Sample records for hemicatenated dna loops

  1. Modulation of DNA loop lifetimes by the free energy of loop formation

    CERN Document Server

    Chen, Yi-Ju; Mulligan, Peter; Spakowitz, Andrew J; Phillips, Rob


    Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for transcriptional regulation in both prokaryotes and eukaryotes, and the speed of such regulations affects the fitness of individuals. Here, we examine the in vitro looping dynamics of the classic Lac repressor gene-regulatory motif. We show that both loop association and loop dissociation at the DNA-repressor junctions depend on the elastic deformation of the DNA and protein, and that both looping and unlooping rates approximately scale with the looping J factor, which reflects the system's deformation free energy. We explain this observation by transition state theory and model the DNA-protein complex as an effective worm-like chain with twist. We introduce a finite protein-DNA binding interaction length, in competition with the characteristic DNA deformation length scale, ...

  2. The Energy Landscape of Hyperstable LacI-DNA Loops (United States)

    Kahn, Jason


    The Escherichia coli LacI protein represses transcription of the lac operon by blocking access to the promoter through binding at a promoter-proximal DNA operator. The affinity of tetrameric LacI (and therefore the repression efficiency) is enhanced by simultaneous binding to an auxiliary operator, forming a DNA loop. Hyperstable LacI-DNA loops were previously shown to be formed on DNA constructs that include a sequence-directed bend flanked by operators. Biochemical experiments showed that two such constructs (9C14 and 11C12) with different helical phasing between the operators and the DNA bend form different DNA loop shapes. The geometry and topology of the loops and the relevance of alternative conformations suggested by probable flexible linkers in LacI remain unclear. Bulk and single molecule fluorescence resonance energy transfer (SM-FRET, with D. English) experiments on a dual fluorophore-labeled 9C14-LacI loop demonstrate that it adopts a single, stable, rigid closed-form loop conformation. Here, we characterize the LacI-9C14 loop by SM-FRET as a function of inducer isopropyl-β,D-thiogalactoside (IPTG) concentration. Energy transfer measurements reveal partial but incomplete destabilization of loop formation by IPTG. Surprisingly, there is no change in the energy transfer efficiency of the remaining looped population. Models for the regulation of the lac operon often assume complete disruption of LacI-operator complexes upon inducer binding to LacI. Our work shows that even at saturating IPTG there is still a significant population of LacI-DNA complexes in a looped state, in accord with previous in vivo experiments that show incomplete induction (with J. Maher). Finally, we will report progress on characterizing the ``energy landscape'' for DNA looping upon systematic variation of the DNA linkers between the operators and the bending locus. Rod mechanics simulations (with N. Perkins) provide testable predictions on loop stability, topology, and FRET.

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

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    Lin Han


    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.

  4. The Role of Entropic Effects on DNA Loop Formation (United States)

    Wilson, David; Tkachenko, Alexei; Lillian, Todd; Perkins, Noel; Meiners, Jens Christian


    The formation of protein mediated DNA loops often regulates gene expression. Typically, a protein is simultaneously bound to two DNA operator sites. An example is the lactose repressor which binds to the Lac operon of E. coli. We characterize the mechanics of this system by calculating the free energy cost of loop formation. We construct a Hamiltonian that describes the change in DNA bending energy due to linear perturbations about the looped and open states, starting from a non-linear mechanical rod model that determines the shape and bending energy of the inter-operator DNA loop while capturing the intrinsic curvature and sequence-dependent elasticity of the DNA. The crystal structure of the LacI protein provides the boundary conditions for the DNA. We then calculate normal modes of the open and closed loops to account for the thermal fluctuations. The ratio of determinants of the two Hamiltonians yields the partition function, and the enthalphic and entropic cost of looping. This calculation goes beyond standard elastic energy models because it fully accounts for the substantial entropic differences between the two states. It also includes effects of sequence dependent curvature and stiffness and allows anisotropic variations in persistence length. From the free energy we then calculate the J-factor and ratio of loop lifetimes.

  5. A Generalized Theory of DNA Looping and Cyclization (United States)

    Wilson, David; Lillian, Todd; Perkins, Noel; Tkachenko, Alexei; Meiners, Jens-Christian


    We have developed a semi-analytic method for calculating the Stockmayer Jacobson J-factor for protein mediated DNA loops. The formation of DNA loops on the order of a few persistence lengths is a key component in many biological regulatory functions. The binding of LacI protein within the Lac Operon of E.coli serves as the canonical example for loop regulated transcription. We use a non-linear rod model to determine the equilibrium shape of the inter-operator DNA loop under prescribed binding constraints while taking sequence-dependent curvature and elasticity into account. Then we construct a Hamiltonian that describes thermal fluctuations about the open and looped equilibrium states, yielding the entropic and enthalpic costs of loop formation. Our work demonstrates that even for short sequences of the order one persistence length, entropic terms contribute substantially to the J factor. We also show that entropic considerations are able to determine the most favorable binding topology. The J factor can be used to compare the relative loop lifetimes of various DNA sequences, making it a useful tool in sequence design. A corollary of this work is the computation of an effective torsional persistence length, which demonstrates how torsion bending coupling in a constrained geometry affects the conversion of writhe to twist.

  6. The free-energy cost of interaction between DNA loops. (United States)

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


    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. Suppression and enhancement of transcriptional noise by DNA looping (United States)

    Vilar, Jose M. G.; Saiz, Leonor


    DNA looping has been observed to enhance and suppress transcriptional noise but it is uncertain which of these two opposite effects is to be expected for given conditions. Here, we derive analytical expressions for the main quantifiers of transcriptional noise in terms of the molecular parameters and elucidate the role of DNA looping. Our results rationalize paradoxical experimental observations and provide the first quantitative explanation of landmark individual-cell measurements at the single molecule level on the classical lac operon genetic system [Choi, L. Cai, K. Frieda, and X. S. Xie, Science 322, 442 (2008), 10.1126/science.1161427].

  8. DNA looping and unlooping by AraC protein. (United States)

    Lobell, R B; Schleif, R F


    Expression of the L-arabinose BAD operon in Escherichia coli is regulated by AraC protein which acts both positively in the presence of arabinose to induce transcription and negatively in the absence of arabinose to repress transcription. The repression of the araBAD promoter is mediated by DNA looping between AraC protein bound at two sites near the promoter separated by 210 base pairs, araI and araO2. In vivo and in vitro experiments presented here show that an AraC dimer, with binding to half of araI and to araO2, maintains the repressed state of the operon. The addition of arabinose, which induces the operon, breaks the loop, and shifts the interactions from the distal araO2 site to the previously unoccupied half of the araI site. The conversion between the two states does not require additional binding of AraC protein and appears to be driven largely by properties of the protein rather than being specified by the slightly different DNA sequences of the binding sites. Slight reorientation of the subunits of AraC could specify looping or unlooping by the protein. Such a mechanism could account for regulation of DNA looping in other systems.

  9. Asymmetric structure of five and six membered DNA hairpin loops (United States)

    Baumann, U.; Chang, S.


    The tertiary structure of nucleic acid hairpins was elucidated by means of the accessibility of the single-strand-specific nuclease from mung bean. This molecular probe has proven especially useful in determining details of the structural arrangement of the nucleotides within a loop. In this study 3'-labeling is introduced to complement previously used 5'-labeling in order to assess and to exclude possible artifacts of the method. Both labeling procedures result in mutually consistent cleavage patterns. Therefore, methodological artifacts can be excluded and the potential of the nuclease as structural probe is increased. DNA hairpins with five and six membered loops reveal an asymmetric loop structure with a sharp bend of the phosphate-ribose backbone between the second and third nucleotide on the 3'-side of a loop. These hairpin structures differ from smaller loops with 3 or 4 members, which reveal this type of bend between the first and second 3' nucleotide, and resemble with respect to the asymmetry anticodon loops of tRNA.

  10. DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics (United States)

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


    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

  11. Effect of DNA hairpin loops on the twist of planar DNA origami tiles. (United States)

    Li, Zhe; Wang, Lei; Yan, Hao; Liu, Yan


    The development of scaffolded DNA origami, a technique in which a long single-stranded viral genome is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides, represents an important milestone in DNA nanotechnology. Recent findings have revealed that two-dimensional (2D) DNA origami structures based on the original design parameters adopt a global twist with respect to the tile plane, which may be because the conformation of the constituent DNA (10.67 bp/turn) deviates from the natural B-type helical twist (10.4 bp/turn). Here we aim to characterize the effects of DNA hairpin loops on the overall curvature of the tile and explore their ability to control, and ultimately eliminate any unwanted curvature. A series of dumbbell-shaped DNA loops were selectively displayed on the surface of DNA origami tiles with the expectation that repulsive interactions among the neighboring dumbbell loops and between the loops and the DNA origami tile would influence the structural features of the underlying tiles. A systematic, atomic force microscopy (AFM) study of how the number and position of the DNA loops influenced the global twist of the structure was performed, and several structural models to explain the results were proposed. The observations unambiguously revealed that the first generation of rectangular shaped origami tiles adopt a conformation in which the upper right (corner 2) and bottom left (corner 4) corners bend upward out of the plane, causing linear superstructures attached by these corners to form twisted ribbons. Our experimental observations are consistent with the twist model predicted by the DNA mechanical property simulation software CanDo. Through the systematic design and organization of various numbers of dumbbell loops on both surfaces of the tile, a nearly planar rectangular origami tile was achieved. © 2011 American Chemical Society

  12. 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.

  13. Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression. (United States)

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


    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.

  14. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. (United States)

    Jiang, Fuguo; Taylor, David W; Chen, Janice S; Kornfeld, Jack E; Zhou, Kaihong; Thompson, Aubri J; Nogales, Eva; Doudna, Jennifer A


    Bacterial adaptive immunity and genome engineering involving the CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) protein Cas9 begin with RNA-guided DNA unwinding to form an RNA-DNA hybrid and a displaced DNA strand inside the protein. The role of this R-loop structure in positioning each DNA strand for cleavage by the two Cas9 nuclease domains is unknown. We determine molecular structures of the catalytically active Streptococcus pyogenes Cas9 R-loop that show the displaced DNA strand located near the RuvC nuclease domain active site. These protein-DNA interactions, in turn, position the HNH nuclease domain adjacent to the target DNA strand cleavage site in a conformation essential for concerted DNA cutting. Cas9 bends the DNA helix by 30°, providing the structural distortion needed for R-loop formation. Copyright © 2016, American Association for the Advancement of Science.

  15. DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations (United States)

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


    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

  16. Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping (United States)

    Lia, Giuseppe; Bensimon, David; Croquette, Vincent; Allemand, Jean-Francois; Dunlap, David; Lewis, Dale E. A.; Adhya, Sankar; Finzi, Laura


    The overall topology of DNA profoundly influences the regulation of transcription and is determined by DNA flexibility as well as the binding of proteins that induce DNA torsion, distortion, and/or looping. Gal repressor (GalR) is thought to repress transcription from the two promoters of the gal operon of Escherichia coli by forming a DNA loop of 40 nm of DNA that encompasses the promoters. Associated evidence of a topological regulatory mechanism of the transcription repression is the requirement for a supercoiled DNA template and the histone-like heat unstable nucleoid protein (HU). By using single-molecule manipulations to generate and finely tune tension in DNA molecules, we directly detected GalR/HU-mediated DNA looping and characterized its kinetics, thermodynamics, and supercoiling dependence. The factors required for gal DNA looping in single-molecule experiments (HU, GalR and DNA supercoiling) correspond exactly to those necessary for gal repression observed both in vitro and in vivo. Our single-molecule experiments revealed that negatively supercoiled DNA, under slight tension, denatured to facilitate GalR/HU-mediated DNA loop formation. Such topological intermediates may operate similarly in other multiprotein complexes of transcription, replication, and recombination.


    Directory of Open Access Journals (Sweden)

    Estu Nugroho


    Full Text Available Variasi genetik ikan kancra yang dikoleksi dari daerah Kuningan (Pesawahan, Gandasoli, dan Ragawacana dan Sumedang di Jawa Barat telah diteliti dengan menggunakan polimorfisme Mitokondria DNA D-loop dan Random Amplified Polymorphism DNA (RAPD. Berdasarkan analisis Mt DNA tidak terdapat perbedaan yang nyata antara ras ikan kancra dari empat lokasi tersebut. Sedangkan analisis RAPD menunjukkan perbedaan yang nyata. Panjang daerah Mt DNA D-loop ikan kancra berkisar antara 700--800 bp. Satu komposit haplotype terdeteksi dengan menggunakan 4 enzim restriksi yaitu Rsa I, Nde II, Taq I, dan Sac I pada sekuens D-loop. Dua dari 20 primer RAPD menunjukkan perbedaan yang nyata di antara keempat populasi ikan kancra. Jarak genetik berdasarkan polimorfisme dua primer tersebut adalah 0,349. The aim of this research was to evaluate genetic variability of Tor soro. The genetic variability of Tor soro collected from Kuningan (Pesawahan, Gandasoli, and Ragawacana and Sumedang, West Java were examined using polymorphism of the mitochondria DNA (MtDNA D-loop and RAPD markers. Based on MtDNA D-loop analysis, there was no significant different among collection. The length size of MtDNA D-loop region was approximately 700--800 bp. A composite haplotype was detected using four endonuclease i.e. Rsa I, Nde II, Taq I, and Sac I. Two of 20 RAPD primers showed significantly different among collections. Average genetic distance based on the polymorphism of two primers was 0.349.

  18. Thermodynamic DNA Looping by a Two-Site Restriction Endonuclease Studied using Optical Tweezers (United States)

    Gemmen, Gregory J.


    Many enzyme-DNA interactions involve multimeric protein complexes that bind at two distant sites such that the DNA is looped. An example is the type IIe restriction enzyme Sau3AI, which requires two recognition sites to cleave the DNA. Here we study this process at the single DNA level using force measuring optical tweezers. We characterize cleavage rates of single DNA molecules in the presence of Sau3AI as a function of enzyme concentration, incubation time, and the fractional extension of the DNA molecule. Activity is completely inhibited by tensions of a few picoNewtons. By replacing Mg^2+ with Ca^2+, the Sau3AI dimers form but do not cleave the DNA, thus trapping DNA loops. We are able to pull apart these loops, measuring the force needed and the length of DNA released for each. We also characterize the number and length distributions of these loops as a function of incubation time and DNA fractional extension. The results of these studies are discussed in the context of a Brownian dynamics model of DNA looping.

  19. Mapping sequences in loops of nuclear DNA by their progressive detachment from the nuclear cage.


    Cook, P R; Brazell, I A


    Nuclear DNA is organised into loops, probably by attachment to a supramolecular structure. We describe a method which enables us to map the position of sequences within a loop relative to the point of attachment. Nuclear DNA is isolated unbroken by lysing HeLa cells in 2M NaCl to release structures which retain many of the morphological features of nuclei. Their DNA is supercoiled and so must remain unbroken and looped during lysis. Nucleoids are digested to various degrees with a restriction...

  20. Roles of the human Rad51 L1 and L2 loops in DNA binding. (United States)

    Matsuo, Yusuke; Sakane, Isao; Takizawa, Yoshimasa; Takahashi, Masayuki; Kurumizaka, Hitoshi


    The human Rad51 protein, a eukaryotic ortholog of the bacterial RecA protein, is a key enzyme that functions in homologous recombination and recombinational repair of double strand breaks. The Rad51 protein contains two flexible loops, L1 and L2, which are proposed to be sites for DNA binding, based on a structural comparison with RecA. In the present study, we performed mutational and fluorescent spectroscopic analyses on the L1 and L2 loops to examine their role in DNA binding. Gel retardation and DNA-dependent ATP hydrolysis measurements revealed that the substitution of the tyrosine residue at position 232 (Tyr232) within the L1 loop with alanine, a short side chain amino acid, significantly decreased the DNA-binding ability of human Rad51, without affecting the protein folding or the salt-induced, DNA-independent ATP hydrolysis. Even the conservative replacement with tryptophan affected the DNA binding, indicating that Tyr232 is involved in DNA binding. The importance of the L1 loop was confirmed by the fluorescence change of a tryptophan residue, replacing the Asp231, Ser233, or Gly236 residue, upon DNA binding. The alanine replacement of phenylalanine at position 279 (Phe279) within the L2 loop did not affect the DNA-binding ability of human Rad51, unlike the Phe203 mutation of the RecA L2 loop. The Phe279 side chain may not be directly involved in the interaction with DNA. However, the fluorescence intensity of the tryptophan replacing the Rad51-Phe279 residue was strongly reduced upon DNA binding, indicating that the L2 loop is also close to the DNA-binding site.

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

    African Journals Online (AJOL)



    Apr 8, 2015 ... 16075, 16104 and 16201 in future may be suitable sources for identification purpose. Key words: D-loop, frequency, north-central Iraq, mitochondrial DNA, polymorphism. INTRODUCTION. Mitochondrial DNA (mtDNA) is a useful genetic marker for answering evolutionary questions due to its high copy.

  2. diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data. (United States)

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


    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 Supplementary data are available at Bioinformatics online.

  3. Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses. (United States)

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


    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.

  4. Real-time observation of DNA looping dynamics of type IIE restriction enzymes NaeI and NarI

    NARCIS (Netherlands)

    van den Broek, B.; Vanzi, F.; Normanno, D.; Pavone, F. S.; Wuite, G.J.L.


    Many restriction enzymes require binding of two copies of a recognition sequence for DNA cleavage, thereby introducing a loop in the DNA. We investigated looping dynamics of Type IIE restriction enzymes NaeI and NarI by tracking the Brownian motion of single tethered DNA molecules. DNA containing

  5. Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs (United States)

    Strom, Shane; Shiskova, Evgenia; Hahm, Yaeeun


    Bulge loops are common features of RNA structures that are involved in the formation of RNA tertiary structures and are often sites for interactions with proteins and ions. Minimal thermodynamic data currently exist on the bulge size and sequence effects. Using thermal denaturation methods, thermodynamic properties of 1- to 5-nt adenine and guanine bulge loop constructs were examined in 10 mM MgCl2 or 1 M KCl. The ΔG37∘ loop parameters for 1- to 5-nt purine bulge loops in RNA constructs were between 3.07 and 5.31 kcal/mol in 1 M KCl buffer. In 10 mM magnesium ions, the ΔΔG° values relative to 1 M KCl were 0.47–2.06 kcal/mol more favorable for the RNA bulge loops. The ΔG37∘ loop parameters for 1- to 5-nt purine bulge loops in DNA constructs were between 4.54 and 5.89 kcal/mol. Only 4- and 5-nt guanine constructs showed significant change in stability for the DNA constructs in magnesium ions. A linear correlation is seen between the size of the bulge loop and its stability. New prediction models are proposed for 1- to 5-nt purine bulge loops in RNA and DNA in 1 M KCl. We show that a significant stabilization is seen for small bulge loops in RNA in the presence of magnesium ions. A prediction model is also proposed for 1- to 5-nt purine bulge loop RNA constructs in 10 mM magnesium chloride. PMID:26022248

  6. Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs. (United States)

    Strom, Shane; Shiskova, Evgenia; Hahm, Yaeeun; Grover, Neena


    Bulge loops are common features of RNA structures that are involved in the formation of RNA tertiary structures and are often sites for interactions with proteins and ions. Minimal thermodynamic data currently exist on the bulge size and sequence effects. Using thermal denaturation methods, thermodynamic properties of 1- to 5-nt adenine and guanine bulge loop constructs were examined in 10 mM MgCl(2) or 1 M KCl. The [Formula: see text] loop parameters for 1- to 5-nt purine bulge loops in RNA constructs were between 3.07 and 5.31 kcal/mol in 1 M KCl buffer. In 10 mM magnesium ions, the ΔΔG° values relative to 1 M KCl were 0.47-2.06 kcal/mol more favorable for the RNA bulge loops. The [Formula: see text] loop parameters for 1- to 5-nt purine bulge loops in DNA constructs were between 4.54 and 5.89 kcal/mol. Only 4- and 5-nt guanine constructs showed significant change in stability for the DNA constructs in magnesium ions. A linear correlation is seen between the size of the bulge loop and its stability. New prediction models are proposed for 1- to 5-nt purine bulge loops in RNA and DNA in 1 M KCl. We show that a significant stabilization is seen for small bulge loops in RNA in the presence of magnesium ions. A prediction model is also proposed for 1- to 5-nt purine bulge loop RNA constructs in 10 mM magnesium chloride. © 2015 Strom et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

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

    DEFF Research Database (Denmark)

    Stella, Stefano; Alcón, Pablo; Montoya, Guillermo


    Cpf1 is an RNA-guided endonuclease that is emerging as a powerful genome-editing tool. Here we provide insight into its DNA-targeting mechanism by determining the structure of Francisella novicida Cpf1 with the triple-stranded R-loop generated after DNA cleavage. The structure reveals the machine...... 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....

  8. Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage. (United States)

    Stella, Stefano; Alcón, Pablo; Montoya, Guillermo


    Cpf1 is an RNA-guided endonuclease that is emerging as a powerful genome-editing tool. Here we provide insight into its DNA-targeting mechanism by determining the structure of Francisella novicida Cpf1 with the triple-stranded R-loop generated after DNA cleavage. The structure reveals the machinery 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 into the double-stranded DNA. Unzipping of the double-stranded DNA occurs in a cleft arranged by acidic and hydrophobic residues facilitating the crRNA-DNA hybrid formation. The PAM single-stranded DNA is funnelled towards the nuclease site through a mixed hydrophobic and basic cavity. In this catalytic conformation, the PAM-interacting domain and the helix-loop-helix motif in the REC1 domain adopt a 'rail' shape and 'flap-on' conformations, respectively, channelling the PAM strand into the cavity. A steric barrier between the RuvC-II and REC1 domains forms the 'septum', separating the displaced PAM strand 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.

  9. Senataxin Mutation Reveals How R-Loops Promote Transcription by Blocking DNA Methylation at Gene Promoters. (United States)

    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


    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.

  10. 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


    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...... maintenance. The DNA-PK complex also functions in both DNA double strand break repair and telomere maintenance. Interaction between WRN and the DNA-PK complex has been reported in DNA double strand break repair, but their possible cooperation at telomeres has not been reported. This study analyzes thein vitro...... 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....

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

    Directory of Open Access Journals (Sweden)

    М. I. Chopei


    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.

  12. Simultaneous elimination of carryover contamination and detection of DNA with uracil-DNA-glycosylase-supplemented loop-mediated isothermal amplification (UDG-LAMP). (United States)

    Hsieh, Kuangwen; Mage, Peter L; Csordas, Andrew T; Eisenstein, Michael; Soh, H Tom


    We report a one-pot, closed-vessel enzymatic assay that eliminates carryover contamination while preserving robust DNA amplification in loop-mediated isothermal amplification (LAMP), providing reliable and rapid detection of target DNA in contaminated samples.

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

    NARCIS (Netherlands)

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


    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

  14. Tightly bound DNA-protein complexes representing stable attachment sites of large DNA loops to components of the matrix. (United States)

    Patriotis, C; Djondjurov, L


    This study describes tightly bound DNA-protein complexes in DNA of matrices isolated from Friend erythroleukemia cells. When after radio-iodination of the associated proteins, such DNA is electrophoresed on agarose and the gel is subsequently subjected to autoradiography, the protein components of three or four complexes are visualized. Their two-dimensional electrophoretic analysis revealed that each possesses a simple but specific polypeptide composition, including a set of five non-histone proteins, characteristic for the matrix, and the core histones H3 and H4. Since the polypeptides dissociate from DNA by treatment with SDS, it is suggested that the linkage is not covalent. Reassociation and hybridization analysis of the DNA of the complexes indicated that it is enriched in highly repetitive, satellite sequences. The latter were found to be, to a great extent, similar to sequences localized at the base of large, dehistonized DNA loops obtained by high-salt extraction of isolated nuclei. Further experiments emphasized the complete conservation of this type of attachment throughout erythroid differentiation of Friend cells. It is proposed that the complexes represent attachment sites of basic, 30-100-kbp loop units of DNA.

  15. DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation (United States)

    Boedicker, James Q.; Garcia, Hernan G.; Johnson, Stephanie; Phillips, Rob


    As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as through nucleosome positioning. Here we examine the sequence-dependent flexibility of DNA in bacterial transcription factor-mediated looping, a context for which the role of sequence remains poorly understood. Using a suite of synthetic constructs repressed by the Lac repressor and two well-known sequences that show large flexibility differences in vitro, we make precise statistical mechanical predictions as to how DNA sequence influences loop formation and test these predictions using in vivo transcription and in vitro single-molecule assays. Surprisingly, sequence-dependent flexibility does not affect in vivo gene regulation. By theoretically and experimentally quantifying the relative contributions of sequence and the DNA-bending protein HU to DNA mechanical properties, we reveal that bending by HU dominates DNA mechanics and masks intrinsic sequence-dependent flexibility. Such a quantitative understanding of how mechanical regulatory information is encoded in the genome will be a key step towards a predictive understanding of gene regulation at single-base pair resolution. PMID:24231252


    Directory of Open Access Journals (Sweden)

    M. F. Harlistyo


    Full Text Available This study was aimed to find out the diversity of mtDNA D-loop at Kejobong goat. The completemtDNA D-loop sequence of 12 goat blood samples were analyzed from 4 different location inPurbalingga Regency, Central Java province, sub-districts Kejobong, Pangadegan, Bukateja, andKaligondang. The mtDNA D-loop was extracted from blood sample. DNA obtained were amplified byPCR (Polymerase Chain Reaction method using primers (5’-tcactatcagcacccaaagc-3’ as forward and(5’-ggcattttcagtgccttgct-3’ as reverse and subsequently sequenced. After nucleotide sequencing analysisconducted, 548 bp along was obtained. Nucleotides were then aligned with Capra hircus (GenBankAccess No.: KF952601.1 and apparently there were 11 different sites on the segment of mtDNA Dloop.Five sites could be used as a specific marker to distinguish between the Capra hircus andKejobong goat, namely at the site of 317 (A-G, 403 (T-C, 434 (T-C, 537 (C-T, and 553 (A-G.Nucleotide sequence analysis also contained seven different haplotypes. It was concluded that thedistribution of the different sites showed different haplotype patterns in Kejobong goat.

  17. Loop-mediated isothermal amplification (LAMP) shield for Arduino DNA detection. (United States)

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


    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.

  18. 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.

  19. Genetic characterization of the Aceh cattle using phenotypic, mitochondrial DNA of D-loop region and microsatellite DNA analyses. (United States)

    Abdullah, M A N; Martojo, H; Noor, R R; Solihin, D D


    The present study reports the phenotypic variation of body weight and body size, the genetic variation of D-loop of mtDNA and microsatellite DNA allele in Aceh cattle in Indonesia within the frame of the design of a conservation programme for this indigenous species. Aceh cattle differ from Bali, Madura, Java-Ongole and Pesisir cattle, but its ancestry relates it closest to Pesisir, thus adding more information to its entry from the Indian sub-continent. © 2012 Blackwell Verlag GmbH.

  20. 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.


    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

  1. Detection of capripoxvirus DNA using a novel loop-mediated isothermal amplification assay. (United States)

    Murray, Lee; Edwards, Lorraine; Tuppurainen, Eeva S M; Bachanek-Bankowska, Katarzyna; Oura, Chris A L; Mioulet, Valerie; King, Donald P


    Sheep poxvirus (SPPV), Goat poxvirus (GTPV) and Lumpy skin disease virus (LSDV) are the most serious poxviruses of ruminants. They are double stranded DNA viruses of the genus Capripoxvirus, (subfamily Chordopoxvirinae) within the family Poxviridae. The aim of this study was to develop a Loop-mediated isothermal AMPlification (LAMP) assay for the detection of Capripoxvirus (CaPV) DNA. A single LAMP assay targeting a conserved region of the CaPV P32 gene was selected from 3 pilot LAMP assays and optimised by adding loop primers to accelerate the reaction time. This LAMP assay successfully detected DNA prepared from representative CaPV isolates (SPPV, GTPV and LSDV), and did not cross-react with DNA extracted from other mammalian poxviruses. The analytical sensitivity of the LAMP assay was determined to be at least 163 DNA copies/μl which is equivalent to the performance reported for diagnostic real-time PCR currently used for the detection of CaPV. LAMP reactions were monitored with an intercalating dye using a real-time PCR machine, or by agarose-gel electrophoresis. Furthermore, dual labelled LAMP products (generated using internal LAMP primers that were conjugated with either biotin or fluorescein) could be readily visualised using a lateral-flow device. This study provides a simple and rapid approach to detect CaPV DNA that may have utility for use in the field, or in non-specialised laboratories where expensive equipment is not available.

  2. Stem-loop structures of the repetitive DNA sequences located at human centromeres

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    Gupta, G.; Garcia, A.E.; Ratliff, R.; Moyzis, R.K. [Los Alamos National Lab., NM (United States); Catasti, P.; Hong, Lin; Yau, P. [California Univ., Davis, CA (United States). Dept. of Biological Chemistry; Bradbury, E.M. [Los Alamos National Lab., NM (United States)]|[California Univ., Davis, CA (United States). Dept. of Biological Chemistry


    The presence of the highly conserved repetitive DNA sequences in the human centromeres argues for a special role of these sequences in their biological functions - most likely achieved by the formation of unusual structures. This prompted us to carry out quantitative one- and two-dimensional nuclear magnetic resonance (lD/2D NMR) spectroscopy to determine the structural properties of the human centromeric repeats, d(AATGG){sub n.d}(CCATT){sub n}. The studies on centromeric DNAs reveal that the complementary sequence, d(AATGG){sub n.d}(CCATT){sub n}, adopts the usual Watson-Crick B-DNA duplex and the pyrimidine-rich d(CCATT){sub n} strand is essentially a random coil. However, the purine-rich d(AATGG){sub n} strand is shown to adopt unusual stem-loop structures for repeat lengths, n=2,3,4, and 6. In addition to normal Watson-Crick A{center_dot}T pairs, the stem-loop structures are stabilized by mismatch A{center_dot}G and G{center_dot}G pairs in the stem and G-G-A stacking in the loop. Stem-loop structures of d(AATGG)n are independently verified by gel electrophoresis and nuclease digestion studies. Thermal melting studies show that the DNA repeats, d(AATGG){sub n}, are as stable as the corresponding Watson-Crick duplex d(AATGG){sub n.d}(CCATT){sub n}. Therefore, the sequence d(AATGG){sub n} can, indeed, nucleate a stem-loop structure at little free-energy cost and if, during mitosis, they are located on the chromosome surface they can provide specific recognition sites for kinetochore function.

  3. Mechanism of retinoic acid-induced transcription: histone code, DNA oxidation and formation of chromatin loops. (United States)

    Zuchegna, Candida; Aceto, Fabiana; Bertoni, Alessandra; Romano, Antonella; Perillo, Bruno; Laccetti, Paolo; Gottesman, Max E; Avvedimento, Enrico V; Porcellini, Antonio


    Histone methylation changes and formation of chromatin loops involving enhancers, promoters and 3' end regions of genes have been variously associated with active transcription in eukaryotes. We have studied the effect of activation of the retinoic A receptor, at the RARE-promoter chromatin of CASP9 and CYP26A1 genes, 15 and 45 min following RA exposure, and we found that histone H3 lysines 4 and 9 are demethylated by the lysine-specific demethylase, LSD1 and by the JMJ-domain containing demethylase, D2A. The action of the oxidase (LSD1) and a dioxygenase (JMJD2A) in the presence of Fe++ elicits an oxidation wave that locally modifies the DNA and recruits the enzymes involved in base and nucleotide excision repair (BER and NER). These events are essential for the formation of chromatin loop(s) that juxtapose the RARE element with the 5' transcription start site and the 3' end of the genes. The RARE bound-receptor governs the 5' and 3' end selection and directs the productive transcription cycle of RNA polymerase. These data mechanistically link chromatin loops, histone methylation changes and localized DNA repair with transcription. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Genetic diversity of Lombok chickens based on D-loop mitochondrial DNA sequences

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    M. Syamsul Arifin Zein


    Full Text Available Mitochondrial DNA (mtDNA displacement (D-loop sequences were used to study the genetic diversity and relationship of Lombok chickens. A total of 45 individuals were sampled. The D-loop segment was PCR amplified and subsequently sequenced. The sequences of the 785 nucleotides were used for analysis. Twelve haplotypes were identified from 25 polymorphic sites with polymorphism between nucleotides 200 and 400 contributing to 80% of the variation. Fu’s Fs value was - 8.768 (all samples, P = 0, indicating high genetic diversity and population expansion, a conclusion supported by a neighbor– joining analysis of the haplotypes. Nucleotides diversity of the Lombok chicken were 0.00221 and haplotype diversity were 0.654 + 0.08. The dominant haplotype found among the Lombok chickens was haplotype B (62% and genetic distances value ranged from 0.001 to 0.017.

  5. DNA replication catalyzed by herpes simplex virus type 1 proteins reveals trombone loops at the fork. (United States)

    Bermek, Oya; Willcox, Smaranda; Griffith, Jack D


    Using purified replication factors encoded by herpes simplex virus type 1 and a 70-base minicircle template, we obtained robust DNA synthesis with leading strand products of >20,000 nucleotides and lagging strand fragments from 600 to 9,000 nucleotides as seen by alkaline gel electrophoresis. ICP8 was crucial for the synthesis on both strands. Visualization of the deproteinized products using electron microscopy revealed long, linear dsDNAs, and in 87%, one end, presumably the end with the 70-base circle, was single-stranded. The remaining 13% had multiple single-stranded segments separated by dsDNA segments 500 to 1,000 nucleotides in length located at one end. These features are diagnostic of the trombone mechanism of replication. Indeed, when the products were examined with the replication proteins bound, a dsDNA loop was frequently associated with the replication complex located at one end of the replicated DNA. Furthermore, the frequency of loops correlated with the fraction of DNA undergoing Okazaki fragment synthesis. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Genetic diversity of native chicken based on analysis of D-Loop mtDNA marker

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    Tike Sartika


    Full Text Available Production was carried out using control region/D-loop mtDNA marker. The base population of native chicken was selected from subpopulation at Cianjur, Jatiwangi, Depok, Bogor I, and Bogor 2. Samples from each population was 10 heads and 2 samples Green Jungle Fowl (Gallus various from East Java as out Group samples. Two primers binding conserved tRNA Phenylalanine gene and tRNA Glutamine gene were DNA Heavy stranded HI255 (5'-CATCTTGGCATCTTCAGTGCC-3' and DNA Light stranded Ll6750 (5'-AGGACTACGGCTTGAAAAGC-3' was used to amplify D-Ioop mtDNA chicken. PCR-RFLP methods with 6 restriction enzymes 4 cutter such as, Alul (AG↓CT, Hpall (C↓CGG, Mbol (↓GATC, Rsal (GT↓AC, NlaIII (CATG↓ and HaeIII (GG↓CC were used to detect polymorphism within and between subpopulation. Result of experiment show that mtDNA which was amplified by PCR was 1320 bp, consist of 1227 bp control region/D-loop, 45 bp tRNA Glutamine gene and 48 bp tRNA Phenylalananine gene. PCR product which were digested from 6 endonucleases enzyme show that native chicken within and between population was monomorphic and if its compare with Green Jungle Fowl was polymorphic.

  7. R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli. (United States)

    Wimberly, Hallie; Shee, Chandan; Thornton, P C; Sivaramakrishnan, Priya; Rosenberg, Susan M; Hastings, P J


    Double-stranded DNA ends, often from replication, drive genomic instability, yet their origin in non-replicating cells is unknown. Here we show that transcriptional RNA/DNA hybrids (R-loops) generate DNA ends that underlie stress-induced mutation and amplification. Depleting RNA/DNA hybrids with overproduced RNase HI reduces both genomic changes, indicating RNA/DNA hybrids as intermediates in both. An Mfd requirement and inhibition by translation implicate transcriptional R-loops. R-loops promote instability by generating DNA ends, shown by their dispensability when ends are provided by I-SceI endonuclease. Both R-loops and single-stranded endonuclease TraI are required for end formation, visualized as foci of a fluorescent end-binding protein. The data suggest that R-loops prime replication forks that collapse at single-stranded nicks, producing ends that instigate genomic instability. The results illuminate how DNA ends form in non-replicating cells, identify R-loops as the earliest known mutation/amplification intermediate, and suggest that genomic instability during stress could be targeted to transcribed regions, accelerating adaptation.

  8. Sequence motifs capable of forming DNA stem-loop structures act as a replication diode. (United States)

    Shirak, Andrey; Seroussi, Uri; Gootwine, Elisha; Seroussi, Eyal


    Calculating peak-height ratios between single-nucleotide polymorphisms (SNP) alleles in sequencing chromatograms is a practical method for estimating their copy number proportions (CNPs). However, it is surprising that sequencing DNA from different directions might yield different results. We analyzed three adjacent SNPs within the ovine period circadian-clock 2 (PER2) gene that displayed such behavior. We compared Sanger and DNA-seq sequencing for this locus and applied high-resolution melt and MFOLD analyses to point to the DNA secondary structure that underlined this phenomenon. A synthetic system of oligonucleotides cloned into plasmids was used to further test the effect of such structures on sequencing. Our analyses indicated that a stem-loop structure capable of G-T pairing mediated the orientation bias by stabilizing this structure for specific alleles in heterozygous situations. We propose that this wobble-like pairing hinders DNA polymerase passage on one strand while, on the complementary strand, the nonpaired A-C nucleotide counterparts allow unobstructed replication. Experimentation with synthetic amplicons that form similar stem-loop structures supported our hypothesis. We coined the term 'replication diode' for this effect and demonstrated that we can minimize it by lowering DNA and salt concentration. We also demonstrated that common genomic palindromes might induce the replication diode effect by applying bidirectional sequencing to an amplicon containing the palindrome within the human miRNA 1-1 gene. Hence, to obtain reliable peak-height ratios, bidirectional sequencing should be practiced at the lowest possible ionic strength whenever estimating CNPs. Further research is needed to determine whether the observed variable stem-loop structures affect PER2 regulation in vivo.

  9. Quantitative model of R-loop forming structures reveals a novel level of RNA–DNA interactome complexity (United States)

    Wongsurawat, Thidathip; Jenjaroenpun, Piroon; Kwoh, Chee Keong; Kuznetsov, Vladimir


    R-loop is the structure co-transcriptionally formed between nascent RNA transcript and DNA template, leaving the non-transcribed DNA strand unpaired. This structure can be involved in the hyper-mutation and dsDNA breaks in mammalian immunoglobulin (Ig) genes, oncogenes and neurodegenerative disease related genes. R-loops have not been studied at the genome scale yet. To identify the R-loops, we developed a computational algorithm and mapped R-loop forming sequences (RLFS) onto 66 803 sequences defined by UCSC as ‘known’ genes. We found that ∼59% of these transcribed sequences contain at least one RLFS. We created R-loopDB (, the database that collects all RLFS identified within over half of the human genes and links to the UCSC Genome Browser for information integration and visualisation across a variety of bioinformatics sources. We found that many oncogenes and tumour suppressors (e.g. Tp53, BRCA1, BRCA2, Kras and Ptprd) and neurodegenerative diseases related genes (e.g. ATM, Park2, Ptprd and GLDC) could be prone to significant R-loop formation. Our findings suggest that R-loops provide a novel level of RNA–DNA interactome complexity, playing key roles in gene expression controls, mutagenesis, recombination process, chromosomal rearrangement, alternative splicing, DNA-editing and epigenetic modifications. RLFSs could be used as a novel source of prospective therapeutic targets. PMID:22121227

  10. Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity. (United States)

    Wongsurawat, Thidathip; Jenjaroenpun, Piroon; Kwoh, Chee Keong; Kuznetsov, Vladimir


    R-loop is the structure co-transcriptionally formed between nascent RNA transcript and DNA template, leaving the non-transcribed DNA strand unpaired. This structure can be involved in the hyper-mutation and dsDNA breaks in mammalian immunoglobulin (Ig) genes, oncogenes and neurodegenerative disease related genes. R-loops have not been studied at the genome scale yet. To identify the R-loops, we developed a computational algorithm and mapped R-loop forming sequences (RLFS) onto 66,803 sequences defined by UCSC as 'known' genes. We found that ∼59% of these transcribed sequences contain at least one RLFS. We created R-loopDB (, the database that collects all RLFS identified within over half of the human genes and links to the UCSC Genome Browser for information integration and visualisation across a variety of bioinformatics sources. We found that many oncogenes and tumour suppressors (e.g. Tp53, BRCA1, BRCA2, Kras and Ptprd) and neurodegenerative diseases related genes (e.g. ATM, Park2, Ptprd and GLDC) could be prone to significant R-loop formation. Our findings suggest that R-loops provide a novel level of RNA-DNA interactome complexity, playing key roles in gene expression controls, mutagenesis, recombination process, chromosomal rearrangement, alternative splicing, DNA-editing and epigenetic modifications. RLFSs could be used as a novel source of prospective therapeutic targets.

  11. Genetic Characteristic of Indonesian Local Ducks Based on Single Nucleotide Polymorphism (SNP) Analysis in D-loop Region Mitochondria DNA


    Purwantini, Dattadewi; Ismoyowati, Ismoyowati


    . Penelitian ini bertujuan untuk mengetahui karakteristik genetik dan polimorfisme itik lokal Indonesia yaitu itik Magelang, Tegal, Mojosari, Bali dan Alabio berdasarkan analisis Single Nucleotide Polymorphism (SNP) daerah D-loop mtDNA. Tujuan jangka panjangnya adalah menetapkan marker atau penanda genetik berdasarkan SNP daerah D-loop mtDNA spesifik yang dapat membedakan itik-itik lokal yang ada di Indonesia. Selanjutnya digunakan sebagai alat bantu seleksi untuk konservasi, pembibitan da...

  12. Human ribonuclease H1 resolves R-loops and thereby enables progression of the DNA replication fork. (United States)

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


    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.

  13. Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping. (United States)

    Zhang, Yongli; McEwen, Abbye E; Crothers, Donald M; Levene, Stephen D


    Interactions of E. coli lac repressor (LacR) with a pair of operator sites on the same DNA molecule can lead to the formation of looped nucleoprotein complexes both in vitro and in vivo. As a major paradigm for loop-mediated gene regulation, parameters such as operator affinity and spacing, repressor concentration, and DNA bending induced by specific or non-specific DNA-binding proteins (e.g., HU), have been examined extensively. However, a complete and rigorous model that integrates all of these aspects in a systematic and quantitative treatment of experimental data has not been available. Applying our recent statistical-mechanical theory for DNA looping, we calculated repression as a function of operator spacing (58-156 bp) from first principles and obtained excellent agreement with independent sets of in-vivo data. The results suggest that a linear extended, as opposed to a closed v-shaped, LacR conformation is the dominant form of the tetramer in vivo. Moreover, loop-mediated repression in wild-type E. coli strains is facilitated by decreased DNA rigidity and high levels of flexibility in the LacR tetramer. In contrast, repression data for strains lacking HU gave a near-normal value of the DNA persistence length. These findings underscore the importance of both protein conformation and elasticity in the formation of small DNA loops widely observed in vivo, and demonstrate the utility of quantitatively analyzing gene regulation based on the mechanics of nucleoprotein complexes.

  14. Comparison between Mt-DNA D-Loop and Cyt B primers for porcine DNA detection in meat products (United States)

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


    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.

  15. Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D-loop Sequences

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    Full Text Available The Mitochondrial DNA (mtDNA displacement (D-loop sequences were used to study the genetic diversity and relationship of Indonesian indigenous chickens. A total of 483 individuals belonging to 15 population breeds and 43 individuals belonging to 6 populations of jungle fowl (2 populations of Gallus gallus and 4 populations of Gallus varius were sampled. The hypervariable I (HVI segment of the D-loop was PCR amplified and subsequently sequenced. The sequences of the first 397 nucleotides were used for analysis. Sixty nine haplotypes were identified from 54 polymorphic sites with polymorphism between nucleotides 167 and 397 contributing to 94.5% of the sequence variation. Phylogenetic analysis indicates that Indonesian indigenous chickens can be grouped into five distinct clades (clade I, II, IIIc, IIId, and IV of the previously identified seven clades (clade I, II, IIIa, IIIb, IIIc, IIId, and IV in Asian indigenous chickens. Fifty haplotypes belong to clade II, seven haplotypes are in clade IV, six are in clade IIId, three are in clade I and one haploype is in clade IIIc. There was no breed-specific clade. Analysis of Molecular Variance (AMOVA based on partial D-loop sequences of Indonesian chicken indicates that 67.85% of the total sequence variation between haplotypes was present within the population and 32.15% between populations. One of the haplotypes (represented by PLC4 was shared by all populations, suggesting that these populations may share the same maternal ancestor. These results show a high mitochondrial D-loop diversity and indicate multiple maternal origins for Indonesian indigenous chickens.

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

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    Aron Batubara


    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. [Screening of the gene mutation in D-loop region of mitochondrial DNA in oral squamous cell carcinoma]. (United States)

    Sun, Yang; Yuan, Rong-tao; Chen, Wan-tao; Bu, Ling-xue; Jia, Mu-yun


    To investigate the gene mutation in D-loop region of mitochondrial DNA (mtDNA) in oral squamous cell carcinoma (OSCC) tissue and to explore the role of the gene mutation in D-loop region in the OSCC tumorigenesis. mtDNA was obtained from cancer, paracancerous and normal mucosa tissues of thirty patients with OSCC. The D-loop regions of mtDNA were amplified with PCR, sequencing and then analyzed by Chromas software and BLAST to identify the mutation site. Mutation in the D-loop region was found in eight cases, with the mutation rate of 27%. There were nine mutations totally, including one point mutation, two base deletions, three insertion mutations, three heterozygous mutations. In these mutations, base deletions were different from each other and heterozygous mutations had no same mutation form, while the three insertion mutations were same, the insertion of base C. One case had T/A heterozygous mutation and base C insertion at the same time. There were mutations in mtDNA D-loop in OSCC, but the relationship between occurrence of OSCC and mutation of mtDNA needs further study.

  18. Enhanced electrostatic force microscopy reveals higher-order DNA looping mediated by the telomeric protein TRF2. (United States)

    Kaur, Parminder; Wu, Dong; Lin, Jiangguo; Countryman, Preston; Bradford, Kira C; Erie, Dorothy A; Riehn, Robert; Opresko, Patricia L; Wang, Hong


    Shelterin protein TRF2 modulates telomere structures by promoting dsDNA compaction and T-loop formation. Advancement of our understanding of the mechanism underlying TRF2-mediated DNA compaction requires additional information regarding DNA paths in TRF2-DNA complexes. To uncover the location of DNA inside protein-DNA complexes, we recently developed the Dual-Resonance-frequency-Enhanced Electrostatic force Microscopy (DREEM) imaging technique. DREEM imaging shows that in contrast to chromatin with DNA wrapping around histones, large TRF2-DNA complexes (with volumes larger than TRF2 tetramers) compact DNA inside TRF2 with portions of folded DNA appearing at the edge of these complexes. Supporting coarse-grained molecular dynamics simulations uncover the structural requirement and sequential steps during TRF2-mediated DNA compaction and result in folded DNA structures with protruding DNA loops as seen in DREEM imaging. Revealing DNA paths in TRF2 complexes provides new mechanistic insights into structure-function relationships underlying telomere maintenance pathways.

  19. In vitro molecular machine learning algorithm via symmetric internal loops of DNA. (United States)

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


    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. [Polymorphism of hypervariable region in D-loop of mitochondrial DNA]. (United States)

    Takada, Y; Mukaida, M


    DNA sequences of PCR products from mitochondrial DNA (mtDNA) of 80 healthy Japanese volunteers (40 pairs, mother and child) were determined by the direct sequencing method for polymorphism. Thirty (15 pairs) of 80 samples analyzed showed a T-to-C transition at position 16189 (T16189C) of the C-stretch region in the hyper-variable region of mtDNA. For seven pairs randomly selected from the 15 T16189C pairs (C-stretch) and a single pair without the transition (non C-stretch), PCR products from the D-loop region were cloned and then sequenced. The repeat number of C in the C-stretch region was found to show heteroplasmy by sequencing multiples clones from each mtDNA. Statistical analyses of the distribution patterns of the repeat number revealed no significant differences between the mother and child in each lineage but significant differences between the lineages. The seven lineages could be then classified into four groups. The result of our data confirmed the existence of heteroplasmic polymorphism in the C-stretch region and the inheritance of the heteroplasmy from mother to child. Therefore, the analysis of heteroplasmy is applicable to individual identification.

  1. Regulation of mitochondrial genome replication by hypoxia: The role of DNA oxidation in D-loop region. (United States)

    Pastukh, Viktor M; Gorodnya, Olena M; Gillespie, Mark N; Ruchko, Mykhaylo V


    Mitochondria of mammalian cells contain multiple copies of mitochondrial (mt) DNA. Although mtDNA copy number can fluctuate dramatically depending on physiological and pathophysiologic conditions, the mechanisms regulating mitochondrial genome replication remain obscure. Hypoxia, like many other physiologic stimuli that promote growth, cell proliferation and mitochondrial biogenesis, uses reactive oxygen species as signaling molecules. Emerging evidence suggests that hypoxia-induced transcription of nuclear genes requires controlled DNA damage and repair in specific sequences in the promoter regions. Whether similar mechanisms are operative in mitochondria is unknown. Here we test the hypothesis that controlled oxidative DNA damage and repair in the D-loop region of the mitochondrial genome are required for mitochondrial DNA replication and transcription in hypoxia. We found that hypoxia had little impact on expression of mitochondrial proteins in pulmonary artery endothelial cells, but elevated mtDNA content. The increase in mtDNA copy number was accompanied by oxidative modifications in the D-loop region of the mitochondrial genome. To investigate the role of this sequence-specific oxidation of mitochondrial genome in mtDNA replication, we overexpressed mitochondria-targeted 8-oxoguanine glycosylase Ogg1 in rat pulmonary artery endothelial cells, enhancing the mtDNA repair capacity of transfected cells. Overexpression of Ogg1 resulted in suppression of hypoxia-induced mtDNA oxidation in the D-loop region and attenuation of hypoxia-induced mtDNA replication. Ogg1 overexpression also reduced binding of mitochondrial transcription factor A (TFAM) to both regulatory and coding regions of the mitochondrial genome without altering total abundance of TFAM in either control or hypoxic cells. These observations suggest that oxidative DNA modifications in the D-loop region during hypoxia are important for increased TFAM binding and ensuing replication of the mitochondrial

  2. Analisis D-loop DNA Mitokondria untuk Memposisikan Ayam Hutan Merah dalam Domestikasi Ayam di Indonesia

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    S. Sulandari


    Full Text Available The current poultry is a domesticated chickens used for both meat and egg production. Pedigree investigation is an important part to understand the process of chicken domestication in Indonesia. Molecular DNA approach using D-loop Mitochondrial DNA marker (hypervariable 1 segment was used in this analysis. The objective of the study was to construct the pedigree analysis of Indonesian chicken. Four hundreds and eighty four (434 samples belonging to 15 breeds of Indonesian local chicken (Cemani, Kedu, Kedu Putih, Pelung, Sentul, Wareng, Merawang, Kapas, Kate, Arab Silver, Arab Gold, Gaok, Nunukan, Kalosi and Tolaki and 9 samples of Red jungle fowls (Gallus gallus gallus were extracted, PCR amplified and subsequently sequenced. Four sequence references from GeneBank, Gallus gallus (NCBI, accession number AB0986688. G. gallus (GenBank accession number AB098668, G. gallus spadiceus (GenBank accession number AB007721, and G. gallus bankiva (GenBank accession number AB007718 were included in this analysis. The sequences of the first 397 nucleotides were used for analysis. The results show that 72 haplotypes were identified from 56 polymorphic sites. Phylogenetic analysis showed that Indonesian chicken have a close relationship with 2 subspecies of Gallus gallus (G. gallus gallus and G. gallus spadiceus. Our results suggest that D-loop region is highly variable in Indonesian chicken with large number of haplotypes.

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

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


    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

  4. A DNA sequence recognition loop on APOBEC3A controls substrate specificity.

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    Eric C Logue

    Full Text Available APOBEC3A (A3A, one of the seven-member APOBEC3 family of cytidine deaminases, lacks strong antiviral activity against lentiviruses but is a potent inhibitor of adeno-associated virus and endogenous retroelements. In this report, we characterize the biochemical properties of mammalian cell-produced and catalytically active E. coli-produced A3A. The enzyme binds to single-stranded DNA with a Kd of 150 nM and forms dimeric and monomeric fractions. A3A, unlike APOBEC3G (A3G, deaminates DNA substrates nonprocessively. Using a panel of oligonucleotides that contained all possible trinucleotide contexts, we identified the preferred target sequence as TC (A/G. Based on a three-dimensional model of A3A, we identified a putative binding groove that contains residues with the potential to bind substrate DNA and to influence target sequence specificity. Taking advantage of the sequence similarity to the catalytic domain of A3G, we generated A3A/A3G chimeric proteins and analyzed their target site preference. We identified a recognition loop that altered A3A sequence specificity, broadening its target sequence preference. Mutation of amino acids in the predicted DNA binding groove prevented substrate binding, confirming the role of this groove in substrate binding. These findings shed light on how APOBEC3 proteins bind their substrate and determine which sites to deaminate.

  5. A novel loop-mediated isothermal amplification-based test for detecting Neospora caninum DNA. (United States)

    Ramos, Andrea Estefanía; Muñoz, Marina; Cortés-Vecino, Jesús Alfredo; Barato, Paola; Patarroyo, Manuel Alfonso


    Neospora caninum is a cyst-forming, coccidian parasite which is known to cause neurological disorders in dogs and abortion and neonatal mortality in cows and other livestock. This study reports the development of a loop-mediated isothermal amplification (LAMP) assay based on the Neospora caninum Nc-5 gene and compares its efficacy for detecting DNA to that of a semi-nested PCR test. Six primers were designed based on the Nc-5 repeat region of N. caninum. Specific LAMP primers led to successful amplification of N. caninum DNA at 63 °C in 30 min. The LAMP assay was highly specific (i.e. it did not reveal cross-reactivity with other parasite species) and had a low N. caninum plasmid DNA limit of detection (1 fg), which is ten times higher than that for the semi-nested PCR. LAMP applicability was evaluated using a set of naturally-infected samples (59 from canine faeces and five from bovine abortions). Thirty-nine percent (25/64) of the naturally-infected samples were positive for N. caninum DNA by LAMP and 36% (23/64) by semi-nested PCR. However, the LAMP assay is much faster to perform than semi-nested PCR and provides results in 30 min. The optimized reaction conditions described in this study resulted in a sensitive, specific and rapid technique for detecting N. caninum DNA. Considering the advantages of LAMP for detecting N. caninum DNA, further assays aimed at testing its usefulness on a wider range of field samples are recommended.

  6. Keragaman Genetik Amfibia Kodok (Rana Nicobariensis) Di Ecology Park, Cibinong Berdasarkan Sekuen DNA Dari Mitokondria D-loop


    Astuti, Dwi; Kurniati, Hellen


    Genetic Diversity of Amphibia (Rana nicobariensis) at Ecology Park, Cibinong Based onDNA Sequences of Mitochomndrial d-Loop. The 397- base pairs from ten nucleotide sequencesof mitochondrial d-loop region were determined and analyzed in object to study the geneticdiversity of frog Rana nicobariensis at Ecology Park, Cibinong, West Java. There were sixhaplotypes from 10 individuals collected from Ecology Park. Haplotype and nucleotide oramino acid diversities in Ecology Park were 0.964 and 0.0...

  7. Development of an in situ loop-mediated isothermal amplification technique for chromosomal localization of DNA sequences (United States)

    Meng, Qinglei; Wang, Shi; Zhang, Lingling; Huang, Xiaoting; Bao, Zhenmin


    In situ loop-mediated isothermal amplification (in situ LAMP) combines in situ hybridization and loop-mediated isothermal amplification (LAMP) techniques for chromosomal localization of DNA sequences. In situ LAMP is a method that is generally more specific and sensitive than conventional techniques such as fluorescence in situ hybridization (FISH), primed in situ labeling (PRINS), and cycling primed in situ labeling (C-PRINS). Here, we describe the development and application of in situ LAMP to identify the chromosomal localization of DNA sequences. To benchmark this technique, we successfully applied this technique to localize the major ribosomal RNA gene on the chromosomes of the Zhikong scallop ( Chlamys farreri).

  8. Genetic variations of East Kalimantan Orangutan based on D-Loop mitochondria DNA

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    Full Text Available Analysis of the variation of D-Loop mtDNA of East Kalimantan orangutan was done to provided the genetic information data from endangerd species in order to support their population conservation efforts. The reason using mtDNA in this research is caused by higher level of mutation ( 5 – 10 trimes when compared with nuclear DNA and it enable to transmited via maternal transmission without experience in recombination. From the analysis conducted on 38 samples resulting eight types of haplotype that is A, B, C, D, E, G, H and I haplotype. Level of variation of the haplotype at East Kutai district was more uniform when compared by variation in Kutai district. From the paternal analysis had been got three cluster with the nearer among cluster IADG and cluster EH compared by cluster BC. Dissociation time between haplotype are 250.000-400.000 years ago, and known the population of East Kalimantan orangutan separated from Sumatran orangutan (X97708 since 1.158.300 years ago.

  9. Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair (United States)

    Shinohara, Takeshi; Ikawa, Shukuko; Iwasaki, Wakana; Hiraki, Toshiki; Hikima, Takaaki; Mikawa, Tsutomu; Arai, Naoto; Kamiya, Nobuo; Shibata, Takehiko


    In all organisms, RecA-family recombinases catalyze homologous joint formation in homologous genetic recombination, which is essential for genome stability and diversification. In homologous joint formation, ATP-bound RecA/Rad51-recombinases first bind single-stranded DNA at its primary site and then interact with double-stranded DNA at another site. The underlying reason and the regulatory mechanism for this conserved binding order remain unknown. A comparison of the loop L1 structures in a DNA-free RecA crystal that we originally determined and in the reported DNA-bound active RecA crystals suggested that the aspartate at position 161 in loop L1 in DNA-free RecA prevented double-stranded, but not single-stranded, DNA-binding to the primary site. This was confirmed by the effects of the Ala-replacement of Asp-161 (D161A), analyzed directly by gel-mobility shift assays and indirectly by DNA-dependent ATPase activity and SOS repressor cleavage. When RecA/Rad51-recombinases interact with double-stranded DNA before single-stranded DNA, homologous joint-formation is suppressed, likely by forming a dead-end product. We found that the D161A-replacement reduced this suppression, probably by allowing double-stranded DNA to bind preferentially and reversibly to the primary site. Thus, Asp-161 in the flexible loop L1 of wild-type RecA determines the preference for single-stranded DNA-binding to the primary site and regulates the DNA-binding order in RecA-catalyzed recombinase reactions. PMID:25561575

  10. Single genetic stock of kawakawa Euthynnus affinis (Cantor, 1849) along the Indian coast inferred from sequence analyses of mitochondrial DNA D-loop region

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

    , genetic variation was assessed using sequence analyses of Mitochondrial DNA (mtDNA) D-loop region. A 500 bp segment of D-loop region was sequenced in 400 samples collected from eight localities (Veraval (VE), Ratnagiri (RA), Kochi (KO), Kavaratti (KA...

  11. The detection of Plasmodiophora brassicae using loop-mediated isothermal DNA amplification

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    Joanna Kaczmarek


    Full Text Available Plasmodiophora brassicae, the cause of clubroot, is a very serious problem preventing from successful and profitable cultivation of oilseed rape in Poland. The pathogen was found in all main growing areas of oilseed rape; it also causes considerable problems in growing of vegetable brassicas. The aim of this work was to elaborate fast, cheap and reliable screening method to detect P. brassicae. To achieve this aim the Loop-mediated isothermal DNA amplification (LAMP technique has been elaborated. The set of three primer pairs was designed using LAMP software. The detection was performed with the GspSSD polymerase, isolated from bacteria Geobacillus sp., with strand displacement activity. DNA extraction from clubbed roots obtained from farmers’ fields of oilseed rape infected by P. brassicae was done using a modified CTAB method. The reaction was performed for 60 min at 62oC. The visual detection was done using CFX96 Real Time PCR Detection System (BioRad or Gerie II Amplicatior (Optigen. The detection with LAMP proved its usefulness; it was easy, fast and accurate and independent of plant age. The detection limit was 5 spores per 1 µl of the spore suspension, so LAMP was less sensitive than quantitative PCR tests reported in the literature. However, the method is cheap and simple, so it is a good alternative, when it comes to practical use and the assessment of numerous samples.

  12. A novel thermostable polymerase for RNA and DNA loop-mediated isothermal amplification (LAMP). (United States)

    Chander, Yogesh; Koelbl, Jim; Puckett, Jamie; Moser, Michael J; Klingele, Audrey J; Liles, Mark R; Carrias, Abel; Mead, David A; Schoenfeld, Thomas W


    Meeting the goal of providing point of care (POC) tests for molecular detection of pathogens in low resource settings places stringent demands on all aspects of the technology. OmniAmp DNA polymerase (Pol) is a thermostable viral enzyme that enables true POC use in clinics or in the field by overcoming important barriers to isothermal amplification. In this paper, we describe the multiple advantages of OmniAmp Pol as an isothermal amplification enzyme and provide examples of its use in loop-mediated isothermal amplification (LAMP) for pathogen detection. The inherent reverse transcriptase activity of OmniAmp Pol allows single enzyme detection of RNA targets in RT-LAMP. Common methods of nucleic acid amplification are highly susceptible to sample contaminants, necessitating elaborate nucleic acid purification protocols that are incompatible with POC or field use. OmniAmp Pol was found to be less inhibited by whole blood components typical in certain crude sample preparations. Moreover, the thermostability of the enzyme compared to alternative DNA polymerases (Bst) and reverse transcriptases allows pretreatment of complete reaction mixes immediately prior to amplification, which facilitates amplification of highly structured genome regions. Compared to Bst, OmniAmp Pol has a faster time to result, particularly with more dilute templates. Molecular diagnostics in field settings can be challenging due to the lack of refrigeration. The stability of OmniAmp Pol is compatible with a dry format that enables long term storage at ambient temperatures. A final requirement for field operability is compatibility with either commonly available instruments or, in other cases, a simple, inexpensive, portable detection mode requiring minimal training or power. Detection of amplification products is shown using lateral flow strips and analysis on a real-time PCR instrument. Results of this study show that OmniAmp Pol is ideally suited for low resource molecular detection of

  13. A novel thermostable polymerase for RNA and DNA Loop-mediated isothermal amplification (LAMP

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    Yogesh eChander


    Full Text Available Meeting the goal of providing point of care (POC tests for molecular detection of pathogens in low resource settings places stringent demands on all aspects of the technology. OmniAmp DNA polymerase (Pol is a thermostable viral enzyme that enables true POC use in clinics or in field by overcoming important barriers to isothermal amplification. In this paper, we describe the multiple advantages of OmniAmp Pol as an isothermal amplification enzyme and provide examples of its use in loop-mediated isothermal amplification (LAMP for pathogen detection. The inherent reverse transcriptase activity of OmniAmp Pol allows single enzyme detection of RNA targets in RT-LAMP. Common methods of nucleic acid amplification are highly susceptible to sample contaminants, necessitating elaborate nucleic acid purification protocols that are incompatible with POC or field use. OmniAmp Pol was found to be less inhibited by whole blood components typical in certain crude sample preparations . Moreover, the thermostability of the enzyme compared to alternative DNA polymerases (Bst and reverse transcriptases allows pretreatment of complete reaction mixes immediately prior to amplification, which facilitates amplification of highly structured genome regions. Compared to Bst, OmniAmp Pol has a faster time to result, particularly with more dilute templates. Molecular diagnostics in field settings can be challenging due to the lack of refrigeration. The stability of OmniAmp Pol is compatible with a dry format that enables long term storage at ambient temperatures. A final requirement for field operability is compatibility with either commonly available instruments or, in other cases, a simple, inexpensive, portable detection mode requiring minimal training or power. Detection of amplification products is shown using lateral flow strips and analysis on a real-time PCR instrument. Results of this study show that OmniAmp Pol is ideally suited for low resource molecular

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


    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.

  15. Genetic relationship and population structure of three Indian local chicken populations as revealed by mtDNA D-loop. (United States)

    Sahu, P K; Das, B; Sahoo, L; Senapati, S; Nayak, G D


    The genetic information obtained from the mitochondrial DNA D-loop region has paramount importance in understanding the evolution of closely related individuals, and designing proper breeding or conservation plans. The present study was conducted using partial D-loop sequences of three local poultry populations from Odisha, India. The partial D-loop sequences were found to be highly polymorphic having 164 polymorphic sites with 89 singletons and 75 parsimony informative sites. Furthermore, 25 insertion and deletion sites were observed. High genetic diversity was observed within three local chicken populations. Highest genetic difference was observed between Gujuri and Kalua population (0.2230) followed by Gujuri and Hansli (0.199) and Kalua with Hansli (0.166). The pairwise mismatch distribution showed that all populations are of constant size over time. Phylogenetic tree analysis indicated that the said three populations were close to the referred population of China, Sri Lanka, Indonesia and Japan than Aseel and Kadaknath (Indian native breeds).

  16. Role of loop residues and cations on the formation and stability of dimeric DNA G-quadruplexes. (United States)

    Cevec, Mirko; Plavec, Janez


    Formation of guanine-quadruplexes by four DNA oligonucleotides with common sequence dG4-loop-dG4 has been studied by a combination of NMR and UV spectroscopy. The loops consisted of 1',2'-dideoxyribose, propanediol, hexaethylene glycol, and thymine residues. The comparison of data on modified and parent oligonucleotides gave insight into the role of loop residues on formation and stability of dimeric G-quadruplexes. All modified oligonucleotides fold into dimeric fold-back G-quadruplexes in the presence of sodium ions. Multiple structures form in the presence of potassium and ammonium ions, which is in contrast to the parent oligonucleotide with dT4 loop. 15N-filtered 1H NMR spectra demonstrate that all studied G-quadruplexes exhibit three 15NH4(+) ion binding sites. Topology of intermolecular G-quadruplexes was evaluated by NMR measurements and diffusion experiments. The spherical, prolate-ellipsoid and symmetric cylinder models were used to interpret experimental translational diffusion constants in terms of diameters and lengths of unfolded oligonucleotides and their respective G-quadruplexes. UV melting and annealing curves show that oligonucleotides with non-nucleosidic loop residues fold faster, exhibit no hysteresis, and are less stable than dimeric d(G4T4G4)2 which can be attributed to the absence of H-bonds, stacking between loop residues and the outer G-quartets as well as cation-pi interactions. Oligonucleotide consisting of hexaethylene glycol linkage with only two phosphate groups in the loop exhibits higher melting temperature and more negative deltaH(o) and deltaG(o) values than oligonucleotides with four 1',2'-dideoxyribose or propanediol residues.

  17. Meat Species Identification using Loop-mediated Isothermal Amplification Assay Targeting Species-specific Mitochondrial DNA. (United States)

    Cho, Ae-Ri; Dong, Hee-Jin; Cho, Seongbeom


    Meat source fraud and adulteration scandals have led to consumer demands for accurate meat identification methods. Nucleotide amplification assays have been proposed as an alternative method to protein-based assays for meat identification. In this study, we designed Loop-mediated isothermal amplification (LAMP) assays targeting species-specific mitochondrial DNA to identify and discriminate eight meat species; cattle, pig, horse, goat, sheep, chicken, duck, and turkey. The LAMP primer sets were designed and the target genes were discriminated according to their unique annealing temperature generated by annealing curve analysis. Their unique annealing temperatures were found to be 85.56±0.07℃ for cattle, 84.96±0.08℃ for pig, and 85.99±0.05℃ for horse in the BSE-LAMP set (Bos taurus, Sus scrofa domesticus and Equus caballus); 84.91±0.11℃ for goat and 83.90±0.11℃ for sheep in the CO-LAMP set (Capra hircus and Ovis aries); and 86.31±0.23℃ for chicken, 88.66±0.12℃ for duck, and 84.49±0.08℃ for turkey in the GAM-LAMP set (Gallus gallus, Anas platyrhynchos and Meleagris gallopavo). No cross-reactivity was observed in each set. The limits of detection (LODs) of the LAMP assays in raw and cooked meat were determined from 10 pg/μL to 100 fg/μL levels, and LODs in raw and cooked meat admixtures were determined from 0.01% to 0.0001% levels. The assays were performed within 30 min and showed greater sensitivity than that of the PCR assays. These novel LAMP assays provide a simple, rapid, accurate, and sensitive technology for discrimination of eight meat species.

  18. Single-molecule imaging reveals the translocation and DNA looping dynamics of hepatitis C virus NS3 helicase. (United States)

    Lin, Chang-Ting; Tritschler, Felix; Lee, Kyung Suk; Gu, Meigang; Rice, Charles M; Ha, Taekjip


    Non-structural protein 3 (NS3) is an essential enzyme and a therapeutic target of hepatitis C virus (HCV). Compared to NS3-catalyzed nucleic acids unwinding, its translation on single stranded nucleic acids have received relatively little attention. To investigate the NS3h translocation with single-stranded nucleic acids substrates directly, we have applied a hybrid platform of single-molecule fluorescence detection combined with optical trapping. With the aid of mechanical manipulation and fluorescence localization, we probed the translocase activity of NS3h on laterally stretched, kilobase-size single-stranded DNA and RNA. We observed that the translocation rate of NS3h on ssDNA at a rate of 24.4 nucleotides per second, and NS3h translocates about three time faster on ssRNA, 74 nucleotides per second. The translocation speed was minimally affected by the applied force. A subpopulation of NS3h underwent a novel translocation mode on ssDNA where the stretched DNA shortened gradually and then recovers its original length abruptly before repeating the cycle repetitively. The speed of this mode of translocation was reduced with increasing force. With corroborating data from single-molecule fluorescence resonance energy transfer (smFRET) experiments, we proposed that NS3h can cause repetitive looping of DNA. The smFRET dwell time analysis showed similar translocation time between sole translocation mode versus repetitive looping mode, suggesting that the motor domain exhibits indistinguishable enzymatic activities between the two translocation modes. We propose a potential secondary nucleic acids binding site at NS3h which might function as an anchor point for translocation-coupled looping. © 2017 The Protein Society.

  19. 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.


    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

  20. Srs2 promotes synthesis-dependent strand annealing by disrupting DNA polymerase δ-extending D-loops. (United States)

    Liu, Jie; Ede, Christopher; Wright, William D; Gore, Steven K; Jenkins, Shirin S; Freudenthal, Bret D; Todd Washington, M; Veaute, Xavier; Heyer, Wolf-Dietrich


    Synthesis-dependent strand annealing (SDSA) is the preferred mode of homologous recombination in somatic cells leading to an obligatory non-crossover outcome, thus avoiding the potential for chromosomal rearrangements and loss of heterozygosity. Genetic analysis identified the Srs2 helicase as a prime candidate to promote SDSA. Here, we demonstrate that Srs2 disrupts D-loops in an ATP-dependent fashion and with a distinct polarity. Specifically, we partly reconstitute the SDSA pathway using Rad51, Rad54, RPA, RFC, DNA Polymerase δ with different forms of PCNA. Consistent with genetic data showing the requirement for SUMO and PCNA binding for the SDSA role of Srs2, Srs2 displays a slight but significant preference to disrupt extending D-loops over unextended D-loops when SUMOylated PCNA is present, compared to unmodified PCNA or monoubiquitinated PCNA. Our data establish a biochemical mechanism for the role of Srs2 in crossover suppression by promoting SDSA through disruption of extended D-loops.

  1. Investigation of the diversity and origins of Chinese dairy goats via the mitochondrial DNA D-loop. (United States)

    Wang, G Z; Pi, X S; Ji, Z B; Qin, Z J; Hou, L; Chao, T L; Wang, J M


    To determine the genetic diversity, origins, and the phylogeography of Chinese dairy goats, we analyzed 162 complete mitochondrial DNA (mtDNA) D- loop sequences from 9 dairy goat breeds and compared them with 8 goat sequences that were previously reported in GenBank. The length of the mtDNA D-loop was 1,212 to 1,215 bp, and 97 polymorphic sites were identified. We also defined 62 haplotypes, including 35 unique haplotypes. The haplotype diversity value of all the dairy goats was 0.952, and the nucleotide diversity was 0.011 per site. Phylogenetic analyses revealed that Chinese dairy goats were divided into haplogroups A and B, with haplogroup A serving as the predominant group. Median-joining network and analyses of molecular variance indicated that Chinese dairy goats were more weakly phylogeographically structured than other domestic goats. A mismatch distribution analysis and Fu's test revealed that at least 1 population expansion event occurred in the demographic history of Chinese dairy goats.

  2. Replication Fidelity of Escherichia Coli DNA Polymerase III Holoenzyme in Vitro and Repair of Heteroduplex DNA with Multibase Loops in Vivo. (United States)

    Carraway, Margaretha Bernardina Maria

    The genetic integrity of an organism is maintained by accurate replication and correction of asymmetry in the DNA. To study replication fidelity, single-stranded plasmid DNA containing the mnt gene, was replicated in vitro with DNA polymerase III holoenzyme by extension of a complimentary annealed primer. On this plasmid the mnt region is fused to a promoterless tet gene. Accurate replication of mnt generates a tetracycline sensitive phenotype, errors in replication are identified by mutation to tetracycline resistance. Mismatch repair deficient mutH cells were transformed to ampicillin-resistance by replicated circles. The mutations in mnt were identified by replica plating and selecting for tetracycline resistant cells. The mutation rate was 1 in 100,000. DNA sequence analysis of 65 isolates identified 33 single base changes, 20 deletions and 12 concurrent deletions and insertions. Except for the deletions and substitutions, identical mutations were isolated in vivo in mismatch repair deficient cells. Therefore, in vitro replication errors resemble those isolated in vivo. Heteroduplexes with loops occur as a result of replication or recombination. To examine if E. coli converts these molecules to a homoduplex via DNA repair, plasmid heteroduplexes with loops of 5, 7, 9, 192, 410 or 514 bases in mnt were constructed. Conversion was examined by tranforming the plasmid heteroduplexes into E. coli lysogens which had a non-functional mnt gene fused to a promoterless lac gene. Repair of the heteroduplex to wild type yields white/tetracycline sensitive colonies; repair to the mutant yields red/tetracycline resistant colonies and no repair results in red-white (mixed)/tetracycline resistant colonies. No significant change in colony color distribution was observed when the heteroduplexes were transformed into wild type and the following mutant strains: pcnB, mutS, recA, recD, recBC sbcBC, recF, recJ, recR, recN, recO, recG ruvC, ruvB, lexA3, lexA51, uvrA, recBC sbcBC rec

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

    African Journals Online (AJOL)



    Apr 8, 2015 ... the degree of variation characteristic of a fragment. FTA® Technology (FTA™ paper DNA extraction) was utilized to extract DNA. PCR products were purified by EZ-10 spin column then sequenced and detected by using the ABI 3730xL DNA Analyzer. Novel polymorphisms discovered at positions 16037,.

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

    African Journals Online (AJOL)

    the degree of variation characteristic of a fragment. FTA® Technology (FTA™ paper DNA extraction) was utilized to extract DNA. PCR products were purified by EZ-10 spin column then sequenced and detected by using the ABI 3730xL DNA Analyzer. Novel polymorphisms discovered at positions 16037, 16075, 16104 and ...

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

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


    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.

  6. 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


    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

  7. Single nucleotide polymorphisms in the D-loop region of mitochondrial DNA is associated with the kidney survival time in chronic kidney disease patients. (United States)

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


    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.

  8. Extra views on structure and dynamics of DNA loops on nucleosomes studied with molecular simulations. (United States)

    Pasi, Marco; Angelov, Dimitar; Bednar, Jan; Dimitrov, Stefan; Lavery, Richard


    It has been shown experimentally that the action of the RSC chromatin remodeler leads to the formation of an irregular, partially remodeled nucleosome, termed a remosome. The remosome contains an extra 30-40 base pairs of DNA compared to a canonical nucleosome. Large-scale molecular simulations have provided information on the probable structure of remosomes and have explained why they remain stable in the absence of RSC. Here we explain how these simulations were carried out and what the resulting remosome models imply in terms of the mechanism of action of RSC. We notably show that local kinks within DNA are key in explaining how extra DNA can be in added to nucleosomes without unduly disturbing DNA-histone binding.

  9. Rapid genotyping of carcinogenic human papillomavirus by loop-mediated isothermal amplification using a new automated DNA test (Clinichip HPV™). (United States)

    Satoh, Toyomi; Matsumoto, Koji; Fujii, Takuma; Sato, Osamu; Gemma, Nobuhiro; Onuki, Mamiko; Saito, Hiroshi; Aoki, Daisuke; Hirai, Yasuo; Yoshikawa, Hiroyuki


    This study was designed to evaluate the Clinichip HPV test, a new DNA test that detects carcinogenic human papillomavirus (HPV) rapidly by loop-mediated isothermal amplification and performs genotyping of all 13 carcinogenic types using automated DNA chip technology with an assay time 2.5h. Using this test, 247 Japanese women (109 with normal cytology, 43 with cervical intraepithelial neoplasia grade 1, 60 with cervical intraepithelial neoplasia grade 2/3 and 35 with invasive cervical cancer) were tested for carcinogenic HPV genotypes. The results were compared to those obtained by the polymerase chain reaction-amplified DNA sequencing using 13 type-specific primers. Overall, there was very good agreement for the detection of carcinogenic HPV between the Clinichip test and direct sequencing, with 95.5% total agreement and a kappa value of 0.91. Comparison of the detection of individual HPV types shows that the overall agreement was also high (range: 96.8-100%). In women with cervical intraepithelial neoplasia grade 2 or worse, the detection rate of carcinogenic HPV was 95.7% by both the Clinichip test and the direct-sequencing method, indicating complete agreement between the two methods. In conclusion, it was found that the Clinichip test is a promising new laboratory method for genotyping of carcinogenic HPV. Copyright © 2012 Elsevier B.V. All rights reserved.




    Abstract Aims: tissue defects, resulting from surgical resection of oral squamous cell carcinoma (OSCC), are routinely reconstructed with skin graft. OSCC arising from the grafted skin have been described, however, it is still unclear whether primary and second tumours have a common clonal origin. By screening mitochondrial DNA D-loop region (mtDNA), we evaluated the clonal relationship between the primary OSCC and the second neoplastic features appearing in the skin graft in three...

  11. PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation. (United States)

    Belotserkovskii, Boris P; Hanawalt, Philip C


    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.

  12. Counterion and polythymidine loop-length-dependent folding and thermodynamic stability of DNA hairpins reveal the unusual counterion-dependent stability of tetraloop hairpins. (United States)

    Nayak, Rajesh K; Van Orden, Alan


    Stem-loop DNA hairpins containing a 5-base-pair (bp) stem and single-stranded polythymidine loop were investigated using thermodynamic melting analysis and stopped-flow kinetics. These studies revealed the thermodynamic stability and folding kinetics as a function of loop length and counterion concentration. Our results show the unusually high thermodynamic stability for tetraloop or 4 poly(dT) loop hairpin as compared with longer loop length hairpins. Furthermore, this exceptional stability is highly counterion-dependent. For example, in the higher counterion concentration regime of 50 mM NaCl and above, the tetraloop hairpin displays enhanced stability as compared with longer loop length hairpins. However, at lower counterion concentration of 25 mM NaCl and below, the thermal stability of tetraloop hairpin is consistent with the longer loop hairpins. The enhanced stability of tetraloop hairpins at higher counterion concentration can be explained on the basis of the combined entropic effect of loop closure as well as base stacking in the loop regions. The stability of longer loop length hairpins at all counterion concentrations as well as tetraloop hairpin at lower counterion concentration can be explained on the basis of entropic effect of loop closure alone. The thermodynamic parameters at lower and higher counterion concentrations were determined to quantify the enhanced stability of base-stacking effects occurring at higher counterion concentrations. For example, for 100 mM NaCl, excess Gibbs energy and enthalpy due to base stacking within the tetraloops were measured to be -1.2 ± 0.14 and -3.28 ± 0.32 kcal/mol, respectively, whereas, no excess of Gibbs energy and enthalpy was observed for 0, 5, 10, and 25 mM NaCl. These findings suggest significant base-stacking interactions occurring in the loop region of the tetraloop hairpins at higher counterion concentration and less significant base-stacking interactions in the lower counterion concentration regime

  13. 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. (United States)

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


    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

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

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


    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. DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity (United States)

    Gonzalez-Huici, Victor; Szakal, Barnabas; Urulangodi, Madhusoodanan; Psakhye, Ivan; Castellucci, Federica; Menolfi, Demis; Rajakumara, Eerappa; Fumasoni, Marco; Bermejo, Rodrigo; Jentsch, Stefan; Branzei, Dana


    DNA replication is sensitive to damage in the template. To bypass lesions and complete replication, cells activate recombination-mediated (error-free) and translesion synthesis-mediated (error-prone) DNA damage tolerance pathways. Crucial for error-free DNA damage tolerance is template switching, which depends on the formation and resolution of damage-bypass intermediates consisting of sister chromatid junctions. Here we show that a chromatin architectural pathway involving the high mobility group box protein Hmo1 channels replication-associated lesions into the error-free DNA damage tolerance pathway mediated by Rad5 and PCNA polyubiquitylation, while preventing mutagenic bypass and toxic recombination. In the process of template switching, Hmo1 also promotes sister chromatid junction formation predominantly during replication. Its C-terminal tail, implicated in chromatin bending, facilitates the formation of catenations/hemicatenations and mediates the roles of Hmo1 in DNA damage tolerance pathway choice and sister chromatid junction formation. Together, the results suggest that replication-associated topological changes involving the molecular DNA bender, Hmo1, set the stage for dedicated repair reactions that limit errors during replication and impact on genome stability. PMID:24473148

  16. Insight into G-DNA Structural Polymorphism and Folding from Sequence and Loop Connectivity through Free Energy Analysis (United States)


    The lengths of G-tracts and their connecting loop sequences determine G-quadruplex folding and stability. Complete understanding of the sequence–structure relationships remains elusive. Here, single-loop G-quadruplexes were investigated using explicit solvent molecular dynamics (MD) simulations to characterize the effect of loop length, loop sequence, and G-tract length on the folding topologies and stability of G-quadruplexes. Eight loop types, including different variants of lateral, diagonal, and propeller loops, and six different loop sequences [d0 (i.e., no intervening residues in the loop), dT, dT2, dT3, dTTA, and dT4] were considered through MD simulation and free energy analysis. In most cases the free energetic estimates agree well with the experimental observations. The work also provides new insight into G-quadruplex folding and stability. This includes reporting the observed instability of the left propeller loop, which extends the rules for G-quadruplex folding. We also suggest a plausible explanation why human telomere sequences predominantly form hybrid-I and hybrid-II type structures in K+ solution. Overall, our calculation results indicate that short loops generally are less stable than longer loops, and we hypothesize that the extreme stability of sequences with very short loops could possibly derive from the formation of parallel multimers. The results suggest that free energy differences, estimated from MD and free energy analysis with current force fields and simulation protocols, are able to complement experiment and to help dissect and explain loop sequence, loop length, and G-tract length and orientation influences on G-quadruplex structure. PMID:21761922

  17. Morphology And Genetic Diversity Of Mitochondrial Dna D-loop Region Using Pcr-rflp Analysis In Magelang Duck And Other Native Duck


    D. Purwantini; T. Yuwanta; T. Hartatik; Ismoyowati, I


    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 ...

  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). (United States)

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


    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.


    Directory of Open Access Journals (Sweden)

    D. Purwantini


    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.


    Directory of Open Access Journals (Sweden)

    D. Purwantini


    Full Text Available The aim of this study was to investigate the different of plumage colors on morphological diversity of Magelang duck and genetic diversity using PCR-RFLP mtDNA D-loop region analysis of Magelang duck and four others native duck population (Tegal, Mojosari, Bali and Alabio duck in Indonesia. Blood sample was taken from 50 Magelang ducks and 20 of each native ducks. Morphological characteristics of body measurement, production ability and egg quality of Magelang duck were analyzed using Completely Randomized Design with 11 plumage colors as treatments. PCR technique was administered to amplify fragments in mtDNA D-loop region and PCR products were digested with endonuclease restriction enzyme AluI and HaeIII. The result showed that morphology diversity of Magelang duck was statistically affected by different plumage colors. PCR-RFLP analysis using AluI and HaeIII restriction enzyme 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 the other native ducks. In conclusion, the different plumage colors affected morphology diversity of Magelang duck. Genetic diversity of Indonesian native duck population could be identified by using PCR-RFLP analysis on mtDNA D-loop region.

  1. 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


    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.

  2. Genetic Diversity and Phylogenetic Analysis of South-East Asian Duck Populations Based on the mtDNA D-loop Sequences

    Directory of Open Access Journals (Sweden)

    H. Sultana


    Full Text Available The maternally inherited mitochondrial DNA (mtDNA D–loop region is widely used for exploring genetic relationships and for investigating the origin of various animal species. Currently, domestic ducks play an important role in animal protein supply. In this study, partial mtDNA D–loop sequences were obtained from 145 samples belonging to six South-East Asian duck populations and commercial duck population. All these populations were closely related to the mallard duck (Anas platyrhynchos, as indicated by their mean overall genetic distance. Sixteen nucleotide substitutions were identified in sequence analyses allowing the distinction of 28 haplotypes. Around 42.76% of the duck sequences were classified as Hap_02, which completely matched with Anas platyrhynchos duck species. The neighbor-joining phylogenetic tree also revealed that South-East Asian duck populations were closely related to Anas platyrhynchos. Network profiles were also traced using the 28 haplotypes. Overall, results showed that those duck populations D-loop haplotypes were shared between several duck breeds from Korea and Bangladesh sub continental regions. Therefore, these results confirmed that South-East Asian domestic duck populations have been domesticated from Anas platyrhynchos duck as the maternal origins.

  3. Association between a common mitochondrial DNA D-loop polycytosine variant and alteration of mitochondrial copy number in human peripheral blood cells. (United States)

    Liou, C-W; Lin, T-K; Chen, J-B; Tiao, M-M; Weng, S-W; Chen, S-D; Chuang, Y-C; Chuang, J-H; Wang, P-W


    A T-to-C transition at mitochondrial DNA (mtDNA) nucleotide position 16189 can generate a variable length polycytosine tract (poly-C). This tract variance has been associated with disease. A suggested pathogenesis is that it interferes with the replication process of mtDNA, which in turn decreases the mtDNA copy number and generates disease. In this study, 837 healthy adults' blood samples were collected and determined for their mtDNA D-loop sequence. The mtDNA copy number in the leucocytes and serum levels of oxidative thiobarbituric acid reactive substance (TBARS) and antioxidative thiols were measured. All subjects were then categorised into three groups: wild type or variant mtDNA with presence of an interrupted/uninterrupted poly-C at 16180-16195 segment. A step-wise multiple linear regression analysis identified factors affecting expression of mtDNA copy number including TBARS, thiols, age, body mass index and the mtDNA poly-C variant. Subjects harbouring a variant uninterrupted poly-C showed lowest mean (SD) mtDNA copy number (330 (178)), whereas an increased copy number was noted in subjects harbouring variant, interrupted poly-C (420 (273)) in comparison with wild type (358 (215)). The difference between the three groups and between the uninterrupted poly-C and the composite data from the interrupted poly-C and wild type remained consistent after adjustment for TBARS, thiols, age and body mass index (p=0.001 and p=0.011, respectively). A trend for decreased mtDNA copy number in association with increased number of continuous cytosine within the 16180-16195 segment was noted (p(trend)16189 variant can cause alteration of mtDNA copy number in human blood cells.

  4. 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


    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.

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

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


    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.

  6. Identification of human DNA in forensic evidence by loop-mediated isothermal amplification combined with a colorimetric gold nanoparticle hybridization probe. (United States)

    Watthanapanpituck, Khanistha; Kiatpathomchai, Wansika; Chu, Eric; Panvisavas, Nathinee


    A DNA test based on loop-mediated isothermal amplification (LAMP) and colorimetric gold nanoparticle (AuNP) hybridization probe to detect the presence of human DNA in forensic evidence was developed. The LAMP primer set targeted eight regions of the human cytochrome b, and its specificity was verified against the DNA of 11 animal species, which included animals closely related to humans, such as chimpanzee and orangutan. By using the AuNP probe, sequence-specific LAMP product could be detected and the test result could be visualized through the change in color. The limit of detection was demonstrated with reproducibility to be as low as 718 fg of genomic DNA, which is equivalent to approximately 100 plasmid DNA copies containing the cytochrome b DNA target region. A simple DNA extraction method for the commonly found forensic biological samples was also devised to streamline the test process. This LAMP-AuNP human DNA test showed to be a robust, specific, and cost-effective tool for the forensic identification of human specimens without requiring sophisticated laboratory instruments.

  7. 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.

  8. Identification of sequence polymorphism in the D-Loop region of mitochondrial DNA as a risk factor for hepatocellular carcinoma with distinct etiology

    Directory of Open Access Journals (Sweden)

    Zhang Ruixing


    Full Text Available Abstract Background Hepatocellular carcinoma (HCC is frequently preceded by hepatitis virus infection or alcohol abuse. Genetic backgrounds may increase susceptibility to HCC from these exposures. Methods Mitochondrial DNA (mtDNA of peripheral blood, tumor, and/or adjacent non-tumor tissue from 49 hepatitis B virus-related and 11 alcohol-related HCC patients, and from 38 controls without HCC were examined for single nucleotide polymorphisms (SNPs and mutations in the D-Loop region. Results Single nucleotide polymorphisms (SNPs in the D-loop region of mt DNA were examined in HCC patients. Individual SNPs, namely the 16266C/T, 16293A/G, 16299A/G, 16303G/A, 242C/T, 368A/G, and 462C/T minor alleles, were associated with increased risk for alcohol- HCC, and the 523A/del was associated with increased risks of both HCC types. The mitochondrial haplotypes under the M haplogroup with a defining 489C polymorphism were detected in 27 (55.1% of HBV-HCCand 8 (72.7% of alcohol- HCC patients, and in 15 (39.5% of controls. Frequencies of the 489T/152T, 489T/523A, and 489T/525C haplotypes were significantly reduced in HBV-HCC patients compared with controls. In contrast, the haplotypes of 489C with 152T, 249A, 309C, 523Del, or 525Del associated significantly with increase of alcohol-HCC risk. Mutations in the D-Loop region were detected in 5 adjacent non-tumor tissues and increased in cancer stage (21 of 49 HBV-HCC and 4 of 11 alcohol- HCC, p Conclusions In sum, mitochondrial haplotypes may differentially predispose patients to HBV-HCC and alcohol-HCC. Mutations of the mitochondrial D-Loop sequence may relate to HCC development.

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

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Alice Kar Lai, E-mail: [Program of Biochemistry, School of Life Sciences, The Chinese University of Hong Kong (Hong Kong); Lu, Haifei, E-mail: [Center for Advanced Research in Photonics, Department of Electronic Engineering, The Chinese University of Hong Kong (Hong Kong); Wu, Shu Yuen, E-mail: [Center for Advanced Research in Photonics, Department of Electronic Engineering, The Chinese University of Hong Kong (Hong Kong); Kwok, Ho Chin, E-mail: [Center for Advanced Research in Photonics, Department of Electronic Engineering, The Chinese University of Hong Kong (Hong Kong); Ho, Ho Pui, E-mail: [Center for Advanced Research in Photonics, Department of Electronic Engineering, The Chinese University of Hong Kong (Hong Kong); Yu, Samuel, E-mail: [The MacDiarmid Institute for Advanced Materials and Nanotechnology, Christchurch (New Zealand); Izon Science, PO Box 39-168, Harewood, Christchurch 8545 (New Zealand); Cheung, Anthony Ka Lun, E-mail: [Program of Biochemistry, School of Life Sciences, The Chinese University of Hong Kong (Hong Kong); Kong, Siu Kai, E-mail: [Program of Biochemistry, School of Life Sciences, The Chinese University of Hong Kong (Hong Kong)


    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.

  10. Highly sensitive electrochemical detection of genomic DNA based on stem loop probes structured for magnetic collection and measurement via metalised hollow polyelectrolyte shells. (United States)

    Khunrattanaporn, Naphat; Rijiravanich, Patsamon; Somasundrum, Mithran; Surareungchai, Werasak


    We report a highly sensitive method for the electrochemical detection of genomic DNA, based on the employment of two sub-micron oligonucleotide labels - one for magnetic collection and the other for voltammetric detection - and their incorporation onto a stem loop DNA probe. The magnetic label consists of a latex particle of mean diameter 441±6 nm, bearing magnetic Fe3O4 particles and approx. 3.5×10(5) anti-DIG antibodies. The voltammetric label is a hollow polyelectrolyte shell containing approx. 1.0×10(11) Au atoms in the form of well dispersed Au nanoparticles. A DIG tag on one arm of the stem loop enables binding to the magnetic label, while a thiol tag on the other arm enables attachment to the Au nanoparticles. Due to steric hindrance from the two relatively large labels, attachment of both moieties is dependant on target-probe hybridisation straightening the loop. Once attached, sensitive DNA measurement is facilitated by magnetic collection of the DNA into a small volume and by the high quantity of Au atoms available for detection. Using differential pulse anodic stripping voltammetry we calibrated a 30 mer sequence common to 71 strains of Escherichia coli across the concentration range from 0.1 aM to 100 pM with a LOD of 1.8 aM. Three strains of E. coli, BL 21, ATCC8739, O157:H7, when spiked into UHT milk and fermented palm juice, could be detected with LODs of approx. 2-4 CFU mL(-1) in an assay time of approx. 140 min. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Mitochondrial myopathy associated with high levels of mitochondrial DNA harboring a 260 bp tandem duplication in the D-loop region

    Energy Technology Data Exchange (ETDEWEB)

    Manfredi, G.; Shanske, S.; Schon, E.A. [Columbia Univ., NY (United States)] [and others


    Low levels of a 260 bp duplication in the D-loop of the mitochondrial DNA (mtDNA) were reported in some patients with mitochondrial disorders harboring large-scale mtDNA deletions. Because the same duplication was observed in unaffected mothers of these patients, it was suggested that the 260 bp duplication predispose mtDNA to deletion. More recently, PCR-levels of this duplication were also observed in a subgroup of normal Caucasions. To test the hypothesis that this genetic abnormality may be prevalent in patients with large-scale deletions of the mitochondrial genome, we used a semi-quantitative PCR protocol to search for the 260 by duplication in 34 patients with, and 35 without mtDNA deletions. Our results do not support the hypothesis that the 260 bp duplication precedes large-scale deletions of mtDNA. They suggest, however, that the duplication may be pathogenic per se, if its level reaches a specific threshold. We are presently trying to test this hypothesis, as well as the stability of the duplication, in a cell culture system.

  12. Sensitive and specific detection of Cryptosporidium species in PCR-negative samples by loop-mediated isothermal DNA amplification and confirmation of generated LAMP products by sequencing. (United States)

    Bakheit, Mohammed A; Torra, Dena; Palomino, Lily A; Thekisoe, Oriel M M; Mbati, Peter A; Ongerth, Jerry; Karanis, Panagiotis


    Three LAMP (loop-mediated isothermal DNA amplification) assays were applied to detect Cryptosporidium species DNA in a total number of 270 fecal samples originating from cattle, sheep and horses in South Africa. DNA was extracted from 0.5 g of fecal material. Results of LAMP detection were compared to those obtained by nested PCR targeting the Cryptosporidium 18 small subunit rRNA (18S) gene. All samples were negative by nested PCR, while up to one-third of samples were positive by LAMP assays. The SAM-1 LAMP assay, shown to detect C. parvum, C. hominis and C. meleagridis, amplified Cryptosporidium DNA in 36 of 107 cattle (33.64%), in 26 of 85 sheep (30.5%) and in 17 of 78 horses (21.79%). The HSP LAMP specific to C. muris and C. andersoni, amplified Cryptosporidium DNA in one cow (0.9%), five sheep (5.8%) and seven horses (8.9%). The gp60 LAMP assay, shown to detect C. parvum produced no amplified Cryptosporidium DNA, likely due to low sample DNA concentrations. The specificity of LAMP assays was confirmed by sequencing of the LAMP products generated in positive samples. Sequence products from the three LAMP assays showed high identity to the target gene sequences confirming the specificity of LAMP. In this study, the LAMP procedure was clearly superior to nested PCR in the detection of Cryptosporidium species DNA. Use of LAMP is proposed as an efficient and effective tool for epidemiologic survey studies including screening of healthy animals in which Cryptosporidium oocyst shedding is characteristically low and likely below the detection limit of PCR in conventional sample concentrates.

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

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


    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.

  14. Uracil-DNA glycosylase-treated reverse transcription loop-mediated isothermal amplification for rapid detection of avian influenza virus preventing carry-over contamination. (United States)

    Kim, Eun-Mi; Jeon, Hyo-Sung; Kim, Ji-Jung; Shin, Yeun-Kyung; Lee, Youn-Jeong; Yeo, Sang-Geon; Park, Choi-Kyu


    Here, we describe a uracil-DNA glycosylase (UNG)-treated reverse transcription loop-mediated isothermal amplification (uRT-LAMP) for the visual detection of all subtypes of avian influenza A virus (AIV). The uRT-LAMP assay can prevent unwanted amplification by carryover contamination of the previously amplified DNA, although the detection limit of the uRT-LAMP assay is 10-fold lower than that of the RT-LAMP without a UNG treatment. To the best of our knowledge, this is the first successful application of deoxyuridine triphosphate/UNG strategy in RT-LAMP for AIV detection, and the assay can be applied for the rapid, and reliable diagnosis of AIVs, even in contaminated samples.

  15. Phylogenetic relationships of intraspecific forms of the house mouse Mus musculus: Analysis of variability of the control region (D-loop) of mitochondrial DNA. (United States)

    Maltsev, A N; Stakheev, V V; Bogdanov, A S; Fomina, E S; Kotenkova, E V


    Analysis of the control region of mitochondrial DNA (mtDNA) or D-loop of 96 house mice (Mus musculus) from Russia, Moldova, Armenia, Azerbaijan, Kazakhstan, and Turkmenistan has been used to reconstruct the phylogenetic relationships and phylogeographic patterns of intraspecific forms. New data on the phylogenetic structure of the house mouse are presented. Three phylogroups can be reliably distinguished in the eastern part of the M. musculus species range, the first one mainly comprising the haplotypes of mice from Transcaucasia (Armenia); the second one, the haplotypes of mice from Kazakhstan; and the third one, the haplotypes of mice from Siberia and some other regions. The morphological subspecies M. m. wagneri and M. m. gansuensis have proved to be genetically heterogeneous and did not form discrete phylogroups in the phylogenetic tree.

  16. [Genetic diversity and relatives of the goitered gazelle (Gazella subgutturosa) groups from Uzbekistan, Turkmenistan, and Azerbaijan: analysis of the D-loop of mitochondrial DNA]. (United States)

    Sorokin, P A; Soldatova, N V; Lukarevskiĭ, V S; Kholodova, M V


    Polymorphism of the nucleotide sequence of a hypervariable fragment of the D-loop (985 bp) of mtDNA in 76 Goitered gazelles of subspecies Gazella subgutturosa subgutturosa from Uzbekistan, Turkmenistan, and Azerbaijan was studied. The genetic similarity of gazelles from Turkmenistan and Uzbekistan has been identified. The population of gazelles from Shirvanskaya steppe reserve (Azerbaijan) is unique and strictly isolated from other groups studied. A high haplotypic (H = 0.9649 +/- 0.0091) and relatively low nucleotide diversity (pi = 0.0212 +/- 0.0105) were noted for all investigated groups of gazelle based on this mtDNA fragment, which is probably related to ecological peculiarities of the species and the history of formation of regional populations.

  17. Protein distributions from a stochastic model of the lac operon of E. coli with DNA looping: analytical solution and comparison with experiments.

    Directory of Open Access Journals (Sweden)

    Krishna Choudhary

    Full Text Available Although noisy gene expression is widely accepted, its mechanisms are subjects of debate, stimulated largely by single-molecule experiments. This work is concerned with one such study, in which Choi et al., 2008, obtained real-time data and distributions of Lac permease in E. coli. They observed small and large protein bursts in strains with and without auxiliary operators. They also estimated the size and frequency of these bursts, but these were based on a stochastic model of a constitutive promoter. Here, we formulate and solve a stochastic model accounting for the existence of auxiliary operators and DNA loops. We find that DNA loop formation is so fast that small bursts are averaged out, making it impossible to extract their size and frequency from the data. In contrast, we can extract not only the size and frequency of the large bursts, but also the fraction of proteins derived from them. Finally, the proteins follow not the negative binomial distribution, but a mixture of two distributions, which reflect the existence of proteins derived from small and large bursts.

  18. Advanced loop-mediated isothermal amplification method for sensitive and specific detection of Tomato chlorosis virus using a uracil DNA glycosylase to control carry-over contamination. (United States)

    Kil, Eui-Joon; Kim, Sunhoo; Lee, Ye-Ji; Kang, Eun-Ha; Lee, Minji; Cho, Sang-Ho; Kim, Mi-Kyeong; Lee, Kyeong-Yeoll; Heo, Noh-Youl; Choi, Hong-Soo; Kwon, Suk-Tae; Lee, Sukchan


    In 2013, Tomato chlorosis virus (ToCV) was identified in symptomatic tomato plants in Korea. In the present study, a loop-mediated isothermal amplification (LAMP) method was developed using four specific primers designed against ORF6 in ToCV RNA2 to detect ToCV rapidly and with high sensitivity. The optimized reaction involved incubation of a reaction mixture containing 2U Bst DNA polymerase and 4mM MgSO4 for 1h at 60-62 °C. Although specific and rapid detection of ToCV by LAMP was confirmed, false-positive reactions caused by carry-over contamination sometimes occurred because of the high sensitivity of LAMP compared with other detection methods. To prevent false-positive reactions, dUTP was substituted for dTTP and uracil-DNA glycosylase (UDG) was added to the LAMP reaction. First, the LAMP reaction was conducted successfully with substitution of dUTP for dTTP. Before the next reaction, LAMP products with incorporated dUTP were cleaved selectively by UDG without any effect on thymine-containing DNA (template DNA). This modified LAMP method complemented with UDG treatment to prevent carry-over contamination offers a potentially powerful method for detecting plant viruses. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Green tea (Camellia sinensis) alleviates arsenic-induced damages to DNA and intestinal tissues in rat and in situ intestinal loop by reinforcing antioxidant system. (United States)

    Acharyya, Nirmallya; Sajed Ali, Sk; Deb, Bimal; Chattopadhyay, Sandip; Maiti, Smarajit


    This study elucidates the protective role of Green tea (Camellia sinensis or CS) against arsenic-induced mutagenic DNA-breakage/intestinal (small) damages in female rats. Intestinal epithelial cells receive ingested arsenic initially. Though, the possibility of damages in this tissue is immense and the therapeutic strategies against this damage are of great concern, reports on either issue are scanty. Our earlier study on arsenic-exposed human unveils a link between carcinogenesis and mutagenic DNA damage. Here, we demonstrate that supplementation of CS-extract (10 mg/mL water) with NaAsO2 (0.6 ppm)/100 g b.w. for 28 days to rats offered a significant protection against arsenic-induced oxidative damages to DNA and intestinal (small) tissues by buttressing antioxidant systems. Necrotic and apoptotic damages and their CS-protection are shown in DNA-fragmentation, comet-assay, and histoarchitecture (hematoxylin and eosin and periodic acid-schiff staining) results. Only arsenic exposure significantly decreased intestinal superoxide dismutase, catalase activities, and level of soluble thiol with a concomitant increase in malondialdehyde/conjugated dienes. Alteration of serum necrotic marker lactate dehydrogenase and the metabolic inflammatory marker c-reactive protein also indicate the impairment may be occurring at transcription and/or cellular signal transduction level. In addition, in situ incubation in rat intestinal loop filled for 24 h with NaAsO2 alone (250 µM) or with aqueous CS-extract (250 mg/mL) suggests that small intestinal epithelial cells are significantly protected by CS against arsenic-associated necrotic/mutagenic damages, which is observed in DNA-breakage studies. In conclusion, besides intensifying endogenous antioxidant system, CS polyphenols also offer a direct role on free radical scavenging activity that is associated to the protection from mutagenic DNA-breakages and prevention of tissue necrosis/carcinogenesis generated by arsenic. © 2014

  20. DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner. (United States)

    Wiedemann, Eva-Maria; Peycheva, Mihaela; Pavri, Rushad


    Class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) locus generates antibody isotypes. CSR depends on double-strand breaks (DSBs) induced by activation-induced cytidine deaminase (AID). Although DSB formation and repair machineries are active in G1 phase, efficient CSR is dependent on cell proliferation and S phase entry; however, the underlying mechanisms are obscure. Here, we show that efficient CSR requires the replicative helicase, the Mcm complex. Mcm proteins are enriched at IgH switch regions during CSR, leading to assembly of facultative replication origins that require Mcm helicase function for productive CSR. Assembly of CSR-associated origins is facilitated by R loops and promotes the physical proximity (synapsis) of recombining switch regions, which is reduced by R loop inhibition or Mcm complex depletion. Thus, R loops contribute to replication origin specification that promotes DSB resolution in CSR. This suggests a mechanism for the dependence of CSR on S phase and cell division. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  1. Study of the genetic origin of the Mexican creole donkey (Equus asinus) by means of the analysis of the D-loop region of mitochondrial DNA. (United States)

    Lopez Lopez, C; Alonso, R; de Aluja, A S


    The aim of this work was to analyse the genetic origin of the Mexican Creole donkey, as well as its genetic diversity, by comparison with Spanish and African donkey populations by means of the D-loop region of mitochondrial DNA. To this end, the genomic DNA of 68 Mexican Creole donkeys from eight geographical regions in six States of the Republic of Mexico and from a Sicilian donkey was obtained. By the polymerase chain-reaction technique (PCR) a fragment of 541 bp was amplified, corresponding to the most informative region of the mitochondrial DNA, the D-loop. The fragments were subsequently sequenced. The analysed sequences revealed 10 new Mexican haplotypes that were different from those of the Spanish and African breeds with which they were compared, showing high levels of genetic diversity. Analysis of the phylogenetic relationships in the different Creole varieties showed a tendency of origin towards Spanish breeds, mainly the Andaluza, Zamorano-Leonesa and Majorera from the Canary Islands; these in turn showed an African origin, seven Mexican haplotypes and three haplotypes similar to those analysed by Aranguren and colleagues (2004) of Spanish and African breeds being obtained. This work allows us to reach the preliminary conclusion that the origin of Mexican Creole donkey populations in the different states of the Republic of Mexico is clearly of Iberian origin, the Spanish donkey breed Andaluza being the main one contributing to the populations of the Mexican Creole donkeys, followed by the Spanish breeds Zamorano-Leonesa and Majorera from the Canary Islands, and that the populations possess high levels of genetic diversity.

  2. Microscale loop-mediated isothermal amplification of viral DNA with real-time monitoring on solution-gated graphene FET microchip. (United States)

    Han, Dawoon; Chand, Rohit; Kim, Yong-Sang


    Rapid and reliable molecular analysis of DNA for disease diagnosis is highly sought-after. FET-based sensors fulfill the demands of future point-of-care devices due to its sensitive charge sensing and possibility of integration with electronic instruments. However, most of the FETs are unstable in aqueous conditions, less sensitive and requires conventional Ag/AgCl electrode for gating. In this work, we propose a solution-gated graphene FET (SG-FET) for real-time monitoring of microscale loop-mediated isothermal amplification of DNA. The SG-FET was fabricated effortlessly with graphene as an active layer, on-chip co-planar electrodes, and polydimethylsiloxane-based microfluidic reservoir. A linear response of about 0.23V/pH was seen when the buffers from pH 5-9 were analyzed on the SG-FET. To evaluate the performance of SG-FET, we monitored the amplification of Lambda phage gene as a proof-of-concept. During amplification, protons are released, which gradually alters the Dirac point voltage (V Dirac ) of SG-FET. The resulting device was highly sensitive with a femto-level limit of detection. The SG-FET could easily produce a positive signal within 16.5min of amplification. An amplification of 10ng/μl DNA for 1h produced a ∆V Dirac of 0.27V. The sensor was tested within a range of 2×10 2 copies/μl (10 fg/μl) to 2×10 8 copies/μl (10ng/μl) of target DNA. Development of this sensing technology could significantly lower the time, cost, and complications of DNA detection. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation. (United States)

    Swadling, Jacob B; Ishii, Kunihiko; Tahara, Tahei; Kitao, Akio


    Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) have remarkably similar chemical structures, but despite this, they play significantly different roles in modern biology. In this article, we explore the possible conformations of DNA and RNA hairpins to better understand the fundamental differences in structure formation and stability. We use large parallel temperature replica exchange molecular dynamics ensembles to sample the full conformational landscape of these hairpin molecules so that we can identify the stable structures formed by the hairpin sequence. Our simulations show RNA adopts a narrower distribution of folded structures compared to DNA at room temperature, which forms both hairpins and many unfolded conformations. RNA is capable of forming twice as many hydrogen bonds than DNA which results in a higher melting temperature. We see that local chemical differences lead to emergent molecular properties such as increased persistence length in RNA that is weakly temperature dependant. These discoveries provide fundamental insight into how RNA forms complex folded tertiary structures which confer enzymatic-like function in ribozymes, whereas DNA retains structural motifs in order to facilitate function such as translation of sequence.

  4. Innate immune recognition of an AT-rich stem-loop DNA motif in the Plasmodium falciparum genome. (United States)

    Sharma, Shruti; DeOliveira, Rosane B; Kalantari, Parisa; Parroche, Peggy; Goutagny, Nadege; Jiang, Zhaozhao; Chan, Jennie; Bartholomeu, Daniella C; Lauw, Fanny; Hall, J Perry; Barber, Glen N; Gazzinelli, Ricardo T; Fitzgerald, Katherine A; Golenbock, Douglas T


    Although Toll-like receptor 9 (TLR9) has been implicated in cytokine and type I interferon (IFN) production during malaria in humans and mice, the high AT content of the Plasmodium falciparum genome prompted us to examine the possibility that malarial DNA triggered TLR9-independent pathways. Over 6000 ATTTTTAC ("AT-rich") motifs are present in the genome of P. falciparum, which we show here potently induce type I IFNs. Parasite DNA, parasitized erythrocytes and oligonucleotides containing the AT-rich motif induce type I IFNs via a pathway that did not involve the previously described sensors TLR9, DAI, RNA polymerase-III or IFI16/p204. Rather, AT-rich DNA sensing involved an unknown receptor that coupled to the STING, TBK1 and IRF3-IRF7 signaling pathway. Mice lacking IRF3, IRF7, the kinase TBK1 or the type I IFN receptor were resistant to otherwise lethal cerebral malaria. Collectively, these observations implicate AT-rich DNA sensing via STING, TBK1 and IRF3-IRF7 in P. falciparum malaria. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Origin and genetic diversity of Egyptian native chickens based on complete sequence of mitochondrial DNA D-loop region. (United States)

    Osman, Sayed A-M; Yonezawa, Takahiro; Nishibori, Masahide


    Domestic chickens (Gallus gallus) play a significant role, ranging from food and entertainment to religion and ornamentation. However, the details on their domestication process are still controversial, especially the origin and evolution of African chickens. Egypt is thought to be important place for this event because of its geographic location as well as its long history of civilization. However, the genetic component and structure of Egyptian native chicken (ENC) have not been studied so far. The aim of this study is to clarify the origin and evolution of African chickens through assessing the genetic diversities and structure of five ENC breeds using the mitochondrial D-loop sequences. Our results suggest there is genetic differentiation between the pure native breeds and the improved native breeds. The latter breeds were established by the hybridization of the pure native and the exotic breeds. The pure native breeds were estimated to be established about 800 years ago. Subsequently, we extensively analyzed the D-loop sequences from the ENC as well as the globally collected chickens (2,010 individuals in total). Our phylogenetic tree among the regional populations shows African chickens can be separated to two distinct clades. The first clade consists of North African (Egypt), Central African (Sudan and Cameroon), European, and West (and Central) Asian chickens. The second clade consists of East African (Kenya, Malawi, and Zimbabwe) and Pacific chickens. It suggests the dual origins of African native chickens. The first group was probably originated from South Asia, and then migrated to West Asia, and finally arrived to Africa thorough Egypt. The second group migrated from Pacific to East Africa via Indian Ocean probably by Austronesian people. This dual origin hypothesis as well as estimated divergence times in this study is harmonious with the archaeological and historical evidences. Our migration analysis suggests there is limited gene flow within African

  6. An integrated rotary microfluidic system with DNA extraction, loop-mediated isothermal amplification, and lateral flow strip based detection for point-of-care pathogen diagnostics. (United States)

    Park, Byung Hyun; Oh, Seung Jun; Jung, Jae Hwan; Choi, Goro; Seo, Ji Hyun; Kim, Do Hyun; Lee, Eun Yeol; Seo, Tae Seok


    Point-of-care (POC) molecular diagnostics plays a pivotal role for the prevention and treatment of infectious diseases. In spite of recent advancement in microfluidic based POC devices, there are still rooms for development to realize rapid, automatic and cost-effective sample-to-result genetic analysis. In this study, we propose an integrated rotary microfluidic system that is capable of performing glass microbead based DNA extraction, loop mediated isothermal amplification (LAMP), and colorimetric lateral flow strip based detection in a sequential manner with an optimized microfluidic design and a rotational speed control. Rotation direction-dependent coriolis force and siphon valving structures enable us to perform the fluidic control and metering, and the use of the lateral flow strip as a detection method renders all the analytical processes for nucleic acid test simplified and integrated without the need of expensive instruments or human intervention. As a proof of concept for point-of-care DNA diagnostics, we identified the food-borne bacterial pathogen which was contaminated in water or milk. Not only monoplex Salmonella Typhimurium but also multiplex Salmonella Typhimurium and Vibrio parahaemolyticus were analysed on the integrated rotary genetic analysis microsystem with a limit of detection of 50 CFU in 80min. In addition, three multiple samples were simultaneously analysed on a single device. The sample-to-result capability of the proposed microdevice provides great usefulness in the fields of clinical diagnostics, food safety and environment monitoring. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Development and Evaluation of Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Tylenchulus semipenetrans Using DNA Extracted from Soil

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    Zhi-Qiang Song


    Full Text Available Tylenchulus semipenetrans is an important and widespread plant-parasitic nematode of citrus worldwide and can cause citrus slow decline disease leading to significant reduction in tree growth and yield. Rapid and accurate detection of T. semipenetrans in soil is important for the disease forecasting and management. In this study, a loop-mediated isothermal amplification (LAMP assay was developed to detect T. semipenetrans using DNA extracted from soil. A set of five primers was designed from the internal transcribed spacer region (ITS1 of rDNA, and was highly specific to T. semipenetrans. The LAMP reaction was performed at 63°C for 60 min. The LAMP product was visualized directly in one reaction tube by adding SYBR Green I. The detection limit of the LAMP assay was 10−2 J2/0.5 g of soil, which was 10 times more sensitive than conventional PCR (10−1 J2/0.5 g of soil. Examination of 24 field soil samples revealed that the LAMP assay was applicable to a range of soils infested naturally with T. semipenetrans, and the total assay time was less than 2.5 h. These results indicated that the developed LAMP assay is a simple, rapid, sensitive, specific and accurate technique for detection of T. semipenetrans in field soil, and contributes to the effective management of citrus slow decline disease.

  8. An improved and robust DNA immunization method to develop antibodies against extra-cellular loops of multi-transmembrane proteins (United States)

    Hazen, Meredith; Bhakta, Sunil; Vij, Rajesh; Randle, Steven; Kallop, Dara; Chiang, Vicki; Hötzel, Isidro; Jaiswal, Bijay S; Ervin, Karen E; Li, Bing; Weimer, Robby M; Polakis, Paul; Scheller, Richard H; Junutula, Jagath R; Hongo, Jo-Anne S


    Multi-transmembrane proteins are especially difficult targets for antibody generation largely due to the challenge of producing a protein that maintains its native conformation in the absence of a stabilizing membrane. Here, we describe an immunization strategy that successfully resulted in the identification of monoclonal antibodies that bind specifically to extracellular epitopes of a 12 transmembrane protein, multi-drug resistant protein 4 (MRP4). These monoclonal antibodies were developed following hydrodynamic tail vein immunization with a cytomegalovirus (CMV) promoter-based plasmid expressing MRP4 cDNA and were characterized by flow cytometry. As expected, the use of the immune modulators fetal liver tyrosine kinase 3 ligand (Flt3L) and granulocyte-macrophage colony-stimulating factor positively enhanced the immune response against MRP4. Imaging studies using CMV-based plasmids expressing luciferase showed that the in vivo half-life of the target antigen was less than 48 h using CMV-based plasmids, thus necessitating frequent boosting with DNA to achieve an adequate immune response. We also describe a comparison of plasmids, which contained MRP4 cDNA with either the CMV or CAG promoters, used for immunizations. The observed luciferase activity in this comparison demonstrated that the CAG promoter-containing plasmid pCAGGS induced prolonged constitutive expression of MRP4 and an increased anti-MRP4 specific immune response even when the plasmid was injected less frequently. The method described here is one that can be broadly applicable as a general immunization strategy to develop antibodies against multi-transmembrane proteins, as well as target antigens that are difficult to express or purify in native and functionally active conformation. PMID:24121517

  9. DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation. (United States)

    Giovan, Stefan M; Hanke, Andreas; Levene, Stephen D


    For much of the last three decades, Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, J, or J factor, for DNA models having sequence-dependent bends or inhomogeneous bending flexibility. Within the last 10 years approaches based on harmonic analysis of semi-flexible polymer models have been introduced, which offer much greater computational efficiency than Monte Carlo techniques. These methods consider the ensemble of molecular conformations in terms of harmonic fluctuations about a well-defined elastic-energy minimum. However, the harmonic approximation is only applicable for small systems, because the accessible conformation space of larger systems is increasingly dominated by anharmonic contributions. In the case of computed values of the J factor, deviations of the harmonic approximation from the exact value of J as a function of DNA length have not been characterized. Using a recent, numerically exact method that accounts for both anharmonic and harmonic contributions to J for wormlike chains of arbitrary size, we report here the apparent error that results from neglecting anharmonic behavior. For wormlike chains having contour lengths less than four times the persistence length, the error in J arising from the harmonic approximation is generally small, amounting to free energies less than the thermal energy, kB T. For larger systems, however, the deviations between harmonic and exact J values increase approximately linearly with size. © 2015 Wiley Periodicals, Inc.

  10. A novel mechanism of FSH regulation of DNA synthesis in the granulosa cells of hamster preantral follicles. Involvement of a protein kinase C mediated MAP kinase 3/1 self- activation loop (United States)

    Yang, Peixin; Roy, Shyamal K.


    Summary FSH- or EGF-induced granulosa cell proliferation in intact preantral follicles depends on a novel PKC-mediated MAPK3/1 self-activation loop. The objective was to reveal whether a PKC-mediated self-sustaining MAPK3/1 activation loop was necessary for FSH- or EGF-induced DNA synthesis in the granulosa cells of intact preantral follicles. For this purpose, hamster preantral follicles were cultured with FSH or EGF in the presence of selective kinase inhibitors. FSH or EGF phosphorylated RAF1, MAP2K1 and MAPK3/1. However, relatively higher dose of EGF was necessary to sustain the MAPK3/1 activity, which was essential for CDK4 activation and DNA synthesis. In intact preantral follicles, FSH or EGF stimulated DNA synthesis only in the granulosa cells. Sustained activation of MAPK3/1 beyond 3h was independent of EGFR kinase activity, but dependent on PKC activity, which appeared to form a self-sustaining MAPK3/1 activation loop by activating RAF1, MAP2K1 and PLA2G4. Inhibition of PKC activity as late as 4h after the administration of FSH or EGF arrested DNA synthesis, which corresponded with attenuated phosphorylation of RAF1 and MAPK3/1, thus suggesting an essential role of PKC in MAPK3/1 activation. Collectively, these data present a novel self-sustaining mechanism comprised of MAPK3/1, PLA2G4, PKC and RAF1 for CDK4 activation leading to DNA synthesis in granulosa cells. Either FSH or EGF can activate the loop to activate CDK4 and initiate DNA synthesis; however, consistent with our previous findings, FSH effect seems to be mediated by EGF, which initiates the event by stimulating EGFR kinase. PMID:16525034

  11. A novel method for the purification of DNA by capturing nucleic acid and magnesium complexes on non-woven fabric filters under alkaline conditions for the gene diagnosis of tuberculosis by loop-mediated isothermal amplification (LAMP). (United States)

    Fukasawa, Tadashi; Oda, Naozumi; Wada, Yasunao; Tamaru, Aki; Fukushima, Yukari; Nakajima, Chie; Suzuki, Yasuhiko


    A novel method for purifying DNA from clinical samples based on the complex formation of DNA and magnesium ion (Mg(2+)) was developed for the detection of Mycobacterium tuberculosis. The formation of a DNA-Mg(2+) complex under alkaline conditions was observed by analyzing electrophoretic mobility reduction of DNA on agarose gel. The DNA-Mg(2+) complex increases the efficacy of DNA recovery from the sample solution on polyethylene terephthalate non-woven fabric (PNWF) filters. Among the various divalent metal cations, only Mg(2+) was associated with this effect. The applicability of DNA recovered on the PNWF filter was examined for the gene amplification method; loop-mediated isothermal amplification (LAMP). DNA on the PNWF filter could be used for the amplification of specific DNA fragments without elution from the filter. Using this method, DNA was directly purified from M. tuberculosis spiked sputum and examined by LAMP assay, showing a high sensitivity in comparison to the commercially available DNA extraction kit. These results indicated that the method developed in this study is useful for rapid gene diagnosis of tuberculosis.

  12. Detection of Schistosoma mansoni and Schistosoma haematobium DNA by Loop-Mediated Isothermal Amplification: Identification of Infected Snails from Early Prepatency (United States)

    Abbasi, Ibrahim; King, Charles H.; Muchiri, Eric M.; Hamburger, Joseph


    Monitoring post-control transmission of schistosomes by examining humans becomes less effective as infection rates among humans decrease. Molecular monitoring of prepatent schistosome infection in snails by the polymerase chain reaction (PCR) has been used for studying human-to-snail transmission, and snail prepatent infection rates were found to correspond to infection prevalence and average intensity in human populations contacting the sites studied. We have now developed loop-mediated isothermal amplification (LAMP) assays for identifying Schistosoma mansoni and S. haematobium to facilitate large-scale evaluation of post-intervention transmission potential. LAMP primers were designed based on the Sm1-7 and DraI repeated sequences of the corresponding schistosomes, and amplification by LAMP of these 121-basepair highly abundant sequences provided a detection sensitivity of 0.1 fg of genomic DNA. When these LAMP assays were applied for examining infected laboratory snails, it was possible to identify infection from the first day after exposure to miracidia. The potential advantages of these assays are discussed. PMID:20682894

  13. TNFα-senescence initiates a STAT-dependent positive feedback loop, leading to a sustained interferon signature, DNA damage, and cytokine secretion (United States)

    Kandhaya-Pillai, Renuka; Miro-Mur, Francesc; Alijotas-Reig, Jaume; Tchkonia, Tamara; Kirkland, James L.; Schwartz, Simo


    Cellular senescence is a cell fate program that entails essentially irreversible proliferative arrest in response to damage signals. Tumor necrosis factor-alpha (TNFα), an important pro-inflammatory cytokine secreted by some types of senescent cells, can induce senescence in mouse and human cells. However, downstream signaling pathways linking TNFα-related inflammation to senescence are not fully characterized. Using human umbilical vein endothelial cells (HUVECs) as a model, we show that TNFα induces permanent growth arrest and increases p21CIP1, p16INK4A, and SA-β-gal, accompanied by persistent DNA damage and ROS production. By gene expression profiling, we identified the crucial involvement of inflammatory and JAK/STAT pathways in TNFα-mediated senescence. We found that TNFα activates a STAT-dependent autocrine loop that sustains cytokine secretion and an interferon signature to lock cells into senescence. Furthermore, we show STAT1/3 activation is necessary for cytokine and ROS production during TNFα-induced senescence. However, inhibition of STAT1/3 did not rescue cells from proliferative arrest, but rather suppressed cell cycle regulatory genes and altered TNFα-induced senescence. Our findings suggest a positive feedback mechanism via the STAT pathway that sustains cytokine production and reveal a reciprocal regulatory role of JAK/STAT in TNFα-mediated senescence. PMID:29176033

  14. Sensitive Visual Detection of AHPND Bacteria Using Loop-Mediated Isothermal Amplification Combined with DNA-Functionalized Gold Nanoparticles as Probes.

    Directory of Open Access Journals (Sweden)

    Narong Arunrut

    Full Text Available Acute hepatopancreatic necrosis disease (AHPND is a component cause of early mortality syndrome (EMS of shrimp. In 2013, the causative agent was found to be unique isolates of Vibrio parahaemolyticus (VPAHPND that contained a 69 kbp plasmid (pAP1 carrying binary Pir-like toxin genes PirvpA and PirvpB. In Thailand, AHPND was first recognized in 2012, prior to knowledge of the causative agent, and it subsequently led to a precipitous drop in shrimp production. After VPAHPND was characterized, a major focus of the AHPND control strategy was to monitor broodstock shrimp and post larvae for freedom from VPAHPND by nucleic acid amplification methods, most of which required use of expensive and sophisticated equipment not readily available in a shrimp farm setting. Here, we describe a simpler but equally sensitive approach for detection of VPAHPND based on loop-mediated isothermal amplification (LAMP combined with unaided visual reading of positive amplification products using a DNA-functionalized, ssDNA-labled nanogold probe (AuNP. The target for the special set of six LAMP primers used was the VPAHPND PirvpA gene. The LAMP reaction was carried out at 65°C for 45 min followed by addition of the red AuNP solution and further incubation at 65°C for 5 min, allowing any PirvpA gene amplicons present to hybridize with the probe. Hybridization protected the AuNP against aggregation, so that the solution color remained red upon subsequent salt addition (positive test result while unprotected AuNP aggregated and underwent a color change from red to blue and eventually precipitated (negative result. The total assay time was approximately 50 min. The detection limit (100 CFU was comparable to that of other commonly-used methods for nested PCR detection of VPAHPND and 100-times more sensitive than 1-step PCR detection methods (104 CFU that used amplicon detection by electrophoresis or spectrophotometry. There was no cross reaction with DNA templates derived

  15. Construction of an Infectious cDNA Clone of Aichi Virus (a New Member of the Family Picornaviridae) and Mutational Analysis of a Stem-Loop Structure at the 5′ End of the Genome (United States)

    Sasaki, Jun; Kusuhara, Yasuhiro; Maeno, Yoshimasa; Kobayashi, Nobumichi; Yamashita, Teruo; Sakae, Kenji; Takeda, Naokazu; Taniguchi, Koki


    Aichi virus is the type species of a new genus, Kobuvirus, of the family Picornaviridae. In this study, we constructed a full-length cDNA clone of Aichi virus whose in vitro transcripts were infectious to Vero cells. During construction of the infectious cDNA clone, a novel sequence of 32 nucleotides was identified at the 5′ end of the genome. Computer-assisted prediction of the secondary structure of the 5′ end of the genome, including the novel sequence, suggested the formation of a stable stem-loop structure consisting of 42 nucleotides. The function of this stem-loop in virus replication was investigated using various site-directed mutants derived from the infectious cDNA clone. Our data indicated that correct folding of the stem-loop at the 5′ end of the positive strand, but not at the 3′ end of the negative strand, is critical for viral RNA replication. The primary sequence in the lower part of the stem was also suggested to be crucial for RNA replication. In contrast, nucleotide changes in the loop segment did not so severely reduce the efficiency of virus replication. A double mutant, in which both nucleotide stretches of the middle part of the stem were replaced by their complementary nucleotides, had efficient RNA replication and translation abilities but was unable to produce viruses. These results indicate that the stem-loop at the 5′ end of the Aichi virus genome is an element involved in both viral RNA replication and production of infectious virus particles. PMID:11483747

  16. 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.

  17. Diagnostic accuracy of loop-mediated isothermal amplification (LAMP for detection of Leishmania DNA in buffy coat from visceral leishmaniasis patients

    Directory of Open Access Journals (Sweden)

    Khan Md Gulam Musawwir


    Full Text Available Abstract Background Visceral leishmaniasis (VL remains as one of the most neglected tropical diseases with over 60% of the world’s total VL cases occurring in the Indian subcontinent. Due to the invasive risky procedure and technical expertise required in the classical parasitological diagnosis, the goal of the VL experts has been to develop noninvasive procedure(s applicable in the field settings. Several serological and molecular biological approaches have been developed over the last decades, but only a few are applicable in field settings that can be performed with relative ease. Recently, loop-mediated isothermal amplification (LAMP has emerged as a novel nucleic acid amplification method for diagnosis of VL. In this study, we have evaluated the LAMP assay using buffy coat DNA samples from VL patients in Bangladesh and compared its performance with leishmania nested PCR (Ln-PCR, an established molecular method with very high diagnostic indices. Methods Seventy five (75 parasitologically confirmed VL patients by spleen smear microcopy and 101 controls (endemic healthy controls −25, non-endemic healthy control-26, Tuberculosis-25 and other diseases-25 were enrolled in this study. LAMP assay was carried out using a set of four primers targeting L. donovani kinetoplast minicircle DNA under isothermal (62 °C conditions in a heat block. For Ln-PCR, we used primers targeting the parasite’s small-subunit rRNA region. Results LAMP assay was found to be positive in 68 of 75 confirmed VL cases, and revealed its diagnostic sensitivity of 90.7% (95.84-81.14, 95% CI, whereas all controls were negative by LAMP assay, indicating a specificity of 100% (100–95.43, 95% CI. The Ln-PCR yielded a sensitivity of 96% (98.96-87.97, 95% CI and a specificity of 100% (100–95.43, 95% CI. Conclusion High diagnostic sensitivity and excellent specificity were observed in this first report of LAMP diagnostic evaluation from Bangladesh. Considering its many fold

  18. Loop-to-loop coupling.

    Energy Technology Data Exchange (ETDEWEB)

    Warne, Larry Kevin; Lucero, Larry Martin; Langston, William L.; Salazar, Robert Austin; Coleman, Phillip Dale; Basilio, Lorena I.; Bacon, Larry Donald


    This report estimates inductively-coupled energy to a low-impedance load in a loop-to-loop arrangement. Both analytical models and full-wave numerical simulations are used and the resulting fields, coupled powers and energies are compared. The energies are simply estimated from the coupled powers through approximations to the energy theorem. The transmitter loop is taken to be either a circular geometry or a rectangular-loop (stripline-type) geometry that was used in an experimental setup. Simple magnetic field models are constructed and used to estimate the mutual inductance to the receiving loop, which is taken to be circular with one or several turns. Circuit elements are estimated and used to determine the coupled current and power (an equivalent antenna picture is also given). These results are compared to an electromagnetic simulation of the transmitter geometry. Simple approximate relations are also given to estimate coupled energy from the power. The effect of additional loads in the form of attached leads, forming transmission lines, are considered. The results are summarized in a set of susceptibility-type curves. Finally, we also consider drives to the cables themselves and the resulting common-to-differential mode currents in the load.

  19. Development of a Loop-Mediated Isothermal Amplification Method for Detecting Streptococcus equi subsp. zooepidemicus and Analysis of Its Use with Three Simple Methods of Extracting DNA from Equine Respiratory Tract Specimens (United States)

    KINOSHITA, Yuta; NIWA, Hidekazu; KATAYAMA, Yoshinari


    ABSTRACT Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) is a dominant pathogenic bacterium in equine pneumonia. We developed a specific loop-mediated isothermal amplification (LAMP) method, which targets the gene encoding sorbitol-6-phosphate 2-dehydrogenase (sorD), for detecting S. zooepidemicus and examined the clinical efficacies of its use in combination with each of 3 DNA extraction methods easily used by veterinary practitioners, namely the Loopamp PURE DNA Extraction Kit, InstaGene Matrix and a conventional boiling method. The LAMP method plus the Loopamp PURE DNA Extraction Kit gave higher rates of positivity than the other combinations in both clinical and spiked samples containing clinically significant concentrations (>1 × 104 CFU/ml) of S. zooepidemicus. PMID:24871644

  20. Analysis of full-length mitochondrial DNA D-loop sequences from Macaca fascicularis of different geographical origin reveals novel haplotypes. (United States)

    Badhan, Anjna; Eichstaedt, Christina A; Almond, Neil M; Knapp, Leslie A; Rose, Nicola J


    Cynomolgus macaques are indigenous to Asia occupying a range of geographical areas. A non-indigenous population established on Mauritius approximately 500 years ago. Mauritian cynomolgus macaques are recognised as having low genetic diversity compared to Indonesian macaques, from which they originated. As cynomolgus macaques are widely used as a biomedical model, there have been many studies of their genetic relationships. However, population diversity and relationships have only been assessed through analysis of either the hypervariable region I or II separately within the D-loop region of the mitochondrial genome in these macaques. Using sequencing, we defined haplotypes encompassing the full D-loop sequence for Mauritian and Indonesian cynomolgus macaques. We evaluated the haplotype relationships by constructing a median-joining network based on full-length D-loop sequences, which has not been reported previously. Our data allow a complete D-loop haplotype, including a hereto unreported polymorphic region, to be defined to aid the resolution of populations of cynomolgus macaques and which highlights the value in analysing both D-loop hypervariable regions in concert. © 2015 The Authors. Journal of Medical Primatology Published by John Wiley & Sons Ltd.

  1. High levels of genetic variability and differentiation in hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes populations revealed by PCR-RFLP analysis of the mitochondrial DNA D-loop region

    Directory of Open Access Journals (Sweden)

    Sabuj Kanti Mazumder


    Full Text Available The hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes is an important anadromous clupeid species from the Western division of the Indo-Pacific region. It constitutes the largest single fishable species in Bangladesh. Information on genetic variability and population structure is very important for both management and conservation purposes. Past reports on the population structure of T. ilisha involving morphometric, allozyme and RAPD analyses are contradictory. We examined genetic variability and divergence in two riverine (the Jamuna and the Meghna, two estuarine (Kuakata and Sundarbans and one marine (Cox's Bazar populations of T. ilisha by applying PCR-RFLP analysis of the mtDNA D-loop region. The amplified PCR products were restricted with four restriction enzymes namely, XbaI, EcoRI, EcoRV, and HaeIII. High levels of haplotype and gene diversity within and significant differentiations among, populations of T. ilisha were observed in this study. Significant F ST values indicated differentiation among the river, estuary and marine populations. The UPGMA dendrogram based on genetic distance resulted in two major clusters, although, these were subsequently divided into three, corresponding to the riverine, estuarine and marine populations. The study underlines the usefulness of RFLP of mtDNA D-loop region as molecular markers, and detected at least two differentiated populations of T. ilisha in Bangladesh waters.

  2. R-loops: targets for nuclease cleavage and repeat instability. (United States)

    Freudenreich, Catherine H


    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.

  3. Alternative loop rings

    CERN Document Server

    Goodaire, EG; Polcino Milies, C


    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

  4. Analytical sensitivity and specificity of a loop-mediated isothermal amplification (LAMP) kit prototype for detection of Trypanosoma cruzi DNA in human blood samples (United States)

    Besuschio, Susana A.; Llano Murcia, Mónica; Benatar, Alejandro F.; Monnerat, Severine; Cruz, Israel; Picado, Albert; Curto, María de los Ángeles; Kubota, Yutaka; Wehrendt, Diana P.; Pavia, Paula; Mori, Yasuyoshi; Puerta, Concepción; Ndung'u, Joseph M.


    This study aimed to assess analytical parameters of a prototype LAMP kit that was designed for detection of Trypanosoma cruzi DNA in human blood. The prototype is based on the amplification of the highly repetitive satellite sequence of T.cruzi in microtubes containing dried reagents on the inside of the caps. The reaction is carried out at 65°C during 40 minutes. Calcein allows direct detection of amplified products with the naked eye. Inclusivity and selectivity were tested in purified DNA from Trypanosoma cruzi stocks belonging to the six discrete typing units (DTUs), in DNA from other protozoan parasites and in human DNA. Analytical sensitivity was estimated in serial dilutions of DNA samples from Sylvio X10 (Tc I) and CL Brener (Tc VI) stocks, as well as from EDTA-treated or heparinized blood samples spiked with known amounts of cultured epimastigotes (CL Brener). LAMP sensitivity was compared after DNA extraction using commercial fiberglass columns or after “Boil & Spin” rapid preparation. Moreover, the same DNA and EDTA-blood spiked samples were subjected to standardized qPCR based on the satellite DNA sequence for comparative purposes. A panel of peripheral blood specimens belonging to Chagas disease patients, including acute, congenital, chronic and reactivated cases (N = 23), as well as seronegative controls (N = 10) were evaluated by LAMP in comparison to qPCR. LAMP was able to amplify DNAs from T. cruzi stocks representative of the six DTUs, whereas it did not amplify DNAs from Leishmania sp, T. brucei sp, T. rangeli KPN+ and KPN-, P. falciparum and non-infected human DNA. Analytical sensitivity was 1x10-2 fg/μL of both CL Brener and Sylvio X10 DNAs, whereas qPCR detected up to 1x 10−1 fg/μL of CL Brener DNA and 1 fg/μl of Sylvio X10 DNA. LAMP detected 1x10-2 parasite equivalents/mL in spiked EDTA blood and 1x10-1 par.eq/mL in spiked heparinized blood using fiberglass columns for DNA extraction, whereas qPCR detected 1x10-2 par.eq./mL in EDTA

  5. 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.

    , Foster City, CA, USA). Representative sequences have been deposited in GenBank, with accession numbers JN398671- JN399010. Data analyses DNA sequences were edited with the program BioEdit (version 7.0.1, Hall 1999) and aligned using the Clustal.... Molecular diversity indices, such as transitions, transversions, substitutions, and indels were obtained using program Arlequin version 3.11 (Excoffier et al. 2005). The aligned sequences were used to analyze the population structure and genetic variation...

  6. Genetic variation in Yellowfin Tuna Thunnus albacares (Bonnaterre, 1788) along Indian coast using PCR-RFLP analysis of mitochondrial DNA D–Loop region

    Digital Repository Service at National Institute of Oceanography (India)

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

    . 26 IJSR - INTERNATIONAL JOURNAL OF SCIENTIFIC RESEARCH Volume : 3 | Issue : 1 | January 2014 • ISSN No 2277 - 8179 Research Paper Data Analyses The mtDNA haplotypes (mitotypes) generated by each restric-tion endonuclease were designated by a... - INTERNATIONAL JOURNAL OF SCIENTIFIC RESEARCH 25 Volume : 3 | Issue : 1 | January 2014 • ISSN No 2277 - 8179 Research Paper Biology Swaraj Priyaranjan Kunal National Institute of Oceanography, Dona Paula, Goa 403004, India Girish Kumar National Institute...

  7. 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


    -2d-restricted cytotoxic T lymphocyte (CTL) epitope. In an attempt to improve the immunogenicity of V3 in DNA vaccines, a plasmid expressing MN V3 as a fusion protein with the highly immunogenic middle (pre-S2 + S) surface antigen of hepatitis B virus (HBsAg) was constructed. Epidermal inoculation......The gp120-derived V3 loop of HIV-1 is involved in co-receptor interaction, it guides cell tropism, and contains an epitope for antibody neutralization. Thus, HIV-1 V3 is an attractive vaccine candidate. The V3 of the MN strain (MN V3) contains both B- and T-cell epitopes, including a known mouse H...... by gene gun was used for genetic immunization in a mouse model. Antibody and CTL responses to MN V3 and HBsAg were measured and compared with the immune responses obtained after vaccination with plasmids encoding the complete HIV-1 MN gp160 and HBsAg (pre-S2 + S), respectively. DNA vaccination...

  8. 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.


    -2d-restricted cytotoxic T lymphocyte (CTL) epitope. In an attempt to improve the immunogenicity of V3 in DNA vaccines, a plasmid expressing MN V3 as a fusion protein with the highly immunogenic middle (pre-S2+S) surface antigen of hepatitis B virus (HBsAg) was constructed. Epidermal inoculation......The gp120-derived V3 loop of HIV-1 is involved in co-receptor interaction, it guides cell tropism, and contains an epitope for antibody neutralization. Thus, HIV-1 V3 is an attractive vaccine candidate. The V3 of the MN strain (MN V3) contains both B- and T-cell epitopes, including a known mouse H...... by gene gun was used for genetic immunization in a mouse model. Antibody and CTL responses to MN V3 and HBsAg were measured and compared with the immune responses obtained after vaccination with plasmids encoding the complete HIV-1 MN gp160 and HBsAg (pre-S2+S), respectively. DNA vaccination with the HIV...

  9. A comparison of the reliability of two gene targets in loop-mediated isothermal amplification assays for detecting leptospiral DNA in canine urine. (United States)

    Gentilini, Fabio; Zanoni, Renato Giulio; Zambon, Elisa; Turba, Maria Elena


    We compared 2 novel loop-mediated isothermal amplification (LAMP) assays that target either the 16S ribosomal RNA ( rrs) gene or the gene encoding a 32-kDa leptospiral lipoprotein ( lipL32) in order to assess the effect of the target on the accuracy of the LAMP assays. The most sensitive assay was the rrs assay with a limit of detection (LOD) of 1.2 × 101 genome equivalents per reaction. The novel lipL32 assay showed an LOD of 1.2 × 102 genome equivalents per reaction. Both assays showed adequate specificity when tested against a collection of bacteria commonly found in voided canine urine. However, when field samples were assayed, the rrs assays gave many false-positive results and a poor positive predictive value of 8.33%. In conclusion, even if the LAMP assay is used in low prevalence areas, the lipL32 assay would be preferable. Conversely, the higher analytical sensitivity of the rrs assay could be effectively used as a screening test in endemic areas with high disease prevalence, followed by confirmation of the positive results using the lipL32 assay.

  10. DNA methylation of germ-cell-specific basic helix-loop-helix (HLH) transcription factors, Sohlh2 and Figlα during gametogenesis. (United States)

    Pan, Bo; Chao, Huhe; Chen, Bo; Zhang, Lianjun; Li, Lan; Sun, Xiaofeng; Shen, Wei


    Regulation of germ-cell-specific transcription is essential for the differentiation and other physiological processes of germ cells. Germ-cell-specific transcription factors, Sohlh2 and Figla, play key roles in gametogenesis. To elucidate whether an epigenetic mechanism is involved in the controlled expression of Sohlh2 and Figlα, we examined the dynamics of DNA methylation at two gene loci. Results showed changes in methylation patterns in the promoter regions of both genes during the period of germ cell differentiation, while the methylation patterns in first exons and first introns (near the transcription initiation sites) remained constant. The methylation reprogramming at the cytosine-phosphate-guanine (CpG) locus in the Figlα promoters (P1: -812 to -568 bp and P2: -692 to -438 bp) and in the Sohlh2 promoter (sohlh2-P: -202 to 173 bp) was found to correlate with the expression of Figlα and Sohlh2 transcripts, respectively. Data therefore suggested that a dynamic DNA CpG methylation in the Sohlh2 and Figlα promoters, but not in the intron and exon sequences, is linked to the regulation of gene expressions, even though CpG islands are also present in their introns or exons. © The Author 2011. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved.

  11. Analysis of a polycytosine tract and heteroplasmic length variation in the mitochondrial DNA D-loop of patients with diabetes, MELAS syndrome and race-matched controls. (United States)

    Gill-Randall, R; Sherratt, E J; Thomas, A W; Gagg, J W; Lee, A; Alcolado, J C


    The T to C substitution at position 16189 nt of the human mitochondrial genome has been associated with the development of heteroplasmic length variation in the control region of mtDNA. Previous reports have suggested that this defect may be associated with the development of other pathogenic mtDNA mutations, including the diabetogenic A to G mutation in the tRNALEU(UUR). Recently the 16189 nt variant has also been associated with insulin resistance in British adult men. In order to investigate these associations further we studied 23 patients with the 3243 nt mutation, 150 patients with Type 2 diabetes and 149 non-diabetic controls. The region around 16189 nt was investigated by polymerase chain reaction-restriction fragment length polymorphism analysis and automated sequencing. We find that the T to C substitution at 16189 nt is associated with heteroplasmic length variation only when the resultant polycytosine tract is not interrupted by a second mutation. There are no significant differences in the prevalence of the 16189 nt variant or heteroplasmic length variation between patients with the 3243 nt mutation, patients with Type 2 diabetes or race-matched normal controls. We conclude that these variants are likely to represent normal polymorphisms and that previously reported associations should be treated with caution unless they can be replicated in other populations.

  12. Approximate Loop Unrolling


    Rodriguez-Cancio, Marcelino; Combemale, Benoit; Baudry, Benoit


    We introduce Approximate Unrolling, a loop optimization that reduces execution time and energy consumption, exploiting the existence of code regions that can endure some degree of approximation while still producing acceptable results. This work focuses on a specific kind of forgiving region: counted loops that map a given functions over the elements of an array. Approximate Unrolling transforms loops in a similar way Loop Unrolling does. However, unlike its exact counterpart, our optimizatio...

  13. Blind Loop Syndrome (United States)

    ... breeding ground for bacteria. The bacteria may produce toxins as well as block the absorption of nutrients. The greater the length of small bowel involved in the blind loop, the greater the chance of bacterial overgrowth. What triggers blind loop syndrome? Blind loop ...

  14. The first detection of Toxoplasma gondii DNA in environmental air samples using gelatine filters, real-time PCR and loop-mediated isothermal (LAMP) assays: qualitative and quantitative analysis. (United States)

    Lass, Anna; Szostakowska, Beata; Korzeniewski, Krzysztof; Karanis, Panagiotis


    Toxoplasma gondii infections are acquired through the ingestion of oocysts present in the environment. However, there is no data about their occurrence in the air or about airborne transmission of these infections. In the present paper, we report on the identification of T. gondii using rapid molecular detection methods, supported by microscopic analysis, in environmental air samples. A total of 71 samples were collected, using gelatine filters, from kitchen gardens, recreational areas and sandpits located in northern and north-eastern Poland. Material recovered from the filters was analysed using real-time PCR and loop-mediated isothermal assays targeting the T. gondii B1 gene. Toxoplasma gondii DNA was found in two samples, as confirmed by both molecular assays. Genotyping at the SAG2 locus showed Toxoplasma SAG2 type I. Moreover, the presence of T. gondii oocysts was confirmed in one of the positive samples with the use of microscopy. The results showed that T. gondii may be present in environmental air samples and that respiratory tract infections may play a role in the high prevalence of toxoplasmosis in humans and animals. To the best of our knowledge, this is the first epidemiological evidence that oro-fecal and foodborne toxoplasmosis may be traceable to an airborne respiratory origin and that this may represent a new, previously unknown transmission route for this disease.

  15. Force distribution in a semiflexible loop

    CERN Document Server

    Waters, James T


    Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in terms of free energy, an average quantity, but it may also be impacted by local fluctuating forces acting within these systems. The full distribution of these forces can thus give us insights into mechanochemistry beyond the predictive capability of thermodynamics. In this paper, we study the force exerted by an inextensible semiflexible polymer constrained in a looped state. By using a novel simulation method termed "phase-space sampling", we generate the equilibrium distribution of chain conformations in both position and momentum space. We compute the constraint forces between the two ends of the loop in this chain ensemble using Lagrangian mechanics, and show that the mean of these forces is equal to the thermodynamic force. By analyzing kinetic and potential contribution...

  16. Mitotic chromosome compaction via active loop extrusion (United States)

    Goloborodko, Anton; Imakaev, Maxim; Marko, John; Mirny, Leonid; MIT-Northwestern Team

    During cell division, two copies of each chromosome are segregated from each other and compacted more than hundred-fold into the canonical X-shaped structures. According to earlier microscopic observations and the recent Hi-C study, chromosomes are compacted into arrays of consecutive loops of ~100 kilobases. Mechanisms that lead to formation of such loop arrays are largely unknown. Here we propose that, during cell division, chromosomes can be compacted by enzymes that extrude loops on chromatin fibers. First, we use computer simulations and analytical modeling to show that a system of loop-extruding enzymes on a chromatin fiber self-organizes into an array of consecutive dynamic loops. Second, we model the process of loop extrusion in 3D and show that, coupled with the topo II strand-passing activity, it leads to robust compaction and segregation of sister chromatids. This mechanism of chromosomal condensation and segregation does not require additional proteins or specific DNA markup and is robust against variations in the number and properties of such loop extruding enzymes. Work at NU was supported by the NSF through Grants DMR-1206868 and MCB-1022117, and by the NIH through Grants GM105847 and CA193419. Work at MIT was supported by the NIH through Grants GM114190 R01HG003143.

  17. The Arabidopsis Basic/Helix-Loop-Helix Transcription Factor Family

    National Research Council Canada - National Science Library

    Gabriela Toledo-Ortiz; Enamul Huq; Peter H. Quail


    The basic/helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that bind as dimers to specific DNA target sites and that have been well characterized in nonplant eukaryotes as important regulatory components...

  18. Loop-mediated isothermal amplification using self-avoiding molecular recognition systems and antarctic thermal sensitive uracil-DNA-glycosylase for detection of nucleic acid with prevention of carryover contamination. (United States)

    Wang, Yi; Liu, Dongxin; Deng, Jianping; Wang, Yan; Xu, Jianguo; Ye, Changyun


    Loop-mediated isothermal amplification (LAMP) is the most popular technique to amplify nucleic acid sequence without the use of temperature cycling. However, LAMP is often confounded by false-positive results, arising from interactions between (hetero-dimer) or within (self-dimerization) primers, off-target hybrids and carryover contaminants. Here, we devised a new LAMP technique that is self-avoiding molecular recognition system (SAMRS) components and antarctic thermal sensitive uracil-DNA-glycosylase (AUDG) enzyme-assisted, termed AUDG-SAMRS-LAMP. Incorporating SAMRS components into 3'-ends of LAMP primers can improve assay's specificity, which completely prevents the non-specific amplification yielding from off-target hybrids and undesired interactions between or within primers. Adding AUDG into reaction mixtures can effectively eliminate the false-positive results arising from carryover contamination, thus the genuine positive reactions are generated from the amplification of target templates. Furthermore, AUDG-SAMRS-LAMP results are confirmed using a new analysis strategy, which is developed for detecting LAMP amplicons by lateral flow biosensor (LFB). Only a single labeled primer is required in the analysis system, thus the false positive results arising from hybridization (the labeled primer and probe, or between two labeled primers) are avoided. Hence, the SAMRS components, AUDG and LFB convert traditional LAMP from a technique suited for the research laboratory into one that has practical value in the field of diagnosis. Human Tuberculosis (TB) is caused by infection with members of Mycobacterium tuberculosis complex (MTC), which are detected by the AUDG-SAMRS-LAMP technique to demonstrate the availability of target analysis. The proof-of-concept method can be reconfigured to detect various nucleic acids by redesigning the specific primers. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Top3-Rmi1 dissolve Rad51-mediated D loops by a topoisomerase-based mechanism. (United States)

    Fasching, Clare L; Cejka, Petr; Kowalczykowski, Stephen C; Heyer, Wolf-Dietrich


    The displacement loop (D loop) is a DNA strand invasion product formed during homologous recombination. Disruption of nascent D loops prevents recombination, and during synthesis-dependent strand annealing (SDSA), disruption of D loops extended by DNA polymerase ensures a non-crossover outcome. The proteins implicated in D loop disruption are DNA motor proteins/helicases that act by moving DNA junctions. Here we report that D loops can also be disrupted by DNA topoisomerase 3 (Top3), and this disruption depends on Top3's catalytic activity. Yeast Top3 specifically disrupts D loops mediated by yeast Rad51/Rad54; protein-free D loops or D loop mediated by bacterial RecA protein or human RAD51/RAD54 resist dissolution. Also, the human Topoisomerase IIIa-RMI1-RMI2 complex is capable of dissolving D loops. Consistent with genetic data, we suggest that the extreme growth defect and hyper-recombination phenotype of Top3-deficient yeast cells is partially a result of unprocessed D loops. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Introduction to Loop Heat Pipes (United States)

    Ku, Jentung


    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.

  1. Blind Loop Syndrome (United States)

    ... of tissue that protrude through the intestinal wall (diverticulosis) Certain medical conditions, including Crohn's disease, radiation enteritis, ... History of radiation therapy to the abdomen Diabetes Diverticulosis of the small intestine A blind loop can ...

  2. When DNA Topology Turns Deadly - RNA Polymerases Dig in Their R-Loops to Stand Their Ground: New Positive and Negative (Super)Twists in the Replication-Transcription Conflict. (United States)

    Kuzminov, Andrei


    Head-on replication-transcription conflict is especially bitter in bacterial chromosomes, explaining why actively transcribed genes are always co-oriented with replication. The mechanism of this conflict remains unclear, besides the anticipated accumulation of positive supercoils between head-on-conflicting polymerases. Unexpectedly, experiments in bacterial and human cells reveal that head-on replication-transcription conflict induces R-loops, indicating hypernegative supercoiling [(-)sc] in the region - precisely the opposite of that assumed. Further, as a result of these R-loops, both replication and transcription in the affected region permanently stall, so the failure of R-loop removal in RNase H-deficient bacteria becomes lethal. How hyper(-)sc emerges in the middle of a positively supercoiled chromosomal domain is a mystery that requires rethinking of topoisomerase action around polymerases. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. The Cinderella loop project (United States)

    Schmelz, J. T.; Beene, J.; Coyle, T.; Douglass, J.; Nasraoui, K.; O'Connor, J.; Roames, J.; Scott, M.


    The solar loop that formed off the northeast limb of the Sun on 1999 November 6 (a.k.a. the Cinderella loop) is one of the few examples of a loop on the limb observed with all three of the following imaging instruments: the Transition Region and Coronal Explorer (TRACE), the SOHO Extreme-ultraviolet Imaging Telescope (EIT), and the Yohkoh Soft X-ray Telescope (SXT). In this project we investigate the temperature differences that result when examining the Cinderella loop with one instrument compared with another. For example, what temperature differences result from the increased spatial resolution between the two EUV imagers? More specifically, given that TRACE and EIT have almost identical temperature response to coronal plasma, does the different spatial resolution of TRACE (with 0.5″ pixels) and EIT (with 2.6″ pixels) produce statistically different results? We find that the answer is no, and that our results do not change after background subtraction. In addition, the spatial resolution of EIT and SXT is similar, but the temperature responses of the two instruments are quite different. The two instruments do not seem to be viewing the same loop strands, and the plasma temperature differences are significant.

  4. Closing global material loops

    DEFF Research Database (Denmark)

    Prosman, Ernst-Jan; Wæhrens, Brian Vejrum; Liotta, Giacomo


    Replacing virgin materials with waste materials, a practice known as Industrial Symbiosis (IS), has been identified as a key strategy for closing material loops. This article adopts a critical view on geographic proximity and external coordinators – two key enablers of IS. By ‘uncovering’ a case...... for geographic proximity and external coordinators. In doing so, our insights into firm-level challenges of long-distance IS exchanges contribute to closing global material loops by increasing the number of potential circular pathways....

  5. Hidden-loop colostomy. (United States)

    Rombeau, J L; Turnbul, R B


    Records of 15 patients having hidden-loop colostomies were reviewed. All patients had metastatic colonic cancers with impending obstructions. Six colostomies were subsequently opened because of obstructions due to cancer. All colostomy openings were done using local anesthesia in the emergency room. This technique prevented six major celiotomies and provided additional time of living without a stoma. There were two postoperative stomal prolapses, one of which necessitated reoperation. A hidden-loop colostomy is easily constructed and readily opened. It should be considered at celiotomy for selected patients who have metastatic colonic cancer with impending obstruction.

  6. Loop Quantum Gravity

    Directory of Open Access Journals (Sweden)

    Rovelli Carlo


    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.


    African Journals Online (AJOL)

    Then the right ureter was laparoscopically spa- tulated and anastomosed to the ileostomy opening using interrupted 4/0 vicryl sutures. After finishing half the circumference of the anastomotic line, a 4 Fr. ureteric catheter was introduced through the external stoma of the loop up to the site of the anastomosis with the aid of a ...

  8. Improving Loop Dependence Analysis

    DEFF Research Database (Denmark)

    Jensen, Nicklas Bo; Karlsson, Sven


    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...

  9. Top3-Rmi1 dissolve Rad51-mediated D-loops by a topoisomerase-based mechanism (United States)

    Fasching, Clare L.; Cejka, Petr; Kowalczykowski, Stephen C.; Heyer, Wolf-Dietrich


    Summary The displacement loop (D-loop) is the DNA strand invasion product formed during homologous recombination. Disruption of nascent D-loops represents a mechanism of anti-recombination. During Synthesis-Dependent Strand Annealing D-loop disruption after extension of the invading strand is an integral step of the pathway and ensures a non-crossover outcome. The proteins implicated in D-loop disruption are DNA motor proteins/helicases acting by migrating DNA junctions. Here we report an unanticipated mechanism of D-loop dissolution mediated by DNA topoisomerase 3 (Top3) and dependent on its catalytic activity. D-loop dissolution catalyzed by yeast Top3 is highly specific for yeast Rad51/Rad54-mediated D-loops, whereas protein-free D-loops or D-loop mediated by bacterial RecA protein or human RAD51/RAD54 resist dissolution. Also the human Topoisomerase IIIα-RMI1–RMI2 complex is capable of dissolving D-loops. Consistent with genetic data, we suggest that the extreme growth defect and hyper-recombination phenotype of Top3-deficient yeast cells is in part a result of unprocessed D-loops. PMID:25699708

  10. Loop Quantum Cosmology. (United States)

    Bojowald, Martin


    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.

  11. PAR Loop Schedule Review

    Energy Technology Data Exchange (ETDEWEB)

    Schaffer, Jr.; W.F.


    The schedule for the installation of the PAR slurry loop experiment in the South Facility of the ORR has been reviewed and revised. The design, fabrications and Installation is approximately two weeks behind schedule at this time due to many factors; however, indications are that this time can be made up. Design is estimated to be 75% complete, fabrication 32% complete and installation 12% complete.

  12. Loop Quantum Cosmology

    Directory of Open Access Journals (Sweden)

    Bojowald Martin


    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.

  13. Loop Quantum Cosmology

    Directory of Open Access Journals (Sweden)

    Bojowald Martin


    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.

  14. Cosmic string loop microlensing (United States)

    Bloomfield, Jolyon K.; Chernoff, David F.


    Cosmic superstring loops within the galaxy microlens background point sources lying close to the observer-string line of sight. For suitable alignments, multiple paths coexist and the (achromatic) flux enhancement is a factor of two. We explore this unique type of lensing by numerically solving for geodesics that extend from source to observer as they pass near an oscillating string. We characterize the duration of the flux doubling and the scale of the image splitting. We probe and confirm the existence of a variety of fundamental effects predicted from previous analyses of the static infinite straight string: the deficit angle, the Kaiser-Stebbins effect, and the scale of the impact parameter required to produce microlensing. Our quantitative results for dynamical loops vary by O(1) factors with respect to estimates based on infinite straight strings for a given impact parameter. A number of new features are identified in the computed microlensing solutions. Our results suggest that optical microlensing can offer a new and potentially powerful methodology for searches for superstring loop relics of the inflationary era.

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

    KAUST Repository

    Messih, Mario Abdel


    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) data are available at Bioinformatics online.

  16. Autosomal mutations affecting Y chromosome loops in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Petrucci Romano


    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.

  17. Nascent Connections: R-Loops and Chromatin Patterning. (United States)

    Chédin, Frédéric


    RNA molecules, such as long noncoding RNAs (lncRNAs), have critical roles in regulating gene expression, chromosome architecture, and the modification states of chromatin. Recent developments suggest that RNA also influences gene expression and chromatin patterns through the interaction of nascent transcripts with their DNA template via the formation of co-transcriptional R-loop structures. R-loop formation over specific, conserved, hotspots occurs at thousands of genes in mammalian genomes and represents an important and dynamic feature of mammalian chromatin. Here, focusing primarily on mammalian systems, I describe the accumulating connections and possible mechanisms linking R-loop formation and chromatin patterning. The possible contribution of aberrant R-loops to pathological conditions is also discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Coupled dual loop absorption heat pump (United States)

    Sarkisian, Paul H.; Reimann, Robert C.; Biermann, Wendell J.


    A coupled dual loop absorption system which utilizes two separate complete loops. Each individual loop operates at three temperatures and two pressures. This low temperature loop absorber and condenser are thermally coupled to the high temperature loop evaporator, and the high temperature loop condenser and absorber are thermally coupled to the low temperature generator.

  19. Wilson loops as precursors

    Energy Technology Data Exchange (ETDEWEB)

    Susskind, Leonard [Department of Physics, Stanford University, Stanford, California 94305-4060 (United States); Toumbas, Nicolaos [Department of Physics, Stanford University, Stanford, California 94305-4060 (United States)


    There is substantial evidence that string theory on AdS{sub 5}xS{sub 5} is a holographic theory in which the number of degrees of freedom scales as the area of the boundary in Planck units. Precisely how the theory can describe bulk physics using only surface degrees of freedom is not well understood. A particularly paradoxical situation involves an event deep in the interior of the bulk space. The event must be recorded in the (Schroedinger picture) state vector of the boundary theory long before a signal, such as a gravitational wave, can propagate from the event to the boundary. In a previous paper with Polchinski, we argued that the ''precursor'' operators which carry information stored in the wave during the time when it vanishes in a neighborhood of the boundary are necessarily non-local. In this paper we argue that the precursors cannot be products of local gauge invariant operators such as the energy momentum tensor. In fact gauge theories have a class of intrinsically non-local operators which cannot be built from local gauge invariant objects. These are the Wilson loops. We show that the precursors can be identified with Wilson loops whose spatial size is dictated by the UV-IR connection. (c) 2000 The American Physical Society.

  20. High temperature storage loop :

    Energy Technology Data Exchange (ETDEWEB)

    Gill, David Dennis; Kolb, William J.


    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

  1. 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


    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

  2. SIRT7 and the DEAD-box helicase DDX21 cooperate to resolve genomic R loops and safeguard genome stability. (United States)

    Song, Chenlin; Hotz-Wagenblatt, Agnes; Voit, Renate; Grummt, Ingrid


    R loops are three-stranded nucleic acid structures consisting of an RNA:DNA heteroduplex and a "looped-out" nontemplate strand. As aberrant formation and persistence of R loops block transcription elongation and cause DNA damage, mechanisms that resolve R loops are essential for genome stability. Here we show that the DEAD (Asp-Glu-Ala-Asp)-box RNA helicase DDX21 efficiently unwinds R loops and that depletion of DDX21 leads to accumulation of cellular R loops and DNA damage. Significantly, the activity of DDX21 is regulated by acetylation. Acetylation by CBP inhibits DDX21 activity, while deacetylation by SIRT7 augments helicase activity and overcomes R-loop-mediated stalling of RNA polymerases. Knockdown of SIRT7 leads to the same phenotype as depletion of DDX21 (i.e., increased formation of R loops and DNA double-strand breaks), indicating that SIRT7 and DDX21 cooperate to prevent R-loop accumulation, thus safeguarding genome integrity. Moreover, DDX21 resolves estrogen-induced R loops on estrogen-responsive genes in breast cancer cells, which prevents the blocking of transcription elongation on these genes. © 2017 Song et al.; Published by Cold Spring Harbor Laboratory Press.

  3. Sequence Affects the Cyclization of DNA Minicircles. (United States)

    Wang, Qian; Pettitt, B Montgomery


    Understanding how the sequence of a DNA molecule affects its dynamic properties is a central problem affecting biochemistry and biotechnology. The process of cyclizing short DNA, as a critical step in molecular cloning, lacks a comprehensive picture of the kinetic process containing sequence information. We have elucidated this process by using coarse-grained simulations, enhanced sampling methods, and recent theoretical advances. We are able to identify the types and positions of structural defects during the looping process at a base-pair level. Correlations along a DNA molecule dictate critical sequence positions that can affect the looping rate. Structural defects change the bending elasticity of the DNA molecule from a harmonic to subharmonic potential with respect to bending angles. We explore the subelastic chain as a possible model in loop formation kinetics. A sequence-dependent model is developed to qualitatively predict the relative loop formation time as a function of DNA sequence.

  4. Loop Quantum Gravity. (United States)

    Rovelli, Carlo


    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.

  5. Loop Quantum Gravity

    Directory of Open Access Journals (Sweden)

    Rovelli Carlo


    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.

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

    Directory of Open Access Journals (Sweden)

    Martin Juliette


    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

  7. TRF1 and TRF2 differentially modulate Rad51-mediated telomeric and nontelomeric displacement loop formation in vitro. (United States)

    Bower, Brian D; Griffith, Jack D


    A growing body of literature suggests that the homologous recombination/repair (HR) pathway cooperates with components of the shelterin complex to promote both telomere maintenance and nontelomeric HR. This may be due to the ability of both HR and shelterin proteins to promote strand invasion, wherein a single-stranded DNA (ssDNA) substrate base pairs with a homologous double-stranded DNA (dsDNA) template displacing a loop of ssDNA (D-loop). Rad51 recombinase catalyzes D-loop formation during HR, and telomere repeat binding factor 2 (TRF2) catalyzes the formation of a telomeric D-loop that stabilizes a looped structure in telomeric DNA (t-loop) that may facilitate telomere protection. We have characterized this functional interaction in vitro using a fluorescent D-loop assay measuring the incorporation of Cy3-labeled 90-nucleotide telomeric and nontelomeric substrates into telomeric and nontelomeric plasmid templates. We report that preincubation of a telomeric template with TRF2 inhibits the ability of Rad51 to promote telomeric D-loop formation upon preincubation with a telomeric substrate. This suggests Rad51 does not facilitate t-loop formation and suggests a mechanism whereby TRF2 can inhibit HR at telomeres. We also report a TRF2 mutant lacking the dsDNA binding domain promotes Rad51-mediated nontelomeric D-loop formation, possibly explaining how TRF2 promotes nontelomeric HR. Finally, we report telomere repeat binding factor 1 (TRF1) promotes Rad51-mediated telomeric D-loop formation, which may facilitate HR-mediated replication fork restart and explain why TRF1 is required for efficient telomere replication.

  8. 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 context by reducing to symmetric models like cosmological ones. This leads to several applications where loop effects play a significant role when one is sensitive to the quantum regime. As a consequence, the structure of and the approach to ...

  9. Protein Loop Closure Using Orientational Restraints from NMR Data (United States)

    Tripathy, Chittaranjan; Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    Protein loops often play important roles in biological functions such as binding, recognition, catalytic activities and allosteric regulation. Modeling loops that are biophysically sensible is crucial to determining the functional specificity of a protein. A variety of algorithms ranging from robotics-inspired inverse kinematics methods to fragmentbased homology modeling techniques have been developed to predict protein loops. However, determining the 3D structures of loops using global orientational restraints on internuclear vectors, such as those obtained from residual dipolar coupling (RDC) data in solution Nuclear Magnetic Resonance (NMR) spectroscopy, has not been well studied. In this paper, we present a novel algorithm that determines the protein loop conformations using a minimal amount of RDC data. Our algorithm exploits the interplay between the sphero-conics derived from RDCs and the protein kinematics, and formulates the loop structure determination problem as a system of low-degree polynomial equations that can be solved exactly and in closed form. The roots of these polynomial equations, which encode the candidate conformations, are searched systematically, using efficient and provable pruning strategies that triage the vast majority of conformations, to enumerate or prune all possible loop conformations consistent with the data. Our algorithm guarantees completeness by ensuring that a possible loop conformation consistent with the data is never missed. This data-driven algorithm provides a way to assess the structural quality from experimental data with minimal modeling assumptions. We applied our algorithm to compute the loops of human ubiquitin, the FF Domain 2 of human transcription elongation factor CA150 (FF2), the DNA damage inducible protein I (DinI) and the third IgG-binding domain of Protein G (GB3) from experimental RDC data. A comparison of our results versus those obtained by using traditional structure determination protocols on the

  10. The loop gravity string

    CERN Document Server

    Freidel, Laurent; Pranzetti, Daniele


    In this work we study canonical gravity in finite regions for which we introduce a generalisation of the Gibbons-Hawking boundary term including the Immirzi parameter. We study the canonical formulation on a spacelike hypersuface with a boundary sphere and show how the presence of this term leads to an unprecedented type of degrees of freedom coming from the restoration of the gauge and diffeomorphism symmetry at the boundary. In the presence of a loop quantum gravity state, these boundary degrees of freedom localize along a set of punctures on the boundary sphere. We demonstrate that these degrees of freedom are effectively described by auxiliary strings with a 3-dimensional internal target space attached to each puncture. We show that the string currents represent the local frame field, that the string angular momenta represent the area flux and that the string stress tensor represents the two dimensional metric on the boundary of the region of interest. Finally, we show that the commutators of these broken...

  11. How long is a piece of loop?

    Directory of Open Access Journals (Sweden)

    Yoonjoo Choi


    Full Text Available Loops are irregular structures which connect two secondary structure elements in proteins. They often play important roles in function, including enzyme reactions and ligand binding. Despite their importance, their structure remains difficult to predict. Most protein loop structure prediction methods sample local loop segments and score them. In particular protein loop classifications and database search methods depend heavily on local properties of loops. Here we examine the distance between a loop’s end points (span. We find that the distribution of loop span appears to be independent of the number of residues in the loop, in other words the separation between the anchors of a loop does not increase with an increase in the number of loop residues. Loop span is also unaffected by the secondary structures at the end points, unless the two anchors are part of an anti-parallel beta sheet. As loop span appears to be independent of global properties of the protein we suggest that its distribution can be described by a random fluctuation model based on the Maxwell–Boltzmann distribution. It is believed that the primary difficulty in protein loop structure prediction comes from the number of residues in the loop. Following the idea that loop span is an independent local property, we investigate its effect on protein loop structure prediction and show how normalised span (loop stretch is related to the structural complexity of loops. Highly contracted loops are more difficult to predict than stretched loops.

  12. Basic domain of telomere guardian TRF2 reduces D-loop unwinding whereas Rap1 restores it. (United States)

    Necasová, Ivona; Janoušková, Eliška; Klumpler, Tomáš; Hofr, Ctirad


    Telomeric repeat binding factor 2 (TRF2) folds human telomeres into loops to prevent unwanted DNA repair and chromosome end-joining. The N-terminal basic domain of TRF2 (B-domain) protects the telomeric displacement loop (D-loop) from cleavage by endonucleases. Repressor activator protein 1 (Rap1) binds TRF2 and improves telomeric DNA recognition. We found that the B-domain of TRF2 stabilized the D-loop and thus reduced unwinding by BLM and RPA, whereas the formation of the Rap1-TRF2 complex restored DNA unwinding. To understand how the B-domain of TRF2 affects DNA binding and D-loop processing, we analyzed DNA binding of full-length TRF2 and a truncated TRF2 construct lacking the B-domain. We quantified how the B-domain improves TRF2's interaction with DNA via enhanced long-range electrostatic interactions. We developed a structural envelope model of the B-domain bound on DNA. The model revealed that the B-domain is flexible in solution but becomes rigid upon binding to telomeric DNA. We proposed a mechanism for how the B-domain stabilizes the D-loop. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. A novel mutation in the tRNAIle gene (MTTI) affecting the variable loop in a patient with chronic progressive external ophthalmoplegia (CPEO)


    Berardo, Andres; Çoku, Jorida; Kurt,Bulent; DiMauro, Salvatore; Hirano, Michio


    We describe a 62-year-old woman with chronic progressive external ophthalmoplegia (CPEO), multiple lipomas, diabetes mellitus, and a novel mitochondrial DNA (mtDNA) mutation at nucleotide 4302 (4302A>G) of the tRNAIle gene (MTTI). This is the first mutation at position 44 in the variable loop (V loop) of any mitochondrial tRNA.

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

    Directory of Open Access Journals (Sweden)

    Mohd. Agus Nashri Abdullah


    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.

  15. A Looping-Based Model for Quenching Repression.

    Directory of Open Access Journals (Sweden)

    Yaroslav Pollak


    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.

  16. In vitro assays for DNA pairing and recombination-associated DNA synthesis. (United States)

    Liu, Jie; Sneeden, Jessica; Heyer, Wolf-Dietrich


    Homologous recombination (HR) is a high-fidelity DNA repair pathway that maintains genome integrity, by repairing double strand breaks (DSBs) and single-stranded DNA (ssDNA) gaps and by supporting stalled/collapsed replication forks. The RecA/Rad51 family of proteins are the key enzymes in this homology-directed repair pathway, as they perform DNA strand invasion and exchange, in concert with a host of ancillary factors. In vitro, the RecA/Rad51 family of proteins share similar enzymatic activities including catalyzing ssDNA-stimulated ATP hydrolysis, formation of displacement loops (D-loops), and DNA strand exchange. After successful DNA strand invasion, DNA synthesis restores the lost genetic information using an undamaged DNA template. In this chapter, we describe two well-established biochemical assays to investigate the signature DNA strand transfer activity of RecA/Rad51 family of proteins: the D-loop assay and the DNA strand exchange reaction. Moreover, we describe a D-loop extension assay coupling D-loop formation with DNA synthesis, which can be used to define the roles of DNA polymerases in HR. Additionally, we present a protocol to investigate protein-mediated DNA annealing, a critical step in the synthesis-dependent strand annealing (SDSA) and double-Holliday junction (dHJ) pathways as well as the single-strand annealing (SSA) pathway. The quality of supercoiled plasmid DNA is critical in reconstituted HR reactions, and a protocol describing the preparation of this DNA substrate is included.

  17. Study of loop-loop and loop-edge dislocation interactions in bcc iron

    DEFF Research Database (Denmark)

    Osetsky, Y.N.; Bacon, D.J.; Gao, F.


    that the evolution of heterogeneities such as dislocation decoration and rafts has serious impacts on the mechanical properties on neutron-irradiated metals. In the present work, atomic-scale computer modelling (ASCM) has been applied to study the mechanisms for the formation of such microstructure in bcc iron....... It is shown that glissile clusters with parallel Burgers vectors interact strongly and can form extended immobile complexes, i.e., rafts. Similar attractive interaction exists between dislocation loops and an edge dislocation. These two mechanisms may be responsible for the formation of extended complexes...... of dislocation loops below the extra half-plane of edge dislocations. The interaction energies between loops and between an edge dislocation and loops has been calculated as a function of distance using ASCM and the results for long-range interactions are in good agreement with the results of isotropic...

  18. N -loop running should be combined with N -loop matching (United States)

    Braathen, Johannes; Goodsell, Mark D.; Krauss, Manuel E.; Opferkuch, Toby; Staub, Florian


    We investigate the high-scale behavior of Higgs sectors beyond the Standard Model, pointing out that the proper matching of the quartic couplings before applying the renormalization group equations (RGEs) is of crucial importance for reliable predictions at larger energy scales. In particular, the common practice of leading-order parameters in the RGE evolution is insufficient to make precise statements on a given model's UV behavior, typically resulting in uncertainties of many orders of magnitude. We argue that, before applying N -loop RGEs, a matching should even be performed at N -loop order in contrast to common lore. We show both analytical and numerical results where the impact is sizable for three minimal extensions of the Standard Model: a singlet extension, a second Higgs doublet and finally vector-like quarks. We highlight that the known two-loop RGEs tend to moderate the running of their one-loop counterparts, typically delaying the appearance of Landau poles. For the addition of vector-like quarks we show that the complete two-loop matching and RGE evolution hints at a stabilization of the electroweak vacuum at high energies, in contrast to results in the literature.

  19. Advanced uracil DNA glycosylase-supplemented real-time reverse transcription loop-mediated isothermal amplification (UDG-rRT-LAMP) method for universal and specific detection of Tembusu virus. (United States)

    Tang, Yi; Chen, Hao; Diao, Youxiang


    Tembusu virus (TMUV) is a mosquito-borne flavivirus which threatens both poultry production and public health. In this study we developed a complete open reading frame alignment-based rRT-LAMP method for the universal detection of TUMV. To prevent false-positive results, the reaction was supplemented with uracil DNA glycosylase (UDG) to eliminate carryover contamination. The detection limit of the newly developed UDG-rRT-LAMP for TMUV was as low as 100 copies/reaction of viral RNA and 1 × 10(0.89) - 1 × 10(1.55) tissue culture infectious dose/100 μL of viruses. There were no cross-reactions with other viruses, and the reproducibility of the assay was confirmed by intra- and inter-assay tests with variability ranging from 0.22-3.33%. The new UDG-rRT-LAMP method for TMUV produced the same results as viral isolation combined with RT-PCR as the "gold standard" in 96.88% of cases for 81 clinical samples from subjects with suspected TMUV infection. The addition of UDG can eliminate as much as 1 × 10(-16) g/reaction of contaminants, which can significantly reduce the likelihood of false-positive results during the rRT-LAMP reaction. Our result indicated that our UDG-rRT-LAMP is a rapid, sensitive, specific, and reliable method that can effectively prevent carryover contamination in the detection of TMUV.

  20. Kalman Orbit Optimized Loop Tracking (United States)

    Young, Lawrence E.; Meehan, Thomas K.


    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.

  1. Detection of Botrytis cinerea by loop-mediated isothermal amplification. (United States)

    Tomlinson, J A; Dickinson, M J; Boonham, N


    To develop a sensitive, rapid and simple method for detection of Botrytis cinerea based on loop-mediated isothermal amplification (LAMP) that would be suitable for use outside a conventional laboratory setting. A LAMP assay was designed based on the intergenic spacer of the B. cinerea nuclear ribosomal DNA (rDNA). The resulting assay was characterized in terms of sensitivity and specificity using DNA extracted from cultures. The assay consistently amplified 65 pg B. cinerea DNA. No cross-reactivity was observed with a range of other fungal pathogens, with the exception of the closely related species Botrytis pelargonii. Use of a novel real-time LAMP platform (the OptiGene Genie I) allowed detection of B. cinerea in infected rose petals, with amplification occurring in cut flowers, fruit and vegetables. © 2010 British Crown Copyright. Letters in Applied Microbiology 51, 650-657 © 2010 The Society for Applied Microbiology.

  2. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan


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

  3. Study of the Open Loop and Closed Loop Oscillator Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Imel, George R. [Idaho State Univ., Pocatello, ID (United States); Baker, Benjamin [Idaho National Lab. (INL), Idaho Falls, ID (United States); Riley, Tony [Knolls Atomic Power Lab. (KAPL), Schenectady, NY (United States); Langbehn, Adam [Puget Sound Naval Base, Bremerton, WA (United States); Aryal, Harishchandra [Idaho State Univ., Pocatello, ID (United States); Benzerga, M. Lamine [Idaho State Univ., Pocatello, ID (United States)


    This report presents the progress and completion of a five-year study undertaken at Idaho State University of the measurement of very small worth reactivity samples comparing open and closed loop oscillator techniques.The study conclusively demonstrated the equivalency of the two techniques with regard to uncertainties in reactivity values, i.e., limited by reactor noise. As those results are thoroughly documented in recent publications, in this report we will concentrate on the support work that was necessary. For example, we describe in some detail the construction and calibration of a pilot rod for the closed loop system. We discuss the campaign to measure the required reactor parameters necessary for inverse-kinetics. Finally, we briefly discuss the transfer of the open loop technique to other reactor systems.

  4. Mitochondrial D-loop mutations can be detected in sporadic malignant tumours in dogs

    Directory of Open Access Journals (Sweden)

    Ślaska Brygida


    Full Text Available The aim of this study was to identify mutations in the D-loop region of mtDNA in head, neck, and limb tumours in dogs, and determination of their relationship with the process of neoplastic transformation. Blood and tumour tissue samples from 19 dogs with diagnosed sporadic malignant tumours were analysed. DNA extraction, amplification, and sequencing of the mtDNA D-loop, and bioinformatic analyses were performed. Five mutations and 19 polymorphisms were observed in 68.42% of all tumours. Polymorphic variants were noted in 42.86% of the head and neck tumours and in 58.33% of the limb tumours. Mutations were observed in 21.05% of dogs. The mutations were found in 28.57% of the head and neck tumours and in 16.66% of the limb tumours. The mutations were identified in 50% of the studied epithelial cancers. In the mesenchymal tumours, no mutations in the D-loop region were observed. Mitochondrial haplotype A17 was found in over 40% cases of limb tumours. No association between the age, breed, sex, type of tumour, and detected polymorphic variants were observed. Different mutational changes in the D-loop sequences of mtDNA identified in the blood and tumour tissues may indicate a relationship between the type of tumour and individual changes in the D-loop nucleotide sequences of mtDNA.

  5. DNA Bending elasticity (United States)

    Sivak, David Alexander

    DNA bending elasticity on length scales of tens of basepairs is of critical importance in numerous biological contexts. Even the simplest models of DNA bending admit of few simple analytic results, thus there is a need for numerical methods to calculate experimental observables, such as distance distributions, forces, FRET efficiencies, and timescales of particular large-scale motions. We have implemented and helped develop a coarse-grained representation of DNA and various other covalently-linked groups that allows simple calculation of such observables for varied experimental systems. The simple freely-jointed chain (FJC) model and extremely coarse resolution proved useful in understanding DNA threading through nanopores, identifying steric occlusion by other parts of the chain as a prime culprit for slower capture as distance to the pore decreased. Enhanced sampling techniques of a finer resolution discrete wormlike chain (WLC) model permitted calculation of cyclization rates for small chains and identified the ramifications of a thermodynamically-sound treatment of thermal melts. Adding treatment of double-stranded DNA's helical nature and single-stranded DNA provided a model system that helped demonstrate the importance of statistical fluctuations in even highly-stressed DNA mini-loops, and allowed us to verify that even these constructs show no evidence of excitation-induced softening. Additional incorporation of salt-sensitivity to the model allowed us to calculate forces and FRET efficiencies for such mini-loops and their uncircularized precursors, thereby furthering the understanding of the nature of IHF binding and bending of its recognition sequence. Adding large volume-excluding spheres linked to the ends of the dsDNA permits calculation of distance distributions and thus small-angle X-ray scattering, whereby we demonstrated the validity of the WLC in describing bending fluctuations in DNA chains as short as 42 bp. We also make important connections

  6. Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression.

    Directory of Open Access Journals (Sweden)

    Tuoqi Liu


    Full Text Available According to recent experimental evidence, the interaction between chromatin loops, which can be characterized by three factors-connection pattern, distance between regulatory elements, and communication form, play an important role in determining the level of cell-to-cell variability in gene expression. These quantitative experiments call for a corresponding modeling effect that addresses the question of how changes in these factors affect variability at the expression level in a systematic rather than case-by-case fashion. Here we make such an effort, based on a mechanic model that maps three fundamental patterns for two interacting DNA loops into a 4-state model of stochastic transcription. We first show that in contrast to side-by-side loops, nested loops enhance mRNA expression and reduce expression noise whereas alternating loops have just opposite effects. Then, we compare effects of facilitated tracking and direct looping on gene expression. We find that the former performs better than the latter in controlling mean expression and in tuning expression noise, but this control or tuning is distance-dependent, remarkable for moderate loop lengths, and there is a limit loop length such that the difference in effect between two communication forms almost disappears. Our analysis and results justify the facilitated chromatin-looping hypothesis.

  7. Vertically Polarized Omnidirectional Printed Slot Loop AntennaPrinted Slot Loop Antenna (invited)

    DEFF Research Database (Denmark)

    Kammersgaard, Nikolaj Peter Iversen; Kvist, Søren Helstrup; Thaysen, Jesper


    A novel verticall A novel vertically polarized dpolarize , omnidirection omnidirectional l , printed slot loop antenna h sprinted 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 a...

  8. DNA Sequential Logic Gate Using Two-Ring DNA. (United States)

    Zhang, Cheng; Shen, Linjing; Liang, Chao; Dong, Yafei; Yang, Jing; Xu, Jin


    Sequential DNA detection is a fundamental issue for elucidating the interactive relationships among complex gene systems. Here, a sequential logic DNA gate was achieved by utilizing the two-ring DNA structure, with the ability to recognize "before" and "after" triggering sequences of DNA signals. By taking advantage of a "loop-open" mechanism, separations of two-ring DNAs were controlled. Three triggering pathways with different sequential DNA treatments were distinguished by comparing fluorescent outputs. Programmed nanoparticle arrangement guided by "interlocked" two-ring DNA was also constructed to demonstrate the achievement of designed nanostrucutres. Such sequential logic DNA operation may guide future molecular sensors to monitor more complex gene network in biological systems.

  9. Closed loop obstruction: pictorial essay. (United States)

    Mbengue, A; Ndiaye, A; Soko, T O; Sahnoun, M; Fall, A; Diouf, C T; Régent, D; Diakhaté, I C


    Closed loop obstruction occurs when a segment of bowel is incarcerated at two contiguous points. The diagnosis is based on multiple transitional zones. The incarcerated loops appear in U or C form or present a radial layout around the location of the obstruction. It's very important to specify the type of obstruction because, in patients with simple bowel obstruction, a conservative approach is often advised. On the other hand, a closed loop obstruction immediately requires a surgical approach because of its high morbidity and the risk of death in case of a late diagnosis. Copyright © 2013 Éditions françaises de radiologie. Published by Elsevier Masson SAS. All rights reserved.

  10. Effective potential at three loops (United States)

    Martin, Stephen P.


    I present the effective potential at three-loop order for a general renormalizable theory, using the MS ¯ renormalization scheme and Landau gauge fixing. As applications and illustrative points of reference, the results are specialized to the supersymmetric Wess-Zumino model and to the standard model. In each case, renormalization group scale invariance provides a consistency check. In the Wess-Zumino model, the required vanishing of the minimum vacuum energy yields an additional check. For the standard model, I carry out the resummation of Goldstone boson contributions, which provides yet more opportunities for nontrivial checks, and obtain the minimization condition for the Higgs vacuum expectation value at full three-loop order. An infrared divergence due to doubled photon propagators appears in the three-loop standard model effective potential, but it does not affect the minimization condition or physical observables and can be eliminated by resummation.

  11. LISA Pathfinder: OPD loop characterisation (United States)

    Born, Michael; LPF Collaboration


    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.

  12. Chinese Magic in Loop Integrals


    Ward, B. F. L.


    We present an approach to higher point loop integrals using Chinese magic in the virtual loop integration variable. We show, using the five point function in the important e^+e^-\\to f\\bar{f}+\\gamma process for ISR as a pedagogical vehicle, that we get an expression for it directly reduced to one scalar 5-point function and 4-, 3-, and 2- point integrals, thereby avoiding the computation of the usual three tensor 5-pt Passarino-Veltman reduction. We argue that this offers potential for greater...

  13. Supercoiling DNA Locates Mismatches (United States)

    Dittmore, Andrew; Brahmachari, Sumitabha; Takagi, Yasuharu; Marko, John F.; Neuman, Keir C.


    We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules with 0 to 16 adjacent mismatches at 1 M monovalent salt and 3.6 pN force and show that under these conditions, a single plectoneme forms and is stably pinned at the defect. We use these measurements to estimate the energy and degree of end-loop kinking at defects. From this, we calculate the relative probability of plectoneme pinning at the mismatch under physiologically relevant conditions. Based on this estimate, we propose that DNA supercoiling could contribute to mismatch and damage sensing in vivo.

  14. Pulled Polymer Loops as a Model for the Alignment of Meiotic Chromosomes (United States)

    Lin, Yen Ting; Frömberg, Daniela; Huang, Wenwen; Delivani, Petrina; Chacón, Mariola; Tolić, Iva M.; Jülicher, Frank; Zaburdaev, Vasily


    During recombination, the DNA of parents exchange their genetic information to give rise to a genetically unique offspring. For recombination to occur, homologous chromosomes need to find each other and align with high precision. Fission yeast solves this problem by folding chromosomes in loops and pulling them through the viscous nucleoplasm. We propose a theory of pulled polymer loops to quantify the effect of drag forces on the alignment of chromosomes. We introduce an external force field to the concept of a Brownian bridge and thus solve for the statistics of loop configurations in space.

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

    Directory of Open Access Journals (Sweden)

    Sarah eLuke-Glaser


    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.

  16. Dirac Induction for loop groups

    NARCIS (Netherlands)

    Posthuma, H.


    Using a coset version of the cubic Dirac operators for affine Lie algebras, we give an algebraic construction of the Dirac induction homomorphism for loop group representations. With this, we prove a homogeneous generalization of the Weyl-Kac character formula and show compatibility with Dirac

  17. Loop quantum cosmology and singularities. (United States)

    Struyve, Ward


    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.

  18. Loop quantum gravity and observations

    CERN Document Server

    Barrau, A


    Quantum gravity has long been thought to be completely decoupled from experiments or observations. Although it is true that smoking guns are still missing, there are now serious hopes that quantum gravity phenomena might be tested. We review here some possible ways to observe loop quantum gravity effects either in the framework of cosmology or in astroparticle physics.

  19. Scalar one-loop integrals

    NARCIS (Netherlands)

    Veltman, M.J.G.; Hooft, G. 't


    The completely general one-loop scalar one-, two-, three- and four-point functions are studied. Also an integral occurring in connection with soft bremsstrahlung is considered. Formulas in terms of Spence functions are given. An expansion for Spence functions with complex argument is presented.

  20. Two loops in eleven dimensions

    CERN Document Server

    Green, Michael B.; Vanhove, Pierre; Green, Michael B.; Kwon, Hwang-h.; Vanhove, Pierre


    The two-loop Feynman diagram contribution to the four-graviton amplitude of eleven-dimensional supergravity compactified on a two-torus, T^2, is analyzed in detail. The Schwinger parameter integrations are re-expressed as integration over the moduli space of a second torus, \\hat T^2, which enables the leading low-momentum contribution to be evaluated in terms of maps of \\hat T^2 into T^2. The ultraviolet divergences associated with boundaries of moduli space are regularized in a manner that is consistent with the expected duality symmetries of string theory. This leads to an exact expression for terms of order contraction of four Weyl tensors), thereby extending earlier results for the R^4 term that were based on the one-loop eleven-dimensional amplitude. Precise agreement is found with terms in type IIA and IIB superstring theory that arise from the low energy expansion of the tree-level and one-loop string amplitudes and predictions are made for the coefficients of certain two-loop string theory terms as we...

  1. Loop 2 in Saccharomyces cerevisiae Rad51 protein regulates filament formation and ATPase activity. (United States)

    Zhang, Xiao-Ping; Galkin, Vitold E; Yu, Xiong; Egelman, Edward H; Heyer, Wolf-Dietrich


    Previous studies showed that the K342E substitution in the Saccharomyces cerevisiae Rad51 protein increases the interaction with Rad54 protein in the two-hybrid system, leads to increased sensitivity to the alkylating agent MMS and hyper-recombination in an oligonucleotide-mediated gene targeting assay. K342 localizes in loop 2, a region of Rad51 whose function is not well understood. Here, we show that Rad51-K342E displays DNA-independent and DNA-dependent ATPase activities, owing to its ability to form filaments in the absence of a DNA lattice. These filaments exhibit a compressed pitch of 81 A, whereas filaments of wild-type Rad51 and Rad51-K342E on DNA form extended filaments with a 97 A pitch. Rad51-K342E shows near normal binding to ssDNA, but displays a defect in dsDNA binding, resulting in less stable protein-dsDNA complexes. The mutant protein is capable of catalyzing the DNA strand exchange reaction and is insensitive to inhibition by the early addition of dsDNA. Wild-type Rad51 protein is inhibited under such conditions, because of its ability to bind dsDNA. No significant changes in the interaction between Rad51-K342E and Rad54 could be identified. These findings suggest that loop 2 contributes to the primary DNA-binding site in Rad51, controlling filament formation and ATPase activity.

  2. Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq. (United States)

    Dumelie, Jason G; Jaffrey, Samie R


    R-loops are features of chromatin consisting of a strand of DNA hybridized to RNA, as well as the expelled complementary DNA strand. R-loops are enriched at promoters where they have recently been shown to have important roles in modifying gene expression. However, the location of promoter-associated R-loops and the genomic domains they perturb to modify gene expression remain unclear. To resolve this issue, we developed a bisulfite-based approach, bisDRIP-seq, to map R-loops across the genome at near-nucleotide resolution in MCF-7 cells. We found the location of promoter-associated R-loops is dependent on the presence of introns. In intron-containing genes, R-loops are bounded between the transcription start site and the first exon-intron junction. In intronless genes, the 3' boundary displays gene-specific heterogeneity. Moreover, intronless genes are often associated with promoter-associated R-loop formation. Together, these studies provide a high-resolution map of R-loops and identify gene structure as a critical determinant of R-loop formation.

  3. Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals. (United States)

    Sanz, Lionel A; Hartono, Stella R; Lim, Yoong Wearn; Steyaert, Sandra; Rajpurkar, Aparna; Ginno, Paul A; Xu, Xiaoqin; Chédin, Frédéric


    R-loops are three-stranded nucleic acid structures formed upon annealing of an RNA strand to one strand of duplex DNA. We profiled R-loops using a high-resolution, strand-specific methodology in human and mouse cell types. R-loops are prevalent, collectively occupying up to 5% of mammalian genomes. R-loop formation occurs over conserved genic hotspots such as promoter and terminator regions of poly(A)-dependent genes. In most cases, R-loops occur co-transcriptionally and undergo dynamic turnover. Detailed epigenomic profiling revealed that R-loops associate with specific chromatin signatures. At promoters, R-loops associate with a hyper-accessible state characteristic of unmethylated CpG island promoters. By contrast, terminal R-loops associate with an enhancer- and insulator-like state and define a broad class of transcription terminators. Together, this suggests that the retention of nascent RNA transcripts at their site of expression represents an abundant, dynamic, and programmed component of the mammalian chromatin that affects chromatin patterning and the control of gene expression. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Modified Continuous Loop Technique for microvascular anastomosis

    Directory of Open Access Journals (Sweden)

    Kumar Pramod


    Full Text Available A modified method of continuous loop technique for microvascular anastomosis is described. The handling of loop is easier & even last suture is placed under vision. This makes the microvascular anastomosis easier and simpler.

  5. A True Open-Loop Synchronization Technique

    DEFF Research Database (Denmark)

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


    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....

  6. Estimation of complex permittivity using loop antenna

    DEFF Research Database (Denmark)

    Lenler-Eriksen, Hans-Rudolph; Meincke, Peter


    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....

  7. Loop connectors in dentogenic diastema

    Directory of Open Access Journals (Sweden)

    Sanjna Nayar


    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.

  8. Chiral logarithms to five loops


    Bissegger, Moritz; Fuhrer, Andreas


    We investigate two specific Green functions in the framework of chiral perturbation theory. We show that, using analyticity and unitarity, their leading logarithmic singularities can be evaluated in the chiral limit to any desired order in the chiral expansion, with a modest calculational cost. The claim is illustrated with an evaluation of the leading logarithm for the scalar two-point function to five-loop order.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    Zanotti Marta


    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.

  11. Association of mitochondrial displacement loop polymorphisms with risk of colorectal cancer in south Indian population. (United States)

    Govatati, Suresh; Saradamma, Bulle; Malempati, Sravanthi; Dasi, Divyamaanasa; Thupurani, Murali Krishna; Nagesh, Narayana; Shivaji, Sisinthy; Bhanoori, Manjula; Tamanam, Raghava Rao; Nallanchakravarthula, Varadacharyulu; Pasupuleti, Sreenivasa Rao


    Mitochondrial displacement loop (D-loop) is the hot spot for mitochondrial DNA (mtDNA) alterations which influence the generation of cellular reactive oxygen species. In the present study, we sequenced the entire mitochondrial D-loop region (1124 bp) of colorectal cancer (CRC) patients (n = 174) and controls (n = 170) of south Indian origin to identify significant mutations/polymorphisms. Our results showed 152 polymorphisms in the D-loop region of patients and/or controls. Polymorphisms were predominantly located in hypervariable region I (54.6%) than in II (45.4%) of D-loop region. The frequencies of 310'C' insertion (p = 0.0078), T16189C (p = 0.0097) variants and 310'C'ins/16189C haplotype (p = 0.0029) were significantly higher in cases than in controls. Furthermore, strong linkage disequilibrium was observed between nucleotide position 310 and 16189 in cases (D'=0.68) as compared with controls (D'=0.27). In conclusion, mitochondrial D-loop sequence alterations may constitute inherent risk factor for CRC.

  12. Chemical Looping Technology: Oxygen Carrier Characteristics. (United States)

    Luo, Siwei; Zeng, Liang; Fan, Liang-Shih


    Chemical looping processes are characterized as promising carbonaceous fuel conversion technologies with the advantages of manageable CO2 capture and high energy conversion efficiency. Depending on the chemical looping reaction products generated, chemical looping technologies generally can be grouped into two types: chemical looping full oxidation (CLFO) and chemical looping partial oxidation (CLPO). In CLFO, carbonaceous fuels are fully oxidized to CO2 and H2O, as typically represented by chemical looping combustion with electricity as the primary product. In CLPO, however, carbonaceous fuels are partially oxidized, as typically represented by chemical looping gasification with syngas or hydrogen as the primary product. Both CLFO and CLPO share similar operational features; however, the optimum process configurations and the specific oxygen carriers used between them can vary significantly. Progress in both CLFO and CLPO is reviewed and analyzed with specific focus on oxygen carrier developments that characterize these technologies.

  13. Multiple Lac-mediated loops revealed by Bayesian statistics and tethered particle motion

    CERN Document Server

    Johnson, Stephanie; Phillips, Rob; Wiggins, Chris H; Lindén, Martin


    The bacterial transcription factor LacI loops DNA by binding to two separate locations on the DNA simultaneously. Despite being one of the best-studied model systems for transcriptional regulation, the number and conformations of loop structures accessible to LacI remain unclear, though the importance of multiple co-existing loops has been implicated in interactions between LacI and other cellular regulators of gene expression. To probe this issue, we have developed a new analysis method for tethered particle motion (TPM), a versatile and commonly-used in vitro single-molecule technique. Our method, vbTPM, is based on a variational Bayes treatment of hidden Markov models. It learns the number of distinct states (i.e., DNA-protein conformations) directly from TPM data with better resolution than existing methods, while easily correcting for common experimental artifacts. Studying short (roughly 100 bp) LacI-mediated loops, we are able to resolve three distinct loop structures, more than previously reported at ...

  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


    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. The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability (United States)

    Hamperl, Stephan; Cimprich, Karlene A.


    Accurate DNA replication and DNA repair are crucial for the maintenance of genome stability, and it is generally accepted that failure of these processes is a major source of DNA damage in cells. Intriguingly, recent evidence suggests that DNA damage is more likely to occur at genomic loci with high transcriptional activity. Furthermore, loss of certain RNA processing factors in eukaryotic cells is associated with increased formation of co-transcriptional RNA:DNA hybrid structures known as R-loops, resulting in double-strand breaks (DSBs) and DNA damage. However, the molecular mechanisms by which R-loop structures ultimately lead to DNA breaks and genome instability is not well understood. In this review, we summarize the current knowledge about the formation, recognition and processing of RNA:DNA hybrids, and discuss possible mechanisms by which these structures contribute to DNA damage and genome instability in the cell. PMID:24746923

  16. The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability. (United States)

    Hamperl, Stephan; Cimprich, Karlene A


    Accurate DNA replication and DNA repair are crucial for the maintenance of genome stability, and it is generally accepted that failure of these processes is a major source of DNA damage in cells. Intriguingly, recent evidence suggests that DNA damage is more likely to occur at genomic loci with high transcriptional activity. Furthermore, loss of certain RNA processing factors in eukaryotic cells is associated with increased formation of co-transcriptional RNA:DNA hybrid structures known as R-loops, resulting in double-strand breaks (DSBs) and DNA damage. However, the molecular mechanisms by which R-loop structures ultimately lead to DNA breaks and genome instability is not well understood. In this review, we summarize the current knowledge about the formation, recognition and processing of RNA:DNA hybrids, and discuss possible mechanisms by which these structures contribute to DNA damage and genome instability in the cell. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Scanning probe microscope visualization of t-loop assembly by TRF2 in cells (United States)

    Cao, En-Hua; Guo, Xiao-Fe; Wang, Ju-Jun; Qin, Jing-Fen


    Telomeres are essential nucleoprotein structure at the ends of all eukaryotic chromosomes. Our previous work demonstrated that mammalian telomeres were shown to end in a large t-loop structure in vitro and the formation of t-loops was dependent on the presence of TRF2. In this work, the telomere DNA and its complex of TRF2 in HeLa cells has been direct observed in the nanometer resolution regime by atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM). AFM images showed that the looped structures exited in cell extract containing TRF2, but it disappeared in the protein-deleted samples. When cells were pretreated by UV light plus psoralen, the looped structure could be observed in the protein-deleted samples. SNOM images further demonstrated TRF2 and p53 proteins in cell was bound at the loop junction. Above results suggest that the telomere t-loop structure by TRF2 play a important role in cell-senescence, and might signals p53 protein directly through association with the t-loop junction in cells.

  18. 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.

  19. Singularities in loop quantum cosmology. (United States)

    Cailleteau, Thomas; Cardoso, Antonio; Vandersloot, Kevin; Wands, David


    We show that simple scalar field models can give rise to curvature singularities in the effective Friedmann dynamics of loop quantum cosmology (LQC). We find singular solutions for spatially flat Friedmann-Robertson-Walker cosmologies with a canonical scalar field and a negative exponential potential, or with a phantom scalar field and a positive potential. While LQC avoids big bang or big rip type singularities, we find sudden singularities where the Hubble rate is bounded, but the Ricci curvature scalar diverges. We conclude that the effective equations of LQC are not in themselves sufficient to avoid the occurrence of curvature singularities.

  20. Closed-loop neuromorphic benchmarks

    CSIR Research Space (South Africa)

    Stewart, TC


    Full Text Available the study was exempt from ethical approval procedures.) Did the study presented in the manuscript involve human or animal subjects: No I v i w 1Closed-loop Neuromorphic Benchmarks Terrence C. Stewart 1,∗, Travis DeWolf 1, Ashley Kleinhans 2 and Chris..._link335 program from ev3dev-c ( This allows the EV3 to336 listen for UDP commands that tell it to set motor values and read sensor values. Communication with337 a PC was over a USB link (although the system also...

  1. Holomorphic curves in loop groups

    Energy Technology Data Exchange (ETDEWEB)

    Guest, M.A.; Pressley, A.N.


    It was observed by Atiyah that there is a correspondence between based gauge equivalence classes of SU/sub n/-instantons over S/sup 4/ of charge d on the one hand, and based holomorphic curves of genus zero in ..cap omega..SU/sub n/ of degree d on the other hand. In this paper we study the parameter space of such holomorphic curves which have the additional property that they lie entirely in the subgroup ..cap omega../sub alg/SU/sub n/ of algebraic loops. We describe a cell decomposition of this parameter space, and compute its complex dimension to be (2n-1)d.

  2. 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)


    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.)

  3. Identification of the source of ivory idol by DNA analysis. (United States)

    Gupta, Sandeep Kumar; Thangaraj, Kumarasamy; Singh, Lalji


    In this study, we describe a forensic case dealing with the identification of the source of the processed ivory object by DNA analysis. Two pieces of Lord Krishna's idols from a shop were confiscated by an investigating agency of the Indian government and forwarded to us to identify the source of its origin. We succeeded in isolating DNA from both processed ivory idols by using the phenol/chloroform DNA extraction method. The extracted DNA was subjected to PCR amplification using an elephant-specific mitochondrial DNA (mtDNA) D-loop marker. DNA sequence analysis of the amplified fragment of mtDNA D-loop region confirmed that the idols were consistent with Asian elephant with 99% similarity. © 2011 American Academy of Forensic Sciences.

  4. Polyakov loop modeling for hot QCD (United States)

    Fukushima, Kenji; Skokov, Vladimir


    We review theoretical aspects of quantum chromodynamics (QCD) at finite temperature. The most important physical variable to characterize hot QCD is the Polyakov loop, which is an approximate order parameter for quark deconfinement in a hot gluonic medium. Additionally to its role as an order parameter, the Polyakov loop has rich physical contents in both perturbative and non-perturbative sectors. This review covers a wide range of subjects associated with the Polyakov loop from topological defects in hot QCD to model building with coupling to the Polyakov loop.

  5. Vertically Polarized Omnidirectional Printed Slot Loop Antenna

    DEFF Research Database (Denmark)

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


    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....

  6. Nonlinear Bayesian Tracking Loops for Multipath Mitigation

    Directory of Open Access Journals (Sweden)

    Pau Closas


    Full Text Available This paper studies Bayesian filtering techniques applied to the design of advanced delay tracking loops in GNSS receivers with multipath mitigation capabilities. The analysis includes tradeoff among realistic propagation channel models and the use of a realistic simulation framework. After establishing the mathematical framework for the design and analysis of tracking loops in the context of GNSS receivers, we propose a filtering technique that implements Rao-Blackwellization of linear states and a particle filter for the nonlinear partition and compare it to traditional delay lock loop/phase lock loop-based schemes.

  7. Soft Neutrosophic Loops and Their Generalization

    Directory of Open Access Journals (Sweden)

    Mumtaz Ali


    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.

  8. [Bacteriophage DNA reptation]. (United States)

    Gabashvili, I S; Grosberg, A Iu


    The kinetics of reptation process of dsDNA leaving the phage head is analysed theoretically. It is assumed that the process is caused by DNA free energy decrease when it is leaving the head (DNA has to be in a globular state) for its surroundings where it is transformed into a coil state. For the analysis we have used the results of previous paper on equilibrium theory of DNA intraphage globule. Three possible cases for the ejection process friction are considered: friction in the tail-part channel, that of DNA segments with each other in the whole globule volume (it is essential for the collective way of the globule decondensation with simultaneous movement of all the loops--the first type way), the globule friction with internal capsid surface (it is most essential for the decondensation by the way of the globule rotation as a whole "spool"--the second type way). The first way would correspond to the greatest ejection time. The known experimental data on distinguishing ejection kinetics for phages with short and long tail-parts allow us to formulate arguments in favor of realization of the second way in nature.

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


    Stuckey, Ruth


    [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, ...

  10. UWB communication receiver feedback loop (United States)

    Spiridon, Alex; Benzel, Dave; Dowla, Farid U.; Nekoogar, Faranak; Rosenbury, Erwin T.


    A novel technique and structure that maximizes the extraction of information from reference pulses for UWB-TR receivers is introduced. The scheme efficiently processes an incoming signal to suppress different types of UWB as well as non-UWB interference prior to signal detection. Such a method and system adds a feedback loop mechanism to enhance the signal-to-noise ratio of reference pulses in a conventional TR receiver. Moreover, sampling the second order statistical function such as, for example, the autocorrelation function (ACF) of the received signal and matching it to the ACF samples of the original pulses for each transmitted bit provides a more robust UWB communications method and system in the presence of channel distortions.

  11. Closed loop steam cooled airfoil (United States)

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


    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.

  12. Lose Your Loops with Numpy

    CERN Multimedia

    CERN. Geneva


    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.

  13. Fiber loop ringdown humidity sensor. (United States)

    Alali, Haifa; Wang, Chuji


    An optical fiber relative humidity (RH) sensor based on the evanescent field-fiber loop ringdown (EF-FLRD) technique is demonstrated. The sensor was placed inside a chamber that provides a humidity reference and is monitored by a humidity meter. The presence of moisture in the chamber changes the refractive index of the medium; thus the ringdown time changes due to a change in the EF scattering loss induced in the sensor head. The sensor demonstrated a fast response (∼1  s), high sensitivity, and excellent reproducibility and reversibly. The EF-FLRD sensor can measure RH in a wide dynamic range of 4% to 100% at a constant temperature of 20±1°C.

  14. Multilevel D-loop PCR identification of hunting game

    Directory of Open Access Journals (Sweden)

    V. Parkanyi


    Full Text Available The control region of mtDNA (D-loop was used for hair samples of the five hunting game species identification: red deer (Cervus elaphus, roe deer (Capreolus capreolus, fallow deer (Dama dama, mouflon (Ovis aries musimon, and wild boar (Sus scrofa. For D-loop multilevel PCR detection scheme was applied in six primers (CE CVZV 1 = 5′-GATCACGAGCTTGATCACCA-3′; CE CVZV 2 = 5′-AGGAGTGGGCGATTTTAGGT-3′; DD CVZV 3 = 5′-CGCGTGAAACCAACAACCCGC-3′; DD CVZV 4 = 5′-CCGGGTCGGGGCCTTAGACG-3′; SSW CVZV 5 = 5′-ACACGTGCGTACACGCGCATA-3′; SSW CVZV 6 = 5′-GGTGCCTGCT T TCGTAGCACG-3′ designed to identify unknown biological samples of the hunting game animals. The PCR reaction volume was 25 μl at conditions 95 °C for 2 min, 94 °C for 30 s, 60 °C for 30 s, 72 °C for 30 s, 35 cycles, with last extension at 72 °C for 10 min. D-loop mtDNA amplicons of the game animals are characterized with specific PCR product sizes depending on species: red deer = 163 bp and 140 bp, fallow deer = 280 bp and 138 bp, roe deer = 303 bp, 280 bp, 160 bp and 138 bp, mouflon = 299 bp and 178 bp, wild boar = 137 bp and 229 bp.

  15. Vacuum energy sequestering and graviton loops


    Kaloper, Nemanja; Padilla, Antonio


    We recently formulated a local mechanism of vacuum energy sequester. This mechanism automatically removes all matter loop contributions to vacuum energy from the stress energy tensor which sources the curvature. Here we adapt the local vacuum energy sequestering mechanism to also cancel all the vacuum energy loops involving virtual gravitons, in addition to the vacuum energy generated by matter fields alone.

  16. Loop calculus for lattice gauge theories

    Energy Technology Data Exchange (ETDEWEB)

    Gambini, R.; Leal, L.; Trias, A.


    Hamiltonian calculations are performed using a loop-labeled basis where the full set of identities for the SU(/ital 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.

  17. Newtonian gravity in loop quantum gravity


    Smolin, Lee


    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.

  18. 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)


    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

  19. Holonomy loops, spectral triples and quantum gravity

    DEFF Research Database (Denmark)

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


    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...

  20. Droplet flows through periodic loop networks (United States)

    Jeanneret, Raphael; Schindler, Michael; Bartolo, Denis


    Numerous microfluidic experiments have revealed non-trivial traffic dynamics when droplets flow through a channel including a single loop. A complex encoding of the time intervals between the droplets is achieved by the binary choices they make as they enter the loop. Very surprisingly, another set of experiments has demonstrated that the addition of a second loop does not increase the complexity of the droplet pattern. Conversely, the second loop decodes the temporal signal encrypted by the first loop [1]. In this talk we show that no first principle argument based on symmetry or conservation laws can account for this unexpected decoding process. Then, to better understand how a loop maps time intervals between droplets, we consider a simplified model which has proven to describe accurately microfluidic droplet flows. Combining numerical simulations and analytical calculations for the dynamic of three droplets travelling through N loops: (i) We show that three different traffic regimes exist, yet none of them yields exact decoding. (ii) We uncover that for a wide class of loop geometry, the coding process is analogous to a Hamiltonian mapping: regular orbits are destabilized in island chains and separatrix. (iii) Eventually, we propose a simple explanation to solve the apparent paradox with the coding/decoding dynamics observed in experiments. [1] M.J. Fuerstman, P. Garstecki, and G.M. Whitesides, Science, 315:828, 2007.

  1. BRCA2 Regulates Transcription Elongation by RNA Polymerase II to Prevent R-Loop Accumulation

    Directory of Open Access Journals (Sweden)

    Mahmud K.K. Shivji


    Full Text Available The controlled release of RNA polymerase II (RNAPII from promoter-proximal pausing (PPP sites is critical for transcription elongation in metazoans. We show that the human tumor suppressor BRCA2 interacts with RNAPII to regulate PPP release, thereby preventing unscheduled RNA-DNA hybrids (R-loops implicated in genomic instability and carcinogenesis. BRCA2 inactivation by depletion or cancer-causing mutations instigates RNAPII accumulation and R-loop accrual at PPP sites in actively transcribed genes, accompanied by γH2AX formation marking DNA breakage, which is reduced by ERCC4 endonuclease depletion. BRCA2 inactivation decreases RNAPII-associated factor 1 (PAF1 recruitment (which normally promotes RNAPII release and diminishes H2B Lys120 ubiquitination, impeding nascent RNA synthesis. PAF1 depletion phenocopies, while its overexpression ameliorates, R-loop accumulation after BRCA2 inactivation. Thus, an unrecognized role for BRCA2 in the transition from promoter-proximal pausing to productive elongation via augmented PAF1 recruitment to RNAPII is subverted by disease-causing mutations, provoking R-loop-mediated DNA breakage in BRCA2-deficient cells.

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


    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.

  3. Mass Inflation in the Loop Black Hole

    CERN Document Server

    Brown, Eric G; Modesto, Leonardo


    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 DTR 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 DTR 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.

  4. Feedback Loop Gains and Feedback Behavior (1996)

    DEFF Research Database (Denmark)

    Kampmann, Christian Erik


    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...

  5. Osmotic mechanism of the loop extrusion process (United States)

    Yamamoto, Tetsuya; Schiessel, Helmut


    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.

  6. Carrier tracking algorithm based on joint acquisition of frequency locked loop and phase locked loop

    Directory of Open Access Journals (Sweden)

    Gao Kang


    Full Text Available Aiming at the problem of frequency step in the frequency lock loop (FLL - phase lock loop (PLL carrier tracking algorithm’s conversion state, presenting an improved algorithm: PLL and FLL joint acquisition to replace the single FLL acquires frequency, and deduce the loop state transition threshold. The simulation results show that the improved algorithm is more stable in the conversion process, and the loop performance is optimized. When the SNR is -10dB, and has the acceleration rate, the tracking loop does not have a frequency step at the time of conversion, achieving the design purpose.

  7. 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.

  8. Loops in exceptional field theory

    Energy Technology Data Exchange (ETDEWEB)

    Bossard, Guillaume [Centre de Physique Théorique, Ecole Polytechnique, CNRS, Université Paris-Saclay,91128 Palaiseau cedex (France); Kleinschmidt, Axel [Max-Planck-Institut für Gravitationsphysik (Albert-Einstein-Institut),Am Mühlenberg 1, DE-14476 Potsdam (Germany); International Solvay Institutes,ULB-Campus Plaine CP231, BE-1050 Brussels (Belgium)


    We study certain four-graviton amplitudes in exceptional field theory in dimensions D≥4 up to two loops. As the formulation is manifestly invariant under the U-duality group E{sub 11−D}(ℤ), our resulting expressions can be expressed in terms of automorphic forms. In the low energy expansion, we find terms in the M-theory effective action of type R{sup 4}, ∇{sup 4}R{sup 4} and ∇{sup 6}R{sup 4} with automorphic coefficient functions in agreement with independent derivations from string theory. This provides in particular an explicit integral formula for the exact string theory ∇{sup 6}R{sup 4} threshold function. We exhibit moreover that the usual supergravity logarithmic divergences cancel out in the full exceptional field theory amplitude, within an appropriately defined dimensional regularisation scheme. We also comment on terms of higher derivative order and the role of the section constraint for possible counterterms.

  9. Theory of loop flows and instability (United States)

    Priest, E. R.

    A preliminary theory for the steady and transient coronal loop flows in solar active regions and their magnetohydrodynamic instability is presented. Siphon flow is shown to be possible in the loops if a pressure difference is maintained between the footpoints, and to account for the presence of cool cores and appearances of only half a loop. The evolution of active region magnetic loops is found to lead to the continual evaporation and draining of the plasma contained within them, particularly as a result of an increase in heating rate. Consideration of static models for thermally isolated loops reveals them to be thermally unstable, implying that in the absence of some atmospheric stabilizing mechanism, the loops must be in a dynamic state of thermal activity. It is shown that kilogauss photospheric fields may be formed by an intense magnetic field instability, with an associated transient downflow which may induce coronal flows at enhanced velocities. Magnetohydrodynamic stability analysis suggests that the major cause of magnetic stability may be line-tying of loop footpoints in the dense photosphere.

  10. Iterative structure of finite loop integrals

    Energy Technology Data Exchange (ETDEWEB)

    Caron-Huot, Simon [Institute for Advanced Study, Princeton, NJ 08540 (United States); Niels Bohr International Academy and Discovery Center, Blegdamsvej 17, Copenhagen 2100 (Denmark); Henn, Johannes M. [Institute for Advanced Study, Princeton, NJ 08540 (United States)


    In this paper we develop further and refine the method of differential equations for computing Feynman integrals. In particular, we show that an additional iterative structure emerges for finite loop integrals. As a concrete non-trivial example we study planar master integrals of light-by-light scattering to three loops, and derive analytic results for all values of the Mandelstam variables s and t and the mass m. We start with a recent proposal for defining a basis of loop integrals having uniform transcendental weight properties and use this approach to compute all planar two-loop master integrals in dimensional regularization. We then show how this approach can be further simplified when computing finite loop integrals. This allows us to discuss precisely the subset of integrals that are relevant to the problem. We find that this leads to a block triangular structure of the differential equations, where the blocks correspond to integrals of different weight. We explain how this block triangular form is found in an algorithmic way. Another advantage of working in four dimensions is that integrals of different loop orders are interconnected and can be seamlessly discussed within the same formalism. We use this method to compute all finite master integrals needed up to three loops. Finally, we remark that all integrals have simple Mandelstam representations.

  11. Hexagon Wilson Loop OPE and Harmonic Polylogarithms

    CERN Document Server

    Papathanasiou, Georgios


    A recent, integrability-based conjecture in the framework of the Wilson loop OPE for N=4 SYM theory, predicts the leading OPE contribution for the hexagon MHV remainder function and NMHV ratio function to all loops, in integral form. We prove that these integrals evaluate to a particular basis of harmonic polylogarithms, at any order in the weak coupling expansion. The proof constitutes an algorithm for the direct computation of the integrals, which we employ in order to obtain the full (N)MHV OPE contribution in question up to 6 loops, and certain parts of it up to 12 loops. We attach computer-readable files with our results, as well as an algorithm implementation which may be readily used to generate higher-loop corrections. The feasibility of obtaining the explicit kinematical dependence of the first term in the OPE in principle at arbitrary loop order, offers promise for the suitability of this approach as a non-perturbative description of Wilson loops/scattering amplitudes.

  12. The physics of protein-DNA interaction networks in the control of gene expression (United States)

    Saiz, Leonor


    Protein-DNA interaction networks play a central role in many fundamental cellular processes. In gene regulation, physical interactions and reactions among the molecular components together with the physical properties of DNA control how genes are turned on and off. A key player in all these processes is the inherent flexibility of DNA, which provides an avenue for long-range interactions between distal DNA elements through DNA looping. Such versatility enables multiple interactions and results in additional complexity that is remarkably difficult to address with traditional approaches. This topical review considers recent advances in statistical physics methods to study the assembly of protein-DNA complexes with loops, their effects in the control of gene expression, and their explicit application to the prototypical lac operon genetic system of the E. coli bacterium. In the last decade, it has been shown that the underlying physical properties of DNA looping can actively control transcriptional noise, cell-to-cell variability, and other properties of gene regulation, including the balance between robustness and sensitivity of the induction process. These physical properties are largely dependent on the free energy of DNA looping, which accounts for DNA bending and twisting effects. These new physical methods have also been used in reverse to uncover the actual in vivo free energy of looping double-stranded DNA in living cells, which was not possible with existing experimental techniques. The results obtained for DNA looping by the lac repressor inside the E. coli bacterium showed a more malleable DNA than expected as a result of the interplay of the simultaneous presence of two distinct conformations of looped DNA.

  13. Infectivity analysis of two variable DNA B components of Mungbean ...

    Indian Academy of Sciences (India)


    Mungbean yellow mosaic virus-Vigna; NES, nuclear export signal; NLS, nuclear localization signal; nt, nucleotide; oc, open circu- lar; OD, optical density; ORF ..... upstream of the stem-loop structure in all five DNA Bs of. MYMV-Vig. Four DNA ..... features (3-nt deletion in first iteron and the 18-nt inser- tion) were also found in ...

  14. 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


    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.

  15. Polyakov loop correlator in perturbation theory (United States)

    Berwein, Matthias; Brambilla, Nora; Petreczky, Péter; Vairo, Antonio


    We study the Polyakov loop correlator in the weak coupling expansion and show how the perturbative series reexponentiates into singlet and adjoint contributions. We calculate the order g7 correction to the Polyakov loop correlator in the short distance limit. We show how the singlet and adjoint free energies arising from the reexponentiation formula of the Polyakov loop correlator are related to the gauge invariant singlet and octet free energies that can be defined in pNRQCD, namely we find that the two definitions agree at leading order in the multipole expansion, but differ at first order in the quark-antiquark distance.

  16. Eigenvalue distributions of Wilson loops

    Energy Technology Data Exchange (ETDEWEB)

    Lohmayer, Robert


    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

  17. Loop Diuretics in the Treatment of Hypertension. (United States)

    Malha, Line; Mann, Samuel J


    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.

  18. A theory of desynchronisable closed loop system

    Directory of Open Access Journals (Sweden)

    Harsh Beohar


    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.

  19. The Universal One-Loop Effective Action

    CERN Document Server

    Drozd, Aleksandra; Quevillon, Jérémie; You, Tevong


    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.

  20. Hardware-in-the-Loop Testing (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...

  1. Mathematical Modeling of Loop Heat Pipes (United States)

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


    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.

  2. Nonequilibrium Chromosome Looping via Molecular Slip Links (United States)

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


    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.

  3. TRF2 binds branched DNA to safeguard telomere integrity. (United States)

    Schmutz, Isabelle; Timashev, Leonid; Xie, Wei; Patel, Dinshaw J; de Lange, Titia


    Although t-loops protect telomeres, they are at risk of cleavage by Holliday junction (HJ) resolvases if branch migration converts the three-way t-loop junction into four-way HJs. T-loop cleavage is repressed by the TRF2 basic domain, which binds three- and four-way junctions and protects HJs in vitro. By replacing the basic domain with bacterial-protein domains binding three- and four-way junctions, we demonstrated the in vivo relevance of branched-DNA binding. Branched-DNA binding also repressed PARP1, presumably by masking the PARP1 site in the t-loop junction. Although PARP1 recruits HJ resolvases and promotes t-loop cleavage, PARP1 activation alone did not result in t-loop cleavage, thus suggesting that the basic domain also prevents formation of HJs. Concordantly, removal of HJs by BLM helicase mitigated t-loop cleavage in response to loss of the basic domain. We propose that TRF2 masks and stabilizes the t-loop three-way junction, thereby protecting telomeres from detrimental deletions and PARP1 activation.

  4. New crown motif of an HIV-1 V3 loop sequence from a Ugandan AIDS patient. (United States)

    von Brunn, A; von Brunn, B; Eberle, J; Biryahwaho, B; Downing, R G; Gürtler, L


    HIV-1 V3 loop sequences from Ugandan patients include motifs from subtypes A, B, and D. To characterize further HIV isolates, V3 loop sequences were amplified from HIV-1 isolated in 1987 from peripheral blood mononuclear cells (PBL) of three patients with full-blown AIDS from Kampala, Uganda. The PBL were separated by Ficoll Paque gradients and cocultivated with noninfected donor lymphocytes for two weeks. The HIV was then transferred to HUT-78 cells. From extracted DNA of the permanently-infected HUT-78 cells, nested polymerase chain reaction (PCR) was conducted, with V3 loop sequencing performed directly upon PCR fragments derived from two independent DNA preparations and on cloned fragments. Isolates MVP-9801, -9802, and -9803 show 35.6%, 32.4%, and 29.7% nucleotide sequence divergence from the ELI subtype D sequence; 31.5%, 25.7%, and 18.9% divergence from the Z2Z6 subtype D sequence; and 21.9%, 12.2%, and 12.2% divergence from the subtype D consensus sequence. All three deduced amino acid sequences fit into the subtype D consensus sequence rather than into other V3 loop sequences described for Ugandan subtype A isolates. MVP-9802 and MVP-9803 contain the GSGQA pentapeptide motif at the tip of the V3 loop, while MVP-9801 contains GGRA. This may be explained by a deletion of proline codon between the codons for the two glycine residues. The authors believe that this deletion has not been previously reported. They also note that the deletion does not appear to be associated with a growth difference in vitro or with a difference in pathogenicity in vivo. The immunogenic implications of this altered V3 loop crest remain unclear. The Western blot profiles for the gp160, gp120, and gp41 proteins of the three Ugandan isolates manifest normal molecular weights.

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

  6. Laser welding closed-loop power control

    DEFF Research Database (Denmark)

    Bagger, Claus; Olsen, Flemming Ove


    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. Design configurations of the methanol synthesis loop


    Bøhn, Kristian


    In recent years the chemical industry has undergone considerable changes due to increased environmental regulations and energy costs. This master thesis has evaluated three different design considerations of the methanol synthesis loop using Honeywell's general purpose process simulator UniSim Design (R380 Build 14027) combined with MathWorks programming language MATLAB. The three configurations are Lurgis methanol reactor loop as built on Tjeldbergodden, the use of interstage methanol remova...

  8. Loop residues and catalysis in OMP synthase

    DEFF Research Database (Denmark)

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


    (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...... of the catalytic loop, which when closed, produces rapid and reversible catalysis....

  9. Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus tokodaii and a function of tyrosine 170 in DNA binding. (United States)

    Kawai, Akito; Higuchi, Shigesada; Tsunoda, Masaru; Nakamura, Kazuo T; Yamagata, Yuriko; Miyamoto, Shuichi


    Uracil-DNA glycosylases (UDGs) excise uracil from DNA by catalyzing the N-glycosidic bond hydrolysis. Here we report the first crystal structures of an archaeal UDG (stoUDG). Compared with other UDGs, stoUDG has a different structure of the leucine-intercalation loop, which is important for DNA binding. The stoUDG-DNA complex model indicated that Leu169, Tyr170, and Asn171 in the loop are involved in DNA intercalation. Mutational analysis showed that Tyr170 is critical for substrate DNA recognition. These results indicate that Tyr170 occupies the intercalation site formed after the structural change of the leucine-intercalation loop required for the catalysis. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  10. 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.

  11. 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)


    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.

  12. Space Station evolution study oxygen loop closure (United States)

    Wood, M. G.; Delong, D.


    In the current Space Station Freedom (SSF) Permanently Manned Configuration (PMC), physical scars for closing the oxygen loop by the addition of oxygen generation and carbon dioxide reduction hardware are not included. During station restructuring, the capability for oxygen loop closure was deferred to the B-modules. As such, the ability to close the oxygen loop in the U.S. Laboratory module (LAB A) and the Habitation A module (HAB A) is contingent on the presence of the B modules. To base oxygen loop closure of SSF on the funding of the B-modules may not be desirable. Therefore, this study was requested to evaluate the necessary hooks and scars in the A-modules to facilitate closure of the oxygen loop at or subsequent to PMC. The study defines the scars for oxygen loop closure with impacts to cost, weight and volume and assesses the effects of byproduct venting. In addition, the recommended scenarios for closure with regard to topology and packaging are presented.

  13. A note on two-loop superloop

    Energy Technology Data Exchange (ETDEWEB)

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


    We explore the duality between supersymmetric Wilson loop on null polygonal contours in maximally supersymmetric Yang-Mills theory and next-to-maximal helicity violating (NMHV) scattering amplitudes. Earlier analyses demonstrated that the use of a dimensional regulator for ultraviolet divergences, induced due to presence of the cusps on the loop, yields anomalies that break both conformal symmetry and supersymmetry. At one-loop order, these are present only in Grassmann components localized in the vicinity of a single cusp and result in a universal function for any number of sites of the polygon that can be subtracted away in a systematic manner leaving a well-defined supersymmetric remainder dual to corresponding components of the superamplitude. The question remains though whether components which were free from the aforementioned supersymmetric anomaly at leading order of perturbation theory remain so once computed at higher orders. Presently we verify this fact by calculating a particular component of the null polygonal super Wilson loop at two loops restricting the contour kinematics to a two-dimensional subspace. This allows one to perform all computations in a concise analytical form and trace the pattern of cancellations between individual Feynman graphs in a transparent fashion. As a consequence of our consideration we obtain a dual conformally invariant result for the remainder function in agreement with one-loop NMHV amplitudes.

  14. Super-resolution fluorescence imaging of telomeres reveals TRF2-dependent T-loop formation. (United States)

    Doksani, Ylli; Wu, John Y; de Lange, Titia; Zhuang, Xiaowei


    We have applied a super-resolution fluorescence imaging method, stochastic optical reconstruction microscopy (STORM), to visualize the structure of functional telomeres and telomeres rendered dysfunctional through removal of shelterin proteins. The STORM images showed that functional telomeres frequently exhibit a t-loop configuration. Conditional deletion of individual components of shelterin showed that TRF2 was required for the formation and/or maintenance of t-loops, whereas deletion of TRF1, Rap1, or the POT1 proteins (POT1a and POT1b) had no effect on the frequency of t-loop occurrence. Within the shelterin complex, TRF2 uniquely serves to protect telomeres from two pathways that are initiated on free DNA ends: classical nonhomologous end-joining (NHEJ) and ATM-dependent DNA damage signaling. The TRF2-dependent remodeling of telomeres into t-loop structures, which sequester the ends of chromosomes, can explain why NHEJ and the ATM signaling pathway are repressed when TRF2 is present. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. Telomere Length Determines TERRA and R-Loop Regulation through the Cell Cycle. (United States)

    Graf, Marco; Bonetti, Diego; Lockhart, Arianna; Serhal, Kamar; Kellner, Vanessa; Maicher, André; Jolivet, Pascale; Teixeira, Maria Teresa; Luke, Brian


    Maintenance of a minimal telomere length is essential to prevent cellular senescence. When critically short telomeres arise in the absence of telomerase, they can be repaired by homology-directed repair (HDR) to prevent premature senescence onset. It is unclear why specifically the shortest telomeres are targeted for HDR. We demonstrate that the non-coding RNA TERRA accumulates as HDR-promoting RNA-DNA hybrids (R-loops) preferentially at very short telomeres. The increased level of TERRA and R-loops, exclusively at short telomeres, is due to a local defect in RNA degradation by the Rat1 and RNase H2 nucleases, respectively. Consequently, the coordination of TERRA degradation with telomere replication is altered at shortened telomeres. R-loop persistence at short telomeres contributes to activation of the DNA damage response (DDR) and promotes recruitment of the Rad51 recombinase. Thus, the telomere length-dependent regulation of TERRA and TERRA R-loops is a critical determinant of the rate of replicative senescence. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Hybrid Combustion-Gasification Chemical Looping

    Energy Technology Data Exchange (ETDEWEB)

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


    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

  17. Mitochondrial DNA. (United States)

    Wright, Russell G.; Bottino, Paul J.


    Provides background information for teachers on mitochondrial DNA, pointing out that it may have once been a free-living organism. Includes a ready-to-duplicate exercise titled "Using Microchondrial DNA to Measure Evolutionary Distance." (JN)

  18. Detection of fish nocardiosis by loop-mediated isothermal amplification. (United States)

    Itano, T; Kawakami, H; Kono, T; Sakai, M


    Loop-mediated isothermal amplification (LAMP) is a novel method that amplifies DNA with high specificity and rapidity under isothermal conditions. In this study, using the LAMP method, a protocol for detecting Nocardia seriolae which is a causative agent of fish nocardiosis, was designed. A set of four primers, two inner and two outer, were designed based on the sequence of the 16S-23S ribosomal RNA internal transcribed spacer region of N. seriolae. Time and temperature conditions for detection of N. seriolae were optimized for 60 min at 65 degrees C. Other fish pathogen was not amplified by this LAMP system. The detection of N. seriola using LAMP was found to be more sensitive than that by polymerase chain reaction. LAMP is a highly sensitive and rapid diagnostic procedure for detection of N. seriolae. LAMP is a useful diagnostic method for fish nocardiosis.

  19. Modeling DNA (United States)

    Robertson, Carol


    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…

  20. Dangerous R loops form in the absence of H3K9 methylation

    DEFF Research Database (Denmark)

    Salcini, Anna Elisabetta


    Methylation of histone H3 on lysine 9 (H3K9) is a hallmark of transcriptionally inactive heterochromatin that is deregulated in pathological conditions. A new study shows that complete loss of H3K9 methylation in Caenorhabditis elegans leads to derepression of repetitive elements and formation of...... of DNA:RNA hybrids (R loops), resulting in increased rates of repeat-specific mutation....

  1. Structure of the Rad50 DNA double-strand break repair protein in complex with DNA. (United States)

    Rojowska, Anna; Lammens, Katja; Seifert, Florian U; Direnberger, Carolin; Feldmann, Heidi; Hopfner, Karl-Peter


    The Mre11-Rad50 nuclease-ATPase is an evolutionarily conserved multifunctional DNA double-strand break (DSB) repair factor. Mre11-Rad50's mechanism in the processing, tethering, and signaling of DSBs is unclear, in part because we lack a structural framework for its interaction with DNA in different functional states. We determined the crystal structure of Thermotoga maritima Rad50(NBD) (nucleotide-binding domain) in complex with Mre11(HLH) (helix-loop-helix domain), AMPPNP, and double-stranded DNA. DNA binds between both coiled-coil domains of the Rad50 dimer with main interactions to a strand-loop-helix motif on the NBD. Our analysis suggests that this motif on Rad50 does not directly recognize DNA ends and binds internal sites on DNA. Functional studies reveal that DNA binding to Rad50 is not critical for DNA double-strand break repair but is important for telomere maintenance. In summary, we provide a structural framework for DNA binding to Rad50 in the ATP-bound state. © 2014 The Authors.

  2. Cytosine deamination and base excision repair cause R-loop-induced CAG repeat fragility and instability in Saccharomyces cerevisiae. (United States)

    Su, Xiaofeng A; Freudenreich, Catherine H


    CAG/CTG repeats are structure-forming repetitive DNA sequences, and expansion beyond a threshold of ∼35 CAG repeats is the cause of several human diseases. Expanded CAG repeats are prone to breakage, and repair of the breaks can cause repeat contractions and expansions. In this study, we found that cotranscriptional R-loops formed at a CAG-70 repeat inserted into a yeast chromosome. R-loops were further elevated upon deletion of yeast RNaseH genes and caused repeat fragility. A significant increase in CAG repeat contractions was also observed, consistent with previous human cell studies. Deletion of yeast cytosine deaminase Fcy1 significantly decreased the rate of CAG repeat fragility and contractions in the rnh1Δrnh201Δ background, indicating that Fcy1-mediated deamination is one cause of breakage and contractions in the presence of R-loops. Furthermore, base excision repair (BER) is responsible for causing CAG repeat contractions downstream of Fcy1, but not fragility. The Rad1/XPF and Rad2/XPG nucleases were also important in protecting against contractions, but through BER rather than nucleotide excision repair. Surprisingly, the MutLγ (Mlh1/Mlh3) endonuclease caused R-loop-dependent CAG fragility, defining an alternative function for this complex. These findings provide evidence that breakage at expanded CAG repeats occurs due to R-loop formation and reveal two mechanisms for CAG repeat instability: one mediated by cytosine deamination of DNA engaged in R-loops and the other by MutLγ cleavage. Since disease-causing CAG repeats occur in transcribed regions, our results suggest that R-loop-mediated fragility is a mechanism that could cause DNA damage and repeat-length changes in human cells.

  3. Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris). (United States)

    Zhang, Wenping; Zhang, Zhihe; Shen, Fujun; Hou, Rong; Lv, Xiaoping; Yue, Bisong


    Using oligonucleotide primers designed to match hypervariable segments I (HVS-1) of Panthera tigris mitochondrial DNA (mtDNA), we amplified two different PCR products (500 bp and 287 bp) in the tiger (Panthera tigris), but got only one PCR product (287 bp) in the leopard (Panthera pardus). Sequence analyses indicated that the sequence of 287 bp was a D-loop-like nuclear mitochondrial sequence (Numts), indicating a nuclear transfer that occurred approximately 4.8-17 million years ago in the tiger and 4.6-16 million years ago in the leopard. Although the mtDNA D-loop sequence has a rapid rate of evolution, the 287-bp Numts are highly conserved; they are nearly identical in tiger subspecies and only 1.742% different between tiger and leopard. Thus, such sequences represent molecular 'fossils' that can shed light on evolution of the mitochondrial genome and may be the most appropriate outgroup for phylogenetic analysis. This is also proved by comparing the phylogenetic trees reconstructed using the D-loop sequence of snow leopard and the 287-bp Numts as outgroup.

  4. Students' Understanding of Loops and Nested Loops in Computer Programming: An APOS Theory Perspective (United States)

    Cetin, Ibrahim


    The purpose of this study is to explore students' understanding of loops and nested loops concepts. Sixty-three mechanical engineering students attending an introductory programming course participated in the study. APOS (Action, Process, Object, Schema) is a constructivist theory developed originally for mathematics education. This study is the…

  5. Open-loop versus closed-loop control of MEMS devices: choices and issues (United States)

    Borovic, B.; Liu, A. Q.; Popa, D.; Cai, H.; Lewis, F. L.


    From a controls point of view, micro electromechanical systems (MEMS) can be driven in an open-loop and closed-loop fashion. Commonly, these devices are driven open-loop by applying simple input signals. If these input signals become more complex by being derived from the system dynamics, we call such control techniques pre-shaped open-loop driving. The ultimate step for improving precision and speed of response is the introduction of feedback, e.g. closed-loop control. Unlike macro mechanical systems, where the implementation of the feedback is relatively simple, in the MEMS case the feedback design is quite problematic, due to the limited availability of sensor data, the presence of sensor dynamics and noise, and the typically fast actuator dynamics. Furthermore, a performance comparison between open-loop and closed-loop control strategies has not been properly explored for MEMS devices. The purpose of this paper is to present experimental results obtained using both open- and closed-loop strategies and to address the comparative issues of driving and control for MEMS devices. An optical MEMS switching device is used for this study. Based on these experimental results, as well as computer simulations, we point out advantages and disadvantages of the different control strategies, address the problems that distinguish MEMS driving systems from their macro counterparts, and discuss criteria to choose a suitable control driving strategy.

  6. Quantum hysteresis loops in microscopic system: The loop area as a ...

    Indian Academy of Sciences (India)

    Effects of non-zero temperatures are explored with reference to a symmetric double well potential. The barrier crossing or, relaxation rates are shown to correlate systematically with the area of the loop. The possible use of hysteresis loop area in designing field parameters for optimal control is suggested.

  7. Parameterizing loop fusion for automated empirical tuning

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Y; Yi, Q; Kennedy, K; Quinlan, D; Vuduc, R


    Traditional compilers are limited in their ability to optimize applications for different architectures because statically modeling the effect of specific optimizations on different hardware implementations is difficult. Recent research has been addressing this issue through the use of empirical tuning, which uses trial executions to determine the optimization parameters that are most effective on a particular hardware platform. In this paper, we investigate empirical tuning of loop fusion, an important transformation for optimizing a significant class of real-world applications. In spite of its usefulness, fusion has attracted little attention from previous empirical tuning research, partially because it is much harder to configure than transformations like loop blocking and unrolling. This paper presents novel compiler techniques that extend conventional fusion algorithms to parameterize their output when optimizing a computation, thus allowing the compiler to formulate the entire configuration space for loop fusion using a sequence of integer parameters. The compiler can then employ an external empirical search engine to find the optimal operating point within the space of legal fusion configurations and generate the final optimized code using a simple code transformation system. We have implemented our approach within our compiler infrastructure and conducted preliminary experiments using a simple empirical search strategy. Our results convey new insights on the interaction of loop fusion with limited hardware resources, such as available registers, while confirming conventional wisdom about the effectiveness of loop fusion in improving application performance.

  8. Logical inference techniques for loop parallelization

    KAUST Repository

    Oancea, Cosmin E.


    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.

  9. Numerical simulation of a natural circulation loop

    Energy Technology Data Exchange (ETDEWEB)

    Verissimo, Gabriel L.; Moreira, Maria de Lourdes; Faccini, Jose Luiz H., E-mail: gabrielverissimo@poli.ufrj.b, E-mail:, E-mail: [Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil)


    This work presents a numerical simulation of a natural circulation loop using computational fluid dynamics. The simulated loop is an experimental model in a reduced scale of 1:10 of a passive heat removal system typical of advanced PWR reactors. The loop is composed of a heating vessel containing 52 electric heaters, a vertical shell-tube heat exchanger and a column of expansion. The working fluid is distilled water. Initially it was created a tridimensional geometric model of the loop components. After that, it was generated a tridimensional mesh of finite elements in order to calculate the variables of the problem. The boundaries of the numerical simulation were the power of the electric resistances and the cooling flow in the secondary side of the heat exchanger. The initial conditions were the temperature, the pressure and the fluid velocity at the time just before the power has been switched on. The results of this simulation were compared with the experimental data, in terms of the evolution of the temperatures in different locations of the loop, and of the average natural circulation flow as a function of time for a given power. (author)

  10. Coronal Loops: Observations and Modeling of Confined Plasma

    Directory of Open Access Journals (Sweden)

    Fabio Reale


    Full Text Available Coronal loops are the building blocks of the X-ray bright solar corona. They owe their brightness to the dense confined plasma, and this review focuses on loops mostly as structures confining plasma. After a brief historical overview, the review is divided into two separate but not independent parts: the first illustrates the observational framework, the second reviews the theoretical knowledge. Quiescent loops and their confined plasma are considered, and therefore topics such as loop oscillations and flaring loops (except for non-solar ones which provide information on stellar loops are not specifically addressed here. The observational section discusses loop classification and populations, and then describes the morphology of coronal loops, its relationship with the magnetic field, and the concept of loops as multi-stranded structures. The following part of this section is devoted to the characteristics of the loop plasma and of its thermal structure in particular, according to the classification into hot, warm, and cool loops. Then, temporal analyses of loops and the observations of plasma dynamics and flows are illustrated. In the modeling section some basics of loop physics are provided, supplying some fundamental scaling laws and timescales, a useful tool for consultation. The concept of loop modeling is introduced and models are distinguished between those treating loops as monolithic and static, and those resolving loops into thin and dynamic strands. Then, more specific discussions address modeling the loop fine structure and the plasma flowing along the loops. Special attention is devoted to the question of loop heating, with separate discussion of wave (AC and impulsive (DC heating. Finally, a brief discussion about stellar X-ray emitting structures related to coronal loops is included and followed by conclusions and open questions.

  11. 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)


    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.

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

    KAUST Repository

    Wang, Yong


    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.

  13. 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.

  14. Mitochondrial D310 D-Loop instability and histological subtypes in radiation-induced cutaneous basal cell carcinomas. (United States)

    Boaventura, Paula; Pereira, Dina; Mendes, Adélia; Batista, Rui; da Silva, André Ferreira; Guimarães, Isabel; Honavar, Mrinalini; Teixeira-Gomes, José; Lopes, José Manuel; Máximo, Valdemar; Soares, Paula


    Basal cell carcinoma (BCC) is the most frequent skin cancer. An elevated prevalence of BCC has been associated with radiation, namely after the Tinea capitis epilation treatment, being these tumors described as more aggressive. Mitochondrial DNA (mtDNA) mutations have been reported in many human tumors, but their occurrence in BCC is poorly documented. The purpose of this work was to evaluate BCC histological subtypes in individuals subjected to X-ray epilation for Tinea capitis treatment when compared to non-irradiated patients. Moreover we also wanted to evaluate mitochondrial D-Loop instability in both groups of BCCs in order to compare the frequency of D-Loop mutations in post-irradiation BCC versus sporadic BCC. 228 histological specimens corresponding to BCCs from 75 irradiated patients and 60 non-irradiated patients were re-evaluated for histological subtype. Subsequently, we sequenced the D-Loop 310 repeat in blood, oral mucosa, tumor lesions and, whenever available, non-tumoral adjacent tissue from these patients. The infiltrative subtype of BCC, considered to be more aggressive, was significantly more frequent in irradiated patients. BCC D-Loop D310 mutation rate was significantly higher in irradiated BCCs than in the non-irradiated ones. Moreover, it was associated with a higher irradiation dose. The presence of mtDNA heteroplasmy in patients' blood was associated with a higher mutation rate in the BCCs suggesting that a more unstable genotype could predispose to mtDNA somatic mutation. Our results suggest that radiation-induced BCCs may be considered to be more aggressive tumors. Further studies are needed to clarify the role of mtDNA D-Loop mutations in tumors from irradiated patients. Copyright © 2013 Japanese Society for Investigative Dermatology. Published by Elsevier Ireland Ltd. All rights reserved.

  15. 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)


    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.

  16. Solar flare loops observations and interpretations

    CERN Document Server

    Huang, Guangli; Ji, Haisheng; Ning, Zongjun


    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.

  17. 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 (DESY), Zeuthen (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)


    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.)

  18. Hybrid Models in Loop Quantum Cosmology

    CERN Document Server

    Navascués, B Elizaga; Marugán, G A Mena


    In the framework of Loop Quantum Cosmology, inhomogeneous models are usually quantized by means of a hybrid approach that combines loop quantization techniques with standard quantum field theory methods. This approach is based on a splitting of the phase space in a homogeneous sector, formed by global, zero-modes, and an inhomogeneous sector, formed by the remaining, infinite number of modes, that describe the local degrees of freedom. Then, the hybrid quantization is attained by adopting a loop representation for the homogeneous gravitational sector, while a Fock representation is used for the inhomogeneities. The zero-mode of the Hamiltonian constraint operator couples the homogeneous and inhomogeneous sectors. The hybrid approach, therefore, is expected to provide a suitable quantum theory in regimes where the main quantum effects of the geometry are those affecting the zero-modes, while the inhomogeneities, still being quantum, can be treated in a more conventional way. This hybrid strategy was first prop...

  19. All Digital Phase-Locked Loop

    Directory of Open Access Journals (Sweden)

    Marijan Jurgo


    Full Text Available The paper reviews working principles of phase-locked loop and drawbacks of classical PLL structure in nanometric technologies. It is proposed to replace the classical structure by all-digital phase-locked loop structure. Authors described the main blocks of all-digital phase-locked loop (time to digital converter and digitally controlled oscillator and overviewed the quantization noise arising in these blocks as well as its minimization strategies. The calculated inverter delay in 65 nm CMOS technology was from 8.64 to 27.71 ps and time to digital converter quantization noise was from −104.33 to −82.17 dBc/Hz, with tres = 8.64–27.71 ps, TSVG = 143–333 ps, FREF = 20–60 MHz.Article in Lithuanian

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


    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.

  1. Coronal Loops: Evolving Beyond the Isothermal Approximation (United States)

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


    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.

  2. Relaxed specificity of prokaryotic DNA methyltransferases results in DNA site-specific modification of RNA/DNA heteroduplexes. (United States)

    Wons, Ewa; Mruk, Iwona; Kaczorowski, Tadeusz


    RNA/DNA hybrid duplexes regularly occur in nature, for example in transcriptional R loops. Their susceptibility to modification by DNA-specific or RNA-specific enzymes is, thus, a biologically relevant question, which, in addition, has possible biotechnological implications. In this study, we investigated the activity of four isospecific DNA methyltransferases (M.EcoVIII, M.LlaCI, M.HindIII, M.BstZ1II) toward an RNA/DNA duplex carrying one 5'-AAGCUU-3'/3'-TTCGAA-5' target sequence. The analyzed enzymes belong to the β-group of adenine N6-methyltransferases and recognize the palindromic DNA sequence 5'-AAGCTT-3'/3'-TTCGAA-5'. Under standard conditions, none of these isospecific enzymes could detectibly methylate the RNA/DNA duplex. However, the addition of agents that generally relax specificity, such as dimethyl sulfoxide (DMSO) and glycerol, resulted in substantial methylation of the RNA/DNA duplex by M.EcoVIII and M.LlaCI. Only the DNA strand of the RNA/DNA duplex was methylated. The same was not observed for M.HindIII or M.BstZ1II. This is, to our knowledge, the first report that demonstrates such activity by prokaryotic DNA methyltransferases. Possible applications of these findings in a laboratory practice are also discussed.

  3. Coronal Loops: Observations and Modeling of Confined Plasma

    Directory of Open Access Journals (Sweden)

    Fabio Reale


    Full Text Available Coronal loops are the building blocks of the X-ray bright solar corona. They owe their brightness to the dense confined plasma, and this review focuses on loops mostly as structures confining plasma. After a brief historical overview, the review is divided into two separate but not independent parts: the first illustrates the observational framework, the second reviews the theoretical knowledge. Quiescent loops and their confined plasma are considered and, therefore, topics such as loop oscillations and flaring loops (except for non-solar ones, which provide information on stellar loops are not specifically addressed here. The observational section discusses the classification, populations, and the morphology of coronal loops, its relationship with the magnetic field, and the loop stranded structure. The section continues with the thermal properties and diagnostics of the loop plasma, according to the classification into hot, warm, and cool loops. Then, temporal analyses of loops and the observations of plasma dynamics, hot and cool flows, and waves are illustrated. In the modeling section, some basics of loop physics are provided, supplying fundamental scaling laws and timescales, a useful tool for consultation. The concept of loop modeling is introduced and models are divided into those treating loops as monolithic and static, and those resolving loops into thin and dynamic strands. More specific discussions address modeling the loop fine structure and the plasma flowing along the loops. Special attention is devoted to the question of loop heating, with separate discussion of wave (AC and impulsive (DC heating. Large-scale models including atmosphere boxes and the magnetic field are also discussed. Finally, a brief discussion about stellar coronal loops is followed by highlights and open questions.

  4. Rational Design of Nanobody80 Loop Peptidomimetics

    DEFF Research Database (Denmark)

    Martin, Charlotte; Moors, Samuel L C; Danielsen, Mia


    G protein-coupled receptors (GPCRs) play an important role in many cellular responses; as such, their mechanism of action is of utmost interest. To gain insight into the active conformation of GPCRs, the X-ray crystal structures of nanobody (Nb)-stabilized β2 -adrenergic receptor (β2 AR) have been...... that peptidomimetics of the CDR3 loop might be sufficient for binding to the receptor, inhibiting the interaction of β2 AR with intracellular GPCR interacting proteins (e.g., G proteins). Based on previous crystallographic data, a set of peptidomimetics were synthesized that, similar to the Nb80 CDR3 loop, adopt a β...

  5. On closed loop transient response system identification

    Directory of Open Access Journals (Sweden)

    Christer Dalen


    Full Text Available Some methods for transient closed loop step response system identification presented in the literature are reviewed. Interestingly some errors in a method published in the early 80's where propagated into a recently published method. These methods are reviewed and some improved methods are suggested and presented. The methods are compared against each other on some closed loop system examples, e.g. a well pipeline-riser severe-slugging flow regime example, using Monte Carlo simulations for comparison of the methods.

  6. Thermal coupling within LTP dynamics control loop

    Energy Technology Data Exchange (ETDEWEB)

    Nofrarias, M; Garcia Marin, A F; Heinzel, G; Hewitson, M; Danzmann, K [Max-Planck-Institut fuer Gravitationsphysik, Albert Einstein Institut (AEI), Callinstrasse 38, 30167 Hannover (Germany); Lobo, A; Sanjuan, J [Institut de Ciencies de l' Espai (ICE-CSIC), Facultat de Ciencies, Torre C5, 08193 Bellaterra (Spain); Ramos-Castro, J, E-mail: miquel.nofrarias@aei.mpg.d [Departament d' Enginyeria Electronica, UPC, Campus Nord, Edifici C4, Jordi Girona 1-3, 08034 Barcelona (Spain)


    The Diagnostic Subsytem in the LISA Technology Package (LTP) on board the LISA Pathfinder mission (LPF) will characterise those external disturbances with a potential impact on the performance of the experiment coming from either thermal, magnetic or charged particles perturbations. A correct design of the experiments to measure these effects in flight requires a closed loop analysis that takes into account the dynamics of the test masses, the force applied by the controllers and those noisy terms (coming from sensing or force noise) that enters into the loop. We describe this analysis in the thermal case and we give a first numerical example of the instrument response to controlled thermal inputs.

  7. Automation of one-loop QCD corrections

    CERN Document Server

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


    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.

  8. Magic spinor product methods in loop integrals

    CERN Document Server

    Ward, B F L


    We present an approach to higher point loop integrals using Chinese magic in the virtual loop integration variable. We show, using the five point function in the important e^+e^-\\to f\\bar{f}+\\gamma process for ISR as a pedagogical vehicle, that we get an expression for it directly reduced to one scalar 5-point function and 4-, 3-, and 2- point integrals, thereby avoiding the computation of the usual three tensor 5-pt Passarino-Veltman reduction. We argue that this offers potential for greater numerical stability.

  9. Magic spinor product methods in loop integrals (United States)

    Ward, B. F. L.


    We present an approach to higher point loop integrals using Chinese magic in the virtual loop integration variable. We show, using the five point function in the important e+e-→ff¯+γ process for initial state radiation as a pedagogical vehicle, that we get an expression for it directly reduced to one scalar 5-point function and 4-, 3-, and 2- point integrals, thereby avoiding the computation of the usual three tensor 5-pt Passarino-Veltman reduction. We argue that this offers potential for greater numerical stability.

  10. Tuning OpenACC loop execution

    KAUST Repository

    Feki, Saber


    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

  11. Minimally doubled fermions at one loop (United States)

    Capitani, Stefano; Weber, Johannes; Wittig, Hartmut


    Minimally doubled fermions have been proposed as a cost-effective realization of chiral symmetry at non-zero lattice spacing. Using lattice perturbation theory at one loop, we study their renormalization properties. Specifically, we investigate the consequences of the breaking of hyper-cubic symmetry, which is a typical feature of this class of fermionic discretizations. Our results for the quark self-energy indicate that the four-momentum undergoes a renormalization which is linearly divergent. We also compute renormalization factors for quark bilinears, construct the conserved vector and axial-vector currents and verify that at one loop the renormalization factors of the latter are equal to one.

  12. High-Order Frequency-Locked Loops

    DEFF Research Database (Denmark)

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


    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...

  13. Geometric structures on loop and path spaces

    Indian Academy of Sciences (India)

    in M. This is naturally a Fréchet manifold. The tangent space to L(M) at a loop γ is. Tγ L(M) ∼= (S1,γ∗TM). The loop space L(M) is equipped with a natural section of its tangent bundle defined as ξ: L(M) → T L(M) γ ↦→ γ . Whenever we fix a Riemannian metric g on M, we can define an associated weak metric on the space of ...

  14. A keyboard control method for loop measurement

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Z.W. [Universita Degli Studi di Roma La Sapienza (Italy)


    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.

  15. Human DNA polymerase θ grasps the primer terminus to mediate DNA repair. (United States)

    Zahn, Karl E; Averill, April M; Aller, Pierre; Wood, Richard D; Doublié, Sylvie


    DNA polymerase θ protects against genomic instability via an alternative end-joining repair pathway for DNA double-strand breaks. Polymerase θ is overexpressed in breast, lung and oral cancers, and reduction of its activity in mammalian cells increases sensitivity to double-strand break-inducing agents, including ionizing radiation. Reported here are crystal structures of the C-terminal polymerase domain from human polymerase θ, illustrating two potential modes of dimerization. One structure depicts insertion of ddATP opposite an abasic-site analog during translesion DNA synthesis. The second structure describes a cognate ddGTP complex. Polymerase θ uses a specialized thumb subdomain to establish unique upstream contacts to the primer DNA strand, including an interaction with the 3'-terminal phosphate from one of five distinctive insertion loops. These observations demonstrate how polymerase θ grasps the primer to bypass DNA lesions or extend poorly annealed DNA termini to mediate end-joining.

  16. Fundamental and Harmonic Oscillations in Neighboring Coronal Loops (United States)

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


    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.

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

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


    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. Photocrosslinking of human telomeric G-quadruplex loops by anti cyclobutane thymine dimer formation. (United States)

    Su, Dian G T; Fang, Huafeng; Gross, Michael L; Taylor, John-Stephen A


    The unusual structural forms of telomere DNA, which protect the ends of chromosomes during replication, may render it vulnerable to unprecedented photodamage, possibly involving nonadjacent bases that are made proximate by folding. The G-quadruplex for the human telomere sequence consisting of a repeating d(TTAGGG) is one unusual form. Tel22, d[AGGG(TTAGGG)(3)], forms a basket structure in the presence of Na(+) and may form multiple equilibrating structures in the presence of K(+) with hybrid-type structures predominating. UVB irradiation of d[AGGG(TTAGGG)(3)] in the presence of Na(+) results in a cis,syn thymine dimer between two adjacent Ts in a TTA loop and a mixture of nonadjacent anti thymine dimers between various loops. Irradiation in the presence of K(+), however, produces, in addition to these same products, a large amount of specific anti thymine dimers formed between either T in loop 1 and the central T in loop 3. These latter species were not observed in the presence of Na(+). Interloop-specific anti thymine dimers are incompatible with hybrid-type structures, but could arise from a chair or basket-type structure or from triplex intermediates involved in interconverting these structures. If these unique nonadjacent anti thymine dimer photoproducts also form in vivo, they would constitute a previously unrecognized type of DNA photodamage that may interfere with telomere replication and present a unique challenge to DNA repair. Furthermore, these unusual anti photoproducts may be used to establish the presence of G-quadruplex or quadruplex-like structures in vivo.

  19. Telomeric D-loops containing 8-oxo-2'-deoxyguanosine are preferred substrates for Werner and Bloom syndrome helicases and are bound by POT1. (United States)

    Ghosh, Avik; Rossi, Marie L; Aulds, Jason; Croteau, Deborah; Bohr, Vilhelm A


    8-Oxo-2'-deoxyguanosine (8-oxodG) is one of the most important oxidative DNA lesions, and G-rich telomeric DNA is especially susceptible to oxidative DNA damage. RecQ helicases WRN and BLM and telomere-binding protein POT1 are thought to play roles in telomere maintenance. This study examines the ability of WRN, BLM, and RecQ5 to unwind and POT1 to bind telomeric D-loops containing 8-oxodG. The results demonstrate that WRN and BLM preferentially unwind telomeric D-loops containing 8-oxodG and that POT1 binds with higher affinity to telomeric D-loops with 8-oxodG but shows no preference for telomeric single-stranded DNA with 8-oxodG. We speculate that telomeric D-loops with 8-oxodG may have a greater tendency to form G-quadruplex DNA structures than telomeric DNA lacking 8-oxodG.

  20. Evaluation and Comparison of Biomechanical Properties of Snail Loop with that of Opus Loop and Teardrop Loop for en masse Retraction of Anterior Teeth: FEM Study

    Directory of Open Access Journals (Sweden)

    Parikshit Rajkumar Rao


    Results: Inherently the M/F ratio produced was higher and F/D rate produced was least for opus loop compared to snail loop and teardrop loop. Conclusion: With incorporation of 20°gable bends snail loop prepared in 0.017 × 0.025 inch and 0.019 × 0.025 inch TMA wire is very efficient to deliver M/F ratio required for translatory tooth movement with acceptable F/D rate. Snail loop is easy to fabricate and finer shape morphology prevents tissue impingement.

  1. Logical inference techniques for loop parallelization

    DEFF Research Database (Denmark)

    Oancea, Cosmin Eugen; Rauchwerger, Lawrence


    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....

  2. Loop quantum gravity; Gravedad cuantica de lazos

    Energy Technology Data Exchange (ETDEWEB)

    Pullin, J.


    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)

  3. Phase locked loops design, simulation, and applications

    CERN Document Server

    Best, Roland E


    The Definitive Introduction to Phase-Locked Loops, Complete with Software for Designing Wireless Circuits! The Sixth Edition of Roland Best's classic Phase-Locked Loops has been updated to equip you with today's definitive introduction to PLL design, complete with powerful PLL design and simulation software written by the author. Filled with all the latest PLL advances, this celebrated sourcebook now includes new chapters on frequency synthesis…CAD for PLLs…mixed-signal PLLs…all-digital PLLs…and software PLLs_plus a new collection of sample communications applications. An essential tool for achieving cutting-edge PLL design, the Sixth Edition of Phase-Locked Loops features: A wealth of easy-to-use methods for designing phase-locked loops Over 200 detailed illustrations New to this edition: new chapters on frequency synthesis, including fractional-N PLL frequency synthesizers using sigma-delta modulators; CAD for PLLs, mixed-signal PLLs, all-digital PLLs, and software PLLs; new PLL communications ap...

  4. Closed Loop System Identification with Genetic Algorithms (United States)

    Whorton, Mark S.


    High performance control design for a flexible space structure is challenging since high fidelity plant models are di.cult to obtain a priori. Uncertainty in the control design models typically require a very robust, low performance control design which must be tuned on-orbit to achieve the required performance. Closed loop system identi.cation is often required to obtain a multivariable open loop plant model based on closed-loop response data. In order to provide an accurate initial plant model to guarantee convergence for standard local optimization methods, this paper presents a global parameter optimization method using genetic algorithms. A minimal representation of the state space dynamics is employed to mitigate the non-uniqueness and over-parameterization of general state space realizations. This control-relevant system identi.cation procedure stresses the joint nature of the system identi.cation and control design problem by seeking to obtain a model that minimizes the di.erence between the predicted and actual closed-loop performance.

  5. Aesthetic rehabilitation with multiple loop connectors

    Directory of Open Access Journals (Sweden)

    Ashish Kalra


    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.

  6. String loop corrected hypermultiplet moduli spaces

    NARCIS (Netherlands)

    Robles-Llana, D.; Saueressig, Frank; Vandoren, S.


    Using constraints from supersymmetry and string perturbation theory, we determine the string loop corrections to the hypermultiplet moduli space of type II strings compactified on a generic Calabi-Yau threefold. The corresponding quaternion-Kähler manifolds are completely encoded in terms of a

  7. Semiclassical analysis of loop quantum gravity

    Energy Technology Data Exchange (ETDEWEB)

    Conrady, F.


    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.)

  8. Introduction to Loop Quantum Gravity and Cosmology (United States)

    Ashtekar, Abhay

    The goal of the lecture is to present a broad perspective on loop quantum gravity and cosmology for young researchers which would serve as an introduction to lectures by Rovelli and Bojowald. The first part is addressed to beginning students and the second to young researchers who are already working in quantum gravity.

  9. Closing the loop: towards strategic defence management

    NARCIS (Netherlands)

    de Spiegeleire, S.; van Hooft, P.; Culpepper, C.; Willems, R.


    How do defence-organisations (or organisations with comparable profiles) of other countries map out policy goals and how are policy goals related to activities and capabilities and the required financial means, and finally how does the feedback loop on the performance in all these areas take place?

  10. Closed-loop control of magnetotactic bacteria

    NARCIS (Netherlands)

    Khalil, I.S.M.; Pichel, Marc Philippe; Pichel, M.P.; Abelmann, Leon; Misra, Sarthak

    Realization of point-to-point positioning of a magnetotactic bacterium (MTB) necessitates the application of a relatively large magnetic field gradients to decrease its velocity in the vicinity of a reference position. We investigate an alternative closed-loop control approach to position the MTB.

  11. Geometry of the analytic loop group

    NARCIS (Netherlands)

    De Concini, C.; Hernandez, D.; Reshetikhin, N.


    We introduce and study a notion of analytic loop group with a Riemann-Hilbert factorization relevant for the representation theory of quantum affine algebras at roots of unity View the MathML source with non-trivial central charge. We introduce a Poisson structure and study properties of its Poisson

  12. Selective purge for hydrogenation reactor recycle loop (United States)

    Baker, Richard W.; Lokhandwala, Kaaeid A.


    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.

  13. Thermal instabilities in magnetically confined plasmas - Solar coronal loops (United States)

    Habbal, S. R.; Rosner, R.


    The thermal stability of confined solar coronal structures ('loops') is investigated, following both normal mode and a new, global instability analysis. It is demonstrated that: (1) 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; (2) 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.

  14. Loop Evolution Observed with AIA and Hi-C (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


    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.

  15. DNA glue

    DEFF Research Database (Denmark)

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


    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...

  16. DNA Vaccines

    Indian Academy of Sciences (India)

    research interests include: eukaryotic gene expres- sion and infectious diseases. Keywords. DNA vaccine, immune response, antibodies, infectious diseases. GENERAL I ... T -cells: Lymphocytes that differentiate primarily in the thymus and are central to the control and ... enhance DNA delivery into skeletal muscle.

  17. Mitochondrial DNA Content Varies with Pathological Characteristics of Breast Cancer

    Directory of Open Access Journals (Sweden)

    Ren-Kui Bai


    Full Text Available Changes in mitochondrial DNA (mtDNA content in cancers have been reported with controversial results, probably due to small sample size and variable pathological conditions. In this study, mtDNA content in 302 breast tumor/surrounding normal tissue pairs were evaluated and correlated with the clinico-pathological characteristics of tumors. Overall, mtDNA content in tumor tissues is significantly lower than that in the surrounding normal tissues, P50 cm3, mtDNA content started to increase. Similarly, mtDNA content decreased from grades 0 and I to grade II tumors, but increased from grade II to grade III tumors. Tumors with somatic mtDNA alterations in coding region have significantly higher mtDNA content than tumors without somatic mtDNA alterations (P<0.001. Tumors with somatic mtDNA alterations in the D-Loop region have significantly lower mtDNA content (P<0.001. Patients with both low and high mtDNA content in tumor tissue have significantly higher hazard of death than patients with median levels of mtDNA content. mtDNA content in tumor tissues change with tumor size, grade, and ER/PR status; significant deviation from the median level of mtDNA content is associated with poor survival.

  18. R-loops cause genomic instability in T helper lymphocytes from patients with Wiskott-Aldrich syndrome. (United States)

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


    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 TH cell deficiency and genomic instability in the XLT/WAS clinical spectrum. In human TH1- or TH2-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 TH1 cells relative to TH2 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 (TH1 genes) in TH1 cells. These aberrations accompany increased unspliced (intron-retained) and decreased spliced mRNA of IFNG and TBX21 but not IL13 (TH2 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 TH1 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 and could be

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

    KAUST Repository

    Ariel, Federico D.


    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.

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

    Directory of Open Access Journals (Sweden)

    Wen-Pin Chou


    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.

  1. Negative Regulators of an RNAi-Heterochromatin Positive Feedback Loop Safeguard Somatic Genome Integrity in Tetrahymena. (United States)

    Suhren, Jan H; Noto, Tomoko; Kataoka, Kensuke; Gao, Shan; Liu, Yifan; Mochizuki, Kazufumi


    RNAi-mediated positive feedback loops are pivotal for the maintenance of heterochromatin, but how they are downregulated at heterochromatin-euchromatin borders is not well understood. In the ciliated protozoan Tetrahymena, heterochromatin is formed exclusively on the sequences that are removed from the somatic genome by programmed DNA elimination, and an RNAi-mediated feedback loop is important for assembling heterochromatin on the eliminated sequences. In this study, we show that the heterochromatin protein 1 (HP1)-like protein Coi6p, its interaction partners Coi7p and Lia5p, and the histone demethylase Jmj1p are crucial for confining the production of small RNAs and the formation of heterochromatin to the eliminated sequences. The loss of Coi6p, Coi7p, or Jmj1p causes ectopic DNA elimination. The results provide direct evidence for the existence of a dedicated mechanism that counteracts a positive feedback loop between RNAi and heterochromatin at heterochromatin-euchromatin borders to maintain the integrity of the somatic genome. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  2. Rotation-Induced Macromolecular Spooling of DNA (United States)

    Shendruk, Tyler N.; Sean, David; Berard, Daniel J.; Wolf, Julian; Dragoman, Justin; Battat, Sophie; Slater, Gary W.; Leslie, Sabrina R.


    Genetic information is stored in a linear sequence of base pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we discover that rotation-induced macromolecular spooling of DNA around a rotating microwire can monotonically order genomic bases, overcoming this challenge. We use single-molecule fluorescence microscopy to directly visualize long DNA strands deforming and elongating in shear flow near a rotating microwire, in agreement with numerical simulations. While untethered DNA is observed to elongate substantially, in agreement with our theory and numerical simulations, strong extension of DNA becomes possible by introducing tethering. For the case of tethered polymers, we show that increasing the rotation rate can deterministically spool a substantial portion of the chain into a fully stretched, single-file conformation. When applied to DNA, the fraction of genetic information sequentially ordered on the microwire surface will increase with the contour length, despite the increased entropy. This ability to handle long strands of DNA is in contrast to modern DNA sample preparation technologies for sequencing and mapping, which are typically restricted to comparatively short strands, resulting in challenges in reconstructing the genome. Thus, in addition to discovering new rotation-induced macromolecular dynamics, this work inspires new approaches to handling genomic-length DNA strands.

  3. Supercritical water loop for in-pile materials testing

    Energy Technology Data Exchange (ETDEWEB)

    Ruzickova, M.; Vsolak, R.; Hajek, P.; Zychova, M.; Fukac, R. [Research Centre Rez Ltd., Husinec-Rez (Czech Republic)


    The Supercritical Water Loop (SCWL) has been designed and built within the HPLWR Phase 2 project, with the objective of testing materials under supercritical water conditions and radiation. The design parameters are set to 25MPa and 600{sup o}C in the testing area, where material samples shall be located. The loop has recently undergone pressure and leakage tests, during which the strength and tightness of the loop were proved. The loop has been also subjected to the first trial operation at nearly maximum operating parameters (temperature 550 {sup o}C was reached); loop operation was steady during several days. Presently, loop operation is envisaged in order to test the loop's long term operation ability. Samples of a material that needs further testing under out- of-pile conditions shall be exposed in the loop; the choice shall be made in agreement with the results of the WP4 - Materials of the HPLWR Phase 2 project. (author)

  4. Vapor Compressor Driven Hybrid Two-Phase Loop Project (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...

  5. Multi-loop calculations: numerical methods and applications (United States)

    Borowka, S.; Heinrich, G.; Jahn, S.; Jones, S. P.; Kerner, M.; Schlenk, J.


    We briefly review numerical methods for calculations beyond one loop and then describe new developments within the method of sector decomposition in more detail. We also discuss applications to two-loop integrals involving several mass scales.

  6. Stability in Real Food Webs: Weak Links in Long Loops

    National Research Council Canada - National Science Library

    Anje-Margriet Neutel; Johan A. P. Heesterbeek; Peter C. de Ruiter


    ... of these patterns, how they come about, and why they influence stability. We show that in real food webs, interaction strengths are organized in trophic loops in such a way that long loops contain relatively many weak links...

  7. The Seasonality Of The Loop Current (United States)

    Hall, Cody Alan

    A total of 20 Loop Current eddy separation event dates were derived from Seasat and ERS-1 satellite altimetry, Coastal Zone Color Scanner chlorophyll-a images, Advanced Very High Resolution Radiometer sea surface temperature images, Horizon Marine, Inc. EddyWatch(TM) reports, and Climatology and Simulation of Eddies Eddy Joint Industry Project Gulf Eddy Model analyses spanning mid-1978 - 1992. There were many inconsistencies between the new "pre-altimetry" reanalysis dates derived from mostly non-altimeter data and dates published in past literature based on earlier versions of the pre-altimetry record. The reanalysis dates were derived from a larger compilation of data types and, consequently, were not as affected by intermittent and seasonal data outages common with past records. Therefore, the reanalysis dates are likely more accurate. About 30 Loop Current eddy separation dates were derived from altimetry data spanning 1993 -- 2012. The pre-altimetry and altimetry reanalysis dates along with similar altimetry dates published in other literature exhibit statistically significant seasonality. Eddy separation events are more likely in the months March, August, and September, and less likely in December. Reanalysis event dates were objectively divided into "spring" and "fall" seasons using a k-means clustering algorithm. The estimated spring and fall season centers are March 2nd and August 23 rd, respectively, with seasonal boundaries on May 22nd and December 3rd. The altimetry data suggest that Loop Current intrusion/retreat is dominantly an annual process. Loop Current metrics such as maximum northern boundary latitude and area are relatively high from January through about July and low in September and October. February metrics are statistically different than metrics in either October or November or both. This annual process is primarily driven by and dynamically linked to geostrophic currents seaward of the Campeche Bank shelf break forced by Kelvin waves

  8. Magnetic Monopoles and the Loop Group. (United States)

    Norbury, Paul Timothy

    My thesis relates three major works in gauge theory and geometry. I use a technique involving jumping lines in the study of holomorphic bundles over the projective plane to gain information about the loop group and hyperbolic monopoles. I also turn this around and get some information on the jumping lines of a holomorphic bundle. Hurtubise studied the local geometry of a holomorphic bundle on the projective plane around a jumping line, encoding this information into the Toeplitz space. Milgram identified a stratum of the projectivized Toeplitz space with a quotient of the space of rational maps from the two-sphere to itself. I associate the Toeplitz space to the loop group and use Milgram's result to get a description of a stratum of the loop group. By studying their jumping lines I construct those holomorphic bundles on the projective plane which are invariant under a circle action so in particular correspond to hyperbolic monopoles. Again I use Milgram's result to get a new proof of the theorem of Atiyah where he obtains a homeomorphism between the space of hyperbolic monopoles and the space of rational maps from the two-sphere to itself that fix infinity. Conversely using Atiyah's theorem I get a new proof of Milgram's result. This equivalence between the theorems of Milgram and Atiyah generalises to the case of higher rank so I get new results on the local geometry of jumping lines of a holomorphic bundle over the projective plane. There are two main ways to describe holomorphic bundles over the projective plane. Using the loop group I produce a third way to describe such bundles. With this description I show that there is a deeper equivalence between the theorems of Milgram and Atiyah. This work originated from questions about the relationship between the instantons of two dynamical theories --gauge theory over the four-sphere and holomorphic curves in the loop group. I study the gradient flows of the energy functional on the loop group and show how they

  9. Mitochondrial DNA variants in obesity.

    Directory of Open Access Journals (Sweden)

    Nadja Knoll

    Full Text Available Heritability estimates for body mass index (BMI variation are high. For mothers and their offspring higher BMI correlations have been described than for fathers. Variation(s in the exclusively maternally inherited mitochondrial DNA (mtDNA might contribute to this parental effect. Thirty-two to 40 mtDNA single nucleotide polymorphisms (SNPs were available from genome-wide association study SNP arrays (Affymetrix 6.0. For discovery, we analyzed association in a case-control (CC sample of 1,158 extremely obese children and adolescents and 435 lean adult controls. For independent confirmation, 7,014 population-based adults were analyzed as CC sample of n = 1,697 obese cases (BMI ≥ 30 kg/m2 and n = 2,373 normal weight and lean controls (BMI<25 kg/m2. SNPs were analyzed as single SNPs and haplogroups determined by HaploGrep. Fisher's two-sided exact test was used for association testing. Moreover, the D-loop was re-sequenced (Sanger in 192 extremely obese children and adolescents and 192 lean adult controls. Association testing of detected variants was performed using Fisher's two-sided exact test. For discovery, nominal association with obesity was found for the frequent allele G of m.8994G/A (rs28358887, p = 0.002 located in ATP6. Haplogroup W was nominally overrepresented in the controls (p = 0.039. These findings could not be confirmed independently. For two of the 252 identified D-loop variants nominal association was detected (m.16292C/T, p = 0.007, m.16189T/C, p = 0.048. Only eight controls carried the m.16292T allele, five of whom belonged to haplogroup W that was initially enriched among these controls. m.16189T/C might create an uninterrupted poly-C tract located near a regulatory element involved in replication of mtDNA. Though follow-up of some D-loop variants still is conceivable, our hypothesis of a contribution of variation in the exclusively maternally inherited mtDNA to the observed larger correlations for BMI between mothers and

  10. Closed-loop fiber optic gyroscope with homodyne detection (United States)

    Zhu, Yong; Qin, BingKun; Chen, Shufen


    Interferometric fiber optic gyroscope (IFOG) has been analyzed with autocontrol theory in this paper. An open-loop IFOG system is not able to restrain the bias drift, but a closed-loop IFOG system can do it very well using negative feedback in order to suppress zero drift. The result of our theoretic analysis and computer simulation indicate that the bias drift of a closed-loop system is smaller than an open- loop one.

  11. Polyakov loops, Gross-Witten like point and Hagedorn states


    Zakout, I.; Greiner, C.


    The phase transition for a finite volume system that incorporates the Polyakov loops and maintains the colorless state is explored using the Polyakov-loop extended Nambu-Jona-Lasinio (PNJL) model. The order parameter for Polyakov loops is demonstrated to signal the appearance of a transition for $SU(3)_{c}$ analogous to Gross-Witten (GW-) phase transition instead of the deconfinement phase transition to quark-gluon plasma. The asymptotic restoration of Polyakov loops is conjectured to be a th...

  12. Probing the dynamics of restriction endonuclease NgoMIV-DNA interaction by single-molecule FRET. (United States)

    Tutkus, Marijonas; Sasnauskas, Giedrius; Rutkauskas, Danielis


    Many type II restriction endonucleases require two copies of their recognition sequence for optimal activity. Concomitant binding of two DNA sites by such an enzyme produces a DNA loop. Here we exploit single-molecule Förster resonance energy transfer (smFRET) of surface-immobilized DNA fragments to study the dynamics of DNA looping induced by tetrameric endonuclease NgoMIV. We have employed a DNA fragment with two NgoMIV recognition sites and a FRET dye pair such that upon protein-induced DNA looping the dyes are brought to close proximity resulting in a FRET signal. The dynamics of DNA-NgoMIV interactions proved to be heterogeneous, with individual smFRET trajectories exhibiting broadly different average looped state durations. Distinct types of the dynamics were attributed to different types of DNA-protein complexes, mediated either by one NgoMIV tetramer simultaneously bound to two specific sites ("slow" trajectories) or by semi-specific interactions of two DNA-bound NgoMIV tetramers ("fast" trajectories), as well as to conformational heterogeneity of individual NgoMIV molecules. © 2017 Wiley Periodicals, Inc.

  13. Loop-loop interactions govern multiple steps in indole-3-glycerol phosphate synthase catalysis. (United States)

    Zaccardi, Margot J; O'Rourke, Kathleen F; Yezdimer, Eric M; Loggia, Laura J; Woldt, Svenja; Boehr, David D


    Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis and molecular dynamic simulations had previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (ssIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic ssIGPS enzyme. Although there were only modest changes in the overall steady-state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate-determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps-ns and µs-ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether, our studies provide structural, dynamic and functional rationales for the coevolution of residues on the β1α1 and β2α2 loops, and highlight the multiple roles that the β1α1 loop plays in IGPS catalysis. Thus, substitution of covarying residues in the active-site β1α1 and β2α2 loops of indole-3-glycerol phosphate synthase results in functional, structural, and dynamic changes, highlighting the multiple roles that the β1α1 loop plays in enzyme catalysis and the importance of regulating the structural dynamics of this loop through noncovalent

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

    Directory of Open Access Journals (Sweden)

    Yu J. Shen


    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.

  15. The mitochondrial C16069T polymorphism, not mitochondrial D310 (D-loop) mononucleotide sequence variations, is associated with bladder cancer. (United States)

    Shakhssalim, Nasser; Houshmand, Massoud; Kamalidehghan, Behnam; Faraji, Abolfazl; Sarhangnejad, Reza; Dadgar, Sepideh; Mobaraki, Maryam; Rosli, Rozita; Sanati, Mohammad Hossein


    Bladder cancer is a relatively common and potentially life-threatening neoplasm that ranks ninth in terms of worldwide cancer incidence. The aim of this study was to determine deletions and sequence variations in the mitochondrial displacement loop (D-loop) region from the blood specimens and tumoral tissues of patients with bladder cancer, compared to adjacent non-tumoral tissues. The DNA from blood, tumoral tissues and adjacent non-tumoral tissues of twenty-six patients with bladder cancer and DNA from blood of 504 healthy controls from different ethnicities were investigated to determine sequence variation in the mitochondrial D-loop region using multiplex polymerase chain reaction (PCR), DNA sequencing and southern blotting analysis. From a total of 110 variations, 48 were reported as new mutations. No deletions were detected in tumoral tissues, adjacent non-tumoral tissues and blood samples from patients. Although the polymorphisms at loci 16189, 16261 and 16311 were not significantly correlated with bladder cancer, the C16069T variation was significantly present in patient samples compared to control samples (p  0.05) of C variations, including C7TC6, C8TC6, C9TC6 and C10TC6, in D310 mitochondrial DNA between patients and control samples. Our study suggests that 16069 mitochondrial DNA D-Loop mutations may play a significant role in the etiology of bladder cancer and facilitate the definition of carcinogenesis-related mutations in human cancer.

  16. Solutions of selected pseudo loop equations in water distribution ...

    African Journals Online (AJOL)

    This paper demonstrated the use of Microsoft Excel Solver (a computer package) in solving selected pseudo loop equations in pipe network analysis problems. Two pipe networks with pumps and overhead tanks were used to demonstrate the use of Microsoft Excel Solver in solving pseudo loops (open loops; networks with ...

  17. The autoregulatory loop: A common mechanism of regulation of key ...

    Indian Academy of Sciences (India)

    ... an autoregulatory positive feedback loop. In this review, by taking examples from various insects, we propose the hypothesis that autoregulatory loop mechanisms of sex determination might be a general strategy. We also discuss the possible reasons for the evolution of autoregulatory loops in sex determination cascades ...

  18. Rare Case of Double Looped Ansa Cervicalis Associated with its ...

    African Journals Online (AJOL)

    fibers of C1‑C3 nerves arose from this loop and ran obliquely downwards superficial to CCA and branched out to supply the infrahyoid muscles. Rare Case of Double Looped Ansa ... Keywords: Ansa cervicalis, Double loop, Nerve muscle transplant, Variation ... categorized as type 3 with the prevalence of 4% and double.

  19. Closed-Loop Optimal Control Implementations for Space Applications (United States)


    COVERED Master’s thesis , Jan-Dec 2016 4. TITLE AND SUBTITLE CLOSED-LOOP OPTIMAL CONTROL IMPLEMENTATIONS FOR SPACE APPLICATIONS 5. FUNDING NUMBERS... Mechanical and Aerospace Engineering iv THIS PAGE INTENTIONALLY LEFT BLANK v ABSTRACT This thesis explores concepts for a closed-loop optimal...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release. Distribution is unlimited. CLOSED-LOOP

  20. Modulation of RNA polymerase activity through trigger loop folding


    Miropolskaya, Nataliya; Nikiforov, Vadim; Klimašauskas, Saulius; Artsimovitch, Irina; Kulbachinskiy, Andrey


    Folding of the trigger loop of RNA polymerase promotes nucleotide addition through creating a closed, catalytically competent conformation of the active center. Here, we discuss the impact of adjacent RNA polymerase elements, including the F loop and the jaw domain, as well as external regulatory factors on the trigger loop folding and catalysis.

  1. Capillary pumped loop body heat exchanger (United States)

    Swanson, Theodore D. (Inventor); Wren, deceased, Paul (Inventor)


    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.

  2. A new vacuum for Loop Quantum Gravity

    CERN Document Server

    Dittrich, Bianca


    We construct a new vacuum for loop quantum gravity, which is dual to the Ashtekar-Lewandowski vacuum. Because it is based on BF theory, this new vacuum 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 which is cylindrically consistent with respect to the notion of refinement by time evolution suggested in [1]. This supports the proposal for a construction of a physical vacuum made in [1,2], also 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.

  3. Loop transfer recovery for general observer architecture

    DEFF Research Database (Denmark)

    Niemann, Hans Henrik; Søgaard-Andersen, Per; Stoustrup, Jakob


    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...

  4. Loop quantization of the Schwarzschild black hole. (United States)

    Gambini, Rodolfo; Pullin, Jorge


    We quantize spherically symmetric vacuum gravity without gauge fixing the diffeomorphism constraint. Through a rescaling, we make the algebra of Hamiltonian constraints Abelian, and therefore the constraint algebra is a true Lie algebra. This allows the completion of the Dirac quantization procedure using loop quantum gravity techniques. We can construct explicitly the exact solutions of the physical Hilbert space annihilated by all constraints. New observables living in the bulk appear at the quantum level (analogous to spin in quantum mechanics) that are not present at the classical level and are associated with the discrete nature of the spin network states of loop quantum gravity. The resulting quantum space-times resolve the singularity present in the classical theory inside black holes.

  5. MBNL expression in autoregulatory feedback loops. (United States)

    Konieczny, Patryk; Stepniak-Konieczna, Ewa; Sobczak, Krzysztof


    Muscleblind-like (MBNL) proteins bind to hundreds of pre- and mature mRNAs to regulate their alternative splicing, alternative polyadenylation, stability and subcellular localization. Once MBNLs are withheld from transcript regulation, cellular machineries generate products inapt for precise embryonal/adult developmental tasks and myotonic dystrophy, a devastating multi-systemic genetic disorder, develops. We have recently demonstrated that all three MBNL paralogs are capable of fine-tuning cellular content of one of the three MBNL paralogs, MBNL1, by binding to the first coding exon (e1) of its pre-mRNA. Intriguingly, this autoregulatory feedback loop grounded on alternative splicing of e1 appears to play a crucial role in delaying the onset of myotonic dystrophy. Here, we describe this process in the context of other autoregulatory and regulatory loops that maintain the content and diverse functions of MBNL proteins at optimal level in health and disease, thus supporting the overall cellular homeostasis.

  6. Dynamical Casimir effect and loop corrections (United States)

    Akhmedov, E. T.; Alexeev, S. O.


    We calculate quantum loop corrections to the stress-energy flux caused by moving mirrors. We consider massless, self-interacting, ϕ4, real scalar theory. In these calculations we encounter new and quite unexpected subtleties due to the absence of global hyperbolicity in the presence of mirrors. We attempt to clearly phrase as many hidden assumptions and complications as possible that appear while solving the problem in question. On top of that, we find that quantum loop corrections to the stress-energy flux grow with time and are not suppressed in comparison with the semiclassical contributions. Thus, we observe the breakdown of the perturbation theory, and we discuss its physical origin and ways to deal with such a situation. As a byproduct, we observe a similarity of the problem in question with that for the minimally coupled, massless scalar field in de Sitter space.

  7. The gluon beam function at two loops (United States)

    Gaunt, Jonathan R.; Stahlhofen, Maximilian; Tackmann, Frank J.


    The virtuality-dependent beam function is a universal ingredient in the resummation for observables probing the virtuality of incoming partons, including N -jettiness and beam thrust. We compute the gluon beam function at two-loop order. Together with our previous results for the two-loop quark beam function, this completes the full set of virtuality-dependent beam functions at next-to-next-to-leading order (NNLO). Our results are required to account for all collinear initial-state radiation effects on the N -jettiness event shape through N3LL order. We present numerical results for both the quark and gluon beam functions up to NNLO and N3LL order. Numerically, the NNLO matching corrections are important. They reduce the residual matching scale dependence in the resummed beam function by about a factor of two.

  8. The gluon beam function at two loops

    Energy Technology Data Exchange (ETDEWEB)

    Gaunt, Jonathan R.; Stahlhofen, Maximilian; Tackmann, Frank J. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Theory Group


    The virtuality-dependent beam function is a universal ingredient in the resummation for observables probing the virtuality of incoming partons, including N-jettiness and beam thrust. We compute the gluon beam function at two-loop order. Together with our previous results for the two-loop quark beam function, this completes the full set of virtuality-dependent beam functions at next-to-next-to-leading order (NNLO). Our results are required to account for all collinear ISR effects to the N-jettiness event shape through N{sup 3}LL order. We present numerical results for both the quark and gluon beam functions up to NNLO and N{sup 3}LL order. Numerically, the NNLO matching corrections are important. They reduce the residual matching scale dependence in the resummed beam function by about a factor of two.

  9. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian


    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...

  10. DNA data (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.,...

  11. DNA nanotechnology (United States)

    Seeman, Nadrian C.; Sleiman, Hanadi F.


    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.

  12. Harmonic Oscillator SUSY Partners and Evolution Loops

    Directory of Open Access Journals (Sweden)

    David J. Fernández


    Full Text Available Supersymmetric quantum mechanics is a powerful tool for generating exactly solvable potentials departing from a given initial one. If applied to the harmonic oscillator, a family of Hamiltonians ruled by polynomial Heisenberg algebras is obtained. In this paper it will be shown that the SUSY partner Hamiltonians of the harmonic oscillator can produce evolution loops. The corresponding geometric phases will be as well studied.

  13. Two-loop statsum of superstrings (United States)

    Morozov, A.


    We discuss, whether there is a choice of odd moduli on super-Riemann surfaces of genus p≳2, which leads to the vanishing of statistical sums of superstrings before integration over the space of even moduli. The answer is shown to be positive at least for p=2, when odd moduli are localized at ramification points. The relation between various definitions of many-loop statistical sums in superstring theory is discussed.

  14. DNA Chip

    Indian Academy of Sciences (India)

    involved in the pathology of schizophrenia. In the human ge- nome, the ratio between coding and non-coding DNA is very low (less than 3% of the human .... construction of a Tm-specific chip, i.e. all the oligos/cDNA on the chip will hybridize at the same temperature. The techniques available are still not able to create a chip ...

  15. NMR studies of artificial double-crossover DNA tiles. (United States)

    Veerapandian, Murugan; Kim, Byeonghoon; Amin, Rashid; Lee, Junwye; Yun, Kyusik; Park, Sung Ha


    This report documents the design and characterization of DNA molecular nanoarchitectures consisting of artificial double crossover DNA tiles with different geometry and chemistry. The Structural characterization of the unit tiles, including normal, biotinylated and hairpin loop structures, are morphologically studied by atomic force microscopy. The specific proton resonance of the individual tiles and their intra/inter nucleotide relationships are verified by proton nuclear magnetic resonance spectroscopy and 2-dimensional correlation spectral studies, respectively. Significant up-field and down-field shifts in the resonance signals of the individual residues at various temperatures are discussed. The results suggest that with artificially designed DNA tiles it is feasible to obtain structural information of the relative base sequences. These tiles were later fabricated into 2D DNA lattice structures for specific applications such as protein arrangement by biotinylated bulged loops or pattern generation using a hairpin structure.

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

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


    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. Transverse loop colostomy and colonic motility. (United States)

    Pucciani, F; Ringressi, M N; Maltinti, G; Bechi, P


    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.

  18. 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)


    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.

  19. Quantum Loop Topography for Machine Learning (United States)

    Zhang, Yi; Kim, Eun-Ah


    Despite rapidly growing interest in harnessing machine learning in the study of quantum many-body systems, training neural networks to identify quantum phases is a nontrivial challenge. The key challenge is in efficiently extracting essential information from the many-body Hamiltonian or wave function and turning the information into an image that can be fed into a neural network. When targeting topological phases, this task becomes particularly challenging as topological phases are defined in terms of nonlocal properties. Here, we introduce quantum loop topography (QLT): a procedure of constructing a multidimensional image from the "sample" Hamiltonian or wave function by evaluating two-point operators that form loops at independent Monte Carlo steps. The loop configuration is guided by the characteristic response for defining the phase, which is Hall conductivity for the cases at hand. Feeding QLT to a fully connected neural network with a single hidden layer, we demonstrate that the architecture can be effectively trained to distinguish the Chern insulator and the fractional Chern insulator from trivial insulators with high fidelity. In addition to establishing the first case of obtaining a phase diagram with a topological quantum phase transition with machine learning, the perspective of bridging traditional condensed matter theory with machine learning will be broadly valuable.

  20. Leptogenesis from loop effects in curved spacetime (United States)

    McDonald, Jamie I.; Shore, Graham M.


    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.

  1. The quark beam function at two loops (United States)

    Gaunt, Jonathan R.; Stahlhofen, Maximilian; Tackmann, Frank J.


    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 the usual longitudinal momentum fraction. 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 N3LL 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 of 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.

  2. The quark beam function at two loops

    Energy Technology Data Exchange (ETDEWEB)

    Gaunt, Jonathan R.; Stahlhofen, Maximilian; Tackmann, Frank J.


    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{sup 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.

  3. The quark beam function at two loops

    Energy Technology Data Exchange (ETDEWEB)

    Gaunt, Jonathan R.; Stahlhofen, Maximilian; Tackmann, Frank J. [Theory Group, Deutsches Elektronen-Synchrotron (DESY),D-22607 Hamburg (Germany)


    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 the usual longitudinal momentum fraction. 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{sup 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 of 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.

  4. Visualizing the Formation and Collapse of DNA Toroids (United States)

    van den Broek, Bram; Noom, Maarten C.; van Mameren, Joost; Battle, Christopher; MacKintosh, Fred C.; Wuite, Gijs J.L.


    Abstract In living organisms, DNA is generally confined into very small volumes. In most viruses, positively charged multivalent ions assist the condensation of DNA into tightly packed toroidal structures. Interestingly, such cations can also induce the spontaneous formation of DNA toroids in vitro. To resolve the condensation dynamics and stability of DNA toroids, we use a combination of optical tweezers and fluorescence imaging to visualize in real-time spermine-induced (de)condensation in single DNA molecules. By actively controlling the DNA extension, we are able to follow (de)condensation under tension with high temporal and spatial resolution. We show that both processes occur in a quantized manner, caused by individual DNA loops added onto or removed from a toroidal condensate that is much smaller than previously observed in similar experiments. Finally, we present an analytical model that qualitatively captures the experimentally observed features, including an apparent force plateau. PMID:20441754

  5. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van


    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

  6. Mutations of the kissing-loop dimerization sequence influence the site specificity of murine leukemia virus recombination in vivo

    DEFF Research Database (Denmark)

    Mikkelsen, J G; Lund, Anders Henrik; Duch, M


    The genetic information of retroviruses is retained within a dimeric RNA genome held together by intermolecular RNA-RNA interactions near the 5' ends. Coencapsidation of retrovirus-derived RNA molecules allows frequent template switching of the virus-encoded reverse transcriptase during DNA...... synthesis in newly infected cells. We have previously shown that template shifts within the 5' leader of murine leukemia viruses occur preferentially within the kissing stem-loop motif, a cis element crucial for in vitro RNA dimer formation. By use of a forced recombination approach based on single...... specificity of recombination within the highly structured 5' leader region. In addition, we find that an intact kissing-loop sequence favors optimal RNA encapsidation and vector transduction. Our data are consistent with the kissing-loop dimerization model and suggest that a direct intermolecular RNA...

  7. Therapeutic effect of green tea extract on alcohol induced hepatic mitochondrial DNA damage in albino wistar rats

    Directory of Open Access Journals (Sweden)

    Hymavathi Reddyvari


    Full Text Available The present study principally sought to investigate the effect of green tea extract (GTE supplementation on hepatic mitochondrial DNA (mtDNA damage in alcohol receiving rats. MtDNA was isolated from hepatic tissues of albino wistar rats after alcohol treatment with and without GTE supplementation. Entire displacement loop (D-loop of mtDNA was screened by PCR-Sanger’s sequencing method. In addition, mtDNA deletions and antioxidant activity were measured in hepatic tissue of all rats. Results showed increased frequency of D-loop mutations in alcoholic rats (ALC. DNA mfold analysis predicted higher free energy for 15507C and 16116C alleles compared to their corresponding wild alleles which represents less stable secondary structures with negative impact on overall mtDNA function. Interestingly, D-loop mutations observed in ALC rats were successfully restored on GTE supplementation. MtDNA deletions were observed in ALC rats, but intact native mtDNA was found in ALC + GTE group suggesting alcohol induced oxidative damage of mtDNA and ameliorative effect of GTE. Furthermore, markedly decreased activities of glutathione peroxidise, superoxide dismutase, catalase and glutathione content were identified in ALC rats; however, GTE supplementation significantly (P < 0.05 restored these levels close to normal. In conclusion, green tea could be used as an effective nutraceutical against alcohol induced mitochondrial DNA damage.

  8. Gravitational smoothing of kinks on cosmic string loops

    CERN Document Server

    Wachter, Jeremy M


    We analyze the effect of gravitational back reaction on cosmic string loops with kinks, which is an important determinant of the shape, and thus the potential observability, of string loops which may exist in the universe today. Kinks are not rounded off, but may be straightened out. In some loops, symmetries prevent even this process, so that the loop evaporates in a self-similar fashion and the kinks are unchanged. As an example, we give results for the rectangular Garfinkle-Vachaspati loop.

  9. On Vanishing Two Loop Cosmological Constants in Nonsupersymmetric Strings

    Energy Technology Data Exchange (ETDEWEB)

    Kachru, S


    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.

  10. Simulaciones numéricas en modelos de loops


    Serna Martínez, Pablo


    El objetivo de esta tesis consiste en el estudio de varias familias de modelos de loops en dos y tres dimensiones, donde se encuentran dos fases diferentes: una con loops finitos y otra donde hay al menos uno infinito. En concreto, se han estudiado tres clases de modelos de loops. El primero, un modelo de loops tridimensionales con orientación y color, definidos en redes con número de coordinación cuatro. El segundo, una modificación de estos modelos de loops que es un firme candidato ...

  11. Atomic Force Microscopy Studies on DNA Structural Changes Induced by Vincristine Sulfate and Aspirin (United States)

    Zhu, Yi; Zeng, Hu; Xie, Jianming; Ba, Long; Gao, Xiang; Lu, Zuhong


    We report that atomic force microscopy (AFM) studies on structural variations of a linear plasmid DNA interact with various concentrations of vincristine sulfate and aspirin. The different binding images show that vincrinstine sulfate binding DNA chains caused some loops and cleavages of the DNA fragments, whereas aspirin interaction caused the width changes and conformational transition of the DNA fragments. Two different DNA structural alternations could be explained by the different mechanisms of the interactions with these two components. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.

  12. What Is Mitochondrial DNA? (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 ...

  13. On the loop-loop scattering amplitudes in Abelian and non-Abelian gauge theories

    Energy Technology Data Exchange (ETDEWEB)

    Meggiolaro, Enrico [Dipartimento di Fisica, Universita di Pisa, Largo Pontecorvo 3, I-56127 Pisa (Italy)]. E-mail:


    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.

  14. Sperm DNA damage measured by comet assay. (United States)

    Simon, Luke; Carrell, Douglas T


    Measurement of sperm DNA damage is a useful tool in the evaluation of male infertility, as the sperm nucleus lacks protection against oxidative stress and is vulnerable to oxidation-mediated DNA damage. The Comet assay or single-cell gel electrophoresis is a relatively simple and sensitive method for measuring strand breaks in DNA in individual sperm. During this procedure, sperm cells are embedded in a thin layer of agarose on a microscope slide and lysed with detergent under high salt conditions. This process removes protamines and histones allowing the nucleus to form a nucleoid-like structure containing supercoiled loops of DNA. Alkaline pH conditions result in unwinding of double-stranded DNA, and subsequent electrophoresis results in the migration of broken strands towards the anode, forming a comet tail, when observed under fluorescence microscope. The amount of DNA in the head and tail is reflected by its fluorescent intensity. The relative fluorescence in the tail compared with its head serves as a measure of the level of DNA damage. In this chapter, we describe the alkaline version of the Comet assay, which is highly sensitive for measuring single- and double-strand DNA breaks.

  15. Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA. (United States)

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


    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

  16. Gauge and Gravity Amplitudes from Trees to Loops

    DEFF Research Database (Denmark)

    Huang, Rijun

    This thesis describes two subjects that I mainly work on during my PhD study. They are both about scattering amplitudes, covering gravity and gauge theories, tree and loop level, with or without supersymmetry. The rst subject is Kawai-Lewellen-Tye(KLT) relation in field theory, which mysteriously...... a special type of two-loop and three-loop diagrams where equations of maximal unitarity cut de ne complex curve. Geometry genus of complex curve is a topological invariant, and characterizes the property of curve. We compute the genus of complex curve for some two-loop and three-loop diagrams from...... for vanishing identities of Yang-Mills amplitudes as violation of linear symmetry groups based on KLT relation argument. The second subject is integrand reduction of multi-loop amplitude. The recent methods based on computational algebraic geometry make it possible to systematically study multi-loop amplitude...

  17. Optimatization of loop heat pipe for cooling of electrotechnical box (United States)

    Roman, Banovcan; Tomas, Puchor; Andrej, Kapjor; Milan, Malcho


    The paper deals with use of LOOP thermosyphon heat pipe to transfer heat from electrotechnical box and describe of construction individual types of LOOP heat pipes. The LOOP heat pipe is very good cooling device which requires no mechanical parts in their design. LOOP heat pipe use only phase change during heat transfer, without a compressor, fan or pump. LOOP heat pipe is more energy saving compared to conventional cooling systems with forced convection. The main advantage of cooling by heat pipe is that electrotechnical box can be hermetically closed (dust -free construction), because dust reduces the lifetime of electrotechnical elements in box. Lifetime of LOOP heat pipe equals to the lifetime of construction material. The paper describes mathematical model of LOOP thermosyphon heat pipe (condenser). Compares selected types of working fluids which are filled with a heat pipe and construction materials of heat pipe.

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

  19. Analytical on shell QED results 3-loop vacuum polarization, 4-loop $\\beta$-function and the muon anomaly

    CERN Document Server

    Broadhurst, D J; Tarasov, O V


    We present the results of analytical calculations of the 3-loop contributions to the asymptotic photon vacuum polarization function, in the on shell scheme, and of the 4-loop contributions to the on shell QED beta-function. These are used to evaluate various 4-loop and 5-loop contributions to the muon anomaly. Our analytical contributions to (g-2)_\\mu differ significantly from previous numerical results. A very recent numerical re-evaluation of 4-loop muon-anomaly contributions has yielded results much closer to ours.

  20. Current systems of coronal loops in 3D MHD simulations (United States)

    Warnecke, J.; Chen, F.; Bingert, S.; Peter, H.


    Aims: We study the magnetic field and current structure associated with a coronal loop. Through this we investigate to what extent the assumptions of a force-free magnetic field break down and where they might be justified. Methods: We analyze a three-dimensional (3D) magnetohydrodynamic (MHD) model of the solar corona in an emerging active region with the focus on the structure of the forming coronal loops. The lower boundary of this simulation is taken from a model of an emerging active region. As a consequence of the emerging magnetic flux and the horizontal motions at the surface a coronal loop forms self-consistently. We investigate the current density along magnetic field lines inside (and outside) this loop and study the magnetic and plasma properties in and around this loop. The loop is defined as the bundle of field lines that coincides with enhanced emission in extreme UV. Results: We find that the total current along the emerging loop changes its sign from being antiparallel to parallel to the magnetic field. This is caused by the inclination of the loop together with the footpoint motion. Around the loop, the currents form a complex non-force-free helical structure. This is directly related to a bipolar current structure at the loop footpoints at the base of the corona and a local reduction of the background magnetic field (I.e., outside the loop) caused by the plasma flow into and along the loop. Furthermore, the locally reduced magnetic pressure in the loop allows the loop to sustain a higher density, which is crucial for the emission in extreme UV. The action of the flow on the magnetic field hosting the loop turns out to also be responsible for the observed squashing of the loop. Conclusions: The complex magnetic field and current system surrounding it can only be modeled in 3D MHD models where the magnetic field has to balance the plasma pressure. A one-dimensional coronal loop model or a force-free extrapolation cannot capture the current system

  1. Phylogenetic analysis of Aceh cattle breed of Indonesia through mitochondrial D-Loop region

    Directory of Open Access Journals (Sweden)

    Eka Meutia Sari


    Full Text Available The objective of this research was to find the basic data on genetic diversity of mtDNA D-Loop in Aceh cattle and its association with Bhutanese, Chinese, and Indian cattle. There were sixty samples of DNA which had been sequenced; i.e. Banda Aceh (11, Saree (20, and Indrapuri (29. To the best of our knowledge this is the first published data on the complete mitochondrial D-Loop sequence of Aceh cattle. Results show that Aceh cattle have the closest relationship to Bos indicus and have been influenced by Bos taurus. The closest genetic ranges among Aceh cattle, Bhutanese, Chinese, Indian and Zebu were Aceh–Zebu (0.0138, Aceh–Bhutanese (0.0156, Aceh–Chinese (0.0190 and Aceh–Indian (0.0193. D-Loop mtDNA analyses showed that there were 27 haplotypes in which twenty-one samples spread in haplotype 1, two samples were in haplotype 2, and the other four haplotypes had various samples in the range of three to seventeen samples. One sample of Aceh cattle from Saree has a closest maternal genetic with B. taurus. One of the four mutations among the star-shaped clusters on median joining network was a new specific haploid-group in Aceh cattle. From this finding it could be assumed that Aceh cattle form a specific haplotype and it can be conclude that Aceh cattle are animal genetic resources from Aceh in Sumatera Island that have to be preserved.

  2. TRF2 is required for repair of nontelomeric DNA double-strand breaks by homologous recombination


    Mao, Zhiyong; Seluanov, Andrei; Jiang, Ying; Gorbunova, Vera


    TRF2 (telomeric repeat binding factor 2) is an essential component of the telomeric cap, where it forms and stabilizes the T-loop junctions. TRF2 forms the T-loops by stimulating strand invasion of the 3′ overhang into duplex DNA. TRF2 also has been shown to localize to nontelomeric DNA double-strand breaks, but its functional role in DNA repair has not been examined. Here, we present evidence that TRF2 is involved in homologous recombination (HR) repair of nontelomeric double-strand breaks. ...

  3. Pemakaian Crown Loop dan Band Loop di Rahang Bawah Anak Usia Enam Tahun (Laporan Kasus

    Directory of Open Access Journals (Sweden)

    Rivi Isabela


    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.

  4. The 1/2 BPS Wilson loop in ABJM theory at two loops


    Bianchi, Marco S.; Giribet, Gaston Enrique; Leoni Olivera, Matías; Penati, Silvia


    We compute the expectation value of the 1/2 BPS circular Wilson loop in ABJM theory at two loops in perturbation theory. The result shows perfect agreement with the prediction from localization and the proposed framing factor. Fil: Bianchi, Marco S.. Institut für Physik. Humboldt-Universität zu Berlin; Alemania; Fil: Giribet, Gaston Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Bue...

  5. LISA Pathfinder closed-loop analysis: a model breakdown of the in-loop observables (United States)

    LISA Pathfinder Collaboration


    This paper describes a methodology to analyze, in the frequency domain, the steady-state control performances of the LISA Pathfinder mission. In particular, it provides a technical framework to give a comprehensive understanding of the spectra of all the degrees of freedom by breaking them down into their various physical origins, hence bringing out the major contributions of the control residuals. A reconstruction of the measured in-loop output, extracted from a model of the closed-loop system, is shown as an instance to illustrate the potential of such a model breakdown of the data.

  6. Open-loop and closed-loop control of flying qubits

    Energy Technology Data Exchange (ETDEWEB)

    Lucamarini, M; Di Giuseppe, G; Vitali, D; Tombesi, P, E-mail: [School of Science and Technology, Physics Division, University of Camerino, I-62032 Camerino (Italy)


    We describe two recent techniques, along with related experiments, to control and reduce the noise affecting a photon polarization qubit. The first is based on the open-loop 'bang-bang' method, where suitably tailored pulses are implemented on the system to prevent polarization decoherence. This requires only passive elements when the physical system is a photon and the operation is performed in space rather than in time. The second technique is based on closed-loop 'asymmetric feedback', where some quantities are measured and used for a real-time correction of the system dynamics. This technique necessarily requires active electronics to work.

  7. Loop securities of arthroscopic sliding-knot techniques when the suture loop is not evenly tensioned. (United States)

    Kim, Sae Hoon; Glaser, Diana; Doan, Josh; Chung, Seok Won; Choi, Hye Yeon; Oh, Joo Han; Hargens, Alan R


    The purpose of this study was to evaluate the loop security of arthroscopic sliding knots when tension is only applied to the post strand and not the loop strand. Six different locking sliding knots (Weston, Nicky, Roeder, SMC, San Diego, and Dines) were included. Loop securities were evaluated in 2 ways: with a conventional method (equal tension applied to the suture loop) and with a worst-case scenario (WCS) method (only the post strand of the suture loop was tensioned). Differences between test methods were evaluated for significance. To help assess the applicability of each test method, loop-security testing in a cadaveric shoulder was performed with 1 type of knot (SMC). Loop securities with the conventional method versus the WCS method were as follows: 10.74 ± 4.20 N versus 6.90 ± 3.90 N for Weston, 21.25 ± 14.74 N versus 8.73 ± 3.35 N for Nicky, 26.14 ± 15.57 N versus 7.95 ± 4.23 N for Roeder, 42.67 ± 22.96 N versus 8.67 ± 4.33 N for SMC, 52.99 ± 21.36 N versus 18.25 ± 10.58 N for San Diego, and 89.27 ± 27.96 N versus 12.48 ± 3.40 N for Dines (P security of 5.53 ± 6.06 N, which was similar to the WCS setting. The locking mechanism of the sliding knots is maintained when the suture loop is evenly tensioned at both post and non-post strands. When tension is not applied to the non-post strand side, the knots slide more easily and fail at lower loads than previously reported. When surgeons tie locking sliding knots in single-row rotator cuff repair, they should be aware that the knots could fail at much lower loads than previously reported. Copyright © 2013 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

  8. Closing the loop of deep brain stimulation

    Directory of Open Access Journals (Sweden)

    Romain eCARRON


    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.

  9. Gas Test Loop Booster Fuel Hydraulic Testing

    Energy Technology Data Exchange (ETDEWEB)

    Gas Test Loop Hydraulic Testing Staff


    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.

  10. Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model (United States)

    Noguchi, Yasunori; Yuan, Zuanning; Bai, Lin; Schneider, Sarah; Zhao, Gongpu; Li, Huilin


    During replication initiation, the core component of the helicase—the Mcm2-7 hexamer—is loaded on origin DNA as a double hexamer (DH). The two ring-shaped hexamers are staggered, leading to a kinked axial channel. How the origin DNA interacts with the axial channel is not understood, but the interaction could provide key insights into Mcm2-7 function and regulation. Here, we report the cryo-EM structure of the Mcm2-7 DH on dsDNA and show that the DNA is zigzagged inside the central channel. Several of the Mcm subunit DNA-binding loops, such as the oligosaccharide–oligonucleotide loops, helix 2 insertion loops, and presensor 1 (PS1) loops, are well defined, and many of them interact extensively with the DNA. The PS1 loops of Mcm 3, 4, 6, and 7, but not 2 and 5, engage the lagging strand with an approximate step size of one base per subunit. Staggered coupling of the two opposing hexamers positions the DNA right in front of the two Mcm2–Mcm5 gates, with each strand being pressed against one gate. The architecture suggests that lagging-strand extrusion initiates in the middle of the DH that is composed of the zinc finger domains of both hexamers. To convert the Mcm2-7 DH structure into the Mcm2-7 hexamer structure found in the active helicase, the N-tier ring of the Mcm2-7 hexamer in the DH-dsDNA needs to tilt and shift laterally. We suggest that these N-tier ring movements cause the DNA strand separation and lagging-strand extrusion. PMID:29078375

  11. Observational constraints on loop quantum cosmology. (United States)

    Bojowald, Martin; Calcagni, Gianluca; Tsujikawa, Shinji


    In the inflationary scenario of loop quantum cosmology in the presence of inverse-volume corrections, we give analytic formulas for the power spectra of scalar and tensor perturbations convenient to compare with observations. Since inverse-volume corrections can provide strong contributions to the running spectral indices, inclusion of terms higher than the second-order runnings in the power spectra is crucially important. Using the recent data of cosmic microwave background and other cosmological experiments, we place bounds on the quantum corrections.

  12. Mercury Thermal Hydraulic Loop (MTHL) Summary Report

    Energy Technology Data Exchange (ETDEWEB)

    Felde, David K. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Crye, Jason Michael [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Wendel, Mark W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Yoder, Jr, Graydon L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Farquharson, George [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Jallouk, Philip A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); McFee, Marshall T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Pointer, William David [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ruggles, Art E. [Univ. of Tennessee, Knoxville, TN (United States); Carbajo, Juan J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)


    The Spallation Neutron Source (SNS) is a high-power linear accelerator built at Oak Ridge National Laboratory (ORNL) which incorporates the use of a flowing liquid mercury target. The Mercury Thermal Hydraulic Loop (MTHL) was constructed to investigate and verify the heat transfer characteristics of liquid mercury in a rectangular channel. This report provides a compilation of previously reported results from the water-cooled and electrically heated straight and curved test sections that simulate the geometry of the window cooling channel in the target nose region.

  13. Loops in Reeb Graphs of 2-Manifolds

    Energy Technology Data Exchange (ETDEWEB)

    Cole-McLaughlin, K; Edelsbrunner, H; Harer, J; Natarajan, V; Pascucci, V


    Given a Morse function f over a 2-manifold with or without boundary, the Reeb graph is obtained by contracting the connected components of the level sets to points. We prove tight upper and lower bounds on the number of loops in the Reeb graph that depend on the genus, the number of boundary components, and whether or not the 2-manifold is orientable. We also give an algorithm that constructs the Reeb graph in time O(n log n), where n is the number of edges in the triangulation used to represent the 2-manifold and the Morse function.

  14. Frequency acquisition techniques for phase locked loop

    CERN Document Server

    Talbot, Daniel


    Many good phaselocked loops (PLL) books exist. However, how to acquire the input frequency from an unlocked state is rarely covered. This book explores the methods for achieving this locked state for a variety of conditions. Using a minimum of mathematics, it introduces engineers to performance limitations of phase/frequency detector based PLL, the quadricorrelator method for both continuous and sampled mode, sawtooth ramp-and-sample phase detector, self-sweeping self-extinguishing topology, and sweep methods using quadrature mixer based lock detection. Digital implementations versus analog are also considered.

  15. Chemical Looping Combustion of Rice Husk


    Rashmeet Singh Monga; Ganesh R. Kale


    A thermodynamic investigation of direct chemical looping combustion (CLC) of rice husk is presented in this paper. Both steam and CO2 are used for gasification within the temperature range of 500–1200˚C and different amounts of oxygen carriers. Chemical equilibrium model was considered for the CLC fuel reactor. The trends in product compositions of the fuel reactor, were determined. Rice husk gasification using 3 moles H2O and 0 moles CO2 per mole carbon (in rice husk) at 1 bar pr...

  16. Towards a four-loop form factor


    Boels, Rutger; Kniehl, Bernd A.; YANG, GANG


    The four-loop, two-point form factor contains the first non-planar correction to the lightlike cusp anomalous dimension. This anomalous dimension is a universal function which appears in many applications. Its planar part in N = 4 SYM is known, in principle, exactly from AdS/CFT and integrability while its non-planar part has been conjectured to vanish. The integrand of the form factor of the stress-tensor multiplet in N = 4 SYM including the non-planar part was obtained in previous work. We ...

  17. Thermoelectric power generator with intermediate loop (United States)

    Bell, Lon E; Crane, Douglas Todd


    A thermoelectric power generator is disclosed for use to generate electrical power from heat, typically waste heat. An intermediate heat transfer loop forms a part of the system to permit added control and adjustability in the system. This allows the thermoelectric power generator to more effectively and efficiently generate power in the face of dynamically varying temperatures and heat flux conditions, such as where the heat source is the exhaust of an automobile, or any other heat source with dynamic temperature and heat flux conditions.

  18. Advanced Hardware Protection of Metallic Loops

    Directory of Open Access Journals (Sweden)

    Mach Václav


    Full Text Available This article deals with the advanced protection of metallic loops using addition electronic components. The main goal of this article is to improve especially Advanced Technology Zone (ATZ, which is the most applied method. The improvement consists of protection against overvoltage which can destroy the Control and Indicating Equipment (CIE and it consist of adding more states which have the impact of numbers of connected detectors. All ideas are introduced with technical details, schematic and every idea also comes with an explanation.

  19. Gauge and Integrable Theories in Loop Spaces


    Ferreira, L. A.; Luchini, G.


    We propose an integral formulation of the equations of motion of a large class of field theories which leads in a quite natural and direct way to the construction of conservation laws. The approach is based on generalized non-abelian Stokes theorems for p-form connections, and its appropriate mathematical language is that of loop spaces. The equations of motion are written as the equality of an hyper-volume ordered integral to an hyper-surface ordered integral on the border of that hyper-volu...

  20. Wilson loop invariants from WN conformal blocks

    Directory of Open Access Journals (Sweden)

    Oleg Alekseev


    Full Text Available Knot and link polynomials are topological invariants calculated from the expectation value of loop operators in topological field theories. In 3D Chern–Simons theory, these invariants can be found from crossing and braiding matrices of four-point conformal blocks of the boundary 2D CFT. We calculate crossing and braiding matrices for WN conformal blocks with one component in the fundamental representation and another component in a rectangular representation of SU(N, which can be used to obtain HOMFLY knot and link invariants for these cases. We also discuss how our approach can be generalized to invariants in higher-representations of WN algebra.

  1. Loop quasi-invariant chunk detection

    DEFF Research Database (Denmark)

    Moyen, Jean-Yves; Rubiano, Thomas; Seiller, Thomas


    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 computational complexity of the overall program can be decreased. In this paper, we introduce the theory around this concept and present a prototype analysis pass implemented on LLVM. We already implemented a proof of concept on a toy C parser ( analysing...

  2. 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

  3. Nanoscale dislocation shear loops at static equilibrium and finite temperature (United States)

    Dang, Khanh; Capolungo, Laurent; Spearot, Douglas E.


    Atomistic simulations are used to determine the resolved shear stress necessary for equilibrium and the resulting geometry of nanoscale dislocation shear loops in Al. Dislocation loops with different sizes and shapes are created via superposition of elemental triangular dislocation displacement fields in the presence of an externally imposed shear stress. First, a bisection algorithm is developed to determine systematically the resolved shear stress necessary for equilibrium at 0 K. This approach allows for the identification of dislocation core structure and a correlation between dislocation loop size, shape and the computed shear stress for equilibrium. It is found, in agreement with predictions made by Scattergood and Bacon, that the equilibrium shape of a dislocation loop becomes more circular with increasing loop size. Second, the bisection algorithm is extended to study the influence of temperature on the resolved shear stress necessary for stability. An approach is presented to compute the effective lattice friction stress, including temperature dependence, for dislocation loops in Al. The temperature dependence of the effective lattice friction stress can be reliably computed for dislocation loops larger than 16.2 nm. However, for dislocation loops smaller than this threshold, the effective lattice friction stress shows a dislocation loop size dependence caused by significant overlap of the stress fields on the interior of the dislocation loops. Combined, static and finite temperature atomistic simulations provide essential data to parameterize discrete dislocation dynamics simulations.

  4. Development of a Loop Mediated Isothermal Amplification for Diagnosis of Ascaris lumbricoides in Fecal Samples

    Directory of Open Access Journals (Sweden)

    Esther A. Shiraho


    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.

  5. Highly Sensitive Loop-Mediated Isothermal Amplification for the Detection of Leptospira

    Directory of Open Access Journals (Sweden)

    Hua-Wei Chen


    Full Text Available Leptospirosis is a worldwide zoonosis caused by an infection with the pathogenic species of Leptospira. We have developed a loop-mediated isothermal amplification (LAMP assay to detect the DNA of Leptospira spp. Six sets of primers targeting the gene of the subsurface protein, lipL32, were evaluated for their detection sensitivity. The best primer set detected less than 25 copies of lipL32 per reaction of both plasmid DNA template and purified leptospiral genomic DNA. By combining primers targeting lipL32 with the previously published primer set targeting lipL41, the sensitivity of the assay was improved to 12 copies of L. interrogans. The specificity of the LAMP assay was evaluated by using the genomic DNA from other clinically encountered bacterial species such as different strains of Orientia tsutsugamushi, Rickettsia typhi, Rickettsia conorii, Rickettsia rickettsii, Coxiella burnetii, and Bartonella bacilliformis. These genomic DNA samples were all negative in our LAMP assay. The sensitivity of the LAMP assay was very similar to that of quantitative real time PCR. Several detection methods for the amplified product of LAMP assay were performed to demonstrate the simplicity of the assay. In summary, our results have suggested that this assay is rapid, robust, and easy to perform and has the potential to be used in endemic locations.

  6. Rapid and Sensitive Identification of the Herbal Tea Ingredient Taraxacum formosanum Using Loop-Mediated Isothermal Amplification

    Directory of Open Access Journals (Sweden)

    Guan-Hua Lai


    Full Text Available Taraxacum formosanum (TF is a medicinal plant used as an important component of health drinks in Taiwan. In this study, a rapid, sensitive and specific loop-mediated isothermal amplification (LAMP assay for authenticating TF was established. A set of four specific LAMP primers was designed based on the nucleotide sequence of the internal transcribed spacer 2 (ITS2 nuclear ribosomal DNA (nrDNA of TF. LAMP amplicons were successfully amplified and detected when purified genomic DNA of TF was added in the LAMP reaction under isothermal condition (65 °C within 45 min. These specific LAMP primers have high specificity and can accurately discriminate Taraxacum formosanum from other adulterant plants; 1 pg of genomic DNA was determined to be the detection limit of the LAMP assay. In conclusion, using this novel approach, TF and its misused plant samples obtained from herbal tea markets were easily identified and discriminated by LAMP assay for quality control.

  7. Shaping chromosomes by DNA capture and release: gating the SMC rings. (United States)

    Gruber, Stephan


    SMC proteins organize chromosomes to coordinate essential nuclear processes such as gene expression and DNA recombination as well as to segregate chromosomes during cell division. SMC mediated DNA bridging keeps sister chromatids aligned for much of the cell cycle, while the active extrusion of DNA loops by SMC presumably compacts chromosomes. Chromosome superstructure is thus given by the number of DNA linkages and the size of chromosomal DNA loops, which in turn depend on the dynamics of SMC loading and unloading. The latter is regulated by the intrinsic SMC ATPase activity, multiple external factors and post-translational modification. Here, I highlight recent advances in our understanding of DNA capture and release by SMC-with a focus on cohesin. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    KAUST Repository

    Deng, Dong


    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.

  9. Quantum hysteresis loops in microscopic system: The loop area as a ...

    Indian Academy of Sciences (India)

    Quantum hysteresis; stochastic resonance; quantum dynamics; Fourier grid methods; stochastically perturbed systems. ... That means we make use of pure state dynamical description of our quantum system. Let the quantum system be .... Apparently, it breaks into a number of smaller loops. The total enclosed area, ...

  10. Innovative hybrid pile oscillator technique in the Minerve reactor: open loop vs. closed loop

    Directory of Open Access Journals (Sweden)

    Geslot Benoit


    Full Text Available Pile oscillator techniques are powerful methods to measure small reactivity worth of isotopes of interest for nuclear data improvement. This kind of experiments has long been implemented in the Mineve experimental reactor, operated by CEA Cadarache. A hybrid technique, mixing reactivity worth estimation and measurement of small changes around test samples is presented here. It was made possible after the development of high sensitivity miniature fission chambers introduced next to the irradiation channel. A test campaign, called MAESTRO-SL, took place in 2015. Its objective was to assess the feasibility of the hybrid method and investigate the possibility to separate mixed neutron effects, such as fission/capture or scattering/capture. Experimental results are presented and discussed in this paper, which focus on comparing two measurements setups, one using a power control system (closed loop and another one where the power is free to drift (open loop. First, it is demonstrated that open loop is equivalent to closed loop. Uncertainty management and methods reproducibility are discussed. Second, results show that measuring the flux depression around oscillated samples provides valuable information regarding partial neutron cross sections. The technique is found to be very sensitive to the capture cross section at the expense of scattering, making it very useful to measure small capture effects of highly scattering samples.

  11. Innovative hybrid pile oscillator technique in the Minerve reactor: open loop vs. closed loop (United States)

    Geslot, Benoit; Gruel, Adrien; Bréaud, Stéphane; Leconte, Pierre; Blaise, Patrick


    Pile oscillator techniques are powerful methods to measure small reactivity worth of isotopes of interest for nuclear data improvement. This kind of experiments has long been implemented in the Mineve experimental reactor, operated by CEA Cadarache. A hybrid technique, mixing reactivity worth estimation and measurement of small changes around test samples is presented here. It was made possible after the development of high sensitivity miniature fission chambers introduced next to the irradiation channel. A test campaign, called MAESTRO-SL, took place in 2015. Its objective was to assess the feasibility of the hybrid method and investigate the possibility to separate mixed neutron effects, such as fission/capture or scattering/capture. Experimental results are presented and discussed in this paper, which focus on comparing two measurements setups, one using a power control system (closed loop) and another one where the power is free to drift (open loop). First, it is demonstrated that open loop is equivalent to closed loop. Uncertainty management and methods reproducibility are discussed. Second, results show that measuring the flux depression around oscillated samples provides valuable information regarding partial neutron cross sections. The technique is found to be very sensitive to the capture cross section at the expense of scattering, making it very useful to measure small capture effects of highly scattering samples.

  12. Improved arrhythmia detection in implantable loop recorders

    DEFF Research Database (Denmark)

    Brignole, M.; Black, C.L.B.; Sutton, R.


    Improved Arrhythmia Detection. Introduction: Implantable loop recorders (ILR) have an automatic arrhythmia detection feature that can be compromised by inappropriately detected episodes. This study evaluated a new ILR sensing and detection scheme for automatically detecting asystole, bradyarrhyth......Improved Arrhythmia Detection. Introduction: Implantable loop recorders (ILR) have an automatic arrhythmia detection feature that can be compromised by inappropriately detected episodes. This study evaluated a new ILR sensing and detection scheme for automatically detecting asystole......, bradyarrhythmia, and tachyarrhythmia events, which is implemented in the next generation device (Reveal DX/XT). Methods and Results: The new scheme employs an automatically adjusting R-wave sensing threshold, enhanced noise rejection, and algorithms to detect asystole, bradyarrhythmia, and tachyarrhythmia....... Performance of the new algorithms was evaluated using 2,613 previously recorded, automatically detected Reveal Plus episodes from 533 patients. A total of 71.9% of episodes were inappropriately detected by the original ILR, and at least 88.6% of patients had one or more inappropriate episodes, with most...

  13. Massive loop corrections for collider physics

    Energy Technology Data Exchange (ETDEWEB)

    Yundin, Valery


    In this thesis we discuss the problem of evaluation of tensor integrals appearing in a typical one-loop Feynman diagram calculation. We present a computer library for the numerical evaluation of tensor integrals with up to 5 legs and arbitrary kinematics. The code implements algorithms based on the formalism which avoids the appearance of inverse Gram determinants in the reduction of pentagon diagrams. The Gram determinants of box integrals are isolated in the set of new basis integrals by using dimensional recurrence relations. These integrals are then evaluated by dimensional recurrence or expansion in small Gram determinant, which is improved by Pade extrapolation. A cache system allows reuse of identical building blocks and increases the efficiency. After describing the cross checks and accuracy tests, we show a sample application to the evaluation of five gluon helicity amplitudes, which is compared with the output of the program NGluon. In the last part the program is applied to the calculation of the one-loop virtual corrections to the muon pair production with hard photon emission. The computation method is explained, followed by a discussion of renormalization and pole structure. Finally, we present numerical results for differential cross sections with kinematics of the KLOE and BaBar detectors.


    Synthetic musk compounds have been found in surface water, fish tissues, and human breast milk. Current techniques for separating these compounds from fish tissues require tedious sample clean-upprocedures A simple method for the deterrnination of these compounds in fish tissues has been developed. Closed-loop stripping of saponified fish tissues in a I -L Wheaton purge-and-trap vessel is used to strip compounds with high vapor pressures such as synthetic musks from the matrix onto a solid sorbent (Abselut Nexus). This technique is useful for screening biological tissues that contain lipids for musk compounds. Analytes are desorbed from the sorbent trap sequentially with polar and nonpolar solvents, concentrated, and directly analyzed by high resolution gas chromatography coupled to a mass spectrometer operating in the selected ion monitoring mode. In this paper, we analyzed two homogenized samples of whole fish tissues with spiked synthetic musk compounds using closed-loop stripping analysis (CLSA) and pressurized liquid extraction (PLE). The analytes were not recovered quantitatively but the extraction yield was sufficiently reproducible for at least semi-quantitative purposes (screening). The method was less expensive to implement and required significantly less sample preparation than the PLE technique. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water,

  15. Black holes in loop quantum gravity (United States)

    Perez, Alejandro


    This is a review of results on black hole physics in the context of loop quantum gravity. The key feature underlying these results is the discreteness of geometric quantities at the Planck scale predicted by this approach to quantum gravity. Quantum discreteness follows directly from the canonical quantization prescription when applied to the action of general relativity that is suitable for the coupling of gravity with gauge fields, and especially with fermions. Planckian discreteness and causal considerations provide the basic structure for the understanding of the thermal properties of black holes close to equilibrium. Discreteness also provides a fresh new look at more (at the moment) speculative issues, such as those concerning the fate of information in black hole evaporation. The hypothesis of discreteness leads, also, to interesting phenomenology with possible observational consequences. The theory of loop quantum gravity is a developing program; this review reports its achievements and open questions in a pedagogical manner, with an emphasis on quantum aspects of black hole physics.

  16. Black holes in loop quantum gravity. (United States)

    Perez, Alejandro


    This is a review of results on black hole physics in the context of loop quantum gravity. The key feature underlying these results is the discreteness of geometric quantities at the Planck scale predicted by this approach to quantum gravity. Quantum discreteness follows directly from the canonical quantization prescription when applied to the action of general relativity that is suitable for the coupling of gravity with gauge fields, and especially with fermions. Planckian discreteness and causal considerations provide the basic structure for the understanding of the thermal properties of black holes close to equilibrium. Discreteness also provides a fresh new look at more (at the moment) speculative issues, such as those concerning the fate of information in black hole evaporation. The hypothesis of discreteness leads, also, to interesting phenomenology with possible observational consequences. The theory of loop quantum gravity is a developing program; this review reports its achievements and open questions in a pedagogical manner, with an emphasis on quantum aspects of black hole physics.

  17. Thermohaline feedback loops and Natural Capital

    Directory of Open Access Journals (Sweden)

    Tom Sawyer Hopkins


    Full Text Available Human interference now represents an inextricable component of all major ecosystems. Whether this is through top-down overharvesting of ecosystem production or bottom-up alteration (deliberate or inadvertent of the abiotic conditions, the planet´s ecosphere is in a vicious degradation cycle. For our economy to shift from exploiting to sustaining the natural systems, the solution, if there is to be one, will involve incorporation of the value of natural capital into the economic and political feedback loop. For the science sector, this will involve developing methodologies to evaluate the nonlinear and behavioral dynamics of entire systems in ways that can be coupled with economic models. One essential characteristic of systems science involves the interactions between internal components and external systems. Thermohaline circulations and their feedback loops illustrate a class of such interactive pathways. Examples from the Arctic, Mediterranean, and the US East Coast along with some of their associated ecological impacts are reviewed. Understanding how thermohaline interactions provide stability to the marine biotic environment and under what conditions this stability could be destabilized is a fundamental step toward evaluating the non-linear response of marine systems to anthropogenic stress.

  18. Keeping Energy Savings in the LOOP

    Energy Technology Data Exchange (ETDEWEB)

    Parrish, Kristen [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Mercado, Andrea [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)


    Mesa Lane Partners (MLP) partnered with the U.S. Department of Energy (DOE) to develop and implement solutions to a build a new, low-energy mixed-use building that consumes at least 50% less energy than requirements set by Energy Standard 90.1-2007 of the American Society of Heating, Refrigerating, and Air-conditioning Engineers (ASHRAE), the American National Standards Institute (ANSI), and the Illuminating Engineering Society of America (IESNA), as part of DOE’s Commercial Building Partnerships (CBP)3 Program. Lawrence Berkeley National Laboratory (LBNL) provided technical expertise in support of this DOE program. The privately developed 46,000-square-foot LOOP project, which is intended to provide affordable off-campus student housing in an underserved community next to University of California at Santa Barbara, will contain more than 7,000 square feet of retail space, a roof deck, an event space, a gym, and 48 apartments. The project developer, MLP, is aiming to exceed CBP requirement, targeting energy consumption that is at least 65% less than that required by the standard. If the LOOP meets this goal, it is expected to achieve Leadership in Energy and Environmental Design (LEED) Gold certification. To meet this goal, the project design incorporates a variety of energy efficiency measures (EEMs) that address the needs of the multiple use types that the project will house.

  19. Loop-Effects in Pseudo-Supersymmetry

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Matthias


    We analyze the transmission of supersymmetry breaking in brane-world models of pseudo-supersymmetry. In these models two branes preserve different halves of the bulk supersymmetry. Thus supersymmetry is broken although each sector of the model is supersymmetric when considered separately. The world-volume theory on one brane feels the breakdown of supersymmetry only through two-loop interactions involving a coupling to fields from the other brane. In a 5D toy model with bulk vectors, we compute the diagrams that contribute to scalar masses on one brane and find that the masses are proportional to the compactification scale up to logarithmic corrections, m{sup 2} {infinity} (2{pi}R){sup -2} (ln(2{pi}R m{sub S}) - 1.1), where m{sub s} is an ultraviolet cutoff. Thus, for large compactification radii, where this result is valid, the brane scalars acquire a positive mass squared. We also compute the three-loop diagrams relevant to the Casimir energy between the two branes and find E {infinity} (2{pi}R){sup -4}((ln(2{pi}R m{sub S}) - 1.7){sup 2} + 0.2). For large radii, this yields a repulsive Casimir force.

  20. Theoretical study on a solar collector loop during stagnation

    DEFF Research Database (Denmark)

    Chen, Ziqian; Dragsted, Janne; Furbo, Simon

    A mathematical model simulating the stagnation behavior of a pressurized solar collector loop with solar collectors with a good emptying behavior is developed. Based on the pre-pressure of the expansion vessel, the system filling pressure of the solar collector loop and the design of the solar...... collector loop, the mass of the fluid flowing into the pressurized expansion vessel and the pressures at the top part and at the bottom part of the solar collector loop during stagnation for the solar collector loop are calculated. The theoretically calculated results are compared with experimental results....... There is a good agreement between calculations and measurements. The developed simulation model is therefore suitable to determine the behavior of solar collector loops during stagnation....

  1. High Dynamic Optimized Carrier Loop Improvement for Tracking Doppler Rates

    Directory of Open Access Journals (Sweden)

    Amirhossein Fereidountabar


    Full Text Available Mathematical analysis and optimization of a carrier tracking loop are presented. Due to fast changing of the carrier frequency in some satellite systems, such as Low Earth Orbit (LEO or Global Positioning System (GPS, or some planes like Unmanned Aerial Vehicles (UAVs, high dynamic tracking loops play a very important role. In this paper an optimized tracking loop consisting of a third-order Phase Locked Loop (PLL assisted by a second-order Frequency Locked Loop (FLL for UAVs is proposed and discussed. Based on this structure an optimal loop has been designed. The main advantages of this approach are the reduction of the computation complexity and smaller phase error. The paper shows the simulation results, comparing them with a previous work.

  2. Coronal Loop Evolution Observed with AIA and Hi-C (United States)

    Mulu-Moore, Fana; Winebarger, A.; Cirtain, J.; Kobayashi, K.; Korreck, K.; Golub, L.; Kuzin. S.; Walsh, R.; DeForest, C.; DePontieu, B.; hide


    Despite much progress toward understanding the dynamics of the solar corona, the physical properties of coronal loops are not yet fully understood. Recent investigations and observations from different instruments have yielded contradictory results about the true physical properties of coronal loops. In the past, the evolution of 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 poster we discuss the first results of loop analysis comparing AIA and Hi-C data. We find signatures of cooling in a pixel selected along a loop structure in the AIA multi-filter observations. However, unlike previous studies, we find that the cooling time is much longer than the draining time. This is inconsistent with previous cooling models.

  3. Tree-loop duality relation beyond single poles

    Energy Technology Data Exchange (ETDEWEB)

    Bierenbaum, Isabella [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Buchta, Sebastian; Draggiotis, Petros; Malamos, Ioannis; Rodrigo, German [Valencia Univ. Paterna (Spain). Inst. de Fisica Corpuscular


    We develop the Tree-Loop Duality Relation for two- and three-loop integrals with multiple identical propagators (multiple poles). This is the extension of the Duality Relation for single poles and multi-loop integrals derived in previous publications. We prove a generalization of the formula for single poles to multiple poles and we develop a strategy for dealing with higher-order pole integrals by reducing them to single pole integrals using Integration By Parts.

  4. The Quantum Configuration Space of Loop Quantum Cosmology


    Velhinho, J. M.


    The article gives an account of several aspects of the space known as the Bohr compactification of the line, featuring as the quantum configuration space in loop quantum cosmology, as well as of the corresponding configuration space realization of the so-called polymer representation. Analogies with loop quantum gravity are explored, providing an introduction to (part of) the mathematical structure of loop quantum gravity, in a technically simpler context.

  5. The quantum configuration space of loop quantum cosmology (United States)

    Velhinho, J. M.


    This paper gives an account of several aspects of the space known as the Bohr compactification of the line, featuring as the quantum configuration space in loop quantum cosmology, as well as of the corresponding configuration space realization of the so-called polymer representation. Analogies with loop quantum gravity are explored, providing an introduction to (part of) the mathematical structure of loop quantum gravity, in a technically simpler context.

  6. Exploiting loop level parallelism in nonprocedural dataflow programs (United States)

    Gokhale, Maya B.


    Discussed are how loop level parallelism is detected in a nonprocedural dataflow program, and how a procedural program with concurrent loops is scheduled. Also discussed is a program restructuring technique which may be applied to recursive equations so that concurrent loops may be generated for a seemingly iterative computation. A compiler which generates C code for the language described below has been implemented. The scheduling component of the compiler and the restructuring transformation are described.

  7. Direct-contact closed-loop heat exchanger

    Energy Technology Data Exchange (ETDEWEB)

    Berry, Gregory F. (Naperville, IL); Minkov, Vladimir (Skokie, IL); Petrick, Michael (Joliet, IL)


    A high temperature heat exchanger with a closed loop and a heat transfer liquid within the loop, the closed loop having a first horizontal channel with inlet and outlet means for providing direct contact of a first fluid at a first temperature with the heat transfer liquid, a second horizontal channel with inlet and outlet means for providing direct contact of a second fluid at a second temperature with the heat transfer liquid, and means for circulating the heat transfer liquid.

  8. Ladder exponentiation for generic large symmetric representation Wilson loops


    Correa, Diego; Massolo, Fidel(Instituto de Física La Plata, CONICET, Universidad Nacional de La Plata, C.C. 67, La Plata, 1900, Argentina)


    A recent proposal was made for a large representation rank limit for which the expectation values of N = 4 $$ \\mathcal{N}=4 $$ super Yang-Mills Wilson loops are given by the exponential of the 1-loop result. We verify the validity of this exponentiation in the strong coupling limit using the holographic D3-brane description for straight Wilson loops following an arbitrary internal space trajectory.

  9. Minor magnetization loops in two-dimensional dipolar Ising model

    Energy Technology Data Exchange (ETDEWEB)

    Sarjala, M. [Aalto University, Department of Applied Physics, P.O. Box 14100, FI-00076 Aalto (Finland); Seppaelae, E.T., E-mail: [Nokia Research Center, Itaemerenkatu 11-13, FI-00180 Helsinki (Finland); Alava, M.J., E-mail: mikko.alava@tkk.f [Aalto University, Department of Applied Physics, P.O. Box 14100, FI-00076 Aalto (Finland)


    The two-dimensional dipolar Ising model is investigated for the relaxation and dynamics of minor magnetization loops. Monte Carlo simulations show that in a stripe phase an exponential decrease can be found for the magnetization maxima of the loops, M{approx}exp(-{alpha}N{sub l}) where N{sub l} is the number of loops. We discuss the limits of this behavior and its relation to the equilibrium phase diagram of the model.

  10. DNA Length Modulates the Affinity of Fragments of Genomic DNA for the Nuclear Matrix In Vitro. (United States)

    García-Vilchis, David; Aranda-Anzaldo, Armando


    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.

  11. Tuning genetic clocks employing DNA binding sites.

    Directory of Open Access Journals (Sweden)

    Shridhar Jayanthi

    Full Text Available Periodic oscillations play a key role in cell physiology from the cell cycle to circadian clocks. The interplay of positive and negative feedback loops among genes and proteins is ubiquitous in these networks. Often, delays in a negative feedback loop and/or degradation rates are a crucial mechanism to obtain sustained oscillations. How does nature control delays and kinetic rates in feedback networks? Known mechanisms include proper selection of the number of steps composing a feedback loop and alteration of protease activity, respectively. Here, we show that a remarkably simple means to control both delays and effective kinetic rates is the employment of DNA binding sites. We illustrate this design principle on a widely studied activator-repressor clock motif, which is ubiquitous in natural systems. By suitably employing DNA target sites for the activator and/or the repressor, one can switch the clock "on" and "off" and precisely tune its period to a desired value. Our study reveals a design principle to engineer dynamic behavior in biomolecular networks, which may be largely exploited by natural systems and employed for the rational design of synthetic circuits.

  12. Assessing catchment connectivity using hysteretic loops (United States)

    Davis, Jason; Masselink, Rens; Goni, Mikel; Gimenez, Rafael; Casali, Javier; Seeger, Manuel; Keesstra, Saskia


    Storm events mobilize large proportions of sediments in catchment systems. Therefore understanding catchment sediment dynamics throughout the continuity of storms and how initial catchment states act as controls on the transport of sediment to catchment outlets is important for effective catchment management. Sediment connectivity is a concept which can explain the origin, pathways and sinks of sediments within catchments (Baartman et al., 2013; Parsons et al., 2015; Masselink et al., 2016a,b; Mekonnen et al., 2016). However, sediment connectivity alone does not provide a practicable mechanism by which the catchment's initial state - and thus the location of entrained sediment in the sediment transport cascade - can be characterized. Studying the dynamic relationship between water discharge (Q) and suspended sediment (SS) at the catchment outlet can provide a valuable research tool to infer the likely source areas and flow pathways contributing to sediment transport because the relationship can be characterized by predictable hysteresis patterns. Hysteresis is observed when the sediment concentration associated with a certain flow rate is different depending on the direction in which the analysis is performed - towards the increase or towards the diminution of the flow. However, the complexity of the phenomena and factors which determine the hysteresis make its interpretation ambiguous. Previous work has described various types of hysteretic loops as well as the cause for the shape of the loop, mainly pointing to the origin of the sediments. The data set for this study comes from four experimental watersheds in Navarre (Spain), owned and maintained by the Government of Navarre. These experimental watersheds have been monitored and studied since 1996 (La Tejería and Latxaga) and 2001 (Oskotz principal and Oskotz woodland). La Tejería and Latxaga watersheds are similar to each other regarding size (approximately 200 ha), geology (marls and sandstones), soils (fine

  13. Impact of looping on middle school science standardized achievement tests (United States)

    Barger, Tammy M.

    Looping may be defined as a teacher remaining with a group of students for multiple academic years. In this quantitative study, looping was examined as a factor on science achievement. State-wide eighth grade school level 2010 Pennsylvania System of School Assessment (PSSA) data were used. By responding to a mailing, school administrators indicated if 2010 eighth grade students had or had not been looped. The schools' percentage of advanced and proficient Science PSSA data were used to determine if the independent variable had a significant impact on science achievement. The results of the independent t-test analysis suggest that looping does not contribute to science achievement for this study sample.

  14. Dynamics of closed-loop systems containing flexible bodies (United States)

    Tadikonda, Sivakumar S. K.; Singh, Ramendra P.


    An important characteristic of flexible multibody systems containing closed-loop topologies is that the component modes used to describe individual bodies will no longer be independent because of loop closure constraints. Thus, the issue of component modal selection becomes even more complicated. In addition, the foreshortening effect that has been studied extensively in the literature in the context of open-loop topologies will also be present in these constraint equations. Simulation results presented demonstrate the effects of modal selection and foreshortening on the dynamic response of closed-loop flexible systems.

  15. Multi-loop Integrand Reduction with Computational Algebraic Geometry

    CERN Document Server

    Badger, Simon; Zhang, Yang


    We discuss recent progress in multi-loop integrand reduction methods. Motivated by the possibility of an automated construction of multi-loop amplitudes via generalized unitarity cuts we describe a procedure to obtain a general parameterisation of any multi-loop integrand in a renormalizable gauge theory. The method relies on computational algebraic geometry techniques such as Gr\\"obner bases and primary decomposition of ideals. We present some results for two and three loop amplitudes obtained with the help of the Macaulay2 computer algebra system and the Mathematica package BasisDet.

  16. Two-loop off-shell QCD amplitudes in FDR

    CERN Document Server

    Page, Ben


    We link the FDR treatment of ultraviolet (UV) divergences to dimensional regularization up to two loops in QCD. This allows us to derive the one-loop and two-loop coupling constant and quark mass shifts necessary to translate infrared finite quantities computed in FDR to the MSbar renormalization scheme. As a by-product of our analysis, we solve a problem analogous to the breakdown of unitarity in the Four Dimensional Helicity (FDH) method beyond one loop. A fix to FDH is then presented that preserves the renormalizability properties of QCD without introducing evanescent quantities.

  17. Enhanced Loop Structure of NFC Antenna for Mobile Handset Applications

    Directory of Open Access Journals (Sweden)

    Byungje Lee


    Full Text Available A new structure of an NFC loop antenna for mobile handset applications is proposed. The proposed antenna consists of conventional loop elements and a parasitic loop embedded capacitor to enhance its performance. Although the sintered ferrite sheets with higher relative permeability (μr≈200 have been used to reduce the performance deterioration due to the eddy current on the battery pack of a mobile handset, their costs are high, and they are considerably breakable. In this paper, with the proposed structure, we effectively enhance the performance of an NFC loop antenna by employing the ferrite-polymer composite with lower relative permeability (μr≈55.

  18. Lattice corrections to the quark quasidistribution at one loop (United States)

    Carlson, Carl E.; Freid, Michael


    We calculate radiative corrections to the quark quasidistribution in lattice perturbation theory at one loop to leading orders in the lattice spacing. We also consider one-loop corrections in continuum Euclidean space. We find that the infrared behavior of the corrections in Euclidean and Minkowski space are different. We explore features of momentum loop integrals and demonstrate why loop corrections from the lattice perturbation theory and Euclidean continuum do not correspond with their Minkowski brethren, and comment on a recent suggestion for transcending the differences in the results. Further, we examine the role of the lattice spacing a and of the r parameter in the Wilson action in these radiative corrections.

  19. Inverse spin Hall effect in a closed loop circuit

    Energy Technology Data Exchange (ETDEWEB)

    Omori, Y.; Auvray, F.; Wakamura, T.; Niimi, Y., E-mail: [Institute for Solid State Physics, University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8581 (Japan); Fert, A. [Unité Mixte de Physique CNRS/Thales, 91767 Palaiseau France associée à l' Université de Paris-Sud, 91405 Orsay (France); Otani, Y. [Institute for Solid State Physics, University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8581 (Japan); RIKEN-CEMS, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)


    We present measurements of inverse spin Hall effects (ISHEs), in which the conversion of a spin current into a charge current via the ISHE is detected not as a voltage in a standard open circuit but directly as the charge current generated in a closed loop. The method is applied to the ISHEs of Bi-doped Cu and Pt. The derived expression of ISHE for the loop structure can relate the charge current flowing into the loop to the spin Hall angle of the SHE material and the resistance of the loop.

  20. Finding the positive feedback loops underlying multi-stationarity. (United States)

    Feliu, Elisenda; Wiuf, Carsten


    Bistability is ubiquitous in biological systems. For example, bistability is found in many reaction networks that involve the control and execution of important biological functions, such as signaling processes. Positive feedback loops, composed of species and reactions, are necessary for bistability, and generally for multi-stationarity, to occur. These loops are therefore often used to illustrate and pinpoint the parts of a multi-stationary network that are relevant ('responsible') for the observed multi-stationarity. However positive feedback loops are generally abundant in reaction networks but not all of them are important for understanding the network's dynamics. We present an automated procedure to determine the relevant positive feedback loops of a multi-stationary reaction network. The procedure only reports the loops that are relevant for multi-stationarity (that is, when broken multi-stationarity disappears) and not all positive feedback loops of the network. We show that the relevant positive feedback loops must be understood in the context of the network (one loop might be relevant for one network, but cannot create multi-stationarity in another). Finally, we demonstrate the procedure by applying it to several examples of signaling processes, including a ubiquitination and an apoptosis network, and to models extracted from the Biomodels database. The procedure is implemented in Maple. We have developed and implemented an automated procedure to find relevant positive feedback loops in reaction networks. The results of the procedure are useful for interpretation and summary of the network's dynamics.

  1. Comments on Pinched Hysteresis Loops of Memristive Elements

    Directory of Open Access Journals (Sweden)

    Z. Biolek


    Full Text Available The hysteresis loops pinched in the v-i origin belong to well-known fingerprints of memristive elements driven by bipolar periodical signals. Some element properties follow from the loop behavior in the close neighborhood of the origin. The paper analyzes this behavior of the memristive elements that produce steady-state hysteresis loops under harmonic excitation. It is shown that there is a connection between the frequency content of the state variable waveform and the type of the loop being pinched.

  2. Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs

    Directory of Open Access Journals (Sweden)

    Daniel P. Aalberts


    Full Text Available The free energy of an RNA fold is a combination of favorable base pairing and stacking interactions competing with entropic costs of forming loops. Here we show how loop entropy, surprisingly, can promote tertiary order. A general formula for the free energy of forming multibranch and other RNA loops is derived with a polymer-physics based theory. We also derive a formula for the free energy of coaxial stacking in the context of a loop. Simulations support the analytic formulas. The effects of stacking of unpaired bases are also studied with simulations.

  3. Time Optimal Synchronization Procedure and Associated Feedback Loops

    CERN Document Server

    Angoletta, Maria Elena; CERN. Geneva. ATS Department


    A procedure to increase the speed of currently used synchronization loops in a synchrotron by an order of magnitude is presented. Beams dynamics constraint imposes an upper limit on excursions in stable phase angle, and the procedure presented exploits this limit to arrive in the synchronized state from an arbitrary initial state in the fastest possible way. Detailed corrector design for beam phase loop, differential frequency loop and final synchronization loop is also presented. Finally, an overview of the synchronization methods currently deployed in some other CERN’s machines is provided, together with a brief comparison with the newly proposed time-optimal algorithm.

  4. Cloning of two sea urchin DNA-binding proteins involved in mitochondrial DNA replication and transcription. (United States)

    Loguercio Polosa, Paola; Megli, Fiammetta; Di Ponzio, Barbara; Gadaleta, Maria Nicola; Cantatore, Palmiro; Roberti, Marina


    The cloning of the cDNA for two mitochondrial proteins involved in sea urchin mtDNA replication and transcription is reported here. The cDNA for the mitochondrial D-loop binding protein (mtDBP) from the sea urchin Strongylocentrotus purpuratus has been cloned by a polymerase chain reaction-based approach. The protein displays a very high similarity with the Paracentrotus lividus homologue as it contains also the two leucine zipper-like domains which are thought to be involved in intramolecular interactions needed to expose the two DNA binding domains in the correct position for contacting DNA. The cDNA for the mitochondrial single-stranded DNA-binding protein (mtSSB) from P. lividus has been also cloned by a similar approach. The precursor protein is 146 amino acids long with a presequence of 16 residues. The deduced amino acid sequence shows the highest homology with the Xenopus laevis protein and the lowest with the Drosophila mtSSB. The computer modeling of the tertiary structure of P. lividus mtSSB shows a structure very similar to that experimentally determined for human mtSSB, with the conservation of the main residues involved in protein tetramerization and in DNA binding.

  5. Retinal mitochondrial DNA mismatch repair in the development of diabetic retinopathy, and its continued progression after termination of hyperglycemia. (United States)

    Mishra, Manish; Kowluru, Renu A


    Mitochondrial DNA (mtDNA) is damaged in the retina in diabetes, and mitochondria copy numbers are decreased. The displacement-loop (D-loop) of the mtDNA, the region with transcription/replication elements, experiences more damage than other regions of mtDNA. Our aim was to examine the role of DNA mismatch repair (MMR) in mitochondria homeostasis in diabetic retinopathy, and in its continued progression after cessation of hyperglycemia. Effect of hyperglycemia on sequence variants in the D-loop region was investigated in retinal endothelial cells and in the retina from streptozotocin-induced diabetic rats using mismatch-specific surveyor nuclease. The role of MMR machinery in mtDNA damage and mitochondrial respiration was investigated in retinal endothelial cells overexpressing Mlh1, an MMR enzyme mainly associated with mtDNA polymerase gamma, or Msh2 (associated with nuclear polymerase beta). Hyperglycemia increased sequence variants in the D-loop region. While overexpression of Mlh1 in endothelial cells ameliorated glucose-induced increase in D-loop sequence variants, decrease in respiration rate and increase in apoptosis, overexpression of Msh2 did not protect the mitochondria damage. Termination of hyperglycemia failed to reverse decrease in MMR enzymes and increase in D-loop sequence variants. Due to a compromised MMR system, the sequence variants in the D-loop region were not repaired, and that resulted in impaired mtDNA transcription. Mitochondria become dysfunctional, and they continued to be dysfunctional even after hyperglycemia was terminated, contributing to the development, and progression of diabetic retinopathy. Thus, strategies targeting mitochondrial MMR machinery could help maintain mitochondria homeostasis, and inhibit the development of diabetic retinopathy and its continued progression. Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

  6. Top-level dynamics and the regulated gene response of feed-forward loop transcriptional motifs. (United States)

    Mayo, Michael; Abdelzaher, Ahmed; Perkins, Edward J; Ghosh, Preetam


    Feed-forward loops are hierarchical three-node transcriptional subnetworks, wherein a top-level protein regulates the activity of a target gene via two paths: a direct-regulatory path, and an indirect route, whereby the top-level proteins act implicitly through an intermediate transcription factor. Using a transcriptional network of the model bacterium Escherichia coli, we confirmed that nearly all types of feed-forward loop were significantly overrepresented in the bacterial network. We then used mathematical modeling to study their dynamics by manipulating the rise times of the top-level protein concentration, termed the induction time, through alteration of the protein destruction rates. Rise times of the regulated proteins exhibited two qualitatively different regimes, depending on whether top-level inductions were "fast" or "slow." In the fast regime, rise times were nearly independent of rapid top-level inductions, indicative of biological robustness, and occurred when RNA production rate-limits the protein yield. Alternatively, the protein rise times were dependent upon slower top-level inductions, greater than approximately one bacterial cell cycle. An equation is given for this crossover, which depends upon three parameters of the direct-regulatory path: transcriptional cooperation at the DNA-binding site, a protein-DNA dissociation constant, and the relative magnitude of the top-level protien concentration.

  7. Parallelizing More Loops with Compiler Guided Refactoring

    DEFF Research Database (Denmark)

    Larsen, Per; Ladelsky, Razya; Lidman, Jacob


    with target-specific optimizations. Furthermore, comparing the first benchmark to manually-parallelized, handoptimized pthreads and OpenMP versions, we find that code generated using our approach typically outperforms the pthreads code (within 93-339%). It also performs competitively against the OpenMP code...... 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......, resulting in scalable parallelized code that runs up to 8.3 times faster on an eightcore 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 be combined...

  8. Simple Device for Treating Prolapsing Loop Colostomy

    Directory of Open Access Journals (Sweden)

    Ming-Yu Hsieh


    Full Text Available Stoma prolapse is a common complication of intestinal stoma. Although various surgical methods yield satisfactory results, nonsurgical treatment may be better for a temporary stoma. We report a case of a patient with a distal limb prolapse of a right transverse colostomy who received nonsurgical treatment with satisfactory results. For the treatment of a temporary transverse loop colostomy with distal limb prolapse, we designed a simple device consisting of a pediatric plastic medicine cup, which was rolled into a towel to shape the bottom of the cup into a compressor. The towel was put on the stoma outside of the colostomy bag with the compressor above the prolapsing limb of the colostomy. An abdominal binder was applied to fix the towel.

  9. Geothermal Loop Experimental Facility. Final report

    Energy Technology Data Exchange (ETDEWEB)


    Research at the Geothermal Loop Experimental Facility was successfully concluded in September 1979. In 13,000 hours of operation over a three and one half year period, the nominal 10 megawatt electrical equivalent GLEF provided the opportunity to identify problems in working with highly saline geothermal fluids and to develop solutions that could be applied to a commercial geothermal power plant producing electricity. A seven and one half year period beginning in April 1972, with early well flow testing and ending in September 1979, with the completion of extensive facility and reservoir operations is covered. During this period, the facility was designed, constructed and operated in several configurations. A comprehensive reference document, addressing or referencing documentation of all the key areas investigated is presented.

  10. ABJM Wilson loops in arbitrary representations

    Energy Technology Data Exchange (ETDEWEB)

    Hatsuda, Yasuyuki [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Theory Group; Tokyo Institute of Technology (Japan). Dept. of Physics; Honda, Masazumi [High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki (Japan); Moriyama, Sanefumi [Nagoya Univ. (Japan). Kobayashi Maskawa Inst. and Graduate School of Mathematics; Okuyama, Kazumi [Shinshu Univ., Matsumoto, Nagano (Japan). Dept. of Physics


    We study vacuum expectation values (VEVs) of circular half BPS Wilson loops in arbitrary representations in ABJM theory. We find that those in hook representations are reduced to elementary integrations thanks to the Fermi gas formalism, which are accessible from the numerical studies similar to the partition function in the previous studies. For non-hook representations, we show that the VEVs in the grand canonical formalism can be exactly expressed as determinants of those in the hook representations. Using these facts, we can study the instanton effects of the VEVs in various representations. Our results are consistent with the worldsheet instanton effects studied from the topological string and a prescription to include the membrane instanton effects by shifting the chemical potential, which has been successful for the partition function.

  11. Cosmological perturbations in teleparallel Loop Quantum Cosmology

    CERN Document Server

    Haro, Jaime


    Cosmological perturbations in Loop Quantum Cosmology (LQC) could be studied from two totally different ways. The first one, called holonomy corrected LQC, is performed in the Hamiltonian framework, where the Asthekar connection is replaced by a suitable sinus function (holonomy correction), in order to have a well-defined quantum analogue. The alternative approach is based in the fact that isotropic LQC could be also obtained as a particular case of teleparallel $F(T)$ gravity (teleparallel LQC). Then, working in the Lagrangian framework and using the well-know perturbation equations in $F(T)$ gravity, we have obtained, in teleparallel LQC, the equations for scalar and tensor perturbations, and the corresponding Mukhanov-Sasaki equations. For scalar perturbations, our equation only differs from the one obtained by holonomy corrections in the velocity of sound, leading both formulations, essentially to the same scale invariant power spectrum when a matter-dominated universe is considered. However for tensor pe...

  12. Effective scenario of loop quantum cosmology. (United States)

    Ding, You; Ma, Yongge; Yang, Jinsong


    Semiclassical states in isotropic loop quantum cosmology are employed to show that the improved dynamics has the correct classical limit. The effective Hamiltonian for the quantum cosmological model with a massless scalar field is thus obtained, which incorporates also the next to leading order quantum corrections. The possibility that the higher order correction terms may lead to significant departure from the leading order effective scenario is revealed. If the semiclassicality of the model is maintained in the large scale limit, there are great possibilities for a k=0 Friedmann expanding universe to undergo a collapse in the future due to the quantum gravity effect. Thus the quantum bounce and collapse may contribute a cyclic universe in the new scenario.

  13. Loops in the Sun’s orbit

    Directory of Open Access Journals (Sweden)

    Marjanov Milutin


    Full Text Available Besides translation, spin around its axis and rotation around center of the Milky Way, the Sun performs relative motion in the solar system Laplacian plane, also. This motion was anticipated by Newton himself, in his Principia. The form of the Sun’s orbit is substantially different from the other solar system bodies’ orbits. Namely, the Sun moves along the path composed of the chain of large and small loops [1, 2, 6, 9]. This chain is situated within the circular outline with the diameter approximately twice as large as the Sun’s is. Under supposition that the solar system is stable, the Sun is going to move along it, in the same region, for eternity, never reitereiting the same path. It was also shown in this work that velocity and acceleration of the Sun’s center of mass are completely defined by the relative velocities and accelerations of the planets with respect to the Sun.

  14. Area Law from Loop Quantum Gravity

    CERN Document Server

    Hamma, Alioscia; Marciano, Antonino; Zhang, Mingyi


    We explore the constraints following from requiring the Area Law in the entanglement entropy in the context of loop quantum gravity. We find a unique solution to the single link wave-function in the large j limit, believed to be appropriate in the semi-classical limit. We then generalize our considerations to multi-link coherent states, and find that the area law is preserved very generically using our single link wave-function as a building block. Finally, we develop the framework that generates families of multi-link states that preserve the area law while avoiding macroscopic entanglement, the space-time analogue of "Schroedinger cat". We note that these states, defined on a given set of graphs, are the ground states of some local Hamiltonian that can be constructed explicitly. This can potentially shed light on the construction of the appropriate Hamiltonian constraints in the LQG framework.

  15. Looped energy harvester for human motion (United States)

    Geisler, M.; Boisseau, S.; Gasnier, P.; Willemin, J.; Gobbo, C.; Despesse, G.; Ait-Ali, I.; Perraud, S.


    The development of energy harvesters for smart wearables is a challenging topic, with a difficult combination of ergonomics constraints, lifetime and electrical requirements. In this work, we focus on an inertial inductive structure, composed of a magnetic ball circulating inside a closed-loop guide and converting the kinetic energy of the user’s limbs into electricity during the run. A specific induction issue related to the free self-rotation of the ball is underlined and addressed using a ferromagnetic ‘rail’ component. From a 2 g moving ball, a 5 cm-diameter 21 cm3 prototype generated up to 4.8 mW of average power when worn by someone running at 8 km h-1. This device is demonstrated to charge a 2.4 V NiMH battery and supply an acceleration and temperature Wireless Sensor Node at 20 Hz.

  16. Closed loop supply chain in printing operation

    Directory of Open Access Journals (Sweden)

    Marcius Fabius Henriques Carvalho


    Full Text Available There is a clear change in focus in large companies, previously dedicated primarily to the production of physical goods, toward offering complimentary services and changing their focus toward more service-oriented businesses, in order to increase their competitiveness. At the same time, companies are facing increasing product returns due to various reasons leading to reverse logistics practices and toward the introduction of a Closed Loop Supply Chain management perspective. The purpose of this work is to identify, using a case study in the printing industry,  specific characteristics, regarding product returns, both in a product-oriented and a service-oriented operation. Furthermore, the current work performs a diagnosis of current practices applications of CLSC models in the two operating models. The paper concludes that indeed there are relevant differences in managing the CLSC for each case and identify the main gaps for each operation.

  17. Subleading soft graviton theorem for loop amplitudes (United States)

    Sen, Ashoke


    Superstring field theory gives expressions for heterotic and type II string loop amplitudes that are free from ultraviolet and infrared divergences when the number of non-compact space-time dimensions is five or more. We prove the subleading soft graviton theorem in these theories to all orders in perturbation theory for S-matrix elements of arbitrary number of finite energy external states but only one external soft graviton. We also prove the leading soft graviton theorem for arbitrary number of finite energy external states and arbitrary number of soft gravitons. Since our analysis is based on general properties of one particle irreducible effective action, the results are valid in any theory of quantum gravity that gives finite result for the S-matrix order by order in perturbation theory without violating general coordinate invariance.

  18. 't Hooft loops and perturbation theory

    CERN Document Server

    De Forcrand, Philippe; Noth, D; Forcrand, Philippe de; Lucini, Biagio; Noth, David


    We show that high-temperature perturbation theory describes extremely well the area law of SU(N) spatial 't Hooft loops, or equivalently the tension of the interface between different Z_N vacua in the deconfined phase. For SU(2), the disagreement between Monte Carlo data and lattice perturbation theory for sigma(T)/T^2 is less than 2%, down to temperatures O(10) T_c. For SU(N), N>3, the ratios of interface tensions, (sigma_k/sigma_1)(T), agree with perturbation theory, which predicts tiny deviations from the ratio of Casimirs, down to nearly T_c. In contrast, individual tensions differ markedly from the perturbative expression. In all cases, the required precision Monte Carlo measurements are made possible by a simple but powerful modification of the 'snake' algorithm.

  19. An integrated tool for loop calculations: AITALC (United States)

    Lorca, Alejandro; Riemann, Tord


    AITALC, a new tool for automating loop calculations in high energy physics, is described. The package creates Fortran code for two-fermion scattering processes automatically, starting from the generation and analysis of the Feynman graphs. We describe the modules of the tool, the intercommunication between them and illustrate its use with three examples. Program summaryTitle of the program:AITALC version 1.2.1 (9 August 2005) Catalogue identifier:ADWO Program summary URL: Program obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland Computer:PC i386 Operating system:GNU/ LINUX, tested on different distributions SuSE 8.2 to 9.3, Red Hat 7.2, Debian 3.0, Ubuntu 5.04. Also on SOLARIS Programming language used:GNU MAKE, DIANA, FORM, FORTRAN77 Additional programs/libraries used:DIANA 2.35 ( QGRAF 2.0), FORM 3.1, LOOPTOOLS 2.1 ( FF) Memory required to execute with typical data:Up to about 10 MB No. of processors used:1 No. of lines in distributed program, including test data, etc.:40 926 No. of bytes in distributed program, including test data, etc.:371 424 Distribution format:tar gzip file High-speed storage required:from 1.5 to 30 MB, depending on modules present and unfolding of examples Nature of the physical problem:Calculation of differential cross sections for ee annihilation in one-loop approximation. Method of solution:Generation and perturbative analysis of Feynman diagrams with later evaluation of matrix elements and form factors. Restriction of the complexity of the problem:The limit of application is, for the moment, the 2→2 particle reactions in the electro-weak standard model. Typical running time:Few minutes, being highly depending on the complexity of the process and the FORTRAN compiler.

  20. Fermions in hybrid loop quantum cosmology (United States)

    Elizaga Navascués, Beatriz; Mena Marugán, Guillermo A.; Martín-Benito, Mercedes


    This work pioneers the quantization of primordial fermion perturbations in hybrid loop quantum cosmology (LQC). We consider a Dirac field coupled to a spatially flat, homogeneous, and isotropic cosmology, sourced by a scalar inflaton, and treat the Dirac field as a perturbation. We describe the inhomogeneities of this field in terms of creation and annihilation variables, chosen to admit a unitary evolution if the Dirac fermion were treated as a test field. Considering instead the full system, we truncate its action at quadratic perturbative order and construct a canonical formulation. In particular this implies that, in the global Hamiltonian constraint of the model, the contribution of the homogeneous sector is corrected with a quadratic perturbative term. We then adopt the hybrid LQC approach to quantize the full model, combining the loop representation of the homogeneous geometry with the Fock quantization of the inhomogeneities. We assume a Born-Oppenheimer ansatz for physical states and show how to obtain a Schrödinger equation for the quantum evolution of the perturbations, where the role of time is played by the homogeneous inflaton. We prove that the resulting quantum evolution of the Dirac field is indeed unitary, despite the fact that the underlying homogeneous geometry has been quantized as well. Remarkably, in such evolution, the fermion field couples to an infinite sequence of quantum moments of the homogeneous geometry. Moreover, the evolved Fock vacuum of our fermion perturbations is shown to be an exact solution of the Schrödinger equation. Finally, we discuss in detail the quantum backreaction that the fermion field introduces in the global Hamiltonian constraint. For completeness, our quantum study includes since the beginning (gauge-invariant) scalar and tensor perturbations, that were studied in previous works.