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Sample records for hemicatenated dna loops

  1. Proteins mediating DNA loops effectively block transcription.

    Science.gov (United States)

    Vörös, Zsuzsanna; Yan, Yan; Kovari, Daniel T; Finzi, Laura; Dunlap, David

    2017-07-01

    Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop-mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  2. Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription.

    Science.gov (United States)

    Gerasimova, N S; Pestov, N A; Kulaeva, O I; Clark, D J; Studitsky, V M

    2016-05-26

    RNA polymerase II (Pol II) transcription through chromatin is accompanied by formation of small intranucleosomal DNA loops. Pol II captured within a small loop drives accumulation of DNA supercoiling, facilitating further transcription. DNA breaks relieve supercoiling and induce Pol II arrest, allowing detection of DNA damage hidden in chromatin structure.

  3. Studying DNA looping by single-molecule FRET.

    Science.gov (United States)

    Le, Tung T; Kim, Harold D

    2014-06-28

    Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA.

  4. Concentration and length dependence of DNA looping in transcriptional regulation.

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    Lin Han

    2009-05-01

    Full Text Available In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA loops: Binding at two or more sites on the DNA results in the formation of a loop, which can bring the transcription factor into the immediate neighborhood of the relevant promoter. These processes are important in settings ranging from the historic bacterial examples (bacterial metabolism and the lytic-lysogeny decision in bacteriophage, to the modern concept of gene regulation to regulatory processes central to pattern formation during development of multicellular organisms. Though there have been a variety of insights into the combinatorial aspects of transcriptional control, the mechanism of DNA looping as an agent of combinatorial control in both prokaryotes and eukaryotes remains unclear. We use single-molecule techniques to dissect DNA looping in the lac operon. In particular, we measure the propensity for DNA looping by the Lac repressor as a function of the concentration of repressor protein and as a function of the distance between repressor binding sites. As with earlier single-molecule studies, we find (at least two distinct looped states and demonstrate that the presence of these two states depends both upon the concentration of repressor protein and the distance between the two repressor binding sites. We find that loops form even at interoperator spacings considerably shorter than the DNA persistence length, without the intervention of any other proteins to prebend the DNA. The concentration measurements also permit us to use a simple statistical mechanical model of DNA loop formation to determine the free energy of DNA looping, or equivalently, the for looping.

  5. Studying DNA Looping by Single-Molecule FRET

    OpenAIRE

    Le, Tung T.; Kim, Harold D.

    2014-01-01

    Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can als...

  6. The free-energy cost of interaction between DNA loops.

    Science.gov (United States)

    Huang, Lifang; Liu, Peijiang; Yuan, Zhanjiang; Zhou, Tianshou; Yu, Jianshe

    2017-10-03

    From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.

  7. Binding of histone H1 to DNA is differentially modulated by redox state of HMGB1.

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    Eva Polanská

    Full Text Available HMGB1 is an architectural protein in chromatin, acting also as a signaling molecule outside the cell. Recent reports from several laboratories provided evidence that a number of both the intracellular and extracellular functions of HMGB1 may depend on redox-sensitive cysteine residues of the protein. In this study we demonstrate that redox state of HMGB1 can significantly modulate the ability of the protein to bind and bend DNA, as well as to promote DNA end-joining. We also report a high affinity binding of histone H1 to hemicatenated DNA loops and DNA minicircles. Finally, we show that reduced HMGB1 can readily displace histone H1 from DNA, while oxidized HMGB1 has limited capacity for H1 displacement. Our results suggested a novel mechanism for the HMGB1-mediated modulation of histone H1 binding to DNA. Possible biological consequences of linker histones H1 replacement by HMGB1 for the functioning of chromatin are discussed.

  8. DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

    Science.gov (United States)

    Laurens, Niels; Rusling, David A.; Pernstich, Christian; Brouwer, Ineke; Halford, Stephen E.; Wuite, Gijs J. L.

    2012-01-01

    Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond. PMID:22373924

  9. Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression.

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    Aze, Antoine; Sannino, Vincenzo; Soffientini, Paolo; Bachi, Angela; Costanzo, Vincenzo

    2016-06-01

    Half of the human genome is made up of repetitive DNA. However, mechanisms underlying replication of chromosome regions containing repetitive DNA are poorly understood. We reconstituted replication of defined human chromosome segments using bacterial artificial chromosomes in Xenopus laevis egg extract. Using this approach we characterized the chromatin assembly and replication dynamics of centromeric alpha-satellite DNA. Proteomic analysis of centromeric chromatin revealed replication-dependent enrichment of a network of DNA repair factors including the MSH2-6 complex, which was required for efficient centromeric DNA replication. However, contrary to expectations, the ATR-dependent checkpoint monitoring DNA replication fork arrest could not be activated on highly repetitive DNA due to the inability of the single-stranded DNA binding protein RPA to accumulate on chromatin. Electron microscopy of centromeric DNA and supercoil mapping revealed the presence of topoisomerase I-dependent DNA loops embedded in a protein matrix enriched for SMC2-4 proteins. This arrangement suppressed ATR signalling by preventing RPA hyper-loading, facilitating replication of centromeric DNA. These findings have important implications for our understanding of repetitive DNA metabolism and centromere organization under normal and stressful conditions.

  10. Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage

    DEFF Research Database (Denmark)

    Stella, Stefano; Alcón, Pablo; Montoya, Guillermo

    2017-01-01

    involved in DNA unwinding to form a CRISPR RNA (crRNA)-DNA hybrid and a displaced DNA strand. The protospacer adjacent motif (PAM) is recognized by the PAM-interacting domain. The loop-lysine helix-loop motif in this domain contains three conserved lysine residues that are inserted in a dentate manner...... and the crRNA-DNA hybrid, avoiding DNA re-annealing. Mutations in key residues reveal a mechanism linking the PAM and DNA nuclease sites. Analysis of the Cpf1 structures proposes a singular working model of RNA-guided DNA cleavage, suggesting new avenues for redesign of Cpf1....

  11. Whole-loop mitochondrial DNA D-loop sequence variability in Egyptian Arabian equine matrilines

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    Hudson, William

    2017-01-01

    Background Egyptian Arabian horses have been maintained in a state of genetic isolation for over a hundred years. There is only limited genetic proof that the studbook records of female lines of Egyptian Arabian pedigrees are reliable. This study characterized the mitochondrial DNA (mtDNA) signatures of 126 horses representing 14 matrilines in the Egyptian Agricultural Organization (EAO) horse-breeding program. Findings Analysis of the whole D-loop sequence yielded additional information compared to hypervariable region-1 (HVR1) analysis alone, with 42 polymorphic sites representing ten haplotypes compared to 16 polymorphic sites representing nine haplotypes, respectively. Most EAO haplotypes belonged to ancient haplogroups, suggesting origin from a wide geographical area over many thousands of years, although one haplotype was novel. Conclusions Historical families share haplotypes and some individuals from different strains belonged to the same haplogroup: the classical EAO strain designation is not equivalent to modern monophyletic matrilineal groups. Phylogenetic inference showed that the foundation mares of the historical haplotypes were highly likely to have the same haplotypes as the animals studied (p > 0.998 in all cases), confirming the reliability of EAO studbook records and providing the opportunity for breeders to confirm the ancestry of their horses. PMID:28859174

  12. DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations

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    Rusling, David A.; Laurens, Niels; Pernstich, Christian; Wuite, Gijs J. L.; Halford, Stephen E.

    2012-01-01

    Most restriction endonucleases, including FokI, interact with two copies of their recognition sequence before cutting DNA. On DNA with two sites they act in cis looping out the intervening DNA. While many restriction enzymes operate symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic site. The directionality of its sequence means that two FokI sites can be bridged in either parallel or anti-parallel alignments. Here we show by biochemical and single-molecule biophysical methods that FokI aligns two recognition sites on separate DNA molecules in parallel and that the parallel arrangement holds for sites in the same DNA regardless of whether they are in inverted or repeated orientations. The parallel arrangement dictates the topology of the loop trapped between sites in cis: the loop from inverted sites has a simple 180° bend, while that with repeated sites has a convoluted 360° turn. The ability of FokI to act at asymmetric sites thus enabled us to identify the synapse geometry for sites in trans and in cis, which in turn revealed the relationship between synapse geometry and loop topology. PMID:22362745

  13. DNA loop domain organization in nucleoids from cells of different types.

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    Afanasieva, Katerina; Chopei, Marianna; Lozovik, Alexandra; Semenova, Anastasia; Lukash, Lyubov; Sivolob, Andrei

    2017-01-29

    The loop domain organization of chromatin plays an important role in transcription regulation and thus may be assumed to vary in cells of different types. We investigated the kinetics of DNA loop migration during single cell gel electrophoresis (the comet assay) for nucleoids obtained from human lymphocytes, lymphoblasts and glioblastoma T98G cells. The results confirm our previous observation that there are three parts of DNA in nucleoids: DNA on the nucleoid surface, loops up to ∼150 kb inside the nucleoid, and larger loops that cannot migrate. However, the relative amounts of the three parts were found to be very different for different cell types. The distributions of the loop length up to 150 kb were shown to be exponential, with the distribution parameter, the loop density, to be dependent on the cell type. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data.

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    Lareau, Caleb A; Aryee, Martin J; Berger, Bonnie

    2018-02-15

    The 3D architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in DNA looping structure are associated with variation in gene expression and cell state. To systematically assess changes in DNA looping architecture between samples, we introduce diffloop, an R/Bioconductor package that provides a suite of functions for the quality control, statistical testing, annotation, and visualization of DNA loops. We demonstrate this functionality by detecting differences between ENCODE ChIA-PET samples and relate looping to variability in epigenetic state. Diffloop is implemented as an R/Bioconductor package available at https://bioconductor.org/packages/release/bioc/html/diffloop.html. aryee.martin@mgh.harvard.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  15. Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses.

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    Hamperl, Stephan; Bocek, Michael J; Saldivar, Joshua C; Swigut, Tomek; Cimprich, Karlene A

    2017-08-10

    Conflicts between transcription and replication are a potent source of DNA damage. Co-transcriptional R-loops could aggravate such conflicts by creating an additional barrier to replication fork progression. Here, we use a defined episomal system to investigate how conflict orientation and R-loop formation influence genome stability in human cells. R-loops, but not normal transcription complexes, induce DNA breaks and orientation-specific DNA damage responses during conflicts with replication forks. Unexpectedly, the replisome acts as an orientation-dependent regulator of R-loop levels, reducing R-loops in the co-directional (CD) orientation but promoting their formation in the head-on (HO) orientation. Replication stress and deregulated origin firing increase the number of HO collisions leading to genome-destabilizing R-loops. Our findings connect DNA replication to R-loop homeostasis and suggest a mechanistic basis for genome instability resulting from deregulated DNA replication, observed in cancer and other disease states. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome

    Science.gov (United States)

    Walter, Jean-Charles; Walliser, Nils-Ole; David, Gabriel; Dorignac, Jérôme; Geniet, Frédéric; Palmeri, John; Parmeggiani, Andrea; Wingreen, Ned S.; Broedersz, Chase P.

    2018-03-01

    The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the looping and clustering model, which employs a statistical physics approach to describe protein-DNA complexes. The looping and clustering model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and loop closure entropy of this protein-DNA cluster on the one hand, and the positional entropy for placing loops within the cluster on the other. Indeed, we show that the protein interaction strength determines the ‘tightness’ of the loopy protein-DNA complex. Thus, our model provides a theoretical framework for quantitatively computing the binding profiles of ParB-like proteins around a cognate (parS) binding site.

  17. RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes.

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    NandyMazumdar, Monali; Nedialkov, Yuri; Svetlov, Dmitri; Sevostyanova, Anastasia; Belogurov, Georgiy A; Artsimovitch, Irina

    2016-12-27

    Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β' clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.

  18. Senataxin Mutation Reveals How R-Loops Promote Transcription by Blocking DNA Methylation at Gene Promoters.

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    Grunseich, Christopher; Wang, Isabel X; Watts, Jason A; Burdick, Joshua T; Guber, Robert D; Zhu, Zhengwei; Bruzel, Alan; Lanman, Tyler; Chen, Kelian; Schindler, Alice B; Edwards, Nancy; Ray-Chaudhury, Abhik; Yao, Jianhua; Lehky, Tanya; Piszczek, Grzegorz; Crain, Barbara; Fischbeck, Kenneth H; Cheung, Vivian G

    2018-02-01

    R-loops are three-stranded nucleic acid structures found abundantly and yet often viewed as by-products of transcription. Studying cells from patients with a motor neuron disease (amyotrophic lateral sclerosis 4 [ALS4]) caused by a mutation in senataxin, we uncovered how R-loops promote transcription. In ALS4 patients, the senataxin mutation depletes R-loops with a consequent effect on gene expression. With fewer R-loops in ALS4 cells, the expression of BAMBI, a negative regulator of transforming growth factor β (TGF-β), is reduced; that then leads to the activation of the TGF-β pathway. We uncovered that genome-wide R-loops influence promoter methylation of over 1,200 human genes. DNA methyl-transferase 1 favors binding to double-stranded DNA over R-loops. Thus, in forming R-loops, nascent RNA blocks DNA methylation and promotes further transcription. Hence, our results show that nucleic acid structures, in addition to sequences, influence the binding and activity of regulatory proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Cooperation of DNA-PKcs and WRN helicase in the maintenance of telomeric D-loops

    DEFF Research Database (Denmark)

    Kusumoto-Matsuo, Rika; Opresko, Patricia L; Ramsden, Dale

    2010-01-01

    Werner syndrome is an inherited human progeriod syndrome caused by mutations in the gene encoding the Werner Syndrome protein, WRN. It has both 3'-5' DNA helicase and exonuclease activities, and is suggested to have roles in many aspects of DNA metabolism, including DNA repair and telomere...... D-loop model substrate. In addition, the length of telomeric G-tails decreases in DNA-PKcs knockdown cells, and this phenotype is reversed by overexpression of WRN helicase. These results suggest that WRN and DNA-PKcs may cooperatively prevent G-tail shortening in vivo....

  20. Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

    Science.gov (United States)

    2017-01-01

    We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory. PMID:28475322

  1. Protein intercalation in DNA as one of main modes of fixation of the most stable chromatin loop domains

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    М. I. Chopei

    2014-08-01

    Full Text Available The main mechanism of DNA track formation during comet assay of nucleoids, obtained after removal of cell membranes and most of proteins, is the extension to anode of negatively supercoiled DNA loops attached to proteins, remaining in nucleoid after lysis treatment. The composition of these residual protein structures and the nature of their strong interaction with the loop ends remain poorly studied. In this work we investigated the influence of chloroquine intercalation and denaturation of nucleoid proteins on the efficiency of electrophoretic track formation during comet assay. The results obtained suggest that even gentle protein denaturation is sufficient to reduce considerably the effectiveness of the DNA loop migration due to an increase in the loops size. The same effect was observed under local DNA unwinding upon chloroquine intercalation around the sites of the attachment of DNA to proteins. The topological interaction (protein intercalation into the double helix between DNA loop ends and nucleoid proteins is discussed.

  2. R-loops and initiation of DNA replication in human cells: a missing link?

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    Rodrigo eLombraña

    2015-04-01

    Full Text Available The unanticipated widespread occurrence of stable hybrid DNA/RNA structures (R-loops in human cells and the increasing evidence of their involvement in several human malignancies have invigorated the research on R-loop biology in recent years. Here we propose that physiological R-loop formation at CpG island promoters can contribute to DNA replication origin specification at these regions, the most efficient replication initiation sites in mammalian cells. Quite likely, this occurs by the strand-displacement reaction activating the formation of G-quadruplex structures that target the Origin Recognition Complex (ORC in the single-stranded conformation. In agreement with this, we found that R-loops co-localize with the ORC within the same CpG island region in a significant fraction of these efficient replication origins, precisely at the position displaying the highest density of G4 motifs. This scenario builds on the connection between transcription and replication in human cells and suggests that R-loop dysregulation at CpG island promoter-origins might contribute to the phenotype of DNA replication abnormalities and loss of genome integrity detected in cancer cells.

  3. Loop-mediated isothermal amplification (LAMP) shield for Arduino DNA detection

    NARCIS (Netherlands)

    Velders, Aldrik H.; Schoen, Cor; Saggiomo, Vittorio

    2018-01-01

    Objective: Loop-mediated isothermal amplification (LAMP) of DNA is gaining relevance as a method to detect nucleic acids, as it is easier, faster, and more powerful than conventional Polymerase Chain Reaction. However, LAMP is still mostly used in laboratory settings, because of the lack of a cheap

  4. Loop-mediated isothermal amplification (LAMP) shield for Arduino DNA detection.

    Science.gov (United States)

    Velders, Aldrik H; Schoen, Cor; Saggiomo, Vittorio

    2018-02-01

    Loop-mediated isothermal amplification (LAMP) of DNA is gaining relevance as a method to detect nucleic acids, as it is easier, faster, and more powerful than conventional Polymerase Chain Reaction. However, LAMP is still mostly used in laboratory settings, because of the lack of a cheap and easy, one-button device that can perform LAMP experiments. Here we show how to build and program an Arduino shield for a LAMP and detection of DNA. The here described Arduino Shield is cheap, easy to assemble, to program and use, it is battery operated and the detection of DNA is done by naked-eye so that it can be used in field.

  5. RTEL1 dismantles T loops and counteracts telomeric G4-DNA to maintain telomere integrity.

    Science.gov (United States)

    Vannier, Jean-Baptiste; Pavicic-Kaltenbrunner, Visnja; Petalcorin, Mark I R; Ding, Hao; Boulton, Simon J

    2012-05-11

    T loops and telomeric G-quadruplex (G4) DNA structures pose a potential threat to genome stability and must be dismantled to permit efficient telomere replication. Here we implicate the helicase RTEL1 in the removal of telomeric DNA secondary structures, which is essential for preventing telomere fragility and loss. In the absence of RTEL1, T loops are inappropriately resolved by the SLX4 nuclease complex, resulting in loss of the telomere as a circle. Depleting SLX4 or blocking DNA replication abolished telomere circles (TCs) and rescued telomere loss in RTEL1(-/-) cells but failed to suppress telomere fragility. Conversely, stabilization of telomeric G4-DNA or loss of BLM dramatically enhanced telomere fragility in RTEL1-deficient cells but had no impact on TC formation or telomere loss. We propose that RTEL1 performs two distinct functions at telomeres: it disassembles T loops and also counteracts telomeric G4-DNA structures, which together ensure the dynamics and stability of the telomere. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Phosphate-methylated DNA aimed at HIV-1 RNA loops and integrated DNA inhibits viral infectivity

    NARCIS (Netherlands)

    Buck, H. M.; Koole, L. H.; van Genderen, M. H.; Smit, L.; Geelen, J. L.; Jurriaans, S.; Goudsmit, J.

    1990-01-01

    Phosphate-methylated DNA hybridizes strongly and specifically to natural DNA and RNA. Hybridization to single-stranded and double-stranded DNA leads to site-selective blocking of replication and transcription. Phosphate-methylated DNA was used to interrupt the life cycle of the human

  7. Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells.

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    Zach Hensel

    Full Text Available DNA looping mediated by transcription factors plays critical roles in prokaryotic gene regulation. The "genetic switch" of bacteriophage λ determines whether a prophage stays incorporated in the E. coli chromosome or enters the lytic cycle of phage propagation and cell lysis. Past studies have shown that long-range DNA interactions between the operator sequences O(R and O(L (separated by 2.3 kb, mediated by the λ repressor CI (accession number P03034, play key roles in regulating the λ switch. In vitro, it was demonstrated that DNA segments harboring the operator sequences formed loops in the presence of CI, but CI-mediated DNA looping has not been directly visualized in vivo, hindering a deep understanding of the corresponding dynamics in realistic cellular environments. We report a high-resolution, single-molecule imaging method to probe CI-mediated DNA looping in live E. coli cells. We labeled two DNA loci with differently colored fluorescent fusion proteins and tracked their separations in real time with ∼40 nm accuracy, enabling the first direct analysis of transcription-factor-mediated DNA looping in live cells. Combining looping measurements with measurements of CI expression levels in different operator mutants, we show quantitatively that DNA looping activates transcription and enhances repression. Further, we estimated the upper bound of the rate of conformational change from the unlooped to the looped state, and discuss how chromosome compaction may impact looping kinetics. Our results provide insights into transcription-factor-mediated DNA looping in a variety of operator and CI mutant backgrounds in vivo, and our methodology can be applied to a broad range of questions regarding chromosome conformations in prokaryotes and higher organisms.

  8. Mapping the structural and dynamical features of multiple p53 DNA binding domains: insights into loop 1 intrinsic dynamics.

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    Suryani Lukman

    Full Text Available The transcription factor p53 regulates cellular integrity in response to stress. p53 is mutated in more than half of cancerous cells, with a majority of the mutations localized to the DNA binding domain (DBD. In order to map the structural and dynamical features of the DBD, we carried out multiple copy molecular dynamics simulations (totaling 0.8 μs. Simulations show the loop 1 to be the most dynamic element among the DNA-contacting loops (loops 1-3. Loop 1 occupies two major conformational states: extended and recessed; the former but not the latter displays correlations in atomic fluctuations with those of loop 2 (~24 Å apart. Since loop 1 binds to the major groove whereas loop 2 binds to the minor groove of DNA, our results begin to provide some insight into the possible mechanism underpinning the cooperative nature of DBD binding to DNA. We propose (1 a novel mechanism underlying the dynamics of loop 1 and the possible tread-milling of p53 on DNA and (2 possible mutations on loop 1 residues to restore the transcriptional activity of an oncogenic mutation at a distant site.

  9. RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage.

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    Cristini, Agnese; Groh, Matthias; Kristiansen, Maiken S; Gromak, Natalia

    2018-05-08

    R-loops comprise an RNA/DNA hybrid and displaced single-stranded DNA. They play important biological roles and are implicated in pathology. Even so, proteins recognizing these structures are largely undefined. Using affinity purification with the S9.6 antibody coupled to mass spectrometry, we defined the RNA/DNA hybrid interactome in HeLa cells. This consists of known R-loop-associated factors SRSF1, FACT, and Top1, and yet uncharacterized interactors, including helicases, RNA processing, DNA repair, and chromatin factors. We validate specific examples of these interactors and characterize their involvement in R-loop biology. A top candidate DHX9 helicase promotes R-loop suppression and transcriptional termination. DHX9 interacts with PARP1, and both proteins prevent R-loop-associated DNA damage. DHX9 and other interactome helicases are overexpressed in cancer, linking R-loop-mediated DNA damage and disease. Our RNA/DNA hybrid interactome provides a powerful resource to study R-loop biology in health and disease. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  10. Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds.

    Science.gov (United States)

    Guo, H W; Li, C; Wang, X N; Li, Z J; Sun, G R; Li, G X; Liu, X J; Kang, X T; Han, R L

    2017-10-01

    1. To explore the genetic diversity of Chinese indigenous chicken breeds, a 585 bp fragment of the mitochondrial DNA (mtDNA) region was sequenced in 102 birds from the Xichuan black-bone chicken, Yunyang black-bone chicken and Lushi chicken. In addition, 30 mtDNA D-loop sequences of Silkie fowls were downloaded from NCBI. The mtDNA D-loop sequence polymorphism and maternal origin of 4 chicken breeds were analysed in this study. 2. The results showed that a total of 33 mutation sites and 28 haplotypes were detected in the 4 chicken breeds. The haplotype diversity and nucleotide diversity of these 4 native breeds were 0.916 ± 0.014 and 0.012 ± 0.002, respectively. Three clusters were formed in 4 Chinese native chickens and 12 reference breeds. Both the Xichuan black-bone chicken and Yunyang black-bone chicken were grouped into one cluster. Four haplogroups (A, B, C and E) emerged in the median-joining network in these breeds. 3. It was concluded that these 4 Chinese chicken breeds had high genetic diversity. The phylogenetic tree and median network profiles showed that Chinese native chickens and its neighbouring countries had at least two maternal origins, one from Yunnan, China and another from Southeast Asia or its surrounding area.

  11. Human ribonuclease H1 resolves R-loops and thereby enables progression of the DNA replication fork.

    Science.gov (United States)

    Parajuli, Shankar; Teasley, Daniel C; Murali, Bhavna; Jackson, Jessica; Vindigni, Alessandro; Stewart, Sheila A

    2017-09-15

    Faithful DNA replication is essential for genome stability. To ensure accurate replication, numerous complex and redundant replication and repair mechanisms function in tandem with the core replication proteins to ensure DNA replication continues even when replication challenges are present that could impede progression of the replication fork. A unique topological challenge to the replication machinery is posed by RNA-DNA hybrids, commonly referred to as R-loops. Although R-loops play important roles in gene expression and recombination at immunoglobulin sites, their persistence is thought to interfere with DNA replication by slowing or impeding replication fork progression. Therefore, it is of interest to identify DNA-associated enzymes that help resolve replication-impeding R-loops. Here, using DNA fiber analysis, we demonstrate that human ribonuclease H1 (RNH1) plays an important role in replication fork movement in the mammalian nucleus by resolving R-loops. We found that RNH1 depletion results in accumulation of RNA-DNA hybrids, slowing of replication forks, and increased DNA damage. Our data uncovered a role for RNH1 in global DNA replication in the mammalian nucleus. Because accumulation of RNA-DNA hybrids is linked to various human cancers and neurodegenerative disorders, our study raises the possibility that replication fork progression might be impeded, adding to increased genomic instability and contributing to disease. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Comparison between Mt-DNA D-Loop and Cyt B primers for porcine DNA detection in meat products

    Science.gov (United States)

    Hamzah, Azhana; Mutalib, Sahilah Abd.; Babji, Abdul Salam

    2013-11-01

    This study was conducted to detect the presence of porcine DNA in meat products in the market using conventional polymerase chain reaction (PCR) and commercial PCR-southern hybridization analysis. Porcine DNA detection in meat products was tested due to some issues associated with the adulteration of food products in Malaysia. This is an important issue especially for Halal authentication which is required for some religious practices such as in Islam and Hinduisms. Many techniques have been developed for determining the Halal status of food products. In this paper, mt-DNA D-loop primer and cytochrome (cyt) b were used to detect the presence of porcine DNA in meat products. Positive and negative controls were always present for each batch of extraction. DNA of raw pork meat was used as a positive control while nucleus free water is used as negative control. A pair of oligonucleotide primer was used namely Pork1 and Pork2 which produced amplicon of 531 base pair (bp) in size. While, PCR-southern hybridization was conducted using primers readily supplied by commercial PCR-Southern hybridization and produced amplicon with 276 bp in size. In the present study, demonstrated that none of the samples were contaminated with porcine residuals but selected samples with pork meat were positive. The species-specific PCR amplification yielded excellent results for identification of pork derivatives in food products and it is a potentially reliable and suitable technique in routine food analysis for Halal certification.

  13. Detection of bovine mastitis pathogens by loop-mediated isothermal amplification and an electrochemical DNA chip.

    Science.gov (United States)

    Kawai, Kazuhiro; Inada, Mika; Ito, Keiko; Hashimoto, Koji; Nikaido, Masaru; Hata, Eiji; Katsuda, Ken; Kiku, Yoshio; Tagawa, Yuichi; Hayashi, Tomohito

    2017-12-22

    Bovine mastitis causes significant economic losses in the dairy industry. Effective prevention of bovine mastitis requires an understanding of the infection status of a pathogenic microorganism in a herd that has not yet shown clinical signs of mastitis and appropriate treatment specific for the pathogenic microorganism. However, bacterial identification by culture has drawbacks in that the sensitivity may be low and the procedure can be complex. In this study, we developed a genetic detection method to identify mastitis pathogens using a simple and highly sensitive electrochemical DNA chip which can specifically detect bacterial DNA in milk specimens. First, we selected microorganisms belonging to 12 families and/or genera associated with mastitis for which testing should be performed. Next, we optimized the conditions for amplifying microorganism DNA by loop-mediated isothermal amplification (LAMP) using 32 primers and the use of a DNA chip capable of measuring all pathogens simultaneously. Sample detection could be completed in just a few hours using this method. Comparison of the results obtained with our DNA chip method and those obtained by bacterial culture verified that when the culture method was set to 100%, the total positive concordance rate of the DNA chip was 85.0% and the total negative concordance rate was 86.9%. Furthermore, the proposed method allows both rapid and highly sensitive detection of mastitis pathogens. We believe that this method will contribute to the development of an effective mastitis control program.

  14. DNA binding specificity of the basic-helix-loop-helix protein MASH-1.

    Science.gov (United States)

    Meierhan, D; el-Ariss, C; Neuenschwander, M; Sieber, M; Stackhouse, J F; Allemann, R K

    1995-09-05

    Despite the high degree of sequence similarity in their basic-helix-loop-helix (BHLH) domains, MASH-1 and MyoD are involved in different biological processes. In order to define possible differences between the DNA binding specificities of these two proteins, we investigated the DNA binding properties of MASH-1 by circular dichroism spectroscopy and by electrophoretic mobility shift assays (EMSA). Upon binding to DNA, the BHLH domain of MASH-1 underwent a conformational change from a mainly unfolded to a largely alpha-helical form, and surprisingly, this change was independent of the specific DNA sequence. The same conformational transition could be induced by the addition of 20% 2,2,2-trifluoroethanol. The apparent dissociation constants (KD) of the complexes of full-length MASH-1 with various oligonucleotides were determined from half-saturation points in EMSAs. MASH-1 bound as a dimer to DNA sequences containing an E-box with high affinity KD = 1.4-4.1 x 10(-14) M2). However, the specificity of DNA binding was low. The dissociation constant for the complex between MASH-1 and the highest affinity E-box sequence (KD = 1.4 x 10(-14) M2) was only a factor of 10 smaller than for completely unrelated DNA sequences (KD = approximately 1 x 10(-13) M2). The DNA binding specificity of MASH-1 was not significantly increased by the formation of an heterodimer with the ubiquitous E12 protein. MASH-1 and MyoD displayed similar binding site preferences, suggesting that their different target gene specificities cannot be explained solely by differential DNA binding. An explanation for these findings is provided on the basis of the known crystal structure of the BHLH domain of MyoD.

  15. LAVA: An Open-Source Approach To Designing LAMP (Loop-Mediated Isothermal Amplification DNA Signatures

    Directory of Open Access Journals (Sweden)

    Gardner Shea N

    2011-06-01

    Full Text Available Abstract Background We developed an extendable open-source Loop-mediated isothermal AMPlification (LAMP signature design program called LAVA (LAMP Assay Versatile Analysis. LAVA was created in response to limitations of existing LAMP signature programs. Results LAVA identifies combinations of six primer regions for basic LAMP signatures, or combinations of eight primer regions for LAMP signatures with loop primers, which can be used as LAMP signatures. The identified primers are conserved among target organism sequences. Primer combinations are optimized based on lengths, melting temperatures, and spacing among primer sites. We compare LAMP signature candidates for Staphylococcus aureus created both by LAVA and by PrimerExplorer. We also include signatures from a sample run targeting all strains of Mycobacterium tuberculosis. Conclusions We have designed and demonstrated new software for identifying signature candidates appropriate for LAMP assays. The software is available for download at http://lava-dna.googlecode.com/.

  16. Molecular characterization of six sub population Indonesian local goats based on mitochondrial DNA D-loop

    Directory of Open Access Journals (Sweden)

    Aron Batubara

    2013-03-01

    Full Text Available Indonesian local goats were spread in some region, but there was still limited data’s known about the characteristics of its genetic diversity and origin. The Mitochondrial DNA D-loop sequences were used to study the genetic diversity and relationships of six sub population Indonesian local goats, namely, Kacang, Marica, Samosir, Jawarandu, Muara and Bengali goats. From 539 blood samples and DNA extraction collections were selected about 60 samples (10 samples each sub populations analyzed by PCR-RFLP methods, followed sequence analyzed about 5 PCR products each sub population. The results of the sequence analyses were edited and acquired about 957 bp of nucleotides length. After the alignment analyses were found 50 polymorphic sites which divided into 19 haplotype groups of mtDNA D-loop region. The value of nucleotide diversity was 0.014 ± 0.002. Analysis of Neighbour Joining with Kimura 2 Parameter methods and bootstrap test with 1000 replication indicated that each sub population groups was significantly different between one groups to the others. The maternal lineages origin of six breeds of Indonesian local goats was included to the group of lineage B. The Lineage B was the maternal origin of the haplogroup of goats in the region of East Asia, South Asia, China, Mongolia, North and South Africa, Malaysia, Indonesia, Pakistan and India.

  17. Identification of sequence polymorphisms in the D-Loop region of mitochondrial DNA as a risk factor for colon cancer.

    Science.gov (United States)

    Guo, Zhanjun; Zhao, Shengnan; Fan, Haiyan; Du, Yanming; Zhao, Yufei; Wang, Guiying

    2016-11-01

    The accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-Loop) of mitochondrial DNA (mtDNA) has been identified for their association with cancer risk in a number of cancers. We investigated the colon cancer risk profile of D-Loop SNPs in a case-control study. The frequent alleles of nucleotides 73G/A, 146T/C, 195T/C, 324C/G, 16261C/T, and 16304T/C as well as the minor allele of 309C/C insert were significantly associated with an increased risk for colon cancer. In conclusion, SNPs in the mtDNA D-Loop were found to be valuable markers for colon cancer risk evaluation.

  18. Absence of correlation between serum CRP levels and mitochondrial D-loop DNA mutations in gastro-oesophageal adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Benjamin H. L. Tan

    2014-01-01

    Full Text Available Introduction: Both inflammation and mitochondrial DNA (mtDNA mutation are thought to play a role in the many human cancers. The aim of this study was to evaluate the relationship between inflammation and accumulation of mitochondrial DNA (mtDNA mutations in the D-loop region in carcinogenesis of gastro-oesophageal adenocarcinomas. Materials and Methods: Blood samples of 20 patients with gastro-oesophageal adenocarcinoma were taken for measurement of serum C-reactive protein (CRP concentration. Direct sequencing of mtDNA in the D-loop region was done in the 20 adenocarcinoma samples and their corresponding surrounding non-cancerous tissue. Sequences were compared with existing mtDNA databases to identify mutations. Results: mtDNA mutations in the D-loop region occur commonly with almost identical frequency in both non-cancerous tissue (3.0 ΁ 1.6 and adenocarcinoma (3.1 ΁ 1.9 (P = 0.916, paired t-test. CRP levels are not predictive of the number of D-loop mutations in both adenocarcinoma (β: -0.131; 95% CI: -2.354-1.364; P = 0.583 and non-cancerous tissue samples (β: 0.130; 95% CI: -1.125-1.933; P = 0.586. Five new mutations were identified that were not recorded previously in mtDNA databases. Conclusion: D-loop mtDNA mutations are common in both gastro-oesophageal adenocarcinoma and surrounding non-cancerous tissue. However, the accumulation of such mutations appears to occur independent of systemic inflammation. The frequency of D-loop mutations is likely not useful as a marker for carcinogenesis in gastro-oesophageal adenocarcinoma.

  19. In vitro molecular machine learning algorithm via symmetric internal loops of DNA.

    Science.gov (United States)

    Lee, Ji-Hoon; Lee, Seung Hwan; Baek, Christina; Chun, Hyosun; Ryu, Je-Hwan; Kim, Jin-Woo; Deaton, Russell; Zhang, Byoung-Tak

    2017-08-01

    Programmable biomolecules, such as DNA strands, deoxyribozymes, and restriction enzymes, have been used to solve computational problems, construct large-scale logic circuits, and program simple molecular games. Although studies have shown the potential of molecular computing, the capability of computational learning with DNA molecules, i.e., molecular machine learning, has yet to be experimentally verified. Here, we present a novel molecular learning in vitro model in which symmetric internal loops of double-stranded DNA are exploited to measure the differences between training instances, thus enabling the molecules to learn from small errors. The model was evaluated on a data set of twenty dialogue sentences obtained from the television shows Friends and Prison Break. The wet DNA-computing experiments confirmed that the molecular learning machine was able to generalize the dialogue patterns of each show and successfully identify the show from which the sentences originated. The molecular machine learning model described here opens the way for solving machine learning problems in computer science and biology using in vitro molecular computing with the data encoded in DNA molecules. Copyright © 2017. Published by Elsevier B.V.

  20. Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping

    International Nuclear Information System (INIS)

    Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.

    2014-01-01

    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases

  1. Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping

    Energy Technology Data Exchange (ETDEWEB)

    Giovan, Stefan M. [Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083 (United States); Scharein, Robert G. [Hypnagogic Software, Vancouver, British Columbia V6K 1V6 (Canada); Hanke, Andreas [Department of Physics and Astronomy, University of Texas at Brownsville, Brownsville, Texas 78520 (United States); Levene, Stephen D., E-mail: sdlevene@utdallas.edu [Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083 (United States); Department of Bioengineering, University of Texas at Dallas, Richardson, Texas 75083 (United States); Department of Physics, University of Texas at Dallas, Richardson, Texas 75083 (United States)

    2014-11-07

    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.

  2. Rapid screening method for male DNA by using the loop-mediated isothermal amplification assay.

    Science.gov (United States)

    Kitamura, Masashi; Kubo, Seiji; Tanaka, Jin; Adachi, Tatsushi

    2017-08-12

    Screening for male-derived biological material from collected samples plays an important role in criminal investigations, especially those involving sexual assaults. We have developed a loop-mediated isothermal amplification (LAMP) assay targeting multi-repeat sequences of the Y chromosome for detecting male DNA. Successful amplification occurred with 0.5 ng of male DNA under isothermal conditions of 61 to 67 °C, but no amplification occurred with up to 10 ng of female DNA. Under the optimized conditions, the LAMP reaction initiated amplification within 10 min and amplified for 20 min. The LAMP reaction was sensitive at levels as low as 1-pg male DNA, and a quantitative LAMP assay could be developed because of the strong correlation between the reaction time and the amount of template DNA in the range of 10 pg to 10 ng. Furthermore, to apply the LAMP assay to on-site screening for male-derived samples, we evaluated a protocol using a simple DNA extraction method and a colorimetric intercalating dye that allows detection of the LAMP reaction by evaluating the change in color of the solution. Using this protocol, samples of male-derived blood and saliva stains were processed in approximately 30 min from DNA extraction to detection. Because our protocol does not require much hands-on time or special equipment, this LAMP assay promises to become a rapid and simple screening method for male-derived samples in forensic investigations.

  3. Phylogenetic relationships of German heavy draught horse breeds inferred from mitochondrial DNA D-loop variation.

    Science.gov (United States)

    Aberle, K S; Hamann, H; Drögemüller, C; Distl, O

    2007-04-01

    We analysed a 610-bp mitochondrial (mt)DNA D-loop fragment in a sample of German draught horse breeds and compared the polymorphic sites with sequences from Arabian, Hanoverian, Exmoor, Icelandic, Sorraia and Przewalski's Horses as well as with Suffolk, Shire and Belgian horses. In a total of 65 horses, 70 polymorphic sites representing 47 haplotypes were observed. The average percentage of polymorphic sites was 11.5% for the mtDNA fragment analysed. In the nine different draught horse breeds including South German, Mecklenburg, Saxon Thuringa coldblood, Rhenisch German, Schleswig Draught Horse, Black Forest Horse, Shire, Suffolk and Belgian, 61 polymorphic sites and 24 haplotypes were found. The phylogenetic analysis failed to show monophyletic groups for the draught horses. The analysis indicated that the draught horse populations investigated consist of diverse genetic groups with respect to their maternal lineage.

  4. Theory on the mechanism of distal action of transcription factors: looping of DNA versus tracking along DNA

    Energy Technology Data Exchange (ETDEWEB)

    Murugan, R, E-mail: rmurugan@gmail.co [Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036 (India)

    2010-10-15

    In this paper, we develop a theory on the mechanism of distal action of the transcription factors, which are bound at their respective cis-regulatory enhancer modules on the promoter-RNA polymerase II (PR) complexes to initiate the transcription event in eukaryotes. We consider both the looping and tracking modes of their distal communication and calculate the mean first passage time that is required for the distal interactions of the complex of enhancer and transcription factor with the PR via both these modes. We further investigate how this mean first passage time is dependent on the length of the DNA segment (L, base-pairs) that connects the cis-regulatory binding site and the respective promoter. When the radius of curvature of this connecting segment of DNA is R that was induced upon binding of the transcription factor at the cis-acting element and RNAPII at the promoter in cis-positions, our calculations indicate that the looping mode of distal action will dominate when L is such that L > 2{pi}R and the tracking mode of distal action will be favored when L < 2{pi}R. The time required for the distal action will be minimum when L = 2{pi}R where the typical value of R for the binding of histones will be R {approx} 16 bps and L {approx} 10{sup 2} bps. It seems that the free energy associated with the binding of the transcription factor with its cis-acting element and the distance of this cis-acting element from the corresponding promoter of the gene of interest is negatively correlated. Our results suggest that the looping and tracking modes of distal action are concurrently operating on the transcription activation and the physics that determines the timescales associated with the looping/tracking in the mechanism of action of these transcription factors on the initiation of the transcription event must put a selection pressure on the distribution of the distances of cis-regulatory modules from their respective promoters of the genes. The computational analysis

  5. Theory on the mechanism of distal action of transcription factors: looping of DNA versus tracking along DNA

    International Nuclear Information System (INIS)

    Murugan, R

    2010-01-01

    In this paper, we develop a theory on the mechanism of distal action of the transcription factors, which are bound at their respective cis-regulatory enhancer modules on the promoter-RNA polymerase II (PR) complexes to initiate the transcription event in eukaryotes. We consider both the looping and tracking modes of their distal communication and calculate the mean first passage time that is required for the distal interactions of the complex of enhancer and transcription factor with the PR via both these modes. We further investigate how this mean first passage time is dependent on the length of the DNA segment (L, base-pairs) that connects the cis-regulatory binding site and the respective promoter. When the radius of curvature of this connecting segment of DNA is R that was induced upon binding of the transcription factor at the cis-acting element and RNAPII at the promoter in cis-positions, our calculations indicate that the looping mode of distal action will dominate when L is such that L > 2πR and the tracking mode of distal action will be favored when L 2 bps. It seems that the free energy associated with the binding of the transcription factor with its cis-acting element and the distance of this cis-acting element from the corresponding promoter of the gene of interest is negatively correlated. Our results suggest that the looping and tracking modes of distal action are concurrently operating on the transcription activation and the physics that determines the timescales associated with the looping/tracking in the mechanism of action of these transcription factors on the initiation of the transcription event must put a selection pressure on the distribution of the distances of cis-regulatory modules from their respective promoters of the genes. The computational analysis of the upstream sequences of promoters of various genes in the human and mouse genomes for the presence of putative cis-regulatory elements for a set of known transcription factors using

  6. Molecular Characterization of Sudanese and Southern Sudanese Chicken Breeds Using mtDNA D-Loop

    Directory of Open Access Journals (Sweden)

    Charles E. Wani

    2014-01-01

    Full Text Available The objective of this study was to assess the genetic relationships and diversity and to estimate the amount of gene flow among the five chicken populations from Sudan and South Sudan and commercial strain of egg line White Leghorn chickens. The chicken populations were genotyped using mtDNA D-loop as a molecular marker. PCR product of the mtDNA D-loop segment was 600 bp and 14 haplotypes were identified. The neighbor-joining phylogenetic tree indicated that the indigenous Sudanese chickens can be grouped into two clades, IV and IIIa only. Median joining networks analysis showed that haplotype LBB49 has the highest frequency. The hierarchal analysis of molecular variance (AMOVA showed that genetic variation within the population was 88.6% and the differentiation among the population was 11.4%. When the populations was redefined into two geographical zones, rich and poor Savanna, the results were fractioned into three genetic variations: between individuals within population 95.5%, between populations within the group 0.75%, and genetic variation between groups 3.75%. The pair wise Fst showed high genetic difference between Betwil populations and the rest with Fst ranging from 0.1492 to 0.2447. We found that there is large number of gene exchanges within the Sudanese indigenous chicken (Nm=4.622.

  7. Label-free fluorescence strategy for sensitive detection of adenosine triphosphate using a loop DNA probe with low background noise.

    Science.gov (United States)

    Lin, Chunshui; Cai, Zhixiong; Wang, Yiru; Zhu, Zhi; Yang, Chaoyong James; Chen, Xi

    2014-07-15

    A simple, rapid, label-free, and ultrasensitive fluorescence strategy for adenosine triphosphate (ATP) detection was developed using a loop DNA probe with low background noise. In this strategy, a loop DNA probe, which is the substrate for both ligation and digestion enzyme reaction, was designed. SYBR green I (SG I), a double-stranded specific dye, was applied for the readout fluorescence signal. Exonuclease I (Exo I) and exonuclease III (Exo III), sequence-independent nucleases, were selected to digest the loop DNA probe in order to minimize the background fluorescence signal. As a result, in the absence of ATP, the loop DNA was completely digested by Exo I and Exo III, leading to low background fluorescence owing to the weak electrostatic interaction between SG I and mononucleotides. On the other hand, ATP induced the ligation of the nicking site, and the sealed loop DNA resisted the digestion of Exo I and ExoIII, resulting in a remarkable increase of fluorescence response. Upon background noise reduction, the sensitivity of the ATP determination was improved significantly, and the detection limitation was found to be 1.2 pM, which is much lower than that in almost all the previously reported methods. This strategy has promise for wide application in the determination of ATP.

  8. Conformation and dynamics of nucleotides in bulges and symmetric internal loops in duplex DNA studied by EPR and fluorescence spectroscopies

    International Nuclear Information System (INIS)

    Cekan, Pavol; Sigurdsson, Snorri Th.

    2012-01-01

    Highlights: ► Bulges and loops were studied by both EPR and fluorescence spectroscopies using the probe Ç/Ç f . ► One-base bulge was in a temperature-dependent equilibrium between looped-out and stacked states. ► Bases in two- and three-base bulges were stacked at all temperatures, resulting in DNA bending. ► Bases were stacked in symmetrical two- to five-base internal loops, according to EPR data. ► Unexpectedly high fluorescence for the smaller loops indicated local structural perturbations. -- Abstract: The dynamics and conformation of base bulges and internal loops in duplex DNA were studied using the bifunctional spectroscopic probe Ç, which becomes fluorescent (Ç f ) upon reduction of the nitroxide functional group, along with EPR and fluorescence spectroscopies. A one-base bulge was in a conformational equilibrium between looped-out and stacked states, the former favored at higher temperature and the latter at lower temperature. Stacking of bulge bases was favored in two- and three-base bulges, independent of temperature, resulting in DNA bending as evidenced by increased fluorescence of Ç f . EPR spectra of Ç-labeled three-, four- and five-base symmetrical interior DNA bulges at 20 °C showed low mobility, indicating that the spin-label was stacked within the loop. The spin-label mobility at 37 °C increased as the loops became larger. A considerable variation in fluorescence between different loops was observed, as well as a temperature-dependence within constructs. Fluorescence unexpectedly increased as the size of the loop decreased at 2 °C. Fluorescence of the smallest loops, where a single T·T mismatch was located between the stem region and the probe, was even larger than for the single strand, indicating a considerable local structural deformation of these loops from regular B-DNA. These results show the value of combining EPR and fluorescence spectroscopy to study non-helical regions of nucleic acids.

  9. Subspecies identification of captive Orang Utan in Melaka based on D-loop mitochondria DNA

    Science.gov (United States)

    Kamaluddin, Siti Norsyuhada; Yaakop, Salmah; Idris, Wan Mohd Razi; Rovie-Ryan, Jeffrine Japning; Md-Zain, Badrul Munir

    2018-04-01

    Mitochondrial DNA of Bornean Orang Utan populations suggests that there are three different subspecies (Pongo pygmaeus pygmaeus; Sarawak & Northwest Kalimantan, P. p. wurmbii; Southern West Kalimantan and Central Kalimantan, P. p. morio; East Kalimantan and Sabah). The subspecies of Orang Utans in captivity are difficult to determine through morphological observation. Thus, misidentification by ranger or zoo staffs leads to unwanted consequences especially towards conservation efforts of Orang Utan. The main objective of this study was to identify the subspecies and the geographic origin of 10 Orang Utans in Zoo Melaka and A' Famosa by using partial mitochondrial D-loop gene sequences. DNA of all individuals was extracted from FTA Card. Data analyses were performed using Maximum Parsimony, MP and Neighbor Joining, NJ. Molecular phylogeny analysis revealed that all the samples likely belong to one species of Sumatran Orang Utan (P. abelii) and three different subspecies of Bornean Orang Utans (P. p. pygmaeus, P. p. morio, and P. p. wurmbii). The results obtained in this study indirectly help the management of zoos in term of conservation and visitor's education.

  10. Genetic distance of Malaysian mousedeer based on mitochondrial DNA cytochrome oxidase I (COI) and D-loop region sequences

    Science.gov (United States)

    Bakar, Mohamad-Azam Akmal Abu; Rovie-Ryan, Jeffrine Japning; Ampeng, Ahmad; Yaakop, Salmah; Nor, Shukor Md; Md-Zain, Badrul Munir

    2018-04-01

    Mousedeer is one of the primitive mammals that can be found mainly in Southeast-Asia region. There are two species of mousedeer in Malaysia which are Tragulus kanchil and Tragulus napu. Both species can be distinguish by size, coat coloration, and throat pattern but clear diagnosis still cannot be found. The objective of the study is to show the genetic distance relationship between T. kanchil and T. napu and their population based on mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and D-loop region. There are 42 sample of mousedeer were used in this study collected by PERHILITAN from different locality. Another 29 D-loop sequence were retrieved from Genbank for comparative analysis. All sample were amplified using universal primer and species-specific primer for COI and D-loop genes via PCR process. The amplified sequences were analyzed to determine genetic distance of T. kanchil and T. napu. From the analysis, the average genetic distance between T. kanchil and T. napu based on locus COI and D-loop were 0.145 and 0.128 respectively. The genetic distance between populations of T. kanchil based on locus COI was between 0.003-0.013. For locus D-loop, genetic distance analysis showed distance in relationship between west-coast populations to east-coast population of T. kanchil. COI and D-loop mtDNA region provided a clear picture on the relationship within the mousedeer species. Last but not least, conservation effort toward protecting this species can be done by study the molecular genetics and prevent the extinction of this species.

  11. Detection of phytoplasma by loop-mediated isothermal amplification of DNA (LAMP).

    Science.gov (United States)

    Obura, E; Masiga, D; Wachira, F; Gurja, B; Khan, Z R

    2011-02-01

    Napier stunt phytoplasma (16SrXI and 16SrIII) in eastern Africa is a serious threat to the expansion of Napier grass (Pennisetum purpureum) farming in the region, where it is widely cultivated as fodder in zero grazing livestock systems. The grass has high potential for bio-fuel production, and has been adopted by farmers as a countermeasure to cereal stem borer Lepidoptera, since it attracts and traps the insect. Diagnosis of stunt phytoplasma have been largely by nested polymerase chain reaction (nPCR) targeting the 16S rRNA gene. However, the method is laborious, costly and technically demanding. This investigation has developed a simpler but effective phytoplasma diagnostic tool, called; loop-mediated isothermal amplification of DNA (LAMP). The assay was tested on 8 symptomatic and 8 asymptomatic plants, while its detection limit was compared to nested PCR using samples serially diluted from 3 ng/μl to 0.38 pg/μl. Molecular typing of LAMP products was determined by BsrI restriction digestion and Southern blot analysis. The assay sensitivity, positive and negative predictive values were estimated, while the specificity was tested on 11 phytoplasma groups. LAMP was specific to 5 phytoplasma groups: 16SrVI, X, XI and XVI. BsrI restriction digestion produced two predicted fragments, and there was specific binding of probe DNA to the LAMP amplicons in Southern blot analysis. The assay sensitivity was 100%, while the positive and negative predictive values were 63 and 100% respectively. LAMP was 20-fold more sensitive than nested PCR. This study validates LAMP for routine diagnosis of Napier stunt and other closely related phytoplasmas. Copyright © 2010 Elsevier B.V. All rights reserved.

  12. Loop-Mediated Isothermal Amplification Targeting Actin DNA of Trichomonas vaginalis.

    Science.gov (United States)

    Goo, Youn-Kyoung; Shin, Won-Sik; Yang, Hye-Won; Joo, So-Young; Song, Su-Min; Ryu, Jae-Sook; Kong, Hyun-Hee; Lee, Won-Ki; Chung, Dong-Il; Hong, Yeonchul

    2016-06-01

    Trichomoniasis caused by Trichomonas vaginalis is a common sexually transmitted disease. Its association with several health problems, including preterm birth, pelvic inflammatory disease, cervical cancer, and transmission of human immunodeficiency virus, emphasizes the importance of improved access to early and accurate detection of T. vaginalis. In this study, a rapid and efficient loop-mediated isothermal amplification-based method for the detection of T. vaginalis was developed and validated, using vaginal swab specimens from subjects suspected to have trichomoniasis. The LAMP assay targeting the actin gene was highly sensitive with detection limits of 1 trichomonad and 1 pg of T. vaginalis DNA per reaction, and specifically amplified the target gene only from T. vaginalis. Validation of this assay showed that it had the highest sensitivity and better agreement with PCR (used as the gold standard) compared to microscopy and multiplex PCR. This study showed that the LAMP assay, targeting the actin gene, could be used to diagnose early infections of T. vaginalis. Thus, we have provided an alternative molecular diagnostic tool and a point-of-care test that may help to prevent trichomoniasis transmission and associated complications.

  13. Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure.

    Science.gov (United States)

    Takahashi, Shuntaro; Sugimoto, Naoki

    2017-12-01

    DNA guanine-quadruplexes (G-quadruplexes) are unique DNA structures formed by guanine-rich sequences. The loop regions of G-quadruplexes play key roles in stability and topology of G-quadruplexes. Here, we investigated volumetric changes induced by pressure in the folding of the G-quadruplex formed by the thrombin binding aptamer (TBA) with mutations within the loop regions. The change of partial molar volume in the transition from coil to G-quadruplex, ∆V tr , of TBA with a mutation from T to A in the 5' most loop (TBA T3A) was 75.5cm 3 mol -1 , which was larger than that of TBA (54.6cm 3 mol -1 ). TBA with a G to T mutation in the central loop (TBA G8T) had thermal stability similar to TBA T3A but a smaller ∆V tr of 41.1cm 3 mol -1 . In the presence of poly(ethylene)glycol 200 (PEG200), ∆V tr values were 14.7cm 3 mol -1 for TBA T3A and 13.2cm 3 mol -1 for TBA G8T. These results suggest that the two mutations destabilize the G-quadruplex structure differently. Thus, volumetric data obtained using pressure-based thermodynamic analyses provides information about the dynamics of the loop regions and the roles of loops in the stabilities and folding of G-quadruplex structures. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing

    Science.gov (United States)

    2018-01-01

    Background The Hungarian draft is a horse breed with a recent mixed ancestry created in the 1920s by crossing local mares with draught horses imported from France and Belgium. The interest in its conservation and characterization has increased over the last few years. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks. Methods To genetically characterize the breed and to set up the basis for a conservation program, in the present study a hypervariable region of the mitochrondial DNA (D-loop) was used to assess genetic diversity in Hungarian draft horses. Two hundred and eighty five sequences obtained in our laboratory and 419 downloaded sequences available from Genbank were analyzed. Results One hundred and sixty-four haplotypes and thirty-six polymorphic sites were observed. High haplotype and nucleotide diversity values (Hd = 0.954 ± 0.004; π = 0.028 ± 0.0004) were identified in Hungarian population, although they were higher within than among the different populations (Hd = 0.972 ± 0.002; π = 0.03097 ± 0.002). Fourteen of the previously observed seventeen haplogroups were detected. Discussion Our samples showed a large intra- and interbreed variation. There was no clear clustering on the median joining network figure. The overall information collected in this work led us to consider that the genetic scenario observed for Hungarian draft breed is more likely the result of contributions from ‘ancestrally’ different genetic backgrounds. This study could contribute to the development of a breeding plan for Hungarian draft horses and help to formulate a genetic conservation plan, avoiding inbreeding while. PMID:29404201

  15. Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region.

    Science.gov (United States)

    Liao, Yuying; Mo, Guodong; Sun, Junli; Wei, Fengying; Liao, Dezhong Joshua

    2016-05-01

    The domestic chicken (Gallus gallus domesticus) is an excellent model for genetic studies of phenotypic diversity. The Guangxi Region of China possesses several native chicken breeds displaying a broad range of phenotypes well adapted to the extreme hot-and-wet environments in the region. We thus evaluated the genetic diversity and relationships among six native chicken populations of the Guangxi region and also evaluated two commercial breeds (Arbor Acres and Roman chickens). We analyzed the sequences of the D-loop region of the mitochondrial DNA (mtDNA) and 18 microsatellite loci of 280 blood samples from six Guangxi native chicken breeds and from Arbor Acres and Roman chickens, and used the neighbor-joining method to construct the phylogenetic tree of these eight breeds. Our results showed that the genetic diversity of Guangxi native breeds was relatively rich. The phylogenetic tree using the unweighed pair-group method with arithmetic means (UPGAM) on microsatellite marks revealed two main clusters. Arbor Acres chicken and Roman chicken were in one cluster, while the Guangxi breeds were in the other cluster. Moreover, the UPGAM tree of Guangxi native breeds based on microsatellite loci was more consistent with the genesis, breeding history, differentiation and location than the mtDNA D-loop region. STRUCTURE analysis further confirmed the genetic structure of Guangxi native breeds in the Neighbor-Net dendrogram. The nomenclature of mtDNA sequence polymorphisms suggests that the Guangxi native chickens are distributed across four clades, but most of them are clustered in two main clades (B and E), with the other haplotypes within the clades A and C. The Guangxi native breeds revealed abundant genetic diversity not only on microsatellite loci but also on mtDNA D-loop region, and contained multiple maternal lineages, including one from China and another from Europe or the Middle East.

  16. Visual Detection of Potato leafroll virus by One-step Reverse Transcription Loop-Mediated Isothermal Amplification of DNA with Hydroxynaphthol Blue Dye

    NARCIS (Netherlands)

    Ahmadi, S.; Almasi, A.M.; Fatehi, F.; Struik, P.C.; Moradi, A.

    2013-01-01

    Loop-mediated isothermal amplification (LAMP) assay is a novel technique for amplifying DNA under constant temperature, with high specificity, sensitivity, rapidity and efficiency. We applied reverse transcription loop-mediated isothermal amplification (RT-LAMP) to visually detect Potato leafroll

  17. Maternal phylogenetic relationships and genetic variation among Arabian horse populations using whole mitochondrial DNA D-loop sequencing.

    Science.gov (United States)

    Khanshour, Anas M; Cothran, Ernest Gus

    2013-09-13

    Maternal inheritance is an essential point in Arabian horse population genetics and strains classification. The mitochondrial DNA (mtDNA) sequencing is a highly informative tool to investigate maternal lineages. We sequenced the whole mtDNA D-loop of 251 Arabian horses to study the genetic diversity and phylogenetic relationships of Arabian populations and to examine the traditional strain classification system that depends on maternal family lines using native Arabian horses from the Middle East. The variability in the upstream region of the D-loop revealed additional differences among the haplotypes that had identical sequences in the hypervariable region 1 (HVR1). While the American-Arabians showed relatively low diversity, the Syrian population was the most variable and contained a very rare and old haplogroup. The Middle Eastern horses had major genetic contributions to the Western horses and there was no clear pattern of differentiation among all tested populations. Our results also showed that several individuals from different strains shared a single haplotype, and individuals from a single strain were represented in clearly separated haplogroups. The whole mtDNA D-loop sequence was more powerful for analysis of the maternal genetic diversity in the Arabian horses than using just the HVR1. Native populations from the Middle East, such as Syrians, could be suggested as a hot spot of genetic diversity and may help in understanding the evolution history of the Arabian horse breed. Most importantly, there was no evidence that the Arabian horse breed has clear subdivisions depending on the traditional maternal based strain classification system.

  18. The cytosolic DNA sensor cGAS forms an oligomeric complex with DNA and undergoes switch-like conformational changes in the activation loop.

    Science.gov (United States)

    Zhang, Xu; Wu, Jiaxi; Du, Fenghe; Xu, Hui; Sun, Lijun; Chen, Zhe; Brautigam, Chad A; Zhang, Xuewu; Chen, Zhijian J

    2014-02-13

    The presence of DNA in the cytoplasm is a danger signal that triggers immune and inflammatory responses. Cytosolic DNA binds to and activates cyclic GMP-AMP (cGAMP) synthase (cGAS), which produces the second messenger cGAMP. cGAMP binds to the adaptor protein STING and activates a signaling cascade that leads to the production of type I interferons and other cytokines. Here, we report the crystal structures of human cGAS in its apo form, representing its autoinhibited conformation as well as in its cGAMP- and sulfate-bound forms. These structures reveal switch-like conformational changes of an activation loop that result in the rearrangement of the catalytic site. The structure of DNA-bound cGAS reveals a complex composed of dimeric cGAS bound to two molecules of DNA. Functional analyses of cGAS mutants demonstrate that both the protein-protein interface and the two DNA binding surfaces are critical for cGAS activation. These results provide insights into the mechanism of DNA sensing by cGAS. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  19. The Cytosolic DNA Sensor cGAS Forms an Oligomeric Complex with DNA and Undergoes Switch-like Conformational Changes in the Activation Loop

    Directory of Open Access Journals (Sweden)

    Xu Zhang

    2014-02-01

    Full Text Available The presence of DNA in the cytoplasm is a danger signal that triggers immune and inflammatory responses. Cytosolic DNA binds to and activates cyclic GMP-AMP (cGAMP synthase (cGAS, which produces the second messenger cGAMP. cGAMP binds to the adaptor protein STING and activates a signaling cascade that leads to the production of type I interferons and other cytokines. Here, we report the crystal structures of human cGAS in its apo form, representing its autoinhibited conformation as well as in its cGAMP- and sulfate-bound forms. These structures reveal switch-like conformational changes of an activation loop that result in the rearrangement of the catalytic site. The structure of DNA-bound cGAS reveals a complex composed of dimeric cGAS bound to two molecules of DNA. Functional analyses of cGAS mutants demonstrate that both the protein-protein interface and the two DNA binding surfaces are critical for cGAS activation. These results provide insights into the mechanism of DNA sensing by cGAS.

  20. Detection of novel polymorphisms in the mitochondrial DNA D-Loop ...

    African Journals Online (AJOL)

    aghomotsegin

    2015-04-08

    Apr 8, 2015 ... 1Department of Molecular Biology, Babylon University, Hilla City, Iraq. 2Babylon ... Mitochondrial DNA (mtDNA) is a useful genetic marker for answering .... to you for choosing the project, your enthusiasm for helping us ...

  1. Optimization of loop-mediated isothermal amplification (LAMP) assays for the detection of Leishmania DNA in human blood samples.

    Science.gov (United States)

    Abbasi, Ibrahim; Kirstein, Oscar D; Hailu, Asrat; Warburg, Alon

    2016-10-01

    Visceral leishmaniasis (VL), one of the most important neglected tropical diseases, is caused by Leishmania donovani eukaryotic protozoan parasite of the genus Leishmania, the disease is prevalent mainly in the Indian sub-continent, East Africa and Brazil. VL can be diagnosed by PCR amplifying ITS1 and/or kDNA genes. The current study involved the optimization of Loop-mediated isothermal amplification (LAMP) for the detection of Leishmania DNA in human blood or tissue samples. Three LAMP systems were developed; in two of those the primers were designed based on shared regions of the ITS1 gene among different Leishmania species, while the primers for the third LAMP system were derived from a newly identified repeated region in the Leishmania genome. The LAMP tests were shown to be sufficiently sensitive to detect 0.1pg of DNA from most Leishmania species. The green nucleic acid stain SYTO16, was used here for the first time to allow real-time monitoring of LAMP amplification. The advantage of real time-LAMP using SYTO 16 over end-point LAMP product detection is discussed. The efficacy of the real time-LAMP tests for detecting Leishmania DNA in dried blood samples from volunteers living in endemic areas, was compared with that of qRT-kDNA PCR. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  2. Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis

    NARCIS (Netherlands)

    Hamdan, Samir M.; Loparo, Joseph J.; Takahashi, Masateru; Richardson, Charles C.; Oijen, Antoine M. van

    2009-01-01

    In all organisms, the protein machinery responsible for the replication of DNA, the replisome, is faced with a directionality problem. The antiparallel nature of duplex DNA permits the leading-strand polymerase to advance in a continuous fashion, but forces the lagging-strand polymerase to

  3. Single nucleotide polymorphisms in the D-loop region of mitochondrial DNA is associated with the kidney survival time in chronic kidney disease patients.

    Science.gov (United States)

    Xu, Jinsheng; Guo, Zhanjun; Bai, Yaling; Zhang, Junxia; Cui, Liwen; Zhang, Huiran; Zhang, Shenglei; Ai, Xiaolu

    2015-02-01

    The mitochondrial displacement loop (D-loop) is known to accumulate mutations and SNPs at a higher frequency than other regions of mitochondrial DNA (mtDNA). We had identified chronic kidney disease (CKD) risk-associated SNPs in the D-loop of CKD patients previously. In this study, we investigated the association of SNPs in the D-loop of mtDNA with the kidney survival of CKD. The D-loop region of mtDNA was sequenced for 119 CKD patients from the inpatient of the Fourth Hospital of Hebei Medical University. The Kaplan-Meier method was used to identify disease outcome-associated SNPs in the D-loop of CKD patients. The Cox proportional hazards model was used to identify risk factors for the kidney survival of CKD. In the present study, we identified 20 SNPs with a frequency higher than 5% and assessed the relationship of these SNPs with kidney survival time in CKD patients, a SNP of 146 was identified by log-rank test for statistically significant prediction of the kidney survival time. In an overall multivariate analysis, allele 146 was identified as an independent predictor of kidney survival time in CKD patients. The survival time of kidney in the CKD patients with 146C was significantly shorter than that of kidney in CKD patients with 146T (relative risk, 2.336; 95% CI, 1.319-3.923; p = 0.001). SNPs in the D-loop can predict the kidney survival of CKD patients. Analysis of genetic polymorphisms in the mitochondrial D-loop can help to identify CKD patient subgroup at high risk of a poor disease outcome.

  4. [The mutations of the D-loop hypervariable region II and hypervariable region III of mitochondrial DNA in oral squamous cell carcinoma].

    Science.gov (United States)

    Wang, Yao-Zhong; Jia, Mu-Yun; Yuan, Rong-Tao; Han, Guo-Dong; Bu, Ling-Xue

    2010-06-01

    To investigate the frequency of mitochondrial DNA (mtDNA) D-loop hypervariable region II (HVR II) and hypervariable region III (HVR III) mutations in oral squamous cell carcinoma (OSCC) and their correlation to provide the new targets for the prevention and treatment of OSCC. The D-loop HVR II and HVR III regions of mtDNA in seven cases with OSCC tissues, matched with paracancerous tissues and normal mucosa tissues from the same case, were amplified by polymerase chain raction (PCR), then were detected by direct sequencing to find the mutantsites after the comparison of all sequencing results with the mtDNA Cambridge sequence in the GenBank database. 82 (56 species) nucleotide changes, with 51(26 species) nucleotide polymorphism, were found after the comparison of all sequencing results with the mtDNA Cambridge sequence in the GenBank database. 31(30 species) mutations, with 21 located within the HVR II and HVR III regions, were found in 3 tumor tissue samples, their paracancerous and normal mucosa tissue were found more polymorphic changes but no mutation. The mtDNA D-loop HVR II and HVR III regions mutation rate was 42.9% (3/7) in OSCC. The mtDNA D-loop HVR II and HVR III regions were highly polymorphic and mutable regions in OSCC. It suggested that the D-loop HVR II and HVR III regions of mtDNA might play a significant role in the tumorigenesis of OSCC. It may become new targets for the gene therapy of OSCC by regulating the above indexes.

  5. The flexible loop L1 of the H3K4 demethylase JARID1B ARID domain has a crucial role in DNA-binding activity

    International Nuclear Information System (INIS)

    Yao, Wenming; Peng, Yu; Lin, Donghai

    2010-01-01

    JARID1B, a member of the JmjC demethylase family, has a crucial role in H3K4me3 demethylation. The ARID domain is a potential DNA-binding domain of JARID1B. Previous studies indicate that a GC-rich DNA motif is the specific target of the ARID domain. However, the details of the interaction between the ARID domain and duplex DNA require further study. Here, we utilized NMR spectroscopy to assign the backbone amino acids and mapped the DNA-binding sites of the human JARID1B ARID domain. Perturbations to 1 H- 15 N correlation spectra revealed that the flexible loop L1 of ARID was the main DNA-binding interface. EMSA and intrinsic fluorescence experiments demonstrated that mutations on loop L1 strongly reduced the DNA-binding activity of JARID1B ARID. Furthermore, transfection of mutant forms resulted in a distinct loss of intrinsic H3K4 demethylase activity, implying that the flexible loop L1 made a major contribution to sustaining the DNA-binding ability of JARID1B ARID domain.

  6. Mitochondrial DNA D-loop sequence variation among 5 maternal lines of the Zemaitukai horse breed

    Directory of Open Access Journals (Sweden)

    E. Gus Cothran

    2005-12-01

    Full Text Available Genetic variation in Zemaitukai horses was investigated using mitochondrial DNA (mtDNA sequencing. The study was performed on 421 bp of the mitochondrial DNA control region, which is known to be more variable than other sections of the mitochondrial genome. Samples from each of the remaining maternal family lines of Zemaitukai horses and three random samples for other Lithuanian (Lithuanian Heavy Draught, Zemaitukai large type and ten European horse breeds were sequenced. Five distinct haplotypes were obtained for the five Zemaitukai maternal families supporting the pedigree data. The minimal difference between two different sequence haplotypes was 6 and the maximal 11 nucleotides in Zemaitukai horse breed. A total of 20 nucleotide differences compared to the reference sequence were found in Lithuanian horse breeds. Genetic cluster analysis did not shown any clear pattern of relationship among breeds of different type.

  7. Impact of Somatic Mutations in the D-Loop of Mitochondrial DNA on the Survival of Oral Squamous Cell Carcinoma Patients

    Science.gov (United States)

    Lin, Jin-Ching; Wang, Chen-Chi; Jiang, Rong-San; Wang, Wen-Yi; Liu, Shih-An

    2015-01-01

    Objectives The aim of this study was to investigate somatic mutations in the D-loop of mitochondrial DNA (mtDNA) and their impact on survival in oral squamous cell carcinoma patients. Materials and Methods Surgical specimen confirmed by pathological examination and corresponding non-cancerous tissues were collected from 120 oral squamous cell carcinoma patients. The sequence in the D-loop of mtDNA from non-cancerous tissues was compared with that from paired cancer samples and any sequence differences were recognized as somatic mutations. Results Somatic mutations in the D-loop of mtDNA were identified in 75 (62.5%) oral squamous cell carcinoma patients and most of them occurred in the poly-C tract. Although there were no significant differences in demographic and tumor-related features between participants with and without somatic mutation, the mutation group had a better survival rate (5 year disease-specific survival rate: 64.0% vs. 43.0%, P = 0.0266). Conclusion Somatic mutation in D-loop of mtDNA was associated with a better survival in oral squamous cell carcinoma patients. PMID:25906372

  8. Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella.

    Science.gov (United States)

    Papenfort, Kai; Espinosa, Elena; Casadesús, Josep; Vogel, Jörg

    2015-08-25

    Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution but constitutes a complex process that requires synchronization with the physiological state of the host bacteria. Although several host transcription factors are known to regulate plasmid-borne transfer genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. We describe a posttranscriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two separate seed-pairing domains to activate the mRNAs of both the sigma-factor σ(S) and the RicI protein, a previously uncharacterized membrane protein here shown to inhibit conjugation. Transcription of ricI requires σ(S) and, together, RprA and σ(S) orchestrate a coherent feedforward loop with AND-gate logic to tightly control the activation of RicI synthesis. RicI interacts with the conjugation apparatus protein TraV and limits plasmid transfer under membrane-damaging conditions. To our knowledge, this study reports the first small RNA-controlled feedforward loop relying on posttranscriptional activation of two independent targets and an unexpected role of the conserved RprA small RNA in controlling extrachromosomal DNA transfer.

  9. Time Course of Detection of Human Male DNA from Stained Blood Sample on Various Surfaces by Loop Mediated Isothermal Amplification and Polymerase Chain Reaction

    OpenAIRE

    Panan Kanchanaphum

    2018-01-01

    This study explores determining the sex of humans from blood stains taken from different surfaces and compares the time course of detection with the conventional PCR, Conventional Loop Mediated Isothermal Amplification (LAMP), and LAMP-Lateral Flow Dipstick (LFD). For the DNA templates, 7 male and 7 female blood stained samples were extracted and added to LAMP and PCR reaction solution to amplify the SRY gene. The DNA samples were extracted from the following blood stained materials: cloth, w...

  10. PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation.

    Science.gov (United States)

    Belotserkovskii, Boris P; Hanawalt, Philip C

    2015-11-01

    Peptide Nucleic Acids (PNAs) are artificial DNA mimics with superior nucleic acid binding capabilities. T7 RNA polymerase (T7 RNAP) transcription upon encountering PNA bound to the non-template DNA strand was studied in vitro. A characteristic pattern of blockage signals was observed, extending downstream from the PNA binding site, similar to that produced by G-rich homopurine-homopyrimidine (hPu-hPy) sequences and likely caused by R-loop formation. Since blocked transcription complexes in association with stable R-loops may interfere with replication and in some cases trigger apoptosis, targeted R-loop formation might be employed to inactivate selected cells, such as those in tumors, based upon their unique complement of expressed genes. © 2014 The Authors. Molecular Carcinogenesis published by Wiley Periodicals, Inc.

  11. The development of a loop-mediated isothermal amplification assay for rapid and sensitive detection of abalone herpesvirus DNA.

    Science.gov (United States)

    Chen, M H; Kuo, S T; Renault, T; Chang, P H

    2014-02-01

    A loop-mediated isothermal amplification (LAMP) assay was developed for the detection of abalone herpesvirus DNA. Two pairs of primers were designed, based on the sequence of the DNA polymerase gene of abalone herpesvirus. The reaction temperature and time were optimized to 63°C and 60min, respectively. LAMP amplicons were analyzed by 2% agarose gel electrophoresis or by visual inspection of a colour change emitted by fluorescent dye. The method developed was specific for the detection of abalone herpesvirus, without cross-reactions with other tested herpesviruses including ostreid herpesvirus 1 (OsHV-1), European eel herpesvirus, koi herpesvirus (KHV) and an avian herpesvirus. The LAMP assay was 100 folds more sensitive than a conventional PCR and 10 folds less sensitive than a SYBR Green PCR. These results indicate that the developed LAMP assay is a simple, rapid, sensitive, specific and reliable technique for the detection of abalone herpesvirus. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Yersinia pestis detection by loop-mediated isothermal amplification combined with magnetic bead capture of DNA

    Directory of Open Access Journals (Sweden)

    Na Feng

    Full Text Available ABSTRACT We developed a loop-mediated isothermal amplification (LAMP assay for the detection of Y. pestis by targeting the 3a sequence on chromosome. All 11 species of the genus Yersinia were used to evaluate the specificity of LAMP and PCR, demonstrating that the primers had a high level of specificity. The sensitivity of LAMP or PCR was 2.3 or 23 CFU for pure culture, whereas 2.3 × 104 or 2.3 × 106 CFU for simulated spleen and lung samples. For simulated liver samples, the sensitivity of LAMP was 2.3 × 106 CFU, but PCR was negative at the level of 2.3 × 107 CFU. After simulated spleen and lung samples were treated with magnetic beads, the sensitivity of LAMP or PCR was 2.3 × 103 or 2.3 × 106 CFU, whereas 2.3 × 105 or 2.3 × 107 CFU for magnetic bead-treated liver samples. These results indicated that some components in the tissues could inhibit LAMP and PCR, and liver tissue samples had a stronger inhibition to LAMP and PCR than spleen and lung tissue samples. LAMP has a higher sensitivity than PCR, and magnetic bead capture of DNAs could remarkably increase the sensitivity of LAMP. LAMP is a simple, rapid and sensitive assay suitable for application in the field or poverty areas.

  13. Simple, rapid and sensitive detection of Orientia tsutsugamushi by loop-isothermal DNA amplification.

    Science.gov (United States)

    Paris, Daniel H; Blacksell, Stuart D; Newton, Paul N; Day, Nicholas P J

    2008-12-01

    We present a loop-mediated isothermal PCR assay (LAMP) targeting the groEL gene, which encodes the 60kDa heat shock protein of Orientia tsutsugamushi. Evaluation included testing of 63 samples of contemporary in vitro isolates, buffy coats and whole blood samples from patients with fever. Detection limits for LAMP were assessed by serial dilutions and quantitation by real-time PCR assay based on the same target gene: three copies/microl for linearized plasmids, 26 copies/microl for VERO cell culture isolates, 14 copies/microl for full blood samples and 41 copies/microl for clinical buffy coats. Based on a limited sample number, the LAMP assay is comparable in sensitivity with conventional nested PCR (56kDa gene), with limits of detection well below the range of known admission bacterial loads of patients with scrub typhus. This inexpensive method requires no sophisticated equipment or sample preparation, and may prove useful as a diagnostic assay in financially poor settings; however, it requires further prospective validation in the field setting.

  14. Tip-enhanced fluorescence with radially polarized illumination for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA

    Science.gov (United States)

    Wei, Shih-Chung; Chuang, Tsung-Liang; Wang, Da-Shin; Lu, Hui-Hsin; Gu, Frank X.; Sung, Kung-Bin; Lin, Chii-Wann

    2015-02-01

    A tip nanobiosensor for monitoring DNA replication was presented. The effects of excitation power and polarization on tip-enhanced fluorescence (TEF) were assessed with the tip immersed in fluorescein isothiocyanate solution first. The photon count rose on average fivefold with radially polarized illumination at 50 mW. We then used polymerase-functionalized tips for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA. The amplicon-SYBR Green I complex was detected and compared to real-time loop-mediated isothermal amplification. The signals of the reaction using 4 and 0.004 ng/μl templates were detected 10 and 30 min earlier, respectively. The results showed the potential of TEF in developing a nanobiosensor for real-time DNA amplification.

  15. Microfluidic method for rapid turbidimetric detection of the DNA of Mycobacterium tuberculosis using loop-mediated isothermal amplification in capillary tubes

    International Nuclear Information System (INIS)

    Rafati, Adele; Gill, Pooria

    2015-01-01

    We describe a microfluidic method for rapid isothermal turbidimetric detection of the DNA of Mycobacterium tuberculosis. Loop-mediated isothermal amplification is accomplished in capillary tubes for amplifying DNA in less than 15 min, and sensitivity and specificity were compared to conventional loop-mediated isothermal amplification (LAMP). The method can detect as little as 1 pg mL −1 DNA in a sample. Results obtained with clinical specimens indicated 90 % sensitivity and 95 % specificity for microfluidic LAMP in comparison to culture methods. No interference occurred due to the presence of nonspecific DNAs. The findings demonstrate the power of the new microfluidic LAMP test for rapid molecular detection of microorganisms even when using bare eyes. (author)

  16. Mutations reducing replication from R-loops suppress the defects of growth, chromosome segregation and DNA supercoiling in cells lacking topoisomerase I and RNase HI activity.

    Science.gov (United States)

    Usongo, Valentine; Martel, Makisha; Balleydier, Aurélien; Drolet, Marc

    2016-04-01

    R-loop formation occurs when the nascent RNA hybridizes with the template DNA strand behind the RNA polymerase. R-loops affect a wide range of cellular processes and their use as origins of replication was the first function attributed to them. In Escherichia coli, R-loop formation is promoted by the ATP-dependent negative supercoiling activity of gyrase (gyrA and gyrB) and is inhibited by topoisomerase (topo) I (topA) relaxing transcription-induced negative supercoiling. RNase HI (rnhA) degrades the RNA moiety of R-loops. The depletion of RNase HI activity in topA null mutants was previously shown to lead to extensive DNA relaxation, due to DNA gyrase inhibition, and to severe growth and chromosome segregation defects that were partially corrected by overproducing topo III (topB). Here, DNA gyrase assays in crude cell extracts showed that the ATP-dependent activity (supercoiling) of gyrase but not its ATP-independent activity (relaxation) was inhibited in topA null cells lacking RNase HI. To characterize the cellular event(s) triggered by the absence of RNase HI, we performed a genetic screen for suppressors of the growth defect of topA rnhA null cells. Suppressors affecting genes in replication (holC2::aph and dnaT18::aph) nucleotide metabolism (dcd49::aph), RNA degradation (rne59::aph) and fimbriae synthesis (fimD22::aph) were found to reduce replication from R-loops and to restore supercoiling, thus pointing to a correlation between R-loop-dependent replication in topA rnhA mutants and the inhibition of gyrase activity and growth. Interestingly, the position of fimD on the E. coli chromosome corresponds to the site of one of the five main putative origins of replication from R-loops in rnhA null cells recently identified by next-generation sequencing, thus suggesting that the fimD22::aph mutation inactivated one of these origins. Furthermore, we show that topo III overproduction is unable to complement the growth defect of topA rnhA null mutants at low

  17. Abrupt suppression of the transcription in the mammalian cells by X-irradiation at the violation of topological contraint of DNA superhelical loops

    International Nuclear Information System (INIS)

    Luchnik, A.N.; Dubinina, E.N.; Zbarskij, I.B.; Georgiev, G.P.; AN SSSR, Moscow. Inst. Molekulyarnoj Biologii)

    1987-01-01

    It is supposed that the whole transcription in mammalian cells depends on elastic stresses in constraint DNA loops. It is assumed that a specific molecular mechanism of transcription stop under irradiation is explained as follows: conformation of nucleosomes is changed (including DNA, histon octamer) in actively elastic-stressed chromatin. Elastically stressed DNA can promote stabilization of unfolded nucleosomes. Such nucleosomes do not interfere in RNA-polymerase conducting transcription. Nucleosomes after losing elastic stresses take wither globulra (non-active) conformation or histons dissociate with DNA, and instead of it non-active ocatmers of nucleosomes precipitate on it. The globular octamer prevents RNA-polymerase from conducting transcription through the whole length of nucleoprotein fibril. This hypothesis is substantiated by the facts that X-radiation removes High- and super-sensitivity of active chromatin to DNA-aze I as well as dissociates histons from active minichromosoms

  18. Loop-mediated isothermal amplification (LAMP) assay-A rapid detection tool for identifying red fox (Vulpes vulpes) DNA in the carcasses of harbour porpoises (Phocoena phocoena).

    Science.gov (United States)

    Heers, Teresa; van Neer, Abbo; Becker, André; Grilo, Miguel Luca; Siebert, Ursula; Abdulmawjood, Amir

    2017-01-01

    Carcasses of wild animals are often visited by different scavengers. However, determining which scavenger caused certain types of bite marks is particularly difficult and knowledge thereof is lacking. Therefore, a loop-mediated isothermal amplification (LAMP) assay (target sequence cytochrome b) was developed to detect red fox DNA in carcasses of harbour porpoises. The MSwab™ method for direct testing without prior DNA isolation was validated. As a detection device, the portable real-time fluorometer Genie® II was used, which yields rapid results and can be used in field studies without huge laboratory equipment. In addition to in vitro evaluation and validation, a stranded and scavenged harbour porpoise carcass was successfully examined for red fox DNA residues. The developed LAMP method is a valuable diagnostic tool for confirming presumable red fox bite wounds in harbour porpoises without further DNA isolation steps.

  19. Population genetic structure of skipjack tuna Katsuwonus pelamis from the Indian coast using sequence analysis of the mitochondrial DNA D-loop region

    Digital Repository Service at National Institute of Oceanography (India)

    Menezes, M.R.; Kumar, G.; Kunal, S.P.

    Biology (2012) 80, 2198–2212 doi:10.1111/j.1095-8649.2012.03270.x, available online at wileyonlinelibrary.com Population genetic structure of skipjack tuna Katsuwonus pelamis from the Indian coast using sequence analysis of the mitochondrial DNA D...-loop region M. R. Menezes*, G. Kumar and S. P. Kunal Biological Oceanography Division, National Institute of Oceanography (CSIR), Dona Paula, Goa 403 004, India (Received 26 May 2011, Accepted 14 February 2012) Genetic structure of skipjack tuna Katsuwonus...

  20. Three genetic stocks of frigate tuna Auxis thazard thazard (Lacepede, 1800) along the Indian coast revealed from sequence analyses of mitochondrial DNA D-loop region

    Digital Repository Service at National Institute of Oceanography (India)

    GirishKumar; Kunal, S.P.; Menezes, M.R.; Meena, R.M.

    revealed from sequence analyses of mitochondrial DNA D-loop region Name of authors: 1. Girish Kumar* Biological Oceanography Division (BOD) National Institute of Oceanography (NIO) Dona Paula, Goa 403004, India. Email: girishkumar....nio@gmail.com Tel: +919766548060 2. Swaraj Priyaranjan Kunal Biological Oceanography Division (BOD) National Institute of Oceanography (NIO) Dona Paula, Goa 403004, India. Email: swar.mbt@gmail.com 3. Maria Rosalia Menezes Biological Oceanography...

  1. An Optimized Protocol for DNA Extraction from Wheat Seeds and Loop-Mediated Isothermal Amplification (LAMP to Detect Fusarium graminearum Contamination of Wheat Grain

    Directory of Open Access Journals (Sweden)

    Mohamed Moslem

    2011-06-01

    Full Text Available A simple, rapid, and efficient method for isolating genomic DNA from germinated seeds of wheat that is free from polysaccharides and polyphenols is reported. DNA was extracted, treated with RNase, measured and tested for completeness using agarose gel electrophoresis. DNA purification from wheat grains yielded abundant, amplifiable DNA with yields typically between 100 and 200 ng DNA/mg. The effectiveness and reliability of the method was tested by assessing quantity and quality of the isolated DNA using three PCR-based markers. Inter-simple sequence repeats (ISSRs were used to assess the genetic diversity between different wheat varieties. Specific PCR primer pair Tox5-1/Tox5-2 and a loop-mediated isothermal amplification (LAMP procedure were used to detect genomic DNA of Fusarium graminearum in contaminated wheat seeds. In this method there is no need to use liquid nitrogen for crushing germinated seedlings. The protocol takes approximately one hour to prepare high quality DNA. In combination with the LAMP assay it is a fast and cost-effective alternative to traditional diagnostic methods for the early detection of toxigenic fusaria in cereals.

  2. An optimized protocol for DNA extraction from wheat seeds and Loop-Mediated Isothermal Amplification (LAMP) to detect Fusarium graminearum contamination of wheat grain.

    Science.gov (United States)

    Abd-Elsalam, Kamel; Bahkali, Ali; Moslem, Mohamed; Amin, Osama E; Niessen, Ludwig

    2011-01-01

    A simple, rapid, and efficient method for isolating genomic DNA from germinated seeds of wheat that is free from polysaccharides and polyphenols is reported. DNA was extracted, treated with RNase, measured and tested for completeness using agarose gel electrophoresis. DNA purification from wheat grains yielded abundant, amplifiable DNA with yields typically between 100 and 200 ng DNA/mg. The effectiveness and reliability of the method was tested by assessing quantity and quality of the isolated DNA using three PCR-based markers. Inter-simple sequence repeats (ISSRs) were used to assess the genetic diversity between different wheat varieties. Specific PCR primer pair Tox5-1/Tox5-2 and a loop-mediated isothermal amplification (LAMP) procedure were used to detect genomic DNA of Fusarium graminearum in contaminated wheat seeds. In this method there is no need to use liquid nitrogen for crushing germinated seedlings. The protocol takes approximately one hour to prepare high quality DNA. In combination with the LAMP assay it is a fast and cost-effective alternative to traditional diagnostic methods for the early detection of toxigenic fusaria in cereals.

  3. MORPHOLOGY AND GENETIC DIVERSITY OF MITOCHONDRIAL DNA D-LOOP REGION USING PCR-RFLP ANALYSIS IN MAGELANG DUCK AND OTHER NATIVE DUCK

    Directory of Open Access Journals (Sweden)

    D. Purwantini

    2014-10-01

    Full Text Available The aim of this study was to investigate the different of plumage colors on morphological diversityof Magelang duck and genetic diversity using PCR-RFLP mtDNA D-loop region analysis of Magelangduck and four others native duck population (Tegal, Mojosari, Bali and Alabio duck in Indonesia. Bloodsample was taken from 50 Magelang ducks and 20 of each native ducks. Morphological characteristicsof body measurement, production ability and egg quality of Magelang duck were analyzed usingCompletely Randomized Design with 11 plumage colors as treatments. PCR technique was administeredto amplify fragments in mtDNA D-loop region and PCR products were digested with endonucleaserestriction enzyme AluI and HaeIII. The result showed that morphology diversity of Magelang duck wasstatistically affected by different plumage colors. PCR-RFLP analysis using AluI and HaeIII restrictionenzyme resulted in six combinations of restriction fragment pattern shown in six haplotypes (A, B, C, D,E and F. Haplotype difference showed genetic diversity in the population of Magelang duck and theother native ducks. In conclusion, the different plumage colors affected morphology diversity ofMagelang duck. Genetic diversity of Indonesian native duck population could be identified by usingPCR-RFLP analysis on mtDNA D-loop region.

  4. Phylogenetic relationships of Scomberomorus commerson using sequence analysis of the mtDNA D-loop region in the Persian Gulf, Oman Sea and Arabian Sea

    Directory of Open Access Journals (Sweden)

    Ana Mansourkiaei

    2016-04-01

    Full Text Available Abstract Narrow-barred Spanish mackerel, Scomberomorus commerson, is an epipelagic and migratory species of family Scombridae which have a significant role in terms of ecology and fishery. 100 samples were collected from the Persian Gulf, Oman Sea and Arabian Sea. Part of their dorsal fins was snipped and transferred to micro-tubes containing ethanol; then, DNAs were extracted and HRM-Real Time PCR was performed to designate representative specimens for sequencing. Phylogenetic relationships of S. commerson from Persian Gulf, Oman Sea and Arabian Sea were investigated using sequence data of mitochondrial DNA D-loop region. None clustered Neighbor Joining tree indicated the proximity amid S. commerson in four sites. As numbers demonstrated in sequence analyses of mitochondrial DNA D-Loop region a sublimely high degree of genetic similarity among S. commerson from the Persian Gulf and Oman Sea were perceived, thereafter, having one stock structure of S. commerson in four regions were proved, and this approximation can be merely justified by their migration process along the coasts of Oman Sea and Persian Gulf. Therefore, the assessment of distribution patterns of 20 haplotypes in the constructed phylogenetic tree using mtDNA D-Loop sequences ascertained that no significant clustering according to the sampling sites was concluded.

  5. Genetic Diversity and Phylogenetic Evolution of Tibetan Sheep Based on mtDNA D-Loop Sequences.

    Directory of Open Access Journals (Sweden)

    Jianbin Liu

    Full Text Available The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries is not well understood, and little is known about this species' genetic diversity. This knowledge gap is partly due to the difficulty of sample collection. This is the first work to address this question. Here, the genetic diversity and phylogenetic relationship of 636 individual Tibetan sheep from fifteen populations were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Samples were collected from the Qinghai-Tibetan Plateau area in China, and reference data were obtained from the six reference breed sequences available in GenBank. The length of the sequences varied considerably, between 1031 and 1259 bp. The haplotype diversity and nucleotide diversity were 0.992±0.010 and 0.019±0.001, respectively. The average number of nucleotide differences was 19.635. The mean nucleotide composition of the 350 haplotypes was 32.961% A, 29.708% T, 22.892% C, 14.439% G, 62.669% A+T, and 37.331% G+C. Phylogenetic analysis showed that all four previously defined haplogroups (A, B, C, and D were found in the 636 individuals of the fifteen Tibetan sheep populations but that only the D haplogroup was found in Linzhou sheep. Further, the clustering analysis divided the fifteen Tibetan sheep populations into at least two clusters. The estimation of the demographic parameters from the mismatch analyses showed that haplogroups A, B, and C had at least one demographic expansion in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau.

  6. Detection of Panton-Valentine Leukocidin DNA from methicillin-resistant Staphylococcus aureus by resistive pulse sensing and loop-mediated isothermal amplification with gold nanoparticles

    International Nuclear Information System (INIS)

    Yang, Alice Kar Lai; Lu, Haifei; Wu, Shu Yuen; Kwok, Ho Chin; Ho, Ho Pui; Yu, Samuel; Cheung, Anthony Ka Lun; Kong, Siu Kai

    2013-01-01

    Graphical abstract: -- Highlights: •A novel diagnostic assay is developed to detect the MRSA's Panton-Valentine Leukocidin toxin. •Detection is based on target DNA amplification at one single temperature at 65 °C by LAMP. •Amplicons are then hybridized with 2 Au-nanoparticles with specific DNA probes for sensing. •The supra-assemblies are subsequently sensed by resistive pulse sensing. •Detection limit: ∼200 copies of DNA; time for detection: completed within 2 h. -- Abstract: This report describes a novel diagnostic assay for rapid detection of the Panton-Valentine Leukocidin (PVL) toxin of methicillin-resistant Staphylococcus aureus (MRSA) utilizing resistive pulse sensing (RPS), loop-mediated isothermal DNA amplification (LAMP) in combination with gold nanoparticles (AuNPs). The PVL DNA from MRSA was specifically amplified by LAMP using four primers at one temperature (65 °C). The DNA products with biotin were then conjugated to a first AuNP1 (55 ± 2 nm) through biotin–avidin binding. A second AuNP2 (30 ± 1.5 nm) coated with a specific DNA probe hybridized with the LAMP DNA products at the loop region to enhance assay sensitivity and specificity, to generate supra-AuNP1-DNA-AuNP2 assemblies. Scanning electron microscopy confirmed the presence of these supra-assemblies. Using RPS, detection and quantitation of the agglomerated AuNPs were performed by a tunable fluidic nanopore sensor. The results demonstrate that the LAMP-based RPS sensor is sensitive and rapid for detecting the PVL DNA. This technique could achieve a limit of detection (LOD) up to about 500 copies of genomic DNA from the bacteria MRSA MW2 and the detection can be completed within two hours with a straightforward signal-to-readout setup. It is anticipated that this LAMP-based AuNP RPS may become an effective tool for MRSA detection and a potential platform in clinical laboratory to report the presence or absence of other types of infectious agents

  7. Loop-Mediated Isothermal Amplification on Crude DNA as a Point-of-Care Test for the Diagnosis of Mycoplasma-Related Vaginitis During Early Pregnancy.

    Science.gov (United States)

    Wang, Yichao; Zhang, Bumei; Sun, Yan; Liu, Yunde; Gu, Yajun

    2017-12-20

    Mycoplasma-related vaginitis gradually has been growing as a threat in adults-genitourinary infection contributes to funisitis, spontaneous abortion, and low birth weight. Until now, use of loop-mediated isothermal amplification (LAMP) to detect Ureaplasma urealyticum (UU), Mycoplasma hominis (MH), or Mycoplasma genitalium (MG) has been reported by some researchers. However, previous studies focused on purified DNA as the template for LAMP assay, which is usually extracted via commercial kit. We developed a LAMP assay for rapid detection of UU, MH, and MG genital mycoplasmas using a simple boiling method for DNA extraction, in a cohort of pregnant women with mycoplasma-related vaginitis. We monitored amplicons with the naked eye using SYBR Green I. The cohort in our study showed a prevalence of 22.6% in pregnant women, as detected by UU-LAMP assay. Compared to the polymerase chain reaction (PCR) test with purified DNA, the sensitivity of the UU-LAMP in clinical specimens with crude DNA was 87.5% (95% confidence interval [CI], 64.6%->99.9). For crude DNA specimens, UU-LAMP was more sensitive and reliable than PCR, with a higher agreement rate (96.8%) and Youden index value (0.88). As a point-of-care test, LAMP is a useful, specific, and efficient way to detect genital mycoplasmas in resource-limited settings, especially for crude DNA. © American Society for Clinical Pathology 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

  8. One simple DNA extraction device and its combination with modified visual loop-mediated isothermal amplification for rapid on-field detection of genetically modified organisms.

    Science.gov (United States)

    Zhang, Miao; Liu, Yinan; Chen, Lili; Quan, Sheng; Jiang, Shimeng; Zhang, Dabing; Yang, Litao

    2013-01-02

    Quickness, simplicity, and effectiveness are the three major criteria for establishing a good molecular diagnosis method in many fields. Herein we report a novel detection system for genetically modified organisms (GMOs), which can be utilized to perform both on-field quick screening and routine laboratory diagnosis. In this system, a newly designed inexpensive DNA extraction device was used in combination with a modified visual loop-mediated isothermal amplification (vLAMP) assay. The main parts of the DNA extraction device included a silica gel membrane filtration column and a modified syringe. The DNA extraction device could be easily operated without using other laboratory instruments, making it applicable to an on-field GMO test. High-quality genomic DNA (gDNA) suitable for polymerase chain reaction (PCR) and isothermal amplification could be quickly isolated from plant tissues using this device within 15 min. In the modified vLAMP assay, a microcrystalline wax encapsulated detection bead containing SYBR green fluorescent dye was introduced to avoid dye inhibition and cross-contaminations from post-LAMP operation. The system was successfully applied and validated in screening and identification of GM rice, soybean, and maize samples collected from both field testing and the Grain Inspection, Packers, and Stockyards Administration (GIPSA) proficiency test program, which demonstrated that it was well-adapted to both on-field testing and/or routine laboratory analysis of GMOs.

  9. Loop kinematics

    International Nuclear Information System (INIS)

    Migdal, A.A.

    1982-01-01

    Basic operators acting in the loop space are introduced. The topology of this space and properties of the Stokes type loop functionals are discussed. The parametrically invariant loop calculus developed here is used in the loop dynamics

  10. Comparison of DNA Microarray, Loop-Mediated Isothermal Amplification (LAMP) and Real-Time PCR with DNA Sequencing for Identification of Fusarium spp. Obtained from Patients with Hematologic Malignancies.

    Science.gov (United States)

    de Souza, Marcela; Matsuzawa, Tetsuhiro; Sakai, Kanae; Muraosa, Yasunori; Lyra, Luzia; Busso-Lopes, Ariane Fidelis; Levin, Anna Sara Shafferman; Schreiber, Angélica Zaninelli; Mikami, Yuzuru; Gonoi, Tohoru; Kamei, Katsuhiko; Moretti, Maria Luiza; Trabasso, Plínio

    2017-08-01

    The performance of three molecular biology techniques, i.e., DNA microarray, loop-mediated isothermal amplification (LAMP), and real-time PCR were compared with DNA sequencing for properly identification of 20 isolates of Fusarium spp. obtained from blood stream as etiologic agent of invasive infections in patients with hematologic malignancies. DNA microarray, LAMP and real-time PCR identified 16 (80%) out of 20 samples as Fusarium solani species complex (FSSC) and four (20%) as Fusarium spp. The agreement among the techniques was 100%. LAMP exhibited 100% specificity, while DNA microarray, LAMP and real-time PCR showed 100% sensitivity. The three techniques had 100% agreement with DNA sequencing. Sixteen isolates were identified as FSSC by sequencing, being five Fusarium keratoplasticum, nine Fusarium petroliphilum and two Fusarium solani. On the other hand, sequencing identified four isolates as Fusarium non-solani species complex (FNSSC), being three isolates as Fusarium napiforme and one isolate as Fusarium oxysporum. Finally, LAMP proved to be faster and more accessible than DNA microarray and real-time PCR, since it does not require a thermocycler. Therefore, LAMP signalizes as emerging and promising methodology to be used in routine identification of Fusarium spp. among cases of invasive fungal infections.

  11. Possible role(s) of nuclear matrix and DNA loop organization in fixation or repair of DNA double-strand breaks

    International Nuclear Information System (INIS)

    Malyapa, R.S.; Wright, W.D.; Roti Roti, J.L.

    1995-01-01

    DNA double-strand breaks produced by ionizing radiation are considered to be a critical radiation-induced lesion responsible, in part, for cell killing. However, the manner in which structures within the nucleus involving DNA organization contribute to the balance between fixation or repair of these critical lesions remains largely obscure. The repair process requires both functional enzymes and substrate availability, i.e., access to and orientation of damage sites. Therefore, the ability to repair damaged DNA could be influenced not only by DNA integrity but also by the spatial organization of DNA. Therefore, the authors investigated the possibility that radiation-induced DNA damage differentially affects DNA supercoiling ability in cells of differing radiosensitivities using radioresistant and radiosensitive mutants of different origins. This study was also designed to determine if differences in the composition of the nuclear matrix exist between cell lines of each origin. Results from these studies indicate that differences in the composition of the nuclear matrix proteins and DNA stability might be related to intrinsic radiation resistance

  12. A “four-ferrocene” modified stem-loop structure as a probe for sensitive detection and single-base mismatch discrimination of DNA

    International Nuclear Information System (INIS)

    Chatelain, Grégory; Ripert, Micaël; Farre, Carole; Ansanay-Alex, Salomé; Chaix, Carole

    2012-01-01

    We report the use of a four-ferrocene modified oligonucleotide as a probe for DNA detection with a gold electrode microsystem. This oligonucleotide is synthesized by automated solid-phase synthesis with four successive ferrocene moieties at the 5′-end and a C6-thiol modifier group at the 3′-end. The grafting of this 4Fc-DNA probe on a gold electrode microsystem results in the appearance of the ferrocene redox couple in cyclic voltammetry. The probe sequence is a stem-loop structure that folds efficiently on the electrode, thus optimizing electron transfer. Such architecture serves as sensor for DNA detection which is based on hybridization. The resulting disposable voltammetric sensor allowed direct, reagentless DNA detection in a small volume (20 μL). Electrochemical response upon hybridization with complementary short sequence (30-base length) and long sequence (50-base length) strands was observed by differential pulse voltammetry. Current variations were compared. The longer the sequence, the greater the decrease in current. The system's detection limit was estimated at 3.5 pM (0.07 fmol in 20 μL) with the 50-base length target and provided a dynamic detection range between 3.5 pM and 5 nM. Single mismatch detection showed a good level of sensitivity. The system was regenerated twice with no significant loss of Fc signal. Finally, 1 pM sensitivity was reached with a long chain analog of DNA PCR products of Influenza virus.

  13. Stability of Loop-Mediated Isothermal Amplification (LAMP) Reagents and its Amplification Efficiency on Crude Trypanosome DNA Templates

    OpenAIRE

    Thekisoe, Oriel M. M; Bazie, Raoul S. B; Coronel-Servian, Andrea M; Sugimoto, Chihiro; Kawazu, Shin-ichiro; Inoue, Noboru

    2009-01-01

    This study evaluated the stability of LAMP reagents when stored at 25C and 37C, and also assessed its detection efficiency on different DNA template preparations. Accordingly, LAMP using reagents stored at 25C and 37C amplified DNA of in vitro cultured T. b. brucei (GUTat 3.1) from day 1 to day 15 of reagent storage. There were no significant differences (P>0.05) in detection sensitivity of LAMP among the reagents stored at 25C, 37C and –20C (recommended storage temperature). LAMP usin...

  14. Stability of Loop-Mediated Isothermal Amplification (LAMP) reagents and its amplification efficiency on crude trypanosome DNA templates.

    Science.gov (United States)

    Thekisoe, Oriel M M; Bazie, Raoul S B; Coronel-Servian, Andrea M; Sugimoto, Chihiro; Kawazu, Shin-Ichiro; Inoue, Noboru

    2009-04-01

    This study evaluated the stability of LAMP reagents when stored at 25 degrees C and 37 degrees C, and also assessed its detection efficiency on different DNA template preparations. Accordingly, LAMP using reagents stored at 25 degrees C and 37 degrees C amplified DNA of in vitro cultured T. b. brucei (GUTat 3.1) from day 1 to day 15 of reagent storage. There were no significant differences (P>0.05) in detection sensitivity of LAMP among the reagents stored at 25 degrees C, 37 degrees C and -20 degrees C (recommended storage temperature). LAMP using the reagents stored at above-mentioned temperatures amplified serially diluted DNAs (genomic DNA extracted by phenol-chloroform method, FTA card and hemolysed blood) of T. b. gambiense (IL2343) with high sensitivity. Reactions were conducted on the reagents stored from 1 day to 30 days. LAMP detection sensitivity was poor when fresh blood as DNA template was added directly into reactive solution. Results of this study demonstrated that LAMP has the potential to be used in field conditions for diagnosis of trypanosome infections without being affected by ambient temperatures of tropical and sub-tropical countries where trypanosomosis is endemic.

  15. Time Course of Detection of Human Male DNA from Stained Blood Sample on Various Surfaces by Loop Mediated Isothermal Amplification and Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    Panan Kanchanaphum

    2018-01-01

    Full Text Available This study explores determining the sex of humans from blood stains taken from different surfaces and compares the time course of detection with the conventional PCR, Conventional Loop Mediated Isothermal Amplification (LAMP, and LAMP-Lateral Flow Dipstick (LFD. For the DNA templates, 7 male and 7 female blood stained samples were extracted and added to LAMP and PCR reaction solution to amplify the SRY gene. The DNA samples were extracted from the following blood stained materials: cloth, wood, clay, and tile. Then, the samples were stored at room temperature for 1, 7, 30, and 60 day(s. After the DNA amplification, the gel electrophoresis process was applied to detect LAMP product. The LFD was combined with the LAMP to detect LAMP product on the male cloth samples. For the male samples, the time course of detection on the first and seventh days indicated positive for both LAMP and PCR products on all the surfaces while no DNA amplification was found on any of the female samples. On day 30, positive LAMP product was still found on all the male samples. However, it had faded on the tiles. Moreover, all the male samples, which had tested positive for PCR product, were blurred and unclear. On day 60, LAMP product was still found on all the male samples. Conversely, the PCR method resulted in no bands showing for any of the male samples. However, the LAMP-LFD method detected product on all the male samples of cloth. The results show that the LAMP is an effective, practical, and reliable molecular-biological method. Moreover, the LFD can increase the efficiency and sensitivity of the LAMP, making it more suitable for field studies because gel electrophoresis apparatus is not required.

  16. Phylogenetic and Genetic Analysis of D-loop and Cyt-b Region of mtDNA Sequence in Iranian Sistani, Sarabi and Brown Swiss Cows

    Directory of Open Access Journals (Sweden)

    reza valizadeh

    2016-06-01

    Full Text Available Cattle have an important role in primary human civilization, so molecular studies for more accurate recognition of their origin are effective to identify unknown historical aspects. Cattle can be divided in to 2 main groups including Bos Tuarus and Bos Indicus. Both types of cattle can be found in Iran; therefore study of their origin has particular importance. The aim of this study was to investigate the nucleotide sequences of Cytochrome-b (Cyt-b and HVR1&2 loci of D-loop gene region in mitochondrial DNA of Sistani, Sarabi and Brown Swiss breeds of cattle. Twenty blood samples of each breed, from non-relative individuals were obtained from blood bank of animal science department of Faculty of Agriculture, Ferdowsi University of Mashhad. The DNA content of sample was extracted based on the guanidinium thiocianate-silicagel method. Polymerase Chain Reaction with specific designed primers was performed to amplify Cyt-b and HVR 1&2 loci with 751 and 701 bp lengths, respectively. Sequencing of amplified Cyt-b and HVR 1&2 loci were done based on Sanger method by automatic sequencer machine (ABI 3130. Nucleotide diversity in Brown Swiss, Sarabi and Sistani breeds were estimated 0.0037, 0.0024 and 0.0029, respectively. Sequences of Cyt-b and HVR 1&2 were register in National Center for Biotechnology Institute due to nucleotide differences. Results of phylogenetic test using UPGMA for both loci showed that Sarabi and Sistani breeds are belonging to first group and Brown Swiss breed to other group.

  17. Expression of the helix-loop-helix protein inhibitor of DNA binding-1 (ID-1) is activated by all-trans retinoic acid in normal human keratinocytes

    International Nuclear Information System (INIS)

    Villano, C.M.; White, L.A.

    2006-01-01

    The ID (inhibitor of differentiation or DNA binding) helix-loop-helix proteins are important mediators of cellular differentiation and proliferation in a variety of cell types through regulation of gene expression. Overexpression of the ID proteins in normal human keratinocytes results in extension of culture lifespan, indicating that these proteins are important for epidermal differentiation. Our hypothesis is that the ID proteins are targets of the retinoic acid signaling pathway in keratinocytes. Retinoids, vitamin A analogues, are powerful regulators of cell growth and differentiation and are widely used in the prevention and treatment of a variety of cancers in humans. Furthermore, retinoic acid is necessary for the maintenance of epithelial differentiation and demonstrates an inhibitory action on skin carcinogenesis. We examined the effect of all-trans retinoic acid on expression of ID-1, -2, -3, and -4 in normal human keratinocytes and found that exposure of these cells to all-trans retinoic acid causes an increase in both ID-1 and ID-3 gene expression. Furthermore, our data show that this increase is mediated by increased transcription involving several cis-acting elements in the distal portion of the promoter, including a CREB-binding site, an Egr1 element, and an YY1 site. These data demonstrate that the ID proteins are direct targets of the retinoic acid signaling pathway. Given the importance of the ID proteins to epidermal differentiation, these results suggest that IDs may be mediating some of the effects of all-trans retinoic acid in normal human keratinocytes

  18. Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly.

    Science.gov (United States)

    Chereji, Razvan V; Bharatula, Vasudha; Elfving, Nils; Blomberg, Jeanette; Larsson, Miriam; Morozov, Alexandre V; Broach, James R; Björklund, Stefan

    2017-09-06

    Mediator is a multi-unit molecular complex that plays a key role in transferring signals from transcriptional regulators to RNA polymerase II in eukaryotes. We have combined biochemical purification of the Saccharomyces cerevisiae Mediator from chromatin with chromatin immunoprecipitation in order to reveal Mediator occupancy on DNA genome-wide, and to identify proteins interacting specifically with Mediator on the chromatin template. Tandem mass spectrometry of proteins in immunoprecipitates of mediator complexes revealed specific interactions between Mediator and the RSC, Arp2/Arp3, CPF, CF 1A and Lsm complexes in chromatin. These factors are primarily involved in chromatin remodeling, actin assembly, mRNA 3'-end processing, gene looping and mRNA decay, but they have also been shown to enter the nucleus and participate in Pol II transcription. Moreover, we have found that Mediator, in addition to binding Pol II promoters, occupies chromosomal interacting domain (CID) boundaries and that Mediator in chromatin associates with proteins that have been shown to interact with CID boundaries, such as Sth1, Ssu72 and histone H4. This suggests that Mediator plays a significant role in higher-order genome organization. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Interaction of the host protein NbDnaJ with Potato virus X minus-strand stem-loop 1 RNA and capsid protein affects viral replication and movement.

    Science.gov (United States)

    Cho, Sang-Yun; Cho, Won Kyong; Sohn, Seong-Han; Kim, Kook-Hyung

    2012-01-06

    Plant viruses must interact with host cellular components to replicate and move from cell to cell. In the case of Potato virus X (PVX), it carries stem-loop 1 (SL1) RNA essential for viral replication and movement. Using two-dimensional electrophoresis northwestern blot analysis, we previously identified several host proteins that bind to SL1 RNA. Of those, we further characterized a DnaJ-like protein from Nicotiana benthamiana named NbDnaJ. An electrophoretic mobility shift assay confirmed that NbDnaJ binds only to SL1 minus-strand RNA, and bimolecular fluorescence complementation (BiFC) indicated that NbDnaJ interacts with PVX capsid protein (CP). Using a series of deletion mutants, the C-terminal region of NbDnaJ was found to be essential for the interaction with PVX CP. The expression of NbDnaJ significantly changed upon infection with different plant viruses such as PVX, Tobacco mosaic virus, and Cucumber mosaic virus, but varied depending on the viral species. In transient experiments, both PVX replication and movement were inhibited in plants that over-expressed NbDnaJ but accelerated in plants in which NbDnaJ was silenced. In summary, we suggest that the newly identified NbDnaJ plays a role in PVX replication and movement by interacting with SL1(-) RNA and PVX CP. Copyright © 2011 Elsevier Inc. All rights reserved.

  20. Loop-mediated isothermal DNA amplification for asymptomatic malaria detection in challenging field settings: Technical performance and pilot implementation in the Peruvian Amazon.

    Directory of Open Access Journals (Sweden)

    Elisa Serra-Casas

    Full Text Available Loop-mediated isothermal DNA amplification (LAMP methodology offers an opportunity for point-of-care (POC molecular detection of asymptomatic malaria infections. However, there is still little evidence on the feasibility of implementing this technique for population screenings in isolated field settings.Overall, we recruited 1167 individuals from terrestrial ('road' and hydric ('riverine' communities of the Peruvian Amazon for a cross-sectional survey to detect asymptomatic malaria infections. The technical performance of LAMP was evaluated in a subgroup of 503 samples, using real-time Polymerase Chain Reaction (qPCR as reference standard. The operational feasibility of introducing LAMP testing in the mobile screening campaigns was assessed based on field-suitability parameters, along with a pilot POC-LAMP assay in a riverine community without laboratory infrastructure.LAMP had a sensitivity of 91.8% (87.7-94.9 and specificity of 91.9% (87.8-95.0, and the overall accuracy was significantly better among samples collected during road screenings than riverine communities (p≤0.004. LAMP-based diagnostic strategy was successfully implemented within the field-team logistics and the POC-LAMP pilot in the riverine community allowed for a reduction in the turnaround time for case management, from 12-24 hours to less than 5 hours. Specimens with haemolytic appearance were regularly observed in riverine screenings and could help explaining the hindered performance/interpretation of the LAMP reaction in these communities.LAMP-based molecular malaria diagnosis can be deployed outside of reference laboratories, providing similar performance as qPCR. However, scale-up in remote field settings such as riverine communities needs to consider a number of logistical challenges (e.g. environmental conditions, labour-intensiveness in large population screenings that can influence its optimal implementation.

  1. An HIV-1 encoded peptide mimics the DNA binding loop of NF-κB and binds thioredoxin with high affinity

    International Nuclear Information System (INIS)

    Su Guoping; Wang Min; Taylor, Ethan Will

    2005-01-01

    Pro-fs is a human immunodeficiency virus type 1 (HIV-l)-encoded putative selenoprotein, predicted by a theoretical analysis of the viral genome; it is potentially expressed by a -1 frameshift from the protease coding region. Pro-fs has significant sequence similarity to the DNA binding loop of nuclear factor kappa B (NF-κB), which is known to bind thioredoxin (Trx). We hypothesize that the putative HIV-1 pro-fs gene product functions by mimicry of NF-κB via binding to Trx. The hypothesis was tested in vitro by co-immunoprecipitation and GST-pull down assays, using a purified mutant pro-fs protein, in which the two potential selenocysteine residues were mutated to cysteines, in order to permit expression in bacteria. Both experiments showed that pro-fs binds to human wild type Trx (Trx-wt) with high affinity. Mutation of the two conserved cysteine residues in the Trx active site redox center to serine (Ser) (Trx-CS) weakened but failed to abolish the interaction. In pro-fs-transfected 293T cells, using confocal microscopy and fluorescence resonance energy transfer (FRET), we have observed that pro-fs localizes in cell nuclei and forms oligomers. Upon stimulation by phorbol 12-myristate 13-acetate (PMA), Trx translocates into cell nuclei. Significant FRET efficiency was detected in the nuclei of PMA-stimulated 293T cells co-expressing fluorescence-tagged pro-fs and Trx-wt or Trx-CS. These results indicate that in living cells the double cysteine mutant of pro-fs binds to both Trx and Trx-CS with high affinity, suggesting that Trx-pro-fs binding is a structurally-specific interaction, involving more of the Trx molecule than just its active site cysteine residues. These results establish the capacity for functional mimicry of the Trx binding ability of the NF-κB/Rel family of transcription factors by the putative HIV-1 pro-fs protein

  2. Assessing the performance of a Loop Mediated Isothermal Amplification (LAMP) assay for the detection and subtyping of high-risk suptypes of Human Papilloma Virus (HPV) for Oropharyngeal Squamous Cell Carcinoma (OPSCC) without DNA purification.

    Science.gov (United States)

    Rohatensky, Mitchell G; Livingstone, Devon M; Mintchev, Paul; Barnes, Heather K; Nakoneshny, Steven C; Demetrick, Douglas J; Dort, Joseph C; van Marle, Guido

    2018-02-08

    Oropharyngeal Squamous Cell Carcinoma (OPSCC) is increasing in incidence despite a decline in traditional risk factors. Human Papilloma Virus (HPV), specifically subtypes 16, 18, 31 and 35, has been implicated as the high-risk etiologic agent. HPV positive cancers have a significantly better prognosis than HPV negative cancers of comparable stage, and may benefit from different treatment regimens. Currently, HPV related carcinogenesis is established indirectly through Immunohistochemistry (IHC) staining for p16, a tumour suppressor gene, or polymerase chain reaction (PCR) that directly tests for HPV DNA in biopsied tissue. Loop mediated isothermal amplification (LAMP) is more accurate than IHC, more rapid than PCR and is significantly less costly. In previous work we showed that a subtype specific HPV LAMP assay performed similar to PCR on purified DNA. In this study we examined the performance of this LAMP assay without DNA purification. We used LAMP assays using established primers for HPV 16 and 18, and new primers for HPV 31 and 35. LAMP reaction conditions were tested on serial dilutions of plasmid HPV DNA to confirm minimum viral copy number detection thresholds. LAMP was then performed directly on different human cell line samples without DNA purification. Our LAMP assays could detect 10 5 , 10 3 , 10 4 , and 10 5 copies of plasmid DNA for HPV 16, 18, 31, and 35, respectively. All primer sets were subtype specific, with no cross-amplification. Our LAMP assays also reliably amplified subtype specific HPV DNA from samples without requiring DNA isolation and purification. The high risk OPSCC HPV subtype specific LAMP primer sets demonstrated, excellent clinically relevant, minimum copy number detection thresholds with an easy readout system. Amplification directly from samples without purification illustrated the robust nature of the assay, and the primers used. This lends further support HPV type specific LAMP assays, and these specific primer sets and assays

  3. The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA

    NARCIS (Netherlands)

    Popovic, Matija; Wienk, Hans; Coglievina, Maristella; Boelens, Rolf; Pongor, Sándor; Pintar, Alessandro

    2014-01-01

    Hairy and enhancer of split 1, one of the main downstream effectors in Notch signaling, is a transcriptional repressor of the basic helix-loop-helix (bHLH) family. Using nuclear magnetic resonance methods, we have determined the structure and dynamics of a recombinant protein, H1H, which includes an

  4. R-loops: targets for nuclease cleavage and repeat instability.

    Science.gov (United States)

    Freudenreich, Catherine H

    2018-01-11

    R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias. Recently, it was found that R-loops at an expanded CAG/CTG repeat tract cause DNA breaks as well as repeat instability (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Two factors were identified as causing R-loop-dependent breaks at CAG/CTG tracts: deamination of cytosines and the MutLγ (Mlh1-Mlh3) endonuclease, defining two new mechanisms for how R-loops can generate DNA breaks (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Following R-loop-dependent nicking, base excision repair resulted in repeat instability. These results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. This perspective summarizes mechanisms of R-loop-induced fragility at G-rich repeats and new links between DNA breaks and repeat instability.

  5. Improved humoral and cellular immune response against the gp120 V3 loop of HIV-1 following genetic immunization with a chimeric DNA vaccine encoding the V3 inserted into the hepatites B surface antigen

    DEFF Research Database (Denmark)

    Fomsgaard, A.; Nielsen, H.V.; Bryder, K.

    1998-01-01

    response and a uniform strong anti-HBs CTL response already 1 week p.i. in all mice. DNA vaccination with the chimeric MN V2/HBsAg plasmid elicited humoral responses against both viruses within 3-6 weeks which peaked at 6-12 weeks and remained stable for at least 25 weeks. In addition, specific CTL...... responses were induced in all mice against both MN V3 and HBsAg already within the first 3 weeks, lasting at least 11 weeks. Thus, HBsAg acts as a `genetic vaccine adjuvant' augmenting and accelerating the cellular and humoral immune response against the inserted MN V3 loop. Such chimeric HIV-HbsAg plasmid...

  6. Improved humoral and cellular immune responses against the gp120 V3 loop of HIV-1 following genetic immunization with a chimeric DNA vaccine encoding the V3 inserted into the hepatitis B surface antigen

    DEFF Research Database (Denmark)

    Fomsgaard, A; Nielsen, H V; Bryder, K

    1998-01-01

    response and a uniform strong anti-HBs CTL response already 1 week p.i. in all mice. DNA vaccination with the chimeric MN V3/HBsAg plasmid elicited humoral responses against both viruses within 3-6 weeks which peaked at 6-12 weeks and remained stable for at least 25 weeks. In addition, specific CTL...... responses were induced in all mice against both MN V3 and HBsAg already within the first 3 weeks, lasting at least 11 weeks. Thus, HBsAg acts as a 'genetic vaccine adjuvant' augmenting and accelerating the cellular and humoral immune response against the inserted MN V3 loop. Such chimeric HIV-HBsAg plasmid...

  7. Population structure and genetic diversity of Sinibrama macrops from Ou River and Ling River based on mtDNA D-loop region analysis, China.

    Science.gov (United States)

    Zhao, Liangjie; Chenoweth, Erica L; Liu, Qigen

    2018-03-01

    In order to understand the influence of human activities such as habitat fragmentation on freshwater fish population evolution, we investigated and compared the genetic diversity and phylogeography of Sinibrama macrops populations in the Oujiang River and Ling River. Mitochondrial control region sequences (D-loop region) of 131 specimens from six populations were obtained and analyzed. The diversity of main stream in the Ou River was lower than that in Ling River. Changtan population showed the lowest diversity (H = 0.646 ± 0.077; π = 0.00060 ± 0.00820). Pairwise F ST , gene flow (Nm), and genetic distance (Da) indicated that Longquan and Changtan significantly differentiate from other populations. Nested clade phylogeographical analysis (NCPA) showed some clades and total cladogram experienced isolation by distance. In conclusion, the populations from severely fragmented Ou River have the lower diversity and more intense differentiation than that from the mainstream of Ling River, Changtan population present the lowest diversity and were isolated by the dam construction.

  8. Alternative loop rings

    CERN Document Server

    Goodaire, EG; Polcino Milies, C

    1996-01-01

    For the past ten years, alternative loop rings have intrigued mathematicians from a wide cross-section of modern algebra. As a consequence, the theory of alternative loop rings has grown tremendously. One of the main developments is the complete characterization of loops which have an alternative but not associative, loop ring. Furthermore, there is a very close relationship between the algebraic structures of loop rings and of group rings over 2-groups. Another major topic of research is the study of the unit loop of the integral loop ring. Here the interaction between loop rings and group ri

  9. Loop Transfer Matrix and Loop Quantum Mechanics

    International Nuclear Information System (INIS)

    Savvidy, George K.

    2000-01-01

    The gonihedric model of random surfaces on a 3d Euclidean lattice has equivalent representation in terms of transfer matrix K(Q i ,Q f ), which describes the propagation of loops Q. We extend the previous construction of the loop transfer matrix to the case of nonzero self-intersection coupling constant κ. We introduce the loop generalization of Fourier transformation which allows to diagonalize transfer matrices, that depend on symmetric difference of loops only and express all eigenvalues of 3d loop transfer matrix through the correlation functions of the corresponding 2d statistical system. The loop Fourier transformation allows to carry out the analogy with quantum mechanics of point particles, to introduce conjugate loop momentum P and to define loop quantum mechanics. We also consider transfer matrix on 4d lattice which describes propagation of memebranes. This transfer matrix can also be diagonalized by using the generalized Fourier transformation, and all its eigenvalues are equal to the correlation functions of the corresponding 3d statistical system. In particular the free energy of the 4d membrane system is equal to the free energy of 3d gonihedric system of loops and is equal to the free energy of 2d Ising model. (author)

  10. The Brownian loop soup

    OpenAIRE

    Lawler, Gregory F.; Werner, Wendelin

    2003-01-01

    We define a natural conformally invariant measure on unrooted Brownian loops in the plane and study some of its properties. We relate this measure to a measure on loops rooted at a boundary point of a domain and show how this relation gives a way to ``chronologically add Brownian loops'' to simple curves in the plane.

  11. Selectivity in ligand recognition of G-quadruplex loops.

    Science.gov (United States)

    Campbell, Nancy H; Patel, Manisha; Tofa, Amina B; Ghosh, Ragina; Parkinson, Gary N; Neidle, Stephen

    2009-03-03

    A series of disubstituted acridine ligands have been cocrystallized with a bimolecular DNA G-quadruplex. The ligands have a range of cyclic amino end groups of varying size. The crystal structures show that the diagonal loop in this quadruplex results in a large cavity for these groups, in contrast to the steric constraints imposed by propeller loops in human telomeric quadruplexes. We conclude that the nature of the loop has a significant influence on ligand selectivity for particular quadruplex folds.

  12. R-loops in bacterial transcription: their causes and consequences.

    Science.gov (United States)

    Gowrishankar, J; Leela, J Krishna; Anupama, K

    2013-01-01

    Nascent untranslated transcripts in bacteria are prone to generating RNA-DNA hybrids (R-loops); Rho-dependent transcription termination acts to reduce their prevalence. Here we discuss the mechanisms of R-loop formation and growth inhibition in bacteria.

  13. Renormalization of loop functions for all loops

    International Nuclear Information System (INIS)

    Brandt, R.A.; Neri, F.; Sato, M.

    1981-01-01

    It is shown that the vacuum expectation values W(C 1 ,xxx, C/sub n/) of products of the traces of the path-ordered phase factors P exp[igcontour-integral/sub C/iA/sub μ/(x)dx/sup μ/] are multiplicatively renormalizable in all orders of perturbation theory. Here A/sub μ/(x) are the vector gauge field matrices in the non-Abelian gauge theory with gauge group U(N) or SU(N), and C/sub i/ are loops (closed paths). When the loops are smooth (i.e., differentiable) and simple (i.e., non-self-intersecting), it has been shown that the generally divergent loop functions W become finite functions W when expressed in terms of the renormalized coupling constant and multiplied by the factors e/sup -K/L(C/sub i/), where K is linearly divergent and L(C/sub i/) is the length of C/sub i/. It is proved here that the loop functions remain multiplicatively renormalizable even if the curves have any finite number of cusps (points of nondifferentiability) or cross points (points of self-intersection). If C/sub γ/ is a loop which is smooth and simple except for a single cusp of angle γ, then W/sub R/(C/sub γ/) = Z(γ)W(C/sub γ/) is finite for a suitable renormalization factor Z(γ) which depends on γ but on no other characteristic of C/sub γ/. This statement is made precise by introducing a regularization, or via a loop-integrand subtraction scheme specified by a normalization condition W/sub R/(C-bar/sub γ/) = 1 for an arbitrary but fixed loop C-bar/sub γ/. Next, if C/sub β/ is a loop which is smooth and simple except for a cross point of angles β, then W(C/sub β/) must be renormalized together with the loop functions of associated sets S/sup i//sub β/ = ]C/sup i/ 1 ,xxx, C/sup i//sub p/i] (i = 2,xxx,I) of loops C/sup i//sub q/ which coincide with certain parts of C/sub β/equivalentC 1 1 . Then W/sub R/(S/sup i//sub β/) = Z/sup i/j(β)W(S/sup j//sub β/) is finite for a suitable matrix Z/sup i/j

  14. Random walk loop soup

    OpenAIRE

    Lawler, Gregory F.; Ferreras, José A. Trujillo

    2004-01-01

    The Brownian loop soup introduced in Lawler and Werner (2004) is a Poissonian realization from a sigma-finite measure on unrooted loops. This measure satisfies both conformal invariance and a restriction property. In this paper, we define a random walk loop soup and show that it converges to the Brownian loop soup. In fact, we give a strong approximation result making use of the strong approximation result of Koml\\'os, Major, and Tusn\\'ady. To make the paper self-contained, we include a proof...

  15. On loop extensions and cohomology of loops

    OpenAIRE

    Benítez, Rolando Jiménez; Meléndez, Quitzeh Morales

    2015-01-01

    In this paper are defined cohomology-like groups that classify loop extensions satisfying a given identity in three variables for association identities, and in two variables for the case of commutativity. It is considered a large amount of identities. This groups generalize those defined in works of Nishigori [2] and of Jhonson and Leedham-Green [4]. It is computed the number of metacyclic extensions for trivial action of the quotient on the kernel in one particular case for left Bol loops a...

  16. Neutron transport in irradiation loops (IRENE loop)

    International Nuclear Information System (INIS)

    Sarsam, Maher.

    1980-09-01

    This thesis is composed of two parts with different aspects. Part one is a technical description of the loop and its main ancillary facilities as well as of the safety and operational regulations. The measurement methods on the model of the ISIS reactor and on the loop in the OSIRIS reactor are described. Part two deals with the possibility of calculating the powers dissipated by each rod of the fuel cluster, using appropriate computer codes, not only in the reflector but also in the core and to suggest a method of calculation [fr

  17. Water loop for training

    International Nuclear Information System (INIS)

    Moeller, S.V.

    1983-02-01

    The procedures used to operate the water loop of the Institute of Nuclear Enginering (IEN) in Brazil are presented. The aim is to help future operators of the training water loop in the operation technique and in a better comprehension of the phenomena occured during the execution of an experience. (E.G.) [pt

  18. DNA moves sequentially towards the nuclear matrix during DNA replication in vivo

    Directory of Open Access Journals (Sweden)

    Aranda-Anzaldo Armando

    2011-01-01

    Full Text Available Abstract Background In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM. There is varied evidence indicating that DNA replication occurs in replication factories organized upon the NM and that DNA loops may correspond to the actual replicons in vivo. In normal rat liver the hepatocytes are arrested in G0 but they synchronously re-enter the cell cycle after partial-hepatectomy leading to liver regeneration in vivo. We have previously determined in quiescent rat hepatocytes that a 162 kbp genomic region containing members of the albumin gene family is organized into five structural DNA loops. Results In the present work we tracked down the movement relative to the NM of DNA sequences located at different points within such five structural DNA loops during the S phase and after the return to cellular quiescence during liver regeneration. Our results indicate that looped DNA moves sequentially towards the NM during replication and then returns to its original position in newly quiescent cells, once the liver regeneration has been achieved. Conclusions Looped DNA moves in a sequential fashion, as if reeled in, towards the NM during DNA replication in vivo thus supporting the notion that the DNA template is pulled progressively towards the replication factories on the NM so as to be replicated. These results provide further evidence that the structural DNA loops correspond to the actual replicons in vivo.

  19. Large lithium loop experience

    International Nuclear Information System (INIS)

    Kolowith, R.; Owen, T.J.; Berg, J.D.; Atwood, J.M.

    1981-10-01

    An engineering design and operating experience of a large, isothermal, lithium-coolant test loop are presented. This liquid metal coolant loop is called the Experimental Lithium System (ELS) and has operated safely and reliably for over 6500 hours through September 1981. The loop is used for full-scale testing of components for the Fusion Materials Irradiation Test (FMIT) Facility. Main system parameters include coolant temperatures to 430 0 C and flow to 0.038 m 3 /s (600 gal/min). Performance of the main pump, vacuum system, and control system is discussed. Unique test capabilities of the ELS are also discussed

  20. Natively unstructured loops differ from other loops.

    Directory of Open Access Journals (Sweden)

    Avner Schlessinger

    2007-07-01

    Full Text Available Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. Here, we introduce an approach that uses a neural network in a very different and novel way. We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions differ significantly from regular, well-structured loops, and that a method detecting such features could predict natively unstructured regions. Training our new method, NORSnet, on predicted information rather than on experimental data yielded three major advantages: it removed the overlap between testing and training, it systematically covered entire proteomes, and it explicitly focused on one particular aspect of unstructured regions with a simple structural interpretation, namely that they are loops. Our hypothesis was correct: well-structured and unstructured loops differ so substantially that NORSnet succeeded in their distinction. Benchmarks on previously used and new experimental data of unstructured regions revealed that NORSnet performed very well. Although it was not the best single prediction method, NORSnet was sufficiently accurate to flag unstructured regions in proteins that were previously not annotated. In one application, NORSnet revealed previously undetected unstructured regions in putative targets for structural genomics and may thereby contribute to increasing structural coverage of large eukaryotic families. NORSnet found unstructured regions more often in domain boundaries than expected at random. In another application, we estimated that 50%-70% of all worm proteins observed to have more than seven protein-protein interaction partners have unstructured regions. The comparative analysis between NORSnet and DISOPRED2 suggested

  1. Introduction to Loop Heat Pipes

    Science.gov (United States)

    Ku, Jentung

    2015-01-01

    This is the presentation file for the short course Introduction to Loop Heat Pipes, to be conducted at the 2015 Thermal Fluids and Analysis Workshop, August 3-7, 2015, Silver Spring, Maryland. This course will discuss operating principles and performance characteristics of a loop heat pipe. Topics include: 1) pressure profiles in the loop; 2) loop operating temperature; 3) operating temperature control; 4) loop startup; 4) loop shutdown; 5) loop transient behaviors; 6) sizing of loop components and determination of fluid inventory; 7) analytical modeling; 8) examples of flight applications; and 9) recent LHP developments.

  2. Diffusion of Wilson loops

    International Nuclear Information System (INIS)

    Brzoska, A.M.; Lenz, F.; Thies, M.; Negele, J.W.

    2005-01-01

    A phenomenological analysis of the distribution of Wilson loops in SU(2) Yang-Mills theory is presented in which Wilson loop distributions are described as the result of a diffusion process on the group manifold. It is shown that, in the absence of forces, diffusion implies Casimir scaling and, conversely, exact Casimir scaling implies free diffusion. Screening processes occur if diffusion takes place in a potential. The crucial distinction between screening of fundamental and adjoint loops is formulated as a symmetry property related to the center symmetry of the underlying gauge theory. The results are expressed in terms of an effective Wilson loop action and compared with various limits of SU(2) Yang-Mills theory

  3. Blind loop syndrome

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/001146.htm Blind loop syndrome To use the sharing features on ... Clinical Professor of Medicine, The George Washington University School of Medicine, Washington, DC. Also reviewed by David ...

  4. Mashup the OODA Loop

    National Research Council Canada - National Science Library

    Heier, Jeffrey E

    2008-01-01

    ...) processes via the Observe, Orient, Decide, and Act (OODA) Loop concept. As defined by Wikipedia, a mashup is a Website or application that combines the content from more than one source into an integrated presentation...

  5. Reactor loops at Chalk River

    International Nuclear Information System (INIS)

    Sochaski, R.O.

    1962-07-01

    This report describes broadly the nine in-reactor loops, and their components, located in and around the NRX and NRU reactors at Chalk River. First an introduction and general description is given of the loops and their function, supplemented with a table outlining some loop specifications and nine simplified flow sheets, one for each individual loop. The report then proceeds to classify each loop into two categories, the 'main loop circuit' and the 'auxiliary circuit', and descriptions are given of each circuit's components in turn. These components, in part, are comprised of the main loop pumps, the test section, loop heaters, loop coolers, delayed-neutron monitors, surge tank, Dowtherm coolers, loop piping. Here again photographs, drawings and tables are included to provide a clearer understanding of the descriptive literature and to include, in tables, some specifications of the more important components in each loop. (author)

  6. Dechanneling by dislocation loops

    International Nuclear Information System (INIS)

    Chalant, Gerard.

    1976-09-01

    Ion implantation always induces the creation of dislocation loops. When the damage profile is determined by a backscattering technique, the dechanneling by these loops is implicitely at the origin of these measurements. The dechanneling of alpha particles by dislocation loops produced by the coalescence of quenched-in vacancies in aluminium is studied. The dechanneling and the concentration of loops were determined simultaneously. The dechanneling width around dislocation was found equal to lambda=6A, both for perfect and imperfect loops having a mean diameter d=250A. In the latter case, a dechanneling probability chi=0.34 was determined for the stacking fault, in good agreement with previous determination in gold. A general formula is proposed which takes into account the variation of lambda with the curvature (or the diameter d) of the loops. Finally, by a series of isothermal anneals, the self-diffusion energy ΔH of aluminium was measured. The value obtained ΔH=1.32+-0.10eV is in good agreement with the values obtained by other methods [fr

  7. Conformal boundary loop models

    International Nuclear Information System (INIS)

    Jacobsen, Jesper Lykke; Saleur, Hubert

    2008-01-01

    We study a model of densely packed self-avoiding loops on the annulus, related to the Temperley-Lieb algebra with an extra idempotent boundary generator. Four different weights are given to the loops, depending on their homotopy class and whether they touch the outer rim of the annulus. When the weight of a contractible bulk loop x≡q+q -1 element of (-2,2], this model is conformally invariant for any real weight of the remaining three parameters. We classify the conformal boundary conditions and give exact expressions for the corresponding boundary scaling dimensions. The amplitudes with which the sectors with any prescribed number and types of non-contractible loops appear in the full partition function Z are computed rigorously. Based on this, we write a number of identities involving Z which hold true for any finite size. When the weight of a contractible boundary loop y takes certain discrete values, y r ≡([r+1] q )/([r] q ) with r integer, other identities involving the standard characters K r,s of the Virasoro algebra are established. The connection with Dirichlet and Neumann boundary conditions in the O(n) model is discussed in detail, and new scaling dimensions are derived. When q is a root of unity and y=y r , exact connections with the A m type RSOS model are made. These involve precise relations between the spectra of the loop and RSOS model transfer matrices, valid in finite size. Finally, the results where y=y r are related to the theory of Temperley-Lieb cabling

  8. Detecção do DNA do papilomavírus humano após excisão da zona de transformação com alça diatérmica para tratamento de neoplasia intra-epitelial cervical Human papillomavirus DNA detection after large loop excision of the transformation zone for the treatment of cervical intraepithelial neoplasia

    Directory of Open Access Journals (Sweden)

    Priscila Garcia Figueirêdo

    2003-02-01

    Full Text Available OBJETIVO: avaliar a presença do DNA do papilomavírus humano (HPV de alto risco oncológico antes e quatro meses após excisão da zona de transformação com alça diatérmica em mulheres com neoplasia intra-epitelial cervical (NIC. MÉTODOS: neste estudo clínico prospectivo foram incluídas 78 mulheres submetidas à excisão da zona de transformação tratadas no período de fevereiro a dezembro de 2001. Todas foram submetidas a colposcopia, citologia oncológica e captura híbrida II (CH II antes da cirurgia e após 4±1,25 meses. Para análise estatística utilizou-se o cálculo do odds ratio (OR com intervalo de confiança de 95% (IC 95%. RESULTADOS: antes da excisão, 67 (86% mulheres apresentavam CH II positiva para DNA-HPV de alto risco oncológico e destas, apenas 22 (33% mantiveram a CH II positiva quatro meses após. A detecção do DNA-HPV após o tratamento não se relacionou com a carga viral prévia, presença de doença nas margens da peça cirúrgica ou idade da mulher. Após quatro meses, a detecção do DNA-HPV associou-se significativamente com a presença de alterações citológicas (OR = 4,8; IC 95% = 1,7-13,7, porém não se relacionou com doença residual ou recidiva histológica (OR = 6,0; IC 95% = 0,8-52,3. CONCLUSÃO: após o tratamento da NIC, a detecção do DNA-HPV diminuiu significativamente porém não se observou relação com a presença de doença residual ou recidiva histológica.PURPOSE: to evaluate the detection of high oncogenic risk human papillomavirus DNA (HPV-DNA immediately before and 4±1.25 months after large loop excision of the transformation zone (LLETZ in the treatment of cervical intraepithelial neoplasia (CIN. METHODS: in this clinical prospective study, 78 patients submitted to LLETZ from February to December 2001 were enrolled. All patients were submitted to colposcopic evaluation and had Pap smear and hybrid capture II (HC II specimens collected immediately before LLETZ and four months

  9. Loop quantum gravity

    International Nuclear Information System (INIS)

    Pullin, J.

    2015-01-01

    Loop quantum gravity is one of the approaches that are being studied to apply the rules of quantum mechanics to the gravitational field described by the theory of General Relativity . We present an introductory summary of the main ideas and recent results. (Author)

  10. Blind Loop Syndrome

    Science.gov (United States)

    ... or scleroderma involving the small intestine History of radiation therapy to the abdomen Diabetes Diverticulosis of the small intestine Complications A blind loop can cause escalating problems, including: Poor absorption of fats. Bacteria in your small intestine break down the bile ...

  11. Improving Loop Dependence Analysis

    DEFF Research Database (Denmark)

    Jensen, Nicklas Bo; Karlsson, Sven

    2017-01-01

    Programmers can no longer depend on new processors to have significantly improved single-thread performance. Instead, gains have to come from other sources such as the compiler and its optimization passes. Advanced passes make use of information on the dependencies related to loops. We improve th...

  12. Cytokine loops driving senescence

    Czech Academy of Sciences Publication Activity Database

    Bartek, Jiří; Hodný, Zdeněk; Lukáš, Jan

    2008-01-01

    Roč. 10, č. 8 (2008), s. 887-889 ISSN 1465-7392 Institutional research plan: CEZ:AV0Z50520514 Keywords : cellular senescence * cytokines * autocrine feedback loop Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 17.774, year: 2008

  13. Loop Quantum Gravity

    Directory of Open Access Journals (Sweden)

    Rovelli Carlo

    1998-01-01

    Full Text Available The problem of finding the quantum theory of the gravitational field, and thus understanding what is quantum spacetime, is still open. One of the most active of the current approaches is loop quantum gravity. Loop quantum gravity is a mathematically well-defined, non-perturbative and background independent quantization of general relativity, with its conventional matter couplings. Research in loop quantum gravity today forms a vast area, ranging from mathematical foundations to physical applications. Among the most significant results obtained are: (i The computation of the physical spectra of geometrical quantities such as area and volume, which yields quantitative predictions on Planck-scale physics. (ii A derivation of the Bekenstein-Hawking black hole entropy formula. (iii An intriguing physical picture of the microstructure of quantum physical space, characterized by a polymer-like Planck scale discreteness. This discreteness emerges naturally from the quantum theory and provides a mathematically well-defined realization of Wheeler's intuition of a spacetime ``foam''. Long standing open problems within the approach (lack of a scalar product, over-completeness of the loop basis, implementation of reality conditions have been fully solved. The weak part of the approach is the treatment of the dynamics: at present there exist several proposals, which are intensely debated. Here, I provide a general overview of ideas, techniques, results and open problems of this candidate theory of quantum gravity, and a guide to the relevant literature.

  14. Random walk loop soups and conformal loop ensembles

    NARCIS (Netherlands)

    van de Brug, T.; Camia, F.; Lis, M.

    2016-01-01

    The random walk loop soup is a Poissonian ensemble of lattice loops; it has been extensively studied because of its connections to the discrete Gaussian free field, but was originally introduced by Lawler and Trujillo Ferreras as a discrete version of the Brownian loop soup of Lawler and Werner, a

  15. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  16. Closing the loop.

    Science.gov (United States)

    Dassau, E; Atlas, E; Phillip, M

    2010-02-01

    The dream of closing the loop is actually the dream of creating an artificial pancreas and freeing the patients from being involved with the care of their own diabetes. Insulin-dependent diabetes (type 1) is a chronic incurable disease which requires constant therapy without the possibility of any 'holidays' or insulin-free days. It means that patients have to inject insulin every day of their life, several times per day, and in order to do it safely they also have to measure their blood glucose levels several times per day. Patients need to plan their meals, their physical activities and their insulin regime - there is only very small room for spontaneous activities. This is why the desire for an artificial pancreas is so strong despite the fact that it will not cure the diabetic patients. Attempts to develop a closed-loop system started in the 1960s but never got to a clinical practical stage of development. In recent years the availability of continuous glucose sensors revived those efforts and stimulated the clinician and researchers to believe that closing the loop might be possible nowadays. Many papers have been published over the years describing several different ideas on how to close the loop. Most of the suggested systems have a sensing arm that measures the blood glucose repeatedly or continuously, an insulin delivery arm that injects insulin upon command and a computer that makes the decisions of when and how much insulin to deliver. The differences between the various published systems in the literature are mainly in their control algorithms. However, there are also differences related to the method and site of glucose measurement and insulin delivery. SC glucose measurements and insulin delivery are the most studied option but other combinations of insulin measurements and glucose delivery including intravascular and intraperitoneal (IP) are explored. We tried to select recent publications that we believe had influenced and inspired people interested

  17. Loop Quantum Cosmology.

    Science.gov (United States)

    Bojowald, Martin

    2008-01-01

    Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time. Supplementary material is available for this article at 10.12942/lrr-2008-4.

  18. Loop Quantum Cosmology

    Directory of Open Access Journals (Sweden)

    Bojowald Martin

    2008-07-01

    Full Text Available Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time.

  19. Loop Quantum Cosmology

    Directory of Open Access Journals (Sweden)

    Bojowald Martin

    2005-12-01

    Full Text Available Quantum gravity is expected to be necessary in order to understand situations where classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical space-time inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding space-time is then modified. One particular realization is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. Main effects are introduced into effective classical equations which allow to avoid interpretational problems of quantum theory. They give rise to new kinds of early universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function which allows to extend space-time beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of space-time arising in loop quantum gravity and its application to cosmology sheds new light on more general issues such as time.

  20. An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community

    KAUST Repository

    Wang, Yong; Gao, Zhaoming; Xu, Ying; Li, Guangyu; He, Lisheng; Qian, Peiyuan

    2016-01-01

    -generation-sequencing technology. Using a synthetic bacterial community, the amplification efficiency of the Multiple Annealing and Looping Based Amplification Cycles (MALBAC) kit that is originally developed to amplify the single-cell genomic DNA of mammalian organisms

  1. Autosomal mutations affecting Y chromosome loops in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Petrucci Romano

    2008-04-01

    Full Text Available Abstract Background The Y chromosome of Drosophila melanogaster harbors several genes required for male fertility. The genes for these fertility factors are very large in size and contain conspicuous amounts of repetitive DNA and transposons. Three of these loci (ks-1, kl-3 and kl-5 have the ability to develop giant lampbrush-like loops in primary spermatocytes, a cytological manifestation of their active state in these cells. Y-loops bind a number of non-Y encoded proteins, but the mechanisms regulating their development and their specific functions are still to be elucidated. Results Here we report the results of a screen of 726 male sterile lines to identify novel autosomal genes controlling Y-loop function. We analyzed mutant testis preparations both in vivo and by immunofluorescence using antibodies directed against Y-loop-associated proteins. This screen enabled us to isolate 17 mutations at 15 loci whose wild-type function is required for proper Y-loop morphogenesis. Six of these loci are likely to specifically control loop development, while the others display pleiotropic effects on both loops and meiotic processes such as spermiogenesis, sperm development and maturation. We also determined the map position of the mutations affecting exclusively Y-loop morphology. Conclusion Our cytological screening permitted us to identify novel genetic functions required for male spermatogenesis, some of which show pleiotropic effects. Analysis of these mutations also shows that loop development can be uncoupled from meiosis progression. These data represent a useful framework for the characterization of Y-loop development at a molecular level and for the study of the genetic control of heterochromatin.

  2. LoopIng: a template-based tool for predicting the structure of protein loops.

    KAUST Repository

    Messih, Mario Abdel

    2015-08-06

    Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are not very effective in modeling their structure. However, loops are often involved in protein function, hence inferring their structure is important for predicting protein structure as well as function.We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently available methods, LoopIng is able to achieve similar accuracy for short loops (4-10 residues) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop).www.biocomputing.it/loopinganna.tramontano@uniroma1.itSupplementary data are available at Bioinformatics online.

  3. Wilson loops in minimal surfaces

    International Nuclear Information System (INIS)

    Drukker, Nadav; Gross, David J.; Ooguri, Hirosi

    1999-01-01

    The AdS/CFT correspondence suggests that the Wilson loop of the large N gauge theory with N = 4 supersymmetry in 4 dimensions is described by a minimal surface in AdS 5 x S 5 . The authors examine various aspects of this proposal, comparing gauge theory expectations with computations of minimal surfaces. There is a distinguished class of loops, which the authors call BPS loops, whose expectation values are free from ultra-violet divergence. They formulate the loop equation for such loops. To the extent that they have checked, the minimal surface in AdS 5 x S 5 gives a solution of the equation. The authors also discuss the zig-zag symmetry of the loop operator. In the N = 4 gauge theory, they expect the zig-zag symmetry to hold when the loop does not couple the scalar fields in the supermultiplet. They will show how this is realized for the minimal surface

  4. Wilson loops and minimal surfaces

    International Nuclear Information System (INIS)

    Drukker, Nadav; Gross, David J.; Ooguri, Hirosi

    1999-01-01

    The AdS-CFT correspondence suggests that the Wilson loop of the large N gauge theory with N=4 supersymmetry in four dimensions is described by a minimal surface in AdS 5 xS 5 . We examine various aspects of this proposal, comparing gauge theory expectations with computations of minimal surfaces. There is a distinguished class of loops, which we call BPS loops, whose expectation values are free from ultraviolet divergence. We formulate the loop equation for such loops. To the extent that we have checked, the minimal surface in AdS 5 xS 5 gives a solution of the equation. We also discuss the zigzag symmetry of the loop operator. In the N=4 gauge theory, we expect the zigzag symmetry to hold when the loop does not couple the scalar fields in the supermultiplet. We will show how this is realized for the minimal surface. (c) 1999 The American Physical Society

  5. On some properties of conjugacy closed loops

    International Nuclear Information System (INIS)

    Adeniran, John Olusola

    2002-07-01

    It is shown that central loops are not conjugacy closed loops but instead are loops of units in their loop algebras that are conjugacy closed. It is also shown that certain inner mappings of a conjugacy closed loop are nuclear. Some invariants of left conjugacy closed loops are obtained. (author)

  6. Two-loop polygon Wilson loops in N = 4 SYM

    International Nuclear Information System (INIS)

    Anastasiou, C.; Brandhuber, A.; Heslop, P.; Spence, B.; Travaglini, G.; Khoze, V.V.

    2009-01-01

    We compute for the first time the two-loop corrections to arbitrary n-gon lightlike Wilson loops in N = 4 supersymmetric Yang-Mills theory, using efficient numerical methods. The calculation is motivated by the remarkable agreement between the finite part of planar six-point MHV amplitudes and hexagon Wilson loops which has been observed at two loops. At n = 6 we confirm that the ABDK/BDS ansatz must be corrected by adding a remainder function, which depends only on conformally invariant ratios of kinematic variables. We numerically compute remainder functions for n = 7,8 and verify dual conformal invariance. Furthermore, we study simple and multiple collinear limits of the Wilson loop remainder functions and demonstrate that they have precisely the form required by the collinear factorisation of the corresponding two-loop n-point amplitudes. The number of distinct diagram topologies contributing to the n-gon Wilson loops does not increase with n, and there is a fixed number of 'master integrals', which we have computed. Thus we have essentially computed general polygon Wilson loops, and if the correspondence with amplitudes continues to hold, all planar n-point two-loop MHV amplitudes in the N = 4 theory.

  7. High temperature storage loop :

    Energy Technology Data Exchange (ETDEWEB)

    Gill, David Dennis; Kolb, William J.

    2013-07-01

    A three year plan for thermal energy storage (TES) research was created at Sandia National Laboratories in the spring of 2012. This plan included a strategic goal of providing test capability for Sandia and for the nation in which to evaluate high temperature storage (>650ÀC) technology. The plan was to scope, design, and build a flow loop that would be compatible with a multitude of high temperature heat transfer/storage fluids. The High Temperature Storage Loop (HTSL) would be reconfigurable so that it was useful for not only storage testing, but also for high temperature receiver testing and high efficiency power cycle testing as well. In that way, HTSL was part of a much larger strategy for Sandia to provide a research and testing platform that would be integral for the evaluation of individual technologies funded under the SunShot program. DOEs SunShot program seeks to reduce the price of solar technologies to 6/kWhr to be cost competitive with carbon-based fuels. The HTSL project sought to provide evaluation capability for these SunShot supported technologies. This report includes the scoping, design, and budgetary costing aspects of this effort

  8. Accelerating the loop expansion

    International Nuclear Information System (INIS)

    Ingermanson, R.

    1986-01-01

    This thesis introduces a new non-perturbative technique into quantum field theory. To illustrate the method, I analyze the much-studied phi 4 theory in two dimensions. As a prelude, I first show that the Hartree approximation is easy to obtain from the calculation of the one-loop effective potential by a simple modification of the propagator that does not affect the perturbative renormalization procedure. A further modification then susggests itself, which has the same nice property, and which automatically yields a convex effective potential. I then show that both of these modifications extend naturally to higher orders in the derivative expansion of the effective action and to higher orders in the loop-expansion. The net effect is to re-sum the perturbation series for the effective action as a systematic ''accelerated'' non-perturbative expansion. Each term in the accelerated expansion corresponds to an infinite number of terms in the original series. Each term can be computed explicitly, albeit numerically. Many numerical graphs of the various approximations to the first two terms in the derivative expansion are given. I discuss the reliability of the results and the problem of spontaneous symmetry-breaking, as well as some potential applications to more interesting field theories. 40 refs

  9. Mirror symmetry and loop operators

    Energy Technology Data Exchange (ETDEWEB)

    Assel, Benjamin [Department of Mathematics, King’s College London,The Strand, London WC2R 2LS (United Kingdom); Gomis, Jaume [Perimeter Institute for Theoretical Physics,Waterloo, Ontario, N2L 2Y5 (Canada)

    2015-11-09

    Wilson loops in gauge theories pose a fundamental challenge for dualities. Wilson loops are labeled by a representation of the gauge group and should map under duality to loop operators labeled by the same data, yet generically, dual theories have completely different gauge groups. In this paper we resolve this conundrum for three dimensional mirror symmetry. We show that Wilson loops are exchanged under mirror symmetry with Vortex loop operators, whose microscopic definition in terms of a supersymmetric quantum mechanics coupled to the theory encode in a non-trivial way a representation of the original gauge group, despite that the gauge groups of mirror theories can be radically different. Our predictions for the mirror map, which we derive guided by branes in string theory, are confirmed by the computation of the exact expectation value of Wilson and Vortex loop operators on the three-sphere.

  10. Reactor recirculation pump test loop

    International Nuclear Information System (INIS)

    Taka, Shusei; Kato, Hiroyuki

    1979-01-01

    A test loop for a reactor primary loop recirculation pumps (PLR pumps) has been constructed at Ebara's Haneda Plant in preparation for production of PLR pumps under license from Byron Jackson Pump Division of Borg-Warner Corporation. This loop can simulate operating conditions for test PLR pumps with 130 per cent of the capacity of pumps for a 1100 MWe BWR plant. A main loop, primary cooling system, water demineralizer, secondary cooling system, instrumentation and control equipment and an electric power supply system make up the test loop. This article describes the test loop itself and test results of two PLR pumps for Fukushima No. 2 N.P.S. Unit 1 and one main circulation pump for HAZ Demonstration Test Facility. (author)

  11. 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.

  12. Loop Heat Pipe Startup Behaviors

    Science.gov (United States)

    Ku, Jentung

    2016-01-01

    A loop heat pipe must start successfully before it can commence its service. The startup transient represents one of the most complex phenomena in the loop heat pipe operation. This paper discusses various aspects of loop heat pipe startup behaviors. Topics include the four startup scenarios, the initial fluid distribution between the evaporator and reservoir that determines the startup scenario, factors that affect the fluid distribution between the evaporator and reservoir, difficulties encountered during the low power startup, and methods to enhance the startup success. Also addressed are the pressure spike and pressure surge during the startup transient, and repeated cycles of loop startup and shutdown under certain conditions.

  13. Modeling of compact loop antennas

    International Nuclear Information System (INIS)

    Baity, F.W.

    1987-01-01

    A general compact loop antenna model which treats all elements of the antenna as lossy transmission lines has been developed. In addition to capacitively-tuned resonant double loop (RDL) antennas the model treats stub-tuned resonant double loop antennas. Calculations using the model have been compared with measurements on full-scale mockups of resonant double loop antennas for ATF and TFTR in order to refine the transmission line parameters. Results from the model are presented for RDL antenna designs for ATF, TFTR, Tore Supra, and for the Compact Ignition Tokamak

  14. Mining protein loops using a structural alphabet and statistical exceptionality

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2010-02-01

    recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930 of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. Conclusions We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.

  15. Mining protein loops using a structural alphabet and statistical exceptionality.

    Science.gov (United States)

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

    2010-02-04

    amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.

  16. Vortex loops and Majoranas

    International Nuclear Information System (INIS)

    Chesi, Stefano; Jaffe, Arthur; Loss, Daniel; Pedrocchi, Fabio L.

    2013-01-01

    We investigate the role that vortex loops play in characterizing eigenstates of interacting Majoranas. We give some general results and then focus on ladder Hamiltonian examples as a test of further ideas. Two methods yield exact results: (i) A mapping of certain spin Hamiltonians to quartic interactions of Majoranas shows that the spectra of these two examples coincide. (ii) In cases with reflection-symmetric Hamiltonians, we use reflection positivity for Majoranas to characterize vortices in the ground states. Two additional methods suggest wider applicability of these results: (iii) Numerical evidence suggests similar behavior for certain systems without reflection symmetry. (iv) A perturbative analysis also suggests similar behavior without the assumption of reflection symmetry

  17. Inductance loop and partial

    CERN Document Server

    Paul, Clayton R

    2010-01-01

    "Inductance is an unprecedented text, thoroughly discussing "loop" inductance as well as the increasingly important "partial" inductance. These concepts and their proper calculation are crucial in designing modern high-speed digital systems. World-renowned leader in electromagnetics Clayton Paul provides the knowledge and tools necessary to understand and calculate inductance." "With the present and increasing emphasis on high-speed digital systems and high-frequency analog systems, it is imperative that system designers develop an intimate understanding of the concepts and methods in this book. Inductance is a much-needed textbook designed for senior and graduate-level engineering students, as well as a hands-on guide for working engineers and professionals engaged in the design of high-speed digital and high-frequency analog systems."--Jacket.

  18. Dynamic PID loop control

    International Nuclear Information System (INIS)

    Pei, L.; Klebaner, A.; Theilacker, J.; Soyars, W.; Martinez, A.; Bossert, R.; DeGraff, B.; Darve, C.

    2011-01-01

    The Horizontal Test Stand (HTS) SRF Cavity and Cryomodule 1 (CM1) of eight 9-cell, 1.3GHz SRF cavities are operating at Fermilab. For the cryogenic control system, how to hold liquid level constant in the cryostat by regulation of its Joule-Thompson JT-valve is very important after cryostat cool down to 2.0 K. The 72-cell cryostat liquid level response generally takes a long time delay after regulating its JT-valve; therefore, typical PID control loop should result in some cryostat parameter oscillations. This paper presents a type of PID parameter self-optimal and Time-Delay control method used to reduce cryogenic system parameters oscillation.

  19. Uranyl Nitrate Flow Loop

    International Nuclear Information System (INIS)

    Ladd-Lively, Jennifer L

    2008-01-01

    The objectives of the work discussed in this report were to: (1) develop a flow loop that would simulate the purified uranium-bearing aqueous stream exiting the solvent extraction process in a natural uranium conversion plant (NUCP); (2) develop a test plan that would simulate normal operation and disturbances that could be anticipated in an NUCP; (3) use the flow loop to test commercially available flowmeters for use as safeguards monitors; and (4) recommend a flowmeter for production-scale testing at an NUCP. There has been interest in safeguarding conversion plants because the intermediate products [uranium dioxide (UO 2 ), uranium tetrafluoride (UF 4 ), and uranium hexafluoride (UF 6 )] are all suitable uranium feedstocks for producing special nuclear materials. Furthermore, if safeguards are not applied virtually any nuclear weapons program can obtain these feedstocks without detection by the International Atomic Energy Agency (IAEA). Historically, IAEA had not implemented safeguards until the purified UF 6 product was declared as feedstock for enrichment plants. H. A. Elayat et al. provide a basic definition of a safeguards system: 'The function of a safeguards system on a chemical conversion plant is in general terms to verify that no useful nuclear material is being diverted to use in a nuclear weapons program'. The IAEA now considers all highly purified uranium compounds as candidates for safeguarding. DOE is currently interested in 'developing instruments, tools, strategies, and methods that could be of use to the IAEA in the application of safeguards' for materials found in the front end of the nuclear fuel cycle-prior to the production of the uranium hexafluoride or oxides that have been the traditional starting point for IAEA safeguards. Several national laboratories, including Oak Ridge, Los Alamos, Lawrence Livermore, and Brookhaven, have been involved in developing tools or techniques for safeguarding conversion plants. This study was sponsored by

  20. Loop Quantum Gravity.

    Science.gov (United States)

    Rovelli, Carlo

    2008-01-01

    The problem of describing the quantum behavior of gravity, and thus understanding quantum spacetime , is still open. Loop quantum gravity is a well-developed approach to this problem. It is a mathematically well-defined background-independent quantization of general relativity, with its conventional matter couplings. Today research in loop quantum gravity forms a vast area, ranging from mathematical foundations to physical applications. Among the most significant results obtained so far are: (i) The computation of the spectra of geometrical quantities such as area and volume, which yield tentative quantitative predictions for Planck-scale physics. (ii) A physical picture of the microstructure of quantum spacetime, characterized by Planck-scale discreteness. Discreteness emerges as a standard quantum effect from the discrete spectra, and provides a mathematical realization of Wheeler's "spacetime foam" intuition. (iii) Control of spacetime singularities, such as those in the interior of black holes and the cosmological one. This, in particular, has opened up the possibility of a theoretical investigation into the very early universe and the spacetime regions beyond the Big Bang. (iv) A derivation of the Bekenstein-Hawking black-hole entropy. (v) Low-energy calculations, yielding n -point functions well defined in a background-independent context. The theory is at the roots of, or strictly related to, a number of formalisms that have been developed for describing background-independent quantum field theory, such as spin foams, group field theory, causal spin networks, and others. I give here a general overview of ideas, techniques, results and open problems of this candidate theory of quantum gravity, and a guide to the relevant literature.

  1. Loop Quantum Gravity

    Directory of Open Access Journals (Sweden)

    Rovelli Carlo

    2008-07-01

    Full Text Available The problem of describing the quantum behavior of gravity, and thus understanding quantum spacetime, is still open. Loop quantum gravity is a well-developed approach to this problem. It is a mathematically well-defined background-independent quantization of general relativity, with its conventional matter couplings. Today research in loop quantum gravity forms a vast area, ranging from mathematical foundations to physical applications. Among the most significant results obtained so far are: (i The computation of the spectra of geometrical quantities such as area and volume, which yield tentative quantitative predictions for Planck-scale physics. (ii A physical picture of the microstructure of quantum spacetime, characterized by Planck-scale discreteness. Discreteness emerges as a standard quantum effect from the discrete spectra, and provides a mathematical realization of Wheeler’s “spacetime foam” intuition. (iii Control of spacetime singularities, such as those in the interior of black holes and the cosmological one. This, in particular, has opened up the possibility of a theoretical investigation into the very early universe and the spacetime regions beyond the Big Bang. (iv A derivation of the Bekenstein–Hawking black-hole entropy. (v Low-energy calculations, yielding n-point functions well defined in a background-independent context. The theory is at the roots of, or strictly related to, a number of formalisms that have been developed for describing background-independent quantum field theory, such as spin foams, group field theory, causal spin networks, and others. I give here a general overview of ideas, techniques, results and open problems of this candidate theory of quantum gravity, and a guide to the relevant literature.

  2. A totally diverting loop colostomy.

    Science.gov (United States)

    Merrett, N. D.; Gartell, P. C.

    1993-01-01

    A technique is described where the distal limb of a loop colostomy is tied with nylon or polydioxanone. This ensures total faecal diversion and dispenses with the supporting rod, enabling early application of stoma appliances. The technique does not interfere with the traditional transverse closure of a loop colostomy. PMID:8379632

  3. Higher dimensional loop quantum cosmology

    International Nuclear Information System (INIS)

    Zhang, Xiangdong

    2016-01-01

    Loop quantum cosmology (LQC) is the symmetric sector of loop quantum gravity. In this paper, we generalize the structure of loop quantum cosmology to the theories with arbitrary spacetime dimensions. The isotropic and homogeneous cosmological model in n + 1 dimensions is quantized by the loop quantization method. Interestingly, we find that the underlying quantum theories are divided into two qualitatively different sectors according to spacetime dimensions. The effective Hamiltonian and modified dynamical equations of n + 1 dimensional LQC are obtained. Moreover, our results indicate that the classical big bang singularity is resolved in arbitrary spacetime dimensions by a quantum bounce. We also briefly discuss the similarities and differences between the n + 1 dimensional model and the 3 + 1 dimensional one. Our model serves as a first example of higher dimensional loop quantum cosmology and offers the possibility to investigate quantum gravity effects in higher dimensional cosmology. (orig.)

  4. Genetic instability associated with loop or stem–loop structures within transcription units can be independent of nucleotide excision repair

    Science.gov (United States)

    Burns, John A; Chowdhury, Moinuddin A; Cartularo, Laura; Berens, Christian; Scicchitano, David A

    2018-01-01

    Abstract Simple sequence repeats (SSRs) are found throughout the genome, and under some conditions can change in length over time. Germline and somatic expansions of trinucleotide repeats are associated with a series of severely disabling illnesses, including Huntington's disease. The underlying mechanisms that effect SSR expansions and contractions have been experimentally elusive, but models suggesting a role for DNA repair have been proposed, in particular the involvement of transcription-coupled nucleotide excision repair (TCNER) that removes transcription-blocking DNA damage from the transcribed strand of actively expressed genes. If the formation of secondary DNA structures that are associated with SSRs were to block RNA polymerase progression, TCNER could be activated, resulting in the removal of the aberrant structure and a concomitant change in the region's length. To test this, TCNER activity in primary human fibroblasts was assessed on defined DNA substrates containing extrahelical DNA loops that lack discernible internal base pairs or DNA stem–loops that contain base pairs within the stem. The results show that both structures impede transcription elongation, but there is no corresponding evidence that nucleotide excision repair (NER) or TCNER operates to remove them. PMID:29474673

  5. LoopIng: a template-based tool for predicting the structure of protein loops.

    KAUST Repository

    Messih, Mario Abdel; Lepore, Rosalba; Tramontano, Anna

    2015-01-01

    ) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has

  6. Rogowski Loop design for NSTX

    International Nuclear Information System (INIS)

    McCormack, B.; Kaita, R.; Kugel, H.; Hatcher, R.

    2000-01-01

    The Rogowski Loop is one of the most basic diagnostics for tokamak operations. On the National Spherical Torus Experiment (NSTX), the plasma current Rogowski Loop had the constraints of the very limited space available on the center stack, 5,000 volt isolation, flexibility requirements as it remained a part of the Center Stack assembly after the first phase of operation, and a +120 C temperature requirement. For the second phase of operation, four Halo Current Rogowski Loops under the Center Stack tiles will be installed having +600 C and limited space requirements. Also as part of the second operational phase, up to ten Rogowski Loops will installed to measure eddy currents in the Passive Plate support structures with +350 C, restricted space, and flexibility requirements. This presentation will provide the details of the material selection, fabrication techniques, testing, and installation results of the Rogowski Loops that were fabricated for the high temperature operational and bakeout requirements, high voltage isolation requirements, and the space and flexibility requirements imposed upon the Rogowski Loops. In the future operational phases of NSTX, additional Rogowski Loops could be anticipated that will measure toroidal plasma currents in the vacuum vessel and in the Passive Plate assemblies

  7. Two-loop hard-thermal-loop thermodynamics with quarks

    International Nuclear Information System (INIS)

    Andersen, Jens O.; Petitgirard, Emmanuel; Strickland, Michael

    2004-01-01

    We calculate the quark contribution to the free energy of a hot quark-gluon plasma to two-loop order using hard-thermal-loop (HTL) perturbation theory. All ultraviolet divergences can be absorbed into renormalizations of the vacuum energy and the HTL quark and gluon mass parameters. The quark and gluon HTL mass parameters are determined self-consistently by a variational prescription. Combining the quark contribution with the two-loop HTL perturbation theory free energy for pure glue we obtain the total two-loop QCD free energy. Comparisons are made with lattice estimates of the free energy for N f =2 and with exact numerical results obtained in the large-N f limit

  8. String breaking with Wilson loops?

    CERN Document Server

    Kratochvila, S; Kratochvila, Slavo; Forcrand, Philippe de

    2003-01-01

    A convincing, uncontroversial observation of string breaking, when the static potential is extracted from Wilson loops only, is still missing. This failure can be understood if the overlap of the Wilson loop with the broken string is exponentially small. In that case, the broken string ground state will only be seen if the Wilson loop is long enough. Our preliminary results show string breaking in the context of the 3d SU(2) adjoint static potential, using the L\\"uscher-Weisz exponential variance reduction approach. As a by-product, we measure the fundamental SU(2) static potential with improved accuracy and see clear deviations from Casimir scaling.

  9. BMN correlators by loop equations

    International Nuclear Information System (INIS)

    Eynard, Bertrand; Kristjansen, Charlotte

    2002-01-01

    In the BMN approach to N=4 SYM a large class of correlators of interest are expressible in terms of expectation values of traces of words in a zero-dimensional gaussian complex matrix model. We develop a loop-equation based, analytic strategy for evaluating such expectation values to any order in the genus expansion. We reproduce the expectation values which were needed for the calculation of the one-loop, genus one correction to the anomalous dimension of BMN-operators and which were earlier obtained by combinatorial means. Furthermore, we present the expectation values needed for the calculation of the one-loop, genus two correction. (author)

  10. Hubungan Kekerabatan Sapi Aceh dengan Menggunakan Daerah Displacement-loop

    Directory of Open Access Journals (Sweden)

    Mohd. Agus Nashri Abdullah

    2008-10-01

    Full Text Available Relationship of aceh cattle using displacement-loop region ABSTRACT. The aims of this study were to describe relationship of D-loop of mtDNA Aceh cattle which is useful database for conducting conservation programme. The whole blood samples were collected (8 samples for D-loop analysis from four locations which were Aceh Besar, Pidie, North Aceh regencies and Banda Aceh city. Out group whole blood samples were collected from two samples from Bali cattles (Bali Island, Madura cattle (Madura Island, Pesisir cattle (West Sumatera respectively and one sample from PO cattle (West Java. Amplification of D-loop sequences of mtDNA with BIDLF and BIDLR primary have PCR product 980 bp. The Data were analyzed using Squint 1.02 and MEGA 4.0 programme. Result of analysis indicate that Aceh cattle have nearer relationship with zebu and there is items inset of genetik Bali cattle (Bos javanicus at the end sequences start ke-354 situs up to 483, so that the origin Aceh cattle was from Bos indicus which have hybridization with Bos javanicus.

  11. A Looping-Based Model for Quenching Repression.

    Directory of Open Access Journals (Sweden)

    Yaroslav Pollak

    2017-01-01

    Full Text Available We model the regulatory role of proteins bound to looped DNA using a simulation in which dsDNA is represented as a self-avoiding chain, and proteins as spherical protrusions. We simulate long self-avoiding chains using a sequential importance sampling Monte-Carlo algorithm, and compute the probabilities for chain looping with and without a protrusion. We find that a protrusion near one of the chain's termini reduces the probability of looping, even for chains much longer than the protrusion-chain-terminus distance. This effect increases with protrusion size, and decreases with protrusion-terminus distance. The reduced probability of looping can be explained via an eclipse-like model, which provides a novel inhibitory mechanism. We test the eclipse model on two possible transcription-factor occupancy states of the D. melanogaster eve 3/7 enhancer, and show that it provides a possible explanation for the experimentally-observed eve stripe 3 and 7 expression patterns.

  12. Optical loop framing

    International Nuclear Information System (INIS)

    Kalibjian, R.; Chong, Y.P.; Prono, D.S.; Cavagnolo, H.R.

    1984-06-01

    The ATA provides an electron beam pulse of 70-ns duration at a 1-Hz rate. Our present optical diagnostics technique involve the imaging of the visible light generated by the beam incident onto the plant of a thin sheet of material. It has already been demonstrated that the light generated has a sufficiently fast temporal reponse in performing beam diagnostics. Notwithstanding possible beam emittance degradation due to scattering in the thin sheet, the observation of beam spatial profiles with relatively high efficiencies has provided data complementary to that obtained from beam wall current monitors and from various x-ray probes and other electrical probes. The optical image sensor consists of a gated, intensified television system. The gate pulse of the image intensifier can be appropriately delayed to give frames that are time-positioned from the head to the tail of the beam with a minimum gate time of 5-ns. The spatial correlation of the time frames from pulse to pulse is very good for a stable electron beam; however, when instabilities do occur, it is difficult to properly assess the spatial composition of the head and the tail of the beam on a pulse-to-pulse basis. Multiple gating within a pulse duration becomes desirable but cannot be performed because the recycle time (20-ms) of the TV system is much longer than the beam pulse. For this reason we have developed an optical-loop framing technique that will allow the recording of two frames within one pulse duration with our present gated/intensified TV system

  13. An ATR-dependent function for the Ddx19 RNA helicase in nuclear R-loop metabolism.

    Science.gov (United States)

    Hodroj, Dana; Recolin, Bénédicte; Serhal, Kamar; Martinez, Susan; Tsanov, Nikolay; Abou Merhi, Raghida; Maiorano, Domenico

    2017-05-02

    Coordination between transcription and replication is crucial in the maintenance of genome integrity. Disturbance of these processes leads to accumulation of aberrant DNA:RNA hybrids (R-loops) that, if unresolved, generate DNA damage and genomic instability. Here we report a novel, unexpected role for the nucleopore-associated mRNA export factor Ddx19 in removing nuclear R-loops formed upon replication stress or DNA damage. We show, in live cells, that Ddx19 transiently relocalizes from the nucleopore to the nucleus upon DNA damage, in an ATR/Chk1-dependent manner, and that Ddx19 nuclear relocalization is required to clear R-loops. Ddx19 depletion induces R-loop accumulation, proliferation-dependent DNA damage and defects in replication fork progression. Further, we show that Ddx19 resolves R-loops in vitro via its helicase activity. Furthermore, mutation of a residue phosphorylated by Chk1 in Ddx19 disrupts its interaction with Nup214 and allows its nuclear relocalization. Finally, we show that Ddx19 operates in resolving R-loops independently of the RNA helicase senataxin. Altogether these observations put forward a novel, ATR-dependent function for Ddx19 in R-loop metabolism to preserve genome integrity in mammalian cells. © 2017 The Authors.

  14. Loop equations in the theory of gravitation

    International Nuclear Information System (INIS)

    Makeenko, Yu.M.; Voronov, N.A.

    1981-01-01

    Loop-space variables (matrices of parallel transport) for the theory of gravitation are described. Loop equations, which are equivalent to the Einstein equations, are derived in the classical case. Loop equations are derived for gravity with cosmological constant as well. An analogy with the loop-space approach in Yang-Mills theory is discussed [ru

  15. Kalman Orbit Optimized Loop Tracking

    Science.gov (United States)

    Young, Lawrence E.; Meehan, Thomas K.

    2011-01-01

    Under certain conditions of low signal power and/or high noise, there is insufficient signal to noise ratio (SNR) to close tracking loops with individual signals on orbiting Global Navigation Satellite System (GNSS) receivers. In addition, the processing power available from flight computers is not great enough to implement a conventional ultra-tight coupling tracking loop. This work provides a method to track GNSS signals at very low SNR without the penalty of requiring very high processor throughput to calculate the loop parameters. The Kalman Orbit-Optimized Loop (KOOL) tracking approach constitutes a filter with a dynamic model and using the aggregate of information from all tracked GNSS signals to close the tracking loop for each signal. For applications where there is not a good dynamic model, such as very low orbits where atmospheric drag models may not be adequate to achieve the required accuracy, aiding from an IMU (inertial measurement unit) or other sensor will be added. The KOOL approach is based on research JPL has done to allow signal recovery from weak and scintillating signals observed during the use of GPS signals for limb sounding of the Earth s atmosphere. That approach uses the onboard PVT (position, velocity, time) solution to generate predictions for the range, range rate, and acceleration of the low-SNR signal. The low- SNR signal data are captured by a directed open loop. KOOL builds on the previous open loop tracking by including feedback and observable generation from the weak-signal channels so that the MSR receiver will continue to track and provide PVT, range, and Doppler data, even when all channels have low SNR.

  16. A type of loop algebra and the associated loop algebras

    International Nuclear Information System (INIS)

    Tam Honwah; Zhang Yufeng

    2008-01-01

    A higher-dimensional twisted loop algebra is constructed. As its application, a new Lax pair is presented, whose compatibility gives rise to a Liouville integrable hierarchy of evolution equations by making use of Tu scheme. One of the reduction cases of the hierarchy is an analogous of the well-known AKNS system. Next, the twisted loop algebra, furthermore, is extended to another higher dimensional loop algebra, from which a hierarchy of evolution equations with 11-potential component functions is obtained, whose reduction is just standard AKNS system. Especially, we prove that an arbitrary linear combination of the four Hamiltonian operators directly obtained from the recurrence relations is still a Hamiltonian operator. Therefore, the hierarchy with 11-potential functions possesses 4-Hamiltonian structures. Finally, an integrable coupling of the hierarchy is worked out

  17. Getting in (and out of) the loop: regulating higher order telomere structures.

    Science.gov (United States)

    Luke-Glaser, Sarah; Poschke, Heiko; Luke, Brian

    2012-01-01

    The DNA at the ends of linear chromosomes (the telomere) folds back onto itself and forms an intramolecular lariat-like structure. Although the telomere loop has been implicated in the protection of chromosome ends from nuclease-mediated resection and unscheduled DNA repair activities, it potentially poses an obstacle to the DNA replication machinery during S-phase. Therefore, the coordinated regulation of telomere loop formation, maintenance, and resolution is required in order to establish a balance between protecting the chromosome ends and promoting their duplication prior to cell division. Until recently, the only factor known to influence telomere looping in human cells was TRF2, a component of the shelterin complex. Recent work in yeast and mouse cells has uncovered additional regulatory factors that affect the loop structure at telomeres. In the following "perspective" we outline what is known about telomere looping and highlight the latest results regarding the regulation of this chromosome end structure. We speculate about how the manipulation of the telomere loop may have therapeutic implications in terms of diseases associated with telomere dysfunction and uncontrolled proliferation.

  18. Getting in (and out of the loop: regulating higher order telomere structures

    Directory of Open Access Journals (Sweden)

    Sarah eLuke-Glaser

    2012-11-01

    Full Text Available The DNA at the ends of linear chromosomes (the telomere folds back onto itself and forms an intramolecular lariat-like structure. Although the telomere loop has been implicated in the protection of chromosome ends from nuclease-mediated resection and unscheduled DNA repair activities, it potentially poses an obstacle to the DNA replication machinery during S phase. Therefore, the coordinated regulation of telomere loop formation, maintenance and resolution is required in order to establish a balance between protecting the chromosome ends and promoting their duplication prior to cell division. Until recently, the only factor know to influence telomere looping in human cells was TRF2, a component of the shelterin complex. Recent work in yeast and mouse cells has uncovered additional regulatory factors that affect the loop structure at telomeres. In the following perspective we will outline what is known about telomere looping and highlight the latest results regarding the regulation of this chromosome end structure. We will speculate about how the manipulation of the telomere loop may have therapeutic implications in terms of diseases associated with telomere dysfunction and uncontrolled proliferation.

  19. Tritium Management Loop Design Status

    Energy Technology Data Exchange (ETDEWEB)

    Rader, Jordan D. [ORNL; Felde, David K. [ORNL; McFarlane, Joanna [ORNL; Greenwood, Michael Scott [ORNL; Qualls, A L. [ORNL; Calderoni, Pattrick [Idaho National Laboratory (INL)

    2017-12-01

    This report summarizes physical, chemical, and engineering analyses that have been done to support the development of a test loop to study tritium migration in 2LiF-BeF2 salts. The loop will operate under turbulent flow and a schematic of the apparatus has been used to develop a model in Mathcad to suggest flow parameters that should be targeted in loop operation. The introduction of tritium into the loop has been discussed as well as various means to capture or divert the tritium from egress through a test assembly. Permeation was calculated starting with a Modelica model for a transport through a nickel window into a vacuum, and modifying it for a FLiBe system with an argon sweep gas on the downstream side of the permeation interface. Results suggest that tritium removal with a simple tubular permeation device will occur readily. Although this system is idealized, it suggests that rapid measurement capability in the loop may be necessary to study and understand tritium removal from the system.

  20. Criteria for saturated magnetization loop

    International Nuclear Information System (INIS)

    Harres, A.; Mikhov, M.; Skumryev, V.; Andrade, A.M.H. de; Schmidt, J.E.; Geshev, J.

    2016-01-01

    Proper estimation of magnetization curve parameters is vital in studying magnetic systems. In the present article, criteria for discrimination non-saturated (minor) from saturated (major) hysteresis loops are proposed. These employ the analysis of (i) derivatives of both ascending and descending branches of the loop, (ii) remanent magnetization curves, and (iii) thermomagnetic curves. Computational simulations are used in order to demonstrate their validity. Examples illustrating the applicability of these criteria to well-known real systems, namely Fe_3O_4 and Ni fine particles, are provided. We demonstrate that the anisotropy-field value estimated from a visual examination of an only apparently major hysteresis loop could be more than two times lower than the real one. - Highlights: • Proper estimation of hysteresis-loop parameters is vital in magnetic studies. • We propose criteria for discrimination minor from major hysteresis loops. • The criteria analyze magnetization, remanence and ZFC/FC curves and/or their derivatives. • Examples of their application on real nanoparticles systems are given. • Using the criteria could avoid twofold or bigger saturation-field underestimation errors.

  1. Criteria for saturated magnetization loop

    Energy Technology Data Exchange (ETDEWEB)

    Harres, A. [Departamento de Física, UFSM, Santa Maria, 97105-900 Rio Grande do Sul (Brazil); Mikhov, M. [Faculty of Physics, University of Sofia, 1164 Sofia (Bulgaria); Skumryev, V. [Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona (Spain); Departament de Física, Universitat Autònoma de Barcelona, 08193 Barcelona (Spain); Andrade, A.M.H. de; Schmidt, J.E. [Instituto de Física, UFRGS, Porto Alegre, 91501-970 Rio Grande do Sul (Brazil); Geshev, J., E-mail: julian@if.ufrgs.br [Departament de Física, Universitat Autònoma de Barcelona, 08193 Barcelona (Spain); Instituto de Física, UFRGS, Porto Alegre, 91501-970 Rio Grande do Sul (Brazil)

    2016-03-15

    Proper estimation of magnetization curve parameters is vital in studying magnetic systems. In the present article, criteria for discrimination non-saturated (minor) from saturated (major) hysteresis loops are proposed. These employ the analysis of (i) derivatives of both ascending and descending branches of the loop, (ii) remanent magnetization curves, and (iii) thermomagnetic curves. Computational simulations are used in order to demonstrate their validity. Examples illustrating the applicability of these criteria to well-known real systems, namely Fe{sub 3}O{sub 4} and Ni fine particles, are provided. We demonstrate that the anisotropy-field value estimated from a visual examination of an only apparently major hysteresis loop could be more than two times lower than the real one. - Highlights: • Proper estimation of hysteresis-loop parameters is vital in magnetic studies. • We propose criteria for discrimination minor from major hysteresis loops. • The criteria analyze magnetization, remanence and ZFC/FC curves and/or their derivatives. • Examples of their application on real nanoparticles systems are given. • Using the criteria could avoid twofold or bigger saturation-field underestimation errors.

  2. Assay for Human Rad51-Mediated DNA Displacement Loop Formation

    OpenAIRE

    sprotocols

    2014-01-01

    Authors: Steven Raynard and Patrick Sung Corresponding author ([]()) ### INTRODUCTION Homologous recombination is an important mechanism for the repair of damaged chromosomes, for preventing the demise of damaged replication forks, and for several other aspects of chromosome metabolism and maintenance. The homologous recombination reaction is mediated by the Rad51 recombinase. In the presence of ATP, Rad51 polymerizes on single-stranded D...

  3. Thermodynamics in Loop Quantum Cosmology

    International Nuclear Information System (INIS)

    Li, L.F.; Zhu, J.Y.

    2009-01-01

    Loop quantum cosmology (LQC) is very powerful to deal with the behavior of early universe. Moreover, the effective loop quantum cosmology gives a successful description of the universe in the semiclassical region. We consider the apparent horizon of the Friedmann-Robertson-Walker universe as a thermodynamical system and investigate the thermodynamics of LQC in the semiclassical region. The effective density and effective pressure in the modified Friedmann equation from LQC not only determine the evolution of the universe in LQC scenario but also are actually found to be the thermodynamic quantities. This result comes from the energy definition in cosmology (the Misner-Sharp gravitational energy) and is consistent with thermodynamic laws. We prove that within the framework of loop quantum cosmology, the elementary equation of equilibrium thermodynamics is still valid.

  4. High pressure experimental water loop

    International Nuclear Information System (INIS)

    Grenon, M.

    1958-01-01

    A high pressure experimental water loop has been made for studying the detection and evolution of cladding failure in a pressurized reactor. The loop has been designed for a maximum temperature of 360 deg. C, a maximum of 160 kg/cm 2 and flow rates up to 5 m 3 /h. The entire loop consists of several parts: a main circuit with a canned rotor circulation pump, steam pressurizer, heating tubes, two hydro-cyclones (one de-gasser and one decanter) and one tubular heat exchanger; a continuous purification loop, connected in parallel, comprising pressure reducing valves and resin pots which also allow studies of the stability of resins under pressure, temperature and radiation; following the gas separator is a gas loop for studying the recombination of the radiolytic gases in the steam phase. The preceding circuits, as well as others, return to a low pressure storage circuit. The cold water of the low pressure storage flask is continuously reintroduced into the high pressure main circuit by means of a return pump at a maximum head of 160 kg /cm 2 , and adjusted to the pressurizer level. This loop is also a testing bench for the tight high pressure apparatus. The circulating pump and the connecting flanges (Oak Ridge type) are water-tight. The feed pump and the pressure reducing valves are not; the un-tight ones have a system of leak recovery. To permanently check the tightness the circuit has been fitted with a leak detection system (similar to the HRT one). (author) [fr

  5. Integrable systems and loop coproducts

    International Nuclear Information System (INIS)

    Musso, Fabio

    2010-01-01

    We present a generalization of a framework for the construction of classical integrable systems that we call loop coproduct formulation (Musso 2010 J. Phys. A: Math. Theor. 43 434026). In this paper, the loop coproduct formulation includes systems of Gelfand-Tsetlin type, the linear r-matrix formulation, the Sklyanin algebras, the reflection algebras, the coalgebra symmetry approach and some of its generalizations as particular cases, showing that all these apparently different approaches have a common algebraic origin. On the other hand, all these subcases do not exhaust the domain of applicability of this new technique, so that new possible directions of investigation do naturally emerge in this framework.

  6. Perturbations in loop quantum cosmology

    International Nuclear Information System (INIS)

    Nelson, W; Agullo, I; Ashtekar, A

    2014-01-01

    The era of precision cosmology has allowed us to accurately determine many important cosmological parameters, in particular via the CMB. Confronting Loop Quantum Cosmology with these observations provides us with a powerful test of the theory. For this to be possible, we need a detailed understanding of the generation and evolution of inhomogeneous perturbations during the early, quantum gravity phase of the universe. Here, we have described how Loop Quantum Cosmology provides a completion of the inflationary paradigm, that is consistent with the observed power spectra of the CMB

  7. LISA Pathfinder: OPD loop characterisation

    Science.gov (United States)

    Born, Michael; LPF Collaboration

    2017-05-01

    The optical metrology system (OMS) of the LISA Pathfinder mission is measuring the distance between two free-floating test masses with unprecedented precision. One of the four OMS heterodyne interferometers reads out the phase difference between the reference and the measurement laser beam. This phase from the reference interferometer is common to all other longitudinal interferometer read outs and therefore subtracted. In addition, the phase is fed back via the digital optical pathlength difference (OPD) control loop to keep it close to zero. Here, we analyse the loop parameters and compare them to on-ground measurement results.

  8. LOOP: engineering marvel, economic calamity

    Energy Technology Data Exchange (ETDEWEB)

    Brossard, E B

    1985-01-01

    The Louisiana Offshore Oil Port (LOOP) is the first superport built in the Lower 48. The United States was the only major oil-importing country that did not have a superport, and therefore, could not offload very large crude carriers (VLCCs). Unfortunately, a number of factors changed after it was decided to build LOOP, and these, plus the onerous provisions of the Deepwater Ports Act of 1974, which authorized superports, prevented LOOP from operating economically. LOOP's facilities consist of an offshore platform complex with three single-point-mooring (SPM) system buoys, 19 miles offshore in 110 feet of water, as well as a 32-million-barrel storage terminal 31 miles inland at Clovelly Salt Dome, and connecting pipelines offshore and onshore. By the time LOOP was started-up in May 1981, demand for oil had declined, because of rises in the price of oil, and the source of US oil imports had shifted back to the western hemisphere, away from the eastern hemisphere, closer to the US. The refinery mix in the US also changed, because of up-grading of a number of big refineries, which further reduced demand and made heavier crudes from countries like Mexico and Venezuela more economical. Because of reduced oil imports and shorter hauls, oil shippers started using or continued to use smaller tankers. Smaller tankers are not economical for LOOP, nor do they need LOOP. The start-up of the Trans-Alaska Pipeline System (TAPS) in mid-1977 backed out 1.5 million bd/sup -1/ of foreign imports. TAPS' capacity coincides with LOOP's offloading capacity of 1.4 million bd/sup -1/. US decontrol of domestic crude in 1981 and increased drilling, plus general energy conservation further reduced US oil imports. US consumption declined to 15.1 million bd/sup -1/ in 1983, from 18.8 million bd/sup -1/ in 1978. This award-winning superport needed federal decontrol and increased oil imports along with more VLCCs, in order to operate economically.

  9. Two-Loop Splitting Amplitudes

    International Nuclear Information System (INIS)

    Bern, Z.

    2004-01-01

    Splitting amplitudes govern the behavior of scattering amplitudes at the momenta of external legs become collinear. In this talk we outline the calculation of two-loop splitting amplitudes via the unitarity sewing method. This method retains the simple factorization properties of light-cone gauge, but avoids the need for prescriptions such as the principal value or Mandelstam-Leibbrandt ones. The encountered loop momentum integrals are then evaluated using integration-by-parts and Lorentz invariance identities. We outline a variety of applications for these splitting amplitudes

  10. Two-loop splitting amplitudes

    International Nuclear Information System (INIS)

    Bern, Z.; Dixon, L.J.; Kosower, D.A.

    2004-01-01

    Splitting amplitudes govern the behavior of scattering amplitudes at the momenta of external legs become collinear. In this talk we outline the calculation of two-loop splitting amplitudes via the unitarity sewing method. This method retains the simple factorization properties of light-cone gauge, but avoids the need for prescriptions such as the principal value or Mandelstam-Leibbrandt ones. The encountered loop momentum integrals are then evaluated using integration-by-parts and Lorentz invariance identities. We outline a variety of applications for these splitting amplitudes

  11. Fermions and loops on graphs: I. Loop calculus for determinants

    International Nuclear Information System (INIS)

    Chernyak, Vladimir Y; Chertkov, Michael

    2008-01-01

    This paper is the first in a series devoted to evaluation of the partition function in statistical models on graphs with loops in terms of the Berezin/fermion integrals. The paper focuses on a representation of the determinant of a square matrix in terms of a finite series, where each term corresponds to a loop on the graph. The representation is based on a fermion version of the loop calculus, previously introduced by the authors for graphical models with finite alphabets. Our construction contains two levels. First, we represent the determinant in terms of an integral over anti-commuting Grassmann variables, with some reparametrization/gauge freedom hidden in the formulation. Second, we show that a special choice of the gauge, called the BP (Bethe–Peierls or belief propagation) gauge, yields the desired loop representation. The set of gauge fixing BP conditions is equivalent to the Gaussian BP equations, discussed in the past as efficient (linear scaling) heuristics for estimating the covariance of a sparse positive matrix

  12. Robust fault detection in open loop vs. closed loop

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik; Stoustrup, J.

    1997-01-01

    The robustness aspects of fault detection and isolation (FDI) for uncertain systems are considered. The FDI problem is considered in a standard problem formulation. The FDI design problem is analyzed both in the case where the control input signal is considered as a known external input signal (o...... (open loop) and when the input signal is generated by a feedback controller...

  13. A virtual closed loop method for closed loop identification

    NARCIS (Netherlands)

    Agüero, J.C.; Goodwin, G.C.; Hof, Van den P.M.J.

    2011-01-01

    Indirect methods for the identification of linear plant models on the basis of closed loop data are based on the use of (reconstructed) input signals that are uncorrelated with the noise. This generally requires exact (linear) controller knowledge. On the other hand, direct identification requires

  14. Studies on the effects of persistent RNA priming on DNA replication and genomic stability

    OpenAIRE

    Stuckey, Ruth

    2014-01-01

    [EN]: DNA replication and transcription take place on the same DNA template, and the correct interplay between these processes ensures faithful genome duplication. DNA replication must be highly coordinated with other cell cycle events, such as segregation of fully replicated DNA in order to maintain genomic integrity. Transcription generates RNA:DNA hybrids, transient intermediate structures that are degraded by the ribonuclease H (RNaseH) class of enzymes. RNA:DNA hybrids can form R-loops, ...

  15. Diagnosis of brugian filariasis by loop-mediated isothermal amplification.

    Directory of Open Access Journals (Sweden)

    Catherine B Poole

    Full Text Available In this study we developed and evaluated a Brugia Hha I repeat loop-mediated isothermal amplification (LAMP assay for the rapid detection of Brugia genomic DNA. Amplification was detected using turbidity or fluorescence as readouts. Reactions generated a turbidity threshold value or a clear visual positive within 30 minutes using purified genomic DNA equivalent to one microfilaria. Similar results were obtained using DNA isolated from blood samples containing B. malayi microfilariae. Amplification was specific to B. malayi and B. timori, as no turbidity was observed using DNA from the related filarial parasites Wuchereria bancrofti, Onchocerca volvulus or Dirofilaria immitis, or from human or mosquito. Furthermore, the assay was most robust using a new strand-displacing DNA polymerase termed Bst 2.0 compared to wild-type Bst DNA polymerase, large fragment. The results indicate that the Brugia Hha I repeat LAMP assay is rapid, sensitive and Brugia-specific with the potential to be developed further as a field tool for diagnosis and mapping of brugian filariasis.

  16. Free loop spaces and cyclohedra

    Czech Academy of Sciences Publication Activity Database

    Markl, Martin

    2003-01-01

    Roč. 71, - (2003), s. 151-157 R&D Projects: GA AV ČR IAA1019203 Institutional research plan: CEZ:AV0Z1019905; CEZ:AV0Z1019905 Keywords : cyclohedron * free loop space * recognition Subject RIV: BA - General Mathematics

  17. Feedback - closing the loop digitally

    International Nuclear Information System (INIS)

    Zagel, J.; Chase, B.

    1992-01-01

    Many feedback and feedforward systems are now using microprocessors within the loop. We describe the wide range of possibilities and problems that arise. We also propose some ideas for analysis and testing, including examples of motion control in the Flying Wire systems in Main Ring and Tevatron and Low Level RF control now being built for the Fermilab Linac upgrade. (author)

  18. Morbidity of temporary loop ileostomies

    NARCIS (Netherlands)

    Bakx, R.; Busch, O. R. C.; Bemelman, W. A.; Veldink, G. J.; Slors, J. F. M.; van Lanschot, J. J. B.

    2004-01-01

    Background/Aims: A temporary loop ileostomy is constructed to protect a distal colonic anastomosis. Closure is usually performed not earlier than 8 - 12 weeks after the primary operation. During this period, stoma-related complications can occur and enhance the adverse effect on quality of life. The

  19. Wilson loops in Kerr gravitation

    International Nuclear Information System (INIS)

    Bollini, C.G.; Giambiagi, J.J.; Tiomno, J.

    1981-01-01

    The ordered integrals for several paths in Kerr gravitation is computed in a compact form. When the path is closed its relation with the angular parallel displacement is discussed and the corresponding Wilson loop is calculated. The validity of Mandelstam relations for gauge fields is also explicitly verified. (Author) [pt

  20. Loop quantum cosmology: Recent progress

    Indian Academy of Sciences (India)

    Aspects of the full theory of loop quantum gravity can be studied in a simpler .... group) 1-forms and vector fields and Λ is an SO(3)-matrix indicating the internal ... are p and c which are related to the more familiar scale factor by the relations.

  1. PONDEROMOTIVE ACCELERATION IN CORONAL LOOPS

    Energy Technology Data Exchange (ETDEWEB)

    Dahlburg, R. B.; Obenschain, K. [LCP and FD, Naval Research Laboratory, Washington, DC 20375 (United States); Laming, J. M. [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States); Taylor, B. D. [AFRL Eglin AFB, Pensacola, FL 32542 (United States)

    2016-11-10

    Ponderomotive acceleration has been asserted to be a cause of the first ionization potential (FIP) effect, the well-known enhancement in abundance by a factor of 3–4 over photospheric values of elements in the solar corona with FIP less than about 10 eV. It is shown here by means of numerical simulations that ponderomotive acceleration occurs in solar coronal loops, with the appropriate magnitude and direction, as a “by-product” of coronal heating. The numerical simulations are performed with the HYPERION code, which solves the fully compressible three-dimensional magnetohydrodynamic equations including nonlinear thermal conduction and optically thin radiation. Numerical simulations of coronal loops with an axial magnetic field from 0.005 to 0.02 T and lengths from 25,000 to 75,000 km are presented. In the simulations the footpoints of the axial loop magnetic field are convected by random, large-scale motions. There is a continuous formation and dissipation of field-aligned current sheets, which act to heat the loop. As a consequence of coronal magnetic reconnection, small-scale, high-speed jets form. The familiar vortex quadrupoles form at reconnection sites. Between the magnetic footpoints and the corona the reconnection flow merges with the boundary flow. It is in this region that the ponderomotive acceleration occurs. Mirroring the character of the coronal reconnection, the ponderomotive acceleration is also found to be intermittent.

  2. Loop quantum cosmology and singularities.

    Science.gov (United States)

    Struyve, Ward

    2017-08-15

    Loop quantum gravity is believed to eliminate singularities such as the big bang and big crunch singularity. This belief is based on studies of so-called loop quantum cosmology which concerns symmetry-reduced models of quantum gravity. In this paper, the problem of singularities is analysed in the context of the Bohmian formulation of loop quantum cosmology. In this formulation there is an actual metric in addition to the wave function, which evolves stochastically (rather than deterministically as the case of the particle evolution in non-relativistic Bohmian mechanics). Thus a singularity occurs whenever this actual metric is singular. It is shown that in the loop quantum cosmology for a homogeneous and isotropic Friedmann-Lemaître-Robertson-Walker space-time with arbitrary constant spatial curvature and cosmological constant, coupled to a massless homogeneous scalar field, a big bang or big crunch singularity is never obtained. This should be contrasted with the fact that in the Bohmian formulation of the Wheeler-DeWitt theory singularities may exist.

  3. PONDEROMOTIVE ACCELERATION IN CORONAL LOOPS

    International Nuclear Information System (INIS)

    Dahlburg, R. B.; Obenschain, K.; Laming, J. M.; Taylor, B. D.

    2016-01-01

    Ponderomotive acceleration has been asserted to be a cause of the first ionization potential (FIP) effect, the well-known enhancement in abundance by a factor of 3–4 over photospheric values of elements in the solar corona with FIP less than about 10 eV. It is shown here by means of numerical simulations that ponderomotive acceleration occurs in solar coronal loops, with the appropriate magnitude and direction, as a “by-product” of coronal heating. The numerical simulations are performed with the HYPERION code, which solves the fully compressible three-dimensional magnetohydrodynamic equations including nonlinear thermal conduction and optically thin radiation. Numerical simulations of coronal loops with an axial magnetic field from 0.005 to 0.02 T and lengths from 25,000 to 75,000 km are presented. In the simulations the footpoints of the axial loop magnetic field are convected by random, large-scale motions. There is a continuous formation and dissipation of field-aligned current sheets, which act to heat the loop. As a consequence of coronal magnetic reconnection, small-scale, high-speed jets form. The familiar vortex quadrupoles form at reconnection sites. Between the magnetic footpoints and the corona the reconnection flow merges with the boundary flow. It is in this region that the ponderomotive acceleration occurs. Mirroring the character of the coronal reconnection, the ponderomotive acceleration is also found to be intermittent.

  4. Independent SU(2)-loop variables

    International Nuclear Information System (INIS)

    Loll, R.

    1991-04-01

    We give a reduction procedure for SU(2)-trace variables and introduce a complete set of indepentent, gauge-invariant and almost local loop variables for the configuration space of SU(2)-lattice gauge theory in 2+1 dimensions. (orig.)

  5. An experimental study of dislocation loop nucleation

    International Nuclear Information System (INIS)

    Bounaud, J.Y.; Leteurtre, J.

    1975-01-01

    The nucleation of dislocation loops is experimentally studied by observing the demixion of the Burgers vectors of dislocation loops nucleated in copper whiskers irradiated in flexion by fission fragments at room temperature. The demixion of Burgers vectors is observed by the dimensional effects of dislocation loops: after irradiation, the applied stress is removed; the whisker shows a residual strain that is due to loops because, after an annealing treatment to evaporate dislocation loops, each whisker recovers its initial straight shape. Everywhere along the whisker, the radius of curvature is measured and plotted vs the max. applied stress. Estimations of the interstitial and vacancy dislocation loop nuclei are derived [fr

  6. In situ detection of tandem DNA repeat length

    Energy Technology Data Exchange (ETDEWEB)

    Yaar, R.; Szafranski, P.; Cantor, C.R.; Smith, C.L. [Boston Univ., MA (United States)

    1996-11-01

    A simple method for scoring short tandem DNA repeats is presented. An oligonucleotide target, containing tandem repeats embedded in a unique sequence, was hybridized to a set of complementary probes, containing tandem repeats of known lengths. Single-stranded loop structures formed on duplexes containing a mismatched (different) number of tandem repeats. No loop structure formed on duplexes containing a matched (identical) number of tandem repeats. The matched and mismatched loop structures were enzymatically distinguished and differentially labeled by treatment with S1 nuclease and the Klenow fragment of DNA polymerase. 7 refs., 4 figs.

  7. Two- and three-loop amplitudes in covariant loop calculus

    International Nuclear Information System (INIS)

    Roland, K.

    1988-04-01

    We study 2- and 3-loop vacuum-amplitudes for the closed bosonic string. We compare two sets of expressions for the corresponding density on moduli space: One, based on the covariant Reggeon loop calculus (where modular invariance is not manifest). The other, based on analytic geometry. We want to prove identity between the two sets of expressions. Quite apart from demonstrating modular invariance of the Reggeon results, this would in itself be a remarkable mathematical feature. Identity is established to 'high' order in some moduli and exactly in others. The expansions reveal an essentially number-theoretical structure. Agreement is found only by exploiting the connection between the 4 Jacobi θ-functions and number theory. (orig.)

  8. Two- and three-loop amplitudes in covariant loop calculus

    International Nuclear Information System (INIS)

    Roland, K.

    1989-01-01

    We study two- and three-loop vacuum amplitudes for the closed bosonic string. We compare two sets of expressions for the corresponding density on moduli space. One is based on the covariant reggeon loop calculus (where modular invariance is not manifest). The other is based on analytic geometry. We want to prove identity between the two sets of expressions. Quite apart from demonstrating modular invariance of the reggeon results, this would in itself be a remarkable mathematical feature. Identity is established to ''high'' order in some moduli and exactly in others. The expansions reveal an essentially number-theoretic structure. Agreement is found only by exploiting the connection between the four Jacobi θ-functions and number theory. (orig.)

  9. Mitochondrial D-loop sequence variation among Italian horse breeds

    Directory of Open Access Journals (Sweden)

    Zanotti Marta

    2004-11-01

    Full Text Available Abstract The genetic variability of the mitochondrial D-loop DNA sequence in seven horse breeds bred in Italy (Giara, Haflinger, Italian trotter, Lipizzan, Maremmano, Thoroughbred and Sarcidano was analysed. Five unrelated horses were chosen in each breed and twenty-two haplotypes were identified. The sequences obtained were aligned and compared with a reference sequence and with 27 mtDNA D-loop sequences selected in the GenBank database, representing Spanish, Portuguese, North African, wild horses and an Equus asinus sequence as the outgroup. Kimura two-parameter distances were calculated and a cluster analysis using the Neighbour-joining method was performed to obtain phylogenetic trees among breeds bred in Italy and among Italian and foreign breeds. The cluster analysis indicates that all the breeds but Giara are divided in the two trees, and no clear relationships were revealed between Italian populations and the other breeds. These results could be interpreted as showing the mixed origin of breeds bred in Italy and probably indicate the presence of many ancient maternal lineages with high diversity in mtDNA sequences.

  10. Human mitochondrial DNA (mtDNA) types in Malaysia

    International Nuclear Information System (INIS)

    Lian, L.H.; Koh, C.L.; Lim, M.E.

    2000-01-01

    Each human cell contains hundreds of mitochondria and thousands of double-stranded circular mtDNA. The delineation of human mtDNA variation and genetics over the past decade has provided unique and often startling insights into human evolution, degenerative diseases, and aging. Each mtDNA of 16,569 base pairs, encodes 13 polypeptides essential to the enzymes of the mitochondrial energy generating pathway, plus the necessary tRNAs and rRNAs. The highly polymorphic noncoding D-(displacement) loop region, also called the control region, is approximately 1.2 kb long. It contains two well-characterized hypervariable (HV-) regions, HV1 and HV2. MtDNA identification is usually based on these sequence differences. According to the TWTGDAM (Technical Working Group for DNA Analysis Methods), the minimum requirement for a mtDNA database for HV1 is from positions 16024 to 16365 and for HV2, from positions 00073 to 00340. The targeted Malaysian population subgroups for this study were mainly the Malays, Chinese, Indians, and indigenous Ibans, Bidayuhs, Kadazan-Dusuns, and Bajaus. Research methodologies undertaken included DNA extraction of samples from unrelated individuals, amplification of the specific regions via the polymerase chain reaction (PCR), and preparation of template DNA for sequencing by using an automated DNA sequencer. Sufficient nucleotide sequence data were generated from the mtDNA analysis. When the sequences were analyzed, sequence variations were found to be caused by nucleotide substitutions, insertions, and deletions. Of the three causes of the sequence variations, nucleotide substitutions (86.1%) accounted for the vast majority of polymorphism. It is noted that transitions (83.5%) were predominant when compared to the significantly lower frequencies of transversions (2.6%). Insertions (0.9%) and deletions (13.0%) were rather rare and found only in HV2. The data generated will also form the basis of a Malaysian DNA sequence database of mtDNA D-loop

  11. Estimation of complex permittivity using loop antenna

    DEFF Research Database (Denmark)

    Lenler-Eriksen, Hans-Rudolph; Meincke, Peter

    2004-01-01

    A method for estimating the complex permittivity of materials in the vicinity of a loop antenna is proposed. The method is based on comparing measured and numerically calculated input admittances for the loop antenna.......A method for estimating the complex permittivity of materials in the vicinity of a loop antenna is proposed. The method is based on comparing measured and numerically calculated input admittances for the loop antenna....

  12. A True Open-Loop Synchronization Technique

    DEFF Research Database (Denmark)

    Golestan, Saeed; Vidal, Ana; Yepes, Alejandro G.

    2016-01-01

    Synchronization techniques can be broadly classified into two major categories: Closed-loop and open-loop methods. The open-loop synchronization (OLS) techniques, contrary to the closed-loop ones, are unconditionally stable and benefit from a fast dynamic response. Their performance, however, tends...... is to develop a true OLS (and therefore, unconditionally stable) technique without any need for the calculation of sine and cosine functions. The effectiveness of the proposed synchronization technique is confirmed through the simulation and experimental results....

  13. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  14. Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection

    Directory of Open Access Journals (Sweden)

    Marius Rutkauskas

    2015-03-01

    Full Text Available CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against foreign nucleic acids. In type I CRISPR-Cas systems, invading DNA is detected by a large ribonucleoprotein surveillance complex called Cascade. The crRNA component of Cascade is used to recognize target sites in foreign DNA (protospacers by formation of an R-loop driven by base-pairing complementarity. Using single-molecule supercoiling experiments with near base-pair resolution, we probe here the mechanism of R-loop formation and detect short-lived R-loop intermediates on off-target sites bearing single mismatches. We show that R-loops propagate directionally starting from the protospacer-adjacent motif (PAM. Upon reaching a mismatch, R-loop propagation stalls and collapses in a length-dependent manner. This unambiguously demonstrates that directional zipping of the R-loop accomplishes efficient target recognition by rapidly rejecting binding to off-target sites with PAM-proximal mutations. R-loops that reach the protospacer end become locked to license DNA degradation by the auxiliary Cas3 nuclease/helicase without further target verification.

  15. Automation of loop amplitudes in numerical approach

    International Nuclear Information System (INIS)

    Fujimoto, J.; Ishikawa, T.; Shimizu, Y.; Kato, K.; Nakazawa, N.; Kaneko, T.

    1997-01-01

    An automatic calculating system GRACE-L1 of one-loop Feynman amplitude is reviewed. This system can be applied to 2 to 2-body one-loop processes. A sample calculation of 2 to 3-body one-loop amplitudes is also presented. (orig.)

  16. Fluctuation current in superconducting loops

    International Nuclear Information System (INIS)

    Berger, Jorge

    2012-01-01

    A superconducting loop that encloses noninteger flux holds a permanent current. On the average, this current is also present above T c , and has been measured in recent years. We are able to evaluate the permanent current within the TDGL or the Kramer-Watts-Tobin models for loops of general configuration, i.e., we don't require uniform cross section, material or temperature. We can also consider situations in which the width is not negligible in comparison to the radius. Our results agree with experiments. The situations with which we deal at present include fluctuation superconductivity in two-band superconductors, equilibrium thermal fluctuations of supercurrent along a weak link, and ratchet effects.

  17. Loop connectors in dentogenic diastema

    Directory of Open Access Journals (Sweden)

    Sanjna Nayar

    2015-01-01

    Full Text Available Patients with a missing tooth along with diastema have limited treatment options to restore the edentulous space. The use of a conventional fixed partial denture (FPD to replace the missing tooth may result in too wide anterior teeth leading to poor esthetics. Loss of anterior teeth with existing diastema may result in excess space available for pontic. This condition presents great esthetic challenge for prosthodontist. If implant supported prosthesis is not possible because of inadequate bone support, FPD along with loop connector may be a treatment option to maintain the diastema and provide optimal esthetic restoration. Here, we report a clinical case where FPD along with loop connector was used to achieve esthetic rehabilitation in maxillary anterior region in which midline diastema has been maintained.

  18. In pile helium loop ''COMEDIE''

    International Nuclear Information System (INIS)

    Abassin, J.J.; Blanchard, R.J.; Gentil, J.

    1981-01-01

    The SR1 test in the COMEDIE loop has permitted to demonstrate particularly the device operation reliability with a fuel loading. The post-irradiation examinations have pointed out the good filter efficiency and have enabled to determine the deposition profiles either for the activation products (e.g.: 51 Cr, 60 Co) or for the fission products (e.g.: sup(110m)Ag, 131 I, 134 Cs, 137 Cs). (author)

  19. Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers.

    Directory of Open Access Journals (Sweden)

    Marijn T J van Loenhout

    Full Text Available The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that acts as a scanning probe, is created by looping an optically trapped DNA tether around a DNA molecule that is held with magnetic tweezers. Upon scanning the loop along the λ-DNA molecule, EcoRI proteins were detected with ~17 nm spatial resolution. An offset of 33 ± 5 nm for the detected protein positions was found between back and forwards scans, corresponding to the size of the DNA loop and in agreement with theoretical estimates. At higher applied stretching forces, the scanning loop was able to remove bound proteins from the DNA, showing that the method is in principle also capable of measuring the binding strength of proteins to DNA with a force resolution of 0.1 pN/[Formula: see text]. The use of magnetic tweezers in this assay allows the facile preparation of many single-molecule tethers, which can be scanned one after the other, while it also allows for direct control of the supercoiling state of the DNA molecule, making it uniquely suitable to address the effects of torque on protein-DNA interactions.

  20. Dispersion relations in loop calculations

    International Nuclear Information System (INIS)

    Kniehl, B.A.

    1996-01-01

    These lecture notes give a pedagogical introduction to the use of dispersion relations in loop calculations. We first derive dispersion relations which allow us to recover the real part of a physical amplitude from the knowledge of its absorptive part along the branch cut. In perturbative calculations, the latter may be constructed by means of Cutkosky's rule, which is briefly discussed. For illustration, we apply this procedure at one loop to the photon vacuum-polarization function induced by leptons as well as to the γf anti-f vertex form factor generated by the exchange of a massive vector boson between the two fermion legs. We also show how the hadronic contribution to the photon vacuum polarization may be extracted from the total cross section of hadron production in e + e - annihilation measured as a function of energy. Finally, we outline the application of dispersive techniques at the two-loop level, considering as an example the bosonic decay width of a high-mass Higgs boson. (author)

  1. Dynamic Effects of Topoisomerase I Inhibition on R-Loops and Short Transcripts at Active Promoters.

    Directory of Open Access Journals (Sweden)

    Jessica Marinello

    Full Text Available Topoisomerase I-DNA-cleavage complexes (Top1cc stabilized by camptothecin (CPT have specific effects at transcriptional levels. We recently reported that Top1cc increase antisense transcript (aRNAs levels at divergent CpG-island promoters and, transiently, DNA/RNA hybrids (R-loop in nuclear and mitochondrial genomes of colon cancer HCT116 cells. However, the relationship between R-loops and aRNAs was not established. Here, we show that aRNAs can form R-loops in N-TERA-2 cells under physiological conditions, and that promoter-associated R-loops are somewhat increased and extended in length immediately upon cell exposure to CPT. In contrast, persistent Top1ccs reduce the majority of R-loops suggesting that CPT-accumulated aRNAs are not commonly involved in R-loops. The enhancement of aRNAs by Top1ccs is present both in human colon cancer HCT116 cells and WI38 fibroblasts suggesting a common response of cancer and normal cells. Although Top1ccs lead to DSB and DDR kinases activation, we do not detect a dependence of aRNA accumulation on ATM or DNA-PK activation. However, we showed that the cell response to persistent Top1ccs can involve an impairment of aRNA turnover rather than a higher synthesis rate. Finally, a genome-wide analysis shows that persistent Top1ccs also determine an accumulation of sense transcripts at 5'-end gene regions suggesting an increased occurrence of truncated transcripts. Taken together, the results indicate that Top1 may regulate transcription initiation by modulating RNA polymerase-generated negative supercoils, which can in turn favor R-loop formation at promoters, and that transcript accumulation at TSS is a response to persistent transcriptional stress by Top1 poisoning.

  2. Oscillation damping of chiral string loops

    International Nuclear Information System (INIS)

    Babichev, Eugeny; Dokuchaev, Vyacheslav

    2002-01-01

    Chiral cosmic string loops tend to the stationary (vorton) configuration due to energy loss into gravitational and electromagnetic radiation. We describe the asymptotic behavior of near stationary chiral loops and their fading to vortons. General limits on the gravitational and electromagnetic energy losses by near stationary chiral loops are found. For these loops we estimate the oscillation damping time. We present solvable examples of gravitational radiation energy loss by some chiral loop configurations. The analytical dependence of string energy with time is found in the case of the chiral ring with small amplitude radial oscillations

  3. Modular invariance and covariant loop calculus

    International Nuclear Information System (INIS)

    Petersen, J.L.; Roland, K.O.; Sidenius, J.R.

    1988-01-01

    The covariant loop calculus provides and efficient technique for computing explicit expressions for the density on moduli space corresponding to arbitrary (bosonic string) loop diagrams. Since modular invariance is not manifest, however, we carry out a detailed comparison with known explicit 2- and 3- loop results derived using analytic geometry (1 loop is known to be ok). We establish identity to 'high' order in some moduli and exactly in others. Agreement is found as a result of various non-trivial cancellations, in part related to number theory. We feel our results provide very strong support for the correctness of the covariant loop calculus approach. (orig.)

  4. Algorithm for counting large directed loops

    Energy Technology Data Exchange (ETDEWEB)

    Bianconi, Ginestra [Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34014 Trieste (Italy); Gulbahce, Natali [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, NM 87545 (United States)

    2008-06-06

    We derive a Belief-Propagation algorithm for counting large loops in a directed network. We evaluate the distribution of the number of small loops in a directed random network with given degree sequence. We apply the algorithm to a few characteristic directed networks of various network sizes and loop structures and compare the algorithm with exhaustive counting results when possible. The algorithm is adequate in estimating loop counts for large directed networks and can be used to compare the loop structure of directed networks and their randomized counterparts.

  5. Functional Fourier transforms and the loop equation

    International Nuclear Information System (INIS)

    Bershadskii, M.A.; Vaisburd, I.D.; Migdal, A.A.

    1986-01-01

    The Migdal-Makeenko momentum-space loop equation is investigated. This equation is derived from the ordinary loop equation by taking the Fourier transform of the Wilson functional. A perturbation theory is constructed for the new equation and it is proved that the action of the loop operator is determined by vertex functions which coincide with those of the previous equation. It is shown how the ghost loop arises in direct iterations of the momentum-space equation with respect to the coupling constant. A simple example is used to illustrate the mechanism of appearance of an integration in the interior loops in transition to observables

  6. Modular invariance and covariant loop calculus

    International Nuclear Information System (INIS)

    Petersen, J.L.; Roland, K.O.; Sidenius, J.R.

    1988-01-01

    The covariant loop calculus provides an efficient technique for computing explicit expressions for the density on moduli space corresponding to arbitrary (bosonic string) loop diagrams. Since modular invariance is not manifest, however, we carry out a detailed comparison with known explicit two- and three-loop results derived using analytic geometry (one loop is known to be okay). We establish identity to 'high' order in some moduli and exactly in others. Agreement is found as a result of various nontrivial cancellations, in part related to number theory. We feel our results provide very strong support for the correctness of the covariant loop calculus approach. (orig.)

  7. Hyperstaticity and loops in frictional granular packings

    Science.gov (United States)

    Tordesillas, Antoinette; Lam, Edward; Metzger, Philip T.

    2009-06-01

    The hyperstatic nature of granular packings of perfectly rigid disks is analyzed algebraically and through numerical simulation. The elementary loops of grains emerge as a fundamental element in addressing hyperstaticity. Loops consisting of an odd number of grains behave differently than those with an even number. For odd loops, the latent stresses are exterior and are characterized by the sum of frictional forces around each loop. For even loops, the latent stresses are interior and are characterized by the alternating sum of frictional forces around each loop. The statistics of these two types of loop sums are found to be Gibbsian with a "temperature" that is linear with the friction coefficient μ when μ<1.

  8. DNA Camouflage

    Science.gov (United States)

    2016-01-08

    1 DNA Camouflage Supplementary Information Bijan Zakeri1,2*, Timothy K. Lu1,2*, Peter A. Carr2,3* 1Department of Electrical Engineering and...ll.mit.edu). Distribution A: Public Release   2 Supplementary Figure 1 DNA camouflage with the 2-state device. (a) In the presence of Cre, DSD-2[α...10 1 + Cre 1 500 1,000 length (bp) chromatogram alignment template − Cre   4 Supplementary Figure 3 DNA camouflage with a switchable

  9. Loop diagrams without γ matrices

    International Nuclear Information System (INIS)

    McKeon, D.G.C.; Rebhan, A.

    1993-01-01

    By using a quantum-mechanical path integral to compute matrix elements of the form left-angle x|exp(-iHt)|y right-angle, radiative corrections in quantum-field theory can be evaluated without encountering loop-momentum integrals. In this paper we demonstrate how Dirac γ matrices that occur in the proper-time ''Hamiltonian'' H lead to the introduction of a quantum-mechanical path integral corresponding to a superparticle analogous to one proposed recently by Fradkin and Gitman. Direct evaluation of this path integral circumvents many of the usual algebraic manipulations of γ matrices in the computation of quantum-field-theoretical Green's functions involving fermions

  10. Perturbation calculations with Wilson loop

    International Nuclear Information System (INIS)

    Peixoto Junior, L.B.

    1984-01-01

    We present perturbative calculations with the Wilson loop (WL). The dimensional regularization method is used with a special attention concerning to the problem of divergences in the WL expansion in second and fourth orders, in three and four dimensions. We show that the residue in the pole, in 4d, of the fourth order graphs contribution sum is important for the charge renormalization. We compute up to second order the exact expression of the WL, in three-dimensional gauge theories with topological mass as well as its assimptotic behaviour for small and large distances. the author [pt

  11. Intersegmental interactions in supercoiled DNA: atomic force microscope study

    Energy Technology Data Exchange (ETDEWEB)

    Shlyakhtenko, Luda S.; Miloseska, Lela; Potaman, Vladimir N.; Sinden, Richard R.; Lyubchenko, Yuri L

    2003-10-15

    Intersegmental interactions in DNA facilitated by the neutralization of electrostatic repulsion was studied as a function of salt concentration and DNA supercoiling. DNA samples with defined superhelical densities were deposited onto aminopropyl mica at different ionic conditions and imaged in air after drying of the samples. Similar to hydrodynamic data, we did not observe a collapse of supercoiled DNA, as proposed earlier by cryo-EM studies. Instead, the formation of the contacts between DNA helices within supercoiled loops with no visible space between the duplexes was observed. The length of such close contacts increased upon increasing NaCl concentration. DNA supercoiling was a critical factor for the stabilization of intersegmental contacts. Implications of the observed effect for understanding DNA compaction in the cell and for regulation DNA transactions via interaction of distantly separated DNA regions are discussed.

  12. Distribution of u.v.-induced repair events in higher-order chromatin loops in human and hamster fibroblasts

    International Nuclear Information System (INIS)

    Mullenders, L.H.F.; Zeeland, A.A. van; Natarajan, A.T.; Kesteren, A.C. van; Bussmann, C.J.M.

    1986-01-01

    The repair of u.v.-induced damage in human and rodent cells was investigated at the level of DNA loops attached to the nuclear matrix. After 2 h post-u.v. incubation, DNase I digestion studies revealed a 3- to 4-fold enrichment of repair-labeled DNA at the nuclear matrix in four xeroderma pigmentosum cell strains belonging to complementation group C. Two xeroderma pigmentosum cell strains of complementation group D and Syrian hamster embryonic cells, as well as in HeLa cells and normal human fibroblasts, no enrichment of repair-labeled DNA at the nuclear matrix was observed. Visualization of repair events in DNA loops by autoradiography of DNA halo - matrix structures confirmed the biochemical observations. The presence or absence of preferential repair of nuclear matrix-associated DNA paralleled the presence or absence of inhomogeneity in the distribution of T4 endonuclease-V-sensitive sites. In xeroderma pigmentosum cells of complementation group C showed that after 2 h post-u.v. incubation, repair events were found at both attachment sites in a limited number of loops and that large domains of loops were not subjected to repair. (author)

  13. Gauge theory loop operators and Liouville theory

    International Nuclear Information System (INIS)

    Drukker, Nadav; Teschner, Joerg

    2009-10-01

    We propose a correspondence between loop operators in a family of four dimensional N=2 gauge theories on S 4 - including Wilson, 't Hooft and dyonic operators - and Liouville theory loop operators on a Riemann surface. This extends the beautiful relation between the partition function of these N=2 gauge theories and Liouville correlators found by Alday, Gaiotto and Tachikawa. We show that the computation of these Liouville correlators with the insertion of a Liouville loop operator reproduces Pestun's formula capturing the expectation value of a Wilson loop operator in the corresponding gauge theory. We prove that our definition of Liouville loop operators is invariant under modular transformations, which given our correspondence, implies the conjectured action of S-duality on the gauge theory loop operators. Our computations in Liouville theory make an explicit prediction for the exact expectation value of 't Hooft and dyonic loop operators in these N=2 gauge theories. The Liouville loop operators are also found to admit a simple geometric interpretation within quantum Teichmueller theory as the quantum operators representing the length of geodesics. We study the algebra of Liouville loop operators and show that it gives evidence for our proposal as well as providing definite predictions for the operator product expansion of loop operators in gauge theory. (orig.)

  14. Gauge theory loop operators and Liouville theory

    Energy Technology Data Exchange (ETDEWEB)

    Drukker, Nadav [Humboldt Univ. Berlin (Germany). Inst. fuer Physik; Gomis, Jaume; Okuda, Takuda [Perimeter Inst. for Theoretical Physics, Waterloo, ON (Canada); Teschner, Joerg [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2009-10-15

    We propose a correspondence between loop operators in a family of four dimensional N=2 gauge theories on S{sup 4} - including Wilson, 't Hooft and dyonic operators - and Liouville theory loop operators on a Riemann surface. This extends the beautiful relation between the partition function of these N=2 gauge theories and Liouville correlators found by Alday, Gaiotto and Tachikawa. We show that the computation of these Liouville correlators with the insertion of a Liouville loop operator reproduces Pestun's formula capturing the expectation value of a Wilson loop operator in the corresponding gauge theory. We prove that our definition of Liouville loop operators is invariant under modular transformations, which given our correspondence, implies the conjectured action of S-duality on the gauge theory loop operators. Our computations in Liouville theory make an explicit prediction for the exact expectation value of 't Hooft and dyonic loop operators in these N=2 gauge theories. The Liouville loop operators are also found to admit a simple geometric interpretation within quantum Teichmueller theory as the quantum operators representing the length of geodesics. We study the algebra of Liouville loop operators and show that it gives evidence for our proposal as well as providing definite predictions for the operator product expansion of loop operators in gauge theory. (orig.)

  15. Contrasting HIV phylogenetic relationships and V3 loop protein similarities

    Energy Technology Data Exchange (ETDEWEB)

    Korber, B. (Los Alamos National Lab., NM (United States) Santa Fe Inst., NM (United States)); Myers, G. (Los Alamos National Lab., NM (United States))

    1992-01-01

    At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

  16. Contrasting HIV phylogenetic relationships and V3 loop protein similarities

    Energy Technology Data Exchange (ETDEWEB)

    Korber, B. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States); Myers, G. [Los Alamos National Lab., NM (United States)

    1992-12-31

    At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

  17. Interplay of protein and DNA structure revealed in simulations of the lac operon.

    Directory of Open Access Journals (Sweden)

    Luke Czapla

    Full Text Available The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gene control. The molecular simulations presented here examine two likely structural contributions to the in-vivo looping of bacterial DNA: the distortions of the double helix introduced upon association of the highly abundant, nonspecific nucleoid protein HU and the large-scale deformations of the repressor detected in low-resolution experiments. The computations take account of the three-dimensional arrangements of nucleotides and amino acids found in crystal structures of DNA with the two proteins, the natural rest state and deformational properties of protein-free DNA, and the constraints on looping imposed by the conformation of the repressor and the orientation of bound DNA. The predicted looping propensities capture the complex, chain-length-dependent variation in repression efficacy extracted from gene expression studies and in vitro experiments and reveal unexpected chain-length-dependent variations in the uptake of HU, the deformation of repressor, and the folding of DNA. Both the opening of repressor and the presence of HU, at levels approximating those found in vivo, enhance the probability of loop formation. HU affects the global organization of the repressor and the opening of repressor influences the levels of HU binding to DNA. The length of the loop determines whether the DNA adopts antiparallel or parallel orientations on the repressor, whether the repressor is opened or closed, and how many HU molecules bind to the loop. The collective behavior of proteins and DNA is greater than the sum of the parts and hints of ways in which multiple proteins may coordinate the packaging and processing of genetic information.

  18. Interplay of protein and DNA structure revealed in simulations of the lac operon.

    Science.gov (United States)

    Czapla, Luke; Grosner, Michael A; Swigon, David; Olson, Wilma K

    2013-01-01

    The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gene control. The molecular simulations presented here examine two likely structural contributions to the in-vivo looping of bacterial DNA: the distortions of the double helix introduced upon association of the highly abundant, nonspecific nucleoid protein HU and the large-scale deformations of the repressor detected in low-resolution experiments. The computations take account of the three-dimensional arrangements of nucleotides and amino acids found in crystal structures of DNA with the two proteins, the natural rest state and deformational properties of protein-free DNA, and the constraints on looping imposed by the conformation of the repressor and the orientation of bound DNA. The predicted looping propensities capture the complex, chain-length-dependent variation in repression efficacy extracted from gene expression studies and in vitro experiments and reveal unexpected chain-length-dependent variations in the uptake of HU, the deformation of repressor, and the folding of DNA. Both the opening of repressor and the presence of HU, at levels approximating those found in vivo, enhance the probability of loop formation. HU affects the global organization of the repressor and the opening of repressor influences the levels of HU binding to DNA. The length of the loop determines whether the DNA adopts antiparallel or parallel orientations on the repressor, whether the repressor is opened or closed, and how many HU molecules bind to the loop. The collective behavior of proteins and DNA is greater than the sum of the parts and hints of ways in which multiple proteins may coordinate the packaging and processing of genetic information.

  19. Sequence-specific activation of the DNA sensor cGAS by Y-form DNA structures as found in primary HIV-1 cDNA.

    Science.gov (United States)

    Herzner, Anna-Maria; Hagmann, Cristina Amparo; Goldeck, Marion; Wolter, Steven; Kübler, Kirsten; Wittmann, Sabine; Gramberg, Thomas; Andreeva, Liudmila; Hopfner, Karl-Peter; Mertens, Christina; Zillinger, Thomas; Jin, Tengchuan; Xiao, Tsan Sam; Bartok, Eva; Coch, Christoph; Ackermann, Damian; Hornung, Veit; Ludwig, Janos; Barchet, Winfried; Hartmann, Gunther; Schlee, Martin

    2015-10-01

    Cytosolic DNA that emerges during infection with a retrovirus or DNA virus triggers antiviral type I interferon responses. So far, only double-stranded DNA (dsDNA) over 40 base pairs (bp) in length has been considered immunostimulatory. Here we found that unpaired DNA nucleotides flanking short base-paired DNA stretches, as in stem-loop structures of single-stranded DNA (ssDNA) derived from human immunodeficiency virus type 1 (HIV-1), activated the type I interferon-inducing DNA sensor cGAS in a sequence-dependent manner. DNA structures containing unpaired guanosines flanking short (12- to 20-bp) dsDNA (Y-form DNA) were highly stimulatory and specifically enhanced the enzymatic activity of cGAS. Furthermore, we found that primary HIV-1 reverse transcripts represented the predominant viral cytosolic DNA species during early infection of macrophages and that these ssDNAs were highly immunostimulatory. Collectively, our study identifies unpaired guanosines in Y-form DNA as a highly active, minimal cGAS recognition motif that enables detection of HIV-1 ssDNA.

  20. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  1. Hyperstretching DNA

    NARCIS (Netherlands)

    Schakenraad, Koen; Biebricher, Andreas S.; Sebregts, Maarten; Ten Bensel, Brian; Peterman, Erwin J.G.; Wuite, Gijs J L; Heller, Iddo; Storm, Cornelis; Van Der Schoot, Paul

    2017-01-01

    The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely

  2. Analysis of the distribution of DNA repair patches in the DNA-nuclear matrix complex from human cells

    International Nuclear Information System (INIS)

    Mullenders, L.H.F.

    1983-01-01

    The distribution of ultraviolet-induced repair patches along DNA loops attached to the nuclear matrix, was investigated by digestion with DNA-degrading enzymes and neutral sucrose gradient centrifugation. When DNA was gradually removed by DNAase 1, pulse label incorporated by ultraviolet-irradiated cells during 10 min in the presence of hydroxyurea or hydroxyurea/arabinosylcytosine showed similar degradation kinetics as prelabelled DNA. No preferential association of pulse label with the nuclear matrix was observed, neither within 30 min nor 13 h after iiradiation. When the pulse label was incorporated by replicative synthesis under the same conditions, a preferential association of newly-synthesized DNA with the nuclear matrix was observed. Single-strand specific digestion with nuclease S 1 of nuclear lysates from ultraviolet-irradiated cells, pulse labelled in the presence of hydroxyurea/arabinosylcytosine, caused a release of about 70% of the prelabelled DNA and 90% of the pulse-labelled DNA from the rapidly sedimenting material in sucrose gradients. The results suggest no specific involvement of the nuclear matrix in repair synthesis, a random distribution of repair patches along the DNA loops, and simultaneously multiple incision events per DNA loop. (Auth.)

  3. Analysis of the distribution of DNA repair patches in the DNA-nuclear matrix complex from human cells

    Energy Technology Data Exchange (ETDEWEB)

    Mullenders, L.H.F. (Rijksuniversiteit Leiden (Netherlands). Lab. voor Stralengenetica en Chemische Mutagenese); Zeeland, A.A. van; Natarajan, A.T. (Cohen (J.A.) Inst. voor Radiopathologie en Stralenbescherming, Leiden (Netherlands))

    1983-09-09

    The distribution of ultraviolet-induced repair patches along DNA loops attached to the nuclear matrix, was investigated by digestion with DNA-degrading enzymes and neutral sucrose gradient centrifugation. When DNA was gradually removed by DNAase 1, pulse label incorporated by ultraviolet-irradiated cells during 10 min in the presence of hydroxyurea or hydroxyurea/arabinosylcytosine showed similar degradation kinetics as prelabelled DNA. No preferential association of pulse label with the nuclear matrix was observed, neither within 30 min nor 13 h after irradiation. When the pulse label was incorporated by replicative synthesis under the same conditions, a preferential association of newly-synthesized DNA with the nuclear matrix was observed. Single-strand specific digestion with nuclease S/sub 1/ of nuclear lysates from ultraviolet-irradiated cells, pulse labelled in the presence of hydroxyurea/arabinosylcytosine, caused a release of about 70% of the prelabelled DNA and 90% of the pulse-labelled DNA from the rapidly sedimenting material in sucrose gradients. The results suggest no specific involvement of the nuclear matrix in repair synthesis, a random distribution of repair patches along the DNA loops, and simultaneously multiple incision events per DNA loop.

  4. Loop quantization as a continuum limit

    International Nuclear Information System (INIS)

    Manrique, Elisa; Oeckl, Robert; Weber, Axel; Zapata, Jose A

    2006-01-01

    We present an implementation of Wilson's renormalization group and a continuum limit tailored for loop quantization. The dynamics of loop-quantized theories is constructed as a continuum limit of the dynamics of effective theories. After presenting the general formalism we show as a first explicit example the 2D Ising field theory, an interacting relativistic quantum field theory with local degrees of freedom quantized by loop quantization techniques

  5. Quantum chromodynamics as dynamics of loops

    International Nuclear Information System (INIS)

    Makeenko, Yu.M.; Migdal, A.A.

    1981-01-01

    QCD is entirely reformulated in terms of white composite fields - the traces of the loop products. The 1/N expansion turns out to be the WKB (Hartree-Fock) approximation for these fields. The 'classical' equation describing the N = infinite case is reduced tp a bootstrap form. New, manifestly gauge-invariant perturbation theory in the loop space, reproducing asymptotic freedom, is developed by iterations of this equation. The area law appears to be a self-consistent solution at large loops. (orig.)

  6. Lattice QED in the loop space

    International Nuclear Information System (INIS)

    Fort, H.

    1994-01-01

    We present a survey on the state of the art in the formulation of lattice compact QED in the space of loops. In a first part we review our most recent Hamiltonian results which signal a second order transition for (3+1) compact QED. We devote the second part to the Lagrangian loop formalism, showing the equivalence of the recently proposed loop action with the Villain form. (orig.)

  7. LMFBR with booster pump in pumping loop

    International Nuclear Information System (INIS)

    Rubinstein, H.J.

    1975-01-01

    A loop coolant circulation system is described for a liquid metal fast breeder reactor (LMFBR) utilizing a low head, high specific speed booster pump in the hot leg of the coolant loop with the main pump located in the cold leg of the loop, thereby providing the advantages of operating the main pump in the hot leg with the reliability of cold leg pump operation

  8. Soft Neutrosophic Loops and Their Generalization

    Directory of Open Access Journals (Sweden)

    Mumtaz Ali

    2014-06-01

    Full Text Available Soft set theory is a general mathematical tool for dealing with uncertain, fuzzy, not clearly defined objects. In this paper we introduced soft neutrosophic loop,soft neutosophic biloop, soft neutrosophic N -loop with the discuission of some of their characteristics. We also introduced a new type of soft neutrophic loop, the so called soft strong neutrosophic loop which is of pure neutrosophic character. This notion also found in all the other corresponding notions of soft neutrosophic thoery. We also given some of their properties of this newly born soft structure related to the strong part of neutrosophic theory.

  9. Vertically Polarized Omnidirectional Printed Slot Loop Antenna

    DEFF Research Database (Denmark)

    Kammersgaard, Nikolaj Peter Iversen; Kvist, Søren H.; Thaysen, Jesper

    2015-01-01

    A novel vertically polarized omnidirectional printed slot loop antenna has been designed, simulated, fabricated and measured. The slot loop works as a magnetic loop. The loop is loaded with inductors to insure uniform and in-phase fields in the slot in order to obtain an omnidirectional radiation...... pattern. The antenna is designed for the 2.45 GHz Industrial, Scientific and Medical band. Applications of the antenna are many. One is for on-body applications since it is ideal for launching a creeping waves due to the polarization....

  10. Quantum chromodynamics as dynamics of loops

    International Nuclear Information System (INIS)

    Makeenko, Yu.; Migdal, A.A.

    1980-01-01

    The problem of a possibility of reformulating quantum chromodynamics (QCD) in terms of colourless composite fields instead of coloured quarks and gluons is considered. The role of such fields is played by the gauge invariant loop functionals. The Shwinger equations of motion is derived in the loop space which completely describe dynamics of the loop fields. New manifestly gauge invariant diagram technique in the loop space is developed. These diagrams reproduce asymptotic freedom in the ultraviolet range and are consistent with the confinement law in the infrared range

  11. R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters.

    Science.gov (United States)

    Chen, Liang; Chen, Jia-Yu; Zhang, Xuan; Gu, Ying; Xiao, Rui; Shao, Changwei; Tang, Peng; Qian, Hao; Luo, Daji; Li, Hairi; Zhou, Yu; Zhang, Dong-Er; Fu, Xiang-Dong

    2017-11-16

    R-loop, a three-stranded RNA/DNA structure, has been linked to induced genome instability and regulated gene expression. To enable precision analysis of R-loops in vivo, we develop an RNase-H-based approach; this reveals predominant R-loop formation near gene promoters with strong G/C skew and propensity to form G-quadruplex in non-template DNA, corroborating with all biochemically established properties of R-loops. Transcription perturbation experiments further indicate that R-loop induction correlates to transcriptional pausing. Interestingly, we note that most mapped R-loops are each linked to a nearby free RNA end; by using a ribozyme to co-transcriptionally cleave nascent RNA, we demonstrate that such a free RNA end coupled with a G/C-skewed sequence is necessary and sufficient to induce R-loop. These findings provide a topological solution for RNA invasion into duplex DNA and suggest an order for R-loop initiation and elongation in an opposite direction to that previously proposed. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Urine sample used for detection of toxoplasma gondii infection by loop-mediated isothermal amplification (LAMP).

    Science.gov (United States)

    Hu, Xin; Pan, Chang-Wang; Li, Ya-Fei; Wang, Han; Tan, Feng

    2012-02-01

    In this study, a loop-mediated isothermal amplification (LAMP) assay was established to detect Toxoplasma gondii DNA in mice infected with T. gondii PRU strain. This LAMP assay was based on the sequence of highly repetitive B1 gene. The detection limit of T. gondii LAMP assay was 1 pg of T. gondii DNA, which was evaluated using 10-fold serially diluted DNA of cultured parasites. The LAMP assay was also highly specific for T. gondii and able to detect T. gondii DNA in urine of mice treated with dexamethasone at 90 day post infection (p.i.), although this assay could not detect the DNA in mice urine 2-6 days p.i. These results demonstrated that LAMP is effective for evaluation of therapy effectiveness for T. gondii infection. The established LAMP assay may represent a useful and practical tool for the routine diagnosis and therapeutic evaluation of human toxoplasmosis.

  13. In pile helium loop ''Comedie''

    International Nuclear Information System (INIS)

    Blanchard, R.J.

    1985-01-01

    The loop is located in the SILOE reactor at Centre d'Etudes Nucleaires de Grenoble. The purpose and objectives are divided into two groups, principal and secondary. The primary objective was to provide basic data on the deposition behavior of important condensable fission products on a variety of steel surfaces, i.e. temperature (sorption isotherms) and mass transfer (physical adsorption) dependencies; to provide information concerning the degree of penetration of important fission products into the metals comprising the heat exchanger-recuperator tubes as a function of alloy type and/or metal temperature; to provide complementary information on the reentrainment (liftoff) of important fission and activation products by performing out-of-pile blowdown experiments on tube samples representative of the alloy types used in the heat exchanger-recuperator and of the surface temperatures experienced during plateout. The secondary objective was to provide information concerning the migration of important fission products through graphite. To this end, concentration profiles in the web between the fuel rods containing the fission product source and the coolant channels and in the graphite diffusion sample will be measured to study the corrosion of metallic specimens placed in the conditions of high temperature gas cooled reactor. The first experiment SRO enables to determine the loop characteristics and possibilities related to thermal, thermodynamic, chemical and neutronic properties. The second experiment has been carried out in high temperature gas cooled reactor operating conditions. It enables to determine in particular the deposition axial profile of activation and fission products in the plateout section constituting the heat exchanger, the fission products balance trapped in the different filter components, and the cumulated released fraction of solid fission products. The SR1 test permits to demonstrate in particular the Comedie loop operation reliability, either

  14. Rapid Simulation of Flat Knitting Loops Based On the Yarn Texture and Loop Geometrical Model

    Directory of Open Access Journals (Sweden)

    Lu Zhiwen

    2017-06-01

    Full Text Available In order to create realistic loop primitives suitable for the fast computer-aided design (CAD of the flat knitted fabric, we have a research on the geometric model of the loop as well as the variation of the loop surface. Establish the texture variation model based on the changing process from the normal yarn to loop that provides the realistic texture of the simulative loop. Then optimize the simulative loop based on illumination variation. This paper develops the computer program with the optimization algorithm and achieves the loop simulation of different yarns to verify the feasibility of the proposed algorithm. Our work provides a fast CAD of the flat knitted fabric with loop simulation, and it is not only more realistic but also material adjustable. Meanwhile it also provides theoretical value for the flat knitted fabric computer simulation.

  15. DNA: Polymer and molecular code

    Science.gov (United States)

    Shivashankar, G. V.

    1999-10-01

    gene expression a prime example of a biological code. We developed a novel method of making DNA micro- arrays, the so-called DNA chip. Using the optical tweezer concept, we were able to pattern biomolecules on a solid substrate, developing a new type of sub-micron laser lithography. A laser beam is focused onto a thin gold film on a glass substrate. Laser ablation of gold results in local aggregation of nanometer scale beads conjugated with small DNA oligonucleotides, with sub-micron resolution. This leads to specific detection of cDNA and RNA molecules. We built a simple micro-array fabrication and detection in the laboratory, based on this method, to probe addressable pools (genes, proteins or antibodies). We have lately used molecular beacons (single stranded DNA with a stem-loop structure containing a fluorophore and quencher), for the direct detection of unlabelled mRNA. As a first step towards a study of the dynamics of the biological code, we have begun to examine the patterns of gene expression during virus (T7 phage) infection of E-coli bacteria.

  16. Lose Your Loops with Numpy

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    Developing in python is fast. Computation, however, can often be another story. Or at least that is how it may seem. When working with arrays and numerical datasets one can subvert many of python’s computational limitations by utilizing numpy. Numpy is python’s standard matrix computation library. Many python users only use numpy to store and generate arrays, failing to utilize one of python’s most powerful computational tools. By leveraging numpy’s ufuncs, aggregation, broadcasting and slicing/masking/indexing functionality one can cut back on slow python loops and increase the speed of their programs by as much as 100x. This talk aims at teaching attendees how to use these tools through toy examples.

  17. Closed loop steam cooled airfoil

    Science.gov (United States)

    Widrig, Scott M.; Rudolph, Ronald J.; Wagner, Gregg P.

    2006-04-18

    An airfoil, a method of manufacturing an airfoil, and a system for cooling an airfoil is provided. The cooling system can be used with an airfoil located in the first stages of a combustion turbine within a combined cycle power generation plant and involves flowing closed loop steam through a pin array set within an airfoil. The airfoil can comprise a cavity having a cooling chamber bounded by an interior wall and an exterior wall so that steam can enter the cavity, pass through the pin array, and then return to the cavity to thereby cool the airfoil. The method of manufacturing an airfoil can include a type of lost wax investment casting process in which a pin array is cast into an airfoil to form a cooling chamber.

  18. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  19. DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Castelino, J

    1993-12-31

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

  20. Neocortical electrical stimulation for epilepsy : Closed-loop versus open-loop

    NARCIS (Netherlands)

    Vassileva, Albena; van Blooijs, Dorien; Leijten, Frans; Huiskamp, Geertjan

    2018-01-01

    The aim of this review is to evaluate whether open-loop or closed-loop neocortical electrical stimulation should be the preferred approach to manage seizures in intractable epilepsy. Twenty cases of open-loop neocortical stimulation with an implanted device have been reported, in 5 case studies.

  1. Second-strand cDNA synthesis: classical method

    International Nuclear Information System (INIS)

    Gubler, U.

    1987-01-01

    The classical scheme for the synthesis of double-stranded cDNA as it was reported in 1976 is described. Reverse transcription of mRNA with oligo(dT) as the primer generates first strands with a small loop at the 3' end of the cDNA (the end that corresponds to the 5' end of the mRNA). Subsequent removal of the mRNA by alkaline hydrolysis leaves single-stranded cDNA molecules again with a small 3' loop. This loop can be used by either reverse transcriptase or Klenow fragment of DNA polymerase I as a primer for second-strand synthesis. The resulting products are double-stranded cDNA molecules that are covalently closed at the end corresponding to the 5' end of the original mRNA. Subsequent cleavage of the short piece of single-stranded cDNA within the loop with the single-strand-specific S 1 nuclease generate open double-stranded molecules that can be used for molecular cloning in plasmids or in phage. Useful variations of this scheme have been described

  2. Newtonian gravity in loop quantum gravity

    OpenAIRE

    Smolin, Lee

    2010-01-01

    We apply a recent argument of Verlinde to loop quantum gravity, to conclude that Newton's law of gravity emerges in an appropriate limit and setting. This is possible because the relationship between area and entropy is realized in loop quantum gravity when boundaries are imposed on a quantum spacetime.

  3. Holonomy loops, spectral triples and quantum gravity

    DEFF Research Database (Denmark)

    Johannes, Aastrup; Grimstrup, Jesper Møller; Nest, Ryszard

    2009-01-01

    We review the motivation, construction and physical interpretation of a semi-finite spectral triple obtained through a rearrangement of central elements of loop quantum gravity. The triple is based on a countable set of oriented graphs and the algebra consists of generalized holonomy loops...

  4. Conformal anomaly of super Wilson loop

    Energy Technology Data Exchange (ETDEWEB)

    Belitsky, A.V., E-mail: andrei.belitsky@asu.edu [Department of Physics, Arizona State University, Tempe, AZ 85287-1504 (United States)

    2012-09-11

    Classically supersymmetric Wilson loop on a null polygonal contour possesses all symmetries required to match it onto non-MHV amplitudes in maximally supersymmetric Yang-Mills theory. However, to define it quantum mechanically, one is forced to regularize it since perturbative loop diagrams are not well defined due to presence of ultraviolet divergences stemming from integration in the vicinity of the cusps. A regularization that is adopted by practitioners by allowing one to use spinor helicity formalism, on the one hand, and systematically go to higher orders of perturbation theory is based on a version of dimensional regularization, known as Four-Dimensional Helicity scheme. Recently it was demonstrated that its use for the super Wilson loop at one loop breaks both conformal symmetry and Poincare supersymmetry. Presently, we exhibit the origin for these effects and demonstrate how one can undo this breaking. The phenomenon is alike the one emerging in renormalization group mixing of conformal operators in conformal theories when one uses dimensional regularization. The rotation matrix to the diagonal basis is found by means of computing the anomaly in the Ward identity for the conformal boost. Presently, we apply this ideology to the super Wilson loop. We compute the one-loop conformal anomaly for the super Wilson loop and find that the anomaly depends on its Grassmann coordinates. By subtracting this anomalous contribution from the super Wilson loop we restore its interpretation as a dual description for reduced non-MHV amplitudes which are expressed in terms of superconformal invariants.

  5. Feedback loop compensates for rectifier nonlinearity

    Science.gov (United States)

    1966-01-01

    Signal processing circuit with two negative feedback loops rectifies two sinusoidal signals which are 180 degrees out of phase and produces a single full-wave rectified output signal. Each feedback loop incorporates a feedback rectifier to compensate for the nonlinearity of the circuit.

  6. Loop calculus for lattice gauge theories

    International Nuclear Information System (INIS)

    Gambini, R.; Leal, L.; Trias, A.; Departamento de Fisica Aplicada, Facultad de Ingenieria, Universidad Central de Venezuela, Apartado 47724, Caracas 1051, Venezuela; Departament de Matematiques, Universitat Politecnica de Catalunya, Escuela Tecnica Superior de Enginyers de Telecomunicaciones, Barcelona 08034, Spain)

    1989-01-01

    Hamiltonian calculations are performed using a loop-labeled basis where the full set of identities for the SU(N) gauge models has been incorporated. The loops are classified as clusterlike structures and the eigenvalue problem leads to a linear set of finite-difference equations easily amenable to numerical treatment. Encouraging results are reported for SU(2) at spatial dimension 2

  7. Design Principles for Closed Loop Supply Chains

    NARCIS (Netherlands)

    H.R. Krikke (Harold); C.P. Pappis (Costas); G.T. Tsoulfas; J.M. Bloemhof-Ruwaard (Jacqueline)

    2001-01-01

    textabstractIn this paper we study design principles for closed loop supply chains. Closed loop supply chains aim at closing material flows thereby limiting emission and residual waste, but also providing customer service at low cost. We study 'traditional' and 'new' design principles known in the

  8. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  9. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  10. DNA nanotechnology

    Science.gov (United States)

    Seeman, Nadrian C.; Sleiman, Hanadi F.

    2018-01-01

    DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

  11. Flexible DNA Path in the MCM Double Hexamer Loaded on DNA.

    Science.gov (United States)

    Hizume, Kohji; Kominami, Hiroaki; Kobayashi, Kei; Yamada, Hirofumi; Araki, Hiroyuki

    2017-05-16

    The formation of the pre-replicative complex (pre-RC) during the G1 phase, which is also called the licensing of DNA replication, is the initial and essential step of faithful DNA replication during the subsequent S phase. It is widely accepted that in the pre-RC, double-stranded DNA passes through the holes of two ring-shaped minichromosome maintenance (MCM) 2-7 hexamers; however, the spatial organization of the DNA and proteins involved in pre-RC formation is unclear. Here we reconstituted the pre-RC from purified DNA and proteins and visualized the complex using atomic force microscopy (AFM). AFM revealed that the MCM double hexamers formed elliptical particles on DNA. Analysis of the angle of binding of DNA to the MCM double hexamer suggests that the DNA does not completely pass through both holes of the MCM hexamers, possibly because the DNA exited from the gap between Mcm2 and Mcm5. A DNA loop fastened by the MCM double hexamer was detected in pre-RC samples reconstituted from purified proteins as well as those purified from yeast cells, suggesting a higher-order architecture of the loaded MCM hexamers and DNA strands.

  12. The Wilson loop and some applications

    International Nuclear Information System (INIS)

    Bezerra, V.B.

    1983-04-01

    A simple relation between the classical Wilson loop and the angular deviation in the parallel displacement is found. An example of potentials which give field copies and which suplly the same classical Wilson loop for a particular trajectory is exhibited. The asymptotic behaviour of the Wilson loop for the BPST instanton and the meron, is discussed. By using the dimensional regularization technique to calculate the second order term of the quantum Wilson loop, the influence of geometrical factors for the residue in the pole due to contact points, cuspides and intersections, in function of the space-time ν, is investigated. Charge renormalization in Quantum electrodynamics is finally calculated by using the quantum Wilson loop. (L.C.) [pt

  13. The Wilson loop and some applications

    International Nuclear Information System (INIS)

    Bezerra, V.B.

    1983-01-01

    A simple relation between the classical Wilson loop and the angular deviation in the parallel shift is found. An example of potential which given field copies and which give the same classical Wilson loop for a given trajectory is exchibited. Afterwards, the asymptotic behaviour of the Wilson loop for the BPST instanton and meron is discussed. Using the dimensional regularization technique to calculate the second order term of Quantum Wilson loop, the influence of geometrical factors for the residue in the polo due to contact points, cusp and intersections, in function of the upsilon dimension of the space-time is investigated. Finally, the charge renormalization in Quantum Electrodynamics using Quantum Wilson loop is calculated. (L.C.) [pt

  14. Hydraulic loop: practices using open control systems

    International Nuclear Information System (INIS)

    Carrasco, J.A.; Alonso, L.; Sanchez, F.

    1998-01-01

    The Tecnatom Hydraulic Loop is a dynamic training platform. It has been designed with the purpose of improving the work in teams. With this system, the student can obtain a full scope vision of a system. The hydraulic Loop is a part of the Tecnatom Maintenance Centre. The first objective of the hydraulic Loop is the instruction in components, process and process control using open control system. All the personal of an electric power plant can be trained in the Hydraulic Loop with specific courses. The development of a dynamic tool for tests previous to plant installations has been an additional objective of the Hydraulic Loop. The use of this platform is complementary to the use of full-scope simulators in order to debug and to analyse advanced control strategies. (Author)

  15. Osmotic mechanism of the loop extrusion process

    Science.gov (United States)

    Yamamoto, Tetsuya; Schiessel, Helmut

    2017-09-01

    The loop extrusion theory assumes that protein factors, such as cohesin rings, act as molecular motors that extrude chromatin loops. However, recent single molecule experiments have shown that cohesin does not show motor activity. To predict the physical mechanism involved in loop extrusion, we here theoretically analyze the dynamics of cohesin rings on a loop, where a cohesin loader is in the middle and unloaders at the ends. Cohesin monomers bind to the loader rather frequently and cohesin dimers bind to this site only occasionally. Our theory predicts that a cohesin dimer extrudes loops by the osmotic pressure of cohesin monomers on the chromatin fiber between the two connected rings. With this mechanism, the frequency of the interactions between chromatin segments depends on the loading and unloading rates of dimers at the corresponding sites.

  16. Feedback Loop Gains and Feedback Behavior (1996)

    DEFF Research Database (Denmark)

    Kampmann, Christian Erik

    2012-01-01

    Linking feedback loops and system behavior is part of the foundation of system dynamics, yet the lack of formal tools has so far prevented a systematic application of the concept, except for very simple systems. Having such tools at their disposal would be a great help to analysts in understanding...... large, complicated simulation models. The paper applies tools from graph theory formally linking individual feedback loop strengths to the system eigenvalues. The significance of a link or a loop gain and an eigenvalue can be expressed in the eigenvalue elasticity, i.e., the relative change...... of an eigenvalue resulting from a relative change in the gain. The elasticities of individual links and loops may be found through simple matrix operations on the linearized system. Even though the number of feedback loops can grow rapidly with system size, reaching astronomical proportions even for modest systems...

  17. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  18. A kinematic view of loop closure.

    Science.gov (United States)

    Coutsias, Evangelos A; Seok, Chaok; Jacobson, Matthew P; Dill, Ken A

    2004-03-01

    We consider the problem of loop closure, i.e., of finding the ensemble of possible backbone structures of a chain segment of a protein molecule that is geometrically consistent with preceding and following parts of the chain whose structures are given. We reduce this problem of determining the loop conformations of six torsions to finding the real roots of a 16th degree polynomial in one variable, based on the robotics literature on the kinematics of the equivalent rotator linkage in the most general case of oblique rotators. We provide a simple intuitive view and derivation of the polynomial for the case in which each of the three pair of torsional axes has a common point. Our method generalizes previous work on analytical loop closure in that the torsion angles need not be consecutive, and any rigid intervening segments are allowed between the free torsions. Our approach also allows for a small degree of flexibility in the bond angles and the peptide torsion angles; this substantially enlarges the space of solvable configurations as is demonstrated by an application of the method to the modeling of cyclic pentapeptides. We give further applications to two important problems. First, we show that this analytical loop closure algorithm can be efficiently combined with an existing loop-construction algorithm to sample loops longer than three residues. Second, we show that Monte Carlo minimization is made severalfold more efficient by employing the local moves generated by the loop closure algorithm, when applied to the global minimization of an eight-residue loop. Our loop closure algorithm is freely available at http://dillgroup. ucsf.edu/loop_closure/. Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 510-528, 2004

  19. Structural and dynamic characterization of the upper part of the HIV-1 cTAR DNA hairpin

    OpenAIRE

    Zargarian, Loussin?; Kanevsky, Igor; Bazzi, Ali; Boynard, Jonathan; Chaminade, Fran?oise; Foss?, Philippe; Mauffret, Olivier

    2009-01-01

    First strand transfer is essential for HIV-1 reverse transcription. During this step, the TAR RNA hairpin anneals to the cTAR DNA hairpin; this annealing reaction is promoted by the nucleocapsid protein and involves an initial loop?loop interaction between the apical loops of TAR and cTAR. Using NMR and probing methods, we investigated the structural and dynamic properties of the top half of the cTAR DNA (mini-cTAR). We show that the upper stem located between the apical and the internal loop...

  20. Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

    Science.gov (United States)

    Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

    2010-01-01

    The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

  1. What Is Mitochondrial DNA?

    Science.gov (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  2. Like-charge attraction and opposite-charge decomplexation between polymers and DNA molecules

    OpenAIRE

    Buyukdagli, Sahin

    2016-01-01

    We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test charge theory to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for one-loop level electrostatic correlation effects such as the ionic cloud deformation around the strongly charged DNA molecule as well as image-charge forces induced by the low DNA permittivity. Our model can reproduce and explain various characteristics of the...

  3. TS LOOP ALCOVE VENTILATION ANALYSIS

    International Nuclear Information System (INIS)

    T.M. Lahnalampi

    2000-01-01

    The scope of this analysis is to examine the existing, constructor installed, physical ventilation installations located in each of the Exploratory Studies Facility (ESF) Topopah Springs (TS) Loop Alcoves No.1, No.2, No.3, No.4, No.6, and No.7. Alcove No.5 is excluded from the scope of this analysis since it is an A/E design system. Each ventilation installation will be analyzed for the purpose of determining if requirements for acceptance into the A/E design technical baseline have been met. The ventilation installations will be evaluated using Occupational Safety and Health Administration (OSHA) standards and Exploratory Studies Facility Design Requirements (ESFDR) (YMP 1997) requirements. The end product will be a technical analysis that will define ventilation installation compliance issues, any outstanding field changes, and use-as-is design deviations that are required to bring the ventilation installations into compliance with requirements for acceptance into the A/E design technical baseline. The analysis will provide guidance for alcove ventilation component design modifications to be developed to correct any deficient components that do not meet minimum requirements and standards

  4. Loops in hierarchical channel networks

    Science.gov (United States)

    Katifori, Eleni; Magnasco, Marcelo

    2012-02-01

    Nature provides us with many examples of planar distribution and structural networks having dense sets of closed loops. An archetype of this form of network organization is the vasculature of dicotyledonous leaves, which showcases a hierarchically-nested architecture. Although a number of methods have been proposed to measure aspects of the structure of such networks, a robust metric to quantify their hierarchical organization is still lacking. We present an algorithmic framework that allows mapping loopy networks to binary trees, preserving in the connectivity of the trees the architecture of the original graph. We apply this framework to investigate computer generated and natural graphs extracted from digitized images of dicotyledonous leaves and animal vasculature. We calculate various metrics on the corresponding trees and discuss the relationship of these quantities to the architectural organization of the original graphs. This algorithmic framework decouples the geometric information from the metric topology (connectivity and edge weight) and it ultimately allows us to perform a quantitative statistical comparison between predictions of theoretical models and naturally occurring loopy graphs.

  5. Towards conformal loop quantum gravity

    International Nuclear Information System (INIS)

    Wang, Charles H-T

    2006-01-01

    A discussion is given of recent developments in canonical gravity that assimilates the conformal analysis of gravitational degrees of freedom. The work is motivated by the problem of time in quantum gravity and is carried out at the metric and the triad levels. At the metric level, it is shown that by extending the Arnowitt-Deser-Misner (ADM) phase space of general relativity (GR), a conformal form of geometrodynamics can be constructed. In addition to the Hamiltonian and Diffeomorphism constraints, an extra first class constraint is introduced to generate conformal transformations. This phase space consists of York's mean extrinsic curvature time, conformal three-metric and their momenta. At the triad level, the phase space of GR is further enlarged by incorporating spin-gauge as well as conformal symmetries. This leads to a canonical formulation of GR using a new set of real spin connection variables. The resulting gravitational constraints are first class, consisting of the Hamiltonian constraint and the canonical generators for spin-gauge and conformorphism transformations. The formulation has a remarkable feature of being parameter-free. Indeed, it is shown that a conformal parameter of the Barbero-Immirzi type can be absorbed by the conformal symmetry of the extended phase space. This gives rise to an alternative approach to loop quantum gravity that addresses both the conceptual problem of time and the technical problem of functional calculus in quantum gravity

  6. Biomolecular and Structural Analyses of Cauliflower-like DNAs by Ultraviolet, Circular Dichroism, and Fluorescence Spectroscopies in Comparison with Natural DNA

    OpenAIRE

    Gill, Pooria; Ranjbar, Bijan; Saber, Reza; Khajeh, Khosro; Mohammadian, Mehdi

    2011-01-01

    Cauliflower-like DNAs are stem-loop DNAs that are fabricated periodically in inverted repetitions from deoxyribonucleic acid phosphates (dNTPs) by loop-mediated isothermal amplification (LAMP). Cauliflower-like DNAs have ladder-shape behaviors on gel electrophoresis, and increasing the time of LAMP leads to multiplying the repetitions, stem-loops, and electrophoretic bands. Cauliflower-like DNAs were fabricated via LAMP using two loop primers, two bumper primers, dNTPs, a λ-phage DNA template...

  7. Stability, structure, and evolution of cool loops

    International Nuclear Information System (INIS)

    Cally, P.S.; Robb, T.D.

    1991-01-01

    The criteria for the existence and stability of cool loops are reexamined. It is found that the stability of the loops strongly depends on the form of the heating and radiative loss functions and that if the Ly-alpha peak which appears in most calculations of the radiative loss function is real, cool loops are almost certainly unstable. Removing the hydrogen contribution from the recent loss function Q(T) by Cook et al. (1989) does not produce the much-used result, Q proportional to T-cubed, which is so favorable to cool loop stability. Even using the probably unrealistically favorable loss function Q1 of Cook et al. with the hydrogen contribution removed, the maximum temperature attainable in stable cool loops is a factor of 2-3 too small to account for the excess emission observed in lower transition region lines. Dynamical simulations of cool loop instabilities reveal that the final state of such a model is the hot loop equilibrium. 26 refs

  8. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

    Science.gov (United States)

    Sanborn, Adrian; Rao, Suhas; Huang, Su-Chen; Durand, Neva; Huntley, Miriam; Jewett, Andrew; Bochkov, Ivan; Chinnappan, Dharmaraj; Cutkosky, Ashok; Li, Jian; Geeting, Kristopher; McKenna, Doug; Stamenova, Elena; Gnirke, Andreas; Melnikov, Alexandre; Lander, Eric; Aiden, Erez

    Our recent kilobase-resolution genome-wide maps of DNA self-contacts demonstrated that mammalian genomes are organized into domains and loops demarcated by the DNA-binding protein CTCF. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that domains are inconsistent with equilibrium and fractal models. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during condensation leads to formation of an anisotropic ``tension globule.'' In the other, CTCF and cohesin act together to extrude unknotted loops. Both models are consistent with the observed domains and loops. However, the extrusion model explains a far wider array of observations, such as why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The extrusion model predicts in silico the experimental maps using only CTCF-binding sites. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.

  9. The cell pole: the site of cross talk between the DNA uptake and genetic recombination machinery.

    Science.gov (United States)

    Kidane, Dawit; Ayora, Silvia; Sweasy, Joann B; Graumann, Peter L; Alonso, Juan C

    2012-01-01

    Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as "guardians", protects ssDNA from degradation and limit the RecA recombinase loading. Then, the "mediators" overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by "modulators", catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or "resolver" cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the "rescuers" will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective.

  10. Loop-quantum-gravity vertex amplitude.

    Science.gov (United States)

    Engle, Jonathan; Pereira, Roberto; Rovelli, Carlo

    2007-10-19

    Spin foam models are hoped to provide the dynamics of loop-quantum gravity. However, the most popular of these, the Barrett-Crane model, does not have the good boundary state space and there are indications that it fails to yield good low-energy n-point functions. We present an alternative dynamics that can be derived as a quantization of a Regge discretization of Euclidean general relativity, where second class constraints are imposed weakly. Its state space matches the SO(3) loop gravity one and it yields an SO(4)-covariant vertex amplitude for Euclidean loop gravity.

  11. Technical specification of HANARO fuel test loop

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J. Y

    1998-03-01

    The design and installation of the irradiation test facility for verification test of the fuel performance are very important in connection with maximization of the utilization of HANARO. HANARO fuel test loop was designed in accordance with the same code and standards of nuclear power plant because HANARO FTL will be operated the high pressure and temperature same as nuclear power plant operation conditions. The objective of this study is to confirm the operation limit, safety limit, operation condition and checking points of HANARO fuel test loop. This results will become guidances for the planning of irradiation testing and operation of HANARO fuel test loop. (author). 13 refs., 13 tabs., 8 figs.

  12. Numerical approach to one-loop integrals

    International Nuclear Information System (INIS)

    Fujimoto, Junpei; Shimizu, Yoshimitsu; Kato, Kiyoshi; Oyanagi, Yoshio.

    1992-01-01

    Two numerical methods are proposed for the calculation of one-loop scalar integrals. In the first method, the singularity is cancelled by the symmetrization of the integrand and the integration is done by a Monte-Carlo method. In the second one, after the transform of the integrand into a standard form, the integral is reduced into a regular numerical integral. These methods provide us practical tools to evaluate one-loop Feynman diagrams with desired numerical accuracy. They are extended to the integral with numerator and the treatment of the one-loop virtual correction to the cross section is also presented. (author)

  13. Zero point energy of renormalized Wilson loops

    International Nuclear Information System (INIS)

    Hidaka, Yoshimasa; Pisarski, Robert D.

    2009-01-01

    The quark-antiquark potential, and its associated zero point energy, can be extracted from lattice measurements of the Wilson loop. We discuss a unique prescription to renormalize the Wilson loop, for which the perturbative contribution to the zero point energy vanishes identically. A zero point energy can arise nonperturbatively, which we illustrate by considering effective string models. The nonperturbative contribution to the zero point energy vanishes in the Nambu model, but is nonzero when terms for extrinsic curvature are included. At one loop order, the nonperturbative contribution to the zero point energy is negative, regardless of the sign of the extrinsic curvature term.

  14. Loop corrections to primordial non-Gaussianity

    Science.gov (United States)

    Boran, Sibel; Kahya, E. O.

    2018-02-01

    We discuss quantum gravitational loop effects to observable quantities such as curvature power spectrum and primordial non-Gaussianity of cosmic microwave background (CMB) radiation. We first review the previously shown case where one gets a time dependence for zeta-zeta correlator due to loop corrections. Then we investigate the effect of loop corrections to primordial non-Gaussianity of CMB. We conclude that, even with a single scalar inflaton, one might get a huge value for non-Gaussianity which would exceed the observed value by at least 30 orders of magnitude. Finally we discuss the consequences of this result for scalar driven inflationary models.

  15. Sigma models and renormalization of string loops

    International Nuclear Information System (INIS)

    Tseytlin, A.A.

    1989-05-01

    An extension of the ''σ-model β-functions - string equations of motion'' correspondence to the string loop level is discussed. Special emphasis is made on how the renormalization group acts in string loops and, in particular, on the renormalizability property of the generating functional Z-circumflex for string amplitudes (related to the σ model partition function integrated over moduli). Renormalization of Z-circumflex at one and two loop order is analyzed in some detail. We also discuss an approach to renormalization based on operators of insertion of topological fixtures. (author). 70 refs

  16. Construction of the blowdown and condensation loop

    Energy Technology Data Exchange (ETDEWEB)

    Park, Choon Kyung; Song, Chul Kyung; Cho, Seok; Chun, S. Y.; Chung, Moon Ki

    1997-12-01

    The blowdown and condensation loop (B and C loop) has been constructed to get experimental data for designing the safety depressurization system (SDS) and steam sparger which are considered to implement in the Korea Next Generation Reactor (KNGR). In this report, system description on the B and C loop is given in detail, which includes the drawings and technical specification of each component, instrumentation and control system, and the operational procedures and the results of the performance testing. (author). 7 refs., 11 tabs., 48 figs.

  17. Study of mitochondria D-loop gene to detect the heterogeneity of gemak in Turnicidae family

    Science.gov (United States)

    Setiati, N.; Partaya

    2018-03-01

    As a part of life biodiversity, birds in Turnicidae family should be preserved from the extinction and its type heterogeneity decline. One effort for giving the strategic base of plasma nutfah conservation is through genetic heterogeneity study. The aim of the research is to analyze D-loop gen from DNA mitochondria of gemak bird in Turnicidae family molecularly. From the result of the analysis, it may be known the genetic heterogeneity of gemak bird based on the sequence of D-loop gen. The collection of both types of gemak of Turnicidae family is still easy since we can find them in ricefield area after harvest particularly for Gemakloreng (Turnix sylvatica), it means while gemak tegalan (Turnixsusciator) is getting difficult to find. Based on the above DNA quantification standard, the blood sample of Gemak in this research is mostly grouped into pure blood (ranges from 1,63 – 1,90), and it deserves to be used for PCR analysis. The sequencing analysis has not detected the sequence of nucleotide completely. However, it indicates sequence polymorphism of base as the arranger of D-loop gen. D-loop gen may identify genetic heterogeneity of gemak bird of Turnicidae family, but it is necessary to perform further sequencing analysis with PCR-RFLP technique. This complete nucleotide sequence is obtained and easy to detect after being cut restriction enzyme.

  18. Eigenvalue distributions of Wilson loops

    International Nuclear Information System (INIS)

    Lohmayer, Robert

    2010-01-01

    In the first part of this thesis, we focus on the distribution of the eigenvalues of the unitary Wilson loop matrix in the two-dimensional case at arbitrary finite N. To characterize the distribution of the eigenvalues, we introduce three density functions (the ''symmetric'', the ''antisymmetric'', and the ''true'' eigenvalue density) which differ at finite N but possess the same infinite-N limit, exhibiting the Durhuus-Olesen phase transition. Using expansions of determinants and inverse determinants in characters of totally symmetric or totally antisymmetric representations of SU(N), the densities at finite N can be expressed in terms of simple sums involving only dimensions and quadratic Casimir invariants of certain irreducible representations of SU(N), allowing for a numerical computation of the densities at arbitrary N to any desired accuracy. We find that the true eigenvalue density, adding N oscillations to the monotonic symmetric density, is in some sense intermediate between the symmetric and the antisymmetric density, which in turn is given by a sum of N delta peaks located at the zeros of the average of the characteristic polynomial. Furthermore, we show that the dependence on N can be made explicit by deriving integral representations for the resolvents associated to the three eigenvalue densities. Using saddle-point approximations, we confirm that all three densities reduce to the Durhuus-Olesen result in the infinite-N limit. In the second part, we study an exponential form of the multiplicative random complex matrix model introduced by Gudowska-Nowak et al. Varying a parameter which can be identified with the area of the Wilson loop in the unitary case, the region of non-vanishing eigenvalue density of the N-dimensional complex product matrix undergoes a topological change at a transition point in the infinite-N limit. We study the transition by a detailed analysis of the average of the modulus square of the characteristic polynomial. Furthermore

  19. Eigenvalue distributions of Wilson loops

    Energy Technology Data Exchange (ETDEWEB)

    Lohmayer, Robert

    2010-07-01

    In the first part of this thesis, we focus on the distribution of the eigenvalues of the unitary Wilson loop matrix in the two-dimensional case at arbitrary finite N. To characterize the distribution of the eigenvalues, we introduce three density functions (the ''symmetric'', the ''antisymmetric'', and the ''true'' eigenvalue density) which differ at finite N but possess the same infinite-N limit, exhibiting the Durhuus-Olesen phase transition. Using expansions of determinants and inverse determinants in characters of totally symmetric or totally antisymmetric representations of SU(N), the densities at finite N can be expressed in terms of simple sums involving only dimensions and quadratic Casimir invariants of certain irreducible representations of SU(N), allowing for a numerical computation of the densities at arbitrary N to any desired accuracy. We find that the true eigenvalue density, adding N oscillations to the monotonic symmetric density, is in some sense intermediate between the symmetric and the antisymmetric density, which in turn is given by a sum of N delta peaks located at the zeros of the average of the characteristic polynomial. Furthermore, we show that the dependence on N can be made explicit by deriving integral representations for the resolvents associated to the three eigenvalue densities. Using saddle-point approximations, we confirm that all three densities reduce to the Durhuus-Olesen result in the infinite-N limit. In the second part, we study an exponential form of the multiplicative random complex matrix model introduced by Gudowska-Nowak et al. Varying a parameter which can be identified with the area of the Wilson loop in the unitary case, the region of non-vanishing eigenvalue density of the N-dimensional complex product matrix undergoes a topological change at a transition point in the infinite-N limit. We study the transition by a detailed analysis of the average of the

  20. Detection of HbsAg and hATIII genetically modified goats (Caprahircus) by loop-mediated isothermal amplification.

    Science.gov (United States)

    Tao, Chenyu; Zhang, Qingde; Zhai, Shanli; Liu, Bang

    2013-11-01

    In this study, sensitive and rapid detection systems were designed using a loop-mediated isothermal amplification (LAMP) method to detect the genetically modified goats. A set of 4 primers were designed for each exogenous nucleic acids HBsAg and hATIII. The DNA samples were first amplified with the outer and inner primers and released a single-stranded DNA,of which both ends were stem-loop structure. Then one inner primer hybridized with the loop, and initiated displacement synthesis in less than 1 h. The result could be visualized by both agarose gel electrophoresis and unaided eyes directly after adding SYBR GREEN 1. The detection limit of LAMP was ten copies of target molecules, indicating that LAMP was tenfold more sensitive than the classical PCR. Furthermore, all the samples of genetically modified goats were tested positively by LAMP, and the results demonstrated that the LAMP was a rapid and sensitive method for detecting the genetically modified organism.

  1. Evaluation of a loop-mediated isothermal amplification (LAMP) method for rapid on-site detection of horse meat

    NARCIS (Netherlands)

    Aartse, Aafke; Scholtens-Toma, Ingrid; A, van der Hans J.G.; Boersma-Greve, Monique M.; Prins, Theo W.; Ginkel, van Leen A.; Kok, Esther J.; Bovee, Toine F.H.

    2017-01-01

    Detection of horse DNA by loop-mediated isothermal amplification (LAMP) seems one of the most promising methods to meet the criteria of fast, robust, cost efficient, specific, and sensitive on-site detection. In the present study an assessment of the specificity and sensitivity of the LAMP horse

  2. Loop-mediated isothermal amplification (LAMP): Early detection of Toxoplasma gondii infection in mice

    OpenAIRE

    Kong, Qing-Ming; Lu, Shao-Hong; Tong, Qun-Bo; Lou, Di; Chen, Rui; Zheng, Bin; Kumagai, Takashi; Wen, Li-Yong; Ohta, Nobuo; Zhou, Xiao-Nong

    2012-01-01

    Abstract Background Toxoplasmosis is a widespread zoonotic parasitic disease that occurs in both animals and humans. Traditional molecular assays are often difficult to perform, especially for the early diagnosis of Toxoplasma gondii infections. Here, we established a novel loop-mediated isothermal amplification targeting the 529 bp repeat element (529 bp-LAMP) to detect T. gondii DNA in blood samples of experimental mice infected with tachyzoites of the RH strain. Findings The assay was perf...

  3. An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community

    KAUST Repository

    Wang, Yong

    2016-02-23

    The low biomass in environmental samples is a major challenge for microbial metagenomic studies. The amplification of a genomic DNA was frequently applied to meeting the minimum requirement of the DNA for a high-throughput next-generation-sequencing technology. Using a synthetic bacterial community, the amplification efficiency of the Multiple Annealing and Looping Based Amplification Cycles (MALBAC) kit that is originally developed to amplify the single-cell genomic DNA of mammalian organisms is examined. The DNA template of 10 pg in each reaction of the MALBAC amplification may generate enough DNA for Illumina sequencing. Using 10 pg and 100 pg templates for each reaction set, the MALBAC kit shows a stable and homogeneous amplification as indicated by the highly consistent coverage of the reads from the two amplified samples on the contigs assembled by the original unamplified sample. Although GenomePlex whole genome amplification kit allows one to generate enough DNA using 100 pg of template in each reaction, the minority of the mixed bacterial species is not linearly amplified. For both of the kits, the GC-rich regions of the genomic DNA are not efficiently amplified as suggested by the low coverage of the contigs with the high GC content. The high efficiency of the MALBAC kit is supported for the amplification of environmental microbial DNA samples, and the concerns on its application are also raised to bacterial species with the high GC content.

  4. Genome-Derived Cytosolic DNA Mediates Type I Interferon-Dependent Rejection of B Cell Lymphoma Cells

    Directory of Open Access Journals (Sweden)

    Yu J. Shen

    2015-04-01

    Full Text Available The DNA damage response (DDR induces the expression of type I interferons (IFNs, but the underlying mechanisms are poorly understood. Here, we show the presence of cytosolic DNA in different mouse and human tumor cells. Treatment of cells with genotoxic agents increased the levels of cytosolic DNA in a DDR-dependent manner. Cloning of cytosolic DNA molecules from mouse lymphoma cells suggests that cytosolic DNA is derived from unique genomic loci and has the potential to form non-B DNA structures, including R-loops. Overexpression of Rnaseh1, which resolves R-loops, reduced the levels of cytosolic DNA, type I Ifn transcripts, and type I IFN-dependent rejection of lymphoma cells. Live-cell imaging showed a dynamic contact of cytosolic DNA with mitochondria, an important organelle for innate immune recognition of cytosolic nucleotides. In summary, we found that cytosolic DNA is present in many tumor cells and contributes to the immunogenicity of tumor cells.

  5. A cryptic targeting signal creates a mitochondrial FEN1 isoform with tailed R-Loop binding properties.

    Directory of Open Access Journals (Sweden)

    Lawrence Kazak

    Full Text Available A growing number of DNA transacting proteins is found in the nucleus and in mitochondria, including the DNA repair and replication protein Flap endonuclease 1, FEN1. Here we show a truncated FEN1 isoform is generated by alternative translation initiation, exposing a mitochondrial targeting signal. The shortened form of FEN1, which we term FENMIT, localizes to mitochondria, based on import into isolated organelles, immunocytochemistry and subcellular fractionation. In vitro FENMIT binds to flap structures containing a 5' RNA flap, and prefers such substrates to single-stranded RNA. FENMIT can also bind to R-loops, and to a lesser extent to D-loops. Exposing human cells to ethidium bromide results in the generation of RNA/DNA hybrids near the origin of mitochondrial DNA replication. FENMIT is recruited to the DNA under these conditions, and is released by RNase treatment. Moreover, high levels of recombinant FENMIT expression inhibit mtDNA replication, following ethidium bromide treatment. These findings suggest FENMIT interacts with RNA/DNA hybrids in mitochondrial DNA, such as those found at the origin of replication.

  6. The Universal One-Loop Effective Action

    CERN Document Server

    Drozd, Aleksandra; Quevillon, Jérémie; You, Tevong

    2016-01-01

    We present the universal one-loop effective action for all operators of dimension up to six obtained by integrating out massive, non-degenerate multiplets. Our general expression may be applied to loops of heavy fermions or bosons, and has been checked against partial results available in the literature. The broad applicability of this approach simplifies one-loop matching from an ultraviolet model to a lower-energy effective field theory (EFT), a procedure which is now reduced to the evaluation of a combination of matrices in our universal expression, without any loop integrals to evaluate. We illustrate the relationship of our results to the Standard Model (SM) EFT, using as an example the supersymmetric stop and sbottom squark Lagrangian and extracting from our universal expression the Wilson coefficients of dimension-six operators composed of SM fields.

  7. The universal one-loop effective action

    International Nuclear Information System (INIS)

    Drozd, Aleksandra; Ellis, John; Quevillon, Jérémie; You, Tevong

    2016-01-01

    We present the universal one-loop effective action for all operators of dimension up to six obtained by integrating out massive, non-degenerate multiplets. Our general expression may be applied to loops of heavy fermions or bosons, and has been checked against partial results available in the literature. The broad applicability of this approach simplifies one-loop matching from an ultraviolet model to a lower-energy effective field theory (EFT), a procedure which is now reduced to the evaluation of a combination of matrices in our universal expression, without any loop integrals to evaluate. We illustrate the relationship of our results to the Standard Model (SM) EFT, using as an example the supersymmetric stop and sbottom squark Lagrangian and extracting from our universal expression the Wilson coefficients of dimension-six operators composed of SM fields.

  8. Mathematical Modeling of Loop Heat Pipes

    Science.gov (United States)

    Kaya, Tarik; Ku, Jentung; Hoang, Triem T.; Cheung, Mark L.

    1998-01-01

    The primary focus of this study is to model steady-state performance of a Loop Heat Pipe (LHP). The mathematical model is based on the steady-state energy balance equations at each component of the LHP. The heat exchange between each LHP component and the surrounding is taken into account. Both convection and radiation environments are modeled. The loop operating temperature is calculated as a function of the applied power at a given loop condition. Experimental validation of the model is attempted by using two different LHP designs. The mathematical model is tested at different sink temperatures and at different elevations of the loop. Tbc comparison of the calculations and experimental results showed very good agreement (within 3%). This method proved to be a useful tool in studying steady-state LHP performance characteristics.

  9. CHY loop integrands from holomorphic forms

    Energy Technology Data Exchange (ETDEWEB)

    Gomez, Humberto [Facultad de Ciencias Basicas, Universidad Santiago de Cali,Calle 5 62-00 Barrio Pampalinda, Cali, Valle (Colombia); Perimeter Institute for Theoretical Physics,31 Caroline Street N, Waterloo, ON N2L 2Y5 (Canada); Mizera, Sebastian; Zhang, Guojun [Perimeter Institute for Theoretical Physics,31 Caroline Street N, Waterloo, ON N2L 2Y5 (Canada); Department of Physics & Astronomy, University of Waterloo,Waterloo, ON N2L 3G1 (Canada)

    2017-03-16

    Recently, the Cachazo-He-Yuan (CHY) approach for calculating scattering amplitudes has been extended beyond tree level. In this paper, we introduce a way of constructing CHY integrands for Φ{sup 3} theory up to two loops from holomorphic forms on Riemann surfaces. We give simple rules for translating Feynman diagrams into the corresponding CHY integrands. As a complementary result, we extend the L-algorithm, originally introduced in https://arxiv.org/abs/1604.05373, to two loops. Using this approach, we are able to analytically verify our prescription for the CHY integrands up to seven external particles at two loops. In addition, it gives a natural way of extending to higher-loop orders.

  10. Observing string breaking with Wilson loops

    CERN Document Server

    Kratochvila, S; Kratochvila, Slavo; Forcrand, Philippe de

    2003-01-01

    An uncontroversial observation of adjoint string breaking is proposed, while measuring the static potential from Wilson loops only. The overlap of the Wilson loop with the broken-string state is small, but non-vanishing, so that the broken-string groundstate can be seen if the Wilson loop is long enough. We demonstrate this in the context of the (2+1)d SU(2) adjoint static potential, using an improved version of the Luscher-Weisz exponential variance reduction. To complete the picture we perform the more usual multichannel analysis with two basis states, the unbroken-string state and the broken-string state (two so-called gluelumps). As by-products, we obtain the temperature-dependent static potential measured from Polyakov loop correlations, and the fundamental SU(2) static potential with improved accuracy. Comparing the latter with the adjoint potential, we see clear deviations from Casimir scaling.

  11. Hardware-in-the-Loop Testing

    Data.gov (United States)

    Federal Laboratory Consortium — RTC has a suite of Hardware-in-the Loop facilities that include three operational facilities that provide performance assessment and production acceptance testing of...

  12. Loop Diuretics in the Treatment of Hypertension.

    Science.gov (United States)

    Malha, Line; Mann, Samuel J

    2016-04-01

    Loop diuretics are not recommended in current hypertension guidelines largely due to the lack of outcome data. Nevertheless, they have been shown to lower blood pressure and to offer potential advantages over thiazide-type diuretics. Torsemide offers advantages of longer duration of action and once daily dosing (vs. furosemide and bumetanide) and more reliable bioavailability (vs. furosemide). Studies show that the previously employed high doses of thiazide-type diuretics lower BP more than furosemide. Loop diuretics appear to have a preferable side effect profile (less hyponatremia, hypokalemia, and possibly less glucose intolerance). Studies comparing efficacy and side effect profiles of loop diuretics with the lower, currently widely prescribed, thiazide doses are needed. Research is needed to fill gaps in knowledge and common misconceptions about loop diuretic use in hypertension and to determine their rightful place in the antihypertensive arsenal.

  13. Possible hysteresis loops of resonatorless optical bistability

    International Nuclear Information System (INIS)

    Nguyen Ba An; Le Thi Cat Tuong.

    1990-05-01

    We qualitatively show that hysteresis loops of intrinsic optical bistability phenomena without any additional feedback may be of various shapes including those of a butterfly and a three-winged bow. (author). 15 refs, 4 figs

  14. Closed loop solar chemical heat pipe

    International Nuclear Information System (INIS)

    Levy, M.; Levitan, R.; Rosin, H.; Rubin, R.

    1991-01-01

    The system used for the closed loop operation of the solar chemical heat pipe comprises a reformer, heated by the solar furnace, a methanator and a storage assembly containing a compressor and storage cylinders. (authors). 7 figs

  15. Nonequilibrium Chromosome Looping via Molecular Slip Links

    Science.gov (United States)

    Brackley, C. A.; Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

    2017-09-01

    We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.

  16. A theory of desynchronisable closed loop system

    Directory of Open Access Journals (Sweden)

    Harsh Beohar

    2010-10-01

    Full Text Available The task of implementing a supervisory controller is non-trivial, even though different theories exist that allow automatic synthesis of these controllers in the form of automata. One of the reasons for this discord is due to the asynchronous interaction between a plant and its controller in implementations, whereas the existing supervisory control theories assume synchronous interaction. As a consequence the implementation suffer from the so-called inexact synchronisation problem. In this paper we address the issue of inexact synchronisation in a process algebraic setting, by solving a more general problem of refinement. We construct an asynchronous closed loop system by introducing a communication medium in a given synchronous closed loop system. Our goal is to find sufficient conditions under which a synchronous closed loop system is branching bisimilar to its corresponding asynchronous closed loop system.

  17. Plasmid DNA Delivery: Nanotopography Matters.

    Science.gov (United States)

    Song, Hao; Yu, Meihua; Lu, Yao; Gu, Zhengying; Yang, Yannan; Zhang, Min; Fu, Jianye; Yu, Chengzhong

    2017-12-20

    Plasmid DNA molecules with unique loop structures have widespread bioapplications, in many cases relying heavily on delivery vehicles to introduce them into cells and achieve their functions. Herein, we demonstrate that control over delicate nanotopography of silica nanoparticles as plasmid DNA vectors has significant impact on the transfection efficacy. For silica nanoparticles with rambutan-, raspberry-, and flower-like morphologies composed of spike-, hemisphere-, and bowl-type subunit nanotopographies, respectively, the rambutan-like nanoparticles with spiky surfaces demonstrate the highest plasmid DNA binding capability and transfection efficacy of 88%, higher than those reported for silica-based nanovectors. Moreover, it is shown that the surface spikes of rambutan nanoparticles provide a continuous open space to bind DNA chains via multivalent interactions and protect the gene molecules sheltered in the spiky layer against nuclease degradation, exhibiting no significant transfection decay. This unique protection feature is in great contrast to a commercial transfection agent with similar transfection performance but poor protection capability against enzymatic cleavage. Our study provides new understandings in the rational design of nonviral vectors for efficient gene delivery.

  18. Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA.

    Science.gov (United States)

    Pedersen, Hege Lynum; Johnson, Kenneth A; McVey, Colin E; Leiros, Ingar; Moe, Elin

    2015-10-01

    Uracil-DNA N-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacterium Deinococcus radiodurans (DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity between DrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well diffracting crystals. The DNA in the co-crystal structure contained an abasic site (substrate product) flipped into the active site of the enzyme, with no uracil in the active-site pocket. Despite the high resolution, it was not possible to fit all of the terminal nucleotides of the DNA complex into electron density owing to disorder caused by a lack of stabilizing interactions. However, the DNA which was in contact with the enzyme, close to the active site, was well ordered and allowed detailed analysis of the enzyme-DNA interaction. The complex revealed that the interaction between DrUNG and DNA is similar to that in the previously determined crystal structure of human UNG (hUNG) in complex with DNA [Slupphaug et al. (1996). Nature (London), 384, 87-92]. Substitutions in a (here defined) variable part of the leucine loop result in a shorter loop (eight residues instead of nine) in DrUNG compared with hUNG; regardless of this, it seems to fulfil its role and generate a stabilizing force with the minor groove upon flipping out of the damaged base into the active site. The structure also provides a rationale for the previously observed high catalytic efficiency of DrUNG caused by high substrate affinity by demonstrating an increased number of long-range electrostatic interactions between the enzyme and the DNA. Interestingly, specific interactions between residues

  19. A mitosis-specific and R loop-driven ATR pathway promotes faithful chromosome segregation.

    Science.gov (United States)

    Kabeche, Lilian; Nguyen, Hai Dang; Buisson, Rémi; Zou, Lee

    2018-01-05

    The ataxia telangiectasia mutated and Rad3-related (ATR) kinase is crucial for DNA damage and replication stress responses. Here, we describe an unexpected role of ATR in mitosis. Acute inhibition or degradation of ATR in mitosis induces whole-chromosome missegregation. The effect of ATR ablation is not due to altered cyclin-dependent kinase 1 (CDK1) activity, DNA damage responses, or unscheduled DNA synthesis but to loss of an ATR function at centromeres. In mitosis, ATR localizes to centromeres through Aurora A-regulated association with centromere protein F (CENP-F), allowing ATR to engage replication protein A (RPA)-coated centromeric R loops. As ATR is activated at centromeres, it stimulates Aurora B through Chk1, preventing formation of lagging chromosomes. Thus, a mitosis-specific and R loop-driven ATR pathway acts at centromeres to promote faithful chromosome segregation, revealing functions of R loops and ATR in suppressing chromosome instability. Copyright © 2018, American Association for the Advancement of Science.

  20. Mitochondrial D-loop sequence of domesticated waterfowl in Central Java: goose and muscovy duck

    Science.gov (United States)

    Susanti, R.; Iswari, R. S.

    2018-03-01

    This study aims to determine the genetic characterization of domesticated waterfowl (goose and Muscovy duck) in Central Java based on a D-loop mtDNA gene. The D-loop gene was amplified using PCR technique by specific primer and sequenced using dideoxy termination method. Multiple alignments of D-loop gene obtained were 710 nucleotides at position 74 to 783 at the 5’ end (for goose) and 712 nucleotides at position 48 to 759 at the 5’ end (for Muscovy duck). The results of the polymorphism analysis on D-loop sequences of muscovy duck produced 3 haplotypes. In the D-loop gene of goose does not show polymorphism, with substitution at G117A. Phylogenetic trees reconstructions of goose and Muscovy duck, which was collected during this research compared with another species from Anser, Chairina and Anas was generated 2 forms of clusters. The first group consists of all kind of Muscovy duck together with Chairina moschata and Anas, while the second group consists of all geese and Anser cygnoides the other. The determination of Muscovy duck and geese identity can be distinguished from the genetic marker information. Based on the phylogenetic analysis, it can be concluded that the Muscovy duck is closely related to Chairina moschata, while geese is closely related to Anser cygnoides.

  1. A multiple-pass ring oscillator based dual-loop phase-locked loop

    International Nuclear Information System (INIS)

    Chen Danfeng; Ren Junyan; Deng Jingjing; Li Wei; Li Ning

    2009-01-01

    A dual-loop phase-locked loop (PLL) for wideband operation is proposed. The dual-loop architecture combines a coarse-tuning loop with a fine-tuning one, enabling a wide tuning range and low voltage-controlled oscillator (VCO) gain without poisoning phase noise and reference spur suppression performance. An analysis of the phase noise and reference spur of the dual-loop PLL is emphasized. A novel multiple-pass ring VCO is designed for the dual-loop application. It utilizes both voltage-control and current-control simultaneously in the delay cell. The PLL is fabricated in Jazz 0.18-μm RF CMOS technology. The measured tuning range is from 4.2 to 5.9 GHz. It achieves a low phase noise of -99 dBc/Hz - 1 MHz offset from a 5.5 GHz carrier.

  2. A multiple-pass ring oscillator based dual-loop phase-locked loop

    Energy Technology Data Exchange (ETDEWEB)

    Chen Danfeng; Ren Junyan; Deng Jingjing; Li Wei; Li Ning, E-mail: dfchen@fudan.edu.c [State Key Laboratory of ASIC and System, Fudan University, Shanghai 201203 (China)

    2009-10-15

    A dual-loop phase-locked loop (PLL) for wideband operation is proposed. The dual-loop architecture combines a coarse-tuning loop with a fine-tuning one, enabling a wide tuning range and low voltage-controlled oscillator (VCO) gain without poisoning phase noise and reference spur suppression performance. An analysis of the phase noise and reference spur of the dual-loop PLL is emphasized. A novel multiple-pass ring VCO is designed for the dual-loop application. It utilizes both voltage-control and current-control simultaneously in the delay cell. The PLL is fabricated in Jazz 0.18-{mu}m RF CMOS technology. The measured tuning range is from 4.2 to 5.9 GHz. It achieves a low phase noise of -99 dBc/Hz - 1 MHz offset from a 5.5 GHz carrier.

  3. DNA Vaccines

    Indian Academy of Sciences (India)

    diseases. Keywords. DNA vaccine, immune response, antibodies, infectious diseases. GENERAL .... tein vaccines require expensive virus/protein purification tech- niques as ... sphere continue to remain major health hazards in developing nations. ... significance since it can be produced at a very low cost and can be stored ...

  4. DNA Investigations.

    Science.gov (United States)

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  5. Selfdual strings and loop space Nahm equations

    International Nuclear Information System (INIS)

    Gustavsson, Andreas

    2008-01-01

    We give two independent arguments why the classical membrane fields should be take values in a loop algebra. The first argument comes from how we may construct selfdual strings in the M5 brane from a loop space version of the Nahm equations. The second argument is that there appears to be no infinite set of finite-dimensional Lie algebras (such as su(N) for any N) that satisfies the algebraic structure of the membrane theory

  6. Laser welding closed-loop power control

    DEFF Research Database (Denmark)

    Bagger, Claus; Olsen, Flemming Ove

    2003-01-01

    A closed-loop control system is developed to maintain an even seam width on the root side of a laser weld by continually controlling the output laser power of a 1500 W CO2 laser.......A closed-loop control system is developed to maintain an even seam width on the root side of a laser weld by continually controlling the output laser power of a 1500 W CO2 laser....

  7. FMFT. Fully massive four-loop tadpoles

    Energy Technology Data Exchange (ETDEWEB)

    Pikelner, Andrey [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik

    2017-07-15

    We present FMFT - a package written in FORM that evaluates four-loop fully massive tadpole Feynman diagrams. It is a successor of the MATAD package that has been successfully used to calculate many renormalization group functions at three-loop order in a wide range of quantum field theories especially in the Standard Model. We describe an internal structure of the package and provide some examples of its usage.

  8. Higgs Decay to Photons at Two Loops

    International Nuclear Information System (INIS)

    Fugel, F.

    2007-01-01

    The calculation of the two-loop corrections to the partial width of an intermediate-mass Higgs boson decaying into a pair of photons is reviewed. The main focus lies on the electroweak (EW) contributions. The sum of the EW corrections ranges from -4% to 0% for a Higgs mass between 100 GeV and 150 GeV, while the complete correction at two-loop order amounts to less than ± 1.5% in this regime. (author)

  9. Piles of dislocation loops in real crystals

    International Nuclear Information System (INIS)

    Dubinko, V.I.; Turkin, A.A.; Yanovskij, V.V.

    1985-01-01

    Behaviour of piles of dislocation loops in crystals was studied in order to define metal swelling under irradiation. Energy of pile interaction with point defects and intrinsic pile energy are studied in the framework of the linear elasticity theory. Preference of dislocation pile calculated in the paper decreases with radiation dose hence, material swelling rate also decreases. Creation of conditions, which assume an existence of piles of dislocation loops being stable under irradiation, is of particular interest

  10. Zero Point Energy of Renormalized Wilson Loops

    OpenAIRE

    Hidaka, Yoshimasa; Pisarski, Robert D.

    2009-01-01

    The quark antiquark potential, and its associated zero point energy, can be extracted from lattice measurements of the Wilson loop. We discuss a unique prescription to renormalize the Wilson loop, for which the perturbative contribution to the zero point energy vanishes identically. A zero point energy can arise nonperturbatively, which we illustrate by considering effective string models. The nonperturbative contribution to the zero point energy vanishes in the Nambu model, but is nonzero wh...

  11. FMFT: fully massive four-loop tadpoles

    Science.gov (United States)

    Pikelner, Andrey

    2018-03-01

    We present FMFT - a package written in FORM that evaluates four-loop fully massive tadpole Feynman diagrams. It is a successor of the MATAD package that has been successfully used to calculate many renormalization group functions at three-loop order in a wide range of quantum field theories especially in the Standard Model. We describe an internal structure of the package and provide some examples of its usage.

  12. Quantum Kinematics of Bosonic Vortex Loops

    International Nuclear Information System (INIS)

    Goldin, G.A.; Owczarek, R.; Sharp, D.H.

    1999-01-01

    Poisson structure for vortex filaments (loops and arcs) in 2D ideal incompressible fluid is analyzed in detail. Canonical coordinates and momenta on coadjoint orbits of the area-preserving diffeomorphism group, associated with such vortices, are found. The quantum space of states in the simplest case of ''bosonic'' vortex loops is built within a geometric quantization approach to the description of a quantum fluid. Fock-like structure and non-local creation and annihilation operators of quantum vortex filaments are introduced

  13. Loop space representation of quantum general relativity and the group of loops

    International Nuclear Information System (INIS)

    Gambini, R.

    1991-01-01

    The action of the constraints of quantum general relativity on a general state in the loop representation is coded in terms of loop derivatives. These differential operators are related to the infinitesimal generators of the group of loops and generalize the area derivative first considered by Mandelstam. A new sector of solutions of the physical states space of nonperturbative quantum general relativity is found. (orig.)

  14. Multiple Flow Loop SCADA System Implemented on the Production Prototype Loop

    Energy Technology Data Exchange (ETDEWEB)

    Baily, Scott A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dalmas, Dale Allen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wheat, Robert Mitchell [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Woloshun, Keith Albert [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dale, Gregory E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-11-16

    The following report covers FY 15 activities to develop supervisory control and data acquisition (SCADA) system for the Northstar Moly99 production prototype gas flow loop. The goal of this effort is to expand the existing system to include a second flow loop with a larger production-sized blower. Besides testing the larger blower, this system will demonstrate the scalability of our solution to multiple flow loops.

  15. Liquid Lead-Bismuth Materials Test Loop

    International Nuclear Information System (INIS)

    Tcharnotskaia, Valentina; Ammerman, Curtt; Darling, Timothy; King, Joe; Li, Ning; Shaw, Don; Snodgrass, Leon; Woloshun, Keith

    2002-01-01

    We designed and built the Liquid Lead-Bismuth Materials Test Loop (MTL) to study the materials behavior in a flow of molten lead-bismuth eutectic (LBE). In this paper we present a description of the loop with main components and their functions. Stress distribution in the piping due to sustained, occasional and expansion loads is shown. The loop is designed so that a difference of 100 deg. C can be attained between the coldest and the hottest parts at a nominal flow rate of 8.84 GPM. Liquid LBE flow can be activated by a mechanical sump pump or by natural convection. In order to maintain a self-healing protective film on the surface of the stainless steel pipe, a certain concentration of oxygen has to be maintained in the liquid metal. We developed oxygen sensors and an oxygen control system to be implemented in the loop. The loop is outfitted with a variety of instruments that are controlled from a computer based data acquisition system. Initial experiments include preconditioning the loop, filling it up with LBE, running at uniform temperature and tuning the oxygen control system. We will present some preliminary results and discuss plans for the future tests. (authors)

  16. Distribution of sizes of erased loops for loop-erased random walks

    OpenAIRE

    Dhar, Deepak; Dhar, Abhishek

    1997-01-01

    We study the distribution of sizes of erased loops for loop-erased random walks on regular and fractal lattices. We show that for arbitrary graphs the probability $P(l)$ of generating a loop of perimeter $l$ is expressible in terms of the probability $P_{st}(l)$ of forming a loop of perimeter $l$ when a bond is added to a random spanning tree on the same graph by the simple relation $P(l)=P_{st}(l)/l$. On $d$-dimensional hypercubical lattices, $P(l)$ varies as $l^{-\\sigma}$ for large $l$, whe...

  17. Hybrid Combustion-Gasification Chemical Looping

    Energy Technology Data Exchange (ETDEWEB)

    Herbert Andrus; Gregory Burns; John Chiu; Gregory Lijedahl; Peter Stromberg; Paul Thibeault

    2009-01-07

    For the past several years Alstom Power Inc. (Alstom), a leading world-wide power system manufacturer and supplier, has been in the initial stages of developing an entirely new, ultra-clean, low cost, high efficiency power plant for the global power market. This new power plant concept is based on a hybrid combustion-gasification process utilizing high temperature chemical and thermal looping technology The process consists of the oxidation, reduction, carbonation, and calcination of calcium-based compounds, which chemically react with coal, biomass, or opportunity fuels in two chemical loops and one thermal loop. The chemical and thermal looping technology can be alternatively configured as (i) a combustion-based steam power plant with CO{sub 2} capture, (ii) a hybrid combustion-gasification process producing a syngas for gas turbines or fuel cells, or (iii) an integrated hybrid combustion-gasification process producing hydrogen for gas turbines, fuel cells or other hydrogen based applications while also producing a separate stream of CO{sub 2} for use or sequestration. In its most advanced configuration, this new concept offers the promise to become the technology link from today's Rankine cycle steam power plants to tomorrow's advanced energy plants. The objective of this work is to develop and verify the high temperature chemical and thermal looping process concept at a small-scale pilot facility in order to enable AL to design, construct and demonstrate a pre-commercial, prototype version of this advanced system. In support of this objective, Alstom and DOE started a multi-year program, under this contract. Before the contract started, in a preliminary phase (Phase 0) Alstom funded and built the required small-scale pilot facility (Process Development Unit, PDU) at its Power Plant Laboratories in Windsor, Connecticut. Construction was completed in calendar year 2003. The objective for Phase I was to develop the indirect combustion loop with CO{sub 2

  18. Incremental Closed-loop Identification of Linear Parameter Varying Systems

    DEFF Research Database (Denmark)

    Bendtsen, Jan Dimon; Trangbæk, Klaus

    2011-01-01

    , closed-loop system identification is more difficult than open-loop identification. In this paper we prove that the so-called Hansen Scheme, a technique known from linear time-invariant systems theory for transforming closed-loop system identification problems into open-loop-like problems, can be extended...

  19. High-temperature helium-loop facility

    International Nuclear Information System (INIS)

    Tokarz, R.D.

    1981-09-01

    The high-temperature helium loop is a facility for materials testing in ultrapure helium gas at high temperatures. The closed loop system is capable of recirculating high-purity helium or helium with controlled impurities. The gas loop maximum operating conditions are as follows: 300 psi pressure, 500 lb/h flow rate, and 2100 0 F temperature. The two test sections can accept samples up to 3.5 in. diameter and 5 ft long. The gas loop is fully instrumented to continuously monitor all parameters of loop operation as well as helium impurities. The loop is fully automated to operate continuously and requires only a daily servicing by a qualified operator to replenish recorder charts and helium makeup gas. Because of its versatility and high degree of parameter control, the helium loop is applicable to many types of materials research. This report describes the test apparatus, operating parameters, peripheral systems, and instrumentation system. The experimental capabilities and test conand presents the results that have been obtained. The study has been conducted using a four-phase approach. The first phase develops the solution to the steady-state radon-diffusion equation in one-dimensieered barriers; disposal charge analysis; analysis of spent fuel policy implementation; spent f water. Field measurements and observations are reported for each site. Analytical data and field measurements are presented in tables and maps. Uranium concentrations in the sediments which were above detection limits ranged from 0.10 t 51.2 ppM. The mean of the logarithms of the uranium concentrations was 0.53. A group of high uranium concentrations occurs near the junctions of quadrangles AB, AC, BB, a 200 mK. In case 2), x-ray studies of isotopic phase separation in 3 He-- 4 He bcc solids were carried out by B. A. Fraass

  20. Two-phase Heating in Flaring Loops

    Science.gov (United States)

    Zhu, Chunming; Qiu, Jiong; Longcope, Dana W.

    2018-03-01

    We analyze and model a C5.7 two-ribbon solar flare observed by the Solar Dynamics Observatory, Hinode, and GOES on 2011 December 26. The flare is made of many loops formed and heated successively over one and half hours, and their footpoints are brightened in the UV 1600 Å before enhanced soft X-ray and EUV missions are observed in flare loops. Assuming that anchored at each brightened UV pixel is a half flaring loop, we identify more than 6700 half flaring loops, and infer the heating rate of each loop from the UV light curve at the footpoint. In each half loop, the heating rate consists of two phases: intense impulsive heating followed by a low-rate heating that is persistent for more than 20 minutes. Using these heating rates, we simulate the evolution of their coronal temperatures and densities with the model of the “enthalpy-based thermal evolution of loops.” In the model, suppression of thermal conduction is also considered. This model successfully reproduces total soft X-ray and EUV light curves observed in 15 passbands by four instruments GOES, AIA, XRT, and EVE. In this flare, a total energy of 4.9 × 1030 erg is required to heat the corona, around 40% of this energy is in the slow-heating phase. About two-fifths of the total energy used to heat the corona is radiated by the coronal plasmas, and the other three fifth transported to the lower atmosphere by thermal conduction.

  1. DNA repair

    International Nuclear Information System (INIS)

    Setlow, R.

    1978-01-01

    Some topics discussed are as follows: difficulty in extrapolating data from E. coli to mammalian systems; mutations caused by UV-induced changes in DNA; mutants deficient in excision repair; other postreplication mechanisms; kinds of excision repair systems; detection of repair by biochemical or biophysical means; human mutants deficient in repair; mutagenic effects of UV on XP cells; and detection of UV-repair defects among XP individuals

  2. 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.

  3. The rolling-circle melting-pot model for porcine circovirus DNA replication

    Science.gov (United States)

    A stem-loop structure, formed by a pair of inverted repeats during DNA replication, is a conserved feature at the origin of DNA replication (Ori) among plant and animal viruses, bacteriophages and plasmids that replicate their genomes via the rolling-circle replication (RCR) mechanism. Porcine circo...

  4. An incoherent feedforward loop facilitates adaptive tuning of gene expression.

    Science.gov (United States)

    Hong, Jungeui; Brandt, Nathan; Abdul-Rahman, Farah; Yang, Ally; Hughes, Tim; Gresham, David

    2018-04-05

    We studied adaptive evolution of gene expression using long-term experimental evolution of Saccharomyces cerevisiae in ammonium-limited chemostats. We found repeated selection for non-synonymous variation in the DNA binding domain of the transcriptional activator, GAT1, which functions with the repressor, DAL80 in an incoherent type-1 feedforward loop (I1-FFL) to control expression of the high affinity ammonium transporter gene, MEP2. Missense mutations in the DNA binding domain of GAT1 reduce its binding to the GATAA consensus sequence. However, we show experimentally, and using mathematical modeling, that decreases in GAT1 binding result in increased expression of MEP2 as a consequence of properties of I1-FFLs. Our results show that I1-FFLs, one of the most commonly occurring network motifs in transcriptional networks, can facilitate adaptive tuning of gene expression through modulation of transcription factor binding affinities. Our findings highlight the importance of gene regulatory architectures in the evolution of gene expression. © 2018, Hong et al.

  5. The efficiency of mitochondrial DNA markers in constructing genetic ...

    African Journals Online (AJOL)

    Administrator

    2011-05-30

    May 30, 2011 ... To date, only parts of mitochondrial DNA from cytochrome b, 12S rRNA, 16S rRNA and non-coding D- loop had been sequenced for different species of Oryx. Discrepancy in the genetic relationship among. Oryx species was previously revealed when combinations of these sequences were analyzed. In the.

  6. Triplet repeat DNA structures and human genetic disease: dynamic ...

    Indian Academy of Sciences (India)

    Unknown

    formed at the loop-outs. [Sinden R R, Potaman V N, Oussatcheva E A, Pearson C E, Lyubchenko Y L and Shlyakhtenko L S 2002 Triplet repeat DNA structures .... 36–39. 40–121 Huntingtin/polyglutamine expansion. Spinocerebellar ataxia 1. SCA1. 6p23. (CAG)n. 6–44. –. 39–82 (pure) Ataxin-1/polyglutamine expansion.

  7. Operation of the hot test loop facilities

    International Nuclear Information System (INIS)

    Cheong, Moon Ki; Park, Choon Kyeong; Won, Soon Yeon; Yang, Sun Kyu; Cheong, Jang Whan; Cheon, Se Young; Song, Chul Hwa; Jeon, Hyeong Kil; Chang, Suk Kyu; Jeong, Heung Jun; Cho, Young Ro; Kim, Bok Duk; Min, Kyeong Ho

    1994-12-01

    The objective of this project is to obtain the available experimental data and to develop the measuring techniques through taking full advantage of the facilities. The facilities operated by the thermal hydraulics department have been maintained and repaired in order to carry out the thermal hydraulics tests necessary for providing the available data. The performance tests for double grid type bottom end piece which was improved on the debris filtering effectivity were performed using the PWR-Hot Test Loop. The CANDU-Hot Test Loop was operated to carry out the pressure drop tests and strength tests of fuel. The Cold Test Loop was used to obtain the local velocity data in subchannel within fuel bundle and to understand the characteristic of pressure drop required for improving the nuclear fuel and to develop the advanced measuring techniques. RCS Loop, which is used to measure the CHF, is presently under design and construction. B and C Loop is designed and constructed to assess the automatic depressurization safety system behavior. 4 tabs., 79 figs., 7 refs. (Author) .new

  8. Mass inflation in the loop black hole

    International Nuclear Information System (INIS)

    Brown, Eric G.; Mann, Robert; Modesto, Leonardo

    2011-01-01

    In classical general relativity the Cauchy horizon within a two-horizon black hole is unstable via a phenomenon known as mass inflation, in which the mass parameter (and the spacetime curvature) of the black hole diverges at the Cauchy horizon. Here we study this effect for loop black holes - quantum gravitationally corrected black holes from loop quantum gravity - whose construction alleviates the r=0 singularity present in their classical counterparts. We use a simplified model of mass inflation, which makes use of the generalized Dray-'t Hooft relation, to conclude that the Cauchy horizon of loop black holes indeed results in a curvature singularity similar to that found in classical black holes. The Dray-'t Hooft relation is of particular utility in the loop black hole because it does not directly rely upon Einstein's field equations. We elucidate some of the interesting and counterintuitive properties of the loop black hole, and corroborate our results using an alternate model of mass inflation due to Ori.

  9. One-loop calculations with massive particles

    International Nuclear Information System (INIS)

    Oldenborgh, G.J. van.

    1990-01-01

    In this thesis some techniques for performing one-loop calculations with massive particles are presented. Numerical techniques are presented necessary for evaluating one-loop integrals which occur in one-loop calculations of photon-photon scattering. The algorithms have been coded in FORTRAN (to evaluate the scalar integrals) and the algebraic language FORM (to reduce the tensor integrals to scalar integrals). Applications are made in the theory of the strong interaction, QCD, i.e. in handling one-loop integrals with massive particles, in order to regulate the infinities by mass parameters encountered in this theory. However this simplifies the computation considerably, the description of the proton structure functions have to be renormalized in order to obtain physical results. This renormalization is different from the published results for the gluon and thus has to be redone. The first physics results that have been obtained with these new methods are presented. These concern heavy quark production in semi-leptonic interactions, for instance neutrino charm production and top production at the electron-proton (ep) collider HERA and the proposed LEP/LHC combination. Total and differential cross-sections for one-loop corrections to top production at the HERA and proposed LEP/HLC ep colliders are given and structure functions for charmed quark production are compared with previously published results. (author). 58 refs.; 18 figs.; 5 tabs

  10. Bootstrapping the Three-Loop Hexagon

    Energy Technology Data Exchange (ETDEWEB)

    Dixon, Lance J.; /CERN /SLAC; Drummond, James M.; /CERN /Annecy, LAPTH; Henn, Johannes M.; /Humboldt U., Berlin /Santa Barbara, KITP

    2011-11-08

    We consider the hexagonal Wilson loop dual to the six-point MHV amplitude in planar N = 4 super Yang-Mills theory. We apply constraints from the operator product expansion in the near-collinear limit to the symbol of the remainder function at three loops. Using these constraints, and assuming a natural ansatz for the symbol's entries, we determine the symbol up to just two undetermined constants. In the multi-Regge limit, both constants drop out from the symbol, enabling us to make a non-trivial confirmation of the BFKL prediction for the leading-log approximation. This result provides a strong consistency check of both our ansatz for the symbol and the duality between Wilson loops and MHV amplitudes. Furthermore, we predict the form of the full three-loop remainder function in the multi-Regge limit, beyond the leading-log approximation, up to a few constants representing terms not detected by the symbol. Our results confirm an all-loop prediction for the real part of the remainder function in multi-Regge 3 {yields} 3 scattering. In the multi-Regge limit, our result for the remainder function can be expressed entirely in terms of classical polylogarithms. For generic six-point kinematics other functions are required.

  11. Logical inference techniques for loop parallelization

    KAUST Repository

    Oancea, Cosmin E.

    2012-01-01

    This paper presents a fully automatic approach to loop parallelization that integrates the use of static and run-time analysis and thus overcomes many known difficulties such as nonlinear and indirect array indexing and complex control flow. Our hybrid analysis framework validates the parallelization transformation by verifying the independence of the loop\\'s memory references. To this end it represents array references using the USR (uniform set representation) language and expresses the independence condition as an equation, S = Ø, where S is a set expression representing array indexes. Using a language instead of an array-abstraction representation for S results in a smaller number of conservative approximations but exhibits a potentially-high runtime cost. To alleviate this cost we introduce a language translation F from the USR set-expression language to an equally rich language of predicates (F(S) ⇒ S = Ø). Loop parallelization is then validated using a novel logic inference algorithm that factorizes the obtained complex predicates (F(S)) into a sequence of sufficient-independence conditions that are evaluated first statically and, when needed, dynamically, in increasing order of their estimated complexities. We evaluate our automated solution on 26 benchmarks from PERFECTCLUB and SPEC suites and show that our approach is effective in parallelizing large, complex loops and obtains much better full program speedups than the Intel and IBM Fortran compilers. Copyright © 2012 ACM.

  12. DNA damage mediated transcription arrest: Step back to go forward.

    Science.gov (United States)

    Mullenders, Leon

    2015-12-01

    The disturbance of DNA helix conformation by bulky DNA damage poses hindrance to transcription elongating due to stalling of RNA polymerase at transcription blocking lesions. Stalling of RNA polymerase provokes the formation of R-loops, i.e. the formation of a DNA-RNA hybrid and a displaced single stranded DNA strand as well as displacement of spliceosomes. R-loops are processed into DNA single and double strand breaks by NER factors depending on TC-NER factors leading to genome instability. Moreover, stalling of RNA polymerase induces a strong signal for cell cycle arrest and apoptosis. These toxic and mutagenic effects are counteracted by a rapid recruitment of DNA repair proteins to perform transcription coupled nucleotide excision repair (TC-NER) to remove the blocking DNA lesions and to restore transcription. Recent studies have highlighted the role of backtracking of RNA polymerase to facilitate TC-NER and identified novel factors that play key roles in TC-NER and in restoration of transcription. On the molecular level these factors facilitate stability of the repair complex by promotion and regulation of various post-translational modifications of NER factors and chromatin substrate. In addition, the continuous flow of new factors that emerge from screening assays hints to several regulatory levels to safeguard the integrity of transcription elongation after disturbance by DNA damage that have yet to be explored. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Variational solution of the loop equation in QCD

    International Nuclear Information System (INIS)

    Agishtein, M.E.; Migdal, A.A.

    1988-01-01

    A new technique for the large N loop equation of QCD is worked out. The Wilson loop W(C) is approximated by a Gaussian functional. The parameters are fitted to the loop equation, after which the equation is statisfied up to 0.2%. The resulting Wilson loop corresponds to linearly rising Regge trajectories. The problem of tachyon is still present, but it could be cured by iteration of the loop equation starting from this variational solution. (orig.)

  14. Variational solution of the loop equation in QCD

    International Nuclear Information System (INIS)

    Agishtein, M.E.; Migdal, A.A.

    1988-01-01

    A new technique for the large N loop equation of QCD is worked out. The Wilson loop W(C) is approximated by a Gaussian functional. The parameters are fitted to the loop equation, after which the equation is satisfied up to 0.2%. The resulting Wilson loop corresponds to linearly rising Regge trajectories. The problem of tachyon is still present, but it could be cured by iteration of the loop equation starting from this variational solution

  15. BPS Wilson loops and Bremsstrahlung function in ABJ(M): a two loop analysis

    Energy Technology Data Exchange (ETDEWEB)

    Bianchi, Marco S. [Institut für Physik, Humboldt-Universität zu Berlin,Newtonstraße 15, 12489 Berlin (Germany); Griguolo, Luca [Dipartimento di Fisica e Scienze della Terra, Università di Parmaand INFN Gruppo Collegato di Parma,Viale G.P. Usberti 7/A, 43100 Parma (Italy); Leoni, Matias [Physics Department, FCEyN-UBA & IFIBA-CONICETCiudad Universitaria, Pabellón I, 1428, Buenos Aires (Argentina); Penati, Silvia [Dipartimento di Fisica, Università di Milano-Bicoccaand INFN, Sezione di Milano-Bicocca,Piazza della Scienza 3, I-20126 Milano (Italy); Seminara, Domenico [Dipartimento di Fisica, Università di Firenzeand INFN Sezione di Firenze,via G. Sansone 1, 50019 Sesto Fiorentino (Italy)

    2014-06-19

    We study a family of circular BPS Wilson loops in N=6 super Chern-Simons-matter theories, generalizing the usual 1/2-BPS circle. The scalar and fermionic couplings depend on two deformation parameters and these operators can be considered as the ABJ(M) counterpart of the DGRT latitudes defined in N=4 SYM. We perform a complete two-loop analysis of their vacuum expectation value, discuss the appearance of framing-like phases and propose a general relation with cohomologically equivalent bosonic operators. We make an all-loop proposal for computing the Bremsstrahlung function associated to the 1/2-BPS cusp in terms of these generalized Wilson loops. When applied to our two-loop result it reproduces the known expression. Finally, we comment on the generalization of this proposal to the bosonic 1/6-BPS case.

  16. Preferential repair of nuclear matrix associated DNA in xeroderma pigmentosum complementation group C

    International Nuclear Information System (INIS)

    Mullenders, L.H.F.; Kesteren, A.C. van; Bussmann, C.J.M.; Zeeland, A.A. van; Natarajan, A.T.

    1984-01-01

    The distribution of ultraviolet-induced DNA repair patches in the genome of xeroderma pigmentosum cells of complementation group C was investigated by determining the molecular weight distribution of repair labeled DNA and prelabeled DNA in alkaline sucrose gradients after treatment with the dimer-specific endonuclease V of bacteriophage T 4 . The results suggest that DNA-repair synthesis in xeroderma pigmentosum cells of complementation group C occurs in localized regions of the genome. Analysis of the spatial distribution of ultraviolet-induced repair patches in DNA loops attached to the nuclear matrix revealed that in xeroderma pigmentosum cells of complementation group C repair patches are preferentially situated near the attachment sites of DNA loops at the nuclear matrix. In normal human fibroblasts the authors observed no enrichment of repair-labeled DNA at the nuclear matrix and repair patches appeared to be distributed randomly along the DNA loops. The enrichment of repair-labeled DNA at the nuclear matrix in xeroderma pigmentosum cells of complementation group C may indicate that the residual DNA-repair synthesis in these cells occurs preferentially in regions of the genome. (Auth.)

  17. The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast.

    Science.gov (United States)

    Hartono, Stella R; Malapert, Amélie; Legros, Pénélope; Bernard, Pascal; Chédin, Frédéric; Vanoosthuyse, Vincent

    2018-02-02

    R-loops, which result from the formation of stable DNA:RNA hybrids, can both threaten genome integrity and act as physiological regulators of gene expression and chromatin patterning. To characterize R-loops in fission yeast, we used the S9.6 antibody-based DRIPc-seq method to sequence the RNA strand of R-loops and obtain strand-specific R-loop maps at near nucleotide resolution. Surprisingly, preliminary DRIPc-seq experiments identified mostly RNase H-resistant but exosome-sensitive RNAs that mapped to both DNA strands and resembled RNA:RNA hybrids (dsRNAs), suggesting that dsRNAs form widely in fission yeast. We confirmed in vitro that S9.6 can immuno-precipitate dsRNAs and provide evidence that dsRNAs can interfere with its binding to R-loops. dsRNA elimination by RNase III treatment prior to DRIPc-seq allowed the genome-wide and strand-specific identification of genuine R-loops that responded in vivo to RNase H levels and displayed classical features associated with R-loop formation. We also found that most transcripts whose levels were altered by in vivo manipulation of RNase H levels did not form detectable R-loops, suggesting that prolonged manipulation of R-loop levels could indirectly alter the transcriptome. We discuss the implications of our work in the design of experimental strategies to probe R-loop functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Flat Knitting Loop Deformation Simulation Based on Interlacing Point Model

    Directory of Open Access Journals (Sweden)

    Jiang Gaoming

    2017-12-01

    Full Text Available In order to create realistic loop primitives suitable for the faster CAD of the flat-knitted fabric, we have performed research on the model of the loop as well as the variation of the loop surface. This paper proposes an interlacing point-based model for the loop center curve, and uses the cubic Bezier curve to fit the central curve of the regular loop, elongated loop, transfer loop, and irregular deformed loop. In this way, a general model for the central curve of the deformed loop is obtained. The obtained model is then utilized to perform texture mapping, texture interpolation, and brightness processing, simulating a clearly structured and lifelike deformed loop. The computer program LOOP is developed by using the algorithm. The deformed loop is simulated with different yarns, and the deformed loop is applied to design of a cable stitch, demonstrating feasibility of the proposed algorithm. This paper provides a loop primitive simulation method characterized by lifelikeness, yarn material variability, and deformation flexibility, and facilitates the loop-based fast computer-aided design (CAD of the knitted fabric.

  19. Transition probability spaces in loop quantum gravity

    Science.gov (United States)

    Guo, Xiao-Kan

    2018-03-01

    We study the (generalized) transition probability spaces, in the sense of Mielnik and Cantoni, for spacetime quantum states in loop quantum gravity. First, we show that loop quantum gravity admits the structures of transition probability spaces. This is exemplified by first checking such structures in covariant quantum mechanics and then identifying the transition probability spaces in spin foam models via a simplified version of general boundary formulation. The transition probability space thus defined gives a simple way to reconstruct the discrete analog of the Hilbert space of the canonical theory and the relevant quantum logical structures. Second, we show that the transition probability space and in particular the spin foam model are 2-categories. Then we discuss how to realize in spin foam models two proposals by Crane about the mathematical structures of quantum gravity, namely, the quantum topos and causal sites. We conclude that transition probability spaces provide us with an alternative framework to understand various foundational questions of loop quantum gravity.

  20. Solar flare loops observations and interpretations

    CERN Document Server

    Huang, Guangli; Ji, Haisheng; Ning, Zongjun

    2018-01-01

    This book provides results of analysis of typical solar events, statistical analysis, the diagnostics of energetic electrons and magnetic field, as well as the global behavior of solar flaring loops such as their contraction and expansion. It pays particular attention to analyzing solar flare loops with microwave, hard X-ray, optical and EUV emissions, as well as the theories of their radiation, and electron acceleration/transport. The results concerning influence of the pitch-angle anisotropy of non-thermal electrons on their microwave and hard X-ray emissions, new spectral behaviors in X-ray and microwave bands, and results related to the contraction of flaring loops, are widely discussed in the literature of solar physics. The book is useful for graduate students and researchers in solar and space physics.

  1. Automatic Loop Parallelization via Compiler Guided Refactoring

    DEFF Research Database (Denmark)

    Larsen, Per; Ladelsky, Razya; Lidman, Jacob

    For many parallel applications, performance relies not on instruction-level parallelism, but on loop-level parallelism. Unfortunately, many modern applications are written in ways that obstruct automatic loop parallelization. Since we cannot identify sufficient parallelization opportunities...... for these codes in a static, off-line compiler, we developed an interactive compilation feedback system that guides the programmer in iteratively modifying application source, thereby improving the compiler’s ability to generate loop-parallel code. We use this compilation system to modify two sequential...... benchmarks, finding that the code parallelized in this way runs up to 8.3 times faster on an octo-core Intel Xeon 5570 system and up to 12.5 times faster on a quad-core IBM POWER6 system. Benchmark performance varies significantly between the systems. This suggests that semi-automatic parallelization should...

  2. Microwave emission from flaring magnetic loops

    International Nuclear Information System (INIS)

    Vlahos, L.

    1980-01-01

    The microwave emission from a flaring loop is considered. In particular the author examines the question: What will be the characteristics of the radio emission at centimeter wavelengths from a small compact flaring loop when the mechanism which pumps magnetic energy into the plasma in the form of heating and/or electron acceleration satisfies the conditions: (a) the magnetic energy is released in a small volume compared to the volume of the loop, and the rate at which magnetic energy is transformed into plasma energy is faster than the energy losses from the same volume. This causes a local enhancement of the temperature by as much as one or two orders of magnitude above the coronal temperature; (b) The bulk of the energy released goes into heating the plasma and heats primarily the electrons. (Auth.)

  3. Experimental loop for SH2 (LECS)

    International Nuclear Information System (INIS)

    Strehar, N.R.; Bruzzoni, Pablo; Moras, J.J.; Cogozzo, E.O.

    1981-01-01

    An experimental loop is described for circulation of SH 2 that operates at 2 x 10 6 Pascal and 33 deg C. It was designed and constructed with the purpose of experimentally studying the hydraulic instability phenomenon that can be detected in cold isotopic exchange columns in the Girdler-Sulfide (GS) process of heavy water production. The main features of the different components of the loop are described, as well as the materials, the measurement and control instruments and the auxiliary equipment used, and finally the measuring methods to qualify and quantify the formation of froth. Furthermore, the loop's transportable metallic container is described, which allows to transport and connect it to CNEA's experimental heavy water plant or to any other heavy water plants using the GS method. Some tests made with inert gases that intended to verify the equipment's performance and to select the most adequate sieve trays for its operation are discussed. (M.E.L.) [es

  4. Automated one-loop calculations with GOSAM

    International Nuclear Information System (INIS)

    Cullen, Gavin; Greiner, Nicolas; Heinrich, Gudrun; Reiter, Thomas; Luisoni, Gionata

    2011-11-01

    We present the program package GoSam which is designed for the automated calculation of one-loop amplitudes for multi-particle processes in renormalisable quantum field theories. The amplitudes, which are generated in terms of Feynman diagrams, can be reduced using either D-dimensional integrand-level decomposition or tensor reduction. GoSam can be used to calculate one-loop QCD and/or electroweak corrections to Standard Model processes and offers the flexibility to link model files for theories Beyond the Standard Model. A standard interface to programs calculating real radiation is also implemented. We demonstrate the flexibility of the program by presenting examples of processes with up to six external legs attached to the loop. (orig.)

  5. Automated one-loop calculations with GOSAM

    Energy Technology Data Exchange (ETDEWEB)

    Cullen, Gavin [Edinburgh Univ. (United Kingdom). School of Physics and Astronomy; Deutsches Elektronen-Synchrotron, Zeuthen [DESY; Germany; Greiner, Nicolas [Illinois Univ., Urbana-Champaign, IL (United States). Dept. of Physics; Max-Planck-Institut fuer Physik, Muenchen (Germany); Heinrich, Gudrun; Reiter, Thomas [Max-Planck-Institut fuer Physik, Muenchen (Germany); Luisoni, Gionata [Durham Univ. (United Kingdom). Inst. for Particle Physics Phenomenology; Mastrolia, Pierpaolo [Max-Planck-Institut fuer Physik, Muenchen (Germany); Padua Univ. (Italy). Dipt. di Fisica; Ossola, Giovanni [New York City Univ., NY (United States). New York City College of Technology; New York City Univ., NY (United States). The Graduate School and University Center; Tramontano, Francesco [European Organization for Nuclear Research (CERN), Geneva (Switzerland)

    2011-11-15

    We present the program package GoSam which is designed for the automated calculation of one-loop amplitudes for multi-particle processes in renormalisable quantum field theories. The amplitudes, which are generated in terms of Feynman diagrams, can be reduced using either D-dimensional integrand-level decomposition or tensor reduction. GoSam can be used to calculate one-loop QCD and/or electroweak corrections to Standard Model processes and offers the flexibility to link model files for theories Beyond the Standard Model. A standard interface to programs calculating real radiation is also implemented. We demonstrate the flexibility of the program by presenting examples of processes with up to six external legs attached to the loop. (orig.)

  6. Covariant diagrams for one-loop matching

    International Nuclear Information System (INIS)

    Zhang, Zhengkang

    2016-10-01

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gaugecovariant quantities and are thus dubbed ''covariant diagrams.'' The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  7. Covariant diagrams for one-loop matching

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhengkang [Michigan Center for Theoretical Physics (MCTP), University of Michigan,450 Church Street, Ann Arbor, MI 48109 (United States); Deutsches Elektronen-Synchrotron (DESY),Notkestraße 85, 22607 Hamburg (Germany)

    2017-05-30

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed “covariant diagrams.” The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  8. Defect networks and supersymmetric loop operators

    Energy Technology Data Exchange (ETDEWEB)

    Bullimore, Mathew [Perimeter Institute for Theoretical Physics, 31 Caroline Street North, Waterloo, ON N2L 2Y5 (Canada)

    2015-02-10

    We consider topological defect networks with junctions in A{sub N−1} Toda CFT and the connection to supersymmetric loop operators in N=2 theories of class S on a four-sphere. Correlation functions in the presence of topological defect networks are computed by exploiting the monodromy of conformal blocks, generalising the notion of a Verlinde operator. Concentrating on a class of topological defects in A{sub 2} Toda theory, we find that the Verlinde operators generate an algebra whose structure is determined by a set of generalised skein relations that encode the representation theory of a quantum group. In the second half of the paper, we explore the dictionary between topological defect networks and supersymmetric loop operators in the N=2{sup ∗} theory by comparing to exact localisation computations. In this context, the the generalised skein relations are related to the operator product expansion of loop operators.

  9. Covariant diagrams for one-loop matching

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhengkang [Michigan Univ., Ann Arbor, MI (United States). Michigan Center for Theoretical Physics; Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2016-10-15

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gaugecovariant quantities and are thus dubbed ''covariant diagrams.'' The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  10. Covariant diagrams for one-loop matching

    International Nuclear Information System (INIS)

    Zhang, Zhengkang

    2017-01-01

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed “covariant diagrams.” The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  11. Involvement of DNA mismatch repair in the maintenance of heterochromatic DNA stability in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Basanta K Dahal

    2017-10-01

    Full Text Available Heterochromatin contains a significant part of nuclear DNA. Little is known about the mechanisms that govern heterochromatic DNA stability. We show here that in the yeast Saccharomyces cerevisiae (i DNA mismatch repair (MMR is required for the maintenance of heterochromatic DNA stability, (ii MutLα (Mlh1-Pms1 heterodimer, MutSα (Msh2-Msh6 heterodimer, MutSβ (Msh2-Msh3 heterodimer, and Exo1 are involved in MMR at heterochromatin, (iii Exo1-independent MMR at heterochromatin frequently leads to the formation of Pol ζ-dependent mutations, (iv MMR cooperates with the proofreading activity of Pol ε and the histone acetyltransferase Rtt109 in the maintenance of heterochromatic DNA stability, (v repair of base-base mismatches at heterochromatin is less efficient than repair of base-base mismatches at euchromatin, and (vi the efficiency of repair of 1-nt insertion/deletion loops at heterochromatin is similar to the efficiency of repair of 1-nt insertion/deletion loops at euchromatin.

  12. Coronal Loops: Evolving Beyond the Isothermal Approximation

    Science.gov (United States)

    Schmelz, J. T.; Cirtain, J. W.; Allen, J. D.

    2002-05-01

    Are coronal loops isothermal? A controversy over this question has arisen recently because different investigators using different techniques have obtained very different answers. Analysis of SOHO-EIT and TRACE data using narrowband filter ratios to obtain temperature maps has produced several key publications that suggest that coronal loops may be isothermal. We have constructed a multi-thermal distribution for several pixels along a relatively isolated coronal loop on the southwest limb of the solar disk using spectral line data from SOHO-CDS taken on 1998 Apr 20. These distributions are clearly inconsistent with isothermal plasma along either the line of sight or the length of the loop, and suggested rather that the temperature increases from the footpoints to the loop top. We speculated originally that these differences could be attributed to pixel size -- CDS pixels are larger, and more `contaminating' material would be expected along the line of sight. To test this idea, we used CDS iron line ratios from our data set to mimic the isothermal results from the narrowband filter instruments. These ratios indicated that the temperature gradient along the loop was flat, despite the fact that a more complete analysis of the same data showed this result to be false! The CDS pixel size was not the cause of the discrepancy; rather, the problem lies with the isothermal approximation used in EIT and TRACE analysis. These results should serve as a strong warning to anyone using this simplistic method to obtain temperature. This warning is echoed on the EIT web page: ``Danger! Enter at your own risk!'' In other words, values for temperature may be found, but they may have nothing to do with physical reality. Solar physics research at the University of Memphis is supported by NASA grant NAG5-9783. This research was funded in part by the NASA/TRACE MODA grant for Montana State University.

  13. DNA repair

    International Nuclear Information System (INIS)

    Van Zeeland, A.A.

    1984-01-01

    In this chapter a series of DNA repair pathways are discussed which are available to the cell to cope with the problem of DNA damaged by chemical or physical agents. In the case of microorganisms our knowledge about the precise mechanism of each DNA repair pathway and the regulation of it has been improved considerably when mutants deficient in these repair mechanisms became available. In the case of mammalian cells in culture, until recently there were very little repair deficient mutants available, because in almost all mammalian cells in culture at least the diploid number of chromosomes is present. Therefore the frequency of repair deficient mutants in such populations is very low. Nevertheless because replica plating techniques are improving some mutants from Chinese hamsters ovary cells and L5178Y mouse lymphoma cells are now available. In the case of human cells, cultures obtained from patients with certain genetic diseases are available. A number of cells appear to be sensitive to some chemical or physical mutagens. These include cells from patients suffering from xeroderma pigmentosum, Ataxia telangiectasia, Fanconi's anemia, Cockayne's syndrome. However, only in the case of xeroderma pigmentosum cells, has the sensitivity to ultraviolet light been clearly correlated with a deficiency in excision repair of pyrimidine dimers. Furthermore the work with strains obtained from biopsies from man is difficult because these cells generally have low cloning efficiencies and also have a limited lifespan in vitro. It is therefore very important that more repair deficient mutants will become available from established cell lines from human or animal origin

  14. Structural basis for sequence-specific recognition of DNA by TAL effectors

    KAUST Repository

    Deng, Dong

    2012-01-05

    TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair by using two hypervariable residues [known as repeat variable diresidues (RVDs)] at positions 12 and 13. Here, we report the crystal structures of an 11.5-repeat TAL effector in both DNA-free and DNA-bound states. Each TAL repeat comprises two helices connected by a short RVD-containing loop. The 11.5 repeats form a right-handed, superhelical structure that tracks along the sense strand of DNA duplex, with RVDs contacting the major groove. The 12th residue stabilizes the RVD loop, whereas the 13th residue makes a base-specific contact. Understanding DNA recognition by TAL effectors may facilitate rational design of DNA-binding proteins with biotechnological applications.

  15. DNA Length Modulates the Affinity of Fragments of Genomic DNA for the Nuclear Matrix In Vitro.

    Science.gov (United States)

    García-Vilchis, David; Aranda-Anzaldo, Armando

    2017-12-01

    Classical observations have shown that during the interphase the chromosomal DNA of metazoans is organized in supercoiled loops attached to a compartment known as the nuclear matrix (NM). Fragments of chromosomal DNA able to bind the isolated NM in vitro are known as matrix associated/attachment/addressed regions or MARs. No specific consensus sequence or motif has been found that may constitute a universal, defining feature of MARs. On the other hand, high-salt resistant DNA-NM interactions in situ define true DNA loop anchorage regions or LARs, that might correspond to a subset of the potential MARs but are not necessarily identical to MARs characterized in vitro, since there are several examples of MARs able to bind the NM in vitro but which are not actually bound to the NM in situ. In the present work we assayed the capacity of two LARs, as well as of shorter fragments within such LARs, for binding to the NM in vitro. Paradoxically the isolated (≈2 kb) LARs cannot bind to the NM in vitro while their shorter (≈300 pb) sub-fragments and other non-related but equally short DNA fragments, bind to the NM in a high-salt resistant fashion. Our results suggest that the ability of a given DNA fragment for binding to the NM in vitro primarily depends on the length of the fragment, suggesting that binding to the NM is modulated by the local topology of the DNA fragment in suspension that it is known to depend on the DNA length. J. Cell. Biochem. 118: 4487-4497, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  16. High-Order Frequency-Locked Loops

    DEFF Research Database (Denmark)

    Golestan, Saeed; Guerrero, Josep M.; Quintero, Juan Carlos Vasquez

    2017-01-01

    In very recent years, some attempts for designing high-order frequency-locked loops (FLLs) have been made. Nevertheless, the advantages and disadvantages of these structures, particularly in comparison with a standard FLL and high-order phase-locked loops (PLLs), are rather unclear. This lack...... study, and its small-signal modeling, stability analysis, and parameter tuning are presented. Finally, to gain insight about advantages and disadvantages of high-order FLLs, a theoretical and experimental performance comparison between the designed second-order FLL and a standard FLL (first-order FLL...

  17. Accident analysis of HANARO fuel test loop

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J. Y.; Chi, D. Y

    1998-03-01

    Steady state fuel test loop will be equipped in HANARO to obtain the development and betterment of advanced fuel and materials through the irradiation tests. The HANARO fuel test loop was designed to match the CANDU and PWR fuel operating conditions. The accident analysis was performed by RELAP5/MOD3 code based on FTL system designs and determined the detail engineering specification of in-pile test section and out-pile systems. The accident analysis results of FTL system could be used for the fuel and materials designer to plan the irradiation testing programs. (author). 23 refs., 20 tabs., 178 figs.

  18. A keyboard control method for loop measurement

    International Nuclear Information System (INIS)

    Gao, Z.W.

    1994-01-01

    This paper describes a keyboard control mode based on the DEC VAX computer. The VAX Keyboard code can be found under running of a program was developed. During the loop measurement or multitask operation, it ables to be distinguished from a keyboard code to stop current operation or transfer to another operation while previous information can be held. The combining of this mode, the author successfully used one key control loop measurement for test Dual Input Memory module which is used in a rearrange Energy Trigger system for LEP 8 Bunch operation

  19. Anomaly freedom in perturbative loop quantum gravity

    International Nuclear Information System (INIS)

    Bojowald, Martin; Hossain, Golam Mortuza; Kagan, Mikhail; Shankaranarayanan, S.

    2008-01-01

    A fully consistent linear perturbation theory for cosmology is derived in the presence of quantum corrections as they are suggested by properties of inverse volume operators in loop quantum gravity. The underlying constraints present a consistent deformation of the classical system, which shows that the discreteness in loop quantum gravity can be implemented in effective equations without spoiling space-time covariance. Nevertheless, nontrivial quantum corrections do arise in the constraint algebra. Since correction terms must appear in tightly controlled forms to avoid anomalies, detailed insights for the correct implementation of constraint operators can be gained. The procedures of this article thus provide a clear link between fundamental quantum gravity and phenomenology.

  20. Logical inference techniques for loop parallelization

    DEFF Research Database (Denmark)

    Oancea, Cosmin Eugen; Rauchwerger, Lawrence

    2012-01-01

    the parallelization transformation by verifying the independence of the loop's memory references. To this end it represents array references using the USR (uniform set representation) language and expresses the independence condition as an equation, S={}, where S is a set expression representing array indexes. Using...... of their estimated complexities. We evaluate our automated solution on 26 benchmarks from PERFECT-CLUB and SPEC suites and show that our approach is effective in parallelizing large, complex loops and obtains much better full program speedups than the Intel and IBM Fortran compilers....

  1. Description of the sodium loop ML-3

    International Nuclear Information System (INIS)

    Torre, de la M.; Melches, I; Lapena, J.; Martinez, T.A.; Miguel, de D.; Duran, F.

    1979-01-01

    The sodium loop ML-3 is described. The main objective of this facility is to obtain mechanical property data for LMFBR materials in creep and low cycle fatigue testing in flowing sodium. ML-3 includes 10 test stations for creep and two for fatigue. It is possible to operate simultaneously at three different temperature levels. The maximum operating temperature is 650 deg C at flow velocities up to 5 m/s. The ML-3 loop has been located in a manner that permits the fill/dump tank cover gas and security systems to be shared with an earlier circuit, the ML-1. (author)

  2. Tuning OpenACC loop execution

    KAUST Repository

    Feki, Saber

    2017-01-07

    The purpose of this chapter is to help OpenACC developer who is already familiar with the basic and essential directives to further improve his code performance by adding more descriptive clauses to OpenACC loop constructs. At the end of this chapter the reader will: • Have a better understanding of the purpose of the OpenACC loop construct and its associated clauses illustrated with use cases • Use the acquired knowledge in practice to further improve the performance of OpenACC accelerated codes

  3. Topspin networks in loop quantum gravity

    International Nuclear Information System (INIS)

    Duston, Christopher L

    2012-01-01

    We discuss the extension of loop quantum gravity to topspin networks, a proposal which allows topological information to be encoded in spin networks. We will show that this requires minimal changes to the phase space, C*-algebra and Hilbert space of cylindrical functions. We will also discuss the area and Hamiltonian operators, and show how they depend on the topology. This extends the idea of ‘background independence’ in loop quantum gravity to include topology as well as geometry. It is hoped this work will confirm the usefulness of the topspin network formalism and open up several new avenues for research into quantum gravity. (paper)

  4. Loop quantum gravity in asymptotically flat spaces

    International Nuclear Information System (INIS)

    Arnsdorf, M.

    2000-01-01

    This thesis describes applications and extensions of the loop variable approach to non-perturbative quantum gravity. The common theme of the work presented, is the need to generalise loop quantum gravity to be applicable in cases where space is asymptotically flat, and no longer compact as is usually assumed. This is important for the study of isolated gravitational systems. It also presents a natural context in which to search for the semi-classical limit, one of the main outstanding problems in loop quantum gravity. In the first part of the thesis we study how isolated gravitational systems can be attributed particle-like properties. In particular, we show how spinorial states can arise in pure loop quantum gravity if spatial topology is non-trivial, thus confirming an old conjecture of Friedman and Sorkin. Heuristically, this corresponds to the idea that we can rotate isolated regions of spatial topology relative to the environment at infinity, and that only a 4π-rotation will take us back to the original configuration. To do this we extend the standard loop quantum gravity formalism by introducing a compactification of our non-compact spatial manifold, and study the knotting of embedded graphs. The second part of the thesis takes a more systematic approach to the study of loop quantum gravity on non-compact spaces. We look for new representations of the loop algebra, which give rise to quantum theories that are inequivalent to the standard one. These theories naturally describe excitations of a fiducial background state, which is specified via the choice of its vacuum expectation values. In particular, we can choose background states that describe the geometries of non-compact manifolds. We also discuss how suitable background states can be constructed that can approximate classical phase space data, in our case holonomies along embedded paths and geometrical quantities related to areas and volumes. These states extend the notion of the weave and provide a

  5. Automation of one-loop QCD corrections

    CERN Document Server

    Hirschi, Valentin; Frixione, Stefano; Garzelli, Maria Vittoria; Maltoni, Fabio; Pittau, Roberto

    2011-01-01

    We present the complete automation of the computation of one-loop QCD corrections, including UV renormalization, to an arbitrary scattering process in the Standard Model. This is achieved by embedding the OPP integrand reduction technique, as implemented in CutTools, into the MadGraph framework. By interfacing the tool so constructed, which we dub MadLoop, with MadFKS, the fully automatic computation of any infrared-safe observable at the next-to-leading order in QCD is attained. We demonstrate the flexibility and the reach of our method by calculating the production rates for a variety of processes at the 7 TeV LHC.

  6. R-loops cause genomic instability in T helper lymphocytes from patients with Wiskott-Aldrich syndrome.

    Science.gov (United States)

    Sarkar, Koustav; Han, Seong-Su; Wen, Kuo-Kuang; Ochs, Hans D; Dupré, Loïc; Seidman, Michael M; Vyas, Yatin M

    2017-12-15

    Wiskott-Aldrich syndrome (WAS), X-linked thrombocytopenia (XLT), and X-linked neutropenia, which are caused by WAS mutations affecting Wiskott-Aldrich syndrome protein (WASp) expression or activity, manifest in immunodeficiency, autoimmunity, genomic instability, and lymphoid and other cancers. WASp supports filamentous actin formation in the cytoplasm and gene transcription in the nucleus. Although the genetic basis for XLT/WAS has been clarified, the relationships between mutant forms of WASp and the diverse features of these disorders remain ill-defined. We sought to define how dysfunctional gene transcription is causally linked to the degree of T H cell deficiency and genomic instability in the XLT/WAS clinical spectrum. In human T H 1- or T H 2-skewing cell culture systems, cotranscriptional R-loops (RNA/DNA duplex and displaced single-stranded DNA) and DNA double-strand breaks (DSBs) were monitored in multiple samples from patients with XLT and WAS and in normal T cells depleted of WASp. WASp deficiency provokes increased R-loops and R-loop-mediated DSBs in T H 1 cells relative to T H 2 cells. Mechanistically, chromatin occupancy of serine 2-unphosphorylated RNA polymerase II is increased, and that of topoisomerase 1, an R-loop preventing factor, is decreased at R-loop-enriched regions of IFNG and TBX21 (T H 1 genes) in T H 1 cells. These aberrations accompany increased unspliced (intron-retained) and decreased spliced mRNA of IFNG and TBX21 but not IL13 (T H 2 gene). Significantly, increased cellular load of R-loops and DSBs, which are normalized on RNaseH1-mediated suppression of ectopic R-loops, inversely correlates with disease severity scores. Transcriptional R-loop imbalance is a novel molecular defect causative in T H 1 immunodeficiency and genomic instability in patients with WAS. The study proposes that cellular R-loop load could be used as a potential biomarker for monitoring symptom severity and prognostic outcome in the XLT-WAS clinical spectrum

  7. Multi-loop PWR modeling and hardware-in-the-loop testing using ACSL

    International Nuclear Information System (INIS)

    Thomas, V.M.; Heibel, M.D.; Catullo, W.J.

    1989-01-01

    Westinghouse has developed an Advanced Digital Feedwater Control System (ADFCS) which is aimed at reducing feedwater related reactor trips through improved control performance for pressurized water reactor (PWR) power plants. To support control system setpoint studies and functional design efforts for the ADFCS, an ACSL based model of the nuclear steam supply system (NSSS) of a Westinghouse (PWR) was generated. Use of this plant model has been extended from system design to system testing through integration of the model into a Hardware-in-Loop test environment for the ADFCS. This integration includes appropriate interfacing between a Gould SEL 32/87 computer, upon which the plant model executes in real time, and the Westinghouse Distributed Processing family (WDPF) test hardware. A development program has been undertaken to expand the existing ACSL model to include capability to explicitly model multiple plant loops, steam generators, and corresponding feedwater systems. Furthermore, the program expands the ADFCS Hardware-in-Loop testing to include the multi-loop plant model. This paper provides an overview of the testing approach utilized for the ADFCS with focus on the role of Hardware-in-Loop testing. Background on the plant model, methodology and test environment is also provided. Finally, an overview is presented of the program to expand the model and associated Hardware-in-Loop test environment to handle multiple loops

  8. Fundamental and Harmonic Oscillations in Neighboring Coronal Loops

    Science.gov (United States)

    Li, Hongbo; Liu, Yu; Vai Tam, Kuan

    2017-06-01

    We present observations of multimode (fundamental and harmonic) oscillations in a loop system, which appear to be simultaneously excited by a GOES C-class flare. Analysis of the periodic oscillations reveals that (1) the primary loop with a period of P a ≈ 4 minutes and a secondary loop with two periods of P a ≈ 4 minutes and P b ≈ 2 minutes are detected simultaneously in closely spaced loop strands; (2) both oscillation components have their peak amplitudes near the loop apex, while in the second loop the low-frequency component P a dominates in a loop segment that is two times larger than the high-frequency component P b ; (3) the harmonic mode P b shows the largest deviation from a sinusoidal loop shape at the loop apex. We conclude that multiple harmonic modes with different displacement profiles can be excited simultaneously even in closely spaced strands, similar to the overtones of a violin string.

  9. DNA supercoiling: changes during cellular differentiation and activation of chromatin transcription

    International Nuclear Information System (INIS)

    Luchnik, A.N.; Bakayev, V.V.; Glaser, V.M.; Moscow State Univ., USSR)

    1983-01-01

    In this paper it is reported that elastic DNA torsional tension has been observed in a fraction of isolated SV40 minichromosomes, which are shown to be transcriptionally active, and that the number of DNA topological (titratable superhelical) turns in closed superhelical loops of nuclear DNA decreases during cellular differentiation, which, we propose, may be responsible for the coordinate switch in transcription of genes controlling cellular proliferation. 37 references, 6 figures, 2 tables

  10. Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

    KAUST Repository

    Ariel, Federico D.; Jé gu, Teddy; Latrasse, David; Romero-Barrios, Natali; Christ, Auré lie; Benhamed, Moussa; Crespi, Martí n D.

    2014-01-01

    The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.

  11. Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

    KAUST Repository

    Ariel, Federico D.

    2014-08-01

    The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes. © 2014 Elsevier Inc.

  12. Development of Capillary Loop Convective Polymerase Chain Reaction Platform with Real-Time Fluorescence Detection

    Directory of Open Access Journals (Sweden)

    Wen-Pin Chou

    2017-02-01

    Full Text Available Polymerase chain reaction (PCR has been one of the principal techniques of molecular biology and diagnosis for decades. Conventional PCR platforms, which work by rapidly heating and cooling the whole vessel, need complicated hardware designs, and cause energy waste and high cost. On the other hand, partial heating on the various locations of vessels to induce convective solution flows by buoyancy have been used for DNA amplification in recent years. In this research, we develop a new convective PCR platform, capillary loop convective polymerase chain reaction (clcPCR, which can generate one direction flow and make the PCR reaction more stable. The U-shaped loop capillaries with 1.6 mm inner diameter are designed as PCR reagent containers. The clcPCR platform utilizes one isothermal heater for heating the bottom of the loop capillary and a CCD device for detecting real-time amplifying fluorescence signals. The stable flow was generated in the U-shaped container and the amplification process could be finished in 25 min. Our experiments with different initial concentrations of DNA templates demonstrate that clcPCR can be applied for precise quantification. Multiple sample testing and real-time quantification will be achieved in future studies.

  13. PHOTOSPHERIC PROPERTIES OF WARM EUV LOOPS AND HOT X-RAY LOOPS

    Energy Technology Data Exchange (ETDEWEB)

    Kano, R. [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Ueda, K. [Department of Astronomy, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Tsuneta, S., E-mail: ryouhei.kano@nao.ac.jp [Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Chuo, Sagamihara, Kanagawa 252-5210 (Japan)

    2014-02-20

    We investigate the photospheric properties (vector magnetic fields and horizontal velocity) of a well-developed active region, NOAA AR 10978, using the Hinode Solar Optical Telescope specifically to determine what gives rise to the temperature difference between ''warm loops'' (1-2 MK), which are coronal loops observed in EUV wavelengths, and ''hot loops'' (>3 MK), coronal loops observed in X-rays. We found that outside sunspots, the magnetic filling factor in the solar network varies with location and is anti-correlated with the horizontal random velocity. If we accept that the observed magnetic features consist of unresolved magnetic flux tubes, this anti-correlation can be explained by the ensemble average of flux-tube motion driven by small-scale random flows. The observed data are consistent with a flux tube width of ∼77 km and horizontal flow at ∼2.6 km s{sup –1} with a spatial scale of ∼120 km. We also found that outside sunspots, there is no significant difference between warm and hot loops either in the magnetic properties (except for the inclination) or in the horizontal random velocity at their footpoints, which are identified with the Hinode X-Ray Telescope and the Transition Region and Coronal Explorer. The energy flux injected into the coronal loops by the observed photospheric motion of the magnetic fields is estimated to be 2 × 10{sup 6} erg s{sup –1} cm{sup –2}, which is the same for both warm and hot loops. This suggests that coronal properties (e.g., loop length) play a more important role in giving rise to temperature differences of active-region coronal loops than photospheric parameters.

  14. Detection of circular telomeric DNA without 2D gel electrophoresis.

    Science.gov (United States)

    Dlaska, Margit; Anderl, Conrad; Eisterer, Wolfgang; Bechter, Oliver E

    2008-09-01

    The end of linear chromosomes forms a lasso-like structure called the t-loop. Such t-loops resemble a DNA recombination intermediate, where the single-stranded 3' overhang is arrested in a stretch of duplex DNA. Presumably, such a t-loop can also be deleted via a recombination process. This would result in the occurrence of circular extrachromosomal telomeric DNA (t-circles), which are known to be abundantly present in immortal cells engaging the recombination-based alternative lengthening of telomeres pathway (ALT pathway). Little is known about the basic mechanism of telomeric recombination in these cells and what ultimately causes the generation of such t-circles. Current standard procedures for detecting these molecules involve 2D gel electrophoresis or electron microscopy. However, both methods are labor intense and sophisticated to perform. Here, we present a simpler, faster, and equally sensitive method for detecting t-circles. Our approach is a telomere restriction fragment assay that involves the enzymatic preservation of circular DNA with Klenow enzyme followed by Bal31 degradation of the remaining linear DNA molecules. We show that with this approach t-circles can be detected in ALT cell lines, whereas no t-circles are present in telomerase-positive cell lines. We consider our approach a valid method in which t-circle generation is the experimental readout.

  15. Detection of early and single infections of Schistosoma japonicum in the intermediate host snail, Oncomelania hupensis, by PCR and loop-mediated isothermal amplification (LAMP) assay.

    Science.gov (United States)

    Kumagai, Takashi; Furushima-Shimogawara, Rieko; Ohmae, Hiroshi; Wang, Tian-Ping; Lu, Shaohong; Chen, Rui; Wen, Liyong; Ohta, Nobuo

    2010-09-01

    Polymerase chain reaction (PCR) with the specific primer set amplifying 28S ribosomal DNA (rDNA) of Schistosoma japonicum was able to detect genomic DNA of S. japonicum, but not S. mansoni, at 100 fg. This procedure enabled us to detect the DNA from a single miracidium and a snail infected with one miracidium at just 1 day after infection. We compared these results with those from loop-mediated isothermal amplification (LAMP) targeting 28S rDNA and found similar results. The LAMP could amplify the specific DNA from a group of 100 normal snails mixed with one infected snail A PCR screening of infected snails from endemic regions in Anhui Province revealed schistosomal DNA even in snails found negative by microscopy. PCR and LAMP show promise for monitoring the early infection rate in snails, and they may be useful for predicting the risk of infection in the endemic places.

  16. Loop-mediated isothermal amplification (LAMP) based detection of Colletotrichum falcatum causing red rot in sugarcane.

    Science.gov (United States)

    Chandra, Amaresh; Keizerweerd, Amber T; Que, Youxiong; Grisham, Michael P

    2015-08-01

    Red rot, caused by Colletotrichum falcatum, is a destructive disease prevalent in most sugarcane-producing countries. Disease-free sugarcane planting materials (setts) are essential as the pathogen spreads primarily through infected setts. The present study was undertaken to develop a loop-mediated isothermal amplification (LAMP) assay for the detection of C. falcatum. C. falcatum genomic DNA was isolated from pure mycelium culture and infected tissues. Four sets of primers corresponding to a unique DNA sequence specific to C. falcatum were designed. Specificity of the LAMP test was checked with DNA of another fungal pathogen of sugarcane, Puccinia melanocephala, as well as two closely-related species, Colletotrichum fructivorum and Colletotrichum acutatum. No reaction was found with the three pathogens. When C. falcatum DNA from pure culture was used in a detection limit analysis, sensitivity of the LAMP method was observed to be ten times higher than that of conventional PCR; however, sensitivity was only 5 times higher when DNA from C. falcatum-infected tissues was used. Using the LAMP assay, C. falcatum DNA is amplified with high specificity, efficiency, and rapidity under isothermal conditions. Moreover, visual judgment of color change in <1 h without further post-amplification processing makes the LAMP method convenient, economical, and useful in diagnostic laboratories and the field.

  17. Parallelizing More Loops with Compiler Guided Refactoring

    DEFF Research Database (Denmark)

    Larsen, Per; Ladelsky, Razya; Lidman, Jacob

    2012-01-01

    an interactive compilation feedback system that guides programmers in iteratively modifying their application source code. This helps leverage the compiler’s ability to generate loop-parallel code. We employ our system to modify two sequential benchmarks dealing with image processing and edge detection...

  18. Loop quantum gravity; Gravedad cuantica de lazos

    Energy Technology Data Exchange (ETDEWEB)

    Pullin, J.

    2015-07-01

    Loop quantum gravity is one of the approaches that are being studied to apply the rules of quantum mechanics to the gravitational field described by the theory of General Relativity . We present an introductory summary of the main ideas and recent results. (Author)

  19. Potential drop sensors for sodium loops

    International Nuclear Information System (INIS)

    Selvaraj, R.

    1978-11-01

    Potential drop sensors to detect the presence or the absence of sodium in pipe lines are described. These are very handy during loop charging and dumping operations. Their suitability to detect level surges and to monitor continuous level of liquid metals in certain applications is discussed. (author)

  20. Loop residues and catalysis in OMP synthase

    DEFF Research Database (Denmark)

    Wang, Gary P.; Hansen, Michael Riis; Grubmeyer, Charles

    2012-01-01

    binding of OMP or PRPP in binary complexes was affected little by loop mutation, suggesting that the energetics of ground-state binding have little contribution from the catalytic loop, or that a favorable binding energy is offset by costs of loop reorganization. Pre-steady-state kinetics for mutants...... values for all four substrate molecules. The 20% (i.e., 1.20) intrinsic [1?-3H]OMP kinetic isotope effect (KIE) for WT is masked because of high forward and reverse commitment factors. K103A failed to express intrinsic KIEs fully (1.095 ± 0.013). In contrast, H105A, which has a smaller catalytic lesion...... (preceding paper in this issue, DOI 10.1021/bi300083p)]. The full expression of KIEs by H105A and E107A may result from a less secure closure of the catalytic loop. The lower level of expression of the KIE by K103A suggests that in these mutant proteins the major barrier to catalysis is successful closure...

  1. Quenched Chiral Perturbation Theory to one loop

    NARCIS (Netherlands)

    Colangelo, G.; Pallante, E.

    The divergences of the generating functional of quenched Chiral Perturbation theory (qCHPT) to one loop are computed in closed form. We show how the quenched chiral logarithms can be reabsorbed in the renormalization of the B0 parameter of the leading order Lagrangian. Finally, we do the chiral

  2. CMOS switched current phase-locked loop

    NARCIS (Netherlands)

    Leenaerts, D.M.W.; Persoon, G.G.; Putter, B.M.

    1997-01-01

    The authors present an integrated circuit realisation of a switched current phase-locked loop (PLL) in standard 2.4 µm CMOS technology. The centre frequency is tunable to 1 MHz at a clock frequency of 5.46 MHz. The PLL has a measured maximum phase error of 21 degrees. The chip consumes

  3. Semiclassical analysis of loop quantum gravity

    International Nuclear Information System (INIS)

    Conrady, F.

    2005-01-01

    In this Ph.D. thesis, we explore and develop new methods that should help in determining an effective semiclassical description of canonical loop quantum gravity and spin foam gravity. A brief introduction to loop quantum gravity is followed by three research papers that present the results of the Ph.D. project. In the first article, we deal with the problem of time and a new proposal for implementing proper time as boundary conditions in a sum over histories: we investigate a concrete realization of this formalism for free scalar field theory. In the second article, we translate semiclassical states of linearized gravity into states of loop quantum gravity. The properties of the latter indicate how semiclassicality manifests itself in the loop framework, and how this may be exploited for doing semiclassical expansions. In the third part, we propose a new formulation of spin foam models that is fully triangulation- and background-independent: by means of a symmetry condition, we identify spin foam models whose triangulation-dependence can be naturally removed. (orig.)

  4. Semiclassical analysis of loop quantum gravity

    Energy Technology Data Exchange (ETDEWEB)

    Conrady, F.

    2005-10-17

    In this Ph.D. thesis, we explore and develop new methods that should help in determining an effective semiclassical description of canonical loop quantum gravity and spin foam gravity. A brief introduction to loop quantum gravity is followed by three research papers that present the results of the Ph.D. project. In the first article, we deal with the problem of time and a new proposal for implementing proper time as boundary conditions in a sum over histories: we investigate a concrete realization of this formalism for free scalar field theory. In the second article, we translate semiclassical states of linearized gravity into states of loop quantum gravity. The properties of the latter indicate how semiclassicality manifests itself in the loop framework, and how this may be exploited for doing semiclassical expansions. In the third part, we propose a new formulation of spin foam models that is fully triangulation- and background-independent: by means of a symmetry condition, we identify spin foam models whose triangulation-dependence can be naturally removed. (orig.)

  5. Looping up Professional Reflection in Honours Programmes

    Science.gov (United States)

    Van Dijk, Trijntje

    2012-01-01

    Within the Saxion Universities in the Netherlands, a profile of the "Reflective Professional" comprises a number of competencies that the honours programmes are designed to develop and support. This article describes the process of developing these competencies. The process involves three loops of learning, characterized by three sets of…

  6. Wilson-loop symmetry breaking reexamined

    International Nuclear Information System (INIS)

    Nakamura, A.; Shiraishi, K.

    1988-07-01

    The splitting in the energy of gauge field vacua on non-simply connected space S 3 /Z 2 is reconsidered. We show the calculation to the one-loop level for a Yang-Mills vector with a ghost field. We confirm our previous result and give a solution to the question offered by Freire, Romao and Barroso. (author)

  7. The Alpine loop of the tethys zone

    NARCIS (Netherlands)

    Bemmelen, R.W. van

    The Alpine loop in Europe results from semi-autochthonous crustal movements which are restricted to the mobile Tethys zone. Its evolution cannot be explained by a uniform northward drift and push of the African continent; it has to be sought, in the first place, in geodynamic processes occurring in

  8. Spontaneous fluxoid formation in superconducting loops

    DEFF Research Database (Denmark)

    Monaco, R.; Mygind, Jesper; Rivers, R.

    2009-01-01

    We report on the experimental verification of the Zurek-Kibble scenario in an isolated superconducting ring over a wide parameter range. The probability of creating a single flux quantum spontaneously during the fast normal-superconducting phase transition of a wide Nb loop clearly follows...

  9. Selective purge for hydrogenation reactor recycle loop

    Science.gov (United States)

    Baker, Richard W.; Lokhandwala, Kaaeid A.

    2001-01-01

    Processes and apparatus for providing improved contaminant removal and hydrogen recovery in hydrogenation reactors, particularly in refineries and petrochemical plants. The improved contaminant removal is achieved by selective purging, by passing gases in the hydrogenation reactor recycle loop or purge stream across membranes selective in favor of the contaminant over hydrogen.

  10. String loop effect on the BRST charge

    International Nuclear Information System (INIS)

    Das, A.; Nishino, H.

    1987-07-01

    An effective BRST charge Q BRST which incorporates the string one-loop corrections is presented for the closed bosonic string in an arbitrary background. The effective σ-model action which leads to such a Q BRST is obtained and some consequences are discussed. (author). 14 refs, 1 fig

  11. Logical inference techniques for loop parallelization

    KAUST Repository

    Oancea, Cosmin E.; Rauchwerger, Lawrence

    2012-01-01

    This paper presents a fully automatic approach to loop parallelization that integrates the use of static and run-time analysis and thus overcomes many known difficulties such as nonlinear and indirect array indexing and complex control flow. Our hybrid analysis framework validates the parallelization transformation by verifying the independence of the loop's memory references. To this end it represents array references using the USR (uniform set representation) language and expresses the independence condition as an equation, S = Ø, where S is a set expression representing array indexes. Using a language instead of an array-abstraction representation for S results in a smaller number of conservative approximations but exhibits a potentially-high runtime cost. To alleviate this cost we introduce a language translation F from the USR set-expression language to an equally rich language of predicates (F(S) ⇒ S = Ø). Loop parallelization is then validated using a novel logic inference algorithm that factorizes the obtained complex predicates (F(S)) into a sequence of sufficient-independence conditions that are evaluated first statically and, when needed, dynamically, in increasing order of their estimated complexities. We evaluate our automated solution on 26 benchmarks from PERFECTCLUB and SPEC suites and show that our approach is effective in parallelizing large, complex loops and obtains much better full program speedups than the Intel and IBM Fortran compilers. Copyright © 2012 ACM.

  12. Afferent loop syndrome - a case report

    International Nuclear Information System (INIS)

    Borges, Ana Karina Nascimento; Pinheiro, Marco Antonio Lopes; Galvao, Cristine Norwig

    2000-01-01

    The afferent loop syndrome occurs in patients with previous gastric surgery for tumor, when there is anastomotic edema, use of inappropriate reconstruction technique for gastro jejunostomy or recurrent gastric cancer. Complaints such jaundice, intermittent abdominal distension associated with pain, and vomiting should be investigated in order to rule out this syndrome. (author)

  13. Aesthetic rehabilitation with multiple loop connectors

    Directory of Open Access Journals (Sweden)

    Ashish Kalra

    2013-01-01

    Full Text Available Patients with a missing tooth along with diastema have limited treatment options to restore the edentulous space. The use of a conventional fixed partial denture (FPD to replace the missing tooth may result in too wide anterior teeth leading to poor esthetics. The diastema resulting from the missing central incisors can be managed with implant-supported prosthesis or FPD with loop connectors. An old lady reported with chief complaints of missing upper anterior teeth due to trauma. Her past dental history revealed that she was having generalized spacing between her upper anterior teeth. Considering her esthetic requirement of maintaining the diastema between 12, 11, 22, and 21, the treatment option of 06 units porcelain fused to metal FPD from canine to canine with intermittent loop connectors between 21, 22, 11, 12 was planned. Connectors basically link different parts of FPDs. The modified FPD with loop connectors enhanced the natural appearance of the restoration, maintained the diastemas and the proper emergence profile, and preserve the remaining tooth structure of abutment teeth. This clinical report discussed a method for fabrication of a modified FPD with loop connectors to restore the wide span created by missing central incisors.

  14. Loop quasi-invariant chunk detection

    DEFF Research Database (Denmark)

    Moyen, Jean-Yves; Rubiano, Thomas; Seiller, Thomas

    2017-01-01

    Several techniques for analysis and transformations are used in compilers. Among them, the peeling of loops for hoisting quasi-invariants can be used to optimize generated code, or simply ease developers’ lives. In this paper, we introduce a new concept of dependency analysis borrowed from the fi...

  15. Tuning OpenACC loop execution

    KAUST Repository

    Feki, Saber; Smaoui, Malek

    2017-01-01

    The purpose of this chapter is to help OpenACC developer who is already familiar with the basic and essential directives to further improve his code performance by adding more descriptive clauses to OpenACC loop constructs. At the end

  16. Particle Scattering in Loop Quantum Gravity

    International Nuclear Information System (INIS)

    Modesto, Leonardo; Rovelli, Carlo

    2005-01-01

    We devise a technique for defining and computing n-point functions in the context of a background-independent gravitational quantum field theory. We construct a tentative implementation of this technique in a perturbatively finite model defined using spin foam techniques in the context of loop quantum gravity

  17. Local expressions for one-loop calculations

    International Nuclear Information System (INIS)

    Wasson, D.A.; Koonin, S.E.

    1991-01-01

    We develop local expressions for the contributions of the short-wavelength vacuum modes to the one-loop vacuum energy. These expressions significantly improve the convergence properties of various ''brute-force'' calculational methods. They also provide a continuous series of approximations that interpolate between the brute-force calculations and the derivative expansion

  18. Prediction of protein loop geometries in solution

    NARCIS (Netherlands)

    Rapp, Chaya S.; Strauss, Temima; Nederveen, Aart; Fuentes, Gloria

    2007-01-01

    The ability to determine the structure of a protein in solution is a critical tool for structural biology, as proteins in their native state are found in aqueous environments. Using a physical chemistry based prediction protocol, we demonstrate the ability to reproduce protein loop geometries in

  19. Associated technologies ensures complete loop mediated ...

    African Journals Online (AJOL)

    Loop Mediated Isothermal Amplification (LAMP) assay could be a useful adjunct diagnostic assay along with the conventional methods that would preclude the requirement of continuous maintenance of pure cultures. Moreover, LAMP assay is simple, rapid, specific and sensitive for the detection of pathogens. Having ...

  20. Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA.

    Science.gov (United States)

    Zhang, Jia-yu; Zheng, Ke-wei; Xiao, Shan; Hao, Yu-hua; Tan, Zheng

    2014-01-29

    We recently reported that a DNA:RNA hybrid G-quadruplex (HQ) forms during transcription of DNA that bears two or more tandem guanine tracts (G-tract) on the nontemplate strand. Putative HQ-forming sequences are enriched in the nearby 1000 nt region right downstream of transcription start sites in the nontemplate strand of warm-blooded animals, and HQ regulates transcription under both in vitro and in vivo conditions. Therefore, knowledge of the mechanism of HQ formation is important for understanding the biological function of HQ as well as for manipulating gene expression by targeting HQ. In this work, we studied the mechanism of HQ formation using an in vitro T7 transcription model. We show that RNA synthesis initially produces an R-loop, a DNA:RNA heteroduplex formed by a nascent RNA transcript and the template DNA strand. In the following round of transcription, the RNA in the R-loop is displaced, releasing the RNA in single-stranded form (ssRNA). Then the G-tracts in the RNA can jointly form HQ with those in the nontemplate DNA strand. We demonstrate that the structural cascade R-loop → ssRNA → HQ offers opportunities to intercept HQ formation, which may provide a potential method to manipulate gene expression.

  1. Loop Evolution Observed with AIA and Hi-C

    Science.gov (United States)

    Mulu-Moore, Fana; Winebarger, Amy R.; Cirtain, Jonathan W.; Kobayashi, Ken; Korreck, Kelly E.; Golub, Leon; Kuzin, Sergei; Walsh, Robert William; DeForest, Craig E.; De Pontieu, Bart; hide

    2012-01-01

    In the past decade, the evolution of EUV loops has been used to infer the loop substructure. With the recent launch of High Resolution Coronal Imager (Hi-C), this inference can be validated. In this presentation we discuss the first results of loop analysis comparing AIA and Hi-C data. In the past decade, the evolution of EUV loops has been used to infer the loop substructure. With the recent launch of High Resolution Coronal Imager (Hi-C), this inference can be validated. In this presentation we discuss the first results of loop analysis comparing AIA and Hi-C data.

  2. Cooling Active Region Loops Observed With SXT and TRACE

    OpenAIRE

    Winebarger, Amy R.; Warren, Harry P.

    2005-01-01

    An Impulsive Heating Multiple Strand (IHMS) Model is able to reproduce the observational characteristics of EUV (~ 1 MK) active region loops. This model implies that some of the loops must reach temperatures where X-ray filters are sensitive (> 2.5 MK) before they cool to EUV temperatures. Hence, some bright EUV loops must be preceded by bright X-ray loops. Previous analysis of X-ray and EUV active region observations, however, have concluded that EUV loops are not preceded by X-ray loops. In...

  3. Effect of vacancy loops on swelling of metals under irradiation

    International Nuclear Information System (INIS)

    Golubov, S.I.

    1981-01-01

    Subsequent analysis of vacancy loops formation in metals under irradiation is carried out and effect of vacancy loops on vacancy porosity is studied. Expression for quasistationary function of vacancy loops distribution according to sizes taking into consideration two mechanisms of their initiation-cascade and fluctuational ones - is obtained. It is shown that rate of vacancy absorption and interstitials by vacancy loops in quasiequilibrium state is similar and depends only on summary length of loops, for its calculations the self-coordinated procedure is formulated. For the rate of metal swelling under irradiation obtained is the expression taking into consideration the presence of vacancy loops [ru

  4. Thermal instabilities in magnetically confined plasmas: Solar coronal loops

    International Nuclear Information System (INIS)

    Habbal, S.R.; Rosner, R.

    1979-01-01

    The thermal stability of confined solar coronal structures (''loops'') is investigated, following both normal mode and a new, global instability analysis. We demonstrate that: (a) normal mode analysis shows modes with size scales comparable to that of loops to be unstable, but to be strongly affected by the loop boundary conditions; (b) a global analysis, based upon variation of the total loop energy losses and gains, yields loop stability conditions for global modes dependent upon the coronal loop heating process, with magnetically coupled heating processes giving marginal stability. The connection between the present analysis and the minimum flux corona of Hearn is also discussed

  5. Constructing QCD one-loop amplitudes

    International Nuclear Information System (INIS)

    Forde, D

    2008-01-01

    In the context of constructing one-loop amplitudes using a unitarity bootstrap approach we discuss a general systematic procedure for obtaining the coefficients of the scalar bubble and triangle integral functions of one-loop amplitudes. Coefficients are extracted after examining the behavior of the cut integrand as the unconstrained parameters of a specifically chosen parameterization of the cut loop momentum approach infinity. Measurements of new physics at the forthcoming experimental program at CERN's Large Hadron Collider (LHC) will require a precise understanding of processes at next-to-leading order (NLO). This places increased demands for the computation of new one-loop amplitudes. This in turn has spurred recent developments towards improved calculational techniques. Direct calculations using Feynman diagrams are in general inefficient. Developments of more efficient techniques have usually centered around unitarity techniques [1], where tree amplitudes are effectively 'glued' together to form loops. The most straightforward application of this method, in which the cut loop momentum is in D = 4, allows for the computation of 'cut-constructible' terms only, i.e. (poly)logarithmic containing terms and any related constants. QCD amplitudes contain, in addition to such terms, rational pieces which cannot be derived using such cuts. These 'missing' rational parts can be extracted using cut loop momenta in D = 4-2 (var e psilon). The greater difficulty of such calculations has restricted the application of this approach, although recent developments [3, 4] have provided new promise for this technique. Recently the application of on-shell recursion relations [5] to obtaining the 'missing' rational parts of one-loop processes [6] has provided an alternative very promising solution to this problem. In combination with unitarity methods an 'on-shell bootstrap' approach provides an efficient technique for computing complete one-loop QCD amplitudes [7]. Additionally

  6. LOOP CALCULUS AND BELIEF PROPAGATION FOR Q-ARY ALPHABET: LOOP TOWER

    Energy Technology Data Exchange (ETDEWEB)

    CHERTKOV, MICHAEL [Los Alamos National Laboratory; CHERNYAK, VLADIMIR [Los Alamos National Laboratory

    2007-01-10

    Loop calculus introduced in [1], [2] constitutes a new theoretical tool that explicitly expresses symbol Maximum-A-Posteriori (MAP) solution of a general statistical inference problem via a solution of the Belief Propagation (BP) equations. This finding brought a new significance to the BP concept, which in the past was thought of as just a loop-free approximation. In this paper they continue a discussion of the Loop Calculus, partitioning the results into three Sections. In Section 1 they introduce a new formulation of the Loop Calculus in terms of a set of transformations (gauges) that keeping the partition function of the problem invariant. The full expression contains two terms referred to as the 'ground state' and 'excited states' contributions. The BP equations are interpreted as a special (BP) gauge fixing condition that emerges as a special orthogonality constraint between the ground state and excited states, which also selects loop contributions as the only surviving ones among the excited states. In Section 2 they demonstrate how the invariant interpretation of the Loop Calculus, introduced in Section 1, allows a natural extension to the case of a general q-ary alphabet, this is achieved via a loop tower sequential construction. The ground level in the tower is exactly equivalent to assigning one color (out of q available) to the 'ground state' and considering all 'excited' states colored in the remaining (q-1) colors, according to the loop calculus rule. Sequentially, the second level in the tower corresponds to selecting a loop from the previous step, colored in (q-1) colors, and repeating the same ground vs excited states splitting procedure into one and (q-2) colors respectively. The construction proceeds till the full (q-1)-levels deep loop tower (and the corresponding contributions to the partition function) are established. In Section 3 they discuss an ultimate relation between the loop calculus and the Bethe

  7. WWER type reactor primary loop imitation on large test loop facility in MARIA reactor

    International Nuclear Information System (INIS)

    Moldysh, A.; Strupchevski, A.; Kmetek, Eh.; Spasskov, V.P.; Shumskij, A.M.

    1982-01-01

    At present in Poland in cooperation with USSR a nuclear water loop test facility (WL) in 'MARIA' reactor in Sverke is under construction. The program objective is to investigate processes occuring in WWER reactor under emergency conditions, first of all after the break of the mainprimary loop circulation pipe-line. WL with the power of about 600 kW consists of three major parts: 1) an active loop, imitating the undamaged loops of the WWER reactor; 2) a passive loop assignedfor modelling the broken loop of the WWER reactor; 3) the emergency core cooling system imitating the corresponding full-scale system. The fuel rod bundle consists of 18 1 m long rods. They were fabricated according to the standard WWER fuel technology. In the report some general principles of WWERbehaviour imitation under emergency conditions are given. They are based on the operation experience obtained from 'SEMISCALE' and 'LOFT' test facilities in the USA. A description of separate modelling factors and criteria effects on the development of 'LOCA'-type accident is presented (the break cross-section to the primary loop volume ratio, the pressure differential between inlet and outlet reactor chambers, the pressure drop rate in the loop, the coolant flow rate throuh the core etc.). As an example a comparison of calculated flow rate variations for the WWER-1000 reactor and the model during the loss-of-coolant accident with the main pipe-line break at the core inlet is given. Calculations have been carried out with the use of TECH'-M code [ru

  8. Computational stability appraisal of rectangular natural circulation loop: Effect of loop inclination

    International Nuclear Information System (INIS)

    Krishnani, Mayur; Basu, Dipankar N.

    2017-01-01

    Highlights: • Computational model developed for single-phase rectangular natural circulation loop. • Role of loop inclination to vertical on thermalhydraulic stability is explored. • Inclination has strong stabilizing effect due to lower effective gravitation force. • Increase in tilt angle reduces settling time and highest amplitude of oscillation. • An angle of 15° is suggested for the selected loop geometry. - Abstract: Controlling stability behavior of single-phase natural circulation loops, without significantly affecting its steady-state characteristics, is a topic of wide research interest. Present study explores the role of loop inclination on a particular loop geometry. Accordingly a 3D computational model of a rectangular loop is developed and transient conservation equations are solved to obtain the temporal variation in flow parameters. Starting from the quiescent state, simulations are performed for selected sets of operating conditions and also with a few selected inclination angles. System experiences instability at higher heater powers and also with higher sink temperatures. Inclination is found to have a strong stabilizing influence owing to the reduction in the effective gravitational acceleration and subsequent decline in local buoyancy effects. The settling time and highest amplitude of oscillations substantially reduces for a stable system with a small inclination. Typically-unstable systems can also suppress the oscillations, when subjected to tilting, within a reasonable period of time. It is possible to stabilize the loop within shorter time span by increasing the tilt angle, but at the expense of reduction in steady-state flow rate. Overall a tilt angle of 15° is suggested for the selected geometry. Results from the 3D model is compared with the predictions from an indigenous 1D code. While similar qualitative influence of inclination is observed, the 1D model predicts early appearance of the stability threshold and hence hints

  9. Single Molecule Study of DNA Organization and Recombination

    Science.gov (United States)

    Xiao, Botao

    We have studied five projects related to DNA organization and recombination using mainly single molecule force-spectroscopy and statistical tools. First, HU is one of the most abundant DNA-organizing proteins in bacterial chromosomes and participates in gene regulation. We report experiments that study the dependence of DNA condensation by HU on force, salt and HU concentration. A first important result is that at physiological salt levels, HU only bends DNA, resolving a previous paradox of why a chromosome-compacting protein should have a DNA-stiffening function. A second major result is quantitative demonstration of strong dependencies of HU-DNA dissociation on both salt concentration and force. Second, we have used a thermodynamic Maxwell relation to count proteins driven off large DNAs by tension, an effect important to understanding DNA organization. Our results compare well with estimates of numbers of proteins HU and Fis in previous studies. We have also shown that a semi-flexible polymer model describes our HU experimental data well. The force-dependent binding suggests mechano-chemical mechanisms for gene regulation. Third, the elusive role of protein H1 in chromatin has been clarified with purified H1 and Xenopus extracts. We find that H1 compacts DNA by both bending and looping. Addition of H1 enhances chromatin formation and maintains the plasticity of the chromatin. Fourth, the topology and mechanics of DNA twisting are critical to DNA organization and recombination. We have systematically measured DNA extension as a function of linking number density from 0.08 to -2 with holding forces from 0.2 to 2.4 pN. Unlike previous proposals, the DNA extension decreases with negative linking number. Finally, DNA recombination is a dynamic process starting from enzyme-DNA binding. We report that the Int-DBD domain of lambda integrase binds to DNA without compaction at low Int-DBD concentration. High concentration of Int-DBD loops DNA below a threshold force

  10. Vapor Compressor Driven Hybrid Two-Phase Loop, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This Small Business Innovation Research Phase I project will demonstrate a vapor compressor driven hybrid two-phase loop technology. The hybrid two-phase loop...

  11. Wilson loops to 20th order numerical stochastic perturbation theory

    Energy Technology Data Exchange (ETDEWEB)

    Horsley, R. [Edinburgh Univ. (United Kingdom). School of Physics; Hotzel, G.; Perlt, H.; Schiller, A. [Leipzig Univ. (Germany). Inst. fuer Theoretische Physik; Ilgenfritz, E.M. [Humboldt-Universitaet, Berlin (Germany). Inst. fuer Physik; Joint Institute for Nuclear Research, VBLHEP, Dubna (Russian Federation); Millo, R.; Rakow, P.E.L. [Liverpool Univ. (Germany). Theoretical Physics Div.; Nakamura, Y. [RIKEN Advanced Institute for Computational Science, Kobe, Hyogo (Japan); Schierholz, G. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2012-05-15

    We calculate Wilson loops of various sizes up to 20 loops in SU(3) pure lattice gauge theory at different lattice sizes for Wilson gauge action using the technique of numerical stochastic perturbation theory. This allows us to investigate the perturbative series for various Wilson loops at high loop orders. We observe differences in the behavior of those series as function of the loop order. Up to n=20 we do not find evidence for the factorial growth of the expansion coefficients often assumed to characterize an asymptotic series. Based on the actually observed behavior we sum the series in a model parametrized by hypergeometric functions. Alternatively we estimate the total series in boosted perturbation theory using information from the first 14 loops. We introduce generalized ratios of Wilson loops of different sizes. Together with the corresponding Wilson loops from standard Monte Carlo measurements they enable us to assess their non-perturbative parts.

  12. DNA Repair Systems

    Indian Academy of Sciences (India)

    DNA molecule which makes it ideal for storage and propagation of genetic information. ... of these errors are broadly referred to as DNA repair. DNA can ... changes occur in the human genome per day. ..... nails, frequent physical and mental.

  13. Synthesis of DNA

    Science.gov (United States)

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  14. SU(2) string tension from large Wilson loops

    International Nuclear Information System (INIS)

    Karsch, F.; Lang, C.B.

    1984-01-01

    We determine expectation values of Wilson loops and correlations of Polyakov loops on lattices of size 10 X 16 3 and 8 X 16 3 at β values 2.25 and 2.375. Utilizing a recently proposed method to reduce the variance of loop expectation values, we are able to measure loops up to 6 X 6. We find Λsub(L) = 0.0151 +- 0.0006√sub(K) at β = 2.375. (orig.)

  15. Sodium characterization during the starting period of a sodium loop

    International Nuclear Information System (INIS)

    Lievens, F.; Parmentier, C.; Soenen, M.

    1976-01-01

    A sodium loop for analytical chemistry studies has been built by S.C.K./C.E.N. at Mol Belgium. Its first working period was used to test analytical methods, to characterize the sodium and to define the operating parameters of the loop. This report covers the working parameters of the loop, the characterization of the filling sodium and its purity evolution during the first working period of the loop

  16. XLOOPS - a package calculating one- and two-loop diagrams

    International Nuclear Information System (INIS)

    Bruecher, L.

    1997-01-01

    A program package for calculating massive one- and two-loop diagrams is introduced. It consists of five parts: - a graphical user interface, - routines for generating diagrams from particle input, - procedures for calculating one-loop integrals both analytically and numerically, - routines for massive two-loop integrals, - programs for numerical integration of two-loop diagrams. Here the graphical user interface and the text interface to Maple are presented. (orig.)

  17. Rapid and Simple Detection of Hot Spot Point Mutations of Epidermal Growth Factor Receptor, BRAF, and NRAS in Cancers Using the Loop-Hybrid Mobility Shift Assay

    Science.gov (United States)

    Matsukuma, Shoichi; Yoshihara, Mitsuyo; Kasai, Fumio; Kato, Akinori; Yoshida, Akira; Akaike, Makoto; Kobayashi, Osamu; Nakayama, Haruhiko; Sakuma, Yuji; Yoshida, Tsutomu; Kameda, Yoichi; Tsuchiya, Eiju; Miyagi, Yohei

    2006-01-01

    A simple and rapid method to detect the epidermal growth factor receptor hot spot mutation L858R in lung adenocarcinoma was developed based on principles similar to the universal heteroduplex generator technology. A single-stranded oligonucleotide with an internal deletion was used to generate heteroduplexes (loop-hybrids) bearing a loop in the complementary strand derived from the polymerase chain reaction product of the normal or mutant allele. By placing deletion in the oligonucleotide adjacent to the mutational site, difference in electrophoretic mobility between loop-hybrids with normal and mutated DNA was distinguishable in a native polyacrylamide gel. The method was also modified to detect in-frame deletion mutations of epidermal growth factor receptor in lung adenocarcinomas. In addition, the method was adapted to detect hot spot mutations in the B-type Raf kinase (BRAF) at V600 and in a Ras-oncogene (NRAS) at Q61, the mutations commonly found in thyroid carcinomas. Our mutation detection system, designated the loop-hybrid mobility shift assay was sensitive enough to detect mutant DNA comprising 7.5% of the total DNA. As a simple and straightforward mutation detection technique, loop-hybrid mobility shift assay may be useful for the molecular diagnosis of certain types of clinical cancers. Other applications are also discussed. PMID:16931592

  18. Loop-mediated isothermal amplification (LAMP): early detection of Toxoplasma gondii infection in mice.

    Science.gov (United States)

    Kong, Qing-Ming; Lu, Shao-Hong; Tong, Qun-Bo; Lou, Di; Chen, Rui; Zheng, Bin; Kumagai, Takashi; Wen, Li-Yong; Ohta, Nobuo; Zhou, Xiao-Nong

    2012-01-03

    Toxoplasmosis is a widespread zoonotic parasitic disease that occurs in both animals and humans. Traditional molecular assays are often difficult to perform, especially for the early diagnosis of Toxoplasma gondii infections. Here, we established a novel loop-mediated isothermal amplification targeting the 529 bp repeat element (529 bp-LAMP) to detect T. gondii DNA in blood samples of experimental mice infected with tachyzoites of the RH strain. The assay was performed with Bst DNA polymerase at 65°C for 1 h. The detection limit of the 529 bp-LAMP assay was as low as 0.6 fg of T. gondii DNA. The sensitivity of this assay was 100 and 1000 fold higher than that of the LAMP targeting B1 gene (B1-LAMP) and nested PCR targeting 529 bp repeat element (529 bp-nested PCR), respectively. The specificity of the 529 bp-LAMP assay was determined using the DNA samples of Trypanosoma evansi, Plasmodium falciparum, Paragonimus westermani, Schistosoma japonicum, Fasciola hepatica and Angiostrongylus cantonensis. No cross-reactivity with the DNA of any parasites was found. The assay was able to detect T. gondii DNA in all mouse blood samples at one day post infection (dpi). We report the following findings: (i) The detection limit of the 529 bp-LAMP assay is 0.6 fg of T. gondii DNA; (ii) The assay does not involve any cross-reactivity with the DNA of other parasites; (iii) This is the first report on the application of the LAMP assay for early diagnosis of toxoplasmosis in blood samples from experimentally infected mice. Due to its simplicity, sensitivity and cost-effectiveness for common use, we suggest that this assay should be used as an early diagnostic tool for health control of toxoplasmosis.

  19. Inheritance of mitochondrial DNA in serially recloned pigs by somatic cell nuclear transfer (SCNT)

    Energy Technology Data Exchange (ETDEWEB)

    Do, Minhwa; Jang, Won-Gu; Hwang, Jeong Hee; Jang, Hoon; Kim, Eun-Jung; Jeong, Eun-Jeong [Regenerative Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305 806 (Korea, Republic of); Shim, Hosup [Department of Physiology, Dankook University School of Medicine, Cheonan 330 714 (Korea, Republic of); Hwang, Sung Soo; Oh, Keon Bong; Byun, Sung June [Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Suwon (Korea, Republic of); Kim, Jin-Hoi [Department of Animal Biotechnology, Konkuk University, Seoul 143 701 (Korea, Republic of); Lee, Jeong Woong, E-mail: jwlee@kribb.re.kr [Regenerative Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305 806 (Korea, Republic of)

    2012-08-10

    Highlights: Black-Right-Pointing-Pointer We success serial SCNT through the third generation using pig fibroblasts. Black-Right-Pointing-Pointer Donor-specific mtDNA in the recloned pigs was detected. Black-Right-Pointing-Pointer SCNT affect mtDNA mounts. -- Abstract: Somatic cell nuclear transfer (SCNT) has been established for the transmission of specific nuclear DNA. However, the fate of donor mitochondrial DNA (mtDNA) remains unclear. Here, we examined the fate of donor mtDNA in recloned pigs through third generations. Fibroblasts of recloned pigs were obtained from offspring of each generation produced by fusion of cultured fibroblasts from a Minnesota miniature pig (MMP) into enucleated oocytes of a Landrace pig. The D-loop regions from the mtDNA of donor and recipient differ at nucleotide sequence positions 16050 (A{yields}T), 16062 (T{yields}C), and 16135 (G{yields}A). In order to determine the fate of donor mtDNA in recloned pigs, we analyzed the D-loop region of the donor's mtDNA by allele-specific PCR (AS-PCR) and real-time PCR. Donor mtDNA was successfully detected in all recloned offspring (F1, F2, and F3). These results indicate that heteroplasmy that originate from donor and recipient mtDNA is maintained in recloned pigs, resulting from SCNT, unlike natural reproduction.

  20. Loop-space quantum formulation of free electromagnetism

    International Nuclear Information System (INIS)

    Di Bartolo, C.; Nori, F.; Gambini, R.; Trias, A.

    1983-01-01

    A procedure for direct quantization of free electromagnetism in the loop-space is proposed. Explicit solutions for the loop-dependent vacuum and the Wilson loop-average are given. It is shown that elementary lines of magnetic field appear as extremals in the vacuum state as a result of the regularization procedure

  1. Loop expansion in massless three-dimensional QED

    International Nuclear Information System (INIS)

    Guendelman, E.I.; Radulovic, Z.M.

    1983-01-01

    It is shown how the loop expansion in massless three-dimensional QED can be made finite, up to three loops, by absorbing the infrared divergences in a gauge-fixing term. The same method removes leading and first subleading singularities to all orders of perturbation theory, and all singularities of the fermion self-energy to four loops

  2. Automated computation of one-loop integrals in massless theories

    International Nuclear Information System (INIS)

    Hameren, A. van; Vollinga, J.; Weinzierl, S.

    2005-01-01

    We consider one-loop tensor and scalar integrals, which occur in a massless quantum field theory, and we report on the implementation into a numerical program of an algorithm for the automated computation of these one-loop integrals. The number of external legs of the loop integrals is not restricted. All calculations are done within dimensional regularization. (orig.)

  3. Numerical evaluation of one-loop QCD amplitudes

    DEFF Research Database (Denmark)

    Badger, Simon David; Biedermann, Benedikt; Uwer, Peter

    2012-01-01

    We present the publicly available program NGluon allowing the numerical evaluation of primitive amplitudes at one-loop order in massless QCD. The program allows the computation of one-loop amplitudes for an arbitrary number of gluons. The focus of the present article is the extension to one-loop ...

  4. Loop transfer recovery for general observer architecture

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik; Søgaard-Andersen, Per; Stoustrup, Jakob

    1991-01-01

    A general and concise formulation is given of the loop transfer recovery (LTR) design problem based on recovery errors. Three types of recovery errors are treated: open loop recovery, sensitivity recovery and input-output recovery errors. The three corresponding versions of the asymptotic recovery...... recovery cases. This general recovery formulation covers all known observer based compensator types as special cases. The conditions given in this setting are effectively the aim of all known LTR design methods. The recovery formulation is interpreted in terms of a modelmatching problem as well, which...... is examined by means of the Q-parametrization. It is shown how the general controller obtained by the Q-parametrization can be written as a Luenberger observer based controller. In all cases, n controller states suffice to achieve recovery. The compensators are characterized for errors both on the input...

  5. Symmetry reduction of loop quantum gravity

    International Nuclear Information System (INIS)

    Brunnemann, Johannes; Koslowski, Tim A

    2011-01-01

    The relation between standard loop quantum cosmology (LQC) and full loop quantum gravity (LQG) fails already at the first nontrivial step: the configuration space of LQC cannot be embedded into the configuration space of full LQG due to a topological obstruction. We investigate this obstruction in detail, because many topological obstructions are the source of physical effects. For this, we derive the topology of a large class of subspaces of the LQG configuration space. This allows us to find the extension of the standard LQC configuration space that admits an embedding in agreement with Fleischhack (arXiv:1010.0449v1 [math-ph]). We then construct the embedding for flat FRW LQC and find the reassuring result that it coincides asymptotically with standard LQC. (paper)

  6. A new vacuum for loop quantum gravity

    International Nuclear Information System (INIS)

    Dittrich, Bianca; Geiller, Marc

    2015-01-01

    We construct a new vacuum and representation for loop quantum gravity. Because the new vacuum is based on BF theory, it is physical for (2+1)-dimensional gravity, and much closer to the spirit of spin foam quantization in general. To construct this new vacuum and the associated representation of quantum observables, we introduce a modified holonomy–flux algebra that is cylindrically consistent with respect to the notion of refinement by time evolution suggested in Dittrich and Steinhaus (2013 arXiv:1311.7565). This supports the proposal for a construction of the physical vacuum made in Dittrich and Steinhaus (2013 arXiv:1311.7565) and Dittrich (2012 New J. Phys. 14 123004), and for (3+1)-dimensional gravity. We expect that the vacuum introduced here will facilitate the extraction of large scale physics and cosmological predictions from loop quantum gravity. (fast track communication)

  7. Scalar one-loop integrals for QCD

    International Nuclear Information System (INIS)

    Ellis, R. Keith; Zanderighi, Giulia

    2008-01-01

    We construct a basis set of infra-red and/or collinearly divergent scalar one-loop integrals and give analytic formulas, for tadpole, bubble, triangle and box integrals, regulating the divergences (ultra-violet, infra-red or collinear) by regularization in D = 4-2ε dimensions. For scalar triangle integrals we give results for our basis set containing 6 divergent integrals. For scalar box integrals we give results for our basis set containing 16 divergent integrals. We provide analytic results for the 5 divergent box integrals in the basis set which are missing in the literature. Building on the work of van Oldenborgh, a general, publicly available code has been constructed, which calculates both finite and divergent one-loop integrals. The code returns the coefficients of 1/ε 2 ,1/ε 1 and 1/ε 0 as complex numbers for an arbitrary tadpole, bubble, triangle or box integral

  8. Multitarget multisensor closed-loop tracking

    Science.gov (United States)

    Sanders-Reed, John N.

    2004-07-01

    This paper describes a closed-loop tracking system using multiple co-located sensors to develop multi-sensor track histories on multiple targets. The use of multiple, co-aligned sensors to track multiple, possibly maneuvering targets, presents a number of tracker design challenges and opportunities. Many of these problems have been addressed individually in the published literature from a theoretical point of view. However, no one has yet addressed the design and implementation of a specific tracker to meet all of these requirements at once. Specific questions addressed in this paper include how to assign N detections in a current frame to M active tracks, how to initiate new tracks and terminate dead tracks, how to combine information from multiple sensors into a single integrated picture, represented by a global track file, and how to perform these functions in a timely manner to support a precision closed loop tracking system.

  9. Penguin loops with confined quark propagators

    International Nuclear Information System (INIS)

    Eeg, J.O.

    1984-12-01

    The ΔS = 1 penguin diagram is calculated by representing the internal quark lines in the loop by bag model wave functions. Because of the involved GIM-mecanism, only the lowest internal quark modes are kept in the loop. The result depends cruically on the values of the strong coupling constant and the quark energy of the bag model wave functions. With reasonable values of parameters, contributions corresponding to effective penguin coeffisient values of approximately two to five times the standard pertubative ones, have been found. Thus the theoretical value for the ratio between ΔI = 1/2 and ΔI = 3/2 amplitudes seems to be improved

  10. Capillary pumped loop body heat exchanger

    Science.gov (United States)

    Swanson, Theodore D. (Inventor); Wren, deceased, Paul (Inventor)

    1998-01-01

    A capillary pumped loop for transferring heat from one body part to another body part, the capillary pumped loop comprising a capillary evaporator for vaporizing a liquid refrigerant by absorbing heat from a warm body part, a condenser for turning a vaporized refrigerant into a liquid by transferring heat from the vaporized liquid to a cool body part, a first tube section connecting an output port of the capillary evaporator to an input of the condenser, and a second tube section connecting an output of the condenser to an input port of the capillary evaporator. A wick may be provided within the condenser. A pump may be provided between the second tube section and the input port of the capillary evaporator. Additionally, an esternal heat source or heat sink may be utilized.

  11. Loop optimization for tensor network renormalization

    Science.gov (United States)

    Yang, Shuo; Gu, Zheng-Cheng; Wen, Xiao-Gang

    We introduce a tensor renormalization group scheme for coarse-graining a two-dimensional tensor network, which can be successfully applied to both classical and quantum systems on and off criticality. The key idea of our scheme is to deform a 2D tensor network into small loops and then optimize tensors on each loop. In this way we remove short-range entanglement at each iteration step, and significantly improve the accuracy and stability of the renormalization flow. We demonstrate our algorithm in the classical Ising model and a frustrated 2D quantum model. NSF Grant No. DMR-1005541 and NSFC 11274192, BMO Financial Group, John Templeton Foundation, Government of Canada through Industry Canada, Province of Ontario through the Ministry of Economic Development & Innovation.

  12. Cosmological footprints of loop quantum gravity.

    Science.gov (United States)

    Grain, J; Barrau, A

    2009-02-27

    The primordial spectrum of cosmological tensor perturbations is considered as a possible probe of quantum gravity effects. Together with string theory, loop quantum gravity is one of the most promising frameworks to study quantum effects in the early universe. We show that the associated corrections should modify the potential seen by gravitational waves during the inflationary amplification. The resulting power spectrum should exhibit a characteristic tilt. This opens a new window for cosmological tests of quantum gravity.

  13. The Re-injection Loop concept

    DEFF Research Database (Denmark)

    Holst Fischer, Christian; Malmgren-Hansen, Bjørn; Uellendahl, Hinrich

    per ton. Based on previous studies on using pretreatment for enhancing the biogas yield of these feedstocks, a new concept called Re-Injection Loop was developed by combining separation and recirculation of the digested fiber fraction with pretreatment of the recalcitrant lignocellulosic fiber...... fraction. The EU project BIOMAN is currently investigating different technologies for separation, mechanical pretreatment and enzymatic hydrolysis to establish an economically viable concept for manure-based biogas plants....

  14. Dynamic response of IPEN experimental water loop

    International Nuclear Information System (INIS)

    Faya, A.J.G.; Bassel, W.S.

    1982-10-01

    A mathematical model has been developed to analyze the transient thermal response of the I.P.E.N. water loop during change of power operations. The model is capable of estimating the necessary test section power and heat exchanger mass flow rate for a given operating temperature. It can also determine the maximum heating or cooling rate to avoid thermal shocks in pipes and components. (Author) [pt

  15. Pumped two-phase heat transfer loop

    Science.gov (United States)

    Edelstein, Fred

    1988-01-01

    A pumped loop two-phase heat transfer system, operating at a nearly constant temperature throughout, includes several independently operating grooved capillary heat exchanger plates supplied with working fluid through independent flow modulation valves connected to a liquid supply line, a vapor line for collecting vapor from the heat exchangers, a condenser between the vapor and the liquid lines, and a fluid circulating pump between the condenser and the heat exchangers.

  16. Loop equations and 1/N expansion

    International Nuclear Information System (INIS)

    Migdal, A.A.

    1983-01-01

    This article consists of two parts. The purpose of the first part is to provide an introduction to loop dynamics; some kind of a textbook. In original papers we usually omit the details and do not explain successive steps, leading to this or that result. Here, on the contrary, we concentrate on the basic notions and discuss alternatives. As for the applications and for the parallel developments, those are briefly discussed in the second part. (orig./HSI)

  17. Optimal tests for electroweak loop effects

    International Nuclear Information System (INIS)

    Aoki, Kenichi; Aoyama, Hideaki; Harvard Univ., Cambridge, MA

    1986-01-01

    A statistical analysis is given for the experimental precision necessary for establishing loop effects in the electroweak theory. Cases with three observables, gauge boson masses and the Weinberg angle, is analyzed by an optimised test. An information on the Weinberg angle with even 5% error (+-.01 in sin 2 thetasub(W)) is shown to reduce the requirement for the measurements of gauge boson masses significantly. (orig.)

  18. Fundamental Structure of Loop Quantum Gravity

    Science.gov (United States)

    Han, Muxin; Ma, Yongge; Huang, Weiming

    In the recent twenty years, loop quantum gravity, a background independent approach to unify general relativity and quantum mechanics, has been widely investigated. The aim of loop quantum gravity is to construct a mathematically rigorous, background independent, non-perturbative quantum theory for a Lorentzian gravitational field on a four-dimensional manifold. In the approach, the principles of quantum mechanics are combined with those of general relativity naturally. Such a combination provides us a picture of, so-called, quantum Riemannian geometry, which is discrete on the fundamental scale. Imposing the quantum constraints in analogy from the classical ones, the quantum dynamics of gravity is being studied as one of the most important issues in loop quantum gravity. On the other hand, the semi-classical analysis is being carried out to test the classical limit of the quantum theory. In this review, the fundamental structure of loop quantum gravity is presented pedagogically. Our main aim is to help non-experts to understand the motivations, basic structures, as well as general results. It may also be beneficial to practitioners to gain insights from different perspectives on the theory. We will focus on the theoretical framework itself, rather than its applications, and do our best to write it in modern and precise langauge while keeping the presentation accessible for beginners. After reviewing the classical connection dynamical formalism of general relativity, as a foundation, the construction of the kinematical Ashtekar-Isham-Lewandowski representation is introduced in the content of quantum kinematics. The algebraic structure of quantum kinematics is also discussed. In the content of quantum dynamics, we mainly introduce the construction of a Hamiltonian constraint operator and the master constraint project. At last, some applications and recent advances are outlined. It should be noted that this strategy of quantizing gravity can also be extended to

  19. Flipped spinfoam vertex and loop gravity

    Energy Technology Data Exchange (ETDEWEB)

    Engle, Jonathan; Pereira, Roberto [CPT, CNRS Case 907, Universite de la Mediterranee, F-13288 Marseille (France); Rovelli, Carlo [CPT, CNRS Case 907, Universite de la Mediterranee, F-13288 Marseille (France)], E-mail: rovelli@cpt.univ-mrs.fr

    2008-07-21

    We introduce a vertex amplitude for 4d loop quantum gravity. We derive it from a conventional quantization of a Regge discretization of euclidean general relativity. This yields a spinfoam sum that corrects some difficulties of the Barrett-Crane theory. The second class simplicity constraints are imposed weakly, and not strongly as in Barrett-Crane theory. Thanks to a flip in the quantum algebra, the boundary states turn out to match those of SO(3) loop quantum gravity-the two can be identified as eigenstates of the same physical quantities-providing a solution to the problem of connecting the covariant SO(4) spinfoam formalism with the canonical SO(3) spin-network one. The vertex amplitude is SO(3) and SO(4)-covariant. It rectifies the triviality of the intertwiner dependence of the Barrett-Crane vertex, which is responsible for its failure to yield the correct propagator tensorial structure. The construction provides also an independent derivation of the kinematics of loop quantum gravity and of the result that geometry is quantized.

  20. The quark beam function at two loops

    International Nuclear Information System (INIS)

    Gaunt, Jonathan R.; Stahlhofen, Maximilian; Tackmann, Frank J.

    2014-01-01

    In differential measurements at a hadron collider, collinear initial-state radiation is described by process-independent beam functions. They are the field-theoretic analog of initial-state parton showers. Depending on the measured observable they are differential in the virtuality and/or transverse momentum of the colliding partons in addition to their usual longitudinal momentum fractions. Perturbatively, the beam functions can be calculated by matching them onto standard quark and gluon parton distribution functions. We calculate the inclusive virtuality-dependent quark beam function at NNLO, which is relevant for any observables probing the virtuality of the incoming partons, including N-jettiness and beam thrust. For such observables, our results are an important ingredient in the resummation of large logarithms at N 3 LL order, and provide all contributions enhanced by collinear t-channel singularities at NNLO for quark-initiated processes in analytic form. We perform the calculation in both Feynman and axial gauge and use two different methods to evaluate the discontinuity in the two-loop Feynman diagrams, providing nontrivial checks of the calculation. As part of our results we reproduce the known two-loop QCD splitting functions and confirm at two loops that the virtuality-dependent beam and final-state jet functions have the same anomalous dimension.

  1. One-loop effective lagrangians after matching

    Energy Technology Data Exchange (ETDEWEB)

    Aguila, F. del; Santiago, J. [Universidad de Granada, Departamento de Fisica Teorica y del Cosmos and CAFPE, Granada (Spain); Kunszt, Z. [ETH Zuerich, Institute for Theoretical Physics, Zuerich (Switzerland)

    2016-05-15

    We discuss the limitations of the covariant derivative expansion prescription advocated to compute the one-loop Standard Model (SM) effective lagrangian when the heavy fields couple linearly to the SM. In particular, one-loop contributions resulting from the exchange of both heavy and light fields must be explicitly taken into account through matching because the proposed functional approach alone does not account for them. We review a simple case with a heavy scalar singlet of charge -1 to illustrate the argument. As two other examples where this matching is needed and this functional method gives a vanishing result, up to renormalization of the heavy sector parameters, we re-evaluate the one-loop corrections to the T-parameter due to a heavy scalar triplet with vanishing hypercharge coupling to the Brout-Englert-Higgs boson and to a heavy vector-like quark singlet of charged 2/3 mixing with the top quark, respectively. In all cases we make use of a new code for matching fundamental and effective theories in models with arbitrary heavy field additions. (orig.)

  2. Two loop integrals and QCD scattering

    International Nuclear Information System (INIS)

    Anastasiou, C.

    2001-04-01

    We present the techniques for the calculation of one- and two-loop integrals contributing to the virtual corrections to 2→2 scattering of massless particles. First, tensor integrals are related to scalar integrals with extra powers of propagators and higher dimension using the Schwinger representation. Integration By Parts and Lorentz Invariance recurrence relations reduce the number of independent scalar integrals to a set of master integrals for which their expansion in ε = 2 - D/2 is calculated using a combination of Feynman parameters, the Negative Dimension Integration Method, the Differential Equations Method, and Mellin-Barnes integral representations. The two-loop matrix-elements for light-quark scattering are calculated in Conventional Dimensional Regularisation by direct evaluation of the Feynman diagrams. The ultraviolet divergences are removed by renormalising with the MS-bar scheme. Finally, the infrared singular behavior is shown to be in agreement with the one anticipated by the application of Catani's formalism for the infrared divergences of generic QCD two-loop amplitudes. (author)

  3. Toward precision holography with supersymmetric Wilson loops

    Energy Technology Data Exchange (ETDEWEB)

    Faraggi, Alberto [Instituto de Física, Pontificia Universidad Católica de Chile,Casilla 306, Santiago (Chile); Zayas, Leopoldo A. Pando [The Abdus Salam International Centre for Theoretical Physics,Strada Costiera 11, 34014 Trieste (Italy); Michigan Center for Theoretical Physics, Department of Physics,University of Michigan, Ann Arbor, MI 48109 (United States); Silva, Guillermo A. [Instituto de Física de La Plata - CONICET & Departamento de Física - UNLP,C.C. 67, 1900 La Plata (Argentina); Trancanelli, Diego [Institute of Physics, University of São Paulo,05314-970 São Paulo (Brazil)

    2016-04-11

    We consider certain 1/4 BPS Wilson loop operators in SU(N)N=4 supersymmetric Yang-Mills theory, whose expectation value can be computed exactly via supersymmetric localization. Holographically, these operators are mapped to fundamental strings in AdS{sub 5}×S{sup 5}. The string on-shell action reproduces the large N and large coupling limit of the gauge theory expectation value and, according to the AdS/CFT correspondence, there should also be a precise match between subleading corrections to these limits. We perform a test of such match at next-to-leading order in string theory, by deriving the spectrum of quantum fluctuations around the classical string solution and by computing the corresponding 1-loop effective action. We discuss in detail the supermultiplet structure of the fluctuations. To remove a possible source of ambiguity in the ghost zero mode measure, we compare the 1/4 BPS configuration with the 1/2 BPS one, dual to a circular Wilson loop. We find a discrepancy between the string theory result and the gauge theory prediction, confirming a previous result in the literature. We are able to track the modes from which this discrepancy originates, as well as the modes that by themselves would give the expected result.

  4. Operator decision support system for sodium loop

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kwang Hyeang; Park, Kyu Ho; Kim, Tak Kon; Jo, Choong Ho; Seong, Kyeong A; Lee, Keon Myeong; Kim, Yeong Dal; Kim, Chang Beom; Kim, Jong Kyu; Jo, Hee Chang; Lee, Ji Hyeong; Jeong, Yoon Soo; Chio, Jong Hyeong; Jeong, Bong Joon; Hong, Joon Seong; Kim, Bong Wan; Seong, Byeong Hak [Korea Advanced Institute Science and Technology, Taejon (Korea, Republic of)

    1994-07-01

    The objective of this study is to develop an operator decision support system by computerizing the sodium circuit. This study developed graphical display interface for the control panel which provides the safety control of equipment, the recognition of experimental process states and sodium circuit states. In this study, basic work to develop an operator decision support real-time expert system for sodium loop was carried out. Simplification of control commands and effective operation of various real-time data and signals by equipment code standardization are studied. The cost ineffectiveness of the single processor structure provides the ground for the development of cost effective parallel processing system. The important tasks of this study are (1) design and implementation of control state surveillance panel of sodium loop, (2) requirement analysis of operator support real-time expert system for sodium loop, (3) design of standard code rule for operating equipment and research on the cost effective all purpose parallel processing system and (4) requirement analysis of expert system and design of control state variables and user interface for experimental process. 10 refs., 36 figs., 20 tabs.

  5. Stretchable Random Lasers with Tunable Coherent Loops.

    Science.gov (United States)

    Sun, Tzu-Min; Wang, Cih-Su; Liao, Chi-Shiun; Lin, Shih-Yao; Perumal, Packiyaraj; Chiang, Chia-Wei; Chen, Yang-Fang

    2015-12-22

    Stretchability represents a key feature for the emerging world of realistic applications in areas, including wearable gadgets, health monitors, and robotic skins. Many optical and electronic technologies that can respond to large strain deformations have been developed. Laser plays a very important role in our daily life since it was discovered, which is highly desirable for the development of stretchable devices. Herein, stretchable random lasers with tunable coherent loops are designed, fabricated, and demonstrated. To illustrate our working principle, the stretchable random laser is made possible by transferring unique ZnO nanobrushes on top of polydimethylsiloxane (PDMS) elastomer substrate. Apart from the traditional gain material of ZnO nanorods, ZnO nanobrushes were used as optical gain materials so they can serve as scattering centers and provide the Fabry-Perot cavity to enhance laser action. The stretchable PDMS substrate gives the degree of freedom to mechanically tune the coherent loops of the random laser action by changing the density of ZnO nanobrushes. It is found that the number of laser modes increases with increasing external strain applied on the PDMS substrate due to the enhanced possibility for the formation of coherent loops. The device can be stretched by up to 30% strain and subjected to more than 100 cycles without loss in laser action. The result shows a major advance for the further development of man-made smart stretchable devices.

  6. Transverse loop colostomy and colonic motility.

    Science.gov (United States)

    Pucciani, F; Ringressi, M N; Maltinti, G; Bechi, P

    2014-11-01

    The motility of the defunctionalized colon, distal to transverse loop colostomy, has never been studied "in vivo." The aim of our study was to evaluate the influence of transverse loop colostomy on colonic motility. Thirteen patients were examined before stoma closure by means of clinical evaluation and colonic manometry; we studied both the right and distal colon in both fasting and fed patients in order to detect motor activity. Quantitative and qualitative manometric analyses showed that the diverted colon had motor activity even if no regular colonic motor pattern was observed. The spreading of aboral propagated contractions (PCs) was sometimes recorded from the right colon to the distal colon. The response of the proximal and distal colon to a standard meal, when compared to fasting values, increased more than 40 and 35 %, respectively. Stool and gas ejections from the colostomy were never related to a particular type of colonic motility: Motor quiescence such as PCs was chaotically related to stool escape. In conclusion, motility of the defunctionalized colon is preserved in patients with transverse loop colostomy.

  7. Gluon quasidistribution function at one loop

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Wei; Zhao, Shuai [Shanghai Jiao Tong University, INPAC, Shanghai Key Laboratory for Particle Physics and Cosmology, School of Physics and Astronomy, Shanghai (China); Zhu, Ruilin [Shanghai Jiao Tong University, INPAC, Shanghai Key Laboratory for Particle Physics and Cosmology, School of Physics and Astronomy, Shanghai (China); Nanjing Normal University, Department of Physics and Institute of Theoretical Physics, Nanjing, Jiangsu (China)

    2018-02-15

    We study the unpolarized gluon quasidistribution function in the nucleon at one loop level in the large momentum effective theory. For the quark quasidistribution, power law ultraviolet divergences arise in the cut-off scheme and an important observation is that they all are subjected to Wilson lines. However for the gluon quasidistribution function, we first point out that the linear ultraviolet divergences also exist in the real diagram which is not connected to any Wilson line. We then study the one loop corrections to parton distribution functions in both cut-off scheme and dimensional regularization to deal with the ultraviolet divergences. In addition to the ordinary quark and gluon distributions, we also include the quark to gluon and gluon to quark splitting diagrams. The complete one-loop matching factors between the quasi and light cone parton distribution functions are presented in the cut-off scheme. We derive the P{sup z} evolution equation for quasi parton distribution functions, and find that the P{sup z} evolution kernels are identical to the DGLAP evolution kernels. (orig.)

  8. Closed-loop, open-source electrophysiology

    Directory of Open Access Journals (Sweden)

    John D Rolston

    2010-09-01

    Full Text Available Multiple extracellular microelectrodes (multi-electrode arrays, or MEAs effectively record rapidly varying neural signals, and can also be used for electrical stimulation. Multi-electrode recording can serve as artificial output (efferents from a neural system, while complex spatially and temporally targeted stimulation can serve as artificial input (afferents to the neuronal network. Multi-unit or local field potential recordings can not only be used to control real world artifacts, such as prostheses, computers or robots, but can also trigger or alter subsequent stimulation. Real-time feedback stimulation may serve to modulate or normalize aberrant neural activity, to induce plasticity, or to serve as artificial sensory input. Despite promising closed-loop applications, commercial electrophysiology systems do not yet take advantage of the bidirectional capabilities of multi-electrodes, especially for use in freely moving animals. We addressed this lack of tools for closing the loop with NeuroRighter, an open-source system including recording hardware, stimulation hardware, and control software with a graphical user interface. The integrated system is capable of multi-electrode recording and simultaneous patterned microstimulation triggered by recordings with minimal stimulation artifact. The potential applications of closed-loop systems as research tools and clinical treatments are broad; we provide one example where epileptic activity recorded by a multi-electrode probe is used to trigger targeted stimulation, via that probe, to freely moving rodents.

  9. Leptogenesis from loop effects in curved spacetime

    Energy Technology Data Exchange (ETDEWEB)

    McDonald, Jamie I.; Shore, Graham M. [Department of Physics, Swansea University,Singleton Park, Swansea, SA2 8PP (United Kingdom)

    2016-04-05

    We describe a new mechanism — radiatively-induced gravitational leptogenesis — for generating the matter-antimatter asymmetry of the Universe. We show how quantum loop effects in C and CP violating theories cause matter and antimatter to propagate differently in the presence of gravity, and prove this is forbidden in flat space by CPT and translation symmetry. This generates a curvature-dependent chemical potential for leptons, allowing a matter-antimatter asymmetry to be generated in thermal equilibrium in the early Universe. The time-dependent dynamics necessary for leptogenesis is provided by the interaction of the virtual self-energy cloud of the leptons with the expanding curved spacetime background, which violates the strong equivalence principle and allows a distinction between matter and antimatter. We show here how this mechanism is realised in a particular BSM theory, the see-saw model, where the quantum loops involve the heavy sterile neutrinos responsible for light neutrino masses. We demonstrate by explicit computation of the relevant two-loop Feynman diagrams how the size of the radiative corrections relevant for leptogenesis becomes enhanced by increasing the mass hierarchy of the sterile neutrinos, and show how the induced lepton asymmetry may be sufficiently large to play an important rôle in determining the baryon-to-photon ratio of the Universe.

  10. Development of a Loop Mediated Isothermal Amplification for Diagnosis of Ascaris lumbricoides in Fecal Samples

    Directory of Open Access Journals (Sweden)

    Esther A. Shiraho

    2016-01-01

    Full Text Available Ascaris lumbricoides is a nematode parasite that causes the common tropical infection ascariasis in humans. It is also considered among the neglected tropical diseases. Diagnosis relies mainly on microscopy-based methods which are laborious, are limited by low sensitivity, and require high expertise. We have developed a loop mediated isothermal amplification (LAMP for diagnosis of ascariasis in fecal samples, based on the first internal transcribed (ITS-1 spacer region of the ribosomal DNA. We used Primer Explorer V4 software to design primers. Ascaris adult and ova were obtained from naturally infected school children, whose parents/guardians gave consent for their participation in the study. Genomic DNA was extracted using alkaline lysis method and amplified by LAMP at 63°C for 45 minutes. LAMP products were visualized by naked eyes after adding SYBR Green dye and also on agarose gel. LAMP successfully and reliably detected Ascaris DNA from a single egg and in fecal samples. The assay specifically detected Ascaris DNA without amplifying DNA from ova of other parasites which commonly coexist with A. lumbricoides in feces. The developed LAMP assay has great potential for use in ascariasis diagnosis at the point of care and in low infection intensity situation that characterize control and elimination campaigns.

  11. Timing, coordination, and rhythm: Acrobatics at the DNA replication fork

    KAUST Repository

    Hamdan, Samir

    2010-04-09

    In DNA replication, the antiparallel nature of the parental duplex imposes certain constraints on the activity of the DNA polymerases that synthesize new DNA. The leading-strand polymerase advances in a continuous fashion, but the lagging-strand polymerase is forced to restart at short intervals. In several prokaryotic systems studied so far, this problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. The timing of Okazaki fragment synthesis and loop formation is determined by a subtle interplay of enzymatic activities at the fork. Recent developments in single-molecule techniques have enabled the direct observation of these processes and have greatly contributed to a better understanding of the dynamic nature of the replication fork. Here, we will review recent experimental advances, present the current models, and discuss some of the exciting developments in the field. 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Timing, coordination, and rhythm: Acrobatics at the DNA replication fork

    KAUST Repository

    Hamdan, Samir; van Oijen, Antoine M.

    2010-01-01

    In DNA replication, the antiparallel nature of the parental duplex imposes certain constraints on the activity of the DNA polymerases that synthesize new DNA. The leading-strand polymerase advances in a continuous fashion, but the lagging-strand polymerase is forced to restart at short intervals. In several prokaryotic systems studied so far, this problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. The timing of Okazaki fragment synthesis and loop formation is determined by a subtle interplay of enzymatic activities at the fork. Recent developments in single-molecule techniques have enabled the direct observation of these processes and have greatly contributed to a better understanding of the dynamic nature of the replication fork. Here, we will review recent experimental advances, present the current models, and discuss some of the exciting developments in the field. 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Development of a novel loop-mediated isothermal amplification (LAMP) assay for the detection of Salmonella ser. Enteritidis from egg products

    Science.gov (United States)

    Salmonella ser. Enteritidis is a major public health concern worldwide. Loop-mediated isothermal amplification (LAMP) is a novel simple, easy-to-operate detection technology that amplifies DNA with high speed, efficiency, and specificity under isothermal conditions. The objective of this study was t...

  14. THE CORONAL LOOP INVENTORY PROJECT: EXPANDED ANALYSIS AND RESULTS

    Energy Technology Data Exchange (ETDEWEB)

    Schmelz, J. T. [USRA, 7178 Columbia Gateway Drive, Columbia, MD 21046 (United States); Christian, G. M.; Chastain, R. A., E-mail: jschmelz@usra.edu [Physics Department, University of Memphis, Memphis, TN 38152 (United States)

    2016-11-10

    We have expanded upon earlier work that investigates the relative importance of coronal loops with isothermal versus multithermal cross-field temperature distributions. These results are important for determining if loops have substructure in the form of unresolved magnetic strands. We have increased the number of loops targeted for temperature analysis from 19 to 207 with the addition of 188 new loops from multiple regions. We selected all loop segments visible in the 171 Å images of the Atmospheric Imaging Assembly (AIA) that had a clean background. Eighty-six of the new loops were rejected because they could not be reliably separated from the background in other AIA filters. Sixty-one loops required multithermal models to reproduce the observations. Twenty-eight loops were effectively isothermal, that is, the plasma emission to which AIA is sensitive could not be distinguished from isothermal emission, within uncertainties. Ten loops were isothermal. Also, part of our inventory was one small flaring loop, one very cool loop whose temperature distribution could not be constrained by the AIA data, and one loop with inconclusive results. Our survey can confirm an unexpected result from the pilot study: we found no isothermal loop segments where we could properly use the 171-to-193 ratio method, which would be similar to the analysis done for many loops observed with TRACE and EIT. We recommend caution to observers who assume the loop plasma is isothermal, and hope that these results will influence the direction of coronal heating models and the effort modelers spend on various heating scenarios.

  15. Development of Loop-Mediated Isothermal Amplification Assay for Detection of Entamoeba histolytica▿

    Science.gov (United States)

    Liang, Shih-Yu; Chan, Yun-Hsien; Hsia, Kan-Tai; Lee, Jing-Lun; Kuo, Ming-Chu; Hwa, Kuo-Yuan; Chan, Chi-Wen; Chiang, Ting-Yi; Chen, Jung-Sheng; Wu, Fang-Tzy; Ji, Dar-Der

    2009-01-01

    A novel one-step, closed-tube, loop-mediated isothermal amplification (LAMP) assay for detecting Entamoeba histolytica, one of the leading causes of morbidity in developing countries, was developed. The sensitivity of the LAMP assay is 1 parasite per reaction. A total of 130 clinical samples were analyzed, and the results compared with those of conventional nested PCR to validate the practicability of this assay. No DNA was amplified from other diarrheal pathogens, such as other Entamoeba species, bacteria, and viruses. These results indicate that LAMP is a rapid, simple, and valuable diagnostic tool for epidemiological studies of amebiasis. PMID:19321720

  16. Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex

    KAUST Repository

    Ghosh, Sharmistha; Hamdan, Samir; Richardson, Charles C.

    2010-01-01

    The DNA polymerase encoded by bacteriophage T7 has low processivity. Escherichia coli thioredoxin binds to a segment of 76 residues in the thumb subdomain of the polymerase and increases the processivity. The binding of thioredoxin leads to the formation of two basic loops, loops A and B, located within the thioredoxin-binding domain (TBD). Both loops interact with the acidic C terminus of the T7 helicase. A relatively weak electrostatic mode involves the C-terminal tail of the helicase and the TBD, whereas a high affinity interaction that does not involve the C-terminal tail occurs when the polymerase is in a polymerization mode. T7 gene 2.5 single-stranded DNA-binding protein (gp2.5) also has an acidic C-terminal tail. gp2.5 also has two modes of interaction with the polymerase, but both involve the C-terminal tail of gp2.5. An electrostatic interaction requires the basic residues in loops A and B, and gp2.5 binds to both loops with similar affinity as measured by surface plasmon resonance. When the polymerase is in a polymerization mode, the C terminus of gene 2.5 protein interacts with the polymerase in regions outside the TBD.gp2.5 increases the processivity of the polymerase-helicase complex during leading strand synthesis. When loop B of the TBD is altered, abortive DNA products are observed during leading strand synthesis. Loop B appears to play an important role in communication with the helicase and gp2.5, whereas loop A plays a stabilizing role in these interactions. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Two modes of interaction of the single-stranded DNA-binding protein of bacteriophage T7 with the DNA polymerase-thioredoxin complex

    KAUST Repository

    Ghosh, Sharmistha

    2010-04-06

    The DNA polymerase encoded by bacteriophage T7 has low processivity. Escherichia coli thioredoxin binds to a segment of 76 residues in the thumb subdomain of the polymerase and increases the processivity. The binding of thioredoxin leads to the formation of two basic loops, loops A and B, located within the thioredoxin-binding domain (TBD). Both loops interact with the acidic C terminus of the T7 helicase. A relatively weak electrostatic mode involves the C-terminal tail of the helicase and the TBD, whereas a high affinity interaction that does not involve the C-terminal tail occurs when the polymerase is in a polymerization mode. T7 gene 2.5 single-stranded DNA-binding protein (gp2.5) also has an acidic C-terminal tail. gp2.5 also has two modes of interaction with the polymerase, but both involve the C-terminal tail of gp2.5. An electrostatic interaction requires the basic residues in loops A and B, and gp2.5 binds to both loops with similar affinity as measured by surface plasmon resonance. When the polymerase is in a polymerization mode, the C terminus of gene 2.5 protein interacts with the polymerase in regions outside the TBD.gp2.5 increases the processivity of the polymerase-helicase complex during leading strand synthesis. When loop B of the TBD is altered, abortive DNA products are observed during leading strand synthesis. Loop B appears to play an important role in communication with the helicase and gp2.5, whereas loop A plays a stabilizing role in these interactions. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. On Vanishing Two Loop Cosmological Constants in Nonsupersymmetric Strings

    Energy Technology Data Exchange (ETDEWEB)

    Kachru, S

    1998-10-22

    It has recently been suggested that in certain special nonsupersymmetric type II string compactifications, at least the first two perturbative contributions to the cosmological constant Lambda vanish. Support for perturbative vanishing beyond 1-loop (as well as evidence for the absence of some nonperturbative contributions) has come from duality arguments. There was also a direct 2-loop computation which was incomplete; in this note we explain the deficiency of the previous 2-loop calculation and discuss the complete 2-loop computation in two different models. The corrected analysis yields a vanishing 2-loop contribution to Lambda in these models.

  19. On vanishing two loop cosmological constants in nonsupersymmetric strings

    International Nuclear Information System (INIS)

    Kachru, Shamit; Silverstein, Eva

    1998-01-01

    It has recently been suggested that in certain special nonsupersymmetric type II string compactifications, at least the first two perturbative contributions to the cosmological constant Λ vanish. Support for perturbative vanishing beyond 1-loop (as well as evidence for the absence of some nonperturbative contributions) has come from duality arguments. There was also a direct 2-loop computation which was incomplete; in this note we explain the deficiency of the previous 2-loop calculation and discuss the complete 2-loop computation in two different models. The corrected analysis yields a vanishing 2-loop contribution to Λ in these models

  20. The massless two-loop two-point function

    International Nuclear Information System (INIS)

    Bierenbaum, I.; Weinzierl, S.

    2003-01-01

    We consider the massless two-loop two-point function with arbitrary powers of the propagators and derive a representation from which we can obtain the Laurent expansion to any desired order in the dimensional regularization parameter ε. As a side product, we show that in the Laurent expansion of the two-loop integral only rational numbers and multiple zeta values occur. Our method of calculation obtains the two-loop integral as a convolution product of two primitive one-loop integrals. We comment on the generalization of this product structure to higher loop integrals. (orig.)

  1. On the loop-loop scattering amplitudes in Abelian and non-Abelian gauge theories

    International Nuclear Information System (INIS)

    Meggiolaro, Enrico

    2005-01-01

    The high-energy elastic scattering amplitude of two colour-singlet qq-bar pairs is governed by the correlation function of two Wilson loops, which follow the classical straight lines for quark (antiquark) trajectories. This quantity is expected to be free of IR divergences, differently from what happens for the parton-parton elastic scattering amplitude, described, in the high-energy limit, by the expectation value of two Wilson lines. We shall explicitly test this IR finiteness by a direct non-perturbative computation of the loop-loop scattering amplitudes in the (pedagogic, but surely physically interesting) case of quenched QED. The results obtained for the Abelian case will be generalized to the case of a non-Abelian gauge theory with Nc colours, but stopping to the order O(g4) in perturbation theory. In connection with the above-mentioned IR finiteness, we shall also discuss some analytic properties of the loop-loop scattering amplitudes in both Abelian and non-Abelian gauge theories, when going from Minkowskian to Euclidean theory, which can be relevant to the still unsolved problem of the s-dependence of hadron-hadron total cross-sections

  2. Probe DNA-Cisplatin Interaction with Solid-State Nanopores

    Science.gov (United States)

    Zhou, Zhi; Hu, Ying; Li, Wei; Xu, Zhi; Wang, Pengye; Bai, Xuedong; Shan, Xinyan; Lu, Xinghua; Nanopore Collaboration

    2014-03-01

    Understanding the mechanism of DNA-cisplatin interaction is essential for clinical application and novel drug design. As an emerging single-molecule technology, solid-state nanopore has been employed in biomolecule detection and probing DNA-molecule interactions. Herein, we reported a real-time monitoring of DNA-cisplatin interaction by employing solid-state SiN nanopores. The DNA-cisplatin interacting process is clearly classified into three stages by measuring the capture rate of DNA-cisplatin adducts. In the first stage, the negative charged DNA molecules were partially discharged due to the bonding of positive charged cisplatin and forming of mono-adducts. In the second stage, forming of DNA-cisplatin di-adducts with the adjacent bases results in DNA bending and softening. The capture rate increases since the softened bi-adducts experience a lower barrier to thread into the nanopores. In the third stage, complex structures, such as micro-loop, are formed and the DNA-cisplatin adducts are aggregated. The capture rate decreases to zero as the aggregated adduct grows to the size of the pore. The characteristic time of this stage was found to be linear with the diameter of the nanopore and this dynamic process can be described with a second-order reaction model. We are grateful to Laboratory of Microfabrication, Dr. Y. Yao, and Prof. R.C. Yu (Institute of Physics, Chinese Academy of Sciences) for technical assistance.

  3. Abnormal duodenal loop demonstrated by X-ray

    International Nuclear Information System (INIS)

    Thommesen, P.; Funch-Jensen, P.

    1986-01-01

    The occurrence of dyspeptic symptoms has previously been correlated with the shape of the duodenal loop in patients with X-ray-negative dyspepsia. An abnormal duodenal loop was associated with a significantly higher incidence of symtoms provoked by meals, vomiting, regurgitations, heartburn, and the irritable bowel syndrome. 89% of these patients (26 patients with a normal duodenal loop and 39 patients with abnormal duodenal loop) were available for a 5-year follow-up study of symptomatic outcome. The incidence of symptoms provoked by meals was still significantly higher in patients with an abnormal duodenal loop, and there was also a significant difference concerning symptomatic outcome. Approximately 75% of the patients with a normal duodenal loop had improved, and 25% had unchanged clinical conditions. Approximately 50% of the patients with an abnormal duodenal loop had improved, and 50% had an unchanged or even deteriorated clinical condition

  4. Decoding the Mobility and Time Scales of Protein Loops.

    Science.gov (United States)

    Gu, Yina; Li, Da-Wei; Brüschweiler, Rafael

    2015-03-10

    The flexible nature of protein loops and the time scales of their dynamics are critical for many biologically important events at the molecular level, such as protein interaction and recognition processes. In order to obtain a predictive understanding of the dynamic properties of loops, 500 ns molecular dynamics (MD) computer simulations of 38 different proteins were performed and validated using NMR chemical shifts. A total of 169 loops were analyzed and classified into three types, namely fast loops with correlation times Web server (http://spin.ccic.ohio-state.edu/index.php/loop). The results demonstrate that loop dynamics with their time scales can be predicted rapidly with reasonable accuracy, which will allow the screening of average protein structures to help better understand the various roles loops can play in the context of protein-protein interactions and binding.

  5. Understanding the Elementary Steps in DNA Tile-Based Self-Assembly.

    Science.gov (United States)

    Jiang, Shuoxing; Hong, Fan; Hu, Huiyu; Yan, Hao; Liu, Yan

    2017-09-26

    Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios. With more sticky ends, tile attachment becomes more thermostable with an approximately linear decrease in the free energy change (more negative). The total binding free energy of sticky ends is partially compromised by a sequence-independent energy penalty when tile attachment forms a constrained configuration: "loop". The minimal loop is a 2 × 2 tetramer (Loop4). The energy penalty of loops of 4, 6, and 8 tiles was analyzed with the independent loop model assuming no interloop tension, which is generalizable to arbitrary tile configurations. More sticky ends also contribute to a faster on-rate under isothermal conditions when nucleation is the rate-limiting step. Incorrect sticky end contributes to neither the thermostability nor the kinetics. The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.

  6. Relating loop quantum cosmology to loop quantum gravity: symmetric sectors and embeddings

    International Nuclear Information System (INIS)

    Engle, J

    2007-01-01

    In this paper we address the meaning of states in loop quantum cosmology (LQC), in the context of loop quantum gravity. First, we introduce a rigorous formulation of an embedding proposed by Bojowald and Kastrup, of LQC states into loop quantum gravity. Then, using certain holomorphic representations, a new class of embeddings, called b-embeddings, are constructed, following the ideas of Engle (2006 Quantum field theory and its symmetry reduction Class. Quantum Gravity 23 2861-94). We exhibit a class of operators preserving each of these embeddings, and show their consistency with the LQC quantization. In the b-embedding case, the classical analogues of these operators separate points in phase space. Embedding at the gauge and diffeomorphism invariant level is discussed briefly in the conclusions

  7. Stem loop sequences specific to transposable element IS605 are found linked to lipoprotein genes in Borrelia plasmids.

    Directory of Open Access Journals (Sweden)

    Nicholas Delihas

    Full Text Available BACKGROUND: Plasmids of Borrelia species are dynamic structures that contain a large number of repetitive genes, gene fragments, and gene fusions. In addition, the transposable element IS605/200 family, as well as degenerate forms of this IS element, are prevalent. In Helicobacter pylori, flanking regions of the IS605 transposase gene contain sequences that fold into identical small stem loops. These function in transposition at the single-stranded DNA level. METHODOLOGY/PRINCIPAL FINDINGS: In work reported here, bioinformatics techniques were used to scan Borrelia plasmid genomes for IS605 transposable element specific stem loop sequences. Two variant stem loop motifs are found in the left and right flanking regions of the transposase gene. Both motifs appear to have dispersed in plasmid genomes and are found "free-standing" and phylogenetically conserved without the associated IS605 transposase gene or the adjacent flanking sequence. Importantly, IS605 specific stem loop sequences are also found at the 3' ends of lipoprotein genes (PFam12 and PFam60, however the left and right sequences appear to develop their own evolutionary patterns. The lipoprotein gene-linked left stem loop sequences maintain the IS605 stem loop motif in orthologs but only at the RNA level. These show mutations whereby variants fold into phylogenetically conserved RNA-type stem loops that contain the wobble non-Watson-Crick G-U base-pairing. The right flanking sequence is associated with the family lipoprotein-1 genes. A comparison of homologs shows that the IS605 stem loop motif rapidly dissipates, but a more elaborate secondary structure appears to develop in its place. CONCLUSIONS/SIGNIFICANCE: Stem loop sequences specific to the transposable element IS605 are present in plasmid regions devoid of a transposase gene and significantly, are found linked to lipoprotein genes in Borrelia plasmids. These sequences are evolutionarily conserved and/or structurally developed in

  8. Transcription and recombination: when RNA meets DNA.

    Science.gov (United States)

    Aguilera, Andrés; Gaillard, Hélène

    2014-08-01

    A particularly relevant phenomenon in cell physiology and proliferation is the fact that spontaneous mitotic recombination is strongly enhanced by transcription. The most accepted view is that transcription increases the occurrence of double-strand breaks and/or single-stranded DNA gaps that are repaired by recombination. Most breaks would arise as a consequence of the impact that transcription has on replication fork progression, provoking its stalling and/or breakage. Here, we discuss the mechanisms responsible for the cross talk between transcription and recombination, with emphasis on (1) the transcription-replication conflicts as the main source of recombinogenic DNA breaks, and (2) the formation of cotranscriptional R-loops as a major cause of such breaks. The new emerging questions and perspectives are discussed on the basis of the interference between transcription and replication, as well as the way RNA influences genome dynamics. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  9. The QED vacuum polarization function at four loops and the anomalous magnetic moment at five loops

    International Nuclear Information System (INIS)

    Baikov, P.

    2013-07-01

    The anomalous moment of the muon is one of the most fundamental observables. It has been measured experimentally with a very high precision and on theory side the contributions from perturbative QED have been calculated up to five-loop level by numerical methods. Contributions to the muon anomalous magnetic moment from certain diagram classes are also accessible by alternative methods. In this paper we present the evaluation of contributions to the QCD corrections due to insertions of the vacuum polarization function at five-loop level.

  10. Closed-loop conductance scanning tunneling spectroscopy: demonstrating the equivalence to the open-loop alternative.

    Science.gov (United States)

    Hellenthal, Chris; Sotthewes, Kai; Siekman, Martin H; Kooij, E Stefan; Zandvliet, Harold J W

    2015-01-01

    We demonstrate the validity of using closed-loop z(V) conductance scanning tunneling spectroscopy (STS) measurements for the determination of the effective tunneling barrier by comparing them to more conventional open-loop I(z) measurements. Through the development of a numerical model, the individual contributions to the effective tunneling barrier present in these experiments, such as the work function and the presence of an image charge, are determined quantitatively. This opens up the possibility of determining tunneling barriers of both vacuum and molecular systems in an alternative and more detailed manner.

  11. Pemakaian Crown Loop dan Band Loop di Rahang Bawah Anak Usia Enam Tahun (Laporan Kasus

    Directory of Open Access Journals (Sweden)

    Rivi Isabela

    2015-11-01

    Full Text Available The function of space maintainer is to preserve arch length following the premature loss of a primary teeth. Early loss of primary tooth may compromise the eruption of succedaneous teeth if there is a reduction in the arch length. The Band and Crown Loop are used to maintain the loss of primary molar. The report describe a 6 year old girl who has premature loss of second left mandibular primary molar and first right mandibular primary molar treated using crown and band loop space maintainer. The patient still has mastication function from other posterior primary teeth.

  12. The QED vacuum polarization function at four loops and the anomalous magnetic moment at five loops

    Energy Technology Data Exchange (ETDEWEB)

    Baikov, P. [Moscow State Univ. (Russian Federation). D.V. Skobeltsyn Inst. of Nuclear Physics; Maier, A. [Technische Univ. Muenchen, Garching (Germany). Physics Dept. T31; Marquard, P. [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany)

    2013-07-15

    The anomalous moment of the muon is one of the most fundamental observables. It has been measured experimentally with a very high precision and on theory side the contributions from perturbative QED have been calculated up to five-loop level by numerical methods. Contributions to the muon anomalous magnetic moment from certain diagram classes are also accessible by alternative methods. In this paper we present the evaluation of contributions to the QCD corrections due to insertions of the vacuum polarization function at five-loop level.

  13. Closing the loop of deep brain stimulation.

    Science.gov (United States)

    Carron, Romain; Chaillet, Antoine; Filipchuk, Anton; Pasillas-Lépine, William; Hammond, Constance

    2013-12-20

    High-frequency deep brain stimulation is used to treat a wide range of brain disorders, like Parkinson's disease. The stimulated networks usually share common electrophysiological signatures, including hyperactivity and/or dysrhythmia. From a clinical perspective, HFS is expected to alleviate clinical signs without generating adverse effects. Here, we consider whether the classical open-loop HFS fulfills these criteria and outline current experimental or theoretical research on the different types of closed-loop DBS that could provide better clinical outcomes. In the first part of the review, the two routes followed by HFS-evoked axonal spikes are explored. In one direction, orthodromic spikes functionally de-afferent the stimulated nucleus from its downstream target networks. In the opposite direction, antidromic spikes prevent this nucleus from being influenced by its afferent networks. As a result, the pathological synchronized activity no longer propagates from the cortical networks to the stimulated nucleus. The overall result can be described as a reversible functional de-afferentation of the stimulated nucleus from its upstream and downstream nuclei. In the second part of the review, the latest advances in closed-loop DBS are considered. Some of the proposed approaches are based on mathematical models, which emphasize different aspects of the parkinsonian basal ganglia: excessive synchronization, abnormal firing-rate rhythms, and a deficient thalamo-cortical relay. The stimulation strategies are classified depending on the control-theory techniques on which they are based: adaptive and on-demand stimulation schemes, delayed and multi-site approaches, stimulations based on proportional and/or derivative control actions, optimal control strategies. Some of these strategies have been validated experimentally, but there is still a large reservoir of theoretical work that may point to ways of improving practical treatment.

  14. Closing the loop of deep brain stimulation

    Directory of Open Access Journals (Sweden)

    Romain eCARRON

    2013-12-01

    Full Text Available High-frequency deep brain stimulation is used to treat a wide range of brain disorders, like Parkinson's disease. The stimulated networks usually share common electrophysiological signatures, including hyperactivity and/or dysrhythmia. From a clinical perspective, HFS is expected to alleviate clinical signs without generating adverse effects. Here, we consider whether the classical open-loop HFS fulfils these criteria and outline current experimental or theoretical research on the different types of closed-loop DBS that could provide better clinical outcomes. In the first part of the review, the two routes followed by HFS-evoked axonal spikes are explored. In one direction, orthodromic spikes functionally de-afferent the stimulated nucleus from its downstream target networks. In the opposite direction, antidromic spikes prevent this nucleus from being influenced by its afferent networks. As a result, the pathological synchronized activity no longer propagates from the cortical networks to the stimulated nucleus. The overall result can be described as a reversible functional de-afferentation of the stimulated nucleus from its upstream and downstream nuclei. In the second part of the review, the latest advances in closed-loop DBS are considered. Some of the proposed approaches are based on mathematical models, which emphasize different aspects of the parkinsonian basal ganglia: excessive synchronization, abnormal firing-rate rhythms, and a deficient thalamo-cortical relay. The stimulation strategies are classified depending on the control-theory techniques on which they are based: adaptive and on-demand stimulation schemes, delayed and multi-site approaches, stimulations based on proportional and/or derivative control actions, optimal control strategies. Some of these strategies have been validated experimentally, but there is still a large reservoir of theoretical work that may point to ways of improving practical treatment.

  15. Closing the loop of deep brain stimulation

    Science.gov (United States)

    Carron, Romain; Chaillet, Antoine; Filipchuk, Anton; Pasillas-Lépine, William; Hammond, Constance

    2013-01-01

    High-frequency deep brain stimulation is used to treat a wide range of brain disorders, like Parkinson's disease. The stimulated networks usually share common electrophysiological signatures, including hyperactivity and/or dysrhythmia. From a clinical perspective, HFS is expected to alleviate clinical signs without generating adverse effects. Here, we consider whether the classical open-loop HFS fulfills these criteria and outline current experimental or theoretical research on the different types of closed-loop DBS that could provide better clinical outcomes. In the first part of the review, the two routes followed by HFS-evoked axonal spikes are explored. In one direction, orthodromic spikes functionally de-afferent the stimulated nucleus from its downstream target networks. In the opposite direction, antidromic spikes prevent this nucleus from being influenced by its afferent networks. As a result, the pathological synchronized activity no longer propagates from the cortical networks to the stimulated nucleus. The overall result can be described as a reversible functional de-afferentation of the stimulated nucleus from its upstream and downstream nuclei. In the second part of the review, the latest advances in closed-loop DBS are considered. Some of the proposed approaches are based on mathematical models, which emphasize different aspects of the parkinsonian basal ganglia: excessive synchronization, abnormal firing-rate rhythms, and a deficient thalamo-cortical relay. The stimulation strategies are classified depending on the control-theory techniques on which they are based: adaptive and on-demand stimulation schemes, delayed and multi-site approaches, stimulations based on proportional and/or derivative control actions, optimal control strategies. Some of these strategies have been validated experimentally, but there is still a large reservoir of theoretical work that may point to ways of improving practical treatment. PMID:24391555

  16. Wilson loops, instantons and quantum mechanics

    International Nuclear Information System (INIS)

    Schiereck, Marc

    2014-05-01

    In this thesis we examine two different problems. The first is the computation of vacuum expectation values of Wilson loop operators in ABJM theory, the other problem is finding the instanton series of the refined topological string on certain local Calabi-Yau geometries in the Nekrasov-Shatashvili limit. Based on the description of ABJM theory as a matrix model, it is possible to find a description of it in terms of an ideal Fermi gas with a non-trivial one-particle Hamiltonian. The vacuum-expectation-values of Wilson loop operators in ABJM theory correspond to averages of operators in the statistical-mechanical problem. Using the WKB expansion, it is possible to extract the full 1/N expansion of the vevs, up to exponentially small contributions, for arbitrary Chern-Simons coupling. We compute these vevs for the 1/6 and 1/2 BPS Wilson loops at any winding number. These can be written in terms of the Airy function. The expressions we found reproduce the low genus results previously obtained in the 't Hooft expansion. In another problem we use mirror symmetry, quantum geometry and modularity properties of elliptic curves to calculate the refined free energies, given in terms of an instanton sum, in the Nekrasov-Shatashvili limit on non-compact toric Calabi-Yau manifolds, based on del Pezzo surfaces. Quantum geometry here is to be understood as a quantum deformed version of rigid special geometry, which has its origin in the quantum mechanical behavior of branes in the topological string B-model. We argue that in the Seiberg-Witten picture only the Coulomb parameters lead to quantum corrections, while the mass parameters remain uncorrected. In certain cases we also compute the expansion of the free energies at the orbifold point and the conifold locus. We compute the quantum corrections order by order on ℎ by deriving second order differential operators, which act on the classical periods.

  17. Chemical-looping combustion - status of development

    Energy Technology Data Exchange (ETDEWEB)

    Lyngfelt, Anders; Johansson, Marcus; Mattisson, Tobias

    2008-05-15

    Chemical-looping combustion (CLC) is a combustion technology with inherent separation of the greenhouse gas CO{sub 2}. The technique involves the use of a metal oxide as an oxygen carrier which transfers oxygen from combustion air to the fuel, and hence a direct contact between air and fuel is avoided. Two inter-connected fluidized beds, a fuel reactor and an air reactor, are used in the process. In the fuel reactor, the metal oxide is reduced by the reaction with the fuel and in the air reactor; the reduced metal oxide is oxidized with air. The outlet gas from the fuel reactor consists of CO{sub 2} and H{sub 2}O, and almost pure stream of CO{sub 2} is obtained when water is condensed. Considerable research has been conducted on CLC in the last years with respect to oxygen carrier development, reactor design, system efficiencies and prototype testing. In 2002 the process was a paper concept, albeit with some important but limited laboratory work on oxygen carrier particles. Today more than 600 materials have been tested and the technique has been successfully demonstrated in chemical-looping combustors in the size range 0.3 - 50 kW, using different types of oxygen carriers based on the metals Ni, Co, Fe, Cu and Mn. The total time of operational experience is more than a thousand hours. From these tests it can be established that almost complete conversion of the fuel can be obtained and 100% CO{sub 2} capture is possible. Most work so far has been focused on gaseous fuels, but the direct application to solid fuels is also being studied. Moreover, the same principle of oxygen transfer is used in chemical-looping reforming (CLR), which involves technologies to produce hydrogen with inherent CO{sub 2} capture. This paper presents an overview of the research performed on CLC and CLR highlights the current status of the technology

  18. Gas Test Loop Booster Fuel Hydraulic Testing

    International Nuclear Information System (INIS)

    Gas Test Loop Hydraulic Testing Staff

    2006-01-01

    The Gas Test Loop (GTL) project is for the design of an adaptation to the Advanced Test Reactor (ATR) to create a fast-flux test space where fuels and materials for advanced reactor concepts can undergo irradiation testing. Incident to that design, it was found necessary to make use of special booster fuel to enhance the neutron flux in the reactor lobe in which the Gas Test Loop will be installed. Because the booster fuel is of a different composition and configuration from standard ATR fuel, it is necessary to qualify the booster fuel for use in the ATR. Part of that qualification is the determination that required thermal hydraulic criteria will be met under routine operation and under selected accident scenarios. The Hydraulic Testing task in the GTL project facilitates that determination by measuring flow coefficients (pressure drops) over various regions of the booster fuel over a range of primary coolant flow rates. A high-fidelity model of the NW lobe of the ATR with associated flow baffle, in-pile-tube, and below-core flow channels was designed, constructed and located in the Idaho State University Thermal Fluids Laboratory. A circulation loop was designed and constructed by the university to provide reactor-relevant water flow rates to the test system. Models of the four booster fuel elements required for GTL operation were fabricated from aluminum (no uranium or means of heating) and placed in the flow channel. One of these was instrumented with Pitot tubes to measure flow velocities in the channels between the three booster fuel plates and between the innermost and outermost plates and the side walls of the flow annulus. Flow coefficients in the range of 4 to 6.5 were determined from the measurements made for the upper and middle parts of the booster fuel elements. The flow coefficient for the lower end of the booster fuel and the sub-core flow channel was lower at 2.3

  19. RPC gas recovery by open loop method

    International Nuclear Information System (INIS)

    Joshi, Avinash

    2009-01-01

    RPC detectors require to be flushed with small but continuous flow of gas mixture. Dealing with large number of detectors, gas consumption to very large volumes. Gas flow is a running expense and constituent gases are too expensive to be treated as consumables. Exhaust gas mixture from detectors is a potential environmental hazard if discharged directly into the atmosphere. Storage of gases on a large scale also leads to inventory- and safety-related problems. A solution to these problems is the recovery and reuse of exhaust gas mixture from RPC detectors. Close loop method employs recirculation of exhausted gas mixture after purification, analysis and addition of top-up quantities. In open loop method, under consideration here, individual component gases are separated from gas mixture and reused as source. During open loop process, gases liquefiable at low pressures are separated from ones liquefiable at high pressure. The gas phase components within each group are successively separated by either fractional condensation or gravity separation. Gas mixture coming from RPC exhaust is first desiccated by passage through molecular sieve adsorbent type (3A+4A). Subsequent scrubbing over basic activated alumina removes toxic and acidic contaminants such as S 2 F 10 produced during corona (arcing) discharge. In the first stage of separation isobutane and freon are concentrated by diffusion and liquefied by fractional condensation by cooling upto -30 deg. C. Liquefied gases are returned to source tanks. In the second stage of separation, argon and sulphur hexafluoride, the residual gases, are concentrated by settling due to density difference. SF 6 is stored for recovery by condensation at high pressure while argon is further purified by thermal cracking of crossover impurities at 1000 deg. C followed by wet scrubbing.

  20. RPC gas recovery by open loop method

    Energy Technology Data Exchange (ETDEWEB)

    Joshi, Avinash [Alpha Pneumatics, 11, Krishna Kutir, Madanlal Dhigra Road, Panch Pakhadi (India)], E-mail: alpha_pneumatics@hotmail.com

    2009-05-01

    RPC detectors require to be flushed with small but continuous flow of gas mixture. Dealing with large number of detectors, gas consumption to very large volumes. Gas flow is a running expense and constituent gases are too expensive to be treated as consumables. Exhaust gas mixture from detectors is a potential environmental hazard if discharged directly into the atmosphere. Storage of gases on a large scale also leads to inventory- and safety-related problems. A solution to these problems is the recovery and reuse of exhaust gas mixture from RPC detectors. Close loop method employs recirculation of exhausted gas mixture after purification, analysis and addition of top-up quantities. In open loop method, under consideration here, individual component gases are separated from gas mixture and reused as source. During open loop process, gases liquefiable at low pressures are separated from ones liquefiable at high pressure. The gas phase components within each group are successively separated by either fractional condensation or gravity separation. Gas mixture coming from RPC exhaust is first desiccated by passage through molecular sieve adsorbent type (3A+4A). Subsequent scrubbing over basic activated alumina removes toxic and acidic contaminants such as S{sub 2}F{sub 10} produced during corona (arcing) discharge. In the first stage of separation isobutane and freon are concentrated by diffusion and liquefied by fractional condensation by cooling upto -30 deg. C. Liquefied gases are returned to source tanks. In the second stage of separation, argon and sulphur hexafluoride, the residual gases, are concentrated by settling due to density difference. SF{sub 6} is stored for recovery by condensation at high pressure while argon is further purified by thermal cracking of crossover impurities at 1000 deg. C followed by wet scrubbing.