binding Motif: Insights into the Evolutionary Dynamics of the SOS Response

    Directory of Open Access Journals (Sweden)

    Ivan Erill

    2016-07-01

    Full Text Available 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.

  6. 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.

  7. Discriminative Motif Discovery via Simulated Evolution and Random Under-Sampling

    OpenAIRE

    Song, Tao; Gu, Hong

    2014-01-01

    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 sta...

  8. Combined anterior C2-C3 fusion and C2 pedicle screw fixation for the treatment of unstable hangman's fracture: a contrast to anterior approach only.

    Science.gov (United States)

    Xie, Ning; Khoo, Larry T; Yuan, Wen; Ye, Xiao-Jian; Chen, De-Yu; Xiao, Jian-Ru; Ni, Bin

    2010-03-15

    A retrospective clinical study was used to evaluate the effect of a new surgical treatment of the hangman's fractures. To determine the treatment efficacy of combined anterior C2-C3 reduction and fusion and posterior compressive C2 pedicle screw fixation for the management of unstable hangman's fractures. The classification of hangman's fractures as proposed by Levine-Edwards was used to classify and guide the treatment of these injuries. Most of these fractures respond to a variety of conservative therapies, but recently, earlier surgery has been increasingly advocated by authors from several countries for the rapid stabilization of these fractures. If surgery is indicated, an anterior approach using a C2-C3 reduction and fusion is preferred usually. Another well-accepted surgical method is the direct transpedicular osteosynthesis by the dorsal approach. However, there was rare report of the combined use of these 2 techniques. A group of 45 surgical patients were all diagnosed with radiograph, magnetic resonance imaging (MRI), and 3D CT scans. Initial and final radiographs were measured for anterior translation and angulation of the C2-C3 complex. Initial external skull traction with extension was used in all patients after admission to reduce the fracture. Then an anterior C2-C3 discectomy followed by an interbody fusion and locking plate fixation was performed. Intraoperative reduction was confirmed by fluoroscopic control. About 29 patients therefore received anterior surgeries only since satisfactory reduction was achieved during the procedure. For the 16 patients who had persistent large residual gaps after the anterior procedure, additional same stage posterior C2 compressive pedicle screws were placed. Clinical and radiologic comparisons were performed in these 2 groups. The follow-up ranged from 24 to 54 months, with an average 33.6 months. There was radiographic evidence of continuity of the fracture and the bone graft seen at 4.7 months on average. Neck

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

    Science.gov (United States)

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

    2012-01-01

    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 for detecting logical inconsistencies as well as other anomalies represented by the motifs. MOCH represents patterns of multi-type interaction as small labeled (with multiple types of edges) 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, we performed exhaustive analyses of a variety of labeled sub-graph motifs. The quality assurance feature of MOCH comes from the distinct use of a subset of the edges of the graph motifs as constraints for disjointness, whereby bringing in rule-based flavor to the approach as well. With possible disjointness implied by antonyms, we performed manual inspection of the resulting FMA fragments and tracked down sources of abnormal inferred conclusions (logical inconsistencies), which are amendable for programmatic revision of the FMA. Our results demonstrate that MOCH provides 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. PMID:23304382

  10. An analysis of multi-type relational interactions in FMA using graph motifs with disjointness constraints.

    Science.gov (United States)

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

    2012-01-01

    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 for detecting logical inconsistencies as well as other anomalies represented by the motifs. MOCH represents patterns of multi-type interaction as small labeled (with multiple types of edges) 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, we performed exhaustive analyses of a variety of labeled sub-graph motifs. The quality assurance feature of MOCH comes from the distinct use of a subset of the edges of the graph motifs as constraints for disjointness, whereby bringing in rule-based flavor to the approach as well. With possible disjointness implied by antonyms, we performed manual inspection of the resulting FMA fragments and tracked down sources of abnormal inferred conclusions (logical inconsistencies), which are amendable for programmatic revision of the FMA. Our results demonstrate that MOCH provides 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.

  11. A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction.

    Science.gov (United States)

    Guo, Yuchun; Tian, Kevin; Zeng, Haoyang; Guo, Xiaoyun; Gifford, David Kenneth

    2018-04-13

    The representation and discovery of transcription factor (TF) sequence binding specificities is critical for understanding gene regulatory networks and interpreting the impact of disease-associated noncoding genetic variants. We present a novel TF binding motif representation, the k -mer set memory (KSM), which consists of a set of aligned k -mers that are overrepresented at TF binding sites, and a new method called KMAC for de novo discovery of KSMs. We find that KSMs more accurately predict in vivo binding sites than position weight matrix (PWM) models and other more complex motif models across a large set of ChIP-seq experiments. Furthermore, KSMs outperform PWMs and more complex motif models in predicting in vitro binding sites. KMAC also identifies correct motifs in more experiments than five state-of-the-art motif discovery methods. In addition, KSM-derived features outperform both PWM and deep learning model derived sequence features in predicting differential regulatory activities of expression quantitative trait loci (eQTL) alleles. Finally, we have applied KMAC to 1600 ENCODE TF ChIP-seq data sets and created a public resource of KSM and PWM motifs. We expect that the KSM representation and KMAC method will be valuable in characterizing TF binding specificities and in interpreting the effects of noncoding genetic variations. © 2018 Guo et al.; Published by Cold Spring Harbor Laboratory Press.

  12. 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.

  13. Creation of Hybrid Nanorods From Sequences of Natural Trimeric Fibrous Proteins Using the Fibritin Trimerization Motif

    Science.gov (United States)

    Papanikolopoulou, Katerina; van Raaij, Mark J.; Mitraki, Anna

    Stable, artificial fibrous proteins that can be functionalized open new avenues in fields such as bionanomaterials design and fiber engineering. An important source of inspiration for the creation of such proteins are natural fibrous proteins such as collagen, elastin, insect silks, and fibers from phages and viruses. The fibrous parts of this last class of proteins usually adopt trimeric, β-stranded structural folds and are appended to globular, receptor-binding domains. It has been recently shown that the globular domains are essential for correct folding and trimerization and can be successfully substituted by a very small (27-amino acid) trimerization motif from phage T4 fibritin. The hybrid proteins are correctly folded nanorods that can withstand extreme conditions. When the fibrous part derives from the adenovirus fiber shaft, different tissue-targeting specificities can be engineered into the hybrid proteins, which therefore can be used as gene therapy vectors. The integration of such stable nanorods in devices is also a big challenge in the field of biomechanical design. The fibritin foldon domain is a versatile trimerization motif and can be combined with a variety of fibrous motifs, such as coiled-coil, collagenous, and triple β-stranded motifs, provided the appropriate linkers are used. The combination of different motifs within the same fibrous molecule to create stable rods with multiple functions can even be envisioned. We provide a comprehensive overview of the experimental procedures used for designing, creating, and characterizing hybrid fibrous nanorods using the fibritin trimerization motif.

  14. Motif formation and industry specific topologies in the Japanese business firm network

    Science.gov (United States)

    Maluck, Julian; Donner, Reik V.; Takayasu, Hideki; Takayasu, Misako

    2017-05-01

    Motifs and roles are basic quantities for the characterization of interactions among 3-node subsets in complex networks. In this work, we investigate how the distribution of 3-node motifs can be influenced by modifying the rules of an evolving network model while keeping the statistics of simpler network characteristics, such as the link density and the degree distribution, invariant. We exemplify this problem for the special case of the Japanese Business Firm Network, where a well-studied and relatively simple yet realistic evolving network model is available, and compare the resulting motif distribution in the real-world and simulated networks. To better approximate the motif distribution of the real-world network in the model, we introduce both subgraph dependent and global additional rules. We find that a specific rule that allows only for the merging process between nodes with similar link directionality patterns reduces the observed excess of densely connected motifs with bidirectional links. Our study improves the mechanistic understanding of motif formation in evolving network models to better describe the characteristic features of real-world networks with a scale-free topology.

  15. GPUmotif: an ultra-fast and energy-efficient motif analysis program using graphics processing units.

    Science.gov (United States)

    Zandevakili, Pooya; Hu, Ming; Qin, Zhaohui

    2012-01-01

    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/

  16. 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/

  17. Short Arginine Motifs Drive Protein Stickiness in the Escherichia coli Cytoplasm.

    Science.gov (United States)

    Kyne, Ciara; Crowley, Peter B

    2017-09-19

    Although essential to numerous biotech applications, knowledge of molecular recognition by arginine-rich motifs in live cells remains limited. 1 H, 15 N HSQC and 19 F NMR spectroscopies were used to investigate the effects of C-terminal -GR n (n = 1-5) motifs on GB1 interactions in Escherichia coli cells and cell extracts. While the "biologically inert" GB1 yields high-quality in-cell spectra, the -GR n fusions with n = 4 or 5 were undetectable. This result suggests that a tetra-arginine motif is sufficient to drive interactions between a test protein and macromolecules in the E. coli cytoplasm. The inclusion of a 12 residue flexible linker between GB1 and the -GR 5 motif did not improve detection of the "inert" domain. In contrast, all of the constructs were detectable in cell lysates and extracts, suggesting that the arginine-mediated complexes were weak. Together these data reveal the significance of weak interactions between short arginine-rich motifs and the E. coli cytoplasm and demonstrate the potential of such motifs to modify protein interactions in living cells. These interactions must be considered in the design of (in vivo) nanoscale assemblies that rely on arginine-rich sequences.

  18. 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.

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

    Science.gov (United States)

    Song, Tao; Gu, Hong

    2014-01-01

    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.

  20. Improved i-motif thermal stability by insertion of anthraquinone monomers

    DEFF Research Database (Denmark)

    Gouda, Alaa S; Amine, Mahasen S.; Pedersen, Erik Bjerregaard

    2017-01-01

    In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA...... loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends...... unlocked nucleic acid monomers or twisted intercalating nucleic acid. The 2,6-disubstituted anthraquinone linker replacing T10 enabled a significant increase of i-motif thermal melting by 8.2 °C. A substantial increase of 5.0 °C in i-motif thermal melting was recorded when both A6 and T16 were modified...

  1. Fast social-like learning of complex behaviors based on motor motifs

    Science.gov (United States)

    Calvo Tapia, Carlos; Tyukin, Ivan Y.; Makarov, Valeri A.

    2018-05-01

    Social learning is widely observed in many species. Less experienced agents copy successful behaviors exhibited by more experienced individuals. Nevertheless, the dynamical mechanisms behind this process remain largely unknown. Here we assume that a complex behavior can be decomposed into a sequence of n motor motifs. Then a neural network capable of activating motor motifs in a given sequence can drive an agent. To account for (n -1 )! possible sequences of motifs in a neural network, we employ the winnerless competition approach. We then consider a teacher-learner situation: one agent exhibits a complex movement, while another one aims at mimicking the teacher's behavior. Despite the huge variety of possible motif sequences we show that the learner, equipped with the provided learning model, can rewire "on the fly" its synaptic couplings in no more than (n -1 ) learning cycles and converge exponentially to the durations of the teacher's motifs. We validate the learning model on mobile robots. Experimental results show that the learner is indeed capable of copying the teacher's behavior composed of six motor motifs in a few learning cycles. The reported mechanism of learning is general and can be used for replicating different functions, including, for example, sound patterns or speech.

  2. Peptide-binding motifs of two common equine class I MHC molecules in Thoroughbred horses.

    Science.gov (United States)

    Bergmann, Tobias; Lindvall, Mikaela; Moore, Erin; Moore, Eugene; Sidney, John; Miller, Donald; Tallmadge, Rebecca L; Myers, Paisley T; Malaker, Stacy A; Shabanowitz, Jeffrey; Osterrieder, Nikolaus; Peters, Bjoern; Hunt, Donald F; Antczak, Douglas F; Sette, Alessandro

    2017-05-01

    Quantitative peptide-binding motifs of MHC class I alleles provide a valuable tool to efficiently identify putative T cell epitopes. Detailed information on equine MHC class I alleles is still very limited, and to date, only a single equine MHC class I allele, Eqca-1*00101 (ELA-A3 haplotype), has been characterized. The present study extends the number of characterized ELA class I specificities in two additional haplotypes found commonly in the Thoroughbred breed. Accordingly, we here report quantitative binding motifs for the ELA-A2 allele Eqca-16*00101 and the ELA-A9 allele Eqca-1*00201. Utilizing analyses of endogenously bound and eluted ligands and the screening of positional scanning combinatorial libraries, detailed and quantitative peptide-binding motifs were derived for both alleles. Eqca-16*00101 preferentially binds peptides with aliphatic/hydrophobic residues in position 2 and at the C-terminus, and Eqca-1*00201 has a preference for peptides with arginine in position 2 and hydrophobic/aliphatic residues at the C-terminus. Interestingly, the Eqca-16*00101 motif resembles that of the human HLA A02-supertype, while the Eqca-1*00201 motif resembles that of the HLA B27-supertype and two macaque class I alleles. It is expected that the identified motifs will facilitate the selection of candidate epitopes for the study of immune responses in horses.

  3. Measurement of the Deuteron Spin Structure Function g_1^d(x) for 1 (GeV/c)^2 < Q^2 < 40 (GeV/c)^2

    OpenAIRE

    E155 Collaboration

    1999-01-01

    New measurements are reported on the deuteron spin structure function g_1^d. These results were obtained from deep inelastic scattering of 48.3 GeV electrons on polarized deuterons in the kinematic range 0.01 < x < 0.9 and 1 < Q^2 < 40 (GeV/c)^2. These are the first high dose electron scattering data obtained using lithium deuteride (6Li2H) as the target material. Extrapolations of the data were performed to obtain moments of g_1^d, including Gamma_1^d, and the net quark polarization Delta Si...

  4. Measurement of the deuteron spin structure function $g^{d}_1(x)$ for $1\\ (GeV/c)^2 < Q^2 < 40\\ (GeV/c)^2$.

    OpenAIRE

    Anthony , P.L.; Arnold , R.G.; Averett , T.; Band , H.R.; Berisso , M.C.; Borel , H.; Bosted , P.E.; Bultmann , S.L.; Buenerd , M.; Chupp , T.; Churchwell , S.; Court , G.R.; Crabb , D.; Day , D.; Decowski , P.

    1999-01-01

    New measurements are reported on the deuteron spin structure function g_1^d. These results were obtained from deep inelastic scattering of 48.3 GeV electrons on polarized deuterons in the kinematic range 0.01 < x < 0.9 and 1 < Q^2 < 40 (GeV/c)^2. These are the first high dose electron scattering data obtained using lithium deuteride (6Li2H) as the target material. Extrapolations of the data were performed to obtain moments of g_1^d, including Gamma_1^d, and the net quark polarization Delta Si...

  5. Management of C2-C3 fracture subluxation by anterior cervical approach and C2-C3 trans-cortical screw placement

    Directory of Open Access Journals (Sweden)

    Agrawal Amit

    2018-03-01

    Full Text Available Cervical spine injuries are the major cause of morbidity and mortality in trauma victims. Upper cervical spine injuries account for about 24% of acute fractures and dislocations and one third of fractures occur at the level of C2, while one half of injuries occur at the C6 or C7 levels. In contrast to this approach we used the transverse cervical, platysma splitting incision at a lower (C3-C4 disc to expose the upper cervical spine particularly lower border of C3 (entry point for the screw.

  6. Pressure-induced structural transformations and polymerization in ThC2

    Science.gov (United States)

    Guo, Yongliang; Yu, Cun; Lin, Jun; Wang, Changying; Ren, Cuilan; Sun, Baoxing; Huai, Ping; Xie, Ruobing; Ke, Xuezhi; Zhu, Zhiyuan; Xu, Hongjie

    2017-04-01

    Thorium-carbon systems have been thought as promising nuclear fuel for Generation IV reactors which require high-burnup and safe nuclear fuel. Existing knowledge on thorium carbides under extreme condition remains insufficient and some is controversial due to limited studies. Here we systematically predict all stable structures of thorium dicarbide (ThC2) under the pressure ranging from ambient to 300 GPa by merging ab initio total energy calculations and unbiased structure searching method, which are in sequence of C2/c, C2/m, Cmmm, Immm and P6/mmm phases. Among these phases, the C2/m is successfully observed for the first time via in situ synchrotron XRD measurements, which exhibits an excellent structural correspondence to our theoretical predictions. The transition sequence and the critical pressures are predicted. The calculated results also reveal the polymerization behaviors of the carbon atoms and the corresponding characteristic C-C bonding under various pressures. Our work provides key information on the fundamental material behavior and insights into the underlying mechanisms that lay the foundation for further exploration and application of ThC2.

  7. TERAHERTZ SPECTROSCOPY AND GLOBAL ANALYSIS OF THE BENDING VIBRATIONS OF ACETYLENE 12C2D2

    International Nuclear Information System (INIS)

    Yu Shanshan; Drouin, Brian J.; Pearson, John C.; Pickett, Herbert M.; Lattanzi, Valerio; Walters, Adam

    2009-01-01

    Two hundred and fifty-one 12 C 2 D 2 transitions have been measured in the 0.2-1.6 THz region of its ν 5 -ν 4 difference band and 202 of them were observed for the first time. The accuracy of these measurements is estimated to be ranging from 50 kHz to 100 kHz. The 12 C 2 D 2 molecules were generated under room temperature by passing 120-150 mTorr D 2 O vapor through calcium carbide (CaC 2 ) powder. A multistate analysis was carried out for the bending vibrational modes ν 4 and ν 5 of 12 C 2 D 2 , which includes the lines observed in this work and prior microwave, far-infrared and infrared data on the pure bending levels. Significantly improved molecular parameters were obtained for 12 C 2 D 2 by adding the new measurements to the old data set, which had only 10 lines with microwave measurement precision. New frequency and intensity predictions have been made based on the obtained molecular parameters. The more precise measurements and new predictions reported here will support the analyses of astronomical observations by the future high-resolution spectroscopy telescopes such as Herschel, SOFIA, and ALMA, which will work in the terahertz spectral region.

  8. Experimental and Kinetic Modeling Study of C2H2Oxidation at High Pressure

    DEFF Research Database (Denmark)

    Lopez, Jorge Gimenez; Rasmussen, Christian Tihic; Hashemi, Hamid

    2016-01-01

    diagram for C2H3 + O2 by Goldsmith et al. and on new ab initio calculations, respectively. The C2H2 + HO2 reaction involves nine pressure- and temperature-dependent product channels, with formation of triplet CHCHO being dominant under most conditions. The barrier to reaction for C2H2 + O2 was found......A detailed chemical kinetic model for oxidation of acetylene at intermediate temperatures and high pressure has been developed and evaluated experimentally. The rate coefficients for the reactions of C2H2 with HO2 and O2 were investigated, based on the recent analysis of the potential energy...... to be more than 50 kcal mol−1 and predictions of the initiation temperature were not sensitive to this reaction. Experiments were conducted with C2H2/O2 mixtures highly diluted in N2 in a high-pressure flow reactor at 600–900 K and 60 bar, varying the reaction stoichiometry from very lean to fuel...

  9. Mutation effects of C2+ ion irradiation on the greasy Nitzschia sp

    International Nuclear Information System (INIS)

    Yang, Y.N.; Liu, C.L.; Wang, Y.K.; Xue, J.M.

    2013-01-01

    Highlights: • The optimal conditions of C 2+ ion irradiation on Nitzschia sp. were discussed. • Get the “saddle type” survival curve. • One mutant whose lipid content improved significantly was selected. • The C 2+ ion irradiation didn’t change the algae's morphology and growth rate. - Abstract: Screening and nurturing algae with high productivity, high lipid content and strong stress resistance are very important in algae industry. In order to increase the lipid content, the Nitzschia sp. was irradiated with a 3 MeV C 2+ beam. The sample pretreatment method was optimized to obtain the best mutagenic condition and the survival ratio curve. The positive mutants with a significant improvement in lipid content were screened and their C 2+ mutagenic effects were analyzed by comparing the greasiness and growth characteristics with the wild type algae. Results showed that when the Nitzschia sp. was cultivated in nutritious medium containing 10% glycerol solution, and dried on the filter for 5 min after centrifugation, the realization of the microalgae heavy ion mutagenesis could be done. The survival ratio curve caused by C 2+ irradiation was proved to be “saddle-shaped”. A positive mutant was screened among 20 survivals after irradiation, the average lipid content of the mutation increased by 9.8% than the wild type after 4 generations. But the growth rate of the screened mutation didn’t change after the heavy ion implantation compared to the wild type algae

  10. Effect of curcumin Extract on Ttranslocation of Glut 4 in C2C12 Myotubes

    Directory of Open Access Journals (Sweden)

    J Zavarreza

    2013-06-01

    Full Text Available Introduction: Curcumin is a major phenolic compound of Curcuma longa, which has long been used in traditional Indian medicine. Recently, curcumin has been reported to have antihyperglycemic activity in animal models. However, the molecular basis of this action has not been adequatedly described. In the present study the antihyperglycemic effect of curcumin was examined using C2C12 myoblast cells. Methods: The effects of curcumin were investigated in C2C12 myotubes by treating the cells with 40 µM of curcumin for 1.5 h. C2C12 myotubes were homogenized and the subcellular fractionation was prepared using ultracentrifugation; Then protein assay was performed using Bradford method and Glut4 determination was done using SDS-PAGE. Moreover, western immunoblotting techniques were exerted for semi-quantitative measurement. Data analysis was performed via gene tools software of Gel documentation and SPSS. An ANOVA test was used to compare three groups together. Results: Comparison of Glut4 levels in C2C12 myotubes showed that myotubes which were exposed to1.5 hours of 40 µM curcunin had higher Glut4 percentages in both cytosolic and membrane fractions and Glut4 percentages were significant with a confidence interval (CI of 95% ( P<0.05 . Conclusion: The study results showed that curcumin can strongly induce the increase of Glut4 translocation in differentiated C2C12 cells, indicating its possible regulatory role in the glucose metabolism of skeletal muscle cells

  11. DRAGON, a GPI-anchored membrane protein, inhibits BMP signaling in C2C12 myoblasts.

    Science.gov (United States)

    Kanomata, Kazuhiro; Kokabu, Shoichiro; Nojima, Junya; Fukuda, Toru; Katagiri, Takenobu

    2009-06-01

    Bone morphogenetic proteins (BMPs) induce osteoblastic differentiation of myoblasts via binding to cell surface receptors. Repulsive guidance molecules (RGMs) have been identified as BMP co-receptors. We report here that DRAGON/RGMb, a member of the RGM family, suppressed BMP signaling in C2C12 myoblasts via a novel mechanism. All RGMs were expressed in C2C12 cells that were differentiated into myocytes and osteoblastic cells, but RGMc was not detected in immature cells. In C2C12 cells, only DRAGON suppressed ALP and Id1 promoter activities induced by BMP-4 or by constitutively activated BMP type I receptors. This inhibition by DRAGON was dependent on the secretory form of the von Willbrand factor type D domain. DRAGON even suppressed BMP signaling induced by constitutively activated Smad1. Over-expression of neogenin did not alter the inhibitory capacity of DRAGON. Taken together, these findings indicate that DRAGON may be an inhibitor of BMP signaling in C2C12 myoblasts. We also suggest that a novel molecule(s) expressed on the cell membrane may mediate the signal transduction of DRAGON in order to suppress BMP signaling in C2C12 myoblasts.

  12. Whole Device Modeling of Compact Tori: Stability and Transport Modeling of C-2W

    Science.gov (United States)

    Dettrick, Sean; Fulton, Daniel; Lau, Calvin; Lin, Zhihong; Ceccherini, Francesco; Galeotti, Laura; Gupta, Sangeeta; Onofri, Marco; Tajima, Toshiki; TAE Team

    2017-10-01

    Recent experimental evidence from the C-2U FRC experiment shows that the confinement of energy improves with inverse collisionality, similar to other high beta toroidal devices, NSTX and MAST. This motivated the construction of a new FRC experiment, C-2W, to study the energy confinement scaling at higher electron temperature. Tri Alpha Energy is working towards catalysing a community-wide collaboration to develop a Whole Device Model (WDM) of Compact Tori. One application of the WDM is the study of stability and transport properties of C-2W using two particle-in-cell codes, ANC and FPIC. These codes can be used to find new stable operating points, and to make predictions of the turbulent transport at those points. They will be used in collaboration with the C-2W experimental program to validate the codes against C-2W, mitigate experimental risk inherent in the exploration of new parameter regimes, accelerate the optimization of experimental operating scenarios, and to find operating points for future FRC reactor designs.

  13. Molecular basis of the specific subcellular localization of the C2-like domain of 5-lipoxygenase.

    Science.gov (United States)

    Kulkarni, Shilpa; Das, Sudipto; Funk, Colin D; Murray, Diana; Cho, Wonhwa

    2002-04-12

    The activation of 5-lipoxygenase (5-LO) involves its calcium-dependent translocation to the nuclear envelope, where it catalyzes the two-step transformation of arachidonic acid into leukotriene A(4), leading to the synthesis of various leukotrienes. To understand the mechanism by which 5-LO is specifically targeted to the nuclear envelope, we studied the membrane binding properties of the amino-terminal domain of 5-LO, which has been proposed to have a C2 domain-like structure. The model building, electrostatic potential calculation, and in vitro membrane binding studies of the isolated C2-like domain of 5-LO and selected mutants show that this Ca(2+)-dependent domain selectively binds zwitterionic phosphatidylcholine, which is conferred by tryptophan residues (Trp(13), Trp(75), and Trp(102)) located in the putative Ca(2+)-binding loops. The spatiotemporal dynamics of the enhanced green fluorescence protein-tagged C2-like domain of 5-LO and mutants in living cells also show that the phosphatidylcholine selectivity of the C2-like domain accounts for the specific targeting of 5-LO to the nuclear envelope. Together, these results show that the C2-like domain of 5-LO is a genuine Ca(2+)-dependent membrane-targeting domain and that the subcellular localization of the domain is governed in large part by its membrane binding properties.

  14. Tetrahedral silsesquioxane-C2H2Ti complex for hydrogen storage

    Science.gov (United States)

    Konda, Ravinder; Tavhare, Priyanka; Ingale, Nilesh; Chaudhari, Ajay

    2018-04-01

    The interaction of molecular hydrogen with tetrahedral silsesquioxane (T4)-C2H2Ti complex has been studied using Density Functional Theory with M06-2X functional and MP2 method with 6-311++G** basis set. T4-C2H2Ti complex can absorb maximum five hydrogen molecules with the gravimetric hydrogen storage capacity of 3.4 wt %. Adsorption energy calculations show that H2 adsorption on T4-C2H2Ti complex is favorable at room temperature by both the methods. We have studied the effect of temperature and pressure on Gibbs free energy corrected adsorption energies. Molecular dynamics simulations for H2 adsorbed T4-C2H2Ti complex have also been performed at 300K and show that loosely bonded H2 molecule flies away within 1fs. Various interaction energies within the complex are studied. Stability of a complex is predicted by means of a gap between Highest Occupied Molecular Orbital (HUMO) and Lowest Unoccupied Molecular Orbital (LUMO). The H2 desorption temperature for T4-C2H2Ti complex is calculated with Van't Hoff equation and it is found to be 229K.

  15. Structural and Functional Motifs in Influenza Virus RNAs

    Directory of Open Access Journals (Sweden)

    Damien Ferhadian

    2018-03-01

    have now been validated experimentally and their role in the viral life cycle demonstrated. This review aims to compile the structural motifs found in the different RNA classes (vRNA, cRNA, and vmRNA of influenza viruses and their function in the viral replication cycle.

  16. The CC2D1A, a member of a new gene family with C2 domains, is involved in autosomal recessive non-syndromic mental retardation.

    Science.gov (United States)

    Basel-Vanagaite, L; Attia, R; Yahav, M; Ferland, R J; Anteki, L; Walsh, C A; Olender, T; Straussberg, R; Magal, N; Taub, E; Drasinover, V; Alkelai, A; Bercovich, D; Rechavi, G; Simon, A J; Shohat, M

    2006-03-01

    The molecular basis of autosomal recessive non-syndromic mental retardation (NSMR) is poorly understood, mostly owing to heterogeneity and absence of clinical criteria for grouping families for linkage analysis. Only two autosomal genes, the PRSS12 gene on chromosome 4q26 and the CRBN on chromosome 3p26, have been shown to cause autosomal recessive NSMR, each gene in only one family. To identify the gene causing autosomal recessive NSMR on chromosome 19p13.12. The candidate region established by homozygosity mapping was narrowed down from 2.4 Mb to 0.9 Mb on chromosome 19p13.12. A protein truncating mutation was identified in the gene CC2D1A in nine consanguineous families with severe autosomal recessive NSMR. The absence of the wild type protein in the lymphoblastoid cells of the patients was confirmed. CC2D1A is a member of a previously uncharacterised gene family that carries two conserved motifs, a C2 domain and a DM14 domain. The C2 domain is found in proteins which function in calcium dependent phospholipid binding; the DM14 domain is unique to the CC2D1A protein family and its role is unknown. CC2D1A is a putative signal transducer participating in positive regulation of I-kappaB kinase/NFkappaB cascade. Expression of CC2D1A mRNA was shown in the embryonic ventricular zone and developing cortical plate in staged mouse embryos, persisting into adulthood, with highest expression in the cerebral cortex and hippocampus. A previously unknown signal transduction pathway is important in human cognitive development.

  17. The CC2D1A, a member of a new gene family with C2 domains, is involved in autosomal recessive non‐syndromic mental retardation

    Science.gov (United States)

    Basel‐Vanagaite, L; Attia, R; Yahav, M; Ferland, R J; Anteki, L; Walsh, C A; Olender, T; Straussberg, R; Magal, N; Taub, E; Drasinover, V; Alkelai, A; Bercovich, D; Rechavi, G; Simon, A J; Shohat, M

    2006-01-01

    Background The molecular basis of autosomal recessive non‐syndromic mental retardation (NSMR) is poorly understood, mostly owing to heterogeneity and absence of clinical criteria for grouping families for linkage analysis. Only two autosomal genes, the PRSS12 gene on chromosome 4q26 and the CRBN on chromosome 3p26, have been shown to cause autosomal recessive NSMR, each gene in only one family. Objective To identify the gene causing autosomal recessive NSMR on chromosome 19p13.12. Results The candidate region established by homozygosity mapping was narrowed down from 2.4 Mb to 0.9 Mb on chromosome 19p13.12. A protein truncating mutation was identified in the gene CC2D1A in nine consanguineous families with severe autosomal recessive NSMR. The absence of the wild type protein in the lymphoblastoid cells of the patients was confirmed. CC2D1A is a member of a previously uncharacterised gene family that carries two conserved motifs, a C2 domain and a DM14 domain. The C2 domain is found in proteins which function in calcium dependent phospholipid binding; the DM14 domain is unique to the CC2D1A protein family and its role is unknown. CC2D1A is a putative signal transducer participating in positive regulation of I‐κB kinase/NFκB cascade. Expression of CC2D1A mRNA was shown in the embryonic ventricular zone and developing cortical plate in staged mouse embryos, persisting into adulthood, with highest expression in the cerebral cortex and hippocampus. Conclusions A previously unknown signal transduction pathway is important in human cognitive development. PMID:16033914

  18. Empirical Study of Consumers' Purchase Intentions in C2C Electronic Commerce

    Institute of Scientific and Technical Information of China (English)

    HE Dehua; LU Yaobin; ZHOU Deyi

    2008-01-01

    Electronic commerce is becoming increasingly important in business, but lack of intention to purchase has become a main barrier in the development of electronic commerce. Thus, effective measures are needed to promote consumers' intentions to purchase in online consumer to consumer (C2C) stores. This paper postulates that five factors, the perceived ease of use of the website, perceived usefulness of the website, vendor competence, introduction and recommendations of third parties, and vendors' attitude toward customers, influence consumers' intentions to purchase in online C2C stores and this intention directly leads to their action to purchase from online C2C stores. The structural equation modeling (SEM) method was used to analyze empirical data, supporting these hypotheses except for the effect of vendor competence.

  19. Simultaneous occurrence of hereditary C6 and C2 deficiency in a French-Canadian family.

    Science.gov (United States)

    Delâge, J M; Lehner-Netsch, G; Lafleur, R; Simard, J; Brun, G; Prochazka, E

    1979-06-01

    The sera of four sisters were found to lack the sixth component of complement (C6) and the serum of one was also partially deficient in the second component (C2). Two other blood relatives were found to be heterozygous for both deficiencies, while only one sibling had normal values. The father of these eight siblings was heterozygous for C2D and C6D and in the third generation, six children were heterozygous for C6 deficiency was treated for chronic active brucel-transmitted; the C6 deficiency was not linked to the HLA system, while the C2-deficiency segregated with the haplotype A10,B18. The proband, homozygous for C6 deficiency was treated for chronic active Brucellosis and in another sibling with C6 deficiency, toxoplasmosis was diagnosed. Neither bleeding disorders nor a tendency to collagen diseases have been observed and the opsonic activity was normal in the sera of all family members.

  20. Experimental and kinetic modeling study of C2H4 oxidation at high pressure

    DEFF Research Database (Denmark)

    Lopez, Jorge Gimenez; Rasmussen, Christian Lund; Alzueta, Maria

    2009-01-01

    of conditions (0.003-100 bar, 200-3000 K). The results indicate that at 60 bar and medium temperatures vinyl peroxide, rather than CH2O and HCO, is the dominant product. The experiments, involving C2H4/O-2 mixtures diluted in N-2, were carried out in a high pressure flow reactor at 600-900 K and 60 bar, varying......A detailed chemical kinetic model for oxidation of C2H4 in the intermediate temperature range and high pressure has been developed and validated experimentally. New ab initio calculations and RRKM analysis of the important C2H3 + O-2 reaction was used to obtain rate coefficients over a wide range...

  1. The influence of collisional transfer effects on measured C2 Swan band transition probabilities

    International Nuclear Information System (INIS)

    Erman, P.

    1980-01-01

    Lifetime and relative intensities of the C 2 (d - a) Swan bands have been remeasured using the High Frequency Deflection technique, yielding tau(d, γ = 0-6) = 120 +- 4ns. With increasing pressure of the C 2 H 2 target gas strong second lifetime components occur revealing collisional transfers from other C 2 levles with rate coefficients around 6 X 10 -11 cm 3 s -1 mol -1 . These transfers are also observed with a number of other catalyser gases such as He, Ne, Ar, N 2 , and CO 2 . The transfer processes explain the considerably longer lifetimes reported in several earlier lifetime investigations and could be a clue to the formation mechanism of the carbon high pressure bands. (Auth.)

  2. Production of $\\chi_{c2}$ Mesons in Photon-Photon Collisions at LEP

    CERN Document Server

    Ackerstaff, K.; Allison, John; Altekamp, N.; Anderson, K.J.; Anderson, S.; Arcelli, S.; Asai, S.; Ashby, S.F.; Axen, D.; Azuelos, G.; Ball, A.H.; Barberio, E.; Barlow, Roger J.; Bartoldus, R.; Batley, J.R.; Baumann, S.; Bechtluft, J.; Behnke, T.; Bell, Kenneth Watson; Bella, G.; Bellerive, A.; Bentvelsen, S.; Bethke, S.; Betts, S.; Biebel, O.; Biguzzi, A.; Bird, S.D.; Blobel, V.; Bloodworth, I.J.; Bobinski, M.; Bock, P.; Bohme, J.; Boutemeur, M.; Braibant, S.; Bright-Thomas, P.; Brown, Robert M.; Burckhart, H.J.; Burgard, C.; Burgin, R.; Capiluppi, P.; Carnegie, R.K.; Carter, A.A.; Carter, J.R.; Chang, C.Y.; Charlton, David G.; Chrisman, D.; Ciocca, C.; Clarke, P.E.L.; Clay, E.; Cohen, I.; Conboy, J.E.; Cooke, O.C.; Couyoumtzelis, C.; Coxe, R.L.; Cuffiani, M.; Dado, S.; Dallavalle, G.Marco; Davis, R.; De Jong, S.; del Pozo, L.A.; De Roeck, A.; Desch, K.; Dienes, B.; Dixit, M.S.; Dubbert, J.; Duchovni, E.; Duckeck, G.; Duerdoth, I.P.; Eatough, D.; Estabrooks, P.G.; Etzion, E.; Evans, H.G.; Fabbri, F.; Fanfani, A.; Fanti, M.; Faust, A.A.; Fiedler, F.; Fierro, M.; Fleck, I.; Folman, R.; Furtjes, A.; Futyan, D.I.; Gagnon, P.; Gary, J.W.; Gascon, J.; Gascon-Shotkin, S.M.; Gaycken, G.; Geich-Gimbel, C.; Giacomelli, G.; Giacomelli, P.; Gibson, V.; Gibson, W.R.; Gingrich, D.M.; Glenzinski, D.; Goldberg, J.; Gorn, W.; Grandi, C.; Gross, E.; Grunhaus, J.; Gruwe, M.; Hanson, G.G.; Hansroul, M.; Hapke, M.; Harder, K.; Hargrove, C.K.; Hartmann, C.; Hauschild, M.; Hawkes, C.M.; Hawkings, R.; Hemingway, R.J.; Herndon, M.; Herten, G.; Heuer, R.D.; Hildreth, M.D.; Hill, J.C.; Hillier, S.J.; Hobson, P.R.; Hocker, James Andrew; Homer, R.J.; Honma, A.K.; Horvath, D.; Hossain, K.R.; Howard, R.; Huntemeyer, P.; Igo-Kemenes, P.; Imrie, D.C.; Ishii, K.; Jacob, F.R.; Jawahery, A.; Jeremie, H.; Jimack, M.; Jones, C.R.; Jovanovic, P.; Junk, T.R.; Karlen, D.; Kartvelishvili, V.; Kawagoe, K.; Kawamoto, T.; Kayal, P.I.; Keeler, R.K.; Kellogg, R.G.; Kennedy, B.W.; Klier, A.; Kluth, S.; Kobayashi, T.; Kobel, M.; Koetke, D.S.; Kokott, T.P.; Kolrep, M.; Komamiya, S.; Kowalewski, Robert V.; Kress, T.; Krieger, P.; von Krogh, J.; Kuhl, T.; Kyberd, P.; Lafferty, G.D.; Lanske, D.; Lauber, J.; Lautenschlager, S.R.; Lawson, I.; Layter, J.G.; Lazic, D.; Lee, A.M.; Lellouch, D.; Letts, J.; Levinson, L.; Liebisch, R.; List, B.; Littlewood, C.; Lloyd, A.W.; Lloyd, S.L.; Loebinger, F.K.; Long, G.D.; Losty, M.J.; Ludwig, J.; Lui, D.; Macchiolo, A.; Macpherson, A.; Mader, W.; Mannelli, M.; Marcellini, S.; Markopoulos, C.; Martin, A.J.; Martin, J.P.; Martinez, G.; Mashimo, T.; Mattig, Peter; McDonald, W.John; McKenna, J.; Mckigney, E.A.; McMahon, T.J.; McPherson, R.A.; Meijers, F.; Menke, S.; Merritt, F.S.; Mes, H.; Meyer, J.; Michelini, A.; Mihara, S.; Mikenberg, G.; Miller, D.J.; Mir, R.; Mohr, W.; Montanari, A.; Mori, T.; Nagai, K.; Nakamura, I.; Neal, H.A.; Nellen, B.; Nisius, R.; O'Neale, S.W.; Oakham, F.G.; Odorici, F.; Ogren, H.O.; Oreglia, M.J.; Orito, S.; Palinkas, J.; Pasztor, G.; Pater, J.R.; Patrick, G.N.; Patt, J.; Perez-Ochoa, R.; Petzold, S.; Pfeifenschneider, P.; Pilcher, J.E.; Pinfold, J.; Plane, David E.; Poffenberger, P.; Poli, B.; Polok, J.; Przybycien, M.; Rembser, C.; Rick, H.; Robertson, S.; Robins, S.A.; Rodning, N.; Roney, J.M.; Roscoe, K.; Rossi, A.M.; Rozen, Y.; Runge, K.; Runolfsson, O.; Rust, D.R.; Sachs, K.; Saeki, T.; Sahr, O.; Sang, W.M.; Sarkisian, E.K.G.; Sbarra, C.; Schaile, A.D.; Schaile, O.; Scharf, F.; Scharff-Hansen, P.; Schieck, J.; Schmitt, B.; Schmitt, S.; Schoning, A.; Schroder, Matthias; Schumacher, M.; Schwick, C.; Scott, W.G.; Seuster, R.; Shears, T.G.; Shen, B.C.; Shepherd-Themistocleous, C.H.; Sherwood, P.; Siroli, G.P.; Sittler, A.; Skuja, A.; Smith, A.M.; Snow, G.A.; Sobie, R.; Soldner-Rembold, S.; Sproston, M.; Stahl, A.; Stephens, K.; Steuerer, J.; Stoll, K.; Strom, David M.; Strohmer, R.; Surrow, B.; Talbot, S.D.; Tanaka, S.; Taras, P.; Tarem, S.; Teuscher, R.; Thiergen, M.; Thomson, M.A.; von Torne, E.; Torrence, E.; Towers, S.; Trigger, I.; Trocsanyi, Z.; Tsur, E.; Turcot, A.S.; Turner-Watson, M.F.; Van Kooten, Rick J.; Vannerem, P.; Verzocchi, M.; Voss, H.; Wackerle, F.; Wagner, A.; Ward, C.P.; Ward, D.R.; Watkins, P.M.; Watson, A.T.; Watson, N.K.; Wells, P.S.; Wermes, N.; White, J.S.; Wilson, G.W.; Wilson, J.A.; Wyatt, T.R.; Yamashita, S.; Yekutieli, G.; Zacek, V.; Zer-Zion, D.

    1998-01-01

    We present an observation at LEP of the production of chi_c2 mesons in the collisions of two quasi-real photons using the OPAL detector. The chi_c2 mesons are reconstructed in the decay channel Chi_c2 to J/psi gamma to l+l- gamma (with l= e,mu) using all data taken at e+e- centre-of-mass energies of 91 and 183 GeV, corresponding to integrated luminosities of 167 and 55 pb-1 respectively. The two-photon width of the Chi_2 is determined to be 1.76 +- 0.47 +- 0.37 +- 0.15 keV where the first error is statistical, the second is systematic and the third comes from branching ratio uncertainties.

  3. Neutron electric form factor up to Q2 = 1.47 GeV/c2

    International Nuclear Information System (INIS)

    Madey, Richard; Semenov, Andrei; Taylor, S.; Aghalaryan, Aram; Crouse, Erick; MacLachlan, Glen; Plaster, Bradley; Shigeyuki Tajima; William Tireman; Chenyu Yan; Abdellah Ahmidouch; Brian Anderson; Hartmuth Arenhovel; Razmik Asaturyan; Baker, O.; Alan Baldwin; Herbert Breuer; Roger Carlini; Christy, E.; Steve Churchwell; Leon Cole; Areg Danagoulian; Donal Day; Mostafa Elaasar; Rolf Ent; Manouchehr Farkhondeh; Howard Fenker; John Finn; Liping Gan; Kenneth Garrow; Paul Gueye; Calvin Howell; Bitao Hu; Mark Jones; James Kelly; Cynthia Keppel; Mahbubul Khandaker; Wooyoung Kim; Stanley Kowalski; Allison Lung; David Mack; Manley, D.; Pete Markowitz; Joseph Mitchell; Hamlet Mkrtchyan; Allena Opper; Charles Perdrisat; Vina Punjabi; Brian Raue; Tilmann Reichelt; Joerg Reinhold; Julie Roche; Yoshinori Sato; Irina Semenova; Wonick Seo; Neven Simicevic; Smith, G.; Samuel Stepanyan; Vardan Tadevosyan; Liguang Tang; Paul Ulmer; William Vulcan; Watson, J. W.; Steven Wells; Frank Wesselmann; Stephen Wood; Chen Yan; Seunghoon Yang; Lulin Yuan; Wei-Ming Zhang; Hong Guo Zhu; Xiaofeng Zhu

    2003-01-01

    The ratio of the electric to the magnetic form factor of the neutron, g /equiv G En /G Mn , was measured via recoil polarimetry (R.G. Arnold, C.E. Carlson, F. Gross, Phys. Rev. C 23, 363 (1981)) from the quasielastic 2 H (/mathop(e)/limitse' /mathop(n)/limits) 1H reaction at three values of Q 2 (viz, 0.45, 1.15, and 1.47 (GeV/c) 2 ) in Hall C of the Thomas Jefferson National Accelerator Facility. The data reveal that GEn continues to follow the Galster parameterization up to Q 2 = 1.15 (GeV/c) 2 and rises above the Galster parameterization at Q 2 = 1.47 (GeV/c) 2

  4. Occupancy of a C2-C2 type 'zinc-finger' protein domain by copper. Direct observation by electrospray ionization mass spectrometry.

    Science.gov (United States)

    Hutchens, T W; Allen, M H; Li, C M; Yip, T T

    1992-09-07

    The metal ion specificity of most 'zinc-finger' metal binding domains is unknown. The human estrogen receptor protein contains two different C2-C2 type 'zinc-finger' sequences within its DNA-binding domain (ERDBD). Copper inhibits the function of this protein by mechanisms which remain unclear. We have used electrospray ionization mass spectrometry to evaluate directly the 71-residue ERDBD (K180-M250) in the absence and presence of Cu(II) ions. The ERDBD showed a high affinity for Cu and was completely occupied with 4 Cu bound; each Cu ion was evidently bound to only two ligand residues (net loss of only 2 Da per bound Cu). The Cu binding stoichiometry was confirmed by atomic absorption. These results (i) provide the first direct physical evidence for the ability of the estrogen receptor DNA-binding domain to bind Cu and (ii) document a twofold difference in the Zn- and Cu-binding capacity. Differences in the ERDBD domain structure with bound Zn and Cu are predicted. Given the relative intracellular contents of Zn and Cu, our findings demonstrate the need to investigate further the Cu occupancy of this and other zinc-finger domains both in vitro and in vivo.

  5. Dual level reaction-path dynamics calculations on the C2H6 + OH → C2H5 + H2O reaction

    International Nuclear Information System (INIS)

    Coitino, E.L.; Truhlar, D.G.

    1996-01-01

    Interpolated Variational Transition State Theory with Multidimensional Tunneling contributions (IVTST/MT) has been applied to the reaction of C 2 H 6 + OH, and it yields rate constants that agree well with the available experimental information. The main disadvantage of this method is the difficulty of interpolating all required information from a few points along the reaction path. A more recent alternative is Variational Transition State Theory with Multidimensional Tunneling and Interpolated Corrections (VTST/MT-IC, also called dual-level direct dynamics), in which the reaction-path properties are first determined at an economical (lower) level of theory and then open-quotes correctedclose quotes using more accurate information obtained at a higher level for a selected number of points on the reaction path. The VTST/MT-IC method also allows for interpolation through die wider reaction swath when large-curvature tunneling occurs. In the present work we examine the affordability/accuracy tradeoff for several combinations of higher and lower levels for VTST/MT-IC reaction rate calculations on the C 2 H 6 + OH process. Various levels of theory (including NDDO-SRP and ab initio ROMP2, UQCISD, UQCISD(T), and UCCSD) have been employed for the electronic structure calculations. We also compare several semiclassical approaches implemented in the POLYRATE and MORATE programs for taking tunneling effects into account

  6. Characterization of an acute muscle contraction model using cultured C2C12 myotubes.

    Directory of Open Access Journals (Sweden)

    Yasuko Manabe

    Full Text Available A cultured C2C12 myotube contraction system was examined for application as a model for acute contraction-induced phenotypes of skeletal muscle. C2C12 myotubes seeded into 4-well rectangular plates were placed in a contraction system equipped with a carbon electrode at each end. The myotubes were stimulated with electric pulses of 50 V at 1 Hz for 3 ms at 997-ms intervals. Approximately 80% of the myotubes were observed to contract microscopically, and the contractions lasted for at least 3 h with electrical stimulation. Calcium ion (Ca²⁺ transient evoked by the electric pulses was detected fluorescently with Fluo-8. Phosphorylation of protein kinase B/Akt (Akt, 5' AMP-activated protein kinase (AMPK, p38 mitogen-activated protein kinase (p38, and c-Jun NH2-terminal kinase (JNK1/2, which are intracellular signaling proteins typically activated in exercised/contracted skeletal muscle, was observed in the electrically stimulated C2C12 myotubes. The contractions induced by the electric pulses increased glucose uptake and depleted glycogen in the C2C12 myotubes. C2C12 myotubes that differentiated after exogenous gene transfection by a lipofection or an electroporation method retained their normal contractile ability by electrical stimulation. These findings show that our C2C12 cell contraction system reproduces the muscle phenotypes that arise invivo (exercise, in situ (hindlimb muscles in an anesthetized animal, and invitro (dissected muscle tissues in incubation buffer by acute muscle contraction, demonstrating that the system is applicable for the analysis of intracellular events evoked by acute muscle contraction.

  7. Nature of the C2-methylation effect on the properties of imidazolium ionic liquids.

    Science.gov (United States)

    Rodrigues, Ana S M C; Lima, Carlos F R A C; Coutinho, João A P; Santos, Luís M N B F

    2017-02-15

    Methylation at the C2 position of 1,3-disubstituted imidazolium-based ionic liquids (ILs) is one of the structural features that has gained attention due to its drastic impact on thermophysical and transport properties. Several hypotheses have been proposed to explain this effect but there is still much discrepancy. Aiming for the rationalization of the effects of these structural features on the properties of imidazolium ILs, we present a thermodynamic and computational study of two methylated ILs at the C2 position of imidazolium, [ 1 C 4 2 C 1 3 C 1 im][NTf 2 ] and [ 1 C 3 2 C 1 3 C 1 im][NTf 2 ]. The phase behaviour (glass transition and vaporization equilibrium) and computational studies of the anion rotation around the cation and ion pair interaction energies for both ILs were explored. The results have shown that C2-methylation has no impact on the enthalpy of vaporization. However, it decreases the entropy of vaporization, which is a consequence of the change in the ion pair dynamics that affects both the liquid and gas phases. In addition, the more hindered dynamics of the ion pair are also reflected in the increase in the glass transition temperature, T g . The entropic contribution of anion-around-cation rotation in the imidazolium [NTf 2 ] ILs was quantified experimentally by the comparative analysis of the entropy of vaporization, and computationally by the calculation of the entropies of hindered internal rotation. The global results exclude the existence of significant H-bonding in the C2-protonated (non-methylated) ILs and explain the C2-methylation effect in terms of reduced entropy of the ion pair in the liquid and gas phases. In light of these results, the C2-methylation effect is intrinsically entropic and originates from the more hindered anion-around-cation rotation as a consequence of the substitution of the -H with a bulkier -CH 3 group.

  8. Clinical Outcomes of Posterior C1 and C2 Screw-Rod Fixation for Atlantoaxial Instability.

    Science.gov (United States)

    Işik, Hasan Serdar; Sandal, Evren; Çağli, Sedat

    2017-06-14

    In this study, we aimed at sharing our experiences and contributing to the literature by making a retrospective analysis of the patients we operated with screw-rod system for atlantoaxial instability in our clinic. Archive files of adult patients, who were operated for posterior C1-C2 stabilization with screw and rod in our clinic between January 2006 and January 2016, were analyzed. 28 patients, who had pre and post-operative images, follow-up forms and who were followed for at least one year, were analyzed. Preoperative clinical and radiological records, preoperative observations, postoperative complications, and clinical responses were evaluated. The average age of 28 patients (F:13 M:19) was 44.7 (21-73). Fixation was performed with C1-C2 screw-rod system on the basis of the following diagnoses; type 2 odontoid fracture (16), basilar invagination (5), C1-C2 instability (5), and atlantoaxial subluxation secondary to rheumatoid arthritis (2). Lateral mass screws were inserted at C1 segment. C2 screws inserted were bilateral pedicle in 12 cases, bilateral pars in 4, bilateral laminar in 8 and one side pars, one side laminar in 4 cases. There was no screw malposition. Neither implant failure nor recurrent instability was observed during follow-up. Significant clinical improvement was reported according to the assessments done with JOA and VAS scores. C1-C2 screw fixation is regarded as a more successful and safe method than other fixation methods in surgical treatment of atlantoaxial instability considering complications, success in reduction, fusion and fixation strength. C2 laminar screw technique is as successful as the other alternatives in fixation and fusion.

  9. Saturable Absorption in 2D Ti3 C2 MXene Thin Films for Passive Photonic Diodes.

    Science.gov (United States)

    Dong, Yongchang; Chertopalov, Sergii; Maleski, Kathleen; Anasori, Babak; Hu, Longyu; Bhattacharya, Sriparna; Rao, Apparao M; Gogotsi, Yury; Mochalin, Vadym N; Podila, Ramakrishna

    2018-03-01

    MXenes comprise a new class of 2D transition metal carbides, nitrides, and carbonitrides that exhibit unique light-matter interactions. Recently, 2D Ti 3 CNT x (T x represents functional groups such as OH and F) was found to exhibit nonlinear saturable absorption (SA) or increased transmittance at higher light fluences, which is useful for mode locking in fiber-based femtosecond lasers. However, the fundamental origin and thickness dependence of SA behavior in MXenes remain to be understood. 2D Ti 3 C 2 T x thin films of different thicknesses are fabricated using an interfacial film formation technique to systematically study their nonlinear optical properties. Using the open aperture Z-scan method, it is found that the SA behavior in Ti 3 C 2 T x MXene arises from plasmon-induced increase in the ground state absorption at photon energies above the threshold for free carrier oscillations. The saturation fluence and modulation depth of Ti 3 C 2 T x MXene is observed to be dependent on the film thickness. Unlike other 2D materials, Ti 3 C 2 T x is found to show higher threshold for light-induced damage with up to 50% increase in nonlinear transmittance. Lastly, building on the SA behavior of Ti 3 C 2 T x MXenes, a Ti 3 C 2 T x MXene-based photonic diode that breaks time-reversal symmetry to achieve nonreciprocal transmission of nanosecond laser pulses is demonstrated. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Memetic algorithms for de novo motif-finding in biomedical sequences.

    Science.gov (United States)

    Bi, Chengpeng

    2012-09-01

    The objectives of this study are to design and implement a new memetic algorithm for de novo motif discovery, which is then applied to detect important signals hidden in various biomedical molecular sequences. In this paper, memetic algorithms are developed and tested in de novo motif-finding problems. Several strategies in the algorithm design are employed that are to not only efficiently explore the multiple sequence local alignment space, but also effectively uncover the molecular signals. As a result, there are a number of key features in the implementation of the memetic motif-finding algorithm (MaMotif), including a chromosome replacement operator, a chromosome alteration-aware local search operator, a truncated local search strategy, and a stochastic operation of local search imposed on individual learning. To test the new algorithm, we compare MaMotif with a few of other similar algorithms using simulated and experimental data including genomic DNA, primary microRNA sequences (let-7 family), and transmembrane protein sequences. The new memetic motif-finding algorithm is successfully implemented in C++, and exhaustively tested with various simulated and real biological sequences. In the simulation, it shows that MaMotif is the most time-efficient algorithm compared with others, that is, it runs 2 times faster than the expectation maximization (EM) method and 16 times faster than the genetic algorithm-based EM hybrid. In both simulated and experimental testing, results show that the new algorithm is compared favorably or superior to other algorithms. Notably, MaMotif is able to successfully discover the transcription factors' binding sites in the chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) data, correctly uncover the RNA splicing signals in gene expression, and precisely find the highly conserved helix motif in the transmembrane protein sequences, as well as rightly detect the palindromic segments in the primary micro

  11. Endovascular Treatment of a Vertebral Artery Pseudoaneurysm Following Posterior C1-C2 Transarticular Screw Fixation

    International Nuclear Information System (INIS)

    Mendez, Jose C.; Gonzalez-Llanos, Francisco

    2005-01-01

    We present a case of vertebral artery pseudoaneurysm after a posterior C1-C2 transarticular screw fixation procedure that was effectively treated with endovascular coil occlusion. Vertebral artery pseudoaneurysm complicating posterior C1-C2 transarticular fixation is extremely rare, with only one previous case having been reported previously. Endovascular occlusion is better achieved in the subacute phase of the pseudoaneurysm, when the wall of the pseudoaneurysm has matured and stabilized. Further follow-up angiographies are mandatory in order to confirm that there is no recurrence of the lesion

  12. Fragmentation of C2H4 by charge-changing collisions of O2+ ions

    International Nuclear Information System (INIS)

    Sato, S.; Mizuno, T.; Yamada, T.; Imai, M.; Shibata, H.; Itoh, A.; Tsuchida, H.

    2009-01-01

    We investigated molecular fragmentation of C 2 H 4 in charge-changing collisions of 1.14MeV O 2+ ions. Branching ratios associated with decaying from temporary produced (C 2 H 4 ) r+ ions into various fragment channels were obtained. Dissociation via a C-C bond breaking is preferential in 1-electron loss collisions in comparison with 1-electron capture collisions. We confirmed that multiple ionization and dissociation rarely occur in electron capture collisions, while they occur rather strongly in electron loss collisions. (author)

  13. Evidences for existence of a strange meson with the 1627 MeV/c2 mass

    International Nuclear Information System (INIS)

    Karnaukhov, V.M.; Moroz, V.I.; Coca, C.

    1995-01-01

    The narrow structure with Μ=(1627±4) MeV/c 2 and Γ=(12 -12 +14 ) MeV/c 2 is observable in π - p interactions at 16 GeV/c in 6 effective mass spectra of the Kmπ systems. In the summed spectrum the number of standard deviations in the structure region over the background is 10. A performed compilative analysis of paper results on the study of strange meson resonances in various experiments does not contradict indication for the existence of K(1627)-meson, a narrow enhancement is observed in the same mass region. (author). 21 refs., 4 figs

  14. Role of metabolites and calcineurin inhibition on C2 monitoring in renal transplant patients

    DEFF Research Database (Denmark)

    Karamperis, N.; Koefoed-Nielsen, P.; Bagger, Sorensen A.

    2005-01-01

    BACKGROUND: Many transplantation centres have switched to C2 monitoring of cyclosporin-treated renal transplant patients. The rationale is that the C2 correlates best with AUC0-4 (area under the concentration-time curve), which again correlates with rejection and nephrotoxicity. It has also been...... metabolites were added to whole blood from healthy volunteers and the calcineurin phosphatase activity (CaN) was determined. Twenty renal transplant patients at varying times after transplantation had blood samples drawn in the morning before and 1, 2, 3 and 4 h after intake of their usual dose of cyclosporin...

  15. The diabetogenic VPS13C/C2CD4A/C2CD4B rs7172432 variant impairs glucose-stimulated insulin response in 5,722 non-diabetic Danish individuals

    DEFF Research Database (Denmark)

    Grarup, N; Overvad, M; Sparsø, T

    2011-01-01

    A genome-wide association study in the Japanese population reported two genome-wide significant loci associated with type 2 diabetes of which the VPS13C/C2CD4A/C2CD4B locus was replicated in Europeans. We looked for potential associations between the diabetogenic VPS13C/C2CD4A/C2CD4B rs7172432 va...

  16. Disparate requirements for the Walker A and B ATPase motifs of human RAD51D in homologous recombination.

    Science.gov (United States)

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

    2006-01-01

    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 (ICLs). 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.

  17. 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.

  18. 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.

  19. 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.

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

    KAUST Repository

    Alam, Tanvir; Alazmi, Meshari; Gao, Xin; Arold, Stefan T.

    2014-01-01

    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.

  1. Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins

    Science.gov (United States)

    Chatterjee, Raghunath; Zhao, Jianfei; He, Ximiao; Shlyakhtenko, Andrey; Mann, Ishminder; Waterfall, Joshua J.; Meltzer, Paul; Sathyanarayana, B. K.; FitzGerald, Peter C.; Vinson, Charles

    2012-01-01

    Previously, we identified 8-bps long DNA sequences (8-mers) that localize in human proximal promoters and grouped them into known transcription factor binding sites (TFBS). We now examine split 8-mers consisting of two 4-mers separated by 1-bp to 30-bps (X4-N1-30-X4) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif (C/GCCGGAAGCGGAA) and the ETS⇔CRE motif (C/GCGGAAGTGACGTCAC). The nucleotides in bold are part of both TFBS. Molecular modeling shows that the ETS⇔CRE motif can be bound simultaneously by both the ETS and the B-ZIP domains without protein-protein clashes. The electrophoretic mobility shift assay (EMSA) shows that the ETS protein GABPα and the B-ZIP protein CREB preferentially bind to the ETS⇔CRE motif only when the two TFBS overlap precisely. In contrast, the ETS domain of ETV5 and CREB interfere with each other for binding the ETS⇔CRE. The 11-mer (CGGAAGTGACG), the conserved part of the ETS⇔CRE motif, occurs 226 times in the human genome and 83% are in known regulatory regions. In vivo GABPα and CREB ChIP-seq peaks identified the ETS⇔CRE as the most enriched motif occurring in promoters of genes involved in mRNA processing, cellular catabolic processes, and stress response, suggesting that a specific class of genes is regulated by this composite motif. PMID:23050235

  2. 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

  3. Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria.

    Science.gov (United States)

    Sun, Eric I; Leyn, Semen A; Kazanov, Marat D; Saier, Milton H; Novichkov, Pavel S; Rodionov, Dmitry A

    2013-09-02

    In silico comparative genomics approaches have been efficiently used for functional prediction and reconstruction of metabolic and regulatory networks. Riboswitches are metabolite-sensing structures often found in bacterial mRNA leaders controlling gene expression on transcriptional or translational levels.An increasing number of riboswitches and other cis-regulatory RNAs have been recently classified into numerous RNA families in the Rfam database. High conservation of these RNA motifs provides a unique advantage for their genomic identification and comparative analysis. A comparative genomics approach implemented in the RegPredict tool was used for reconstruction and functional annotation of regulons controlled by RNAs from 43 Rfam families in diverse taxonomic groups of Bacteria. The inferred regulons include ~5200 cis-regulatory RNAs and more than 12000 target genes in 255 microbial genomes. All predicted RNA-regulated genes were classified into specific and overall functional categories. Analysis of taxonomic distribution of these categories allowed us to establish major functional preferences for each analyzed cis-regulatory RNA motif family. Overall, most RNA motif regulons showed predictable functional content in accordance with their experimentally established effector ligands. Our results suggest that some RNA motifs (including thiamin pyrophosphate and cobalamin riboswitches that control the cofactor metabolism) are widespread and likely originated from the last common ancestor of all bacteria. However, many more analyzed RNA motifs are restricted to a narrow taxonomic group of bacteria and likely represent more recent evolutionary innovations. The reconstructed regulatory networks for major known RNA motifs substantially expand the existing knowledge of transcriptional regulation in bacteria. The inferred regulons can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. The obtained genome

  4. 14C2H4: distribution of 14C-labeled tissue metabolites in pea seedlings

    International Nuclear Information System (INIS)

    Giaquinta, R.; Beyer, E. Jr.

    1977-01-01

    The 14 C-metabolite distribution pattern following 14 C 2 H 4 metabolism in intact pea seedlings (Pisum sativum L.) was determined under various conditions. After a 24 hr exposure to 14 C 2 H 4 , the majority of 14 C-metabolites were water-soluble (60-70%) with lesser amounts in the protein (10-15%), lipid (1%), and insoluble (1-2%) fractions. Ion exchange chromatography of the water-soluble components into basic, neutral, and acidic fractions revealed a 50:40:10 distribution, respectively. Chromatography of the neutral fraction revealed two regions of radioactivity (Rf=0.38) and 0.63 which did not cochromatograph with twenty-two known sugars or neutral metabolites. Chromatograms of the basic fraction contained 3 regions of radioactivity. Similar distribution patterns were noted when 14 C 2 H 4 exposure was followed by a 6 hr air chase or when 5% CO 2 , an antagonist of ethylene action, was present during the exposure. Marked differences in the 14 C-metabolite distribution patterns were obtained when 14 CO 2 was substituted for 14 C 2 H 4 . These results indicate that the metabolic pathway involved in ethylene metabolism is different from that involved in intermediately carbon metabolism. (auth.)

  5. Crystal-field splitting in coadsorbate systems: c (2x2) CO/K/Ni (100)

    NARCIS (Netherlands)

    Hasselström, J.; Föhlisch, A.; Denecke, R.; Nilsson, A.; Groot, F.M.F. de

    2000-01-01

    It is demonstrated how the crystal field splitting (CFS) fine structure can be used to characterize a coadsor-bate system. We have applied K 2p x-ray absorption spectroscopy (XAS) to the c(2x2) CO/K/Ni(100) system. The CFS fine structure is shown to be sensitive to the the local atomic

  6. Functional aspects of dexamethasone upregulated nicotinic acetylcholine receptors in C2C12 myotubes

    NARCIS (Netherlands)

    Maestrone, E; Lagostena, L; Henning, RH; DenHertog, A; Nobile, M

    Three days of treatment with the glucocorticoid dexamethasone (1 nM-mu M) induced a concentration-dependent up-regulation of muscle nicotinic acetylcholine receptor (nAChR) in C2C12 mouse myotubes (EC(50)=10+/-7.3 nM), as assessed by [H-3]alpha-BuTx binding. The maximum increase in binding amounted

  7. A Proposed Engineering Process and Prototype Toolset for Developing C2-to-Simulation Interoperability Solutions

    NARCIS (Netherlands)

    Gautreau, B.; Khimeche, L.; Reus, N.M. de; Heffner, K.; Mevassvik, O.M.

    2014-01-01

    The Coalition Battle Management Language (C-BML) is an open standard being developed for the exchange of digitized military information among command and control (C2), simulation and autonomous systems by the Simulation Interoperability Standards Organization (SISO). As the first phase of the C-BML

  8. Die 'Proslogion C2-4' van Anselmus van Kantelberg (1033/34-1109 ...

    African Journals Online (AJOL)

    The Proslogion, C2-4 of Anselm of Canterbury (1033/34-1109) In Protestant circles students and lecturers usually know the 'ontological' (a name given by Kant) proof for the existence of God of Anselm, mostly only from selected sentences and critical arguments about this 'proof. In this article the full Latin text of Anselm's ...

  9. Die 'Proslogion C2-4' van Anselmus van Kantelberg (1033/34-1109 ...

    African Journals Online (AJOL)

    The Proslogion, C2-4 of Anselm of Canterbury. (1033/34-1109). In Protestant circles students and lecturers usually know the 'ontological' (a name given by Kant) proof for the existence of God of Anselm, mostly only from selected sentences and critical arguments about this 'proof. In this article the full Latin text of Anselm's ...

  10. 26 CFR 31.3306(c)(2)-1 - Domestic service.

    Science.gov (United States)

    2010-04-01

    ... SOURCE Federal Unemployment Tax Act (Chapter 23, Internal Revenue Code of 1954) § 31.3306(c)(2)-1... maintained by an individual in an apartment house, hotel, or other similar establishment may constitute a... lodging houses, boarding houses, clubs (except local college clubs), hotels, hospitals, eleemosynary...

  11. Oxidation-induced crack healing in Ti3AlC2 ceramics

    NARCIS (Netherlands)

    Song, G.M.; Pei, Y.T.; Sloof, W.G.; Li, S.B.; Hosson, J.Th.M. De; Zwaag, S. van der

    Crack healing of Ti3AlC2 was investigated by oxidizing a partially pre-cracked sample. A crack near a notch was introduced into the sample by tensile deformation. After oxidation at 1100 degrees C in air for 2 h, the crack was completely healed, with oxidation products consisting primarily of

  12. New Ti3C2 aerogel as promising negative electrode materials for asymmetric supercapacitors

    Science.gov (United States)

    Li, Lu; Zhang, Mingyi; Zhang, Xitian; Zhang, Zhiguo

    2017-10-01

    Novel 3D Ti3C2 aerogel has been first synthesized by a simple EDA-assisted self-assembly process. Its inside are channels and pores structure. The interconnected aerogel structure could efficiently restrain restacking of Ti3C2 flakes. Thus, it exhibits a large specific surface area as high as 176.3 m2 g-1. The electrochemical performances have been measured. The Ti3C2 aerogel achieves a quite high areal capacitance of 1012.5 mF cm-2 for the mass loading of 15 mg at a scan rate of 2 mV s-1 in 1 M KOH electrolyte. An asymmetric supercapacitor (ASC) has been assembled by using the Ti3C2 aerogel electrode as the negative electrode and electrospinning carbon nanofiber film as the positive electrode. The device can deliver a high energy density of 120.0 μWh cm-2 and a maximum power density of 26123 μW cm-2. A lamp panel with nineteen red light-emitting diodes has been powered by two ASCs in series.

  13. Impaired ALDH2 activity decreases the mitochondrial respiration in H9C2 cardiomyocytes.

    Science.gov (United States)

    Mali, Vishal R; Deshpande, Mandar; Pan, Guodong; Thandavarayan, Rajarajan A; Palaniyandi, Suresh S

    2016-02-01

    Reactive oxygen species (ROS)-mediated reactive aldehydes induce cellular stress. In cardiovascular diseases such as ischemia-reperfusion injury, lipid-peroxidation derived reactive aldehydes such as 4-hydroxy-2-nonenal (4HNE) are known to contribute to the pathogenesis. 4HNE is involved in ROS formation, abnormal calcium handling and more importantly defective mitochondrial respiration. Aldehyde dehydrogenase (ALDH) superfamily contains NAD(P)(+)-dependent isozymes which can detoxify endogenous and exogenous aldehydes into non-toxic carboxylic acids. Therefore we hypothesize that 4HNE afflicts mitochondrial respiration and leads to cell death by impairing ALDH2 activity in cultured H9C2 cardiomyocyte cell lines. H9C2 cardiomyocytes were treated with 25, 50 and 75 μM 4HNE and its vehicle, ethanol as well as 25, 50 and 75 μM disulfiram (DSF), an inhibitor of ALDH2 and its vehicle (DMSO) for 4 h. 4HNE significantly decreased ALDH2 activity, ALDH2 protein levels, mitochondrial respiration and mitochondrial respiratory reserve capacity, and increased 4HNE adduct formation and cell death in cultured H9C2 cardiomyocytes. ALDH2 inhibition by DSF and ALDH2 siRNA attenuated ALDH2 activity besides reducing ALDH2 levels, mitochondrial respiration and mitochondrial respiratory reserve capacity and increased cell death. Our results indicate that ALDH2 impairment can lead to poor mitochondrial respiration and increased cell death in cultured H9C2 cardiomyocytes. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Selective conversion of synthesis gas into C2-oxygenated products using mixed-metal homogeneous catalysts

    International Nuclear Information System (INIS)

    Whyman, R.

    1986-01-01

    A feature which is a key to any wider utilization of chemistry based on synthesis gas is an understanding of, and more particularly, an ability to control, those factors which determine the selectivity of the C 1 to C 2 transformation during the hydrogenation of carbon monoxide. With the exception of the rhodium-catalyzed conversion of carbon monoxide and hydrogen into ethylene glycol and methanol, in which molar ethylene glycol/methanol selectivities of ca 2/1 may be achieved, other catalyst systems containing metals such as cobalt or ruthenium exhibit only poor selectivities to ethylene glycol. The initial studies in this area were based on the reasoning that, since the reduction of carbon monoxide to C 2 products is a complex, multi-step process, the use of appropriate combinations of metals could generate synergistic effects which might prove more effective (in terms of both catalytic activity and selectivity) than simply the sum of the individual metal components. In particular, the concept of the combination of a good hydrogenation catalyst with a good carbonylation, or ''CO insertion'', catalyst seemed particularly germane. As a result of this approach the authors discovered an unprecedented example of the effect of catalyst promoters, particularly in the enhancement of C 2 /C 1 selectivity, and one which has led to the development of composite mixed-metal homogeneous catalyst systems for the conversion of CO/H 2 into C 2 -oxygenate esters

  15. C2 Product-Centric Approach to Transforming Current C4ISR Information Architectures

    Science.gov (United States)

    2004-06-01

    SAML) Privacy (P3P) Digital Rights Management (XrML) Content Mngmnt (DASL) (WebDAV) Content Syndicat’n (ICE) (RSS) Ontology (OML) (OWL) Resource...RNIF Registry/ Repository BPSS eCommerce XML/EDI Universal Business Language (UBL) Internet & Computing Human Resources (HR-XML) Semantic C2RM

  16. Calcium carbide (CaC2): Effect on fruit set and yield of mango ...

    African Journals Online (AJOL)

    Reviewer

    contains nitrogen in both the ammonium and nitrate form, less subject to ... soil reacts with soil water to produce calcium ion and acetylene (C2H2). ..... nitrification inhibitors on methane and nitrous oxide fluxes in irrigated corn. pp. 278-289.

  17. A functional study of the rat olfactory bulb through autoradiography with 14C-2-deoxyglucose

    International Nuclear Information System (INIS)

    Verrier, Marie; Leveteau, Jean; Giachetti, Ismene; MacLeod, Patrick

    1978-01-01

    The autoradiographic methods has been used in the rat to map active regions in the olfactory bulb after a pulse of 14 C-2-deoxyglucose with electrical stimulation of the lateral olfactory tract. The highest optical densities were found at the external plexiform, mural, internal plexiform and granular layers: the lowest was found in the glomerular layer [fr

  18. Fluoride induces apoptosis in H9c2 cardiomyocytes via the mitochondrial pathway.

    Science.gov (United States)

    Yan, Xiaoyan; Wang, Lu; Yang, Xia; Qiu, Yulan; Tian, Xiaolin; Lv, Yi; Tian, Fengjie; Song, Guohua; Wang, Tong

    2017-09-01

    Numerous studies have shown that chronic excessive fluoride intake can adversely affect different organ systems. In particular, the cardiovascular system is susceptible to disruption by a high concentration of fluoride. The objectives of this study were to explore the mechanism of apoptosis by detecting the toxic effects of different concentrations of sodium fluoride (NaF) in H9c2 cells exposed for up to 96 h. NaF not only inhibited H9c2 cell proliferation but also induced apoptosis and morphological damage. With increasing NaF concentrations, early apoptosis of H9c2 cells was increased while the mitochondrial membrane potential was decreased. Compared with the control group, the mRNA levels of caspase-3, caspase-9, and cytochrome c all increased with increasing concentrations of NaF. In summary, these data suggest that apoptosis is involved in NaF-induced H9c2 cell toxicity and that activation of the mitochondrial pathway may occur. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Observation of the decay $\\overline{B_s^0} \\rightarrow \\chi_{c2} K^+ K^- $

    CERN Document Server

    Aaij, R.; LHCb Collaboration; Adinolfi, M.; Aidala, C.A.; Ajaltouni, Z.; Akar, S.; Albicocco, P.; Albrecht, J.; Alessio, F.; Alexander, M.; Albero, A. Alfonso; Ali, S.; Alkhazov, G.; Alvarez Cartelle, P.; Alves, A.A.; Amato, S.; Amerio, S.; Amhis, Y.; An, L.; Anderlini, L.; Andreassi, G.; Andreotti, M.; Andrews, J.E.; Appleby, R.B.; Archilli, F.; d'Argent, P.; Arnau Romeu, J.; Artamonov, A.; Artuso, M.; Arzymatov, K.; Aslanides, E.; Atzeni, M.; Bachmann, S.; Back, J.J.; Baker, S.; Balagura, V.; Baldini, W.; Baranov, A.; Barlow, R.J.; Barsuk, S.; Barter, W.; Baryshnikov, F.; Batozskaya, V.; Batsukh, B.; Battista, V.; Bay, A.; Beddow, J.; Bedeschi, F.; Bediaga, I.; Beiter, A.; Bel, L.J.; Beliy, N.; Bellee, V.; Belloli, N.; Belous, K.; Belyaev, I.; Ben-Haim, E.; Bencivenni, G.; Benson, S.; Beranek, S.; Berezhnoy, A.; Bernet, R.; Berninghoff, D.; Bertholet, E.; Bertolin, A.; Betancourt, C.; Betti, F.; Bettler, M.O.; van Beuzekom, M.; Bezshyiko, Ia.; Bhasin, S.; Bhom, J.; Bian, L.; Bifani, S.; Billoir, P.; Birnkraut, A.; Bizzeti, A.; Bjørn, M.; Blago, M.P.; Blake, T.; Blanc, F.; Blusk, S.; Bobulska, D.; Bocci, V.; Garcia, O. Boente; Boettcher, T.; Bondar, A.; Bondar, N.; Borghi, S.; Borisyak, M.; Borsato, M.; Bossu, F.; Boubdir, M.; Bowcock, T.J.V.; Bozzi, C.; Braun, S.; Brodski, M.; Brodzicka, J.; Brundu, D.; Buchanan, E.; Buonaura, A.; Burr, C.; Bursche, A.; Buytaert, J.; Byczynski, W.; Cadeddu, S.; Cai, H.; Calabrese, R.; Calladine, R.; Calvi, M.; Calvo Gomez, M.; Camboni, A.; Campana, P.; Perez, D.H. Campora; Capriotti, L.; Carbone, A.; Carboni, G.; Cardinale, R.; Cardini, A.; Carniti, P.; Carson, L.; Carvalho Akiba, K.; Casse, G.; Cassina, L.; Cattaneo, M.; Cavallero, G.; Cenci, R.; Chamont, D.; Chapman, M.G.; Charles, M.; Charpentier, Ph.; Chatzikonstantinidis, G.; Chefdeville, M.; Chekalina, V.; Chen, C.; Chen, S.; Chitic, S.G.; Chobanova, V.; Chrzaszcz, M.; Chubykin, A.; Ciambrone, P.; Cid Vidal, X.; Ciezarek, G.; Clarke, P.E.L.; Clemencic, M.; Cliff, H.V.; Closier, J.; Coco, V.; Coelho, J.A.B.; Cogan, J.; Cogneras, E.; Cojocariu, L.; Collins, P.; Colombo, T.; Comerma-Montells, A.; Contu, A.; Coombs, G.; Coquereau, S.; Corti, G.; Corvo, M.; Costa Sobral, C.M.; Couturier, B.; Cowan, G.A.; Craik, D.C.; Crocombe, A.; Cruz Torres, M.; Currie, R.; D'Ambrosio, C.; Da Cunha Marinho, F.; Da Silva, C.L.; Dall'Occo, E.; Dalseno, J.; Danilina, A.; Davis, A.; De Aguiar Francisco, O.; De Bruyn, K.; De Capua, S.; De Cian, M.; De Miranda, J.M.; De Paula, L.; De Serio, M.; De Simone, P.; Dean, C.T.; Decamp, D.; Del Buono, L.; Delaney, B.; Dembinski, H.P.; Demmer, M.; Dendek, A.; Derkach, D.; Deschamps, O.; Desse, F.; Dettori, F.; Dey, B.; Di Canto, A.; Di Nezza, P.; Didenko, S.; Dijkstra, H.; Dordei, F.; Dorigo, M.; Suárez, A. Dosil; Douglas, L.; Dovbnya, A.; Dreimanis, K.; Dufour, L.; Dujany, G.; Durante, P.; Durham, J.M.; Dutta, D.; Dzhelyadin, R.; Dziewiecki, M.; Dziurda, A.; Dzyuba, A.; Easo, S.; Egede, U.; Egorychev, V.; Eidelman, S.; Eisenhardt, S.; Eitschberger, U.; Ekelhof, R.; Eklund, L.; Ely, S.; Ene, A.; Escher, S.; Esen, S.; Evans, T.; Falabella, A.; Farley, N.; Farry, S.; Fazzini, D.; Federici, L.; Fernandez, G.; Fernandez Declara, P.; Fernandez Prieto, A.; Ferrari, F.; Lopes, L. Ferreira; Ferreira Rodrigues, F.; Ferro-Luzzi, M.; Filippov, S.; Fini, R.A.; Fiorini, M.; Firlej, M.; Fitzpatrick, C.; Fiutowski, T.; Fleuret, F.; Fontana, M.; Fontanelli, F.; Forty, R.; Franco Lima, V.; Frank, M.; Frei, C.; Fu, J.; Funk, W.; Färber, C.; Carvalho, M. Féo Pereira Rivello; Gabriel, E.; Gallas Torreira, A.; Galli, D.; Gallorini, S.; Gambetta, S.; Gan, Y.; Gandelman, M.; Gandini, P.; Gao, Y.; Garcia Martin, L.M.; Plana, B. Garcia; Pardiñas, J. García; Garra Tico, J.; Garrido, L.; Gascon, D.; Gaspar, C.; Gavardi, L.; Gazzoni, G.; Gerick, D.; Gersabeck, E.; Gersabeck, M.; Gershon, T.; Gerstel, D.; Ghez, Ph.; Gianì, S.; Gibson, V.; Girard, O.G.; Giubega, L.; Gizdov, K.; Gligorov, V.V.; Golubkov, D.; Golutvin, A.; Gomes, A.; Gorelov, I.V.; Gotti, C.; Govorkova, E.; Grabowski, J.P.; Graciani Diaz, R.; Granado Cardoso, L.A.; Graugés, E.; Graverini, E.; Graziani, G.; Grecu, A.; Greim, R.; Griffith, P.; Grillo, L.; Gruber, L.; Gruberg Cazon, B.R.; Grünberg, O.; Gu, C.; Gushchin, E.; Guz, Yu.; Gys, T.; Göbel, C.; Hadavizadeh, T.; Hadjivasiliou, C.; Haefeli, G.; Haen, C.; Haines, S.C.; Hainge, J.; Hamilton, B.; Han, X.; Hancock, T.H.; Hansmann-Menzemer, S.; Harnew, N.; Harnew, S.T.; Harrison, T.; Hasse, C.; Hatch, M.; He, J.; Hecker, M.; Heinicke, K.; Heister, A.; Hennessy, K.; Henry, L.; van Herwijnen, E.; Heß, M.; Hicheur, A.; Charman, R. Hidalgo; Hill, D.; Hilton, M.; Hopchev, P.H.; Hu, W.; Huang, W.; Huard, Z.C.; Hulsbergen, W.; Humair, T.; Hushchyn, M.; Hutchcroft, D.; Hynds, D.; Ibis, P.; Idzik, M.; Ilten, P.; Ivshin, K.; Jacobsson, R.; Jalocha, J.; Jans, E.; Jawahery, A.; Jiang, F.; John, M.; Johnson, D.; Jones, C.R.; Joram, C.; Jost, B.; Jurik, N.; Kandybei, S.; Karacson, M.; Kariuki, J.M.; Karodia, S.; Kazeev, N.; Kecke, M.; Keizer, F.; Kelsey, M.; Kenzie, M.; Ketel, T.; Khairullin, E.; Khanji, B.; Khurewathanakul, C.; Kim, K.E.; Kirn, T.; Klaver, S.; Klimaszewski, K.; Klimkovich, T.; Koliiev, S.; Kolpin, M.; Kopecna, R.; Koppenburg, P.; Kostiuk, I.; Kotriakhova, S.; Kozeiha, M.; Kravchuk, L.; Kreps, M.; Kress, F.; Krokovny, P.; Krupa, W.; Krzemien, W.; Kucewicz, W.; Kucharczyk, M.; Kudryavtsev, V.; Kuonen, A.K.; Kvaratskheliya, T.; Lacarrere, D.; Lafferty, G.; Lai, A.; Lancierini, D.; Lanfranchi, G.; Langenbruch, C.; Latham, T.; Lazzeroni, C.; Le Gac, R.; Leflat, A.; Lefrançois, J.; Lefèvre, R.; Lemaitre, F.; Leroy, O.; Lesiak, T.; Leverington, B.; Li, P.R.; Li, T.; Li, Z.; Liang, X.; Likhomanenko, T.; Lindner, R.; Lionetto, F.; Lisovskyi, V.; Liu, X.; Loh, D.; Loi, A.; Longstaff, I.; Lopes, J.H.; Lovell, G.H.; Lucchesi, D.; Lucio Martinez, M.; Lupato, A.; Luppi, E.; Lupton, O.; Lusiani, A.; Lyu, X.; Machefert, F.; Maciuc, F.; Macko, V.; Mackowiak, P.; Maddrell-Mander, S.; Maev, O.; Maguire, K.; Maisuzenko, D.; Majewski, M.W.; Malde, S.; Malecki, B.; Malinin, A.; Maltsev, T.; Manca, G.; Mancinelli, G.; Marangotto, D.; Maratas, J.; Marchand, J.F.; Marconi, U.; Marin Benito, C.; Marinangeli, M.; Marino, P.; Marks, J.; Marshall, P.J.; Martellotti, G.; Martin, M.; Martinelli, M.; Martinez Santos, D.; Vidal, F. Martinez; Massafferri, A.; Materok, M.; Matev, R.; Mathad, A.; Mathe, Z.; Matteuzzi, C.; Mauri, A.; Maurice, E.; Maurin, B.; Mazurov, A.; McCann, M.; McNab, A.; McNulty, R.; Mead, J.V.; Meadows, B.; Meaux, C.; Meier, F.; Meinert, N.; Melnychuk, D.; Merk, M.; Merli, A.; Michielin, E.; Milanes, D.A.; Millard, E.; Minard, M.N.; Minzoni, L.; Mitzel, D.S.; Mogini, A.; Molina Rodriguez, J.; Mombächer, T.; Monroy, I.A.; Monteil, S.; Morandin, M.; Morello, G.; Morello, M.J.; Morgunova, O.; Moron, J.; Morris, A.B.; Mountain, R.; Muheim, F.; Mulder, M.; Murphy, C.H.; Murray, D.; Mödden, A.; Müller, D.; Müller, J.; Müller, K.; Müller, V.; Naik, P.; Nakada, T.; Nandakumar, R.; Nandi, A.; Nanut, T.; Nasteva, I.; Needham, M.; Neri, N.; Neubert, S.; Neufeld, N.; Neuner, M.; Nguyen, T.D.; Nguyen-Mau, C.; Nieswand, S.; Niet, R.; Nikitin, N.; Nogay, A.; O'Hanlon, D.P.; Oblakowska-Mucha, A.; Obraztsov, V.; Ogilvy, S.; Oldeman, R.; Onderwater, C.J.G.; Ossowska, A.; Otalora Goicochea, J.M.; Owen, P.; Oyanguren, A.; Pais, P.R.; Palano, A.; Palutan, M.; Panshin, G.; Papanestis, A.; Pappagallo, M.; Pappalardo, L.L.; Parker, W.; Parkes, C.; Passaleva, G.; Pastore, A.; Patel, M.; Patrignani, C.; Pearce, A.; Pellegrino, A.; Penso, G.; Pepe Altarelli, M.; Perazzini, S.; Pereima, D.; Perret, P.; Pescatore, L.; Petridis, K.; Petrolini, A.; Petrov, A.; Petrucci, S.; Petruzzo, M.; Pietrzyk, B.; Pietrzyk, G.; Pikies, M.; Pili, M.; Pinci, D.; Pinzino, J.; Pisani, F.; Piucci, A.; Placinta, V.; Playfer, S.; Plews, J.; Plo Casasus, M.; Polci, F.; Lener, M. Poli; Poluektov, A.; Polukhina, N.; Polyakov, I.; Polycarpo, E.; Pomery, G.J.; Ponce, S.; Popov, A.; Popov, D.; Poslavskii, S.; Potterat, C.; Price, E.; Prisciandaro, J.; Prouve, C.; Pugatch, V.; Puig Navarro, A.; Pullen, H.; Punzi, G.; Qian, W.; Qin, J.; Quagliani, R.; Quintana, B.; Rachwal, B.; Rademacker, J.H.; Rama, M.; Ramos Pernas, M.; Rangel, M.S.; Ratnikov, F.; Raven, G.; Ravonel Salzgeber, M.; Reboud, M.; Redi, F.; Reichert, S.; dos Reis, A.C.; Reiss, F.; Remon Alepuz, C.; Ren, Z.; Renaudin, V.; Ricciardi, S.; Richards, S.; Rinnert, K.; Robbe, P.; Robert, A.; Rodrigues, A.B.; Rodrigues, E.; Rodriguez Lopez, J.A.; Roehrken, M.; Rogozhnikov, A.; Roiser, S.; Rollings, A.; Romanovskiy, V.; Romero Vidal, A.; Rotondo, M.; Rudolph, M.S.; Ruf, T.; Ruiz Vidal, J.; Saborido Silva, J.J.; Sagidova, N.; Saitta, B.; Salustino Guimaraes, V.; Gras, C. Sanchez; Sanchez Mayordomo, C.; Sanmartin Sedes, B.; Santacesaria, R.; Santamarina Rios, C.; Santimaria, M.; Santovetti, E.; Sarpis, G.; Sarti, A.; Satriano, C.; Satta, A.; Saur, M.; Savrina, D.; Schael, S.; Schellenberg, M.; Schiller, M.; Schindler, H.; Schmelling, M.; Schmelzer, T.; Schmidt, B.; Schneider, O.; Schopper, A.; Schreiner, H.F.; Schubiger, M.; Schune, M.H.; Schwemmer, R.; Sciascia, B.; Sciubba, A.; Semennikov, A.; Sepulveda, E.S.; Sergi, A.; Serra, N.; Serrano, J.; Sestini, L.; Seuthe, A.; Seyfert, P.; Shapkin, M.; Shcheglov, Y.; Shears, T.; Shekhtman, L.; Shevchenko, V.; Shmanin, E.; Siddi, B.G.; Silva Coutinho, R.; Silva de Oliveira, L.; Simi, G.; Simone, S.; Skidmore, N.; Skwarnicki, T.; Smeaton, J.G.; Smith, E.; Smith, I.T.; Smith, M.; Soares, M.; Soares Lavra, l.; Sokoloff, M.D.; Soler, F.J.P.; Souza De Paula, B.; Spaan, B.; Spradlin, P.; Stagni, F.; Stahl, M.; Stahl, S.; Stefko, P.; Stefkova, S.; Steinkamp, O.; Stemmle, S.; Stenyakin, O.; Stepanova, M.; Stevens, H.; Stone, S.; Storaci, B.; Stracka, S.; Stramaglia, M.E.; Straticiuc, M.; Straumann, U.; Strokov, S.; Sun, J.; Sun, L.; Swientek, K.; Syropoulos, V.; Szumlak, T.; Szymanski, M.; T'Jampens, S.; Tang, Z.; Tayduganov, A.; Tekampe, T.; Tellarini, G.; Teubert, F.; Thomas, E.; van Tilburg, J.; Tilley, M.J.; Tisserand, V.; Tolk, S.; Tomassetti, L.; Tonelli, D.; Tou, D.Y.; Aoude, R. Tourinho Jadallah; Tournefier, E.; Traill, M.; Tran, M.T.; Trisovic, A.; Tsaregorodtsev, A.; Tully, A.; Tuning, N.; Ukleja, A.; Usachov, A.; Ustyuzhanin, A.; Uwer, U.; Vacca, C.; Vagner, A.; Vagnoni, V.; Valassi, A.; Valat, S.; Valenti, G.; Vazquez Gomez, R.; Regueiro, P. Vazquez; Vecchi, S.; van Veghel, M.; Velthuis, J.J.; Veltri, M.; Veneziano, G.; Venkateswaran, A.; Verlage, T.A.; Vernet, M.; Veronika, N.V.; Vesterinen, M.; Viana Barbosa, J.V.; Vieira, D.; Vieites Diaz, M.; Viemann, H.; Vilasis-Cardona, X.; Vitkovskiy, A.; Vitti, M.; Volkov, V.; Vollhardt, A.; Voneki, B.; Vorobyev, A.; Vorobyev, V.; de Vries, J.A.; Vázquez Sierra, C.; Waldi, R.; Walsh, J.; Wang, J.; Wang, M.; Wang, Y.; Wang, Z.; Ward, D.R.; Wark, H.M.; Watson, N.K.; Websdale, D.; Weiden, A.; Weisser, C.; Whitehead, M.; Wicht, J.; Wilkinson, G.; Wilkinson, M.; Williams, I.; Williams, M.R.J.; Williams, M.; Williams, T.; Wilson, F.F.; Wimberley, J.; Winn, M.; Wishahi, J.; Wislicki, W.; Witek, M.; Wormser, G.; Wotton, S.A.; Wyllie, K.; Xiao, D.; Xie, Y.; Xu, A.; Xu, M.; Xu, Q.; Xu, Z.; Yang, Z.; Yao, Y.; Yeomans, L.E.; Yin, H.; Yu, J.; Yuan, X.; Yushchenko, O.; Zarebski, K.A.; Zavertyaev, M.; Zhang, D.; Zhang, L.; Zhang, W.C.; Zhang, Y.; Zhelezov, A.; Zheng, Y.; Zhu, X.; Zhukov, V.; Zonneveld, J.B.; Zucchelli, S.

    2018-01-01

    The $\\overline{B_s^0} \\rightarrow \\chi_{c2} K^+ K^- $ decay mode is observed and its branching fraction relative to the corresponding $\\chi_{c1}$ decay mode, in a $\\pm 15 \\textrm{MeV}/c^2$ window around the $\\phi$ mass, is found to be $$\\frac{\\mathcal{B}(\\overline{B_s^0} \\rightarrow \\chi_{c2} K^+ K^-) }{ \\mathcal{B}(\\overline{B_s^0} \\rightarrow \\chi_{c1} K^+K^-)} = (17.1 \\pm 3.1 \\pm 0.4 \\pm 0.9)\\%,$$ where the first uncertainty is statistical, the second systematic and the third due to the knowledge of the branching fractions of radiative $\\chi_c$ decays. The decay mode $\\overline{B_s^0} \\rightarrow \\chi_{c1} K^+ K^- $ allows the $ B_s^0$ mass to be measured as $$m(B_s^0) = 5366.83 \\pm 0.25 \\pm 0.27 \\, \\textrm{MeV}/c^2,$$ where the first uncertainty is statistical and the second systematic.

  20. Overview of C-2W Field-Reversed Configuration Experimental Program

    Science.gov (United States)

    Gota, H.; Binderbauer, M. W.; Tajima, T.; Putvinski, S.; Tuszewski, M.; Dettrick, S.; Korepanov, S.; Romero, J.; Smirnov, A.; Song, Y.; Thompson, M. C.; van Drie, A.; Yang, X.; Ivanov, A. A.; TAE Team

    2017-10-01

    Tri Alpha Energy's research has been devoted to producing a high temperature, stable, long-lived field-reversed configuration (FRC) plasma state by neutral-beam injection (NBI) and edge biasing/control. C-2U experiments have demonstrated drastic improvements in particle and energy confinement properties of FRC's, and the plasma performance obtained via 10 MW NBI has achieved plasma sustainment of up to 5 ms and plasma (diamagnetism) lifetimes of 10 + ms. The emerging confinement scaling, whereby electron energy confinement time is proportional to a positive power of the electron temperature, is very attractive for higher energy plasma confinement; accordingly, verification of the observed Te scaling law will be a key future research objective. The new experimental device, C-2W (now also called ``Norman''), has the following key subsystem upgrades from C-2U: (i) higher injected power, optimum energies, and extended pulse duration of the NBI system; (ii) installation of inner divertors with upgraded edge-biasing systems; (iii) fast external equilibrium/mirror-coil current ramp-up capability; and (iv) installation of trim/saddle coils for active feedback control of the FRC plasma. This paper will review highlights of the C-2W program.

  1. Quantification of C2 cervical spine rotatory fixation by X-ray, MRI and CT

    Energy Technology Data Exchange (ETDEWEB)

    Gradl, Georg [Chirurgische Klinik und Poliklinik der Universitaet Rostock, Abteilung Unfall- und Wiederherstellungschirurgie, Rostock (Germany); Maier-Bosse, Tamara; Staebler, Axel [Institut fuer Radiologische Diagnostik der Universitaet Muenchen, Klinikum Grobetahadern, Munich (Germany); Penning, Randolph [Institut fuer Rechtsmedizin der Universitaet Muenchen, Munich (Germany)

    2005-02-01

    Atlanto-axial rotatory displacement is known to be a cause of childhood torticollis and may as well be responsible for chronic neck pain after rear-end automobile collisions. The objective was to determine whether quantification of C2 malrotation is possible by plain radiographs in comparison to CT as the golden standard. MR imaging was evaluated as to whether it was of equal value in the detection of bony landmarks. C2 vertebra of five human cadaveric cervical spine specimens, ligamentously intact, were rotated using a Steinmann pin in steps of 5 up to 15 right and 15 left. Plain radiographs, CT and MRI images were taken in each rotational step. Data were analyzed for quantification of C2 rotation by three independent examiners. A rotation of 5 led to a spinous process deviation (SPD) from the midline of 3 mm as measured on an a.p. plain radiograph. A coefficient of rotation was calculated (1.62 mm{sup -1}). Data analyzed by three examiners revealed a small coefficient of variation (0.03). MRI and CT measurements showed comparable results for the quantification of rotation; however, in both techniques the 15 rotation was underestimated. Quantification of upper cervical spine malrotation was possible on plain radiographs using the SPD and a rotation coefficient. MRI and CT were equally successful in the assessment of C2 malrotation. (orig.)

  2. BAMBI Promotes C2C12 Myogenic Differentiation by Enhancing Wnt/β-Catenin Signaling

    Directory of Open Access Journals (Sweden)

    Qiangling Zhang

    2015-08-01

    Full Text Available Bone morphogenic protein and activin membrane-bound inhibitor (BAMBI is regarded as an essential regulator of cell proliferation and differentiation that represses transforming growth factor-β and enhances Wnt/β-catenin signaling in various cell types. However, its role in skeletal muscle remains largely unknown. In the current study, we found that the expression level of BAMBI peaked in the early differentiation phase of the C2C12 rodent myoblast cell line. Knockdown of BAMBI via siRNA inhibited C2C12 differentiation, indicated by repressed MyoD, MyoG, and MyHC expression as well as reductions in the differentiation and fusion indices. BAMBI knockdown reduced the activity of Wnt/β-catenin signaling, as characterized by the decreased nuclear translocation of β-catenin and the lowered transcription of Axin2, which is a well-documented target gene of the Wnt/β-catenin signaling pathway. Furthermore, treatment with LiCl, an activator of Wnt/β-catenin signaling, rescued the reduction in C2C12 differentiation caused by BAMBI siRNA. Taken together, our data suggest that BAMBI is required for normal C2C12 differentiation, and that its role in myogenesis is mediated by the Wnt/β-catenin pathway.

  3. O(3P) + C2H4 Potential Energy Surface: Study at the Multireference Level

    Czech Academy of Sciences Publication Activity Database

    West, A. C.; Kretchmer, J. S.; Sellner, B.; Park, K.; Hase, W. L.; Lischka, Hans; Windus, T. L.

    2009-01-01

    Roč. 113, č. 45 (2009), s. 12663-12674 ISSN 1089-5639 Institutional research plan: CEZ:AV0Z40550506 Keywords : hydrogen combustion * multireference methods * O(3P)+C2H4 reaction Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.899, year: 2009

  4. "Operationalizing C2 agility”. Coping with complexity in command and control

    CSIR Research Space (South Africa)

    Oosthuizen, R

    2012-06-01

    Full Text Available . The trend of modern combat is to move away from conventional warfare, increasing the occurrence of “messy” and “wicked” problems. Modern C2 systems require new frameworks and designs to cope with the increase in complexity experienced in warfare. Despite...

  5. Calcium carbide (CaC2): Effect on fruit set and yield of mango ...

    African Journals Online (AJOL)

    Application of slow release calcium carbide (CaC2) to the soil are thought to improve plant growth and yield through the generation of acetylene, which inhibits nitrification, thereby reducing nitrogen losses which may be converted to physiologically significant concentrations of the plant growth regulator ethylene. The effects ...

  6. 76 FR 33798 - Self-Regulatory Organizations; C2 Options Exchange, Incorporated; Order Instituting Proceedings...

    Science.gov (United States)

    2011-06-09

    ... Letter 2''); Michael J. Simon, Secretary, International Securities Exchange, LLC (``ISE''), dated March... C2 introducing a p.m.-settled S&P 500 index option? If commenters think there may be an impact, do... last 30 years? Please provide data to support your answer. How much of the change do commenters think...

  7. A combined crossed molecular beams and theoretical study of the reaction CN + C2H4

    International Nuclear Information System (INIS)

    Balucani, Nadia; Leonori, Francesca; Petrucci, Raffaele; Wang, Xingan; Casavecchia, Piergiorgio; Skouteris, Dimitrios; Albernaz, Alessandra F.; Gargano, Ricardo

    2015-01-01

    Highlights: • The CN + C 2 H 4 reaction was investigated in crossed beam experiments. • Electronic structure calculations of the potential energy surface were performed. • RRKM estimates qualitatively reproduce the experimental C 2 H 3 NC yield. - Abstract: The CN + C 2 H 4 reaction has been investigated experimentally, in crossed molecular beam (CMB) experiments at the collision energy of 33.4 kJ/mol, and theoretically, by electronic structure calculations of the relevant potential energy surface and Rice–Ramsperger–Kassel–Marcus (RRKM) estimates of the product branching ratio. Differently from previous CMB experiments at lower collision energies, but similarly to a high energy study, we have some indication that a second reaction channel is open at this collision energy, the characteristics of which are consistent with the channel leading to CH 2 CHNC + H. The RRKM estimates using M06L electronic structure calculations qualitatively support the experimental observation of C 2 H 3 NC formation at this and at the higher collision energy of 42.7 kJ/mol of previous experiments

  8. Network Centric Warfare Concepts in the Royal Netherlands Army C2 Architecture

    NARCIS (Netherlands)

    Meijden, M.G. van der

    2004-01-01

    The Royal Netherlands Army (RNLA) has been working on its second generation C2 Information System since 2000. Its first generation Integrated Staff Information System (ISIS) that is currently deployed is based on ATCCIS specifications and uses the ATCCIS Replication Mechanism for database to

  9. Quantitative laser diagnostic and modeling study of C2 and CH chemistry in combustion.

    Science.gov (United States)

    Köhler, Markus; Brockhinke, Andreas; Braun-Unkhoff, Marina; Kohse-Höinghaus, Katharina

    2010-04-15

    Quantitative concentration measurements of CH and C(2) have been performed in laminar, premixed, flat flames of propene and cyclopentene with varying stoichiometry. A combination of cavity ring-down (CRD) spectroscopy and laser-induced fluorescence (LIF) was used to enable sensitive detection of these species with high spatial resolution. Previously, CH and C(2) chemistry had been studied, predominantly in methane flames, to understand potential correlations of their formation and consumption. For flames of larger hydrocarbon fuels, however, quantitative information on these small intermediates is scarce, especially under fuel-rich conditions. Also, the combustion chemistry of C(2) in particular has not been studied in detail, and although it has often been observed, its role in potential build-up reactions of higher hydrocarbon species is not well understood. The quantitative measurements performed here are the first to detect both species with good spatial resolution and high sensitivity in the same experiment in flames of C(3) and C(5) fuels. The experimental profiles were compared with results of combustion modeling to reveal details of the formation and consumption of these important combustion molecules, and the investigation was devoted to assist the further understanding of the role of C(2) and of its potential chemical interdependences with CH and other small radicals.

  10. Evaluation of the ion-density measurements by the Indian satellite SROSS-C2

    Science.gov (United States)

    Subrahmanyam, P.; Jain, A. R.; Maini, H. K.; Bahl, M.; Das, Rupesh M.; Garg, S. C.; Niranjan, K.

    2010-12-01

    The ion and electron F region plasma measurements made by the ion and electron Retarding Potential Analyzers (RPAs) onboard the Indian satellite SROSS-C2, have yielded excellent data set over the Indian region for more than half a solar cycle, after the SROSS-C2 launch in May 1994. The absolute ion density, ion temperature, and ion composition parameters are derived from these in situ measurements and used by many workers. In this paper the absolute values of ion density derived from the ion RPA measurements are compared and evaluated with the measurements made by ground-based ionosondes located in the Indian region and close to the SROSS-C2 orbital path. It is shown that a slight adjustment in efficiency factor of the ion RPA sensor brings the in situ measurements much closer to those obtained from the ground-based ionosonde measurements taking into account the model calculations. It may be mentioned that this is a correction to the ion density measurement by SROSS-C2 by a fixed proportion (14-11.4%). The effect of change in efficiency factor on the ion current, which is used to deduce the ion number density, is demonstrated and discussed.

  11. C2-C5 hydrocarbon measurements in the Netherlands 1981-1991

    NARCIS (Netherlands)

    Roemer, M.; Builtjes, P.; Esser, P.; Guicherit, R.; Thijsse, T.

    1999-01-01

    Measurements of C2-C5 hydrocarbons on an hourly basis at the TNO site in Delft from 1982 to 1984 and at Moerdijk over the period 1981-1991 are presented. In combination with meteorological data (wind direction and wind speed) the Delft and Moerdijk series are evaluated to identify source categories,

  12. checkCIF/PLATON report Datablock: ll5182-c2m

    Indian Academy of Sciences (India)

    THIS REPORT IS FOR GUIDANCE ONLY. IF USED AS PART OF A REVIEW PROCEDURE. FOR PUBLICATION, IT SHOULD NOT REPLACE THE EXPERTISE OF AN EXPERIENCED. CRYSTALLOGRAPHIC REFEREE. No syntax errors found. CIF dictionary Interpreting this report. Datablock: ll5182-c2m. Bond precision:.

  13. Synthesis of 2-substituted tryptophans via a C3- to C2-alkyl migration

    Directory of Open Access Journals (Sweden)

    Michele Mari

    2014-08-01

    Full Text Available The reaction of 3-substituted indoles with dehydroalanine (Dha derivatives under Lewis acid-mediated conditions has been investigated. The formation of 2-substituted tryptophans is proposed to occur through a selective alkylative dearomatization–cyclization followed by C3- to C2-alkyl migration and rearomatization.

  14. Spatial distributions of H, CN, and C2 in a diamond growing oxyacetylene flame

    NARCIS (Netherlands)

    Klein-Douwel, R.J.H.; Meulen, ter J.J.

    1998-01-01

    Two-dimensional laser-induced fluorescence (2D-LIF) measurements are applied to the chemical vapor deposition (CVD) of diamond by an oxyacetylene flame to visualize the distributions of atomic hydrogen, C2, and CN in the gas phase during diamond growth. Experiments are carried out in laminar flames

  15. Thermal stability of Ti3SiC2 thin films

    International Nuclear Information System (INIS)

    Emmerlich, Jens; Music, Denis; Eklund, Per; Wilhelmsson, Ola; Jansson, Ulf; Schneider, Jochen M.; Hoegberg, Hans; Hultman, Lars

    2007-01-01

    The thermal stability of Ti 3 SiC 2 (0 0 0 1) thin films is studied by in situ X-ray diffraction analysis during vacuum furnace annealing in combination with X-ray photoelectron spectroscopy, transmission electron microscopy and scanning transmission electron microscopy with energy dispersive X-ray analysis. The films are found to be stable during annealing at temperatures up to ∼1000 deg. C for 25 h. Annealing at 1100-1200 deg. C results in the rapid decomposition of Ti 3 SiC 2 by Si out-diffusion along the basal planes via domain boundaries to the free surface with subsequent evaporation. As a consequence, the material shrinks by the relaxation of the Ti 3 C 2 slabs and, it is proposed, by an in-diffusion of O into the empty Si-mirror planes. The phase transformation process is followed by the detwinning of the as-relaxed Ti 3 C 2 slabs into (1 1 1)-oriented TiC 0.67 layers, which begin recrystallizing at 1300 deg. C. Ab initio calculations are provided supporting the presented decomposition mechanisms

  16. A first interpretation of the Mol 7C/l and Mol 7C/2 experiments

    International Nuclear Information System (INIS)

    Berthier, J.; Carluec, B.; Fortunato, M.; Lemmet, L.

    1983-01-01

    The interpretation of the two experiments MOL 7C/1 and MOL 7C/2 that has been performed at the CEA of Cadarache is presented here: one will find first a recall of the experimental conditions of the MOL experiments, then a short description of the codes that enable the interpretation and finally the results of this interpretation compared to the experimental results

  17. 40 CFR Table C-2 to Subpart C of... - Sequence of Test Measurements

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 5 2010-07-01 2010-07-01 false Sequence of Test Measurements C Table C-2 to Subpart C of Part 53 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Medium. 2 High High. 3 Medium Low. 4 High High. 5 Low Medium. 6 Medium Low. 7 Low Medium. 8 Medium Low. 9...

  18. 26 CFR 301.6229(c)(2)-1T - Substantial omission of income (temporary).

    Science.gov (United States)

    2010-04-01

    ....6229(c)(2)-1T Substantial omission of income (temporary). (a) Partnership return—(1) General rule. (i) If any partnership omits from the gross income stated in its return an amount properly includible... omitted from gross income if information sufficient to apprise the Commissioner of the nature and amount...

  19. Ca-Embedded C2N: an efficient adsorbent for CO2 capture.

    Science.gov (United States)

    Liu, Yuzhen; Meng, Zhaoshun; Guo, Xiaojian; Xu, Genjian; Rao, Dewei; Wang, Yuhui; Deng, Kaiming; Lu, Ruifeng

    2017-10-25

    Carbon dioxide as a greenhouse gas causes severe impacts on the environment, whereas it is also a necessary chemical feedstock that can be converted into carbon-based fuels via electrochemical reduction. To efficiently and reversibly capture CO 2 , it is important to find novel materials for a good balance between adsorption and desorption. In this study, we performed first-principles calculations and grand canonical Monte Carlo (GCMC) simulations, to systematically study metal-embedded carbon nitride (C 2 N) nanosheets for CO 2 capture. Our first-principles results indicated that Ca atoms can be uniformly trapped in the cavity center of C 2 N structure, while the transition metals (Sc, Ti, V, Cr, Mn, Fe, Co) are favorably embedded in the sites off the center of the cavity. The determined maximum number of CO 2 molecules with strong physisorption showed that Ca-embedded C 2 N monolayer is the most promising CO 2 adsorbent among all considered metal-embedded materials. Moreover, GCMC simulations revealed that at room temperature the gravimetric density for CO 2 adsorbed on Ca-embedded C 2 N reached 50 wt% at 30 bar and 23 wt% at 1 bar, higher than other layered materials, thus providing a satisfactory system for the CO 2 capture and utilization.

  20. A Proposed Engineering Process and Prototype Toolset for Developing C2-to-Simulation Interoperability Solutions

    NARCIS (Netherlands)

    Johnsen, F.T.; Bloebaum, T.H.; Meiler, P.P.; Owens, I.; Barz, C.; Jansen, N.

    2013-01-01

    Service Oriented Architecture (SOA) can enable agile C2 functionality. The flexibility and loose coupling offered by the SOA paradigm means that both NATO and many of the NATO nations are basing their future information infrastructures on this paradigm. Web services, the most common and mature

  1. Observations of interstellar C2 toward Chi Oph, HD 154368, 147889 and 149404

    NARCIS (Netherlands)

    Dishoeck, van E.F.; Zeeuw, de P.T.

    1984-01-01

    Interstellar absorption lines of the C2 (2-0) Phillips band at 8750 A have been searched for in the spectra of southern stars. Seventeen lines originating from the lowest eight rotational levels have been detected toward Chi Oph, and eleven lines originating from the lowest five rotational levels

  2. 26 CFR 1.1092(c)-2 - Equity options with flexible terms.

    Science.gov (United States)

    2010-04-01

    ...) INCOME TAX (CONTINUED) INCOME TAXES Wash Sales of Stock Or Securities § 1.1092(c)-2 Equity options with... applicable stock price for Corporation Y stock is $14.75. Using the bench marks for an equity option with..., because the highest available strike price less than the applicable stock price for an equity option with...

  3. Pore Formation Process of Porous Ti3SiC2 Fabricated by Reactive Sintering

    Directory of Open Access Journals (Sweden)

    Huibin Zhang

    2017-02-01

    Full Text Available Porous Ti3SiC2 was fabricated with high purity, 99.4 vol %, through reactive sintering of titanium hydride (TiH2, silicon (Si and graphite (C elemental powders. The reaction procedures and the pore structure evolution during the sintering process were systematically studied by X-ray diffraction (XRD and scanning electron microscope (SEM. Our results show that the formation of Ti3SiC2 from TiH2/Si/C powders experienced the following steps: firstly, TiH2 decomposed into Ti; secondly, TiC and Ti5Si3 intermediate phases were generated; finally, Ti3SiC2 was produced through the reaction of TiC, Ti5Si3 and Si. The pores formed in the synthesis procedure of porous Ti3SiC2 ceramics are derived from the following aspects: interstitial pores left during the pressing procedure; pores formed because of the TiH2 decomposition; pores formed through the reactions between Ti and Si and Ti and C powders; and the pores produced accompanying the final phase synthesized during the high temperature sintering process.

  4. 17 CFR 240.15c2-7 - Identification of quotations.

    Science.gov (United States)

    2010-04-01

    ... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Identification of quotations... quotations. (a) It shall constitute an attempt to induce the purchase or sale of a security by making a “fictitious quotation” within the meaning of section 15(c)(2) of the Act, for any broker or dealer to furnish...

  5. Electron capture by C2+ and Ti2+ ions in H and H2

    International Nuclear Information System (INIS)

    Nutt, W.L.; McCullough, R.W.; Gilbody, H.B.

    1978-01-01

    Cross sections for electron capture by C 2+ and Ti 2+ ions in H and H 2 have been determined within the energy range 0.5 to 14 keV from measurements made using a tungsten-tube furnace to provide a target of highly dissociated hydrogen. (author)

  6. 76 FR 17973 - Self-Regulatory Organizations; C2 Options Exchange, Incorporated; Order Approving Proposed Rule...

    Science.gov (United States)

    2011-03-31

    ... Directors may establish an Advisory Board; and (3) eliminate the C2 Audit Committee. A. Elimination of the... communication between the Exchange and its Trading Permit Holders and to coordinate the activities of Trading... channels, including direct communication with individual Trading Permit Holders, committees established by...

  7. Quantification of C2 cervical spine rotatory fixation by X-ray, MRI and CT

    International Nuclear Information System (INIS)

    Gradl, Georg; Maier-Bosse, Tamara; Staebler, Axel; Penning, Randolph

    2005-01-01

    Atlanto-axial rotatory displacement is known to be a cause of childhood torticollis and may as well be responsible for chronic neck pain after rear-end automobile collisions. The objective was to determine whether quantification of C2 malrotation is possible by plain radiographs in comparison to CT as the golden standard. MR imaging was evaluated as to whether it was of equal value in the detection of bony landmarks. C2 vertebra of five human cadaveric cervical spine specimens, ligamentously intact, were rotated using a Steinmann pin in steps of 5 up to 15 right and 15 left. Plain radiographs, CT and MRI images were taken in each rotational step. Data were analyzed for quantification of C2 rotation by three independent examiners. A rotation of 5 led to a spinous process deviation (SPD) from the midline of 3 mm as measured on an a.p. plain radiograph. A coefficient of rotation was calculated (1.62 mm -1 ). Data analyzed by three examiners revealed a small coefficient of variation (0.03). MRI and CT measurements showed comparable results for the quantification of rotation; however, in both techniques the 15 rotation was underestimated. Quantification of upper cervical spine malrotation was possible on plain radiographs using the SPD and a rotation coefficient. MRI and CT were equally successful in the assessment of C2 malrotation. (orig.)

  8. Energy of ions 3{<=}Z{<=}10 in Ilford C2 nuclear emulsions; Parcours - energie des ions 3{<=}Z{<=}10 dans les emulsions nucleaires ilford C2

    Energy Technology Data Exchange (ETDEWEB)

    Papineau, A [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1956-07-01

    The relationship between the path and energy of ions with 3{<=}Z{<=}10 in Ilford C2 nuclear emulsions is studied. It determined the average state of charge of ions in each velocity intervals. Results are given in a table for {sub 2}He, {sub 3}Li, {sub 4}Be, {sub 5}B, {sub 6}C, {sub 7}N, {sub 8}O and {sub 10}Ne. For each velocity interval, it is possible to apply the Blackett relation which links, for the same velocity, the path {delta}R of a particle with M (mass) and Z (charge) to the path {delta}R' of a particle with M' and Z'. Results are given in tables and graphics representing the particles energy with the particles path. (M.P.)

  9. The Rate Constant for the Reaction H + C2H5 at T = 295 - 150K

    Science.gov (United States)

    Pimentel, Andre S.; Payne, Walter A.; Nesbitt, Fred L.; Cody, Regina J.; Stief, Louis J.

    2004-01-01

    The reaction between the hydrogen atom and the ethyl (C2H3) radical is predicted by photochemical modeling to be the most important loss process for C2H5 radicals in the atmospheres of Jupiter and Saturn. This reaction is also one of the major sources for the methyl radicals in these atmospheres. These two simplest hydrocarbon radicals are the initial species for the synthesis of larger hydrocarbons. Previous measurements of the rate constant for the H + C2H5 reaction varied by a factor of five at room temperature, and some studies showed a dependence upon temperature while others showed no such dependence. In addition, the previous studies were at higher temperatures and generally higher pressures than that needed for use in planetary atmospheric models. The rate constant for the reaction H + C2H5 has been measured directly at T = 150, 202 and 295 K and at P = 1.0 Torr He for all temperatures and additionally at P = 0.5 and 2.0 Torr He at T = 202 K. The measurements were performed in a discharge - fast flow system. The decay of the C2H5 radical in the presence of excess hydrogen was monitored by low-energy electron impact mass spectrometry under pseudo-first order conditions. H atoms and C2H5 radicals were generated rapidly and simultaneously by the reaction of fluorine atoms with H2 and C2H6, respectively. The total rate constant was found to be temperature and pressure independent. The measured total rate constant at each temperature are: k(sub 1)(295K) = (1.02+/-0.24)x10(exp -10), k(sub 1)(202K) = (1.02+/-0.22)x10(exp -10) and k(sub 1)(150K) = (0.93+/-0.21)x10(exp -10), all in units of cu cm/molecule/s. The total rate constant derived from all the combined measurements is k(sub 1) = (l.03+/-0.17)x10(exp -10) cu cm/molecule/s. At room temperature our results are about a factor of two higher than the recommended rate constant and a factor of three lower than the most recently published study.

  10. Selective reduction of AKR1C2 in prostate cancer and its role in DHT metabolism.

    Science.gov (United States)

    Ji, Qing; Chang, Lilly; VanDenBerg, David; Stanczyk, Frank Z; Stolz, Andrew

    2003-03-01

    As androgens play an essential role in prostate cancer, we sought to develop a real-time PCR to characterize mRNA expression profiles of human members of the Aldo-Keto Reductase (AKR) 1C gene family, as well as of 5 alpha-steroid reductase Type II (SRD5A2) in prostate cancer samples. Functional activity and regulation of AKR1C2, a 3 alpha-hydroxysteroid dehydrogenase (HSD) type III, was also assessed in prostate cancer cell lines. Gene specific PCR primers were established and relative gene expression of human AKR1C family members was determined in paired samples of cancerous and surrounding unaffected prostate tissue. AKR1C2 preferentially reduces DHT to the weak metabolite 5 alpha-androstane-3 alpha,17 beta-diol (3 alpha-diol) without conversion of 3 alpha-diol to DHT in the PC-3 cell line, and its expression was increased by DHT treatment in LNCaP cells. Selectively reduced expression of AKR1C2 mRNA, but not AKR1C1 (97% sequence identity), was found in approximately half of the pairs whereas AKR1C3 relative expression was not significantly altered. No aberrant expression of AKR1C4 expression or significant differences in SRD5A2 gene expression were found. AKR1C2 functions as a DHT reductase in prostate-derived cells lines and is regulated by DHT. Additional studies are needed to further define the significance of reduced AKR1C2 expression in prostate cancer and its potential role in modulating local availability of DHT. Copyright 2003 Wiley-Liss, Inc.

  11. Apoptosis in differentiating C2C12 muscle cells selectively targets Bcl-2-deficient myotubes

    Science.gov (United States)

    Schoneich, Christian; Dremina, Elena; Galeva, Nadezhda; Sharov, Victor

    2014-01-01

    Muscle cell apoptosis accompanies normal muscle development and regeneration, as well as degenerative diseases and aging. C2C12 murine myoblast cells represent a common model to study muscle differentiation. Though it was already shown that myogenic differentiation of C2C12 cells is accompanied by enhanced apoptosis in a fraction of cells, either the cell population sensitive to apoptosis or regulatory mechanisms for the apoptotic response are unclear so far. In the current study we characterize apoptotic phenotypes of different types of C2C12 cells at all stages of differentiation, and report here that myotubes of differentiated C2C12 cells with low levels of anti-apoptotic Bcl-2 expression are particularly vulnerable to apoptosis even though they are displaying low levels of pro-apoptotic proteins Bax, Bak and Bad. In contrast, reserve cells exhibit higher levels of Bcl-2 and high resistance to apoptosis. The transfection of proliferating myoblasts with Bcl-2 prior to differentiation did not protect against spontaneous apoptosis accompanying differentiation of C2C12 cell but led to Bcl-2 overexpression in myotubes and to significant protection from apoptotic cell loss caused by exposure to hydrogen peroxide. Overall, our data advocate for a Bcl-2-dependent mechanism of apoptosis in differentiated muscle cells. However, downstream processes for spontaneous and hydrogen peroxide induced apoptosis are not completely similar. Apoptosis in differentiating myoblasts and myotubes is regulated not through interaction of Bcl-2 with pro-apoptotic Bcl-2 family proteins such as Bax, Bak, and Bad. PMID:24129924

  12. Molecular cloning, structural analysis and expression of complement component Bf/C2 genes in the nurse shark, Ginglymostoma cirratum.

    Science.gov (United States)

    Shin, Dong-Ho; Webb, Barbara; Nakao, Miki; Smith, Sylvia L

    2007-01-01

    Factor B and C2 are serine proteases that provide the catalytic subunits of C3 and C5 convertases of the alternative (AP) and classical (CP) complement pathways. Two Bf/C2 cDNAs, GcBf/C2-1 and -2 (previously referred to as nsBf/C2-A and nsBf/C2-B), were isolated from the nurse shark, Ginglymostoma cirratum. GcBf/C2-1 and -2 are 3364 and 3082bp in length and encode a leader peptide, three CCPs, one VWFA, the serine protease domain and have a putative factor D/C1s/MASP cleavage site. Southern blots show that there might be up to two Bf/C2-like genes for each of the two GcBf/C2 isoforms. GcBf/C2-1 and -2 are constitutively expressed, albeit at different levels, in all nine tissues examined. Expression in erythrocytes is a novel finding. Structural analysis has revealed that the localization of glycosylation sites in the SP domain of both putative proteins indicates that the molecular organization of the shark molecules is more like C2 than factor B. Phylogenetic analysis indicates that GcBf/C2-1 and -2 and TrscBf of Triakis scyllia (another shark species) originated from a common ancestor and share a remote ancestor with Bf and C2 of mammals and bony fish.

  13. 26 CFR 31.6302(c)-2A - Use of Government depositaries in connection with the railroad unemployment repayment tax.

    Science.gov (United States)

    2010-04-01

    ... with the railroad unemployment repayment tax. 31.6302(c)-2A Section 31.6302(c)-2A Internal Revenue...) § 31.6302(c)-2A Use of Government depositaries in connection with the railroad unemployment repayment...,000,000, such employer shall (except as provided below) deposit his undeposited railroad unemployment...

  14. 75 FR 27973 - Airworthiness Directives; Rolls-Royce plc RB211-524C2 Series Turbofan Engines

    Science.gov (United States)

    2010-05-19

    ... RB211-524C2 Series Turbofan Engines AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Notice... Rolls-Royce plc (RR) model RB211-524C2-19 and RB211-524C2-B-19 turbofan engines. These engines are...

  15. File list: InP.Myo.20.AllAg.C2C12 [Chip-atlas[Archive

    Lifescience Database Archive (English)

    Full Text Available InP.Myo.20.AllAg.C2C12 mm9 Input control Muscle C2C12 SRX262224,SRX262225,SRX148229...695944 http://dbarchive.biosciencedbc.jp/kyushu-u/mm9/assembled/InP.Myo.20.AllAg.C2C12.bed ...

  16. 78 FR 17967 - Self-Regulatory Organizations; C2 Options Exchange, Incorporated; Notice of Filing and Immediate...

    Science.gov (United States)

    2013-03-25

    ...'') and Amazon.com Inc. (``AMZN'') (``mini-options''). The purpose of this proposed rule change is to...://www.c2exchange.com/Legal/ ), at the Exchange's Office of the Secretary, and at the Commission's Public... Web site. The C2 rule filing Web site is located at: http://www.c2exchange.com/Legal/RuleFilings.aspx...

  17. 77 FR 22022 - Self-Regulatory Organizations; C2 Options Exchange, Incorporated; Order Approving a Proposed Rule...

    Science.gov (United States)

    2012-04-12

    ...-rata, and price-time with primary public customer and secondary trade participation right priority and...'') is within designated size and price parameters, as determined by C2 for the individual leg. See C2... within certain parameters determined by C2 and for which the NBBO is within designated size and price...

  18. 76 FR 7598 - Self-Regulatory Organizations; C2 Options Exchange, Incorporated; Notice of Filing of a Proposed...

    Science.gov (United States)

    2011-02-10

    ... its Bylaws to eliminate its Audit Committee. The text of the proposed amendments to C2's Bylaws and... the C2 Audit Committee. (a) Elimination of Office of Vice Chairman of the Board Based on the Exchange... role in facilitating communication between C2 and its Trading Permit Holders and in coordinating the...

  19. Efficient sequential and parallel algorithms for finding edit distance based motifs.

    Science.gov (United States)

    Pal, Soumitra; Xiao, Peng; Rajasekaran, Sanguthevar

    2016-08-18

    Motif search is an important step in extracting meaningful patterns from biological data. The general problem of motif search is intractable and there is a pressing need to develop efficient, exact and approximation algorithms to solve this problem. In this paper, we present several novel, exact, sequential and parallel algorithms for solving the (l,d) Edit-distance-based Motif Search (EMS) problem: given two integers l,d and n biological strings, find all strings of length l that appear in each input string with atmost d errors of types substitution, insertion and deletion. One popular technique to solve the problem is to explore for each input string the set of all possible l-mers that belong to the d-neighborhood of any substring of the input string and output those which are common for all input strings. We introduce a novel and provably efficient neighborhood exploration technique. We show that it is enough to consider the candidates in neighborhood which are at a distance exactly d. We compactly represent these candidate motifs using wildcard characters and efficiently explore them with very few repetitions. Our sequential algorithm uses a trie based data structure to efficiently store and sort the candidate motifs. Our parallel algorithm in a multi-core shared memory setting uses arrays for storing and a novel modification of radix-sort for sorting the candidate motifs. The algorithms for EMS are customarily evaluated on several challenging instances such as (8,1), (12,2), (16,3), (20,4), and so on. The best previously known algorithm, EMS1, is sequential and in estimated 3 days solves up to instance (16,3). Our sequential algorithms are more than 20 times faster on (16,3). On other hard instances such as (9,2), (11,3), (13,4), our algorithms are much faster. Our parallel algorithm has more than 600 % scaling performance while using 16 threads. Our algorithms have pushed up the state-of-the-art of EMS solvers and we believe that the techniques introduced in

  20. Through the Portal: Viking Motifs Incorporated in the Romanesque Style in Telemark, Norway

    Directory of Open Access Journals (Sweden)

    Kristine Ødeby

    2013-09-01

    Full Text Available This paper presents the results of an analysis of motifs identified on six carved wooden Romanesque portal panels from the Norwegian county of Telemark. The findings suggest that animal motifs in the Late Viking style survived long into the Late Medieval period and were reused on these medieval portals. Stylistically, late expressions of Viking animal art do not differ a great deal from those of the subsequent Romanesque style. However, their symbolical differences are considered to be significant. The motifs themselves, and the issue of whether the Romanesque style adopted motifs from pre-Christian art, have attracted less attention. The motif portraying Sigurd slaying the dragon is considered in depth. It will be suggested that Sigurd, serving as a mediator between the old and the new beliefs when he appeared in late Viking contexts, was given a new role when portrayed in Christian art. Metaphor and liminality are a central part of this paper, and the theories of Alfred Gell and Margrete Andås suggest that the portal itself affects those who pass through it, and that the iconography is meaningful from a liminal perspective.

  1. Discovery and validation of information theory-based transcription factor and cofactor binding site motifs.

    Science.gov (United States)

    Lu, Ruipeng; Mucaki, Eliseos J; Rogan, Peter K

    2017-03-17

    Data from ChIP-seq experiments can derive the genome-wide binding specificities of transcription factors (TFs) and other regulatory proteins. We analyzed 765 ENCODE ChIP-seq peak datasets of 207 human TFs with a novel motif discovery pipeline based on recursive, thresholded entropy minimization. This approach, while obviating the need to compensate for skewed nucleotide composition, distinguishes true binding motifs from noise, quantifies the strengths of individual binding sites based on computed affinity and detects adjacent cofactor binding sites that coordinate with the targets of primary, immunoprecipitated TFs. We obtained contiguous and bipartite information theory-based position weight matrices (iPWMs) for 93 sequence-specific TFs, discovered 23 cofactor motifs for 127 TFs and revealed six high-confidence novel motifs. The reliability and accuracy of these iPWMs were determined via four independent validation methods, including the detection of experimentally proven binding sites, explanation of effects of characterized SNPs, comparison with previously published motifs and statistical analyses. We also predict previously unreported TF coregulatory interactions (e.g. TF complexes). These iPWMs constitute a powerful tool for predicting the effects of sequence variants in known binding sites, performing mutation analysis on regulatory SNPs and predicting previously unrecognized binding sites and target genes. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. 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.

  3. Do motifs reflect evolved function?--No convergent evolution of genetic regulatory network subgraph topologies.

    Science.gov (United States)

    Knabe, Johannes F; Nehaniv, Chrystopher L; Schilstra, Maria J

    2008-01-01

    Methods that analyse the topological structure of networks have recently become quite popular. Whether motifs (subgraph patterns that occur more often than in randomized networks) have specific functions as elementary computational circuits has been cause for debate. As the question is difficult to resolve with currently available biological data, we approach the issue using networks that abstractly model natural genetic regulatory networks (GRNs) which are evolved to show dynamical behaviors. Specifically one group of networks was evolved to be capable of exhibiting two different behaviors ("differentiation") in contrast to a group with a single target behavior. In both groups we find motif distribution differences within the groups to be larger than differences between them, indicating that evolutionary niches (target functions) do not necessarily mold network structure uniquely. These results show that variability operators can have a stronger influence on network topologies than selection pressures, especially when many topologies can create similar dynamics. Moreover, analysis of motif functional relevance by lesioning did not suggest that motifs were of greater importance to the functioning of the network than arbitrary subgraph patterns. Only when drastically restricting network size, so that one motif corresponds to a whole functionally evolved network, was preference for particular connection patterns found. This suggests that in non-restricted, bigger networks, entanglement with the rest of the network hinders topological subgraph analysis.

  4. The position of the Gly-xxx-Gly motif in transmembrane segments modulates dimer affinity.

    Science.gov (United States)

    Johnson, Rachel M; Rath, Arianna; Deber, Charles M

    2006-12-01

    Although the intrinsic low solubility of membrane proteins presents challenges to their high-resolution structure determination, insight into the amino acid sequence features and forces that stabilize their folds has been provided through study of sequence-dependent helix-helix interactions between single transmembrane (TM) helices. While the stability of helix-helix partnerships mediated by the Gly-xxx-Gly (GG4) motif is known to be generally modulated by distal interfacial residues, it has not been established whether the position of this motif, with respect to the ends of a given TM segment, affects dimer affinity. Here we examine the relationship between motif position and affinity in the homodimers of 2 single-spanning membrane protein TM sequences: glycophorin A (GpA) and bacteriophage M13 coat protein (MCP). Using the TOXCAT assay for dimer affinity on a series of GpA and MCP TM segments that have been modified with either 4 Leu residues at each end or with 8 Leu residues at the N-terminal end, we show that in each protein, centrally located GG4 motifs are capable of stronger helix-helix interactions than those proximal to TM helix ends, even when surrounding interfacial residues are maintained. The relative importance of GG4 motifs in stabilizing helix-helix interactions therefore must be considered not only in its specific residue context but also in terms of the location of the interactive surface relative to the N and C termini of alpha-helical TM segments.

  5. 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.

  6. 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.

  7. Regulation of TCF ETS-domain transcription factors by helix-loop-helix motifs.

    Science.gov (United States)

    Stinson, Julie; Inoue, Toshiaki; Yates, Paula; Clancy, Anne; Norton, John D; Sharrocks, Andrew D

    2003-08-15

    DNA binding by the ternary complex factor (TCF) subfamily of ETS-domain transcription factors is tightly regulated by intramolecular and intermolecular interactions. The helix-loop-helix (HLH)-containing Id proteins are trans-acting negative regulators of DNA binding by the TCFs. In the TCF, SAP-2/Net/ERP, intramolecular inhibition of DNA binding is promoted by the cis-acting NID region that also contains an HLH-like motif. The NID also acts as a transcriptional repression domain. Here, we have studied the role of HLH motifs in regulating DNA binding and transcription by the TCF protein SAP-1 and how Cdk-mediated phosphorylation affects the inhibitory activity of the Id proteins towards the TCFs. We demonstrate that the NID region of SAP-1 is an autoinhibitory motif that acts to inhibit DNA binding and also functions as a transcription repression domain. This region can be functionally replaced by fusion of Id proteins to SAP-1, whereby the Id moiety then acts to repress DNA binding in cis. Phosphorylation of the Ids by cyclin-Cdk complexes results in reduction in protein-protein interactions between the Ids and TCFs and relief of their DNA-binding inhibitory activity. In revealing distinct mechanisms through which HLH motifs modulate the activity of TCFs, our results therefore provide further insight into the role of HLH motifs in regulating TCF function and how the inhibitory properties of the trans-acting Id HLH proteins are themselves regulated by phosphorylation.

  8. Motif finding in DNA sequences based on skipping nonconserved positions in background Markov chains.

    Science.gov (United States)

    Zhao, Xiaoyan; Sze, Sing-Hoi

    2011-05-01

    One strategy to identify transcription factor binding sites is through motif finding in upstream DNA sequences of potentially co-regulated genes. Despite extensive efforts, none of the existing algorithms perform very well. We consider a string representation that allows arbitrary ignored positions within the nonconserved portion of single motifs, and use O(2(l)) Markov chains to model the background distributions of motifs of length l while skipping these positions within each Markov chain. By focusing initially on positions that have fixed nucleotides to define core occurrences, we develop an algorithm to identify motifs of moderate lengths. We compare the performance of our algorithm to other motif finding algorithms on a few benchmark data sets, and show that significant improvement in accuracy can be obtained when the sites are sufficiently conserved within a given sample, while comparable performance is obtained when the site conservation rate is low. A software program (PosMotif ) and detailed results are available online at http://faculty.cse.tamu.edu/shsze/posmotif.

  9. OSR1 regulates a subset of inward rectifier potassium channels via a binding motif variant.

    Science.gov (United States)

    Taylor, Clinton A; An, Sung-Wan; Kankanamalage, Sachith Gallolu; Stippec, Steve; Earnest, Svetlana; Trivedi, Ashesh T; Yang, Jonathan Zijiang; Mirzaei, Hamid; Huang, Chou-Long; Cobb, Melanie H

    2018-04-10

    The with-no-lysine (K) (WNK) signaling pathway to STE20/SPS1-related proline- and alanine-rich kinase (SPAK) and oxidative stress-responsive 1 (OSR1) kinase is an important mediator of cell volume and ion transport. SPAK and OSR1 associate with upstream kinases WNK 1-4, substrates, and other proteins through their C-terminal domains which interact with linear R-F-x-V/I sequence motifs. In this study we find that SPAK and OSR1 also interact with similar affinity with a motif variant, R-x-F-x-V/I. Eight of 16 human inward rectifier K + channels have an R-x-F-x-V motif. We demonstrate that two of these channels, Kir2.1 and Kir2.3, are activated by OSR1, while Kir4.1, which does not contain the motif, is not sensitive to changes in OSR1 or WNK activity. Mutation of the motif prevents activation of Kir2.3 by OSR1. Both siRNA knockdown of OSR1 and chemical inhibition of WNK activity disrupt NaCl-induced plasma membrane localization of Kir2.3. Our results suggest a mechanism by which WNK-OSR1 enhance Kir2.1 and Kir2.3 channel activity by increasing their plasma membrane localization. Regulation of members of the inward rectifier K + channel family adds functional and mechanistic insight into the physiological impact of the WNK pathway.

  10. 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.

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

    KAUST Repository

    AbouEisha, Hassan M.

    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.

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

    KAUST Repository

    Kalkatawi, Manal M.

    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.

  13. Identification of helix capping and β-turn motifs from NMR chemical shifts

    International Nuclear Information System (INIS)

    Shen Yang; Bax, Ad

    2012-01-01

    We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13 C β chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of β-turns: I, II, I′, II′ 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 β-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.

  14. Structural motifs of diiodine complexes with amides and thioamides.

    Science.gov (United States)

    Parigoridi, Ioanna-Efpraxia; Corban, Ghada J; Hadjikakou, Sotiris K; Hadjiliadis, Nick; Kourkoumelis, Nikolaos; Kostakis, George; Psycharis, Vassilis; Raptopoulou, Catherine P; Kubicki, Maciej

    2008-10-14

    The reaction of 2-pyrimidone hydrochloride ([C(4)H(5)N(2)O](+)[Cl](-) or [PMOH(2)](+)[Cl](-)) with diiodine in a dichloromethane-methanol solution resulted in the formation of ([C(4)H(5)N(2)O](+))(2)[I(2)Cl(2)](2-) (1) complex. The compound was characterized by elemental analysis, FT-IR, DTA-TG and conductivity titrations. The crystal structure of 1 was also determined by X-ray diffraction at 294(1) K. Compound 1 is monoclinic, space group P2(1)/n, consisting of two cationic [PMOH(2)](+) species and a [I(2)Cl(2)](2-) counter dianion. The cation is in its keto form. Direct reaction of thiazolidine-2-thione (tzdtH), with diiodine in dichloromethane solution, on the other hand, led to the formation of a crystalline solid which contained two complexes of formulae [(tzdtH)(2)I](+)[I(3)](-).2I(2) (2) and [(tzdtH)I(2)](2).I(2) (2a) in a ratio of 90 to 10%. Complex 2a was characterized by X-ray analysis at 180(2) K. Compound is monoclinic, space group C2/c and contains two units of [(tzdtH)I(2)] "spoke" structures. Compound 1, as well as the known species iodonium salt [(tzdtH)(2)I](+)[I(3)](-).2I(2) (2) and the charge transfer (CT) iodine complexes of formulae [(bztzdtH)I(2)] (3) and [(bztzdtH)I(2)].I(2) (4) (bztzdtH = 2-mercaptobenzothiazole) with "spoke" and extended "spoke" structures respectively, were tested for their oxidizing activity towards 3,5-di-tert-butylcatechol to 3,5-di-tert-butyl-o-benzoquinone.

  15. Force Limited Vibration Testing: Computation C2 for Real Load and Probabilistic Source

    Science.gov (United States)

    Wijker, J. J.; de Boer, A.; Ellenbroek, M. H. M.

    2014-06-01

    To prevent over-testing of the test-item during random vibration testing Scharton proposed and discussed the force limited random vibration testing (FLVT) in a number of publications, in which the factor C2 is besides the random vibration specification, the total mass and the turnover frequency of the load(test item), a very important parameter. A number of computational methods to estimate C2 are described in the literature, i.e. the simple and the complex two degrees of freedom system, STDFS and CTDFS, respectively. Both the STDFS and the CTDFS describe in a very reduced (simplified) manner the load and the source (adjacent structure to test item transferring the excitation forces, i.e. spacecraft supporting an instrument).The motivation of this work is to establish a method for the computation of a realistic value of C2 to perform a representative random vibration test based on force limitation, when the adjacent structure (source) description is more or less unknown. Marchand formulated a conservative estimation of C2 based on maximum modal effective mass and damping of the test item (load) , when no description of the supporting structure (source) is available [13].Marchand discussed the formal description of getting C 2 , using the maximum PSD of the acceleration and maximum PSD of the force, both at the interface between load and source, in combination with the apparent mass and total mass of the the load. This method is very convenient to compute the factor C 2 . However, finite element models are needed to compute the spectra of the PSD of both the acceleration and force at the interface between load and source.Stevens presented the coupled systems modal approach (CSMA), where simplified asparagus patch models (parallel-oscillator representation) of load and source are connected, consisting of modal effective masses and the spring stiffnesses associated with the natural frequencies. When the random acceleration vibration specification is given the CMSA

  16. Cobalt triggers necrotic cell death and atrophy in skeletal C2C12 myotubes

    International Nuclear Information System (INIS)

    Rovetta, Francesca; Stacchiotti, Alessandra; Faggi, Fiorella; Catalani, Simona; Apostoli, Pietro; Fanzani, Alessandro; Aleo, Maria Francesca

    2013-01-01

    Severe poisoning has recently been diagnosed in humans having hip implants composed of cobalt–chrome alloys due to the release of particulate wear debris on polyethylene and ceramic implants which stimulates macrophagic infiltration and destroys bone and soft tissue, leading to neurological, sensorial and muscular impairments. Consistent with this premise, in this study, we focused on the mechanisms underlying the toxicity of Co(II) ions on skeletal muscle using mouse skeletal C2C12 myotubes as an in vitro model. As detected using propidium iodide incorporation, increasing CoCl 2 doses (from 5 to 200 μM) affected the viability of C2C12 myotubes, mainly by cell necrosis, which was attenuated by necrostatin-1, an inhibitor of the necroptotic branch of the death domain receptor signaling pathway. On the other hand, apoptosis was hardly detectable as supported by the lack of caspase-3 and -8 activation, the latter resulting in only faint activation after exposure to higher CoCl 2 doses for prolonged time points. Furthermore, CoCl 2 treatment resulted in atrophy of the C2C12 myotubes which was characterized by the increased expression of HSP25 and GRP94 stress proteins and other typical 'pro-atrophic molecular hallmarks, such as early activation of the NF-kB pathway and down-regulation of AKT phosphorylation, followed by the activation of the proteasome and autophagy systems. Overall, these results suggested that cobalt may impact skeletal muscle homeostasis as an inducer of cell necrosis and myofiber atrophy. - Highlights: • The effects of cobalt on muscle myofibers in vitro were investigated. • Cobalt treatment mainly causes cell necrosis in skeletal C2C12 myotubes. • Cobalt impacts the PI3K/AKT and NFkB pathways and induces cell stress markers. • Cobalt induces atrophy of C2C12 myotubes through the activation of proteasome and autophagy systems. • Co treatment triggers NF-kB and PI3K/AKT pathways in C2C12 myotubes

  17. Cobalt triggers necrotic cell death and atrophy in skeletal C2C12 myotubes

    Energy Technology Data Exchange (ETDEWEB)

    Rovetta, Francesca [Unit of Biotechnologies, Department of Molecular and Translational Medicine, University of Brescia, Brescia I-25123 (Italy); Interuniversity Institute of Myology (IIM) (Italy); Stacchiotti, Alessandra [Institute of Human Anatomy, Department of Clinical and Experimental Sciences, University of Brescia, Brescia I-25123 (Italy); Faggi, Fiorella [Unit of Biotechnologies, Department of Molecular and Translational Medicine, University of Brescia, Brescia I-25123 (Italy); Interuniversity Institute of Myology (IIM) (Italy); Catalani, Simona; Apostoli, Pietro [Unit of Occupational Health and Industrial Hygiene, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia I-25123 (Italy); Fanzani, Alessandro, E-mail: fanzani@med.unibs.it [Unit of Biotechnologies, Department of Molecular and Translational Medicine, University of Brescia, Brescia I-25123 (Italy); Interuniversity Institute of Myology (IIM) (Italy); Aleo, Maria Francesca, E-mail: aleo@med.unibs.it [Unit of Biotechnologies, Department of Molecular and Translational Medicine, University of Brescia, Brescia I-25123 (Italy); Interuniversity Institute of Myology (IIM) (Italy)

    2013-09-01

    Severe poisoning has recently been diagnosed in humans having hip implants composed of cobalt–chrome alloys due to the release of particulate wear debris on polyethylene and ceramic implants which stimulates macrophagic infiltration and destroys bone and soft tissue, leading to neurological, sensorial and muscular impairments. Consistent with this premise, in this study, we focused on the mechanisms underlying the toxicity of Co(II) ions on skeletal muscle using mouse skeletal C2C12 myotubes as an in vitro model. As detected using propidium iodide incorporation, increasing CoCl{sub 2} doses (from 5 to 200 μM) affected the viability of C2C12 myotubes, mainly by cell necrosis, which was attenuated by necrostatin-1, an inhibitor of the necroptotic branch of the death domain receptor signaling pathway. On the other hand, apoptosis was hardly detectable as supported by the lack of caspase-3 and -8 activation, the latter resulting in only faint activation after exposure to higher CoCl{sub 2} doses for prolonged time points. Furthermore, CoCl{sub 2} treatment resulted in atrophy of the C2C12 myotubes which was characterized by the increased expression of HSP25 and GRP94 stress proteins and other typical 'pro-atrophic molecular hallmarks, such as early activation of the NF-kB pathway and down-regulation of AKT phosphorylation, followed by the activation of the proteasome and autophagy systems. Overall, these results suggested that cobalt may impact skeletal muscle homeostasis as an inducer of cell necrosis and myofiber atrophy. - Highlights: • The effects of cobalt on muscle myofibers in vitro were investigated. • Cobalt treatment mainly causes cell necrosis in skeletal C2C12 myotubes. • Cobalt impacts the PI3K/AKT and NFkB pathways and induces cell stress markers. • Cobalt induces atrophy of C2C12 myotubes through the activation of proteasome and autophagy systems. • Co treatment triggers NF-kB and PI3K/AKT pathways in C2C12 myotubes.

  18. Molecular dynamics simulations of electrostatics and hydration distributions around RNA and DNA motifs

    Science.gov (United States)

    Marlowe, Ashley E.; Singh, Abhishek; Semichaevsky, Andrey V.; Yingling, Yaroslava G.

    2009-03-01

    Nucleic acid nanoparticles can self-assembly through the formation of complementary loop-loop interactions or stem-stem interactions. Presence and concentration of ions can significantly affect the self-assembly process and the stability of the nanostructure. In this presentation we use explicit molecular dynamics simulations to examine the variations in cationic distributions and hydration environment around DNA and RNA helices and loop-loop interactions. Our simulations show that the potassium and sodium ionic distributions are different around RNA and DNA motifs which could be indicative of ion mediated relative stability of loop-loop complexes. Moreover in RNA loop-loop motifs ions are consistently present and exchanged through a distinct electronegative channel. We will also show how we used the specific RNA loop-loop motif to design a RNA hexagonal nanoparticle.

  19. PDL1 Signals through Conserved Sequence Motifs to Overcome Interferon-Mediated Cytotoxicity

    Directory of Open Access Journals (Sweden)

    Maria Gato-Cañas

    2017-08-01

    Full Text Available PDL1 blockade produces remarkable clinical responses, thought to occur by T cell reactivation through prevention of PDL1-PD1 T cell inhibitory interactions. Here, we find that PDL1 cell-intrinsic signaling protects cancer cells from interferon (IFN cytotoxicity and accelerates tumor progression. PDL1 inhibited IFN signal transduction through a conserved class of sequence