Knots: attractive places with high path tortuosity in mouse open field exploration.

Directory of Open Access Journals (Sweden)

Anna Dvorkin

2010-01-01

Full Text Available When introduced into a novel environment, mammals establish in it a preferred place marked by the highest number of visits and highest cumulative time spent in it. Examination of exploratory behavior in reference to this "home base" highlights important features of its organization. It might therefore be fruitful to search for other types of marked places in mouse exploratory behavior and examine their influence on overall behavior.Examination of path curvatures of mice exploring a large empty arena revealed the presence of circumscribed locales marked by the performance of tortuous paths full of twists and turns. We term these places knots, and the behavior performed in them-knot-scribbling. There is typically no more than one knot per session; it has distinct boundaries and it is maintained both within and across sessions. Knots are mostly situated in the place of introduction into the arena, here away from walls. Knots are not characterized by the features of a home base, except for a high speed during inbound and a low speed during outbound paths. The establishment of knots is enhanced by injecting the mouse with saline and placing it in an exposed portion of the arena, suggesting that stress and the arousal associated with it consolidate a long-term contingency between a particular locale and knot-scribbling.In an environment devoid of proximal cues mice mark a locale associated with arousal by twisting and turning in it. This creates a self-generated, often centrally located landmark. The tortuosity of the path traced during the behavior implies almost concurrent multiple views of the environment. Knot-scribbling could therefore function as a way to obtain an overview of the entire environment, allowing re-calibration of the mouse's locale map and compass directions. The rich vestibular input generated by scribbling could improve the interpretation of the visual scene.

Probe Knots and Hopf Insulators with Ultracold Atoms

Science.gov (United States)

Deng, Dong-Ling; Wang, Sheng-Tao; Sun, Kai; Duan, L.-M.

2018-01-01

Knots and links are fascinating and intricate topological objects. Their influence spans from DNA and molecular chemistry to vortices in superfluid helium, defects in liquid crystals and cosmic strings in the early universe. Here we find that knotted structures also exist in a peculiar class of three-dimensional topological insulators—the Hopf insulators. In particular, we demonstrate that the momentum-space spin textures of Hopf insulators are twisted in a nontrivial way, which implies the presence of various knot and link structures. We further illustrate that the knots and nontrivial spin textures can be probed via standard time-of-flight images in cold atoms as preimage contours of spin orientations in stereographic coordinates. The extracted Hopf invariants, knots, and links are validated to be robust to typical experimental imperfections. Our work establishes the existence of knotted structures in Hopf insulators, which may have potential applications in spintronics and quantum information processing. D.L.D., S.T.W. and L.M.D. are supported by the ARL, the IARPA LogiQ program, and the AFOSR MURI program, and supported by Tsinghua University for their visits. K.S. acknowledges the support from NSF under Grant No. PHY1402971. D.L.D. is also supported by JQI-NSF-PFC and LPS-MPO-CMTC at the final stage of this paper.

Knots and links

CERN Document Server

Rolfsen, Dale

2003-01-01

Rolfsen's beautiful book on knots and links can be read by anyone, from beginner to expert, who wants to learn about knot theory. Beginners with a basic background find an inviting introduction to the elements of topology, emphasizing the tools needed for understanding knots, the fundamental group and van Kampen's theorem, for example, which are then applied to concrete problems, such as computing knot groups. For experts, Rolfsen explains advanced topics, such as the connections between knot theory and surgery and how they are useful to understanding three-manifolds. Besides providing a guide

A Midsummer Knot's Dream

Science.gov (United States)

Henrich, A.; MacNaughton, N.; Narayan, S.; Pechenik, O.; Silversmith, R.; Townsend, J.

2011-01-01

We introduce playing games on the shadows of knots and demonstrate two novel games, namely, "To Knot or Not to Knot" and "Much Ado about Knotting." We discuss winning strategies for these games on certain families of knot shadows and go on to suggest variations of these games for further study.

Phase behaviour of polyethylene knotted ring chains

International Nuclear Information System (INIS)

Wen Xiao-Hui; Xia A-Gen; Chen Hong-Ping; Zhang Lin-Xi

2011-01-01

The phase behaviour of polyethylene knotted ring chains is investigated by using molecular dynamics simulations. In this paper, we focus on the collapse of the polyethylene knotted ring chain, and also present the results of linear and ring chains for comparison. At high temperatures, a fully extensive knot structure is observed. The mean-square radius of gyration per bond (S 2 )/(Nb 2 ) and the shape factor (δ*) depend on not only the chain length but also the knot type. With temperature decreasing, chain collapse is observed, and the collapse temperature decreases with the chain length increasing. The actual collapse transition can be determined by the specific heat capacity C v , and the knotted ring chain undergoes gas—liquid—solid-like transition directly. The phase transition of a knotted ring chain is only one-stage collapse, which is different from the polyethylene linear and ring chains. This investigation can provide some insights into the statistical properties of knotted polymer chains. (condensed matter: structural, mechanical, and thermal properties)

DNA binding sites recognised in vitro by a knotted class 1 homeodomain protein encoded by the hooded gene, k, in barley (Hordeum vulgare)

DEFF Research Database (Denmark)

Krusell, L; Rasmussen, I; Gausing, K

1997-01-01

of knotted1 from maize was isolated from barley seedlings and expressed as a maltose binding protein fusion in E. coli. The purified HvH21-fusion protein selected DNA fragments with 1-3 copies of the sequence TGAC. Gel shift experiments showed that the TGAC element was required for binding and the results...

A Stevedore's protein knot.

Directory of Open Access Journals (Sweden)

Daniel Bölinger

2010-04-01

Full Text Available Protein knots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Seven distinctly knotted folds have already been identified. It is by and large unclear how these exceptional structures actually fold, and only recently, experiments and simulations have begun to shed some light on this issue. In checking the new protein structures submitted to the Protein Data Bank, we encountered the most complex and the smallest knots to date: A recently uncovered alpha-haloacid dehalogenase structure contains a knot with six crossings, a so-called Stevedore knot, in a projection onto a plane. The smallest protein knot is present in an as yet unclassified protein fragment that consists of only 92 amino acids. The topological complexity of the Stevedore knot presents a puzzle as to how it could possibly fold. To unravel this enigma, we performed folding simulations with a structure-based coarse-grained model and uncovered a possible mechanism by which the knot forms in a single loop flip.

History and science of knots

CERN Document Server

Turner, J C

1996-01-01

This book brings together twenty essays on diverse topics in the history and science of knots. It is divided into five parts, which deal respectively with knots in prehistory and antiquity, non-European traditions, working knots, the developing science of knots, and decorative and other aspects of knots.Its authors include archaeologists who write on knots found in digs of ancient sites (one describes the knots used by the recently discovered Ice Man); practical knotters who have studied the history and uses of knots at sea, for fishing and for various life support activities; a historian of l

Handbook of knot theory

CERN Document Server

Menasco, William

2005-01-01

This book is a survey of current topics in the mathematical theory of knots. For a mathematician, a knot is a closed loop in 3-dimensional space: imagine knotting an extension cord and then closing it up by inserting its plug into its outlet. Knot theory is of central importance in pure and applied mathematics, as it stands at a crossroads of topology, combinatorics, algebra, mathematical physics and biochemistry.* Survey of mathematical knot theory* Articles by leading world authorities* Clear exposition, not over-technical* Accessible to readers with undergraduate background in mathematics

Knots with proprety R+

OpenAIRE

Clark, Bradd Evans

1983-01-01

If we consider the set of manifolds that can be obtained by surgery on a fixed knot K, then we have an associated set of numbers corresponding to the Heegaard genus of these manifolds. It is known that there is an upper bound to this set of numbers. A knot K is said to have Property R+ if longitudinal surgery yields a manifold of highest possible Heegaard genus among those obtainable by surgery on K. In this paper we show that torus knots, 2-bridge knots, and knots which are the connected ...

Electrostatics of DNA-DNA juxtapositions: consequences for type II topoisomerase function

International Nuclear Information System (INIS)

Randall, Graham L; Pettitt, B Montgomery; Buck, Gregory R; Zechiedrich, E Lynn

2006-01-01

Type II topoisomerases resolve problematic DNA topologies such as knots, catenanes, and supercoils that arise as a consequence of DNA replication and recombination. Failure to remove problematic DNA topologies prohibits cell division and can result in cell death or genetic mutation. Such catastrophic consequences make topoisomerases an effective target for antibiotics and anticancer agents. Despite their biological and clinical importance, little is understood about how a topoisomerase differentiates DNA topologies in a molecule that is significantly larger than the topoisomerase itself. It has been proposed that type II topoisomerases recognize angle and curvature between two DNA helices characteristic of knotted and catenated DNA to account for the enzyme's preference to unlink instead of link DNA. Here we consider the electrostatic potential of DNA juxtapositions to determine the possibility of juxtapositions occurring through Brownian diffusion. We found that despite the large negative electrostatic potential formed between two juxtaposed DNA helices, a bulk counterion concentration as small as 50 mM provides sufficient electrostatic screening to prohibit significant interaction beyond an interhelical separation of 3 nm in both hooked and free juxtapositions. This suggests that instead of electrostatics, mechanical forces such as those occurring in anaphase, knots, catenanes, or the writhe of supercoiled DNA may be responsible for the formation of DNA juxtapositions

Knots in Art

OpenAIRE

Jablan, Slavik; Radović, Ljiljana; Sazdanović, Radmila; Zeković, Ana

2012-01-01

We analyze applications of knots and links in the Ancient art, beginning from Babylonian, Egyptian, Greek, Byzantine and Celtic art. Construction methods used in art are analyzed on the examples of Celtic art and ethnical art of Tchokwe people from Angola or Tamil art, where knots are constructed as mirror-curves. We propose different methods for generating knots and links based on geometric polyhedra, suitable for applications in architecture and sculpture.

Proteins analysed as virtual knots

Science.gov (United States)

Alexander, Keith; Taylor, Alexander J.; Dennis, Mark R.

2017-02-01

Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or disappear rapidly under manipulation and interaction. Knotting has been previously identified in protein backbone chains, for which these mechanical constraints are of fundamental importance to their molecular functionality, despite their being open curves in which the knots are not mathematically well defined; knotting can only be identified by closing the termini of the chain somehow. We introduce a new method for resolving knotting in open curves using virtual knots, which are a wider class of topological objects that do not require a classical closure and so naturally capture the topological ambiguity inherent in open curves. We describe the results of analysing proteins in the Protein Data Bank by this new scheme, recovering and extending previous knotting results, and identifying topological interest in some new cases. The statistics of virtual knots in protein chains are compared with those of open random walks and Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important.

Knots in Art

Directory of Open Access Journals (Sweden)

Radmila Sazdanović

2012-06-01

Full Text Available We analyze applications of knots and links in the Ancient art, beginning from Babylonian, Egyptian, Greek, Byzantine and Celtic art. Construction methods used in art are analyzed on the examples of Celtic art and ethnical art of Tchokwe people from Angola or Tamil art, where knots are constructed as mirror-curves. We propose different methods for generating knots and links based on geometric polyhedra, suitable for applications in architecture and sculpture.

Energy of knots and conformal geometry

CERN Document Server

O'Hara, Jun

2003-01-01

Energy of knots is a theory that was introduced to create a "canonical configuration" of a knot - a beautiful knot which represents its knot type. This book introduces several kinds of energies, and studies the problem of whether or not there is a "canonical configuration" of a knot in each knot type. It also considers this problems in the context of conformal geometry. The energies presented in the book are defined geometrically. They measure the complexity of embeddings and have applications to physical knotting and unknotting through numerical experiments. Contents: In Search of the "Optima

Braiding knots with topological strings

International Nuclear Information System (INIS)

Gu, Jie

2015-08-01

For an arbitrary knot in a three-sphere, the Ooguri-Vafa conjecture associates to it a unique stack of branes in type A topological string on the resolved conifold, and relates the colored HOMFLY invariants of the knot to the free energies on the branes. For torus knots, we use a modified version of the topological recursion developed by Eynard and Orantin to compute the free energies on the branes from the Aganagic-Vafa spectral curves of the branes, and find they are consistent with the known colored HOMFLY knot invariants a la the Ooguri-Vafa conjecture. In addition our modified topological recursion can reproduce the correct closed string free energies, which encode the information of the background geometry. We conjecture the modified topological recursion is applicable for branes associated to hyperbolic knots as well, encouraged by the observation that the modified topological recursion yields the correct planar closed string free energy from the Aganagic-Vafa spectral curves of hyperbolic knots. This has implications for the knot theory concerning distinguishing mutant knots with colored HOMFLY invariants. Furthermore, for hyperbolic knots, we present methods to compute colored HOMFLY invariants in nonsymmetric representations of U(N). The key step in this computation is computing quantum 6j-symbols in the quantum group U q (sl N ).

Biomechanical evaluation of the Nice knot

OpenAIRE

Hill, Shannon W.; Chapman, Christopher R.; Adeeb, Samer; Duke, Kajsa; Beaupre, Lauren; Bouliane, Martin J.

2016-01-01

Background: The Nice knot is a bulky double-stranded knot. Biomechanical data supporting its use as well as the number of half hitches required to ensure knot security is lacking. Materials and Methods: Nice knots with, one, two, or three half-hitches were compared with the surgeon′s and Tennessee slider knots with three half hitches. Each knot was tied 10 times around a fixed diameter using four different sutures: FiberWire (Arthrex, Naples, FL), Ultrabraid (Smith and Nephew, Andover, MA...

Knot topology in QCD

International Nuclear Information System (INIS)

Zou, L.P.; Zhang, P.M.; Pak, D.G.

2013-01-01

We consider topological structure of classical vacuum solutions in quantum chromodynamics. Topologically non-equivalent vacuum configurations are classified by non-trivial second and third homotopy groups for coset of the color group SU(N) (N=2,3) under the action of maximal Abelian stability group. Starting with explicit vacuum knot configurations we study possible exact classical solutions. Exact analytic non-static knot solution in a simple CP 1 model in Euclidean space–time has been obtained. We construct an ansatz based on knot and monopole topological vacuum structure for searching new solutions in SU(2) and SU(3) QCD. We show that singular knot-like solutions in QCD in Minkowski space–time can be naturally obtained from knot solitons in integrable CP 1 models. A family of Skyrme type low energy effective theories of QCD admitting exact analytic solutions with non-vanishing Hopf charge is proposed

Knot theory in modern chemistry.

Science.gov (United States)

Horner, Kate E; Miller, Mark A; Steed, Jonathan W; Sutcliffe, Paul M

2016-11-21

Knot theory is a branch of pure mathematics, but it is increasingly being applied in a variety of sciences. Knots appear in chemistry, not only in synthetic molecular design, but also in an array of materials and media, including some not traditionally associated with knots. Mathematics and chemistry can now be used synergistically to identify, characterise and create knots, as well as to understand and predict their physical properties. This tutorial review provides a brief introduction to the mathematics of knots and related topological concepts in the context of the chemical sciences. We then survey the broad range of applications of the theory to contemporary research in the field.

Surface-knots in 4-space an introduction

CERN Document Server

Kamada, Seiichi

2017-01-01

This introductory volume provides the basics of surface-knots and related topics, not only for researchers in these areas but also for graduate students and researchers who are not familiar with the field. Knot theory is one of the most active research fields in modern mathematics. Knots and links are closed curves (one-dimensional manifolds) in Euclidean 3-space, and they are related to braids and 3-manifolds. These notions are generalized into higher dimensions. Surface-knots or surface-links are closed surfaces (two-dimensional manifolds) in Euclidean 4-space, which are related to two-dimensional braids and 4-manifolds. Surface-knot theory treats not only closed surfaces but also surfaces with boundaries in 4-manifolds. For example, knot concordance and knot cobordism, which are also important objects in knot theory, are surfaces in the product space of the 3-sphere and the interval. Included in this book are basics of surface-knots and the related topics of classical knots, the motion picture method, surf...

Topological and metric properties of linear and circular DNA chains in nano-slits and nano-channels

Science.gov (United States)

Orlandini, Enzo; Micheletti, Cristian

2014-03-01

Motivated by recent advancements in single DNA molecule experiments, based on nanofluidic devices, we investigate numerically the metric and topological properties of a modelof open and circular DNA chains confined inside nano-slits and nano-channles. The results reveal an interesting characterization of the metric crossover behaviour in terms of the abundance, type and length of occuring knots. In particular we find that the knotting probability is nonmonotonic for increasing confinement and can be largely enhanced or suppressed, compared to the bulk case, by simply varying the slit or channel trasversal dimension. The observed knot population consists of knots that are far simpler than for DNA chains in spherical (i.e. cavities or capsids) confinement. These results suggest that nanoslits and nanochannels can be properly designed to produce open DNA chains hosting simple knots or to sieve DNA rings according to their knotted state. Finally we discuss the implications that the presence of knots may have on the dynamical properties of confined DNA chains such as chain elongation, injection/ejection processes and entanglement relaxation. We acknowledge financial support from the Italian ministry of education, grant PRIN 2010HXAW77.

Weaving Knotted Vector Fields with Tunable Helicity.

Science.gov (United States)

Kedia, Hridesh; Foster, David; Dennis, Mark R; Irvine, William T M

2016-12-30

We present a general construction of divergence-free knotted vector fields from complex scalar fields, whose closed field lines encode many kinds of knots and links, including torus knots, their cables, the figure-8 knot, and its generalizations. As finite-energy physical fields, they represent initial states for fields such as the magnetic field in a plasma, or the vorticity field in a fluid. We give a systematic procedure for calculating the vector potential, starting from complex scalar functions with knotted zero filaments, thus enabling an explicit computation of the helicity of these knotted fields. The construction can be used to generate isolated knotted flux tubes, filled by knots encoded in the lines of the vector field. Lastly, we give examples of manifestly knotted vector fields with vanishing helicity. Our results provide building blocks for analytical models and simulations alike.

Knots in polymers

Indian Academy of Sciences (India)

Abstract. Knots and topological entanglements play an important role in the statistical mechanics of polymers. While topological entanglement is a global property, it is possible to study the size of a knotted region both numerically and analytically. It can be shown that long-range repulsive interactions, as well as entropy ...

Asymptotic laws for random knot diagrams

Science.gov (United States)

Chapman, Harrison

2017-06-01

We study random knotting by considering knot and link diagrams as decorated, (rooted) topological maps on spheres and pulling them uniformly from among sets of a given number of vertices n, as first established in recent work with Cantarella and Mastin. The knot diagram model is an exciting new model which captures both the random geometry of space curve models of knotting as well as the ease of computing invariants from diagrams. We prove that unknot diagrams are asymptotically exponentially rare, an analogue of Sumners and Whittington’s landmark result for self-avoiding polygons. Our proof uses the same key idea: we first show that knot diagrams obey a pattern theorem, which describes their fractal structure. We examine how quickly this behavior occurs in practice. As a consequence, almost all diagrams are asymmetric, simplifying sampling from this model. We conclude with experimental data on knotting in this model. This model of random knotting is similar to those studied by Diao et al, and Dunfield et al.

Colouring and knot polynomials

International Nuclear Information System (INIS)

Welsh, D.J.A.

1991-01-01

These lectures will attempt to explain a connection between the recent advances in knot theory using the Jones and related knot polynomials with classical problems in combinatorics and statistical mechanics. The difficulty of some of these problems will be analysed in the context of their computational complexity. In particular we shall discuss colourings and groups valued flows in graphs, knots and the Jones and Kauffman polynomials, the Ising, Potts and percolation problems of statistical physics, computational complexity of the above problems. (author). 20 refs, 9 figs

Differential and symplectic topology of knots and curves

CERN Document Server

Tabachnikov, S

1999-01-01

This book presents a collection of papers on two related topics: topology of knots and knot-like objects (such as curves on surfaces) and topology of Legendrian knots and links in 3-dimensional contact manifolds. Featured is the work of international experts in knot theory (""quantum"" knot invariants, knot invariants of finite type), in symplectic and contact topology, and in singularity theory. The interplay of diverse methods from these fields makes this volume unique in the study of Legendrian knots and knot-like objects such as wave fronts. A particularly enticing feature of the volume is

The Mathematics of Knots

CERN Document Server

Banagl, Markus

2011-01-01

The present volume grew out of the Heidelberg Knot Theory Semester, organized by the editors in winter 2008/09 at Heidelberg University. The contributed papers bring the reader up to date on the currently most actively pursued areas of mathematical knot theory and its applications in mathematical physics and cell biology. Both original research and survey articles are presented; numerous illustrations support the text. The book will be of great interest to researchers in topology, geometry, and mathematical physics, graduate students specializing in knot theory, and cell biologists interested

Knot detection in X-ray images of wood planks using dictionary learning

DEFF Research Database (Denmark)

Hansson, Nils Mattias; Enescu, Alexandru; Brandt, Sami Sebastian

2015-01-01

This paper considers a novel application of x-ray imaging of planks, for the purpose of detecting knots in high quality furniture wood. X-ray imaging allows the detection of knots invisible from the surface to conventional cameras. Our approach is based on texture analysis, or more specifically, ......, discriminative dictionary learning. Experiments show that the knot detection and segmentation can be accurately performed by our approach. This is a promising result and can be directly applied in industrial processing of furniture wood.......This paper considers a novel application of x-ray imaging of planks, for the purpose of detecting knots in high quality furniture wood. X-ray imaging allows the detection of knots invisible from the surface to conventional cameras. Our approach is based on texture analysis, or more specifically...

Optical knots and contact geometry II. From Ranada dyons to transverse and cosmetic knots

Energy Technology Data Exchange (ETDEWEB)

Kholodenko, Arkady L., E-mail: string@clemson.edu

2016-08-15

Some time ago Ranada (1989) obtained new nontrivial solutions of the Maxwellian gauge fields without sources. These were reinterpreted in Kholodenko (2015) [10] (part I) as particle-like (monopoles, dyons, etc.). They were obtained by the method of Abelian reduction of the non-Abelian Yang–Mills functional. The developed method uses instanton-type calculations normally employed for the non-Abelian gauge fields. By invoking the electric–magnetic duality it then becomes possible to replace all known charges/masses by the particle-like solutions of the source-free Abelian gauge fields. To employ these results in high energy physics, it is essential to extend Ranada’s results by carefully analyzing and classifying all dynamically generated knotted/linked structures in gauge fields, including those discovered by Ranada. This task is completed in this work. The study is facilitated by the recent progress made in solving the Moffatt conjecture. Its essence is stated as follows: in steady incompressible Euler-type fluids the streamlines could have knots/links of all types. By employing the correspondence between the ideal hydrodynamics and electrodynamics discussed in part I and by superimposing it with the already mentioned method of Abelian reduction, it is demonstrated that in the absence of boundaries only the iterated torus knots and links could be dynamically generated. Obtained results allow to develop further particle-knot/link correspondence studied in Kholodenko (2015) [13].

Open knot-tying skills: residents skills assessed

NARCIS (Netherlands)

van Empel, P.J.; Verdam, M.G.E.; Huirne, J.A.; Bonjer, H.J.; Meijerink, W.J.; Scheele, F.

2013-01-01

Aim: Open knot-tying and suturing skills are fundamental surgical skills, founding many alternative knot-tying techniques. It is therefore mandatory for residents to possess adequate basic open knot-tying skills. The aim of this study was to compare an objective assessment of open knot-tying skills

Integral Suture-Handling Techniques for Arthroscopic Sliding Knots

OpenAIRE

Kanchanatawan, Wichan; Kongtharvonskul, Jatupon; Dorjiee, Gem; Suppauksorn, Sunikom; Pornvoranunt, Umpire; Karchana, Pongsakorn

2016-01-01

In arthroscopic tissue repair, the final step is achieving adequate tissue approximation with a secure knot. The sliding knot is widely preferred over the nonsliding knot, with numerous publications describing knot configurations. However, in the literature there are few published descriptions of suture-handling techniques, even though they are fundamental to arthroscopic knot tying. We describe integral suture-handling techniques for arthroscopic sliding knots to improve the surgeon's perfor...

Intricate knots in proteins: Function and evolution.

Directory of Open Access Journals (Sweden)

Peter Virnau

2006-09-01

Full Text Available Our investigation of knotted structures in the Protein Data Bank reveals the most complicated knot discovered to date. We suggest that the occurrence of this knot in a human ubiquitin hydrolase might be related to the role of the enzyme in protein degradation. While knots are usually preserved among homologues, we also identify an exception in a transcarbamylase. This allows us to exemplify the function of knots in proteins and to suggest how they may have been created.

Virtual knotting in proteins and other open curves

Science.gov (United States)

Alexander, Keith; Taylor, Alexander; Dennis, Mark

Long filaments naturally knot, from string to long-chain molecules. Knotting in a filament affects its properties, and may be very stable or disappear under slight manipulation. Knotting has been identified in protein backbones for which these mechanical constraints are of fundamental importance to their function, although they are open curves in which knots are not mathematically well defined; knotting can only be identified by closing the ends of the chain. We introduce a new method for resolving knotting in open curves using virtual knots, a wider class of topological objects that do not use a classical closure, capturing the topological ambiguity of open curves. Having analysed all proteins in the Protein Data Bank by this new scheme, we recover and extend previous knotting results, and identify topological interest in some new cases. The statistics of virtual knots in proteins are compared with those of Hamiltonian subchains on cubic lattices, identifying a regime of open curves in which the virtual knotting description is likely to be important. This work was supported by the Leverhulme Trust Programme Grant ``Scientific Properties of Complex Knots'' and the EPSRC.

The entropic cost to tie a knot

International Nuclear Information System (INIS)

Baiesi, M; Orlandini, E; Stella, A L

2010-01-01

We estimate by Monte Carlo simulations the configurational entropy of N-step polygons in the cubic lattice with fixed knot type. By collecting rich statistics of configurations with very large values of N we are able to analyse the asymptotic behaviour of the partition function of the problem for different knot types. Our results confirm that, in the large N limit, each prime knot is localized in a small region of the polygon, regardless of the possible presence of other knots. Each prime knot component may slide along the unknotted region contributing to the overall configurational entropy with a term proportional to lnN. Furthermore, we discover that the mere existence of a knot requires a well defined entropic cost that scales exponentially with its minimal length. In the case of polygons with composite knots it turns out that the partition function can be simply factorized in terms that depend only on prime components, with an additional combinatorial factor that takes into account the statistical property that by interchanging two identical prime knot components in the polygon the corresponding set of overall configurations remains unaltered. Finally, the above results allow one to conjecture a sequence of inequalities for the connective constants of polygons whose topology varies within a given family of composite knot types

A DECADE-BASELINE STUDY OF THE PLASMA STATES OF EJECTA KNOTS IN CASSIOPEIA A

Energy Technology Data Exchange (ETDEWEB)

Rutherford, John; Dewey, Daniel; Figueroa-Feliciano, Enectali; Heine, Sarah N. T.; Canizares, C. R.; Bastien, Fabienne A.; Sato, Kosuke, E-mail: enectali@mit.edu, E-mail: jmrv@mit.edu [Department of Physics and Kavli Institute for Astrophysics and Space Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)

2013-05-20

We present the analysis of 21 bright X-ray knots in the Cassiopeia A supernova remnant from observations spanning 10 yr. We performed a comprehensive set of measurements to reveal the kinematic and thermal state of the plasma in each knot, using a combined analysis of two high energy resolution High Energy Transmission Grating (HETG) and four medium energy resolution Advanced CCD Imaging Spectrometer (ACIS) sets of spectra. The ACIS electron temperature estimates agree with the HETG-derived values for approximately half of the knots studied, yielding one of the first comparisons between high resolution temperature estimates and ACIS-derived temperatures. We did not observe the expected spectral evolution-predicted from the ionization age and density estimates for each knot-in all but three of the knots studied. The incompatibility of these measurements with our assumptions has led us to propose a dissociated ejecta model, with the metals unmixed inside the knots, which could place strong constraints on supernova mixing models.

The mathematics and physics of knots

Energy Technology Data Exchange (ETDEWEB)

Kauffman, Louis H [Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607-7045 (United States)

2005-12-01

This paper is an introduction to relationships between knot theory and theoretical physics. We give an exposition of the theory of polynomial invariants of knots and links, the Witten functional integral formulation of knot and link invariants, and the beginnings of topological quantum field theory, and show how the theory of knots is related to a number of key issues in mathematical physics, including loop quantum gravity and quantum information theory. Along with the references cited in the text below, we also recommend the following as sources of background information.

Legendrian and transverse cables of positive torus knots

DEFF Research Database (Denmark)

Etnyre, John; LaFountain, Douglas; Tosun, Bülent

2012-01-01

Thurston-Bennequin invariant is arbitrarily far from maximal. We also exhibit Legendrian knots requiring arbitrarily many stabilizations before they become Legendrian isotopic. Similar new phenomena are observed for transverse knots. To achieve these results we define and study "partially thickenable" tori......In this paper we classify Legendrian and transverse knots in the knot types obtained from positive torus knots by cabling. This classification allows us to demonstrate several new phenomena. Specifically, we show there are knot types that have non-destabilizable Legendrian representatives whose...

Legendrian and transverse cables of positive torus knots

DEFF Research Database (Denmark)

B. Etnyre, John; la Fountain, Douglas James; Tosun, Bulent

In this paper we classify Legendrian and transverse knots in the knot types obtained from positive torus knots by cabling. This classification allows us to demonstrate several new phenomena. Specifically, we show there are knot types that have non-destabilizable Legendrian representatives whose T...

In Search of Functional Advantages of Knots in Proteins.

Science.gov (United States)

Dabrowski-Tumanski, Pawel; Stasiak, Andrzej; Sulkowska, Joanna I

2016-01-01

We analysed the structure of deeply knotted proteins representing three unrelated families of knotted proteins. We looked at the correlation between positions of knotted cores in these proteins and such local structural characteristics as the number of intra-chain contacts, structural stability and solvent accessibility. We observed that the knotted cores and especially their borders showed strong enrichment in the number of contacts. These regions showed also increased thermal stability, whereas their solvent accessibility was decreased. Interestingly, the active sites within these knotted proteins preferentially located in the regions with increased number of contacts that also have increased thermal stability and decreased solvent accessibility. Our results suggest that knotting of polypeptide chains provides a favourable environment for the active sites observed in knotted proteins. Some knotted proteins have homologues without a knot. Interestingly, these unknotted homologues form local entanglements that retain structural characteristics of the knotted cores.

Topological effects on the mechanical properties of polymer knots

Science.gov (United States)

Zhao, Yani; Ferrari, Franco

2017-11-01

The mechanical properties of knotted polymer rings under stretching in a bad or good solvent are investigated by applying a force F to a point of the knot while keeping another point fixed. The Monte Carlo sampling of the polymer conformations is performed on a simple cubic lattice using the Wang-Landau algorithm. The specific energy, specific heat capacity, gyration radius and the force-elongation curves are computed for several knot topologies with lengths up to 120 lattice units. The common features of the mechanical and thermal behavior of stretched short polymer rings forming knots of a given topological type are analyzed as well as the differences arising due to topology and size effects. It is found that these systems admit three different phases depending on the values of the tensile force F and the temperature T. The transitions from one phase to the other are well characterized by the peaks of the specific heat capacity and by the data of the gyration radius and specific energy. At very low temperatures the force-elongation curves show that the stretching of a knot is a stepwise process, which becomes smooth at higher temperatures. Criteria for distinguishing topological and size effects are provided. It turns out from our study that the behavior of short polymer rings is strongly influenced by topological effects. In particular, the swelling and the swelling rate of knots are severely limited by the topological constraints. Several other properties that are affected by topology, like the decay of the specific energy at high tensile forces, are discussed. The fading out of the influences of topological origin with increasing knot lengths has been verified. Some anomalies detected in the plots of the specific heat capacity of very short and complex knots have been explained by the limitations in the number of accessible energy states due to the topological constraints.

Torus knots and mirror symmetry

CERN Document Server

Brini, Andrea; Marino, Marcos

2012-01-01

We propose a spectral curve describing torus knots and links in the B-model. In particular, the application of the topological recursion to this curve generates all their colored HOMFLY invariants. The curve is obtained by exploiting the full Sl(2, Z) symmetry of the spectral curve of the resolved conifold, and should be regarded as the mirror of the topological D-brane associated to torus knots in the large N Gopakumar-Vafa duality. Moreover, we derive the curve as the large N limit of the matrix model computing torus knot invariants.

Knot invariants derived from quandles and racks

OpenAIRE

Kamada, Seiichi

2002-01-01

The homology and cohomology of quandles and racks are used in knot theory: given a finite quandle and a cocycle, we can construct a knot invariant. This is a quick introductory survey to the invariants of knots derived from quandles and racks.

Examining the High-energy Radiation Mechanisms of Knots and Hotspots in Active Galactic Nucleus Jets

Science.gov (United States)

Zhang, Jin; Du, Shen-shi; Guo, Sheng-Chu; Zhang, Hai-Ming; Chen, Liang; Liang, En-Wei; Zhang, Shuang-Nan

2018-05-01

We compile the radio–optical–X-ray spectral energy distributions (SEDs) of 65 knots and 29 hotspots in 41 active galactic nucleus jets to examine their high-energy radiation mechanisms. Their SEDs can be fitted with the single-zone leptonic models, except for the hotspot of Pictor A and six knots of 3C 273. The X-ray emission of 1 hotspot and 22 knots is well explained as synchrotron radiation under the equipartition condition; they usually have lower X-ray and radio luminosities than the others, which may be due to a lower beaming factor. An inverse Compton (IC) process is involved for explaining the X-ray emission of the other SEDs. Without considering the equipartition condition, their X-ray emission can be attributed to the synchrotron-self-Compton process, but the derived jet powers (P jet) are not correlated with L k and most of them are larger than L k, with more than three orders of magnitude, where L k is the jet kinetic power estimated with their radio emission. Under the equipartition condition, the X-ray emission is well interpreted with the IC process for the cosmic microwave background photons (IC/CMB). In this scenario, the derived P jet of knots and hotspots are correlated with and comparable to L k. These results suggest that the IC/CMB model may be a promising interpretation of the X-ray emission. In addition, a tentative knot–hotspot sequence in the synchrotron peak-energy–peak-luminosity plane is observed, similar to the blazar sequence, which may be attributed to the different cooling mechanisms of electrons.

The mystery of knots

CERN Document Server

Aneziris, Charilaos N

1999-01-01

One of the most significant unsolved problems in mathematics is the complete classification of knots. The main purpose of this book is to introduce the reader to the use of computer programming to obtain the table of knots. The author presents this problem as clearly and methodically as possible, starting from the very basics. Mathematical ideas and concepts are extensively discussed, and no advanced background is required.

The dynamic interplay between DNA topoisomerases and DNA topology.

Science.gov (United States)

Seol, Yeonee; Neuman, Keir C

2016-11-01

Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.

Root-knot nematodes in golf course greens of the western United States

Science.gov (United States)

A survey of 238 golf courses in ten of the Western U.S. found root-knot nematodes (Meloidogyne spp.) in 60 % of the putting greens sampled. Sequence and phylogenetic analyses of 18S rRNA, D2-D3 of 28S rRNA, ITS-rRNA and mtDNA gene sequences were used to identify specimens from 110 golf courses. The...

Recognition algorithms in knot theory

International Nuclear Information System (INIS)

Dynnikov, I A

2003-01-01

In this paper the problem of constructing algorithms for comparing knots and links is discussed. A survey of existing approaches and basic results in this area is given. In particular, diverse combinatorial methods for representing links are discussed, the Haken algorithm for recognizing a trivial knot (the unknot) and a scheme for constructing a general algorithm (using Haken's ideas) for comparing links are presented, an approach based on representing links by closed braids is described, the known algorithms for solving the word problem and the conjugacy problem for braid groups are described, and the complexity of the algorithms under consideration is discussed. A new method of combinatorial description of knots is given together with a new algorithm (based on this description) for recognizing the unknot by using a procedure for monotone simplification. In the conclusion of the paper several problems are formulated whose solution could help to advance towards the 'algorithmization' of knot theory

Four-manifolds, geometries and knots

CERN Document Server

Hillman, Jonathan A

2007-01-01

The goal of this book is to characterize algebraically the closed 4-manifolds that fibre nontrivially or admit geometries in the sense of Thurston, or which are obtained by surgery on 2-knots, and to provide a reference for the topology of such manifolds and knots. The first chapter is purely algebraic. The rest of the book may be divided into three parts: general results on homotopy and surgery (Chapters 2-6), geometries and geometric decompositions (Chapters 7-13), and 2-knots (Chapters 14-18). In many cases the Euler characteristic, fundamental group and Stiefel-Whitney classes together form a complete system of invariants for the homotopy type of such manifolds, and the possible values of the invariants can be described explicitly. The strongest results are characterizations of manifolds which fibre homotopically over S^1 or an aspherical surface (up to homotopy equivalence) and infrasolvmanifolds (up to homeomorphism). As a consequence 2-knots whose groups are poly-Z are determined up to Gluck reconstruc...

Knotting probabilities after a local strand passage in unknotted self-avoiding polygons

International Nuclear Information System (INIS)

Szafron, M L; Soteros, C E

2011-01-01

We investigate, both theoretically and numerically, the knotting probabilities after a local strand passage is performed in an unknotted self-avoiding polygon (SAP) on the simple cubic lattice. In the polygons studied, it is assumed that two polygon segments have already been brought close together for the purpose of performing a strand passage. This restricts the polygons considered to those that contain a specific pattern called Θ at a fixed location; an unknotted polygon containing Θ is called a Θ-SAP. It is proved that the number of n-edge Θ-SAPs grows exponentially (with n) at the same rate as the total number of n-edge unknotted SAPs (those with no prespecified strand passage structure). Furthermore, it is proved that the same holds for subsets of n-edge Θ-SAPs that yield a specific after-strand-passage knot-type. Thus, the probability of a given after-strand-passage knot-type does not grow (or decay) exponentially with n. Instead, it is conjectured that these after-strand-passage knot probabilities approach, as n goes to infinity, knot-type dependent amplitude ratios lying strictly between 0 and 1. This conjecture is supported by numerical evidence from Monte Carlo data generated using a composite (aka multiple) Markov chain Monte Carlo BFACF algorithm developed to study Θ-SAPs. A new maximum likelihood method is used to estimate the critical exponents relevant to this conjecture. We also obtain strong numerical evidence that the after-strand-passage knotting probability depends on the local structure around the strand-passage site. If the local structure and the crossing sign at the strand-passage site are considered, then we observe that the more 'compact' the local structure, the less likely the after-strand-passage polygon is to be knotted. This trend for compactness versus knotting probability is consistent with results obtained for other strand-passage models; however, we are the first to note the influence of the crossing-sign information. We

Freely Expanding Knots of X-Ray-emitting Ejecta in Kepler’s Supernova Remnant

Science.gov (United States)

Sato, Toshiki; Hughes, John P.

2017-08-01

We report measurements of proper motion, radial velocity, and elemental composition for 14 compact X-ray-bright knots in Kepler’s supernova remnant (SNR) using archival Chandra data. The knots with the highest speed show both large proper motions (μ ˜ 0.″11-0.″14 yr-1) and high radial velocities (v ˜ 8700-10,020 km s-1). For these knots the estimated space velocities (9100 km s-1 ≲ v 3D ≲ 10,400 km s-1) are similar to the typical Si velocity seen in supernovae (SNe) Ia near maximum light. High-speed ejecta knots appear only in specific locations and are morphologically and kinematically distinct from the rest of the ejecta. The proper motions of five knots extrapolate back over the age of Kepler’s SNR to a consistent central position. This new kinematic center agrees well with previous determinations, but is less subject to systematic errors and denotes a location about which several prominent structures in the remnant display a high degree of symmetry. These five knots are expanding at close to the free expansion rate (expansion indices of 0.75 ≲ m ≲ 1.0), which we argue indicates either that they were formed in the explosion with a high density contrast (more than 100 times the ambient density) or that they have propagated through regions of relatively low density (n H ruled out.

On two-generator satellite knots

OpenAIRE

Bleiler, Steven A.; Jones, Amelia C.

1997-01-01

Techniques are introduced which determine the geometric structure of non-simple two-generator $3$-manifolds from purely algebraic data. As an application, the satellite knots in the $3$-sphere with a two-generator presentation in which at least one generator is represented by a meridian for the knot are classified.

Modeling the Effects of Knots in Structural Timber

DEFF Research Database (Denmark)

Foley, Christina

The main purpose of the pursued research presented in this thesis is to increase knowledge of the effects of knots in structural timber so that characteristics of weaker timber may be determined and applied to improve current grading techniques. In the process, a three-dimensional fiber paradigm...... are given to Shigo's knot formation theory, and thus predicts two separate patterns of fiber direction within annual growth layers related to live knots. In order to determine the possibility to practically and non destructively predict local material directions in structural timber with the three...... was established, which describes variations of radial growth direction and fiber orientation related to knots in timber. The adaptability of the paradigm allows practically any softwood knot and its effect on surrounding wood material to be modeled with an accuracy that is limited only by input data. The knot...

Studying uniform thickness II: Transversely nonsimple iterated torus knots

DEFF Research Database (Denmark)

LaFountain, Douglas

2011-01-01

We prove that an iterated torus knot type in the standard contact 3-sphere fails the uniform thickness property (UTP) if and only if it is formed from repeated positive cablings, which is precisely when an iterated torus knot supports the standard contact structure. This is the first complete UTP...... classification for a large class of knots. We also show that all iterated torus knots that fail the UTP support cabling knot types that are transversely non-simple....

Freely Expanding Knots of X-Ray-emitting Ejecta in Kepler’s Supernova Remnant

Energy Technology Data Exchange (ETDEWEB)

Sato, Toshiki [Department of Physics, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397 (Japan); Hughes, John P., E-mail: toshiki@astro.isas.jaxa.jp, E-mail: jph@physics.rutgers.edu [Department of Physics and Astronomy, Rutgers University, 136 Frelinghuysen Road, Piscataway, NJ 08854-8019 (United States)

2017-08-20

We report measurements of proper motion, radial velocity, and elemental composition for 14 compact X-ray-bright knots in Kepler’s supernova remnant (SNR) using archival Chandra data. The knots with the highest speed show both large proper motions ( μ ∼ 0.″11–0.″14 yr{sup −1}) and high radial velocities ( v ∼ 8700–10,020 km s{sup −1}). For these knots the estimated space velocities (9100 km s{sup −1} ≲ v {sub 3D} ≲ 10,400 km s{sup −1}) are similar to the typical Si velocity seen in supernovae (SNe) Ia near maximum light. High-speed ejecta knots appear only in specific locations and are morphologically and kinematically distinct from the rest of the ejecta. The proper motions of five knots extrapolate back over the age of Kepler’s SNR to a consistent central position. This new kinematic center agrees well with previous determinations, but is less subject to systematic errors and denotes a location about which several prominent structures in the remnant display a high degree of symmetry. These five knots are expanding at close to the free expansion rate (expansion indices of 0.75 ≲ m ≲ 1.0), which we argue indicates either that they were formed in the explosion with a high density contrast (more than 100 times the ambient density) or that they have propagated through regions of relatively low density ( n {sub H} < 0.1 cm{sup −3}) in the ambient medium. X-ray spectral analysis shows that the undecelerated knots have high Si and S abundances, a lower Fe abundance, and very low O abundance, pointing to an origin in the partial Si-burning zone, which occurs in the outer layer of the exploding white dwarf for models of SNe Ia. Other knots show lower speeds and expansion indices consistent with decelerated ejecta knots or features in the ambient medium overrun by the forward shock. Our new accurate location for the explosion site has well-defined positional uncertainties, allowing for a great reduction in the area to be searched for faint

On the universality of knot probability ratios

Energy Technology Data Exchange (ETDEWEB)

Janse van Rensburg, E J [Department of Mathematics and Statistics, York University, Toronto, Ontario M3J 1P3 (Canada); Rechnitzer, A, E-mail: rensburg@yorku.ca, E-mail: andrewr@math.ubc.ca [Department of Mathematics, University of British Columbia, 1984 Mathematics Road, Vancouver, BC V6T 1Z2 (Canada)

2011-04-22

Let p{sub n} denote the number of self-avoiding polygons of length n on a regular three-dimensional lattice, and let p{sub n}(K) be the number which have knot type K. The probability that a random polygon of length n has knot type K is p{sub n}(K)/p{sub n} and is known to decay exponentially with length (Sumners and Whittington 1988 J. Phys. A: Math. Gen. 21 1689-94, Pippenger 1989 Discrete Appl. Math. 25 273-8). Little is known rigorously about the asymptotics of p{sub n}(K), but there is substantial numerical evidence. It is believed that the entropic exponent, {alpha}, is universal, while the exponential growth rate is independent of the knot type but varies with the lattice. The amplitude, C{sub K}, depends on both the lattice and the knot type. The above asymptotic form implies that the relative probability of a random polygon of length n having prime knot type K over prime knot type L. In the thermodynamic limit this probability ratio becomes an amplitude ratio; it should be universal and depend only on the knot types K and L. In this communication we examine the universality of these probability ratios for polygons in the simple cubic, face-centred cubic and body-centred cubic lattices. Our results support the hypothesis that these are universal quantities. For example, we estimate that a long random polygon is approximately 28 times more likely to be a trefoil than be a figure-eight, independent of the underlying lattice, giving an estimate of the intrinsic entropy associated with knot types in closed curves. (fast track communication)

Mutual attraction of magnetic knots

International Nuclear Information System (INIS)

Parker, E.N.

1978-01-01

It is observed that the magnetic knots associated with active regions on the Sun have an attraction for each other during the formative period of the active regions, when new magnetic flux is coming to the surface. The attraction disappears when new flux ceases to rise through the surface. Then the magnetic spots and knots tend to come apart, leading to disintegration of the sunspots previously formed. The dissolution of the fields is to be expected, as a consequence of the magnetic repulsion of knots of like polarity and as a consequence of the hydromagnetic exchange instability.The purpose of this paper is to show that the mutual attraction of knots during the formative stages of a sunspot region may be understood as the mutual hydrodynamic attraction of the rising flux tubes. Two rising tubes attract each other, as a consequence of the wake of the leading tube when one is moving behind the other, and as a consequence of the Bernoulli effect when rising side by side

On the concordance genus of topologically slice knots

OpenAIRE

Hom, Jennifer

2012-01-01

The concordance genus of a knot K is the minimum Seifert genus of all knots smoothly concordant to K. Concordance genus is bounded below by the 4-ball genus and above by the Seifert genus. We give a lower bound for the concordance genus of K coming from the knot Floer complex of K. As an application, we prove that there are topologically slice knots with 4-ball genus equal to one and arbitrarily large concordance genus.

Knotting in stretched polygons

International Nuclear Information System (INIS)

Rensburg, E J Janse van; Orlandini, E; Tesi, M C; Whittington, S G

2008-01-01

The knotting in a lattice polygon model of ring polymers is examined when a stretching force is applied to the polygon. By examining the incidence of cut-planes in the polygon, we prove a pattern theorem in the stretching regime for large applied forces. This theorem can be used to examine the incidence of entanglements such as knotting and writhing. In particular, we prove that for arbitrarily large positive, but finite, values of the stretching force, the probability that a stretched polygon is knotted approaches 1 as the length of the polygon increases. In the case of writhing, we prove that for stretched polygons of length n, and for every function f(n)=o(√n), the probability that the absolute value of the mean writhe is less than f(n) approaches 0 as n → ∞, for sufficiently large values of the applied stretching force

Grid homology for knots and links

CERN Document Server

Ozsváth, Peter S; Szabó, Zoltán

2015-01-01

Knot theory is a classical area of low-dimensional topology, directly connected with the theory of three-manifolds and smooth four-manifold topology. In recent years, the subject has undergone transformative changes thanks to its connections with a number of other mathematical disciplines, including gauge theory; representation theory and categorification; contact geometry; and the theory of pseudo-holomorphic curves. Starting from the combinatorial point of view on knots using their grid diagrams, this book serves as an introduction to knot theory, specifically as it relates to some of the ab

Bounds for the minimum step number of knots confined to slabs in the simple cubic lattice

International Nuclear Information System (INIS)

Ishihara, K; Shimokawa, K; Scharein, R; Arsuaga, J; Vazquez, M; Diao, Y

2012-01-01

Volume confinement is a key determinant of the topology and geometry of a polymer. However, the direct relationship between the two is not fully understood. For instance, recent experimental studies have constructed P4 cosmids, i.e. P4 bacteriophages whose genome sequence and length have been artificially engineered and have shown that upon extraction their DNA knot distribution differs from that of wild-type bacteriophage P4. In particular, it was observed that the complexity of the knots decreases sharply with the length of the packed genome. This problem is the motivation of this paper. Here, a polymer is modeled as a self-avoiding polygon on the simple cubic lattice and the confining condition is such that the polygon is bounded between two parallel planes (i.e. bounded within a slab). We estimate the minimum length required for such a polygon to realize a knot type. Our numerical simulations show that in order to realize a prime knot (with up to ten crossings) in a 1-slab (i.e. a slab of height 1), one needs a polygon of length strictly longer than the minimum length needed to realize the same knot when there is no confining condition. In the case of the trefoil knot, we can in fact establish this result analytically by proving that the minimum length required to tie a trefoil in the 1-slab is 26, which is greater than 24, the known minimum length required to tie a trefoil without a confinement condition. Additionally, we find that in the 1-slab not all geometrical realizations of a given knot type are equivalent under BFACF moves. This suggests that in certain confined volumes, knowing the topology of a polymer is not enough to describe all its states. (paper)

Induction effects of torus knots and unknots

Science.gov (United States)

Oberti, Chiara; Ricca, Renzo L.

2017-09-01

Geometric and topological aspects associated with induction effects of field lines in the shape of torus knots/unknots are examined and discussed in detail. Knots are assumed to lie on a mathematical torus of circular cross-section and are parametrized by standard equations. The induced field is computed by direct integration of the Biot-Savart law. Field line patterns of the induced field are obtained and several properties are examined for a large family of knots/unknots up to 51 crossings. The intensity of the induced field at the origin of the reference system (center of the torus) is found to depend linearly on the number of toroidal coils and reaches maximum values near the boundary of the mathematical torus. New analytical estimates and bounds on energy and helicity are established in terms of winding number and minimum crossing number. These results find useful applications in several contexts when the source field is either vorticity, electric current or magnetic field, from vortex dynamics to astrophysics and plasma physics, where highly braided magnetic fields and currents are present.

Knack knots you need step-by-step instructions for more than 100 of the best sailing, fishing, climbing, camping and decorative knots

CERN Document Server

Tilton, Buck

2008-01-01

Untie the mystery of knot-making with this clever and handy guide. This new compendium presents all the knots you need to know, with brightly colored photographs enabling you to easily follow the instructions. In addition, the book includes copious information on using knots in most popular activities. With its clear step-by-step instructions and friendly tone, this is the one volume you can count on to guide you toward quick success in knot-making.

In Search of Functional Advantages of Knots in Proteins.

OpenAIRE

Dabrowski-Tumanski, P.; Stasiak, A.; Sulkowska, J.I.

2016-01-01

We analysed the structure of deeply knotted proteins representing three unrelated families of knotted proteins. We looked at the correlation between positions of knotted cores in these proteins and such local structural characteristics as the number of intra-chain contacts, structural stability and solvent accessibility. We observed that the knotted cores and especially their borders showed strong enrichment in the number of contacts. These regions showed also increased thermal stability, whe...

Factorization of differential expansion for antiparallel double-braid knots

Science.gov (United States)

Morozov, A.

2016-09-01

Continuing the quest for exclusive Racah matrices, which are needed for evaluation of colored arborescent-knot polynomials in Chern-Simons theory, we suggest to extract them from a new kind of a double-evolution — that of the antiparallel double-braids, which is a simple two-parametric family of two-bridge knots, generalizing the one-parametric family of twist knots. In the case of rectangular representations R = [ r s ] we found an evidence that the corresponding differential expansion miraculously factorizes and can be obtained from that for the twist knots. This reduces the problem of rectangular exclusive Racah to constructing the answers for just a few twist knots. We develop a recent conjecture on the structure of differential expansion for the simplest members of this family (the trefoil and the figure-eight knot) and provide the exhaustive answer for the first unknown case of R = [33]. The answer includes HOMFLY of arbitrary twist and double-braid knots and Racah matrices overline{S} and S — what allows to calculate [33]-colored polynomials for arbitrary arborescent (double-fat) knots. For generic rectangular representations fully described are only the contributions of the single-floor pyramids. One step still remains to be done.

Effects of knot type in the folding of topologically complex lattice proteins

Science.gov (United States)

Soler, Miguel A.; Nunes, Ana; Faísca, Patrícia F. N.

2014-07-01

The folding properties of a protein whose native structure contains a 52 knot are investigated by means of extensive Monte Carlo simulations of a simple lattice model and compared with those of a 31 knot. A 52 knot embedded in the native structure enhances the kinetic stability of the carrier lattice protein in a way that is clearly more pronounced than in the case of the 31 knot. However, this happens at the expense of a severe loss in folding efficiency, an observation that is consistent with the relative abundance of 31 and 52 knots in the Protein Data Bank. The folding mechanism of the 52 knot shares with that of the 31 knot the occurrence of a threading movement of the chain terminus that lays closer to the knotted core. However, co-concomitant knotting and folding in the 52 knot occurs with negligible probability, in sharp contrast to what is observed for the 31 knot. The study of several single point mutations highlights the importance in the folding of knotted proteins of the so-called structural mutations (i.e., energetic perturbations of native interactions between residues that are critical for knotting but not for folding). On the other hand, the present study predicts that mutations that perturb the folding transition state may significantly enhance the kinetic stability of knotted proteins provided they involve residues located within the knotted core.

Appendicular knot causing closed-loop obstruction, volvulus and ...

African Journals Online (AJOL)

Keywords: appendix, appendicular tie/knot syndrome, intestinal obstruction, volvulus, strangulation .... possible contrast reaction and high cost) and its unavailability in some ... morbidity and mortality rise significantly with delay. In. Fevang's ...

Analysis of the tractive force pattern on a knot by force measurement during laparoscopic knot tying.

Science.gov (United States)

Takayasu, Kenta; Yoshida, Kenji; Kinoshita, Hidefumi; Yoshimoto, Syunsuke; Oshiro, Osamu; Matsuda, Tadashi

2017-07-19

Quantifying surgical skills assists novice surgeons when learning operative techniques. We measured the interaction force at a ligation point and clarified the features of the force pattern among surgeons with different skill levels during laparoscopic knot tying. Forty-four surgeons were divided into three groups based on experience: 13 novice (0-5 years), 16 intermediate (6-15 years), and 15 expert (16-30 years). To assess the tractive force direction and volume during knot tying, we used a sensor that measures six force-torque values (x-axis: Fx, y-axis: Fy, z-axis: Fz, and xy-axis: Fxy) attached to a slit Penrose drain. All participants completed one double knot and five single knot sequences. We recorded completion time, force volume (FV), maximum force (MF), time over 1.5 N, duration of non-zero force, and percentage time when vertical force exceeded horizontal force (PTz). There was a significant difference between groups for completion time (p = 0.007); FV (total: p = 0.002; Fx: p = 0.004, Fy: p = 0.007, Fxy: p = 0.004, Fz: p force (p = 0.029); and PTz (p force pattern at the ligation point during suturing by surgeons with three levels of experience using a force measurement system. We revealed that both force volume and force direction differed depending on surgeons' skill level during knot tying. Copyright © 2017. Published by Elsevier Inc.

The mean squared writhe of alternating random knot diagrams

Energy Technology Data Exchange (ETDEWEB)

Diao, Y; Hinson, K [Department of Mathematics and Statistics University of North Carolina at Charlotte, NC 28223 (United States); Ernst, C; Ziegler, U, E-mail: ydiao@uncc.ed [Department of Mathematics and Computer Science, Western Kentucky University, Bowling Green, KY 42101 (United States)

2010-12-10

The writhe of a knot diagram is a simple geometric measure of the complexity of the knot diagram. It plays an important role not only in knot theory itself, but also in various applications of knot theory to fields such as molecular biology and polymer physics. The mean squared writhe of any sample of knot diagrams with n crossings is n when for each diagram at each crossing one of the two strands is chosen as the overpass at random with probability one-half. However, such a diagram is usually not minimal. If we restrict ourselves to a minimal knot diagram, then the choice of which strand is the over- or under-strand at each crossing is no longer independent of the neighboring crossings and a larger mean squared writhe is expected for minimal diagrams. This paper explores the effect on the correlation between the mean squared writhe and the diagrams imposed by the condition that diagrams are minimal by studying the writhe of classes of reduced, alternating knot diagrams. We demonstrate that the behavior of the mean squared writhe heavily depends on the underlying space of diagram templates. In particular this is true when the sample space contains only diagrams of a special structure. When the sample space is large enough to contain not only diagrams of a special type, then the mean squared writhe for n crossing diagrams tends to grow linearly with n, but at a faster rate than n, indicating an intrinsic property of alternating knot diagrams. Studying the mean squared writhe of alternating random knot diagrams also provides some insight into the properties of the diagram generating methods used, which is an important area of study in the applications of random knot theory.

Knotcraft the practical and entertaining art of tying knots

CERN Document Server

Macfarlan, Allan and Paulette

1983-01-01

Comprehensive reference work explains how to tie hundreds of practical (and decorative) knots in clear illustrations and precisely worded written instructions. Ideal for boaters and campers. Also covers knots in history, knot mystery and magic, and games, stunts and tricks with rope. Introduction. Index. 166 black-and-white illustrations.

Khovanov homology for virtual knots with arbitrary coefficients

International Nuclear Information System (INIS)

Manturov, Vassily O

2007-01-01

The Khovanov homology theory over an arbitrary coefficient ring is extended to the case of virtual knots. We introduce a complex which is well-defined in the virtual case and is homotopy equivalent to the original Khovanov complex in the classical case. Unlike Khovanov's original construction, our definition of the complex does not use any additional prescription of signs to the edges of a cube. Moreover, our method enables us to construct a Khovanov homology theory for 'twisted virtual knots' in the sense of Bourgoin and Viro (including knots in three-dimensional projective space). We generalize a number of results of Khovanov homology theory (the Wehrli complex, minimality problems, Frobenius extensions) to virtual knots with non-orientable atoms

Confirming the nature of the knot near the pulsar B1951+32

Science.gov (United States)

Zyuzin, D. A.; Shibanov, Yu A.; Pavlov, G. G.; Danilenko, A. A.

2017-12-01

The energetic and fast-moving radio and γ-ray pulsar B1951+32 is associated with the supernova remnant CTB 80. It powers a complex pulsar wind nebula detected in the radio, Hα and X-rays (Moon et al 2004 ApJ 610 L33). A puzzling optical knot was detected about 0″.5 from the pulsar in the optical and near-IR (Moon et al 2004 ApJ 610 L33; Hester 2000 Bulletin of the AAS 32 1542). It is reminiscent of the unique “inner optical knot” located 0″.6 from the Crab pulsar. Until now there has been no evidence that B1951+32 knot is indeed associated with the pulsar. We observed the pulsar field with the Gemini-North telescope in 2016 to check the association. We performed first near-IR high spatial resolution imaging in the K s band using the NIRI+Altair instrument and deep optical imaging in the gr bands using the GMOS instrument. Our observations showed that the current knot position is shifted by ≈ 0″.6 from the position measured with the HST in 1997. This is consistent with the known pulsar proper motion and is direct evidence of the pulsar-knot connection. We compared the spectral energy distribution of the knot emission with that of the Crab knot. Possible implications of the results are discussed.

On the groundstate energy spectrum of magnetic knots and links

International Nuclear Information System (INIS)

Ricca, Renzo L; Maggioni, Francesca

2014-01-01

By using analytical results for the constrained minimum energy of magnetic knots we determine the influence of internal twist on the minimum magnetic energy levels of knots and links, and by using ropelength data from the RIDGERUNNER tightening algorithm (Ashton et al 2011 Exp. Math. 20 57–90) we obtain the groundstate energy spectra of the first 250 prime knots and 130 prime links. The two spectra are found to follow an almost identical logarithmic law. By assuming that the number of knot types grows exponentially with the topological crossing number, we show that this generic behavior can be justified by a general relationship between ropelength and crossing number, which is in good agreement with former analytical estimates (Buck and Simon 1999 Topol. Appl. 91 245–57, Diao 2003 J. Knot Theory Ramifications 12 1–16). Moreover, by considering the ropelength averaged over a given knot family, we establish a new connection between the averaged ropelength and the topological crossing number of magnetic knots. (paper)

Filtration of the classical knot concordance group and Casson-Gordon invariants

OpenAIRE

Kim, Taehee

2002-01-01

It is known that if any prime power branched cyclic cover of a knot in the 3-sphere is a homology sphere, then the knot has vanishing Casson-Gordon invariants. We construct infinitely many examples of (topologically) non-slice knots in the 3-sphere whose prime power branched cyclic covers are homology spheres. We show that these knots generate an infinite rank subgroup of F_(1.0)/F_(1.5) for which Casson-Gordon invariants vanish in Cochran-Orr-Teichner's filtration of the classical knot conco...

Energy, ropelength, and other physical aspects of equilateral knots

International Nuclear Information System (INIS)

Millett, Kenneth C.; Rawdon, Eric J.

2003-01-01

Closed macromolecular chains may form physically knotted conformations whose relative occurrence and spatial measurements provide insight into their properties and the mechanisms acting upon them. Under the assumption of a degree of structural homogeneity, equilateral spatial polygons are a productive context within which to create mathematical models of these knots and to study their mathematical and physical properties. The ensembles, or spaces, of these knots are models of the settings within which the knots evolve in ways determined by a physical model. In this paper we describe the mathematical foundation of such models as well as such spatial, geometric, statistical, and physical properties of the configurations as mathematical energies, thickness and ropelength, average crossing number, average writhe, and volumes and surfaces areas of standard bodies enclosing the knots. We present methods with which the energy and ropelength are optimized within the families of spatially equivalent equilateral configurations. Numerical results from our implementation of these methods are shown to illustrate connections between the physical measurements and spatial characteristics of the optimized knot configurations. In addition, these data suggest potentially new connections involving their spatial properties

Quandles an introduction to the algebra of knots

CERN Document Server

Elhamdadi, Mohamed

2015-01-01

From prehistory to the present, knots have been used for purposes both artistic and practical. The modern science of Knot Theory has ramifications for biochemistry and mathematical physics and is a rich source of research projects for undergraduate and graduate students and professionals alike. Quandles are essentially knots translated into algebra. This book provides an accessible introduction to quandle theory for readers with a background in linear algebra. Important concepts from topology and abstract algebra motivated by quandle theory are introduced along the way. With elementary self-co

Avian influenza virus antibodies in Pacific Coast Red Knots (Calidris canutus rufa)

Science.gov (United States)

Johnson, James A.; DeCicco, Lucas H.; Ruthrauff, Daniel R.; Krauss, Scott; Hall, Jeffrey S.

2014-01-01

Prevalence of avian influenza virus (AIV) antibodies in the western Atlantic subspecies of Red Knot (Calidris canutus rufa) is among the highest for any shorebird. To assess whether the frequency of detection of AIV antibodies is high for the species in general or restricted only to C. c. rufa, we sampled the northeastern Pacific Coast subspecies of Red Knot (Calidris canutus roselaari) breeding in northwestern Alaska. Antibodies were detected in 90% of adults and none of the chicks sampled. Viral shedding was not detected in adults or chicks. These results suggest a predisposition of Red Knots to AIV infection. High antibody titers to subtypes H3 and H4 were detected, whereas low to intermediate antibody levels were found for subtypes H10 and H11. These four subtypes have previously been detected in shorebirds at Delaware Bay (at the border of New Jersey and Delaware) and in waterfowl along the Pacific Coast of North America.

Knots and Links

Indian Academy of Sciences (India)

in a fashion similar to sound waves, whose medium is air. Ether was believed ..... [3] Colin C Adams, The Knot Book, W H Freeman and Company, New. York. ... [5] Kelly S Chichak, Stuart j CantriU, Antony R Pease, Sheng-Hsien. Chiu, Gareth ...

evaluation of tomato genotypes for resistance to root-knot

African Journals Online (AJOL)

Prof. Adipala Ekwamu

Tomato production in Ghana is threatened by plant parasitic nematodes, especially the root knot ... to be highly resistant to Meloidogyne spp. and also recorded the lowest reproductive factors of 0.71 and 0.53, respectively. ..... VII International.

Filtration of the classical knot concordance group and Casson-Gordon invariants

Science.gov (United States)

Kim, Taehee

2004-09-01

It is known that if every prime power branched cyclic cover of a knot in S(3) is a homology sphere, then the knot has vanishing Casson-Gordon invariants. We construct infinitely many examples of (topologically) non-slice knots in S(3) whose prime power branched cyclic covers are homology spheres. We show that these knots generate an infinite rank subgroup of scrf_{(1.0)}/scrf_{(1.5)} for which Casson-Gordon invariants vanish in Cochran-Orr-Teichner's filtration of the classical knot concordance group. As a corollary, it follows that Casson-Gordon invariants are not a complete set of obstructions to a second layer of Whitney disks.

Knot theory and a physical state of quantum gravity

International Nuclear Information System (INIS)

Liko, Tomas; Kauffman, Louis H

2006-01-01

We discuss the theory of knots, and describe how knot invariants arise naturally in gravitational physics. The focus of this review is to delineate the relationship between knot theory and the loop representation of non-perturbative canonical quantum general relativity (loop quantum gravity). This leads naturally to a discussion of the Kodama wavefunction, a state which is conjectured to be the ground state of the gravitational field with positive cosmological constant. This review can serve as a self-contained introduction to loop quantum gravity and related areas. Our intent is to make the paper accessible to a wider audience that may include topologists, knot theorists, and other persons innocent of the physical background to this approach to quantum gravity. (topical review)

Minimal knotted polygons in cubic lattices

International Nuclear Information System (INIS)

Van Rensburg, E J Janse; Rechnitzer, A

2011-01-01

In this paper we examine numerically the properties of minimal length knotted lattice polygons in the simple cubic, face-centered cubic, and body-centered cubic lattices by sieving minimal length polygons from a data stream of a Monte Carlo algorithm, implemented as described in Aragão de Carvalho and Caracciolo (1983 Phys. Rev. B 27 1635), Aragão de Carvalho et al (1983 Nucl. Phys. B 215 209) and Berg and Foester (1981 Phys. Lett. B 106 323). The entropy, mean writhe, and mean curvature of minimal length polygons are computed (in some cases exactly). While the minimal length and mean curvature are found to be lattice dependent, the mean writhe is found to be only weakly dependent on the lattice type. Comparison of our results to numerical results for the writhe obtained elsewhere (see Janse van Rensburg et al 1999 Contributed to Ideal Knots (Series on Knots and Everything vol 19) ed Stasiak, Katritch and Kauffman (Singapore: World Scientific), Portillo et al 2011 J. Phys. A: Math. Theor. 44 275004) shows that the mean writhe is also insensitive to the length of a knotted polygon. Thus, while these results for the mean writhe and mean absolute writhe at minimal length are not universal, our results demonstrate that these values are quite close the those of long polygons regardless of the underlying lattice and length

Relative symplectic caps, 4-genus and fibered knots

Indian Academy of Sciences (India)

We prove relative versions of the symplectic capping theorem and sufficiency of Giroux's criterion for Stein fillability and use these to study the 4-genus of knots. More precisely, suppose we have a symplectic 4-manifold with convex boundary and a symplectic surface in such that is a transverse knot in .

Teaching and Learning of Knot Theory in School Mathematics

CERN Document Server

Kawauchi, Akio

2012-01-01

This book is the result of a joint venture between Professor Akio Kawauchi, Osaka City University, well-known for his research in knot theory, and the Osaka study group of mathematics education, founded by Professor Hirokazu Okamori and now chaired by his successor Professor Tomoko Yanagimoto, Osaka Kyoiku University. The seven chapters address the teaching and learning of knot theory from several perspectives. Readers will find an extremely clear and concise introduction to the fundamentals of knot theory, an overview of curricular developments in Japan, and in particular a series of teaching

Great Knot Calidris tenuirostris at Lutembe Bay, Uganda

African Journals Online (AJOL)

Unfortunately it became nervous and flew to another island and we were unable to pursue it before darkness fell. I was, however, able to take some record shots. I circulated the best of four poor photographs to a few birding colleagues for their opinion, and the general consensus favoured Red Knot rather than Great Knot.

Total curvature and total torsion of knotted random polygons in confinement

Science.gov (United States)

Diao, Yuanan; Ernst, Claus; Rawdon, Eric J.; Ziegler, Uta

2018-04-01

Knots in nature are typically confined spatially. The confinement affects the possible configurations, which in turn affects the spectrum of possible knot types as well as the geometry of the configurations within each knot type. The goal of this paper is to determine how confinement, length, and knotting affect the total curvature and total torsion of random polygons. Previously published papers have investigated these effects in the unconstrained case. In particular, we analyze how the total curvature and total torsion are affected by (1) varying the length of polygons within a fixed confinement radius and (2) varying the confinement radius of polygons with a fixed length. We also compare the total curvature and total torsion of groups of knots with similar complexity (measured as crossing number). While some of our results fall in line with what has been observed in the studies of the unconfined random polygons, a few surprising results emerge from our study, showing some properties that are unique due to the effect of knotting in confinement.

Lattices gauge theories in terms of knots

International Nuclear Information System (INIS)

Vecernyes, P.

1989-01-01

Cluster expansion is developed in lattice gauge theories with finite gauge groups in d≥3 dimensions where the clusters are connected (d - 2)-dimensional surfaces which can branch along (d - 3)-cells. The interaction between them has a knot theoretical interpretation. It can be many body linking or knotting self-interaction. For small enough gauge coupling g the authors prove analyticity of the correlation functions in the variable exp(-1/g 2

Sectional meeting on Numerical Methods, Calculations and Simulations in Knot Theory and its Applications

CERN Document Server

Millett, Kenneth C; Rawdon, Eric J; Stasiak, Andrzej; Physical and Numerical Models in Knot theory: including Applications to the Life Sciences; Conference on Knots, Random Walks and Biomolecules

2005-01-01

The physical properties of knotted and linked configurations in space have long been of interest to mathematicians. More recently, these properties have become significant to biologists, physicists, and engineers among others. Their depth of importance and breadth of application are now widely appreciated and valuable progress continues to be made each year. This volume presents several contributions from researchers using computers to study problems that would otherwise be intractable. While computations have long been used to analyze problems, formulate conjectures, and search for special structures in knot theory, increased computational power has made them a staple in many facets of the field. The volume also includes contributions concentrating on models researchers use to understand knotting, linking, and entanglement in physical and biological systems. Topics include properties of knot invariants, knot tabulation, studies of hyperbolic structures, knot energies, the exploration of spaces of knots, knot...

Multimedia article. The keys to the new laparoscopic world Thumbs up! knot and Tornado knot.

Science.gov (United States)

Uchida, K; Haruta, N; Okajima, M; Matsuda, M; Yamamoto, M

2005-06-01

Most laparoscopic surgeons feel some anxiety when performing intracorporeal knotting with conventional techniques [1, 2]. Two factors contribute to this anxiety. The first is the necessity of recognizing three dimensions on a two-dimensional monitor. The conventional intracorporeal knotting techniques make loops by twisting the thread with a second pair of forceps. This necessitates cooperative movement of both hands, with the added difficulties of depth perception. Regular touch confirmations reduce problems with depth perception. However, touch confirmation is more complicated in laparoscopic surgery than in laparotomy. The second problem is that tied loops can come loose and escape the instruments, especially with hard thread. This is not only stressful but also increases operation time.

Borromean Triangles and Prime Knots in an Ancient Temple

Indian Academy of Sciences (India)

a computer mouse with cable which forms the logo of the Topo- logical Quantum .... theory of knots stayed on and was developed into a beautiful. Figure 3. A prime knot ... ematics to build bridges with the inner worlds that these temples seek to ...

Intra-vesical knot of bladder catheter in an extremely low birthweight neonate: A case report

Directory of Open Access Journals (Sweden)

Paula M.Y. Tang

2015-07-01

Full Text Available Premature and extremely low birth weight (ELBW neonates are at high risk of developing multiple co-morbidities and often require urinary catheterization for various medical indications. Intra-vesical knotting of bladder catheter is a known but uncommon complication of this procedure. We report a case of an ELBW baby boy with a knotted bladder catheter requiring surgical retrieval. After an elective operation for the closure of patent ductus arteriosus, a 4 French urinary catheter was inserted into an ELBW baby boy for urine output monitoring and left in-situ. Resistance was encountered in attempt to remove the urinary catheter. Abdominal X Ray confirmed intra-vesical knotting of the tube. Knot unravelling by interventional radiology was attempted but was unsuccessful. Open extra-peritoneal bladder exploration was performed for the retrieval of the tightly knotted catheter. A 6 French transurethral Foley catheter was inserted for bladder drainage. Upon removal of the Foley's catheter on day 5 post op, the baby was able to void spontaneously. With literature review, we postulated the potential risk factors resulting in this potentially avoidable iatrogenic unusual complication. Recommendations were suggested to avoid further incidences.

Handbook of knotting and splicing

CERN Document Server

Hasluck, Paul N

2005-01-01

Clearly written and amply illustrated with 208 figures, this classic guide ranges from simple and useful knots to complex varieties. Additional topics include rope splicing, working cordage, hammock making, more.

Dissecting host plant manipulation by cyst and root-knot nematodes

NARCIS (Netherlands)

Karczmarek, A.

2006-01-01

Cyst ( Globodera spp. and Heterodera spp.) and root-knot nematodes ( Meloidogyne spp.), one of the most damaging crop pests, are a perfect example of highly adapted, sophisticated root parasites. These nematodes induces specialized feeding structures (cyst

Motion of charged particles in a knotted electromagnetic field

International Nuclear Information System (INIS)

Arrayas, M; Trueba, J L

2010-01-01

In this paper we consider the classical relativistic motion of charged particles in a knotted electromagnetic field. After reviewing how to construct electromagnetic knots from maps between the three-sphere and the two-sphere, we introduce a mean quadratic radius of the energy density distribution in order to study some properties of this field. We study the classical relativistic motion of electrons in the electromagnetic field of the Hopf map, and compute their trajectories. It is observed that these electrons initially at rest are strongly accelerated by the electromagnetic force, becoming ultrarelativistic in a period of time that depends on the knot energy and size.

Motion of charged particles in a knotted electromagnetic field

Energy Technology Data Exchange (ETDEWEB)

Arrayas, M; Trueba, J L, E-mail: joseluis.trueba@urjc.e [Area de Electromagnetismo, Universidad Rey Juan Carlos, Camino del Molino s/n, 28943 Fuenlabrada, Madrid (Spain)

2010-06-11

In this paper we consider the classical relativistic motion of charged particles in a knotted electromagnetic field. After reviewing how to construct electromagnetic knots from maps between the three-sphere and the two-sphere, we introduce a mean quadratic radius of the energy density distribution in order to study some properties of this field. We study the classical relativistic motion of electrons in the electromagnetic field of the Hopf map, and compute their trajectories. It is observed that these electrons initially at rest are strongly accelerated by the electromagnetic force, becoming ultrarelativistic in a period of time that depends on the knot energy and size.

Knotted solutions for linear and nonlinear theories: Electromagnetism and fluid dynamics

Directory of Open Access Journals (Sweden)

Daniel W.F. Alves

2017-10-01

Full Text Available We examine knotted solutions, the most simple of which is the “Hopfion”, from the point of view of relations between electromagnetism and ideal fluid dynamics. A map between fluid dynamics and electromagnetism works for initial conditions or for linear perturbations, allowing us to find new knotted fluid solutions. Knotted solutions are also found to be solutions of nonlinear generalizations of electromagnetism, and of quantum-corrected actions for electromagnetism coupled to other modes. For null configurations, electromagnetism can be described as a null pressureless fluid, for which we can find solutions from the knotted solutions of electromagnetism. We also map them to solutions of Euler's equations, obtained from a type of nonrelativistic reduction of the relativistic fluid equations.

Ileosigmoid knotting in pregnancy: A case report from Zimbabwe ...

African Journals Online (AJOL)

Ileosigmoid knotting (ISK), also known as compound volvulus, is a rare cause of intestinal obstruction wherein the ileum wraps around the base of the sigmoid colon and forms a knot with rapid progression to gangrene. The worldwide incidence of ISK ranges from 1 in 1500 to 1 in 66,431. ISK is particularly rare in pregnancy ...

True Umbilical Cord Knot Leading to Fetal Demise | Ikechebelu ...

African Journals Online (AJOL)

The incidence of true knot of the umbilical cord is not only very low but it is often undiagnosed antenatally when present despite the availability of prenatal ultrasonography. When the true knot remains tight, it may impede the circulation of the fetus and may result to fetal death in utero especially in labor. We report a very ...

Evaluation of tomato genotypes for resistance to root-knot nematodes

African Journals Online (AJOL)

Tomato (Solanum lycopersicum) is one of the most popular vegetable crops worldwide, owing to its high nutritive value and diversified use. Tomato production in Ghana is threatened by plant parasitic nematodes, especially the root knot nematodes (Meloidogyne spp.), which are responsible for huge economic yield losses.

The Chern-Simons current in time series of knots and links in proteins

Science.gov (United States)

Capozziello, Salvatore; Pincak, Richard

2018-06-01

A superspace model of knots and links for DNA time series data is proposed to take into account the feedback loop from docking to undocking state of protein-protein interactions. In particular, the direction of interactions between the 8 hidden states of DNA is considered. It is a E8 ×E8 unified spin model where the genotype, from active and inactive side of DNA time data series, can be considered for any living organism. The mathematical model is borrowed from loop-quantum gravity and adapted to biology. It is used to derive equations for gene expression describing transitions from ground to excited states, and for the 8 coupling states between geneon and anti-geneon transposon and retrotransposon in trash DNA. Specifically, we adopt a modified Grothendieck cohomology and a modified Khovanov cohomology for biology. The result is a Chern-Simons current in (8 + 3) extradimensions of a given unoriented supermanifold with ghost fields of protein structures. The 8 dimensions come from the 8 hidden states of spinor field of genetic code. The extradimensions come from the 3 types of principle fiber bundle in the secondary protein.

The unique cysteine knot regulates the pleotropic hormone leptin.

Directory of Open Access Journals (Sweden)

Ellinor Haglund

Full Text Available Leptin plays a key role in regulating energy intake/expenditure, metabolism and hypertension. It folds into a four-helix bundle that binds to the extracellular receptor to initiate signaling. Our work on leptin revealed a hidden complexity in the formation of a previously un-described, cysteine-knotted topology in leptin. We hypothesized that this unique topology could offer new mechanisms in regulating the protein activity. A combination of in silico simulation and in vitro experiments was used to probe the role of the knotted topology introduced by the disulphide-bridge on leptin folding and function. Our results surprisingly show that the free energy landscape is conserved between knotted and unknotted protein, however the additional complexity added by the knot formation is structurally important. Native state analyses led to the discovery that the disulphide-bond plays an important role in receptor binding and thus mediate biological activity by local motions on distal receptor-binding sites, far removed from the disulphide-bridge. Thus, the disulphide-bridge appears to function as a point of tension that allows dissipation of stress at a distance in leptin.

Pinus pinaster Knot: A Source of Polyphenols against Plasmopara viticola.

Science.gov (United States)

Gabaston, Julien; Richard, Tristan; Cluzet, Stéphanie; Palos Pinto, Antonio; Dufour, Marie-Cécile; Corio-Costet, Marie-France; Mérillon, Jean-Michel

2017-10-11

Pine knot extract from Pinus pinaster byproducts was characterized by UHPLC-DAD-MS and NMR. Fourteen polyphenols divided into four classes were identified as follows: lignans (nortrachelogenin, pinoresinol, matairesinol, isolariciresinol, secoisolariciresinol), flavonoids (pinocembrin, pinobanksin, dihydrokaempferol, taxifolin), stilbenes (pinosylvin, pinosylvin monomethyl ether, pterostilbene), and phenolic acids (caffeic acid, ferulic acid). The antifungal potential of pine knot extract, as well as the main compounds, was tested in vitro against Plasmopara viticola. The ethanolic extract showed a strong antimildew activity. In addition, pinosylvins and pinocembrin demonstrated significant inhibition of zoospore mobility and mildew development. These findings strongly suggest that pine knot is a potential biomass that could be used as a natural antifungal product.

Design and Assembly of DNA Nano-Objects and 2D DNA Origami Arrays

Science.gov (United States)

Liu, Wenyan

DNA, which plays a central role in biology as the carrier of genetic information, is also an excellent candidate for structural nanotechnology. Researches have proven that a variety of complicated DNA assemblies, such as objects, 2D & 3D crystals, and nanomechanical devices, can be fabricated through the combination of robust branched DNA motifs and sticky ends. This dissertation focuses on the design and construction of DNA nano--objects and 2D DNA origami arrays. In this dissertation, we first describe the formation of a triangular species that has four strands per edge, held together by PX interactions. We demonstrate by nondenaturing gel electrophoresis and by atomic force microscopy (AFM) that we can combine a partial triangle with other strands to form a robust four--stranded molecule. By combining them with a novel three--domain molecule, we also demonstrate by AFM that these triangles can be self--assembled into a linear array. Second, we demonstrate our attempts to design and self--assemble 2D DNA origami arrays using several different strategies. Specifically, we introduce the self--assembly of 2D DNA origami lattices using a symmetric cross--like design. This design strategy resulted in a well--ordered woven latticework array with edge dimensions of 2--3 mum. This size is likely to be large enough to connect bottom-up methods of patterning with top--down approaches. Third, we illustrate the design and construction of DNA nano--objects for exploring the substrate preferences of topoisomerase (topo) II. We designed and fabricated four double rhombus--like DNA molecules, each of which contains a different conformation of crossover in the middle, as possible substrates to establish the structural preferences for topo II. We characterized the formation of each substrate molecule by gel electrophoresis. Finally, we study the effect of M13 DNA knotting on the formation of the DNA origami tiles. We demonstrate by atomic force microscopy (AFM) that knotted M13

Scaling behavior of knotted random polygons and self-avoiding polygons: Topological swelling with enhanced exponent.

Science.gov (United States)

Uehara, Erica; Deguchi, Tetsuo

2017-12-07

We show that the average size of self-avoiding polygons (SAPs) with a fixed knot is much larger than that of no topological constraint if the excluded volume is small and the number of segments is large. We call it topological swelling. We argue an "enhancement" of the scaling exponent for random polygons with a fixed knot. We study them systematically through SAP consisting of hard cylindrical segments with various different values of the radius of segments. Here we mean by the average size the mean-square radius of gyration. Furthermore, we show numerically that the topological balance length of a composite knot is given by the sum of those of all constituent prime knots. Here we define the topological balance length of a knot by such a number of segments that topological entropic repulsions are balanced with the knot complexity in the average size. The additivity suggests the local knot picture.

Knot invariants and higher representation theory

CERN Document Server

Webster, Ben

2018-01-01

The author constructs knot invariants categorifying the quantum knot variants for all representations of quantum groups. He shows that these invariants coincide with previous invariants defined by Khovanov for \\mathfrak{sl}_2 and \\mathfrak{sl}_3 and by Mazorchuk-Stroppel and Sussan for \\mathfrak{sl}_n. The author's technique is to study 2-representations of 2-quantum groups (in the sense of Rouquier and Khovanov-Lauda) categorifying tensor products of irreducible representations. These are the representation categories of certain finite dimensional algebras with an explicit diagrammatic presentation, generalizing the cyclotomic quotient of the KLR algebra. When the Lie algebra under consideration is \\mathfrak{sl}_n, the author shows that these categories agree with certain subcategories of parabolic category \\mathcal{O} for \\mathfrak{gl}_k.

Knot invariants and M-theory: Proofs and derivations

Science.gov (United States)

Errasti Díez, Verónica

2018-01-01

We construct two distinct yet related M-theory models that provide suitable frameworks for the study of knot invariants. We then focus on the four-dimensional gauge theory that follows from appropriately compactifying one of these M-theory models. We show that this theory has indeed all required properties to host knots. Our analysis provides a unifying picture of the various recent works that attempt an understanding of knot invariants using techniques of four-dimensional physics. This is a companion paper to K. Dasgupta, V. Errasti Díez, P. Ramadevi, and R. Tatar, Phys. Rev. D 95, 026010 (2017), 10.1103/PhysRevD.95.026010, covering all but Sec. III C. It presents a detailed mathematical derivation of the main results there, as well as additional material. Among the new insights, those related to supersymmetry and the topological twist are highlighted. This paper offers an alternative, complementary formulation of the contents in the first paper, but is self-contained and can be read independently.

Classification of knotted tori in 2-metastable dimension

KAUST Repository

Cencelj, Matija

2012-11-30

This paper is devoted to the classical Knotting Problem: for a given manifold N and number m describe the set of isotopy classes of embeddings N → Sm. We study the specific case of knotted tori, that is, the embeddings Sp × Sq → Sm. The classification of knotted tori up to isotopy in the metastable dimension range m > p + 3 2 q + 2, p 6 q, was given by Haefliger, Zeeman and A. Skopenkov. We consider the dimensions below the metastable range and give an explicit criterion for the finiteness of this set of isotopy classes in the 2-metastable dimension: Theorem. Assume that p+ 4 3 q +2 < mp+ 3 2 q +2 and m > 2p+q +2. Then the set of isotopy classes of smooth embeddings Sp × Sq → Sm is infinite if and only if either q + 1 or p + q + 1 is divisible by 4. © 2012 RAS(DoM) and LMS.

Classification of knotted tori in 2-metastable dimension

KAUST Repository

Cencelj, Matija; Repovš, Dušan; Skopenkov, Mikhail

2012-01-01

This paper is devoted to the classical Knotting Problem: for a given manifold N and number m describe the set of isotopy classes of embeddings N → Sm. We study the specific case of knotted tori, that is, the embeddings Sp × Sq → Sm. The classification of knotted tori up to isotopy in the metastable dimension range m > p + 3 2 q + 2, p 6 q, was given by Haefliger, Zeeman and A. Skopenkov. We consider the dimensions below the metastable range and give an explicit criterion for the finiteness of this set of isotopy classes in the 2-metastable dimension: Theorem. Assume that p+ 4 3 q +2 < mp+ 3 2 q +2 and m > 2p+q +2. Then the set of isotopy classes of smooth embeddings Sp × Sq → Sm is infinite if and only if either q + 1 or p + q + 1 is divisible by 4. © 2012 RAS(DoM) and LMS.

Knots Untie: Molecular Determinants Involved in Knot Formation Induced by Pseudomonas savastanoi in Woody Hosts

Directory of Open Access Journals (Sweden)

Eloy Caballo-Ponce

2017-06-01

Full Text Available The study of the molecular basis of tree diseases is lately receiving a renewed attention, especially with the emerging perception that pathogens require specific pathogenicity and virulence factors to successfully colonize woody hosts. Pathosystems involving woody plants are notoriously difficult to study, although the use of model bacterial strains together with genetically homogeneous micropropagated plant material is providing a significant impetus to our understanding of the molecular determinants leading to disease. The gammaproteobacterium Pseudomonas savastanoi belongs to the intensively studied Pseudomonas syringae complex, and includes three pathogenic lineages causing tumorous overgrowths (knots in diverse economically relevant trees and shrubs. As it occurs with many other bacteria, pathogenicity of P. savastanoi is dependent on a type III secretion system, which is accompanied by a core set of at least 20 effector genes shared among strains isolated from olive, oleander, and ash. The induction of knots of wild-type size requires that the pathogen maintains adequate levels of diverse metabolites, including the phytohormones indole-3-acetic acid and cytokinins, as well as cyclic-di-GMP, some of which can also regulate the expression of other pathogenicity and virulence genes and participate in bacterial competitiveness. In a remarkable example of social networking, quorum sensing molecules allow for the communication among P. savastanoi and other members of the knot microbiome, while at the same time are essential for tumor formation. Additionally, a distinguishing feature of bacteria from the P. syringae complex isolated from woody organs is the possession of a 15 kb genomic island (WHOP carrying four operons and three other genes involved in degradation of phenolic compounds. Two of these operons mediate the catabolism of anthranilate and catechol and, together with another operon, are required for the induction of full-size tumors

A 'FIREWORK' OF H2 KNOTS IN THE PLANETARY NEBULA NGC 7293 (THE HELIX NEBULA)

International Nuclear Information System (INIS)

Matsuura, M.; Speck, A. K.; McHunu, B. M.; Tanaka, I.; Wright, N. J.; Viti, S.; Wesson, R.; Smith, M. D.; Zijlstra, A. A.

2009-01-01

We present a deep and wide field-of-view (4' x 7') image of the planetary nebula (PN) NGC 7293 (the Helix Nebula) in the 2.12 μm H 2 v = 1 → 0 S(1) line. The excellent seeing (0.''4) at the Subaru Telescope, allows the details of cometary knots to be examined. The knots are found at distances of 2.'2-6.'4 from the central star (CS). At the inner edge and in the inner ring (up to 4.'5 from the CS), the knot often show a 'tadpole' shape, an elliptical head with a bright crescent inside and a long tail opposite to the CS. In detail, there are variations in the tadpole shapes, such as narrowing tails, widening tails, meandering tails, or multipeaks within a tail. In the outer ring (4.'5-6.'4 from the CS), the shapes are more fractured, and the tails do not collimate into a single direction. The transition in knot morphology from the inner edge to the outer ring is clearly seen. The number density of knots governs the H 2 surface brightness in the inner ring: H 2 exists only within the knots. Possible mechanisms which contribute to the shaping of the knots are discussed, including photoionization and streaming motions. A plausible interpretation of our images is that inner knots are being overrun by a faster wind, but that this has not (yet) reached the outer knots. Based on H 2 formation and destruction rates, H 2 gas can survive in knots from formation during the late asymptotic giant branch phase throughout the PN phase. These observations provide new constraints on the formation and evolution of knots, and on the physics of molecular gas embedded within ionized gas.

How to Twist a Knot

DEFF Research Database (Denmark)

Randrup, Thomas; Røgen, Peter

1997-01-01

is an invariant of ambient isotopy measuring the topological twist of the closed strip. We classify closed strips in euclidean 3-space by their knots and their twisting number. We prove that this classification exactly divides closed strips into isotopy classes. Using this classification we point out how some...

A "Firework" of H2 Knots in the Planetary Nebula NGC 7293 (The Helix Nebula)

Science.gov (United States)

Matsuura, M.; Speck, A. K.; McHunu, B. M.; Tanaka, I.; Wright, N. J.; Smith, M. D.; Zijlstra, A. A.; Viti, S.; Wesson, R.

2009-08-01

We present a deep and wide field-of-view (4' × 7') image of the planetary nebula (PN) NGC 7293 (the Helix Nebula) in the 2.12 μm H2 v = 1 → 0 S(1) line. The excellent seeing (0farcs4) at the Subaru Telescope, allows the details of cometary knots to be examined. The knots are found at distances of 2farcm2-6farcm4 from the central star (CS). At the inner edge and in the inner ring (up to 4farcm5 from the CS), the knot often show a "tadpole" shape, an elliptical head with a bright crescent inside and a long tail opposite to the CS. In detail, there are variations in the tadpole shapes, such as narrowing tails, widening tails, meandering tails, or multipeaks within a tail. In the outer ring (4farcm5-6farcm4 from the CS), the shapes are more fractured, and the tails do not collimate into a single direction. The transition in knot morphology from the inner edge to the outer ring is clearly seen. The number density of knots governs the H2 surface brightness in the inner ring: H2 exists only within the knots. Possible mechanisms which contribute to the shaping of the knots are discussed, including photoionization and streaming motions. A plausible interpretation of our images is that inner knots are being overrun by a faster wind, but that this has not (yet) reached the outer knots. Based on H2 formation and destruction rates, H2 gas can survive in knots from formation during the late asymptotic giant branch phase throughout the PN phase. These observations provide new constraints on the formation and evolution of knots, and on the physics of molecular gas embedded within ionized gas. Based on data taken with the Subaru Telescope, National Astronomical Observatory of Japan (proposal ID S07B-054).

Rectangular superpolynomials for the figure-eight knot 41

Science.gov (United States)

Kononov, Ya. A.; Morozov, A. Yu.

2017-11-01

We rewrite the recently proposed differential expansion formula for HOMFLY polynomials of the knot 41 in an arbitrary rectangular representation R = [rs] as a sum over all Young subdiagrams λ of R with surprisingly simple coefficients of the Z factors. Intriguingly, these coefficients are constructed from the quantum dimensions of symmetric representations of the groups SL(r) and SL(s) and restrict the summation to diagrams with no more than s rows and r columns. Moreover, the β-deformation to Macdonald dimensions yields polynomials with positive integer coefficients, which are plausible candidates for the role of superpolynomials for rectangular representations. Both the polynomiality and the positivity of the coefficients are nonobvious, nevertheless true. This generalizes the previously known formulas for symmetric representations to arbitrary rectangular representations. The differential expansion allows introducing additional gradings. For the trefoil knot 31, to which our results for the knot 41 are immediately extended, we obtain the so-called fourth grading of hyperpolynomials. The property of factorization in roots of unity is preserved even in the five-graded case.

Towards effective topological field theory for knots

Directory of Open Access Journals (Sweden)

A. Mironov

2015-10-01

Full Text Available Construction of (colored knot polynomials for double-fat graphs is further generalized to the case when “fingers” and “propagators” are substituting R-matrices in arbitrary closed braids with m-strands. Original version of [25] corresponds to the case m=2, and our generalization sheds additional light on the structure of those mysterious formulas. Explicit expressions are now combined from Racah matrices of the type R⊗R⊗R¯⟶R¯ and mixing matrices in the sectors R⊗3⟶Q. Further extension is provided by composition rules, allowing to glue two blocks, connected by an m-strand braid (they generalize the product formula for ordinary composite knots with m=1.

Successful Treatment of Stent Knot in the Proximal Ureter Using Ureteroscopy and Holmium Laser

Directory of Open Access Journals (Sweden)

Masters M. Richards

2011-01-01

Full Text Available Knotted ureteral stent is rare yet tedious complication that might represent a treatment challenge to the endourologist. Only twelve cases of knotted stent have been reported. Different management options have been reported, including simple traction, ureteroscopy, percutaneous removal, and open surgery. In this paper, we present the successful untying of the knot using ureteroscopy with holmium laser.

Knots and Random Walks in Vibrated Granular Chains

International Nuclear Information System (INIS)

Ben-Naim, E.; Daya, Z. A.; Vorobieff, P.; Ecke, R. E.

2001-01-01

We study experimentally statistical properties of the opening times of knots in vertically vibrated granular chains. Our measurements are in good qualitative and quantitative agreement with a theoretical model involving three random walks interacting via hard-core exclusion in one spatial dimension. In particular, the knot survival probability follows a universal scaling function which is independent of the chain length, with a corresponding diffusive characteristic time scale. Both the large-exit-time and the small-exit-time tails of the distribution are suppressed exponentially, and the corresponding decay coefficients are in excellent agreement with theoretical values

An Indwelling Urethral Catheter Knotted Around a Double-J Ureteral Stent: An Unusual Complication after Kidney Transplantation

Directory of Open Access Journals (Sweden)

E. G. Warmerdam

2011-01-01

Full Text Available Urethral catheterization is a common procedure with a relatively low complication rate. Knotting of an indwelling urethral catheter is a very rare complication, and there are only a few case reports on knotted catheters, most of them concerning children. We report an especially rare case where a urethral catheter formed a knot around a double-J ureteral stent after a kidney transplantation. We will discuss the various risk factors for knotting of a catheter and the methods to untangle a knot.

The Ileosigmoid Knot: A Case Report

African Journals Online (AJOL)

because the clinical signs are difficult to define and the ... describe a case of ileosigmoid knotting in a 40 year old male and .... Prompt relief of obstruction by an emergency laparatomy is a ... the bowel leading to perforation, fecal peritonitis and.

Knot numbers used as labels for identifying subject matter of a khipu

Directory of Open Access Journals (Sweden)

Alberto Saez-Rodriguez

2013-03-01

Full Text Available This investigation presents a new way to look at the numerical khipu, a knotted-string recording device from Pachacamac (Peru, and the types of information it contains. In addition to celestial coordinates, khipu knots apparently pertain to an early form of double-entry accounting. This study hypothesizes that the khipu sample has the recording capacity needed to register double-entry-like accounts. After the identification of its subject matter, the khipu sample was studied in an attempt to ascertain whether the knot values could represent instructions from the Inca state administration to a local accounting center. The results indicate that the numerical information in the pairing quadrants (determined by the distribution of S- and Z-knots should be read from top to bottom along the full length of the string and can then provide certain complementary details regarding the projected corn stocks of the Inca stat

Adhering Pasteuria penetrans endospores affect movements of root-knot nematode juveniles

Directory of Open Access Journals (Sweden)

Ioannis VAGELAS

2013-01-01

Full Text Available Pasteuria penetrans is a biological control agent of root-knot nematodes (Meloidogyne spp., preventing root invasion by second-stage juveniles (J2s, and eventually causing females sterility and death. greatest control effects for P. penetrans depend on the numbers of endospores attached to nematode cuticles. a method based on digital image analysis was used to record the effects of endospore attachment on the movements of juvenile root-knot nematodes, using a model based on the centroid point. Data showed that the numbers of endospores attached to the cuticle influenced nematode movement. At high endospore attachment levels (20‒30 per J2, nematodes did not show directional movement, whereas nematodes encumbered with five to eight spores showed limited directional movement, compared to those without endospores. nematode cephalic region turns were modelled using a markov chain, showing that P. penetrans endospores affected movements. Less nematodes invaded and established on tomato root systems when encumbered with low (five to eight or high numbers (20‒30 of P. penetrans endospores, compared with unencumbered nematodes.

Blue optical continuum associated with a radio knot in 3C346

Science.gov (United States)

Dey, Arjun; van Breugel, Wil J. M.

1994-06-01

We report the discovery of extremely luminous near-UV continuum emission associated with a bright radio knot in the radio galaxy 3C346 (zeta = 0.162). Photometric measurements from U and r' band images and longslit spectra show a spectral energy distribution that steepens at higher frequencies, with radio and optical spectral indices alphar = -0.37 +/- 0.02 and alphao = -1.8 +/- 0.2, respectively. Based on a comparison of the optical properties of this knot with other known cases of optical emission associated with radio structures, we conclude that the continuum emission is optical synchrotron radiation. Our observations are consistent with the suggestion that 3C346 is a foreshortened FR-II radio galaxy with its radio axis oriented close to the line of sight. The optical and radio emission from the knot appear to be associated with a hotspot (at the end of a jet) on the near side. Finally, our U and r' images of 3C346 provide a striking illustration that the optical morphologies of nearby radio galaxies also depend upon wavelength and that studies of these objects are relevant to the interpretation of the alignment effect seen in the high redshift radio galaxies.

A novel knot selection method for the error-bounded B-spline curve fitting of sampling points in the measuring process

International Nuclear Information System (INIS)

Liang, Fusheng; Zhao, Ji; Ji, Shijun; Zhang, Bing; Fan, Cheng

2017-01-01

The B-spline curve has been widely used in the reconstruction of measurement data. The error-bounded sampling points reconstruction can be achieved by the knot addition method (KAM) based B-spline curve fitting. In KAM, the selection pattern of initial knot vector has been associated with the ultimate necessary number of knots. This paper provides a novel initial knots selection method to condense the knot vector required for the error-bounded B-spline curve fitting. The initial knots are determined by the distribution of features which include the chord length (arc length) and bending degree (curvature) contained in the discrete sampling points. Firstly, the sampling points are fitted into an approximate B-spline curve Gs with intensively uniform knot vector to substitute the description of the feature of the sampling points. The feature integral of Gs is built as a monotone increasing function in an analytic form. Then, the initial knots are selected according to the constant increment of the feature integral. After that, an iterative knot insertion (IKI) process starting from the initial knots is introduced to improve the fitting precision, and the ultimate knot vector for the error-bounded B-spline curve fitting is achieved. Lastly, two simulations and the measurement experiment are provided, and the results indicate that the proposed knot selection method can reduce the number of ultimate knots available. (paper)

Hybrid Threat Center of Gravity Analysis: Cutting the Gordian Knot

Science.gov (United States)

2016-04-04

19b. TELEPHONE NUMBER (Include area code) 04/04/2016 Master’s Thesis 22-7-2015 to 04-04-2016 HYBRID THREAT CENTER OF GRAVITY ANALYSIS: CUTTING THE...CENTER OF GRAVITY ANALYSIS: CUTTING THE GORDIAN KNOT By Michael D. Reilly LtCol, USMC Intentionally left blank...HYBRID THREAT CENTER OF GRAVITY ANALYSIS: CUTTING THE GORDIAN KNOT By Michael D. Reilly LtCol, USMC A paper submitted to the Faculty of the Joint Advanced

The volume conjecture, perturbative knot invariants, and recursion relations for topological strings

NARCIS (Netherlands)

Dijkgraaf, R.; Fuji, H.; Manabe, M.

2011-01-01

We study the relation between perturbative knot invariants and the free energies defined by topological string theory on the character variety of the knot. Such a correspondence between SL(2;C) Chern-Simons gauge theory and the topological open string theory was proposed earlier on the basis of the

Knotting and unknotting proteins in the chaperonin cage: Effects of the excluded volume.

Directory of Open Access Journals (Sweden)

Szymon Niewieczerzal

Full Text Available Molecular dynamics simulations are used to explore the effects of chaperonin-like cages on knotted proteins with very low sequence similarity, different depths of a knot but with a similar fold, and the same type of topology. The investigated proteins are VirC2, DndE and MJ0366 with two depths of a knot. A comprehensive picture how encapsulation influences folding rates is provided based on the analysis of different cage sizes and temperature conditions. Neither of these two effects with regard to knotted proteins has been studied by means of molecular dynamics simulations with coarse-grained structure-based models before. We show that encapsulation in a chaperonin is sufficient to self-tie and untie small knotted proteins (VirC2, DndE, for which the equilibrium process is not accessible in the bulk solvent. Furthermore, we find that encapsulation reduces backtracking that arises from the destabilisation of nucleation sites, smoothing the free energy landscape. However, this effect can also be coupled with temperature rise. Encapsulation facilitates knotting at the early stage of folding and can enhance an alternative folding route. Comparison to unknotted proteins with the same fold shows directly how encapsulation influences the free energy landscape. In addition, we find that as the size of the cage decreases, folding times increase almost exponentially in a certain range of cage sizes, in accordance with confinement theory and experimental data for unknotted proteins.

Tightening slip knots in raw and degummed silk to increase toughness without losing strength

OpenAIRE

Pantano, Maria; Berardo, Alice; Pugno, Nicola

2016-01-01

Knots are fascinating topological elements, which can be found in both natural and artificial systems. While in most of the cases, knots cannot be loosened without breaking the strand where they are tightened, herein, attention is focused on slip or running knots, which on the contrary can be unfastened without compromising the structural integrity of their hosting material. Two different topologies are considered, involving opposite unfastening mechanisms, and their influence on the mechanic...

HOMFLYPT polynomial is the best quantifier for topological cascades of vortex knots

Science.gov (United States)

Ricca, Renzo L.; Liu, Xin

2018-02-01

In this paper we derive and compare numerical sequences obtained by adapted polynomials such as HOMFLYPT, Jones and Alexander-Conway for the topological cascade of vortex torus knots and links that progressively untie by a single reconnection event at a time. Two cases are considered: the alternate sequence of knots and co-oriented links (with positive crossings) and the sequence of two-component links with oppositely oriented components (negative crossings). New recurrence equations are derived and sequences of numerical values are computed. In all cases the adapted HOMFLYPT polynomial proves to be the best quantifier for the topological cascade of torus knots and links.

First report of the root-knot nematode Meloidogyne ethiopica on tomato in Slovenia

NARCIS (Netherlands)

Sirca, S.; Urek, G.; Karssen, G.

2004-01-01

The root-knot nematode Meloidogyne ethiopica Whitehead originally described from Tanzania is also distributed in South Africa, Zimbabwe, and Ethiopia (3). Although this species is a relatively unknown root-knot nematode, M. ethiopica parasitizes several economical important crops, such as tomato,

Integrated management of root-knot nematode (Meloidogyne ...

African Journals Online (AJOL)

Integrated management of root-knot nematode (Meloidogyne incognita) for tomato production and productivity. Bayuh Belay1* ... important food and cash crop of the farmers and is ...... some part of the research budget without any reservation.

Computational Elastic Knots

KAUST Repository

Zhao, Xin

2013-05-01

Elastic rods have been studied intensively since the 18th century. Even now the theory of elastic rods is still developing and enjoying popularity in computer graphics and physical-based simulation. Elastic rods also draw attention from architects. Architectural structures, NODUS, were constructed by elastic rods as a new method of form-finding. We study discrete models of elastic rods and NODUS structures. We also develop computational tools to find the equilibria of elastic rods and the shape of NODUS. Applications of elastic rods in forming torus knot and closing Bishop frame are included in this thesis.

Characterization of the psoRPM1 gene for resistance to root-knot ...

African Journals Online (AJOL)

Several root-knot nematode (Meloidogyne spp.) resistance genes have been discovered in different stone fruit crops. However, none of them has yet been cloned and they were only located on the chromosomes. In this study, a candidate root-knot nematode resistance gene (designated as psoRPM1) was isolated from the ...

The mutual attraction of magnetic knots. [solar hydromagnetic instability in sunspot regions

Science.gov (United States)

Parker, E. N.

1978-01-01

It is observed that the magnetic knots associated with active regions on the sun have an attraction for each other during the formative period of the active regions, when new magnetic flux is coming to the surface. The attraction disappears when new flux ceases to rise through the surface. Then the magnetic spots and knots tend to come apart, leading to disintegration of the sunspots previously formed. The dissolution of the fields is to be expected, as a consequence of the magnetic repulsion of knots of like polarity and as a consequence of the hydromagnetic exchange instability. The purpose of this paper is to show that the mutual attraction of knots during the formative stages of a sunspot region may be understood as the mutual hydrodynamic attraction of the rising flux tubes. Two rising tubes attract each other, as a consequence of the wake of the leading tube when one is moving behind the other, and as a consequence of the Bernoulli effect when rising side by side.

Assessment of Multiple Types of DNA Damage in Human Placentas from Smoking and Non-smoking Women in the Czech Republic

Science.gov (United States)

Margaret Pratt, M.; King, Leon C.; Adams, Linda D.; John, Kaarthik; Sirajuddin, Paul; Olivero, Ofelia A.; Manchester, David K.; Sram, Radim J.; DeMarini, David M.; Poirier, Miriam C.

2010-01-01

Three classes of DNA damage were assessed in human placentas collected (in 2000-4) from 51 women living in the Teplice region of the Czech Republic, a mining area considered to have some of the worst environmental pollution in Europe in the 1980s. Polycyclic aromatic hydrocarbon (PAH)-DNA adducts were localized and semiquantified using immunohistochemistry (IHC) and the Automated Cellular Imaging System (ACIS). More generalized DNA damage was measured both by 32P-postlabeling and by abasic (AB) site analysis. Placenta stained with antiserum elicited against DNA modified with r7, t8-dihydroxy-t-9, 10-oxy-7,8,9,10-tetrahydro-benzo[a]pyrene (BPDE) revealed PAH-DNA adduct localization in nuclei of the cytotrophoblast (CT) cells and syncytiotrophoblast (ST) knots lining the chorionic villi. The highest levels of DNA damage, 49–312 PAH-DNA adducts/108 nucleotides, were found by IHC/ACIS in 14 immediately-fixed placenta samples. An additional 37 placenta samples were stored frozen before fixation and embedding, and because PAH-DNA adducts were largely undetectable in these samples, freezing was implicated in the loss of IHC signal. The same placentas (n = 37) contained 1.7 – 8.6 stable/bulky DNA adducts/108 nucleotides and 0.6 – 47.2 AB sites/105 nucleotides. For all methods there was no correlation among types of DNA damage and no difference in extent of DNA damage between smokers and non-smokers. Therefore, the data show that DNA from placentas obtained in Teplice contained multiple types of DNA damage, which likely arose from various environmental exposures. In addition, PAH-DNA adducts were present at high concentrations in the CT cells and ST knots of the chorionic villi. PMID:20839217

A New Euler's Formula for DNA Polyhedra

Science.gov (United States)

Hu, Guang; Qiu, Wen-Yuan; Ceulemans, Arnout

2011-01-01

DNA polyhedra are cage-like architectures based on interlocked and interlinked DNA strands. We propose a formula which unites the basic features of these entangled structures. It is based on the transformation of the DNA polyhedral links into Seifert surfaces, which removes all knots. The numbers of components , of crossings , and of Seifert circles are related by a simple and elegant formula: . This formula connects the topological aspects of the DNA cage to the Euler characteristic of the underlying polyhedron. It implies that Seifert circles can be used as effective topological indices to describe polyhedral links. Our study demonstrates that, the new Euler's formula provides a theoretical framework for the stereo-chemistry of DNA polyhedra, which can characterize enzymatic transformations of DNA and be used to characterize and design novel cages with higher genus. PMID:22022596

Hair-on-hair static friction coefficient can be determined by tying a knot.

Science.gov (United States)

Chevalier, Nicolas R

2017-11-01

Characterizing the tribological properties of the hair-hair interface is important to quantify the manageability of hair and to assess the performance of hair care products. Audoly et al. (Phys. Rev. Lett. 99, 164301, 2007) derived an equation relating the self-friction coefficient of an elastic fiber to the dimensions of a simple, relaxed overhand knot made from this fiber. I experimentally tested and validated their equation using nylon thread and an independent measurement of its self-friction coefficient. I show that this methodology can be applied to provide high-throughput data on the static self-friction coefficient of single hair fibers in various conditions and to quantitatively assess how hair care treatments (conditioner, relaxant) alter frictional properties. I find that treatment of hair with 1M sodium hydroxide leads to a quick, irreversible self-friction coefficient increase; the resulting fine frictional fibers can be used to form very small knots for microsurgical vessel and organ ligature in medicine or embryology. The relaxed overhand knot method can more generally be used to measure the self-friction coefficients of a wide range of elastic fibers from the nano- (e.g. proteins, nanotubes) to the macro-scale (e.g. textile fiber, fiberglass). Copyright © 2017 Elsevier B.V. All rights reserved.

Post-breeding migration and connectivity of red knots in the Western Atlantic

Science.gov (United States)

Lyons, James E.; Winn, Bradford; Keyes, Timothy; Kalasz, Kevin S.

2018-01-01

Red knots (Calidris canutus rufa) have 3 distinct nonbreeding regions: 1 in the southeastern United States and Caribbean, another on the northeast coast of Brazil in the Maranhão region, and a third along the Patagonian coasts of Chile and Argentina. Effective conservation and recovery of this threatened long-distance migrant will require knowledge of population structure, migration ecology, and abundance and distribution throughout the annual cycle. We conducted a stopover population and biogeographic assessment of knots at the Altamaha River Delta, Georgia, an important stopover area in the southeastern United States. We estimated stopover population size and stopover duration during post-breeding migration in 2011 at the Altamaha study area using mark-resight data, and we inferred nonbreeding regions for this stopover population using stable isotope ratios of carbon and nitrogen in feathers, and observations (sightings and captures) during boreal winter from across the hemisphere. With an integrated Bayesian analysis of all these data, we also estimated the number of birds in the southeastern United States and northern Brazil during boreal winter. For mark-resight analyses in Georgia, we made observations of marked individuals during 14 weeks from early August to early November 2011 and detected 814 individually marked birds. We used the Jolly-Seber mark-recapture model and estimated the southbound passage population at approximately 23,400 red knots. In ongoing studies elsewhere, isotope samples were collected from 175 (21%) of the 814 birds detected in our study, and ≥1 sighting or capture record during boreal winter was located in data repositories for 659 birds (81%). Isotopic signatures and boreal winter records indicate that the majority (82–96%) of the birds that stopped at the Altamaha Delta spend the boreal winter in the northern part of the nonbreeding range (southeast USA, Caribbean, and northern Brazil). Knots migrating to the southeastern

Long-slit spectrophotometry of the multiple knots of the polar ring galaxy IIZw71

Science.gov (United States)

Pérez-Montero, E.; García-Benito, R.; Díaz, A. I.; Pérez, E.; Kehrig, C.

2009-04-01

Aims: The blue compact dwarf galaxy IIZw71 is catalogued as a probable polar-ring galaxy, and along its long axis it has several very luminous knots showing recent episodes of star formation. Our main aim is to study the physical properties, the stellar content, and the kinematics in the brightest knots of the polar ring. Methods: We carried out long-slit spectroscopic observations of the polar ring in the spectral range 3500-10 000 Å taken with the William Herschel Telescope (WHT). The spectroscopic observations complemented by the available photometry of the galaxy in narrow Hα filters. Results: We measured the rotation curve of the ring, from which we infer a ratio M/LB ≈ 3.9 inside the star-forming ring. We measured the auroral [Oiii] line in the two brightest knots, allowing us to measure oxygen, sulphur, nitrogen, argon, and neon chemical abundances following the direct method. Different empirical calibrators were used to estimate the oxygen abundance in the two faintest knots where the temperature sensitive lines could not be measured. The metallicities obtained are very similar for all the knots, but lower than previously reported in the literature from integrated spectra. The N/O abundance, as derived from the N2O2 parameter (the ratio of the [Nii] and [Oii] intensities), is remarkably constant over the ring, indicating that local polution processes are not conspicuous. Using synthetic stellar populations (SSPs) calculated with the code STARLIGHT, we studied the age distribution of the stellar populations in each knot, finding that in all of them there is a combination of a very young population with less than 10 Myr, responsible for the ionisation of the gas, with other populations older than 100 Myr, probably responsible for the chemical evolution of the knots. The small differences in metallicity and the age distributions among the different knots are indicative of a common chemical evolution, probably related to the process of interaction with the

Gordian Knots of Prevision: The lessons of history

Science.gov (United States)

Fleming, J. R.

2017-12-01

Atmospheric researchers have long attempted to untie the Gordian Knot of meteorology—that intractable and intertwined tangle of observational imprecision, theoretical uncertainties, and non-linear influences—that, if unraveled, would provide perfect prevision of the weather for ten days, of seasonal conditions for the year, and of climatic conditions for a decade, a century, a millennium, or longer. This presentation, based on Inventing Atmospheric Science (M.I.T. Press, 2016), examines the work of four interconnected generations of scientists (Vilhelm Bjerknes, C.-G. Rossby, Harry Wexler, Ed Lorenz) and the influence of four transformative technologies (radio, nuclear, computation, aerospace) from the dawn of applied fluid dynamics to the emergence of the interdisciplinary atmospheric sciences and the new Gordian Knot of chaos.

Design and performance of the APPLE-Knot undulator

International Nuclear Information System (INIS)

Ji, Fuhao; Chang, Rui; Zhou, Qiaogen; Zhang, Wei; Ye, Mao; Sasaki, Shigemi; Qiao, Shan

2015-01-01

The design and performance of the Apple-Knot undulator which can generate photons with arbitrary polarization and low on-axis heat load are presented. Along with the development of accelerator technology, synchrotron emittance has continuously decreased. This results in increased brightness, but also causes a heavy heat load on beamline optics. Recently, optical surfaces with 0.1 nm micro-roughness and 0.05 µrad slope error (r.m.s.) have become commercially available and surface distortions due to heat load have become a key factor in determining beamline performance, and heat load has become a serious problem at modern synchrotron radiation facilities. Here, APPLE-Knot undulators which can generate photons with arbitrary polarization, with low on-axis heat load, are reported

Design and performance of the APPLE-Knot undulator

Energy Technology Data Exchange (ETDEWEB)

Ji, Fuhao [Department of Physics, State Key Laboratory of Surface Physics, and Laboratory of Advanced Materials, Fudan University, 2005 Songhu Road, Shanghai 200438, People’s Republic of (China); Chang, Rui [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, People’s Republic of (China); Zhou, Qiaogen; Zhang, Wei [Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 239 Zhangheng Road, Shanghai 201204, People’s Republic of (China); Ye, Mao [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, People’s Republic of (China); Sasaki, Shigemi [Hiroshima Synchrotron Radiation Center, Hiroshima University, 2-313 Kagamiyama, Hiroshima 739-0046 (Japan); Qiao, Shan, E-mail: qiaoshan@mail.sim.ac.cn [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, People’s Republic of (China); School of Physical Science and Technology, ShanghaiTech University, 319 Yueyang Road, Shanghai 200031, People’s Republic of (China)

2015-06-09

The design and performance of the Apple-Knot undulator which can generate photons with arbitrary polarization and low on-axis heat load are presented. Along with the development of accelerator technology, synchrotron emittance has continuously decreased. This results in increased brightness, but also causes a heavy heat load on beamline optics. Recently, optical surfaces with 0.1 nm micro-roughness and 0.05 µrad slope error (r.m.s.) have become commercially available and surface distortions due to heat load have become a key factor in determining beamline performance, and heat load has become a serious problem at modern synchrotron radiation facilities. Here, APPLE-Knot undulators which can generate photons with arbitrary polarization, with low on-axis heat load, are reported.

Polynomial invariants for torus knots and topological strings

International Nuclear Information System (INIS)

Labastida, J.M.F.

2001-01-01

We make a precision test of a recently proposed conjecture relating Chern-Simons gauge theory to topological string theory on the resolution of the conifold. First, we develop a systematic procedure to extract string amplitudes from vacuum expectation values (vevs) of Wilson loops in Chern-Simons gauge theory, and then we evaluate these vevs in arbitrary irreducible representations of SU(N) for torus knots. We find complete agreement with the predictions derived from the target space interpretation of the string amplitudes. We also show that the structure of the free energy of topological open string theory gives further constraints on the Chern-Simons vevs. Our work provides strong evidence towards an interpretation of knot polynomial invariants as generating functions associated to enumerative problems. (orig.)

Atmospheres of polygons and knotted polygons

International Nuclear Information System (INIS)

Janse Rensburg, E J Janse; Rechnitzer, A

2008-01-01

In this paper we define two statistics a + (ω) and a - (ω), the positive and negative atmospheres of a lattice polygon ω of fixed length n. These statistics have the property that (a + (ω))/(a - (ω)) = p n+2 /p n , where p n is the number of polygons of length n, counted modulo translations. We use the pivot algorithm to sample polygons and to compute the corresponding average atmospheres. Using these data, we directly estimate the growth constants of polygons in two and three dimensions. We find that μ=2.63805±0.00012 in two dimensions and μ=4.683980±0.000042±0.000067 in three dimensions, where the error bars are 67% confidence intervals, and the second error bar in the three-dimensional estimate of μ is an estimated systematic error. We also compute atmospheres of polygons of fixed knot type K sampled by the BFACF algorithm. We discuss the implications of our results and show that different knot types have atmospheres which behave dramatically differently at small values of n

Prediction of the optimal set of contacts to fold the smallest knotted protein

International Nuclear Information System (INIS)

Dabrowski-Tumanski, P; Jarmolinska, A I; Sulkowska, J I

2015-01-01

Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map. (paper)

Prediction of the optimal set of contacts to fold the smallest knotted protein

Science.gov (United States)

Dabrowski-Tumanski, P.; Jarmolinska, A. I.; Sulkowska, J. I.

2015-09-01

Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map.

360° virtual reality video for the acquisition of knot tying skills: A randomised controlled trial.

Science.gov (United States)

Yoganathan, S; Finch, D A; Parkin, E; Pollard, J

2018-04-10

360° virtual reality (VR) video is an exciting and evolving field. Current technology promotes a totally immersive, 3-dimensional (3D), 360° experience anywhere in the world using simply a smart phone and virtual reality headset. The potential for its application in the field of surgical education is enormous. The aim of this study was to determine knot tying skills taught with a 360-degree VR video compared to conventional 2D video teaching. This trial was a prospective, randomised controlled study. 40 foundation year doctors (first year postgraduate) were randomised to either the 360-degree VR video (n = 20) or 2D video teaching (n = 20). Participants were given 15 min to watch their allocated video. Ability to tie a single handed reef knot was then assessed against a marking criteria developed for the Royal College of Surgeons, England, (RCSeng) Basic Surgical Skills (BSS) course, by a blinded assessor competent in knot tying. Each candidate then underwent further teaching using Peyton's four step model. Knot tying technique was then re-assessed. Knot tying scores were significantly better in the VR video teaching arm when compared with conventional (median knot score 5.0 vs 4.0 p = 0.04). When used in combination with face to face skills teaching this difference persisted (median knot score 9.5 vs 9.0 p = 0.01). More people in the VR arm constructed a complete reef knot than in the 2D arm following face to face teaching (17/20 vs 12/20). No difference between the groups existed in the time taken to construct a reef knot following video and teaching (median time 31.0s vs 30.5s p = 0.89). This study shows there is significant merit in the application of 360-degree VR video technology in surgical training, both as an independent teaching aid and when used as an adjunct to traditional face to face teaching. Copyright © 2018 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

Knots, splices and rope-work an illustrated handbook

CERN Document Server

Verrill, A Hyatt

2006-01-01

This treasury of practical and ornamental knots ranges from easy half-hitches and bow-lines to intricate rope-work projects, such as rope buckles and cask slings. Detailed instructions accompany the 148 drawings.

Knot positioning during McDonald cervical cerclage, does it make a difference? A cohort study.

Science.gov (United States)

Atia, Hytham; Ellaithy, Mohamed; Altraigey, Ahmed; Ibrahim, Heba

2018-05-15

To study the effect of McDonald cerclage knot position on the different maternal and neonatal outcomes. This historical cohort study included women with singleton pregnancy who had a prophylactic McDonald cervical cerclage between 1 May 2010 and 31 September 2017. Maternal and neonatal outcome parameters were compared between the anterior and posterior knot cerclage procedures. The primary outcome measure was the rate of term birth. 550 Women had a prophylactic McDonald cervical cerclage, 306 with anterior knot (Group A) and 244 with posterior knot (Group B). There were no statistically significant differences regarding gestational age (GA) at delivery (36.3 ± 4.2 versus 35.8 ± 5.3 for groups A and B respectively), term birth rate, post-cerclage cervical length, symptomatic vaginitis, urinary tract infection, difficult cerclage removal and cervical lacerations. Similarly, there were no statistically significant differences as regards the studied neonatal outcomes including take home babies, neonatal intensive care admission, respiratory distress syndrome and neonatal sepsis. Survival analysis on GA at delivery demonstrated no statistically significant difference as regards the proportion of term deliveries in the anterior and posterior knot cerclage groups (log-rank test p-value = .478). Knot positioning during McDonald cervical cerclage, anteriorly or posteriorly, didn't significantly impact the studied maternal and neonatal outcomes.

Pierced Lasso Bundles are a new class of knot-like motifs.

Directory of Open Access Journals (Sweden)

Ellinor Haglund

2014-06-01

Full Text Available A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin. When oxidized, leptin contains a disulphide bridge creating a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins. We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structurally homologous proteins in the PDB. We call this new helical family class the Pierced Lasso Bundle (PLB and the knot-like threaded structural motif a Pierced Lasso (PL. In the current study, we use structure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with three unthreaded homologs as the covalent loop (or lasso in leptin is important in folding dynamics and activity. We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. Remarkably, the position of the loop as well as its size influences the native state dynamics, which can impact receptor binding and biological activity. This previously unrecognized complexity of knot-like proteins within the helical bundle family comprises a completely new class within the knot family, and the hidden complexity we unraveled in the PLBs is expected to be found in other protein structures outside the four-helix bundles. The insights gained here provide critical new elements for future investigation of this emerging class of proteins, where function and the energetic landscape can be controlled by hidden topology, and should be take into account in ab initio predictions of newly identified protein targets.

A novel platform based on defect-rich knotted graphene nanotubes for detection of small biomolecules

International Nuclear Information System (INIS)

Lan, Shumin; Song, Yingpan; Chen, Qidi; Guo, Zhiyong; Zhan, Hongbing

2016-01-01

Highlights: • Curvature of the SC-CNTs’ cavities had more local pressure, leading to form k-GNTs. • k-GNTs are divided into sections by knots with abundant edge-plane sites/defects. • k-GNTs exhibited excellent catalytic activity, sensitivity and reproducibility. - Abstract: Detection of disease-related small biomolecules was of great significance for clinical diagnostics and treatment. In this work, we synthesized defect-rich knotted graphene nanotubes (k-GNTs) via chemical oxidative etching of stacked-up carbon nanotubes (SC-CNTs) followed by chemical reduction, to detect disease-related small biomolecules. We further studied the electrochemical properties using three representative redox probes and analyzed their biosensitivity using five biomolecules. The k-GNT-modified electrodes exhibited excellent electrochemical response, with the lowest ΔE p and the highest k 0 . Besides, the modified electrodes could simultaneously detect and discriminate between dopamine (DA), ascorbic acid and uric acid (UA), as well as differentiate phenethylamine (PEA) and epinephrine (EP) existed in newborn rat serum, providing the wide linear detection ranges with high sensitivities for DA, UA, PEA, and EP. These excellent electrocatalytic properties could be ascribe to the unique knotted graphene nanotube structure with high proportion of defect/edge sites, large, accessible, three-dimensional, accessible surface area, fewer oxygen-containing groups and doped N atoms. Our work reveals defect-rich k-GNTs as a promising platform for further applications in electrochemical biosensing and electrocatalysis.

Refined large N duality for knots

DEFF Research Database (Denmark)

Kameyama, Masaya; Nawata, Satoshi

We formulate large N duality of U(N) refined Chern-Simons theory with a torus knot/link in S³. By studying refined BPS states in M-theory, we provide the explicit form of low-energy effective actions of Type IIA string theory with D4-branes on the Ω-background. This form enables us to relate...

Pseudomonas savastanoi pv. savastanoi: some like it knot.

Science.gov (United States)

Ramos, Cayo; Matas, Isabel M; Bardaji, Leire; Aragón, Isabel M; Murillo, Jesús

2012-12-01

Pseudomonas savastanoi pv. savastanoi is the causal agent of olive (Olea europaea) knot disease and an unorthodox member of the P. syringae complex, causing aerial tumours instead of the foliar necroses and cankers characteristic of most members of this complex. Olive knot is present wherever olive is grown; although losses are difficult to assess, it is assumed that olive knot is one of the most important diseases of the olive crop. The last century witnessed a large number of scientific articles describing the biology, epidemiology and control of this pathogen. However, most P. savastanoi pv. savastanoi strains are highly recalcitrant to genetic manipulation, which has effectively prevented the pathogen from benefitting from the scientific progress in molecular biology that has elevated the foliar pathogens of the P. syringae complex to supermodels. A number of studies in recent years have made significant advances in the biology, ecology and genetics of P. savastanoi pv. savastanoi, paving the way for the molecular dissection of its interaction with other nonpathogenic bacteria and their woody hosts. The selection of a genetically pliable model strain was soon followed by the development of rapid methods for virulence assessment with micropropagated olive plants and the analysis of cellular interactions with the plant host. The generation of a draft genome of strain NCPPB 3335 and the closed sequence of its three native plasmids has allowed for functional and comparative genomic analyses for the identification of its pathogenicity gene complement. This includes 34 putative type III effector genes and genomic regions, shared with other pathogens of woody hosts, which encode metabolic pathways associated with the degradation of lignin-derived compounds. Now, the time is right to explore the molecular basis of the P. savastanoi pv. savastanoi-olive interaction and to obtain insights into why some pathovars like it necrotic and why some like it knot

"Nara" knot for suturing of cleft lip in children to make removal easy

Directory of Open Access Journals (Sweden)

Obaidullah

2006-01-01

Full Text Available Cleft patients usually go through a lifetime of repeated hospital admissions and multiple procedures. Suture removal at a tender age and on a sensitive area like the lip becomes a challenge for the nursing staff. It is also emotionally demanding on the part of the parents. Hence, in most centres these patients are at least sedated if not anaesthetised. We have been using a simple knot and running prolene material so that undoing of the knot becomes easy and suture removal more or less atraumatic. We would like to share our experience with readers through this article. An analysis of 53 cleft lip repairs has shown that this knot is safe and easily removable.

Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori

Science.gov (United States)

Wang, Liang-Wei; Liu, Yu-Nan; Lyu, Ping-Chiang; Jackson, Sophie E.; Hsu, Shang-Te Danny

2015-09-01

Understanding the mechanism by which a polypeptide chain thread itself spontaneously to attain a knotted conformation has been a major challenge in the field of protein folding. HP0242 is a homodimeric protein from Helicobacter pylori with intertwined helices to form a unique pseudo-knotted folding topology. A tandem HP0242 repeat has been constructed to become the first engineered trefoil-knotted protein. Its small size renders it a model system for computational analyses to examine its folding and knotting pathways. Here we report a multi-parametric study on the folding stability and kinetics of a library of HP0242 variants, including the trefoil-knotted tandem HP0242 repeat, using far-UV circular dichroism and fluorescence spectroscopy. Equilibrium chemical denaturation of HP0242 variants shows the presence of highly populated dimeric and structurally heterogeneous folding intermediates. Such equilibrium folding intermediates retain significant amount of helical structures except those at the N- and C-terminal regions in the native structure. Stopped-flow fluorescence measurements of HP0242 variants show that spontaneous refolding into knotted structures can be achieved within seconds, which is several orders of magnitude faster than previously observed for other knotted proteins. Nevertheless, the complex chevron plots indicate that HP0242 variants are prone to misfold into kinetic traps, leading to severely rolled-over refolding arms. The experimental observations are in general agreement with the previously reported molecular dynamics simulations. Based on our results, kinetic folding pathways are proposed to qualitatively describe the complex folding processes of HP0242 variants.

Potential of Tissue Culture for Breeding Root-Knot Nematode Resistance into Vegetables

OpenAIRE

Fassuliotis, G.; Bhatt, D. P.

1982-01-01

Plant protoplast technology is being investigated as a means of transferring root-knot nematode resistance factors from Solanum sisymbriifolium into the susceptible S. melongena. Solanum sisymbriifolium plants regenerated from callus lost resistance to Meloidogyne javanica but retained resistance to M. incognita. Tomato plants cloned from leaf discs of the root-knot nematode resistant 'Patriot' were completely susceptible to M. incognita, while sections of stems and leaves rooted in sand in t...

Splitting, linking, knotting, and solitonic escape of topological defects in nematic drops with handles.

Science.gov (United States)

Tasinkevych, Mykola; Campbell, Michael G; Smalyukh, Ivan I

2014-11-18

Topologically nontrivial field excitations, including solitonic, linked, and knotted structures, play important roles in physical systems ranging from classical fluids and liquid crystals, to electromagnetism, classic, and quantum field theories. These excitations can appear spontaneously during symmetry-breaking phase transitions. For example, in cosmological theories, cosmic strings may have formed knotted configurations influencing the Early Universe development, whereas in liquid crystals transient tangled defect lines were observed during isotropic-nematic transitions, eventually relaxing to defect-free states. Knotted and solitonic fields and defects were also obtained using optical manipulation, complex-shaped colloids, and frustrated cholesterics. Here we use confinement of nematic liquid crystal by closed surfaces with varied genus and perpendicular boundary conditions for a robust control of appearance and stability of such field excitations. Theoretical modeling and experiments reveal structure of defect lines as a function of the surface topology and material and geometric parameters, establishing a robust means of controlling solitonic, knotted, linked, and other field excitations.

Hydrodynamic characteristics of knotted and knotless purse seine netting panels as determined in a flume tank.

Science.gov (United States)

Tang, Hao; Xu, Liuxiong; Hu, Fuxiang

2018-01-01

Nylon (PA) netting is widely used in purse seines and other fishing gears due to its high strength and good sinking performance. However, hydrodynamic properties of nylon netting of different characteristics are poorly understood. This study investigated hydrodynamic characteristics of nylon netting of different knot types and solidity ratios under different attack angles and flow velocities. It was found that the hydrodynamic coefficient of netting panels was related to Reynolds number, solidity ratio, attack angle, knot type and twine construction. The solidity ratio was found to positively correlate with drag coefficient when the netting was normal to the flow (CD90), but not the case when the netting was parallel to the flow (CD0). For netting panels inclined to the flow, the inclined drag coefficient had a negative relationship with the solidity ratio for attack angles between 0° and 50°, but a positive relationship for attack angles between 50° and 90°. The lift coefficient increased with the attack angle, reaching the culminating point at an attack angle of 50°, before subsequent decline. We found that the drag generated by knot accounted for 15-25% of total drag, and the knotted netting with higher solidity ratio exhibited a greater CD0, but it was not the case for the knotless netting. Compared to knotless polyethylene (PE) netting, the drag coefficients of knotless PA netting were dominant at higher Reynolds number (Re>2200).

Hydrodynamic characteristics of knotted and knotless purse seine netting panels as determined in a flume tank.

Directory of Open Access Journals (Sweden)

Hao Tang

Full Text Available Nylon (PA netting is widely used in purse seines and other fishing gears due to its high strength and good sinking performance. However, hydrodynamic properties of nylon netting of different characteristics are poorly understood. This study investigated hydrodynamic characteristics of nylon netting of different knot types and solidity ratios under different attack angles and flow velocities. It was found that the hydrodynamic coefficient of netting panels was related to Reynolds number, solidity ratio, attack angle, knot type and twine construction. The solidity ratio was found to positively correlate with drag coefficient when the netting was normal to the flow (CD90, but not the case when the netting was parallel to the flow (CD0. For netting panels inclined to the flow, the inclined drag coefficient had a negative relationship with the solidity ratio for attack angles between 0° and 50°, but a positive relationship for attack angles between 50° and 90°. The lift coefficient increased with the attack angle, reaching the culminating point at an attack angle of 50°, before subsequent decline. We found that the drag generated by knot accounted for 15-25% of total drag, and the knotted netting with higher solidity ratio exhibited a greater CD0, but it was not the case for the knotless netting. Compared to knotless polyethylene (PE netting, the drag coefficients of knotless PA netting were dominant at higher Reynolds number (Re>2200.

Tolerance of a knotted near infrared fluorescent protein to random circular permutation

Science.gov (United States)

Pandey, Naresh; Kuypers, Brianna E.; Nassif, Barbara; Thomas, Emily E.; Alnahhas, Razan N.; Segatori, Laura; Silberg, Jonathan J.

2016-01-01

Bacteriophytochrome photoreceptors (BphP) are knotted proteins that have been developed as near-infrared fluorescent protein (iRFP) reporters of gene expression. To explore how rearrangements in the peptides that interlace into the knot within the BphP photosensory core affect folding, we subjected iRFP to random circular permutation using an improved transposase mutagenesis strategy and screened for variants that fluoresce. We identified twenty seven circularly permuted iRFP that display biliverdin-dependent fluorescence in Escherichia coli. The variants with the brightest whole cell fluorescence initiated translation at residues near the domain linker and knot tails, although fluorescent variants were discovered that initiated translation within the PAS and GAF domains. Circularly permuted iRFP retained sufficient cofactor affinity to fluoresce in tissue culture without the addition of biliverdin, and one variant displayed enhanced fluorescence when expressed in bacteria and tissue culture. This variant displayed a similar quantum yield as iRFP, but exhibited increased resistance to chemical denaturation, suggesting that the observed signal increase arose from more efficient protein maturation. These results show how the contact order of a knotted BphP can be altered without disrupting chromophore binding and fluorescence, an important step towards the creation of near-infrared biosensors with expanded chemical-sensing functions for in vivo imaging. PMID:27304983

BPS counting for knots and combinatorics on words

Science.gov (United States)

Kucharski, Piotr; Sułkowski, Piotr

2016-11-01

We discuss relations between quantum BPS invariants defined in terms of a product decomposition of certain series, and difference equations (quantum A-polynomials) that annihilate such series. We construct combinatorial models whose structure is encoded in the form of such difference equations, and whose generating functions (Hilbert-Poincaré series) are solutions to those equations and reproduce generating series that encode BPS invariants. Furthermore, BPS invariants in question are expressed in terms of Lyndon words in an appropriate language, thereby relating counting of BPS states to the branch of mathematics referred to as combinatorics on words. We illustrate these results in the framework of colored extremal knot polynomials: among others we determine dual quantum extremal A-polynomials for various knots, present associated combinatorial models, find corresponding BPS invariants (extremal Labastida-Mariño-Ooguri-Vafa invariants) and discuss their integrality.

BPS counting for knots and combinatorics on words

Energy Technology Data Exchange (ETDEWEB)

Kucharski, Piotr [Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland); Sułkowski, Piotr [Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland); Walter Burke Institute for Theoretical Physics, California Institute of Technology,Pasadena, CA 91125 (United States)

2016-11-21

We discuss relations between quantum BPS invariants defined in terms of a product decomposition of certain series, and difference equations (quantum A-polynomials) that annihilate such series. We construct combinatorial models whose structure is encoded in the form of such difference equations, and whose generating functions (Hilbert-Poincaré series) are solutions to those equations and reproduce generating series that encode BPS invariants. Furthermore, BPS invariants in question are expressed in terms of Lyndon words in an appropriate language, thereby relating counting of BPS states to the branch of mathematics referred to as combinatorics on words. We illustrate these results in the framework of colored extremal knot polynomials: among others we determine dual quantum extremal A-polynomials for various knots, present associated combinatorial models, find corresponding BPS invariants (extremal Labastida-Mariño-Ooguri-Vafa invariants) and discuss their integrality.

Seasonality in basal metabolic rate and thermal conductance in a long-distance migrant shorebird, the knot (Calidris canutus)

NARCIS (Netherlands)

Piersma, T.; Cadée, N.; Daan, S.

Knots Calidris canutus live highly seasonal lives, breeding solitarily on high arctic tundra and spending the non-breeding season in large social flocks in temperate to tropical estuaries. Their reproductive activities and physiological preparations for long flights are reflected in pronounced

Economic design in a long-distance migrating molluscivore: how fast-fuelling red knots in Bohai Bay, China, get away with small gizzards.

Science.gov (United States)

Yang, Hong-Yan; Chen, Bing; Ma, Zhi-Jun; Hua, Ning; van Gils, Jan A; Zhang, Zheng-Wang; Piersma, Theunis

2013-10-01

We carried out an observational and experimental study to decipher how resource characteristics, in interaction with the predator's phenotype, constrain a fitness-determining performance measure, i.e. refuelling in a migrant bird. Two subspecies of red knot (Calidris canutus rogersi and C. c. piersmai) use northern Bohai Bay, Yellow Sea, China, for the final prebreeding stopover, during their 10,000-15,000 km long migrations between wintering and breeding areas. Here, they feed on small bivalves, especially 2-7 mm long Potamocorbula laevis. With an average stay of 29 days, and the need to store 80 g of fat for the onward flights to high-Arctic breeding grounds, red knots need to refuel fast. Using existing knowledge, we expected them to achieve this on the basis of (1) prey with high flesh to shell mass ratios, (2) large gizzards to crush the ingested molluscs, or (3) a combination of the two. Rejecting all three predictions, we found that red knots staging in Bohai Bay had the smallest gizzards on record (4.9 ± 0.8 g, mean ± s.e.m., N = 27), and also found that prey quality of P. laevis is much lower than predicted for the measured gizzard size (i.e. 1.3 rather than the predicted 4.5 kJ g(-1) dry shell mass, DM(shell)). The estimated handling time of P. laevis (0.2 s) is much shorter than the observed time between two prey ingestions (0.7 s), indicating that prey handling time is no constraint. Based on field observations of dropping rates and on indoor digestion trails, the shell processing rate was estimated at 3.9 mg DM(shell) s(-1), i.e. three times higher the rate previously predicted for red knots eating as fast as they can with the measured gizzard size. This is explained by the small and easily crushed P. laevis enabling high processing rates. As P. laevis also occurred in high densities, the metabolizable energy intake rate of red knots with small gizzards at 5 J s(-1) was as high as at northward staging sites elsewhere in the world. Currently

Microaspiration of esophageal gland cells and cDNA library construction for identifying parasitism genes of plant-parasitic nematodes.

Science.gov (United States)

Hussey, Richard S; Huang, Guozhong; Allen, Rex

2011-01-01

Identifying parasitism genes encoding proteins secreted from a plant-parasitic nematode's esophageal gland cells and injected through its stylet into plant tissue is the key to understanding the molecular basis of nematode parasitism of plants. Parasitism genes have been cloned by directly microaspirating the cytoplasm from the esophageal gland cells of different parasitic stages of cyst or root-knot nematodes to provide mRNA to create a gland cell-specific cDNA library by long-distance reverse-transcriptase polymerase chain reaction. cDNA clones are sequenced and deduced protein sequences with a signal peptide for secretion are identified for high-throughput in situ hybridization to confirm gland-specific expression.

Tolerance of a Knotted Near-Infrared Fluorescent Protein to Random Circular Permutation.

Science.gov (United States)

Pandey, Naresh; Kuypers, Brianna E; Nassif, Barbara; Thomas, Emily E; Alnahhas, Razan N; Segatori, Laura; Silberg, Jonathan J

2016-07-12

Bacteriophytochrome photoreceptors (BphP) are knotted proteins that have been developed as near-infrared fluorescent protein (iRFP) reporters of gene expression. To explore how rearrangements in the peptides that interlace into the knot within the BphP photosensory core affect folding, we subjected iRFPs to random circular permutation using an improved transposase mutagenesis strategy and screened for variants that fluoresce. We identified 27 circularly permuted iRFPs that display biliverdin-dependent fluorescence in Escherichia coli. The variants with the brightest whole cell fluorescence initiated translation at residues near the domain linker and knot tails, although fluorescent variants that initiated translation within the PAS and GAF domains were discovered. Circularly permuted iRFPs retained sufficient cofactor affinity to fluoresce in tissue culture without the addition of biliverdin, and one variant displayed enhanced fluorescence when expressed in bacteria and tissue culture. This variant displayed a quantum yield similar to that of iRFPs but exhibited increased resistance to chemical denaturation, suggesting that the observed increase in the magnitude of the signal arose from more efficient protein maturation. These results show how the contact order of a knotted BphP can be altered without disrupting chromophore binding and fluorescence, an important step toward the creation of near-infrared biosensors with expanded chemical sensing functions for in vivo imaging.

Knot probability of polygons subjected to a force: a Monte Carlo study

International Nuclear Information System (INIS)

Rensburg, E J Janse van; Orlandini, E; Tesi, M C; Whittington, S G

2008-01-01

We use Monte Carlo methods to study the knot probability of lattice polygons on the cubic lattice in the presence of an external force f. The force is coupled to the span of the polygons along a lattice direction, say the z-direction. If the force is negative polygons are squeezed (the compressive regime), while positive forces tend to stretch the polygons along the z-direction (the tensile regime). For sufficiently large positive forces we verify that the Pincus scaling law in the force-extension curve holds. At a fixed number of edges n the knot probability is a decreasing function of the force. For a fixed force the knot probability approaches unity as 1 - exp(-α 0 (f)n + o(n)), where α 0 (f) is positive and a decreasing function of f. We also examine the average of the absolute value of the writhe and we verify the square root growth law (known for f = 0) for all values of f

Use of gadolinium chloride as a contrast agent for imaging spruce knots by magnetic resonance

Science.gov (United States)

Thomas L. Eberhardt; Chi-Leung So; Amy H. Herlihy; Po-Wah So

2006-01-01

Treatments of knot-containing spruce wood blocks with a paramagnetic salt, gadolinium (III) chloride, in combination with solvent pretreatments, were evaluated as strategies to enhance the visualization of wood features by magnetic resonance imaging (MRI). Initial experiments with clear wood and excised knot samples showed differences in moisture uptake after...

All for knots: evaluating the effectiveness of a proficiency-driven, simulation-based knot tying and suturing curriculum for medical students during their third-year surgery clerkship.

Science.gov (United States)

Pender, Cianna; Kiselov, Vladimir; Yu, Qingzhao; Mooney, Jennifer; Greiffenstein, Patrick; Paige, John T

2017-02-01

We evaluated the effectiveness of implementing a proficiency-driven, simulation-based knot tying and suturing curriculum for medical students during their 3rd-year surgery clerkship. Medical students on the 3rd-year surgical clerkship completed a proficiency-driven, simulation-based knot tying and suturing curriculum consisting of 6 tasks. The effectiveness was evaluated by comparing the initial presession scores to the final postsession scores on an 8-item self-efficacy scale and evaluating pass rates on end of clerkship skills testing. A paired t test was used to analyze data. Sixty-five students had matched preintervention and postintervention questionnaires for analysis. Pass rates approached 100% by the 3rd attempt on all tasks. Significant gains on all 8 items of the self-efficacy questionnaire from pretraining to post-training were noted. Timing of the general surgery rotation did not impact results. Implementation of a simulation-based training, proficiency-driven knot tying and suturing curriculum for 3rd-year medical students during the surgery clerkship is feasible and effective in improving student self-efficacy and objective proficiency toward performance of the tasks taught. Copyright © 2016 Elsevier Inc. All rights reserved.

The multivariable Alexander polynomial and modern knot theory

International Nuclear Information System (INIS)

Saleur, H.

1992-01-01

This paper is a summary of several recent works (by the author and collaborators) that study the Conway-Alexander link invariant in the light of quantum groups and topological quantum field theories. Their purpose is to understand connections between modern knot theory and more classical topological concepts

Control of Root-Knot Nematodes on Tomato by the Endoparasitic Fungus Meria coniospora

OpenAIRE

Jansson, Hans-Börje; Jeyaprakash, A.; Zuckerman, Bert M.

1985-01-01

The endoparasitic nematophagous fungus Meria coniospora reduced root-knot nematode galling on tomatoes in greenhouse pot trials. The fungus was introduced to pots by addition of conidia at several inoculum levels directly to the soil or addition of nematodes infected with M. coniospora to the soil; both methods reduced root galling by root-knot nematodes. These studies represent a part of a recently initiated effort to evaluate the potential of endoparasitic nematophagous fungi for biocontrol...

On the species status of the root-knot nematode Meloidogyne ulmi Palmisano & Ambrogioni, 2000 (Nematoda, Meloidogynidae

Directory of Open Access Journals (Sweden)

Mohammed Ahmed

2013-12-01

Full Text Available The root-knot nematode Meloidogyne ulmi is synonymised with Meloidogyne mali based on morphological and morphometric similarities, common hosts, as well as biochemical similarities at both protein and DNA levels. M. mali was first described in Japan on Malus prunifolia Borkh.; and M. ulmi in Italy on Ulmus chenmoui W.C. Cheng. Morphological and morphometric studies of their holo- and paratypes revealed important similarities in the major characters as well as some general variability in a few others. Host test also showed that besides the two species being able to parasitize the type hosts of the other, they share some other common hosts. Our study of the esterase and malate dehydrogenase isozyme phenotypes of some M. ulmi populations gave a perfectly comparable result to that already known for M. mali. Finally, phylogenetic studies of their SSU and LSU rDNA sequence data revealed that the two are not distinguishable at DNA level. All these put together, leave strong evidences to support the fact that M. ulmi is not a valid species, but a junior synonym of M. mali. Brief discussion on the biology and life cycle of M. mali is given. An overview of all known hosts and the possible distribution of M. mali in Europe are also presented.

Developing an Objective Structured Assessment of Technical Skills for Laparoscopic Suturing and Intracorporeal Knot Tying.

Science.gov (United States)

Chang, Olivia H; King, Louise P; Modest, Anna M; Hur, Hye-Chun

2016-01-01

To develop a teaching and assessment tool for laparoscopic suturing and intracorporeal knot tying. We designed an Objective Structured Assessment of Technical Skills (OSATS) tool that includes a procedure-specific checklist (PSC) and global rating scale (GRS) to assess laparoscopic suturing and intracorporeal knot-tying performance. Obstetrics and Gynecology residents at our institution were videotaped while performing a laparoscopic suturing and intracorporeal knot-tying task at a surgical simulation workshop. A total of 2 expert reviewers assessed resident performance using the OSATS tool during live performance and 1 month later using the videotaped recordings. OSATS scores were analyzed using the Wilcoxon rank-sum test. Data are presented as median scores (interquartile range [IQR]). Intrarater and interrater reliabilities were assessed using a Spearman correlation and are presented as an r correlation coefficient and p value. An r ≥ 0.8 was considered as a high correlation. After testing, we received feedback from residents and faculty to improve the OSATS tool as part of an iterative design process. In all, 14 of 21 residents (66.7%) completed the study, with 9 junior residents and 5 senior residents. Junior residents had a lower score on the PSC than senior residents did; however, this was not statistically significant (median = 6.0 [IQR: 4.0-10.0] and median = 13.0 [IQR: 10.0-13.0]; p = 0.09). There was excellent intrarater reliability with our OSATS tool (for PSC component, r = 0.88 for Rater 1 and 0.93 for Rater 2, both p assessment and teaching tool for laparoscopic suturing and intracorporeal knot-tying skills. Overall, good intrarater reliability was demonstrated, suggesting that this tool may be useful for longitudinal assessment of surgical skills. Copyright © 2015 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

The multivariable Alexander polynomial and modern knot theory

International Nuclear Information System (INIS)

Saleur, H.; Yale Univ., New Haven, CT

1991-01-01

This note is a summary of several recent works (by the author and collaborators) that study the Conway Alexander link invariant in the light of quantum groups and topological quantum field theories. Their purpose is to understand connections between ''modern'' knot theory and more classical topological concepts. (author)

Prevalence, incidence and molecular identification of root-knot ...

African Journals Online (AJOL)

Tomato is a widely grown vegetable in Pakistan. However, its production is severely constrained by root knot nematodes (RKNs). Accurate identification of RKNs is essential for an appropriate control program. The current study evaluated the prevalence, incidence and diversity of RKNs of tomato crops grown in the Khyber ...

[Controlling effect of antagonist bioorganic fertilizer on tomato root-knot nematode].

Science.gov (United States)

Zhu, Zhen; Chen, Fang; Xiao, Tong-jian; Wang, Xiao-hui; Ran, Wei; Yang, Xing-ming; Shen, Qi-rong

2011-04-01

Indoor in vitro culture experiment and greenhouse pot experiment were conducted to evaluate the capabilities of three bacterial strains XZ-173 (Bacillus amyloliquefaciens), SL-25 (B. gibsonii), and KS-62 (Paenibacillus polymyxa) that can hydrolyze collagen protein in controlling tomato root-knot nematode. In the in vitro culture experiment, suspensions of XZ-173, SL-25, and KS-62 induced a mortality rate of 75.9%, 66.7%, and 50.0% to the second-stage junior nematode within 24 h, and decreased the egg hatching rate to 17.8%, 28.9% and 37.6% after 7-day incubation, respectively, in contrast to the 17.4% mortality rate and 53.6% egg hatching rate in the control (sterilized water). In the greenhouse pot experiment, the bioorganic fertilizer mixed with equal parts of fermented XZ-173, SL-25, and KS-62 gained the best result, with the root-knot nematode population in rhizosphere soil decreased by 84.0% as compared with the control. The bioorganic fertilizer also decreased the numbers of galls and eggs on tomato roots significantly, and increased the underground and aboveground biomass of tomato. Therefore, antagonist bioorganic fertilizer has promising potential in controlling root-knot nematode.

A high throughput DNA extraction method with high yield and quality

Directory of Open Access Journals (Sweden)

Xin Zhanguo

2012-07-01

Full Text Available Abstract Background Preparation of large quantity and high quality genomic DNA from a large number of plant samples is a major bottleneck for most genetic and genomic analyses, such as, genetic mapping, TILLING (Targeting Induced Local Lesion IN Genome, and next-generation sequencing directly from sheared genomic DNA. A variety of DNA preparation methods and commercial kits are available. However, they are either low throughput, low yield, or costly. Here, we describe a method for high throughput genomic DNA isolation from sorghum [Sorghum bicolor (L. Moench] leaves and dry seeds with high yield, high quality, and affordable cost. Results We developed a high throughput DNA isolation method by combining a high yield CTAB extraction method with an improved cleanup procedure based on MagAttract kit. The method yielded large quantity and high quality DNA from both lyophilized sorghum leaves and dry seeds. The DNA yield was improved by nearly 30 fold with 4 times less consumption of MagAttract beads. The method can also be used in other plant species, including cotton leaves and pine needles. Conclusion A high throughput system for DNA extraction from sorghum leaves and seeds was developed and validated. The main advantages of the method are low cost, high yield, high quality, and high throughput. One person can process two 96-well plates in a working day at a cost of $0.10 per sample of magnetic beads plus other consumables that other methods will also need.

Small home ranges and high site fidelity in red knots (Calidris c. canutus) wintering on the Banc d'Arguin, Mauritania

NARCIS (Netherlands)

Leyrer, J; Spaans, B; Camara, M; Piersma, T

Using automated and manual radio-telemetry and resightings of individual colour-ringed birds, we assessed the daily use of space of red knots Calidris canutus canutus at a tropical wintering area along the Sahara coast, the Banc d'Arguin in Mauritania. Confirming earlier suggestions, we found that

Small home ranges and high site fidelity in red knots (Calidris c. canutus) wintering on the Banc d’Arguin, Mauritania

NARCIS (Netherlands)

Leyrer, Jutta; Spaans, Bernard; Camara, Mohamed; Piersma, Theunis; Bairlein, F.

2006-01-01

Using automated and manual radio-telemetry and resightings of individual colour-ringed birds, we assessed the daily use of space of red knots Calidris canutus canutus at a tropical wintering area along the Sahara coast, the Banc d’Arguin in Mauritania. Confirming earlier suggestions, we found that

A summary of modulus of elasticity and knot size surveys for laminating grades of lumber

Science.gov (United States)

R. W. Wolfe; R. C. Moody

1981-01-01

A summary of modulus of elasticity (MOE) and knot data is presented for grades of lumber commonly used to manufacture glued-laminated (glulam) timber by the laminating Industry. Tabulated values represent 30 different studies covering a time span of over 16 years. Statistical estimates of average and near-maximum knot sizes as well as mean and coefficient of variation...

True Umbilical Cord Knot Leading to Fetal Demise

African Journals Online (AJOL)

weight was 140 kg, height 1.69 m, blood pressure 120 mmHg. The booking ... The fetal heart tones were monitored using Doppler sonicaid. They remained normal throughout .... true knot, seemingly because the umbilical cord vessels can be compressed ... Therefore, the Wharton's jelly surrounding the fetal vessels has the ...

Braid group, knot theory and statistical mechanics II

CERN Document Server

Yang Chen Ning

1994-01-01

The present volume is an updated version of the book edited by C N Yang and M L Ge on the topics of braid groups and knot theory, which are related to statistical mechanics. This book is based on the 1989 volume but has new material included and new contributors.

Particle on a torus knot: Constrained dynamics and semi-classical quantization in a magnetic field

Energy Technology Data Exchange (ETDEWEB)

Das, Praloy, E-mail: praloydasdurgapur@gmail.com; Pramanik, Souvik, E-mail: souvick.in@gmail.com; Ghosh, Subir, E-mail: subirghosh20@gmail.com

2016-11-15

Kinematics and dynamics of a particle moving on a torus knot poses an interesting problem as a constrained system. In the first part of the paper we have derived the modified symplectic structure or Dirac brackets of the above model in Dirac’s Hamiltonian framework, both in toroidal and Cartesian coordinate systems. This algebra has been used to study the dynamics, in particular small fluctuations in motion around a specific torus. The spatial symmetries of the system have also been studied. In the second part of the paper we have considered the quantum theory of a charge moving in a torus knot in the presence of a uniform magnetic field along the axis of the torus in a semiclassical quantization framework. We exploit the Einstein–Brillouin–Keller (EBK) scheme of quantization that is appropriate for multidimensional systems. Embedding of the knot on a specific torus is inherently two dimensional that gives rise to two quantization conditions. This shows that although the system, after imposing the knot condition reduces to a one dimensional system, even then it has manifested non-planar features which shows up again in the study of fractional angular momentum. Finally we compare the results obtained from EBK (multi-dimensional) and Bohr–Sommerfeld (single dimensional) schemes. The energy levels and fractional spin depend on the torus knot parameters that specifies its non-planar features. Interestingly, we show that there can be non-planar corrections to the planar anyon-like fractional spin.

Energy and helicity of magnetic torus knots and braids

Science.gov (United States)

Oberti, Chiara; Ricca, Renzo L.

2018-02-01

By considering steady magnetic fields in the shape of torus knots and unknots in ideal magnetohydrodynamics, we compute some fundamental geometric and physical properties to provide estimates for magnetic energy and helicity. By making use of an appropriate parametrization, we show that knots with dominant toroidal coils that are a good model for solar coronal loops have negligible total torsion contribution to magnetic helicity while writhing number provides a good proxy. Hence, by the algebraic definition of writhe based on crossing numbers, we show that the estimated values of writhe based on image analysis provide reliable information for the exact values of helicity. We also show that magnetic energy is linearly related to helicity, and the effect of the confinement of magnetic field can be expressed in terms of geometric information. These results can find useful application in solar and plasma physics, where braided structures are often present.

Finite-size and asymptotic behaviors of the gyration radius of knotted cylindrical self-avoiding polygons.

Science.gov (United States)

Shimamura, Miyuki K; Deguchi, Tetsuo

2002-05-01

Several nontrivial properties are shown for the mean-square radius of gyration R2(K) of ring polymers with a fixed knot type K. Through computer simulation, we discuss both finite size and asymptotic behaviors of the gyration radius under the topological constraint for self-avoiding polygons consisting of N cylindrical segments with radius r. We find that the average size of ring polymers with the knot K can be much larger than that of no topological constraint. The effective expansion due to the topological constraint depends strongly on the parameter r that is related to the excluded volume. The topological expansion is particularly significant for the small r case, where the simulation result is associated with that of random polygons with the knot K.

Ileosigmoid knot: A case report

International Nuclear Information System (INIS)

Baheti, Akshay D; Patel, Darshana; Hira, Priya; Babu, Donald

2011-01-01

The ileosigmoid knot is an uncommon but life-threatening cause of closed loop intestinal obstruction. Its treatment is different from a simple volvulus in that it has to be operated upon immediately. Preoperative CT scan diagnosis and prompt treatment can lead to a good outcome. Findings of simultaneous ileal and sigmoid ischemia with non-ischemic colon interposed in between should, in an appropriate clinical setting, indicate this condition. The presence of the whirl sign, medially deviated distal descending colon and cecum, and mesenteric vascular structures from the superior mesenteric vessels that converge toward the sigmoid colon on CT scan help clinch the diagnosis

Rather than by direct acquisition via lateral gene transfer, GHF5 cellulases were passed on from early Pratylenchidae to root-knot and cyst nematodes.

Science.gov (United States)

Rybarczyk-Mydłowska, Katarzyna; Maboreke, Hazel Ruvimbo; van Megen, Hanny; van den Elsen, Sven; Mooyman, Paul; Smant, Geert; Bakker, Jaap; Helder, Johannes

2012-11-21

Plant parasitic nematodes are unusual Metazoans as they are equipped with genes that allow for symbiont-independent degradation of plant cell walls. Among the cell wall-degrading enzymes, glycoside hydrolase family 5 (GHF5) cellulases are relatively well characterized, especially for high impact parasites such as root-knot and cyst nematodes. Interestingly, ancestors of extant nematodes most likely acquired these GHF5 cellulases from a prokaryote donor by one or multiple lateral gene transfer events. To obtain insight into the origin of GHF5 cellulases among evolutionary advanced members of the order Tylenchida, cellulase biodiversity data from less distal family members were collected and analyzed. Single nematodes were used to obtain (partial) genomic sequences of cellulases from representatives of the genera Meloidogyne, Pratylenchus, Hirschmanniella and Globodera. Combined Bayesian analysis of ≈ 100 cellulase sequences revealed three types of catalytic domains (A, B, and C). Represented by 84 sequences, type B is numerically dominant, and the overall topology of the catalytic domain type shows remarkable resemblance with trees based on neutral (= pathogenicity-unrelated) small subunit ribosomal DNA sequences. Bayesian analysis further suggested a sister relationship between the lesion nematode Pratylenchus thornei and all type B cellulases from root-knot nematodes. Yet, the relationship between the three catalytic domain types remained unclear. Superposition of intron data onto the cellulase tree suggests that types B and C are related, and together distinct from type A that is characterized by two unique introns. All Tylenchida members investigated here harbored one or multiple GHF5 cellulases. Three types of catalytic domains are distinguished, and the presence of at least two types is relatively common among plant parasitic Tylenchida. Analysis of coding sequences of cellulases suggests that root-knot and cyst nematodes did not acquire this gene directly

Rather than by direct acquisition via lateral gene transfer, GHF5 cellulases were passed on from early Pratylenchidae to root-knot and cyst nematodes

Directory of Open Access Journals (Sweden)

Rybarczyk-Mydłowska Katarzyna

2012-11-01

Full Text Available Abstract Background Plant parasitic nematodes are unusual Metazoans as they are equipped with genes that allow for symbiont-independent degradation of plant cell walls. Among the cell wall-degrading enzymes, glycoside hydrolase family 5 (GHF5 cellulases are relatively well characterized, especially for high impact parasites such as root-knot and cyst nematodes. Interestingly, ancestors of extant nematodes most likely acquired these GHF5 cellulases from a prokaryote donor by one or multiple lateral gene transfer events. To obtain insight into the origin of GHF5 cellulases among evolutionary advanced members of the order Tylenchida, cellulase biodiversity data from less distal family members were collected and analyzed. Results Single nematodes were used to obtain (partial genomic sequences of cellulases from representatives of the genera Meloidogyne, Pratylenchus, Hirschmanniella and Globodera. Combined Bayesian analysis of ≈ 100 cellulase sequences revealed three types of catalytic domains (A, B, and C. Represented by 84 sequences, type B is numerically dominant, and the overall topology of the catalytic domain type shows remarkable resemblance with trees based on neutral (= pathogenicity-unrelated small subunit ribosomal DNA sequences. Bayesian analysis further suggested a sister relationship between the lesion nematode Pratylenchus thornei and all type B cellulases from root-knot nematodes. Yet, the relationship between the three catalytic domain types remained unclear. Superposition of intron data onto the cellulase tree suggests that types B and C are related, and together distinct from type A that is characterized by two unique introns. Conclusions All Tylenchida members investigated here harbored one or multiple GHF5 cellulases. Three types of catalytic domains are distinguished, and the presence of at least two types is relatively common among plant parasitic Tylenchida. Analysis of coding sequences of cellulases suggests that root-knot

A class of non-null toroidal electromagnetic fields and its relation to the model of electromagnetic knots

International Nuclear Information System (INIS)

Arrayás, Manuel; Trueba, José L

2015-01-01

An electromagnetic knot is an electromagnetic field in vacuum in which the magnetic lines and the electric lines coincide with the level curves of a pair of complex scalar fields ϕ and θ (see equations (A.1), (A.2)). When electromagnetism is expressed in terms of electromagnetic knots, it includes mechanisms for the topological quantization of the electromagnetic helicity, the electric charge, the electromagnetic energy inside a cavity and the magnetic flux through a superconducting ring. In the case of electromagnetic helicity, its topological quantization depends on the linking number of the field lines, both electric and magnetic. Consequently, to find solutions of the electromagnetic knot equations with nontrivial topology of the field lines has important physical consequences. We study a new class of solutions of Maxwell's equations in vacuum Arrayás and Trueba (2011 arXiv:1106.1122) obtained from complex scalar fields that can be interpreted as maps S 3 →S 2 , in which the topology of the field lines is that of the whole torus-knot set. Thus this class of solutions is built as electromagnetic knots at initial time. We study some properties of those fields and consider if detection based on the energy and momentum observables is possible. (paper)

Quiet eye training improves surgical knot tying more than traditional technical training: a randomized controlled study.

Science.gov (United States)

Causer, Joe; Harvey, Adrian; Snelgrove, Ryan; Arsenault, Gina; Vickers, Joan N

2014-08-01

We examined the effectiveness of technical training (TT) and quiet eye training (QE) on the performance of one-handed square knot tying in surgical residents. Twenty surgical residents were randomly assigned to the 2 groups and completed pretest, training, retention, and transfer tests. Participants wore a mobile eye tracker that simultaneously recorded their gaze and hand movements. Dependent variables were knot tying performance (%), QE duration (%), number of fixations, total movement time (s), and hand movement phase time (s). The QE training group had significantly higher performance scores, a longer QE duration, fewer fixations, faster total knot tying times, and faster movement phase times compared with the TT group. The QE group maintained performance in the transfer test, whereas the TT group significantly decreased performance from retention to transfer. QE training significantly improved learning, retention, and transfer of surgical knot tying compared with a traditional technical approach. Both performance effectiveness (performance outcome) and movement efficiency (hand movement times) were improved using QE modeling, instruction, and feedback. Copyright © 2014 Elsevier Inc. All rights reserved.

A state enumeration of the foil knot

OpenAIRE

Ramaharo, Franck; Rakotondrajao, Fanja

2017-01-01

We split the crossings of the foil knot and enumerate the resulting states with a generating polynomial. Unexpectedly, the number of such states which consist of two components are given by the lazy caterer's sequence. This sequence describes the maximum number of planar regions that is obtained with a given number of straight lines. We then establish a bijection between this partition of the plane and the concerned foil splits sequence.

Computation of Hyperbolic Structures in Knot Theory

OpenAIRE

Weeks, Jeffrey R.

2003-01-01

This chapter from the upcoming Handbook of Knot Theory (eds. Menasco and Thistlethwaite) shows how to construct hyperbolic structures on link complements and perform hyperbolic Dehn filling. Along with a new elementary exposition of the standard ideas from Thurston's work, the article includes never-before-published explanations of SnapPea's algorithms for triangulating a link complement efficiently and for converging quickly to the hyperbolic structure while avoiding singularities in the par...

Detection of two fungal biocontrol agents against root-knot nematodes by RAPD markers.

Science.gov (United States)

Zhu, Ming Liang; Mo, Ming He; Xia, Zhen Yuan; Li, Yun Hua; Yang, Shu Jun; Li, Tian Fei; Zhang, Ke Qin

2006-05-01

The strain ZK7 of Pochonia chlamydosporia var. chlamydosporia and IPC of Paecilomyces lilacinus are highly effective in the biological control against root-knot nematodes infecting tobacco. When applied, they require a specific monitoring method to evaluate the colonization and dispersal in soil. In this work, the randomly amplified polymorphic DNA (RAPD) technique was used to differentiate between the two individual strains and 95 other isolates, including isolates of the same species and common soil fungi. This approach allowed the selection of specific fragments of 1.2 kb (Vc1200) and 2.0 kb (Vc2000) specific for ZK7, 1.4 kb (P1400) and 0.85 kb (P850) specific for IPC, using the random Primers OPL-02, OPD-05, OPD-05 and OPC-11, respectively. These fragments were cloned, sequenced, and used to design sequence-characterized amplification region (SCAR) primers specific for the two strains. In classical polymerase chain reaction (PCR), with serial dilution of ZK7 and IPC pure culture DNAs template, the detection limits of these oligonucleotide SCAR-PCR primers were found to be 10, 1000, 500, 100 pg, respectively. In the dot blotting, digoxigenin (DIG)-labeled amplicons from these four primers specifically recognized the corresponding fragments in the DNAs template of these two strains. The detection limit of these amplicons were 0.2, 0.2, 0.5, 0.5 mug, respectively.

EXPANSION OF HYDROGEN-POOR KNOTS IN THE BORN-AGAIN PLANETARY NEBULAE A30 AND A78

Energy Technology Data Exchange (ETDEWEB)

Fang, X.; Guerrero, M. A.; Marquez-Lugo, R. A.; Toalá, J. A. [Instituto de Astrofísica de Andalucía (IAA-CSIC), Glorieta de la Astronomía s/n, E-18008 Granada (Spain); Arthur, S. J. [Centro de Radioastronomía y Astrofísica, Universidad Nacional Autónoma de México, Campus Morelia, 58090 Morelia (Mexico); Chu, Y.-H.; Gruendl, R. A. [Department of Astronomy, University of Illinois, 1002 West Green Street, Urbana, IL 61801 (United States); Blair, W. P. [Department of Physics and Astronomy, Johns Hopkins University, Baltimore, MD 21218 (United States); Hamann, W.-R.; Oskinova, L. M.; Todt, H., E-mail: fangx@iaa.es [Institute for Physics and Astronomy, Universität Potsdam, D-14476 Potsdam (Germany)

2014-12-20

We analyze the expansion of hydrogen-poor knots and filaments in the born-again planetary nebulae A30 and A78 based on Hubble Space Telescope (HST) images obtained almost 20 yr apart. The proper motion of these features generally increases with distance to the central star, but the fractional expansion decreases, i.e., the expansion is not homologous. As a result, there is not a unique expansion age, which is estimated to be 610-950 yr for A30 and 600-1140 yr for A78. The knots and filaments have experienced complex dynamical processes: the current fast stellar wind is mass loaded by the material ablated from the inner knots; the ablated material is then swept up until it shocks the inner edges of the outer, hydrogen-rich nebula. The angular expansion of the outer filaments shows a clear dependence on position angle, indicating that the interaction of the stellar wind with the innermost knots channels the wind along preferred directions. The apparent angular expansion of the innermost knots seems to be dominated by the rocket effect of evaporating gas and by the propagation of the ionization front inside them. Radiation-hydrodynamical simulations show that a single ejection of material followed by a rapid onset of the stellar wind and ionizing flux can reproduce the variety of clumps and filaments at different distances from the central star found in A30 and A78.

Gaussian quadrature rules for C 1 quintic splines with uniform knot vectors

KAUST Repository

Bartoň, Michael

2017-03-21

We provide explicit quadrature rules for spaces of C1C1 quintic splines with uniform knot sequences over finite domains. The quadrature nodes and weights are derived via an explicit recursion that avoids numerical solvers. Each rule is optimal, that is, requires the minimal number of nodes, for a given function space. For each of nn subintervals, generically, only two nodes are required which reduces the evaluation cost by 2/32/3 when compared to the classical Gaussian quadrature for polynomials over each knot span. Numerical experiments show fast convergence, as nn grows, to the “two-third” quadrature rule of Hughes et al. (2010) for infinite domains.

Gaussian quadrature rules for C 1 quintic splines with uniform knot vectors

KAUST Repository

Barton, Michael; Ait-Haddou, Rachid; Calo, Victor Manuel

2017-01-01

We provide explicit quadrature rules for spaces of C1C1 quintic splines with uniform knot sequences over finite domains. The quadrature nodes and weights are derived via an explicit recursion that avoids numerical solvers. Each rule is optimal, that is, requires the minimal number of nodes, for a given function space. For each of nn subintervals, generically, only two nodes are required which reduces the evaluation cost by 2/32/3 when compared to the classical Gaussian quadrature for polynomials over each knot span. Numerical experiments show fast convergence, as nn grows, to the “two-third” quadrature rule of Hughes et al. (2010) for infinite domains.

Sensitivity of root-knot nematodes to gamma irradiation, salinity and plant growth regulator, cycocel

Energy Technology Data Exchange (ETDEWEB)

Sweelam, M E [Econ. Entomology Dept., Fac. Agric. Menoufia University Shebin El-Kom, (Egypt)

1995-10-01

The experiment was carried out at the experimental station of the faculty of agriculture, Menoufia Univ. To determine the sensitivity of root-knot nematode, Meloidogyne Javanica infecting tomato plants exposed to different doses of gamma irradiation 0,20,40,60,80 Gy, salinity levels 0. 1000, 2000, 4000 ppm and the plant growth regulator cycocel 0,200 ppm. Treated seeds were planted clay pots and salinity levels and cycocel concentrations were applied. Fresh weights and nematode populations were computed 3 months after application. Results indicated that 20 Gy, 1000 ppm salinity and cycocel gave the highest fresh weight of shoots and roots. The developmental stages and egg-laying females of nematode decreased by the increasing of irradiation dose and salinity levels. Root-knot galls decreased with 40 and 60 Gy, while significant increase was observed with 0 and 80 Gy, salinity levels decreased root galls. Cycocel decreased nematode population, egg-lying females and root-knot galls.

Sensitivity of root-knot nematodes to gamma irradiation, salinity and plant growth regulator, cycocel

International Nuclear Information System (INIS)

Sweelam, M.E.

1995-01-01

The experiment was carried out at the experimental station of the faculty of agriculture, Menoufia Univ. To determine the sensitivity of root-knot nematode, Meloidogyne Javanica infecting tomato plants exposed to different doses of gamma irradiation 0,20,40,60,80 Gy, salinity levels 0. 1000, 2000, 4000 ppm and the plant growth regulator cycocel 0,200 ppm. Treated seeds were planted clay pots and salinity levels and cycocel concentrations were applied. Fresh weights and nematode populations were computed 3 months after application. Results indicated that 20 Gy, 1000 ppm salinity and cycocel gave the highest fresh weight of shoots and roots. The developmental stages and egg-laying females of nematode decreased by the increasing of irradiation dose and salinity levels. Root-knot galls decreased with 40 and 60 Gy, while significant increase was observed with 0 and 80 Gy, salinity levels decreased root galls. Cycocel decreased nematode population, egg-lying females and root-knot galls

Food, feeding, and refuelling of Red Knots during northward migration at San Antonio Oeste, Rio Negro, Argentina

NARCIS (Netherlands)

Gonzalez, PM; Piersma, T; Verkuil, Y; González, Patricia M.

1996-01-01

We studied the food and feeding ecology of Red Knots Calidris canutus rufa on an area of rocky flat, or restinga, near San Antonio Oeste in the northwest of Golfo San Matias, Provincia de Rio Negro, Argentina in March 1992. These Red Knots are on their way north, from ''wintering'' areas in Tierra

Spermatic Cord Knot: A Clinical Finding in Patients with Spermatic Cord Torsion

Directory of Open Access Journals (Sweden)

Abdullatif Al-Terki

2011-01-01

Full Text Available Pertinent history taking and careful examination often taper the differentials of the acute scrotum; congruently the ability to diagnose acute spermatic cord torsion (SCT when radiological adjuncts are not available is highly imperative. This observational study serves to present a series of 46 cases of spermatic cord torsion whereby we hypothesize the identification of a clinical knot on scrotal examination as an important clinical aid in making a decision to surgical exploration in patients with acute and subacute SCT, especially in centers where imaging resources are unavailable.

PRESENCE OF RED KNOT (CALIDRIS CANUTUS) IN ITE WETLANDS, TACNA, PERU

OpenAIRE

Jhonson K. Vizcarra

2012-01-01

The presence of Red Knot (Calidris canutus, Linnaeus 1758) in Ite Wetlands, Tacna, Peru is documented. Two individuals were observed in October 2011. This species had only one occurrence without details in this area.

Evaluation of potential bio-control agents on root-knot nematode ...

African Journals Online (AJOL)

Indigenous strains of Trichoderma viride (ITCC No. 6889), Pseudomonas fluorescens (ITCC No. B0034) and Purpureocillium lilacinum (ITCC No.6887) were isolated from undisturbed forest eco-system of Southern India. These three bio-mediators were evaluated for their antagonism towards root knot nematode, ...

Meloidogyne luci n. sp. (Nematoda: Meloidogynidae), a root-knot nematode parasitising different crops in Brazil, Chile and Iran

NARCIS (Netherlands)

Carneiro, R.M.D.G.; Correa, V.R.; Almeida, M.R.A.; Gomes, A.C.M.M.; Deimi, A.M.; Castagnone-Sereno, P.; Karssen, G.

2014-01-01

A new root-knot nematode parasitising vegetables, flowers and fruits in Brazil, Iran and Chile, is described as Meloidogyne luci n. sp. The female has an oval to squarish perineal pattern with a low to moderately high dorsal arc and without shoulders, similar to M. ethiopica. The female stylet is

Are There Knots in Chromosomes?

Directory of Open Access Journals (Sweden)

Jonathan T. Siebert

2017-08-01

Full Text Available Recent developments have for the first time allowed the determination of three-dimensional structures of individual chromosomes and genomes in nuclei of single haploid mouse embryonic stem (ES cells based on Hi–C chromosome conformation contact data. Although these first structures have a relatively low resolution, they provide the first experimental data that can be used to study chromosome and intact genome folding. Here we further analyze these structures and provide the first evidence that G1 phase chromosomes are knotted, consistent with the fact that plots of contact probability vs sequence separation show a power law dependence that is intermediate between that of a fractal globule and an equilibrium structure.

Being at the right time at the right place: interpreting the annual life cycle of Afro-Siberian red knots

NARCIS (Netherlands)

Leyrer, J.

2011-01-01

This thesis describes the possible selection pressures acting on survival and, indirectly, on reproduction of Afro-Siberian red knots Calidris canutus canutus while wintering and migrating. Afro-Siberian red knots are long-distance migrants. They travel between the West African wintering areas and

Management of Root Knot Nematode on Tomato through Grafting Root Stock of Solanum sisymbriifolium

Directory of Open Access Journals (Sweden)

Suraj Baidya

2017-05-01

Full Text Available The root-knot nematodes (Meloidogyne spp are difficult to manage once established in the field because of their wide host range, and soil-borne nature. Thus, the aim of the present study was to examine the use of resistant root stock of wild brinjal (Solanum sisymbriifolium to reduce the loss caused by the nematodes on tomato. For the management of root-knot nematodes, grafted plant with resistant root stock of the wild brinjal was tested under farmers’ field conditions at Hemza of Kaski district. Grafted and non-grafted plants were produced in root-knot nematode-free soil. Around three week-old grafted and non-grafted tomato plants were transplanted in four different plastic tunnels where root-knot nematodes had been reported previously. The plants were planted in diagonal position to each other as a pair plot in 80 × 60 cm2 spacing in an average of 20 × 7 m2 plastic tunnels. Galling Index (GI was recorded three times in five randomly selected plants in each plot at 60 days intervals. The first observation was recorded two months after transplanting. Total fruit yield was recorded from same plants. In the grafted plants, the root system was totally free from gall whereas in an average of 7.5 GI in 0-10 scale was recorded in the non-grafted plants. Fruits were harvested from time to time and cumulated after final harvest to calculate the total fruit yield. It was estimated that on an average tomato fruit yield was significantly (P>0.05 increased by 37 percent in the grafted plants compared with the non-grafted plants. Grafting technology could be used effectively for cultivation of commonly grown varieties, which are susceptible to root-knot nematodes in disease prone areas. This can be used as an alternative technology for reducing the use of hazardous pesticides for enhancing commercial organic tomato production.

Rapid identification of cyst (Heterodera spp., Globodera spp.) and root-knot (Meloidogyne spp.) nematodes on the basis of ITS2 sequence variation detected by PCR-single-strand conformational polymorphism (PCR-SSCP) in cultures and field samples

NARCIS (Netherlands)

Clapp, J.P.; Van der Stoel, C.D.; Van der Putten, W.H.

2000-01-01

Cyst and root-knot nematodes show high levels of gross morphological similarity. This presents difficulties for the study of their ecology in natural ecosystems. In this study, cyst and root-knot nematode species, as well as some ectoparasitic nematode species, were identified using the second

Azadirachtin powder for control of root-knot nematodes in tomato

Science.gov (United States)

USDA ARS Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, 64 Nowelo St., Hilo, HI 96720. Root-knot nematodes cause root galling and yield reductions in many vegetable crops, including tomato. Three organic treatments to improve root growth and reduce nematode infestation were eval...

New Ways to Cut through Ethical Gordian Knots.

Science.gov (United States)

Howe, Edmund G

2017-01-01

Clinicians and ethicists routinely encounter complex ethical dilemmas that seem intractable, which have been described as ethical Gordian knots. How can they best assist patients and surrogate decision makers who are entangled in struggles around the capacity to make life-or-death treatment decisions? In this article I describe unconventional and unorthodox approaches to help slice through these dilemmas. Copyright 2017 The Journal of Clinical Ethics. All rights reserved.

Effect of soil solarization using plastic mulch in controlling root-knot ...

African Journals Online (AJOL)

PRECIOUS

2009-12-15

Dec 15, 2009 ... effect of soil solarization using plastic mulch in controlling root-knot nematode infestation and yield of ... addition to their increased toxic effects in the soil over the .... thereby promoting conducive environment for the utiliza- ...

3D visualization software to analyze topological outcomes of topoisomerase reactions

Science.gov (United States)

Darcy, I. K.; Scharein, R. G.; Stasiak, A.

2008-01-01

The action of various DNA topoisomerases frequently results in characteristic changes in DNA topology. Important information for understanding mechanistic details of action of these topoisomerases can be provided by investigating the knot types resulting from topoisomerase action on circular DNA forming a particular knot type. Depending on the topological bias of a given topoisomerase reaction, one observes different subsets of knotted products. To establish the character of topological bias, one needs to be aware of all possible topological outcomes of intersegmental passages occurring within a given knot type. However, it is not trivial to systematically enumerate topological outcomes of strand passage from a given knot type. We present here a 3D visualization software (TopoICE-X in KnotPlot) that incorporates topological analysis methods in order to visualize, for example, knots that can be obtained from a given knot by one intersegmental passage. The software has several other options for the topological analysis of mechanisms of action of various topoisomerases. PMID:18440983

A better way to teach knot tying: a randomized controlled trial comparing the kinesthetic and traditional methods.

Science.gov (United States)

Huang, Emily; Chern, Hueylan; O'Sullivan, Patricia; Cook, Brian; McDonald, Erik; Palmer, Barnard; Liu, Terrence; Kim, Edward

2014-10-01

Knot tying is a fundamental and crucial surgical skill. We developed a kinesthetic pedagogical approach that increases precision and economy of motion by explicitly teaching suture-handling maneuvers and studied its effects on novice performance. Seventy-four first-year medical students were randomized to learn knot tying via either the traditional or the novel "kinesthetic" method. After 1 week of independent practice, students were videotaped performing 4 tying tasks. Three raters scored deidentified videos using a validated visual analog scale. The groups were compared using analysis of covariance with practice knots as a covariate and visual analog scale score (range, 0 to 100) as the dependent variable. Partial eta-square was calculated to indicate effect size. Overall rater reliability was .92. The kinesthetic group scored significantly higher than the traditional group for individual tasks and overall, controlling for practice (all P kinesthetic overall mean was 64.15 (standard deviation = 16.72) vs traditional 46.31 (standard deviation = 16.20; P kinesthetic suture handling substantively improved performance on knot tying. We believe this effect can be extrapolated to more complex surgical skills. Copyright © 2014 Elsevier Inc. All rights reserved.

Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

Directory of Open Access Journals (Sweden)

Zdepski Anna

2011-05-01

Full Text Available Abstract Background High throughput sequencing (HTS technologies have revolutionized the field of genomics by drastically reducing the cost of sequencing, making it feasible for individual labs to sequence or resequence plant genomes. Obtaining high quality, high molecular weight DNA from plants poses significant challenges due to the high copy number of chloroplast and mitochondrial DNA, as well as high levels of phenolic compounds and polysaccharides. Multiple methods have been used to isolate DNA from plants; the CTAB method is commonly used to isolate total cellular DNA from plants that contain nuclear DNA, as well as chloroplast and mitochondrial DNA. Alternatively, DNA can be isolated from nuclei to minimize chloroplast and mitochondrial DNA contamination. Results We describe optimized protocols for isolation of nuclear DNA from eight different plant species encompassing both monocot and eudicot species. These protocols use nuclei isolation to minimize chloroplast and mitochondrial DNA contamination. We also developed a protocol to determine the number of chloroplast and mitochondrial DNA copies relative to the nuclear DNA using quantitative real time PCR (qPCR. We compared DNA isolated from nuclei to total cellular DNA isolated with the CTAB method. As expected, DNA isolated from nuclei consistently yielded nuclear DNA with fewer chloroplast and mitochondrial DNA copies, as compared to the total cellular DNA prepared with the CTAB method. This protocol will allow for analysis of the quality and quantity of nuclear DNA before starting a plant whole genome sequencing or resequencing experiment. Conclusions Extracting high quality, high molecular weight nuclear DNA in plants has the potential to be a bottleneck in the era of whole genome sequencing and resequencing. The methods that are described here provide a framework for researchers to extract and quantify nuclear DNA in multiple types of plants.

Spontaneous knot; a rare cause of ventriculoperitoneal shunt blockage.

LENUS (Irish Health Repository)

Mohammed, Wail

2011-02-01

A 14-year old X linked congenital hydrocephalus presented with unexplained headaches and vomiting. He had external ventricular drain and intracranial pressure monitoring (ICP). Subsequently, he underwent exploration and removal of previously inserted ventriculoperitoneal (VP) shunts. On retrieval of peritoneal catheters a double knot was noted between his two distal catheters. This case illustrates a rare cause of ventriculoperitoneal shunt malfunction.

Spontaneous knot; a rare cause of ventriculoperitoneal shunt blockage.

LENUS (Irish Health Repository)

Mohammed, Wail

2012-02-01

A 14-year old X linked congenital hydrocephalus presented with unexplained headaches and vomiting. He had external ventricular drain and intracranial pressure monitoring (ICP). Subsequently, he underwent exploration and removal of previously inserted ventriculoperitoneal (VP) shunts. On retrieval of peritoneal catheters a double knot was noted between his two distal catheters. This case illustrates a rare cause of ventriculoperitoneal shunt malfunction.

Incidence and Identification of Root-Knot Nematode in Plastic-House Fields of Central Area of Korea

Directory of Open Access Journals (Sweden)

Hyoung Rai Ko

2017-12-01

Full Text Available To investigate occurrence of root-knot nematode (RKN in plastic house of central area of Korea, 132 soil samples were collected in cucumber, water melon, tomato, red pepper and strawberry fields from 2013 to 2015. Among 132 soil samples, 65 soil samples (49% were infested with RKN and mean density of RKN was 178 second-stage juveniles per 100 cm³ soil (min. 1 ~ max. 3,947. The frequency of RKN by regional was the highest in Chuncheon with 80%, followed by Cheonan (68%, Nonsan (36%, Buyeo (33% and Yesan (30%. The frequency of RKN by crops was the highest in tomato with 83%, followed by cucumber (61%, strawberry (41%, red pepper (30%, watermelon (26%. To identify the species of RKN, fifteen populations were selected for representative populations. As a phylogenetic analysis of 15 populations, southern root-knot nematode (Meloidogyne incognita, peanut root-knot nematode (M. arenaria and northern root-knot nematode (M. hapla were identified with 47%, 20% and 33% ratio, respectively. In crops, M. incognita, M. arenaria and M. hapla were detected in tomato, M. incognita and M. arenaria were detected in cucumber and watermelon, and M. hapla was detected in strawberry and lettuce. Thus, there should be a continuous management to major species of each crops to prevent dispersal of RKN damages.

Red Knots (Calidris canutus piersmai and C. c. rogersi) depend on a small threatened staging area in Bohai Bay, China

NARCIS (Netherlands)

Rogers, Danny I.; Yang, Hong-Yan; Hassell, Chris J.; Boyle, Adrian N.; Rogers, Ken G.; Chen, Bing; Zhang, Zheng-Wang; Piersma, Theunis

2010-01-01

We monitored numbers of Red Knots (Calidris canutus) staging in Bohai Bay, China (39 degrees 02'N, 118 degrees 15'E) on northward migration. Knots were identified to subspecies, and we systematically searched for colour-banded birds from the non-breeding grounds. We modelled migratory turnover, and

High-Throughput Block Optical DNA Sequence Identification.

Science.gov (United States)

Sagar, Dodderi Manjunatha; Korshoj, Lee Erik; Hanson, Katrina Bethany; Chowdhury, Partha Pratim; Otoupal, Peter Britton; Chatterjee, Anushree; Nagpal, Prashant

2018-01-01

Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm -1 . Here, surface-enhanced Raman spectroscopy is used to demonstrate label-free identification of DNA nucleobases with multiplexed 3D plasmonic nanofocusing. While nanometer-scale mode volumes prevent identification of single nucleobases within a DNA sequence, the block optical technique can identify A, T, G, and C content in DNA k-mers. The content of each nucleotide in a DNA block can be a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single-letter sequencing. Additionally, coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization. These results pave the way for developing a novel, high-throughput block optical sequencing method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of soil solarization using plastic mulch in controlling root-knot ...

African Journals Online (AJOL)

A field experiment was conducted from February to May, 2004 and 2005 planting seasons at the Vegetable Evaluation and Research Station Farm located at Anse Boileau, Seychelles to evaluate the effect of soil solarization using plastic mulch in controlling root-knot nematode infestation and yield of lettuce.

Possible configuration of two-knot auto-localized exciton in strainless and deformed alkali halide crystals

International Nuclear Information System (INIS)

Dzhumanov, S.; Tulepbergenov, S.K.; Shunkeev, K.Sh.

2002-01-01

In the paper molecular component of two-knot auto-localized exciton (TALE) occupying centrosymmetric state in alkali halide crystal cubic lattice with local D 2h symmetry is considered. In is suggested that the symmetry lowering of forming small radius auto-localized exciton (ALE) is realizing in order configuration transformation by the scenario: multi-knot continual ALE (with O h symmetry)→six-halide ALE (with O h symmetry)→TALE (with O h symmetry) or by the scenario O h →D 2h . Then for TALE with local D 2h symmetry normal molecular ion shifts are considered as well

Intraurethral knot in a very-low-birth-weight infant: radiological recognition, surgical management and prevention

International Nuclear Information System (INIS)

Lodha, Abhay; Ly, Linh; McNamara, Patrick J.; Brindle, Mary; Daneman, Alan

2005-01-01

We report a case where a knot developed in a urinary catheter and became lodged within the urethra of a very-low-birth-weight (VLBW) preterm infant. The catheter was removed with the assistance of a urologist. We recommend using caution when placing urinary catheters in VLBW infants and question the appropriateness of feeding tubes as catheters. Recognition on radiographs of malpositioned bladder catheters is vital to the care of these patients. All staff involved in the insertion, maintenance or removal of these catheters should be suitably trained to minimize the risk of knots and related complications. (orig.)

Supporting Third Year Medical Students' Skill Acquisition and Self-Efficacy with Coping Models and Process Feedback during Laparoscopic Knot Tying Simulation.

Science.gov (United States)

Dempsey, Michael S; Kauffman, Douglas F

2017-01-01

Background: During the third year general surgery clerkship, medical students are required to develop laparoscopic knot-tying skills. Knot-tying skills studies often rely on objective variables (e.g., time, materials used, number of iterations) that lend themselves to correlational analysis of pre- and post-intervention skill level. This study differs by examining how instructional interventions-role modeling and feedback-affect medical students' skill acquisition and self-efficacy during a laparoscopic surgical simulation training session. Methods: Seventy-eight surgical clerkship students were assigned randomly to one cell of a 2X2 factorial design. Participants observed one of two types of role modeling (expert vs. coping) and received either process-oriented or outcome-oriented feedback during a 30-min laparoscopic training session. Participants also completed several surveys that assessed their interest in surgery and their self-efficacy for laparoscopic knot tying. Results: Coping model groups tended to perform better on the knot tying task, though this was less the case in the presence of outcome feedback. Expert model groups slightly outperformed the coping model group on the peg transfer task, but in the presence of outcome feedback they reported the lowest satisfaction with their performance and the lowest self-efficacy for the knot tying task. The coping model combined with process feedback had a positive influence on students' efficiency in learning the task, on their satisfaction with their performance, and on their self-efficacy for laparoscopic knot typing. Conclusions: Results are discussed relative to self-regulated learning theory.

Evaluation of edible ginger and turmeric cultivars for root-knot nematode resistance

Science.gov (United States)

Edible ginger and turmeric roots are important agricultural commodities for the State of Hawaii. Bacterial wilt, Ralstonia solanacearum, and root-knot nematodes, Meloidogyne spp. are major factors hindering optimum production. An evaluation of tolerance and resistance to M. incognita was undertake...

PROPER MOTIONS OF THE OUTER KNOTS OF THE HH 80/81/80N RADIO-JET

Energy Technology Data Exchange (ETDEWEB)

Masqué, Josep M.; Rodriguez, Luis F.; Carrasco-González, Carlos [Instituto de Radioastronomía y Astrofísica, Universidad Nacional Autónoma de México, Morelia 58089, México (Mexico); Araudo, Anabella [University of Oxford, Astrophysics, Keble Road, Oxford OX1 3RH (United Kingdom); Estalella, Robert [Departament d’Astronomia i Meteorologia and Institut de Ciències del Cosmos (IEEC-UB), Universitat de Barcelona, Martí i Franquès 1, E-08028 Barcelona, Catalunya (Spain); Anglada, Guillem; Osorio, Mayra [Instituto de Astrofísica de Andalucía (CSIC), Apartado 3004, E-18080 Granada (Spain); Girart, Josep M. [Institut de Ciències de l’Espai (CSIC-IEEC), Campus UAB, Carrer de Can Magrans, S/N, E-08193 Cerdanyola del Vallès, Catalunya (Spain)

2015-11-20

The radio-knots of the Herbig–Haro (HH) 80/81/80N jet extend from the HH 80 object to the recently discovered Source 34 and has a total projected jet size of 10.3 pc, constituting the largest collimated radio-jet system known so far. It is powered by the bright infrared source IRAS 18162−2048 associated with a massive young stellar object. We report 6 cm JVLA observations that, compared with previous 6 cm VLA observations carried out in 1989, allow us to derive proper motions of the HH 80, HH 81, and HH 80N radio knots located about 2.5 pc away in projection from the powering source. For the first time, we measure proper motions of the optically obscured HH 80N object providing evidence that this knot, along with HH 81 and HH 80 are associated with the same radio-jet. We also confirm the presence of Source 34, located further north of HH 80N, previously proposed to belong to the jet.We derived that the tangential velocity of HH 80N is 260 km s{sup −1} and has a direction in agreement with the expected direction of a ballistic precessing jet. The HH 80 and HH 81 objects have tangential velocities of 350 and 220 km s{sup −1}, respectively, but their directions are somewhat deviated from the expected jet path. The velocities of the HH objects studied in this work are significantly lower than those derived for the radio knots of the jet close to the powering source (600–1400 km s{sup −1}) suggesting that the jet is slowing down due to a strong interaction with the ambient medium. As a result, since HH 80 and HH 81 are located near the edge of the cloud, the inhomogeneous and low density medium may contribute to skew the direction of their determined proper motions. The HH 80 and HH 80N emission at 6 cm is, at least in part, probably synchrotron radiation produced by relativistic electrons in a magnetic field of 1 mG. If these electrons are accelerated in a reverse adiabatic shock, we estimate a jet total density of ≲1000 cm{sup −3}. All of these

extraction of high quality dna from polysaccharides-secreting ...

African Journals Online (AJOL)

cistvr

A DNA extraction method using CTAB was used for the isolation of genomic DNA from ten. Xanthomonas campestris pathovars, ten isolates of Xanthomonas albilineans and one isolate of. Pseudomonas rubrisubalbicans. High quality DNA was obtained that was ideal for molecular analy- ses. Extracellular polysaccharides ...

Replication of kinetoplast minicircle DNA

International Nuclear Information System (INIS)

Sheline, C.T.

1989-01-01

These studies describe the isolation and characterization of early minicircle replication intermediates from Crithidia fasciculata, and Leishmania tarentolae, the mitochondrial localization of a type II topoisomerase (TIImt) in C. fasciculata, and the implication of the aforementioned TIImt in minicircle replication in L. tarentolae. Early minicircle replication intermediates from C. fasciculata were identified and characterized using isolated kinetoplasts to incorporate radiolabeled nucleotides into its DNA. The pulse-label in an apparent theta-type intermediate chase into two daughter molecules. A uniquely gapped, ribonucleotide primed, knotted molecule represents the leading strand in the model proposed, and a highly gapped molecule represents the lagging strand. This theta intermediate is repaired in vitro to a doubly nicked catenated dimer which was shown to result from the replication of a single parental molecule. Very similar intermediates were found in the heterogeneous population of minicircles of L. tarentolae. The sites of the Leishmania specific discontinuities were mapped and shown to lie within the universally conserved sequence blocks in identical positions as compared to C. fasciculata and Trypanosoma equiperdum

High resolution optical DNA mapping

Science.gov (United States)

Baday, Murat

Many types of diseases including cancer and autism are associated with copy-number variations in the genome. Most of these variations could not be identified with existing sequencing and optical DNA mapping methods. We have developed Multi-color Super-resolution technique, with potential for high throughput and low cost, which can allow us to recognize more of these variations. Our technique has made 10--fold improvement in the resolution of optical DNA mapping. Using a 180 kb BAC clone as a model system, we resolved dense patterns from 108 fluorescent labels of two different colors representing two different sequence-motifs. Overall, a detailed DNA map with 100 bp resolution was achieved, which has the potential to reveal detailed information about genetic variance and to facilitate medical diagnosis of genetic disease.

Intravesical knotting of feeding tube used as urinary catheter in an infant

Directory of Open Access Journals (Sweden)

Mamatha Basavaraju

2016-09-01

Full Text Available Infant feeding tube is commonly used to temporarily drain the bladder in pediatric population. A case is described where the tube got knotted inside the bladder probably due to over insertion or bladder spasm caused by irritation of catheter.

Explorations in topology map coloring, surfaces and knots

CERN Document Server

Gay, David

2013-01-01

Explorations in Topology, Second Edition, provides students a rich experience with low-dimensional topology (map coloring, surfaces, and knots), enhances their geometrical and topological intuition, empowers them with new approaches to solving problems, and provides them with experiences that will help them make sense of future, more formal topology courses. The book's innovative story-line style models the problem-solving process, presents the development of concepts in a natural way, and engages students in meaningful encounters with the material. The updated end-of-chapter investigation

Recent Advancements in DNA Damage-Transcription Crosstalk and High-Resolution Mapping of DNA Breaks.

Science.gov (United States)

Vitelli, Valerio; Galbiati, Alessandro; Iannelli, Fabio; Pessina, Fabio; Sharma, Sheetal; d'Adda di Fagagna, Fabrizio

2017-08-31

Until recently, DNA damage arising from physiological DNA metabolism was considered a detrimental by-product for cells. However, an increasing amount of evidence has shown that DNA damage could have a positive role in transcription activation. In particular, DNA damage has been detected in transcriptional elements following different stimuli. These physiological DNA breaks are thought to be instrumental for the correct expression of genomic loci through different mechanisms. In this regard, although a plethora of methods are available to precisely map transcribed regions and transcription start sites, commonly used techniques for mapping DNA breaks lack sufficient resolution and sensitivity to draw a robust correlation between DNA damage generation and transcription. Recently, however, several methods have been developed to map DNA damage at single-nucleotide resolution, thus providing a new set of tools to correlate DNA damage and transcription. Here, we review how DNA damage can positively regulate transcription initiation, the current techniques for mapping DNA breaks at high resolution, and how these techniques can benefit future studies of DNA damage and transcription.

Highly efficient DNA extraction method from skeletal remains

Directory of Open Access Journals (Sweden)

Irena Zupanič Pajnič

2011-03-01

Full Text Available Background: This paper precisely describes the method of DNA extraction developed to acquire high quality DNA from the Second World War skeletal remains. The same method is also used for molecular genetic identification of unknown decomposed bodies in routine forensic casework where only bones and teeth are suitable for DNA typing. We analysed 109 bones and two teeth from WWII mass graves in Slovenia. Methods: We cleaned the bones and teeth, removed surface contaminants and ground the bones into powder, using liquid nitrogen . Prior to isolating the DNA in parallel using the BioRobot EZ1 (Qiagen, the powder was decalcified for three days. The nuclear DNA of the samples were quantified by real-time PCR method. We acquired autosomal genetic profiles and Y-chromosome haplotypes of the bones and teeth with PCR amplification of microsatellites, and mtDNA haplotypes 99. For the purpose of traceability in the event of contamination, we prepared elimination data bases including genetic profiles of the nuclear and mtDNA of all persons who have been in touch with the skeletal remains in any way. Results: We extracted up to 55 ng DNA/g of the teeth, up to 100 ng DNA/g of the femurs, up to 30 ng DNA/g of the tibias and up to 0.5 ng DNA/g of the humerus. The typing of autosomal and YSTR loci was successful in all of the teeth, in 98 % dekalof the femurs, and in 75 % to 81 % of the tibias and humerus. The typing of mtDNA was successful in all of the teeth, and in 96 % to 98 % of the bones. Conclusions: We managed to obtain nuclear DNA for successful STR typing from skeletal remains that were over 60 years old . The method of DNA extraction described here has proved to be highly efficient. We obtained 0.8 to 100 ng DNA/g of teeth or bones and complete genetic profiles of autosomal DNA, Y-STR haplotypes, and mtDNA haplotypes from only 0.5g bone and teeth samples.

Percutaneous untying of a knot in a retained Swan-Ganz catheter

International Nuclear Information System (INIS)

Bhatti, Waqar A.; Sinha, Sankar; Rowlands, Peter

2000-01-01

A patient was referred to us with a tightly knotted Swan-Ganz catheter. The catheter could not be removed by conventional simple methods. We describe a minimally invasive means of removal of the catheter using an Amplatz gooseneck snare and an angioplasty balloon. This allowed the Catheter to be removed without trauma.

Habitat use by Red Knots (Calidris canutus rufa): Experiments with oyster racks and reefs on the beach and intertidal of Delaware Bay, New Jersey

Science.gov (United States)

Burger, Joanna; Niles, Lawrence J.

2017-07-01

Sea level rise and increasing human activities have decreased intertidal habitat in many places in the world. The expansion of aquaculture in intertidal areas may impact birds and other organisms using these habitats, leading to questions of sustainability of both aquaculture and functioning estuarine ecosystems. Understanding the effect of oyster culture on shorebird activity, particularly on Red Knots (Calidris canutus rufa), a species on the U.S. Threatened List, is important for adaptive management and the expansion of oyster culture. In May 2013 we experimentally compared Red Knot and shorebird use of a beach section with racks and a control, and in 2016 we compared the use of sections with artificial reefs, oyster racks, and control on Delaware Bay, New Jersey (USA). The data included only times when no workers or other people were present. Censuses, conducted every 30 min throughout the day (279 censuses in 2013, 231 censuses in 2016), included the number of Red Knots and other shorebirds in each treatment section. In 2013, the total number of shorebirds was significantly higher in the rack section than in the control section, except for Red Knots and Ruddy Turnstones (Arenaria interpres) that occurred in higher numbers in the control than in the rack section. In 2016 Red Knot numbers were also significantly lower in the rack section. In 2013, the mean number of Red Knots/census was 13 for racks vs 59 for the control (P racks and over 68 for other treatments (P racks while both foraging and roosting, suggesting that caution should be used before placing oyster racks in areas used for foraging by Red Knots.

Direct Detection of the Helical Magnetic Field Geometry from 3D Reconstruction of Prominence Knot Trajectories

Science.gov (United States)

Zapiór, Maciej; Martínez-Gómez, David

2016-02-01

Based on the data collected by the Vacuum Tower Telescope located in the Teide Observatory in the Canary Islands, we analyzed the three-dimensional (3D) motion of so-called knots in a solar prominence of 2014 June 9. Trajectories of seven knots were reconstructed, giving information of the 3D geometry of the magnetic field. Helical motion was detected. From the equipartition principle, we estimated the lower limit of the magnetic field in the prominence to ≈1-3 G and from the Ampère’s law the lower limit of the electric current to ≈1.2 × 109 A.

Construction of Orthonormal Piecewise Polynomial Scaling and Wavelet Bases on Non-Equally Spaced Knots

Directory of Open Access Journals (Sweden)

Jean Pierre Astruc

2007-01-01

Full Text Available This paper investigates the mathematical framework of multiresolution analysis based on irregularly spaced knots sequence. Our presentation is based on the construction of nested nonuniform spline multiresolution spaces. From these spaces, we present the construction of orthonormal scaling and wavelet basis functions on bounded intervals. For any arbitrary degree of the spline function, we provide an explicit generalization allowing the construction of the scaling and wavelet bases on the nontraditional sequences. We show that the orthogonal decomposition is implemented using filter banks where the coefficients depend on the location of the knots on the sequence. Examples of orthonormal spline scaling and wavelet bases are provided. This approach can be used to interpolate irregularly sampled signals in an efficient way, by keeping the multiresolution approach.

Molecular Dynamics Simulation of High Density DNA Arrays

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Rudolf Podgornik

2018-01-01

Full Text Available Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and

Basal metabolic rate declines during long-distance migratory flight in great knots

NARCIS (Netherlands)

Battley, PF; Dekinga, A; Dietz, MW; Piersma, T; Tang, SX; Hulsman, K; Battley, Phil F.; Tang, Sixian

2001-01-01

Great Knots (Calidris tenuirostris) make one of the longest migratory flights in the avian world, flying almost 5500 km from Australia to China during northward migration. We measured basal metabolic rate (BMR) and body composition in birds before and after this flight and found that BMR decreased

The geometry of periodic knots, polycatenanes and weaving from a chemical perspective: a library for reticular chemistry.

Science.gov (United States)

Liu, Yuzhong; O'Keeffe, Michael; Treacy, Michael M J; Yaghi, Omar M

2018-05-04

The geometry of simple knots and catenanes is described using the concept of linear line segments (sticks) joined at corners. This is extended to include woven linear threads as members of the extended family of knots. The concept of transitivity that can be used as a measure of regularity is explained. Then a review is given of the simplest, most 'regular' 2- and 3-periodic patterns of polycatenanes and weavings. Occurrences in crystal structures are noted but most structures are believed to be new and ripe targets for designed synthesis.

A Novel Low Temperature PCR Assured High-Fidelity DNA Amplification

Directory of Open Access Journals (Sweden)

Shaoxia Zhou

2013-06-01

Full Text Available As previously reported, a novel low temperature (LoTemp polymerase chain reaction (PCR catalyzed by a moderately heat-resistant (MHR DNA polymerase with a chemical-assisted denaturation temperature set at 85 °C instead of the conventional 94–96 °C can achieve high-fidelity DNA amplification of a target DNA, even after up to 120 PCR thermal cycles. Furthermore, such accurate amplification is not achievable with conventional PCR. Now, using a well-recognized L1 gene segment of the human papillomavirus (HPV type 52 (HPV-52 as the template for experiments, we demonstrate that the LoTemp high-fidelity DNA amplification is attributed to an unusually high processivity and stability of the MHR DNA polymerase whose high fidelity in template-directed DNA synthesis is independent of non-existent 3'–5' exonuclease activity. Further studies and understanding of the characteristics of the LoTemp PCR technology may facilitate implementation of DNA sequencing-based diagnostics at the point of care in community hospital laboratories.

Theory of high-force DNA stretching and overstretching.

Science.gov (United States)

Storm, C; Nelson, P C

2003-05-01

Single-molecule experiments on single- and double-stranded DNA have sparked a renewed interest in the force versus extension of polymers. The extensible freely jointed chain (FJC) model is frequently invoked to explain the observed behavior of single-stranded DNA, but this model does not satisfactorily describe recent high-force stretching data. We instead propose a model (the discrete persistent chain) that borrows features from both the FJC and the wormlike chain, and show that it resembles the data more closely. We find that most of the high-force behavior previously attributed to stretch elasticity is really a feature of the corrected entropic elasticity; the true stretch compliance of single-stranded DNA is several times smaller than that found by previous authors. Next we elaborate our model to allow coexistence of two conformational states of DNA, each with its own stretch and bend elastic constants. Our model is computationally simple and gives an excellent fit through the entire overstretching transition of nicked, double-stranded DNA. The fit gives the first value for the bend stiffness of the overstretched state. In particular, we find the effective bend stiffness for DNA in this state to be about 12 nm k(B)T, a value quite different from either the B-form or single-stranded DNA.

Diversity of Knot Solitons in Liquid Crystals Manifested by Linking of Preimages in Torons and Hopfions

Science.gov (United States)

Ackerman, Paul J.; Smalyukh, Ivan I.

2017-01-01

Topological solitons are knots in continuous physical fields classified by nonzero Hopf index values. Despite arising in theories that span many branches of physics, from elementary particles to condensed matter and cosmology, they remain experimentally elusive and poorly understood. We introduce a method of experimental and numerical analysis of such localized structures in liquid crystals that, similar to the mathematical Hopf maps, relates all points of the medium's order parameter space to their closed-loop preimages within the three-dimensional solitons. We uncover a surprisingly large diversity of naturally occurring and laser-generated topologically nontrivial solitons with differently knotted nematic fields, which previously have not been realized in theories and experiments alike. We discuss the implications of the liquid crystal's nonpolar nature on the knot soliton topology and how the medium's chirality, confinement, and elastic anisotropy help to overcome the constraints of the Hobart-Derrick theorem, yielding static three-dimensional solitons without or with additional defects. Our findings will establish chiral nematics as a model system for experimental exploration of topological solitons and may impinge on understanding of such nonsingular field configurations in other branches of physics, as well as may lead to technological applications.

DIRECT DETECTION OF THE HELICAL MAGNETIC FIELD GEOMETRY FROM 3D RECONSTRUCTION OF PROMINENCE KNOT TRAJECTORIES

Energy Technology Data Exchange (ETDEWEB)

Zapiór, Maciej; Martinez-Gómez, David, E-mail: zapior.maciek@gmail.com [Physics Department, University of the Balearic Islands, Cra. de Valldemossa, km 7.5. Palma (Illes Balears), E-07122 (Spain)

2016-02-01

Based on the data collected by the Vacuum Tower Telescope located in the Teide Observatory in the Canary Islands, we analyzed the three-dimensional (3D) motion of so-called knots in a solar prominence of 2014 June 9. Trajectories of seven knots were reconstructed, giving information of the 3D geometry of the magnetic field. Helical motion was detected. From the equipartition principle, we estimated the lower limit of the magnetic field in the prominence to ≈1–3 G and from the Ampère’s law the lower limit of the electric current to ≈1.2 × 10{sup 9} A.

BUBBLES AND KNOTS IN THE KINEMATICAL STRUCTURE OF THE BIPOLAR PLANETARY NEBULA NGC 2818

Energy Technology Data Exchange (ETDEWEB)

Vazquez, Roberto, E-mail: vazquez@astro.unam.mx [Instituto de Astronomia, Universidad Nacional Autonoma de Mexico, Km 103 Carretera Tijuana-Ensenada, 22860 Ensenada, BC (Mexico)

2012-06-01

High-resolution Hubble Space Telescope archive imaging and high-dispersion spectroscopy are used to study the complex morphological and kinematical structure of the planetary nebula, NGC 2818. We analyze narrowband H{alpha}, [O III], [N II], [S II], and He II images, addressing important morphological features. Ground-based long-slit echelle spectra were obtained crossing NGC 2818 at five different positions to precisely determine kinematical features in the structure of the nebula. A distance of 2.5 kpc was used to determine physical scales. Constructing models to fit the data with modern computational tools, we find NGC 2818 is composed of (1) a non-uniform bipolar structure with a semimajor axis of 0.92 pc (75''), possibly deformed by the stellar wind, (2) a 0.17 pc (14'') diameter central region, which is potentially the remnant of an equatorial enhancement, and (3) a great number of cometary knots. These knots are preferentially located inside a radius of 0.24 pc (20'') around the central star. The major axis of the main structure is oriented at i {approx_equal} 60 Degree-Sign with respect to the line of sight and at P.A. = +89 Degree-Sign on the plane of the sky. Expansion velocities of this nebula are V{sub pol} = 105 km s{sup -1} and V{sub eq} = 20 km s{sup -1}, which lead to our estimate of the kinematical age of {tau}{sub k} {approx_equal} 8400 {+-} 3400 yr (assuming homologous expansion). Our observations do not support the idea that high-velocity collimated ejections are responsible for the formation of microstructures inside the nebula. We determine the systemic velocity of NGC 2818 to be V{sub HEL} = +26 {+-} 2 km s{sup -1}.

Lipofection: a highly efficient, lipid-mediated DNA-transfection procedure.

OpenAIRE

Felgner, P L; Gadek, T R; Holm, M; Roman, R; Chan, H W; Wenz, M; Northrop, J P; Ringold, G M; Danielsen, M

1987-01-01

A DNA-transfection protocol has been developed that makes use of a synthetic cationic lipid, N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA). Small unilamellar liposomes containing DOTMA interact spontaneously with DNA to form lipid-DNA complexes with 100% entrapment of the DNA, DOTMA facilitates fusion of the complex with the plasma membrane of tissue culture cells, resulting in both uptake and expression of the DNA. The technique is simple, highly reproducible, and eff...

First report of the root-knot nematode Meloidogyne marylandi on Turfgrasses in Israel

NARCIS (Netherlands)

Oka, Y.; Karssen, G.; Mor, M.

2004-01-01

In a turfgrass nursery in Arava, Israel, a population of root-knot nematodes was isolated from poorly growing Zoysiagrass (Zoysia japonica Steud.) with symptoms of foliar chlorosis and roots with very small, smooth galls and protruding egg masses. The isolated population (genus Meloidogyne) included

Antagonistic Activities of Streptomyces against Root Knot Nematode of Kiwifruit

Directory of Open Access Journals (Sweden)

S. Bashiri

2016-02-01

Full Text Available Introduction: Iran is among the world leading kiwifruit producers with 2.816 ha cultivated and 31.567 tones production. Plant parasitic nematodes cause damages to a variety of agricultural crops throughout the world. Interest in biological control of nematodes has increased because of the need for alternative methods to fumigant and non-fumigant nematicides and overall improvement of IPM programs. Bacterial species with nematicidal activity have also been used with some success for controlling root-knot diseases, including Streptomyces spp., Serratia spp., Bacillus spp. and Pseudomonas spp. The goal of the current study was to isolate, identify and investigate the potential of local Streptomyces bacteria for controlling and reducing root-knot nematode population in the north of Iran. Materials and Methods: In order to evaluate the effect of antagonistic bacteria on control of root-knot nematode of Kiwifruit, 100 isolates of bacteria were collected from Kiwifruit rhizosphere in the north of Iran and screened for pigmented microorganisms especially Streptomyces by applying standard serial dilution plate technique, using starch casein nitrate agar and glycerol asparagine agar. Morphological characterizations were achieved by the microscopic method. The microscopic characterization was done by cover slip culture method. The mycelium structure, color and arrangement of conidiospore and arthrospore on the mycelium were observed through the oil immersion (100X. The observed structure was compared with Bergey’s Manual of Determinative Bacteriology and the organism was identified. Various biochemical tests performed for the identification of the potent isolates are as follows: casein hydrolysis, starch hydrolysis, urea hydrolysis, esculin hydrolysis, acid production from sugar, NaCl resistance, temperature tolerance. Soil samples (100g were collected, and then processed for nematode egg and larvae extraction Hussey method. The suspension was pipetted

High-speed detection of DNA translocation in nanopipettes

Science.gov (United States)

Fraccari, Raquel L.; Ciccarella, Pietro; Bahrami, Azadeh; Carminati, Marco; Ferrari, Giorgio; Albrecht, Tim

2016-03-01

We present a high-speed electrical detection scheme based on a custom-designed CMOS amplifier which allows the analysis of DNA translocation in glass nanopipettes on a microsecond timescale. Translocation of different DNA lengths in KCl electrolyte provides a scaling factor of the DNA translocation time equal to p = 1.22, which is different from values observed previously with nanopipettes in LiCl electrolyte or with nanopores. Based on a theoretical model involving electrophoresis, hydrodynamics and surface friction, we show that the experimentally observed range of p-values may be the result of, or at least be affected by DNA adsorption and friction between the DNA and the substrate surface.We present a high-speed electrical detection scheme based on a custom-designed CMOS amplifier which allows the analysis of DNA translocation in glass nanopipettes on a microsecond timescale. Translocation of different DNA lengths in KCl electrolyte provides a scaling factor of the DNA translocation time equal to p = 1.22, which is different from values observed previously with nanopipettes in LiCl electrolyte or with nanopores. Based on a theoretical model involving electrophoresis, hydrodynamics and surface friction, we show that the experimentally observed range of p-values may be the result of, or at least be affected by DNA adsorption and friction between the DNA and the substrate surface. Electronic supplementary information (ESI) available: Gel electrophoresis confirming lengths and purity of DNA samples, comparison between Axopatch 200B and custom-built setup, comprehensive low-noise amplifier characterization, representative I-V curves of nanopipettes used, typical scatter plots of τ vs. peak amplitude for the four LDNA's used, table of most probable τ values, a comparison between different fitting models for the DNA translocation time distribution, further details on the stochastic numerical simulation of the scaling statistics and the derivation of the extended

Explicit Gaussian quadrature rules for C^1 cubic splines with symmetrically stretched knot sequence

KAUST Repository

Ait-Haddou, Rachid; Barton, Michael; Calo, Victor M.

2015-01-01

We provide explicit expressions for quadrature rules on the space of C^1 cubic splines with non-uniform, symmetrically stretched knot sequences. The quadrature nodes and weights are derived via an explicit recursion that avoids an intervention

Analysis of Gene expression in soybean (Glycine max roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways

Directory of Open Access Journals (Sweden)

Gamal El-Din Abd El Kader Y

2011-05-01

Full Text Available Abstract Background Root-knot nematodes are sedentary endoparasites that can infect more than 3000 plant species. Root-knot nematodes cause an estimated $100 billion annual loss worldwide. For successful establishment of the root-knot nematode in its host plant, it causes dramatic morphological and physiological changes in plant cells. The expression of some plant genes is altered by the nematode as it establishes its feeding site. Results We examined the expression of soybean (Glycine max genes in galls formed in roots by the root-knot nematode, Meloidogyne incognita, 12 days and 10 weeks after infection to understand the effects of infection of roots by M. incognita. Gene expression was monitored using the Affymetrix Soybean GeneChip containing 37,500 G. max probe sets. Gene expression patterns were integrated with biochemical pathways from the Kyoto Encyclopedia of Genes and Genomes using PAICE software. Genes encoding enzymes involved in carbohydrate and cell wall metabolism, cell cycle control and plant defense were altered. Conclusions A number of different soybean genes were identified that were differentially expressed which provided insights into the interaction between M. incognita and soybean and into the formation and maintenance of giant cells. Some of these genes may be candidates for broadening plants resistance to root-knot nematode through over-expression or silencing and require further examination.

The impact of solarisation integrated with plant bio-fermentation on root knot nematodes

International Nuclear Information System (INIS)

Ibrahim, S. K.; Traboulsi, A. F.

2009-01-01

The impact of different freshly/dried chopped medicinal or aromatic plant materials as an organic amendment in pot cultures, as well as integrated with solarisation under greenhouse conditions on the root knot nematodes population was evaluated. Results indicated that application of solarisation alone gave good control (72%) but when integrated with different plant materials, the control level increased to 95% with Allium sativum and 90% with Mentha microphylla and slightly less with other plant materials which ranged from75 to 80%. The results of pot experiments revealed that the most significant effect on the number of nematodes was achieved with Tagetes patula followed by Pimpinella anisum, Melia azadirach and Origanium syriacum reaching 0.0, 1.2, 1.2 and 2.5/g of roots, respectively. Total control was obtained with Allium sativum. Origanium syriacum contained the highest amount of essential oil (6%). Results obtained indicated that integrated approach using solarisation combined with plant materials could be the best alternative control for the root-knot nematodes. (author)

HOMFLY for twist knots and exclusive Racah matrices in representation [333

Science.gov (United States)

Morozov, A.

2018-03-01

Next step is reported in the program of Racah matrices extraction from the differential expansion of HOMFLY polynomials for twist knots: from the double-column rectangular representations R = [ rr ] to a triple-column and triple-hook R = [ 333 ]. The main new phenomenon is the deviation of the particular coefficient f[ 332 ][ 21 ] from the corresponding skew dimension, what opens a way to further generalizations.

X-RAY RADIATION MECHANISMS AND BEAMING EFFECT OF HOT SPOTS AND KNOTS IN ACTIVE GALACTIC NUCLEAR JETS

International Nuclear Information System (INIS)

Zhang Jin; Bai, J. M.; Chen Liang; Liang Enwei

2010-01-01

The observed radio-optical-X-ray spectral energy distributions (SEDs) of 22 hot spots and 45 knots in the jets of 35 active galactic nuclei are complied from the literature and modeled with single-zone lepton models. It is found that the observed luminosities at 5 GHz (L 5 G Hz ) and at 1 keV (L 1 k eV ) are tightly correlated, and the two kinds of sources can be roughly separated with a division of L 1 k eV = L 5 G Hz . Our SED fits show that the mechanisms of the X-rays are diverse. While the X-ray emission of a small fraction of the sources is a simple extrapolation of the synchrotron radiation for the radio-to-optical emission, an inverse Compton (IC) scattering component is necessary to model the X-rays for most of the sources. Considering the sources at rest (the Doppler factor δ = 1), the synchrotron-self-Compton (SSC) scattering would dominate the IC process. This model can interpret the X-rays of some hot spots with a magnetic field strength (B δ= 1 ssc ) being consistent with the equipartition magnetic field (B δ= 1 eq ) in 1 order of magnitude, but an unreasonably low B δ= 1 ssc is required to model the X-rays for all knots. Measuring the deviation between B δ= 1 ssc and B δ= 1 eq with ratio R B ≡ B δ= 1 eq /B δ= 1 ssc , we find that R B is greater than 1 and it is tightly anti-correlated with ratio R L ≡ L 1 k eV /L 5 G Hz for both the knots and the hot spots. We propose that the deviation may be due to the neglect of the relativistic bulk motion for these sources. Considering this effect, the IC/cosmic microwave background (CMB) component would dominate the IC process. We show that the IC/CMB model well explains the X-ray emission for most sources under the equipartition condition. Although the derived beaming factor (δ) and co-moving equipartition magnetic field (B' eq ) of some hot spots are comparable to the knots, the δ values of the hot spots tend to be smaller and their B' eq values tend to be larger than that of the knots, favoring

Root-Knot and Cyst Nematodes Activate Procambium-Associated Genes in Arabidopsis Roots

Directory of Open Access Journals (Sweden)

Yasuka L. Yamaguchi

2017-07-01

Full Text Available Developmental plasticity is one of the most striking features of plant morphogenesis, as plants are able to vary their shapes in response to environmental cues. Biotic or abiotic stimuli often promote organogenesis events in plants not observed under normal growth conditions. Root-knot nematodes (RKNs are known to parasitize multiple species of rooting plants and to induce characteristic tissue expansion called galls or root-knots on the roots of their hosts by perturbing the plant cellular machinery. Galls contain giant cells (GCs and neighboring cells, and the GCs are a source of nutrients for the parasitizing nematode. Highly active cell proliferation was observed in galls. However, the underlying mechanisms that regulate the symptoms triggered by the plant-nematode interaction have not yet been elucidated. In this study, we deciphered the molecular mechanism of gall formation with an in vitro infection assay system using RKN Meloidogyne incognita, and the model plant Arabidopsis thaliana. By taking advantages of this system, we performed next-generation sequencing-based transcriptome profiling, and found that the expression of procambium identity-associated genes were enriched during gall formation. Clustering analyses with artificial xylogenic systems, together with the results of expression analyses of the candidate genes, showed a significant correlation between the induction of gall cells and procambium-associated cells. Furthermore, the promoters of several procambial marker genes such as ATHB8, TDR and WOX4 were activated not only in M. incognita-induced galls, but similarly in M. javanica induced-galls and Heterodera schachtii-induced syncytia. Our findings suggest that phytoparasitic nematodes modulate the host’s developmental regulation of the vascular stem cells during gall formation.

Root-Knot and Cyst Nematodes Activate Procambium-Associated Genes in Arabidopsis Roots.

Science.gov (United States)

Yamaguchi, Yasuka L; Suzuki, Reira; Cabrera, Javier; Nakagami, Satoru; Sagara, Tomomi; Ejima, Chika; Sano, Ryosuke; Aoki, Yuichi; Olmo, Rocio; Kurata, Tetsuya; Obayashi, Takeshi; Demura, Taku; Ishida, Takashi; Escobar, Carolina; Sawa, Shinichiro

2017-01-01

Developmental plasticity is one of the most striking features of plant morphogenesis, as plants are able to vary their shapes in response to environmental cues. Biotic or abiotic stimuli often promote organogenesis events in plants not observed under normal growth conditions. Root-knot nematodes (RKNs) are known to parasitize multiple species of rooting plants and to induce characteristic tissue expansion called galls or root-knots on the roots of their hosts by perturbing the plant cellular machinery. Galls contain giant cells (GCs) and neighboring cells, and the GCs are a source of nutrients for the parasitizing nematode. Highly active cell proliferation was observed in galls. However, the underlying mechanisms that regulate the symptoms triggered by the plant-nematode interaction have not yet been elucidated. In this study, we deciphered the molecular mechanism of gall formation with an in vitro infection assay system using RKN Meloidogyne incognita , and the model plant Arabidopsis thaliana. By taking advantages of this system, we performed next-generation sequencing-based transcriptome profiling, and found that the expression of procambium identity-associated genes were enriched during gall formation. Clustering analyses with artificial xylogenic systems, together with the results of expression analyses of the candidate genes, showed a significant correlation between the induction of gall cells and procambium-associated cells. Furthermore, the promoters of several procambial marker genes such as ATHB8 , TDR and WOX4 were activated not only in M. incognita -induced galls, but similarly in M. javanica induced-galls and Heterodera schachtii -induced syncytia. Our findings suggest that phytoparasitic nematodes modulate the host's developmental regulation of the vascular stem cells during gall formation.

Diversity of Knot Solitons in Liquid Crystals Manifested by Linking of Preimages in Torons and Hopfions

Directory of Open Access Journals (Sweden)

Paul J. Ackerman

2017-01-01

Full Text Available Topological solitons are knots in continuous physical fields classified by nonzero Hopf index values. Despite arising in theories that span many branches of physics, from elementary particles to condensed matter and cosmology, they remain experimentally elusive and poorly understood. We introduce a method of experimental and numerical analysis of such localized structures in liquid crystals that, similar to the mathematical Hopf maps, relates all points of the medium’s order parameter space to their closed-loop preimages within the three-dimensional solitons. We uncover a surprisingly large diversity of naturally occurring and laser-generated topologically nontrivial solitons with differently knotted nematic fields, which previously have not been realized in theories and experiments alike. We discuss the implications of the liquid crystal’s nonpolar nature on the knot soliton topology and how the medium’s chirality, confinement, and elastic anisotropy help to overcome the constraints of the Hobart-Derrick theorem, yielding static three-dimensional solitons without or with additional defects. Our findings will establish chiral nematics as a model system for experimental exploration of topological solitons and may impinge on understanding of such nonsingular field configurations in other branches of physics, as well as may lead to technological applications.

Southward migration and fuel deposition of Red Knots Calidris canutus

OpenAIRE

Helseth, Anders; Lindström, Åke; Stervander, Martin

2005-01-01

We compared the differences between spring and autumn in migration speed, fuelling rates and fuel loads of migrating Red Knots Calidris canutus. As a basis we used ringing data from Ottenby Bird Observatory, southeastern Sweden, collected 1948–2003, with morphometrical data from 1990–2003. Numbers ringed varied between 0 and 301 per year (average 56). Morphometrics, recoveries and recaptures of ringed birds indicated that most birds belonged to the Afro-Siberian subspecies C. c. canutus, poss...

Knots and surfaces a guide to discovering mathematics

CERN Document Server

Farmer, David W

1995-01-01

In most mathematics textbooks, the most exciting part of mathematics-the process of invention and discovery-is completely hidden from the reader. The aim of Knots and Surfaces is to change all that. By means of a series of carefully selected tasks, this book leads readers to discover some real mathematics. There are no formulas to memorize; no procedures to follow. The book is a guide: its job is to start you in the right direction and to bring you back if you stray too far. Discovery is left to you. Suitable for a one-semester course at the beginning undergraduate level, there are no prerequi

Knots on a Torus: A Model of the Elementary Particles

Directory of Open Access Journals (Sweden)

Jack S. Avrin

2012-02-01

Full Text Available Two knots; just two rudimentary knots, the unknot and the trefoil. That’s all we need to build a model of the elementary particles of physics, one with fermions and bosons, hadrons and leptons, interactions weak and strong and the attributes of spin, isospin, mass, charge, CPT invariance and more. There are no quarks to provide fractional charge, no gluons to sequester them within nucleons and no “colors” to avoid violating Pauli’s principle. Nor do we require the importation of an enigmatic Higgs boson to confer mass upon the particles of our world. All the requisite attributes emerge simply (and relativistically invariant as a result of particle conformation and occupation in and of spacetime itself, a spacetime endowed with the imprimature of general relativity. Also emerging are some novel tools for systemizing the particle taxonomy as governed by the gauge group SU(2 and the details of particle degeneracy as well as connections to Hopf algebra, Dirac theory, string theory, topological quantum field theory and dark matter. One exception: it is found necessary to invoke the munificent geometry of the icosahedron in order to provide, as per the group “flavor” SU(3, a scaffold upon which to organize the well-known three generations—no more, no less—of the particle family tree.

Fuzzy knot theory interpretation of Yang-Mills instantons and Witten's 5-Brane model

International Nuclear Information System (INIS)

El Naschie, M.S.

2008-01-01

A knot theory interpretation of 'tHooft's instanton based on hyperbolic volume, crossing numbers and exceptional Lie symmetry groups is given. Subsequently it is shown that although instantons and particle-like states of Heterotic super strings may appear to be different concepts, on a very deep fuzzy level they are not

Lipofection: A Highly Efficient, Lipid-Mediated DNA-Transfection Procedure

Science.gov (United States)

Felgner, Philip L.; Gadek, Thomas R.; Holm, Marilyn; Roman, Richard; Chan, Hardy W.; Wenz, Michael; Northrop, Jeffrey P.; Ringold, Gordon M.; Danielsen, Mark

1987-11-01

A DNA-transfection protocol has been developed that makes use of a synthetic cationic lipid, N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA). Small unilamellar liposomes containing DOTMA interact spontaneously with DNA to form lipid-DNA complexes with 100% entrapment of the DNA. DOTMA facilitates fusion of the complex with the plasma membrane of tissue culture cells, resulting in both uptake and expression of the DNA. The technique is simple, highly reproducible, and effective for both transient and stable expression of transfected DNA. Depending upon the cell line, lipofection is from 5- to >100-fold more effective than either the calcium phosphate or the DEAE-dextran transfection technique.

Overexpression of MIC-3 indicates a direct role for the MIC gene family in mediating Upland cotton (Gossypium hirsutum) resistance to root-knot nematode (Meloidogyne incognita)

Science.gov (United States)

Major quantitative trait loci (QTL) have been mapped to Upland cotton (Gossypium hirsutum L.) chromosomes 11 and 14 that govern the highly resistant phenotype in response to infection by root-knot nematode (RKN; Meloidogyne incognita Chitwood & White); however, nearly nothing is known regarding the ...

High-Throughput DNA sequencing of ancient wood.

Science.gov (United States)

Wagner, Stefanie; Lagane, Frédéric; Seguin-Orlando, Andaine; Schubert, Mikkel; Leroy, Thibault; Guichoux, Erwan; Chancerel, Emilie; Bech-Hebelstrup, Inger; Bernard, Vincent; Billard, Cyrille; Billaud, Yves; Bolliger, Matthias; Croutsch, Christophe; Čufar, Katarina; Eynaud, Frédérique; Heussner, Karl Uwe; Köninger, Joachim; Langenegger, Fabien; Leroy, Frédéric; Lima, Christine; Martinelli, Nicoletta; Momber, Garry; Billamboz, André; Nelle, Oliver; Palomo, Antoni; Piqué, Raquel; Ramstein, Marianne; Schweichel, Roswitha; Stäuble, Harald; Tegel, Willy; Terradas, Xavier; Verdin, Florence; Plomion, Christophe; Kremer, Antoine; Orlando, Ludovic

2018-03-01

Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management. © 2018 John Wiley & Sons Ltd.

Three-dimensional printed knotted reactors enabling highly sensitive differentiation of silver nanoparticles and ions in aqueous environmental samples

International Nuclear Information System (INIS)

Su, Cheng-Kuan; Hsieh, Meng-Hsuan; Sun, Yuh-Chang

2016-01-01

Whether silver nanoparticles (AgNPs) persist or release silver ions (Ag + ) when discharged into a natural environment has remained an unresolved issue. In this study, we employed a low-cost stereolithographic three-dimensional printing (3DP) technology to fabricate the angle-defined knotted reactors (KRs) to construct a simple differentiation scheme for quantitative assessment of Ag + ions and AgNPs in municipal wastewater samples. We chose xanthan/phosphate-buffered saline as a dispersion medium for in situ stabilization of the two silver species, while also facilitating their extraction from complicated wastewater matrices. After method optimization, we measured extraction efficiencies of 54.5 and 32.3% for retaining Ag + ions and AgNPs, respectively, in the printed KR (768-turn), with detection limits (DLs) of 0.86 and 0.52 ng L −1 when determining Ag + ions and AgNPs, respectively (sample run at pH 11 without a rinse solution), and 0.86 ng L −1 when determining Ag + ions alone (sample run at pH 12 with a 1.5-mL rinse solution). The proposed scheme is tolerant of the wastewater matrix and provides more reliable differentiation between Ag + /AgNPs than does a conventional filtration method. The concept and applicability of adopting 3DP technology to renew traditional KR devices were evidently proven by means of these significantly improved analytical performance. Our analytical data suggested that the concentrations of Ag + ions and AgNPs in the tested industrial wastewater sample were both higher than those in domestic wastewater, implying that industrial activity might be a main source of environmental silver species, rather than domestic discharge from AgNP-containing products. - Highlights: • 3D printed knotted reactors are utilized to differentiate AgNPs and Ag + ions. • Xanthan/phosphate-buffered saline is used for stabilizing the two silver species. • Extraction efficiency up to 54.5% is available for retaining Ag + ion species. • The

Sprouty gene dosage influences temporal-spatial dynamics of primary enamel knot formation

Czech Academy of Sciences Publication Activity Database

Lochovská, Kateřina; Peterková, Renata; Pavlíková, Zuzana; Hovořáková, Mária

2015-01-01

Roč. 15, APR 22 (2015), s. 21 ISSN 1471-213X R&D Projects: GA ČR(CZ) GAP305/12/1766; GA ČR GB14-37368G Institutional support: RVO:68378041 Keywords : enamel knot * tooth development * mouse molar * sprouty genes * sonic hedgehog * cre-loxp system * supernumerary tooth Subject RIV: EA - Cell Biology Impact factor: 2.096, year: 2015

Caspase 3 activation in the primary enamel knot of developing molar tooth

Czech Academy of Sciences Publication Activity Database

Matalová, Eva; Kovářů, František; Míšek, Ivan

2006-01-01

Roč. 55, 2 (2006), s. 183-188 ISSN 0862-8408 R&D Projects: GA ČR GA304/04/0101; GA AV ČR KJB500450503; GA MŠk OC B23.001 Institutional research plan: CEZ:AV0Z50450515 Keywords : apoptosis * caspase 3 * primary enamel knot Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.093, year: 2006

Endogenous circannual rhythmicity in body mass, molt, and plumage of Great Knots (Calidris tenuirostris)

NARCIS (Netherlands)

Piersma, Theunis; Brugge, Maarten; Spaans, Bernard; Battley, Phil F.; Handel, C.M.

Four Great Knots (Calidris tenuirostris) were kept for six years in a constant-temperature indoor aviary. For two of those six years, they were kept under photoperiodic conditions that mimicked natural changes in daylength for wild birds, followed by four years under a constant photoperiod

Modelling phenotypic flexibility : an optimality analysis of gizzard size in Red Knots Calidris canutus

NARCIS (Netherlands)

van Gils, Jan A.; Piersma, Theunis; Dekinga, Anne; Battley, Phil F.

2006-01-01

Reversible phenotypic changes, such as those observed in nutritional organs of long-distance migrants, increasingly receive the attention of ornithologists. In this paper we review the cost-benefit studies that have been performed on the flexible gizzard of Red Knots Calidris cunutus. By varying the

Modelling phenotypic flexibility: an optimality analysis of gizzard size in Red Knots (Calidris canutus)

NARCIS (Netherlands)

Van Gils, J.A.; Piersma, T.; Dekinga, A.; Battley, P.F.

2006-01-01

Reversible phenotypic changes, such as those observed in nutritional organs of long-distance migrants, increasingly receive the attention of ornithologists. In this paper we review the cost-benefit studies that have been performed on the flexible gizzard of Red Knots Calidris canutus. By varying the

First report of the root-knot nematode Meloidogyne minor on turfgrass in Belgium

NARCIS (Netherlands)

Viaene, N.; Wiseborn, D.B.; Karssen, G.

2007-01-01

The root-knot nematode, Meloidogyne minor, was described during 2004 after it was found on potato roots in a field in the Netherlands and in golf courses in England, Wales, and Ireland (2). Since it is associated with yellow patch disease in turf grass and causes deformation of potato tubers (2), it

Day and night feeding habitat of Red Knots in Patagonia : Profitability versus safety?

NARCIS (Netherlands)

Sitters, HP; Gonzalez, PM; Piersma, T; Baker, AJ; Price, DJ; Sitters, Humphrey P.; González, Patricia M.; Baker, Allan J.; Price, David J.

2001-01-01

By radio-tracking and recording the movements of flocks. the distribution of feeding Red Knots (Calidris canutus rufa) was studied day and night at a migration stopover site near San Antonio Oeste, Rio Negro, Argentina in March and April 1998. By day, the birds fed in dense flocks of 500-4000 on an

Polycyclic Aromatic Hydrocarbon (PAH Exposure and DNA Adduct Semi-Quantitation in Archived Human Tissues

Directory of Open Access Journals (Sweden)

M. Margaret Pratt

2011-06-01

Full Text Available Polycyclic aromatic hydrocarbons (PAHs are combustion products of organic materials, mixtures of which contain multiple known and probable human carcinogens. PAHs occur in indoor and outdoor air, as well as in char-broiled meats and fish. Human exposure to PAHs occurs by inhalation, ingestion and topical absorption, and subsequently formed metabolites are either rendered hydrophilic and excreted, or bioactivated and bound to cellular macromolecules. The formation of PAH-DNA adducts (DNA binding products, considered a necessary step in PAH-initiated carcinogenesis, has been widely studied in experimental models and has been documented in human tissues. This review describes immunohistochemistry (IHC studies, which reveal localization of PAH-DNA adducts in human tissues, and semi-quantify PAH-DNA adduct levels using the Automated Cellular Imaging System (ACIS. These studies have shown that PAH-DNA adducts concentrate in: basal and supra-basal epithelium of the esophagus, cervix and vulva; glandular epithelium of the prostate; and cytotrophoblast cells and syncitiotrophoblast knots of the placenta. The IHC photomicrographs reveal the ubiquitous nature of PAH-DNA adduct formation in human tissues as well as PAH-DNA adduct accumulation in specific, vulnerable, cell types. This semi-quantative method for PAH-DNA adduct measurement could potentially see widespread use in molecular epidemiology studies.

Effect of Emamectin Benzoate on Root-Knot Nematodes and Tomato Yield

OpenAIRE

Cheng, Xingkai; Liu, Xiumei; Wang, Hongyan; Ji, Xiaoxue; Wang, Kaiyun; Wei, Min; Qiao, Kang

2015-01-01

Southern root-knot nematode (Meloidogyne incognita) is an obligate, sedentary endoparasite of more than 3000 plant species, that causes heavy economic losses and limit the development of protected agriculture of China. As a biological pesticide, emamectin benzoate has effectively prevented lepidopteran pests; however, its efficacy to control M. incognita remains unknown. The purpose of the present study was to test soil application of emamectin benzoate for management of M. incognita in labor...

A baseline correction algorithm for Raman spectroscopy by adaptive knots B-spline

International Nuclear Information System (INIS)

Wang, Xin; Fan, Xian-guang; Xu, Ying-jie; Wang, Xiu-fen; He, Hao; Zuo, Yong

2015-01-01

The Raman spectroscopy technique is a powerful and non-invasive technique for molecular fingerprint detection which has been widely used in many areas, such as food safety, drug safety, and environmental testing. But Raman signals can be easily corrupted by a fluorescent background, therefore we presented a baseline correction algorithm to suppress the fluorescent background in this paper. In this algorithm, the background of the Raman signal was suppressed by fitting a curve called a baseline using a cyclic approximation method. Instead of the traditional polynomial fitting, we used the B-spline as the fitting algorithm due to its advantages of low-order and smoothness, which can avoid under-fitting and over-fitting effectively. In addition, we also presented an automatic adaptive knot generation method to replace traditional uniform knots. This algorithm can obtain the desired performance for most Raman spectra with varying baselines without any user input or preprocessing step. In the simulation, three kinds of fluorescent background lines were introduced to test the effectiveness of the proposed method. We showed that two real Raman spectra (parathion-methyl and colza oil) can be detected and their baselines were also corrected by the proposed method. (paper)

A new class of magnetic confinement device in the shape of a knot

Energy Technology Data Exchange (ETDEWEB)

Hudson, S. R., E-mail: shudson@pppl.gov; Startsev, E.; Feibush, E. [Princeton Plasma Physics Laboratory, PO Box 451, Princeton, New Jersey 08543 (United States)

2014-01-15

We describe a new class of magnetic confinement device, with the magnetic axis in the shape of a knot. We call such devices “knotatrons.” An example is given that has a large volume filled with magnetic surfaces, with significant rotational-transform, and with the magnetic field produced entirely by external circular coils.

A biomechanical comparison of 2 technical variations of double-row rotator cuff fixation: the importance of medial row knots.

Science.gov (United States)

Busfield, Benjamin T; Glousman, Ronald E; McGarry, Michelle H; Tibone, James E; Lee, Thay Q

2008-05-01

Previous studies have shown comparable biomechanical properties of double-row fixation versus double-row fixation with a knotless lateral row. SutureBridge is a construct that secures the cuff with medial row mattress suture anchors and knotless lateral row fixation of the medial suture ends. Recent completely knotless constructs may lead to lesser clinical outcomes if the construct properties are compromised from lack of suture knots. A completely knotless construct without medial row knots will compromise the biomechanical properties in both cyclic and failure-testing parameters. Controlled laboratory study. Six matched pairs of cadaveric shoulders were randomized to 2 groups of double row fixation with SutureBridge: group 1 with medial row knots, and group 2 without medial row knots. The specimens were placed in a materials test system at 30 degrees of abduction. Cyclic testing to 180 N at 1 mm/sec for 30 cycles was performed, followed by tensile testing to failure at 1 mm/sec. Data included cyclic and failure data from the materials test system and gap data using a video digitizing system. All data from paired specimens were compared using paired Student t tests. Group 1 had a statistically significant difference (P row failure, whereas all group 1 specimens failed at the clamp. Although lateral row knotless fixation has been shown not to sacrifice structural integrity of this construct, the addition of a knotless medial row compromises the construct leading to greater gapping and failure at lower loads. This may raise concerns regarding recently marketed completely knotless double row constructs.

Numerical simulation of the knotted nylon netting panel

Directory of Open Access Journals (Sweden)

Li Yuwei

2016-01-01

Full Text Available A piece of netting, consists of the 8 8 meshes, fixed on a square frame, was simulated and the tensions and their distribution, the positions of knots and netting shape were calculated by means of MATLAB in computer. The dynamic mathematic model was developed based on lumped mass method, the netting was treated as spring-mass system, the Runge-Kutta fifth-order and sixth-order method was used to solve the differential equations for every step, then the displacement and tension of each mass point were obtained. For verify this model, the tests have been carried out in a flume tank. The results of the numerical simulation fully agreed with the experiments.

Automated knot detection with visual post-processing of Douglas-fir veneer images

Science.gov (United States)

C.L. Todoroki; Eini C. Lowell; Dennis Dykstra

2010-01-01

Knots on digital images of 51 full veneer sheets, obtained from nine peeler blocks crosscut from two 35-foot (10.7 m) long logs and one 18-foot (5.5 m) log from a single Douglas-fir tree, were detected using a two-phase algorithm. The algorithm was developed using one image, the Development Sheet, refined on five other images, the Training Sheets, and then applied to...

Growth and yield of grafted cucumbers in soil infested with root-knot nematodes

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Smiljana Goreta Ban

2014-03-01

Full Text Available The aim of this study was to determine the effect of rootstocks on the growth and yield of cucumber (Cucumis sativus L. plants in soils infested with root-knot nematodes (Meloidogyne spp. Cucumber 'Adrian' was grown with its own roots or was grafted onto three rootstocks of Lagenariasiceraria (Molina Standi. ('Emphasis', 'S-1', and 'Gourd', two interspecific hybrid rootstocks of Cucurbita maxima Duchesne x C. moschata Duchesne ('Strong Tosa' and 'RS 841 Improved' and zucchini Cucurbita pepo L. ('Romanesco Zucchini'. The experiments were conducted in commercial greenhouse, with cucumber grafted onto three rootstocks in the first season and onto six rootstocks in the second spring-summer season. The number of leaves was considerably affected by the rootstock in both seasons, and was the highest for the plants grafted onto interspecific rootstocks (28.0 in the first and 44.9 in the second season. The plants grafted onto 'Strong Tosa' had higher total number of fruits (19.9 and yield (5.38 kg compared to other rootstocks or non-grafted plants in first season, and the same result was found for two interspecific rootstocks in the second season (6.96 kg and more than 28.9 fruits per plant. The total soluble solids, pH and electrical conductivity of the fruit were not affected by rootstock, while titratable acidity changed with the rootstock type. The grafting of cucumber plants onto different rootstocks was confirmed as an acceptable non-chemical method to compete with the limitations of soils infected with root-knot nematodes, but the effect was highly dependent on the choice of the rootstock.

High efficiency hydrodynamic DNA fragmentation in a bubbling system

NARCIS (Netherlands)

Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; Van Den Berg, Albert; Eijkel, Jan C.T.; Shui, Lingling

2017-01-01

DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling

High molecular weight DNA assembly in vivo for synthetic biology applications.

Science.gov (United States)

Juhas, Mario; Ajioka, James W

2017-05-01

DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.

High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

Science.gov (United States)

Inagaki, Soichi; Henry, Isabelle M; Lieberman, Meric C; Comai, Luca

2015-01-01

Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

Personalized Video Feedback and Repeated Task Practice Improve Laparoscopic Knot-Tying Skills: Two Controlled Trials.

Science.gov (United States)

Abbott, Eduardo F; Thompson, Whitney; Pandian, T K; Zendejas, Benjamin; Farley, David R; Cook, David A

2017-11-01

Compare the effect of personalized feedback (PF) vs. task demonstration (TD), both delivered via video, on laparoscopic knot-tying skills and perceived workload; and evaluate the effect of repeated practice. General surgery interns and research fellows completed four repetitions of a simulated laparoscopic knot-tying task at one-month intervals. Midway between repetitions, participants received via e-mail either a TD video (demonstration by an expert) or a PF video (video of their own performance with voiceover from a blinded senior surgeon). Each participant received at least one video per format, with sequence randomly assigned. Outcomes included performance scores and NASA Task Load Index (NASA-TLX) scores. To evaluate the effectiveness of repeated practice, scores from these trainees on a separate delayed retention test were compared against historical controls who did not have scheduled repetitions. Twenty-one trainees completed the randomized study. Mean change in performance scores was significantly greater for those receiving PF (difference = 23.1 of 150 [95% confidence interval (CI): 0, 46.2], P = .05). Perceived workload was also significantly reduced (difference = -3.0 of 20 [95% CI: -5.8, -0.3], P = .04). Compared with historical controls (N = 93), the 21 with scheduled repeated practice had higher scores on the laparoscopic knot-tying assessment two weeks after the final repetition (difference = 1.5 of 10 [95% CI: 0.2, 2.8], P = .02). Personalized video feedback improves trainees' procedural performance and perceived workload compared with a task demonstration video. Brief monthly practice sessions support skill acquisition and retention.

Optimizing the efficacy of Paecilomyces lilacinus (strain 251) for the control of root-knot nematodes.

Science.gov (United States)

Kiewnick, S; Sikora, R A

2004-01-01

The egg pathogenic fungus Paecilomyces lilacinus (strain 251) is a biocontrol fungus with a potential range of activity to control the worldwide most important plant parasitic nematodes. This biological nematicide may be an useful tool in an integrated approach to control mainly sedentary nematodes. Greenhouse experiments were conducted with the root-knot nematodes Meloidogyne incognita and M. hapla on tomato. P. lilacinus, formulated as WG (BIOACT WG), was incorporated into soil inoculated with root-knot nematode eggs prior to transplanting the susceptible tomato cultivar "Hellfrucht". Furthermore, soil treatments were combined with seedling treatments 24 hours before transplanting and a soil drench 2 weeks after planting, respectively. Seedling and post planting treatment was also combined with a soil treatment at planting. All single or combination treatments tested decreased the gall index and the number of egg masses compared to the untreated control 12 weeks after planting. However, the combination of the seedling treatment with a pre- or at-planting application of P. lilacinus was necessary to achieve higher levels of control. Additional post plant drenching resulted in only a slight increase In efficacy. To the feasibility of this modified application system for the control of root-knot nematodes, a yield experiment was conducted with M. hapla and the susceptible cultivar "Gnom F1 Hybrid". It could be demonstrated that the above mentioned combination of pre-planting application plus the seedling and one post plant drench gave the best control and resulted in a significant fruit yield increase in concurrence with a decrease in number of galls per root.

Novel Inhibitor Cystine Knot Peptides from Momordica charantia

Science.gov (United States)

Clark, Richard J.; Tang, Jun; Zeng, Guang-Zhi; Franco, Octavio L.; Cantacessi, Cinzia; Craik, David J.; Daly, Norelle L.; Tan, Ning-Hua

2013-01-01

Two new peptides, MCh-1 and MCh-2, along with three known trypsin inhibitors (MCTI-I, MCTI-II and MCTI-III), were isolated from the seeds of the tropical vine Momordica charantia. The sequences of the peptides were determined using mass spectrometry and NMR spectroscopy. Using a strategy involving partial reduction and stepwise alkylation of the peptides, followed by enzymatic digestion and tandem mass spectrometry sequencing, the disulfide connectivity of MCh-1 was elucidated to be CysI-CysIV, CysII-CysV and CysIII-CysVI. The three-dimensional structures of MCh-1 and MCh-2 were determined using NMR spectroscopy and found to contain the inhibitor cystine knot (ICK) motif. The sequences of the novel peptides differ significantly from peptides previously isolated from this plant. Therefore, this study expands the known peptide diversity in M. charantia and the range of sequences that can be accommodated by the ICK motif. Furthermore, we show that a stable two-disulfide intermediate is involved in the oxidative folding of MCh-1. This disulfide intermediate is structurally homologous to the proposed ancestral fold of ICK peptides, and provides a possible pathway for the evolution of this structural motif, which is highly prevalent in nature. PMID:24116036

Novel inhibitor cystine knot peptides from Momordica charantia.

Directory of Open Access Journals (Sweden)

Wen-Jun He

Full Text Available Two new peptides, MCh-1 and MCh-2, along with three known trypsin inhibitors (MCTI-I, MCTI-II and MCTI-III, were isolated from the seeds of the tropical vine Momordica charantia. The sequences of the peptides were determined using mass spectrometry and NMR spectroscopy. Using a strategy involving partial reduction and stepwise alkylation of the peptides, followed by enzymatic digestion and tandem mass spectrometry sequencing, the disulfide connectivity of MCh-1 was elucidated to be CysI-CysIV, CysII-CysV and CysIII-CysVI. The three-dimensional structures of MCh-1 and MCh-2 were determined using NMR spectroscopy and found to contain the inhibitor cystine knot (ICK motif. The sequences of the novel peptides differ significantly from peptides previously isolated from this plant. Therefore, this study expands the known peptide diversity in M. charantia and the range of sequences that can be accommodated by the ICK motif. Furthermore, we show that a stable two-disulfide intermediate is involved in the oxidative folding of MCh-1. This disulfide intermediate is structurally homologous to the proposed ancestral fold of ICK peptides, and provides a possible pathway for the evolution of this structural motif, which is highly prevalent in nature.

A free-knot spline modeling framework for piecewise linear logistic regression in complex samples with body mass index and mortality as an example

Directory of Open Access Journals (Sweden)

Scott W. Keith

2014-09-01

Full Text Available This paper details the design, evaluation, and implementation of a framework for detecting and modeling nonlinearity between a binary outcome and a continuous predictor variable adjusted for covariates in complex samples. The framework provides familiar-looking parameterizations of output in terms of linear slope coefficients and odds ratios. Estimation methods focus on maximum likelihood optimization of piecewise linear free-knot splines formulated as B-splines. Correctly specifying the optimal number and positions of the knots improves the model, but is marked by computational intensity and numerical instability. Our inference methods utilize both parametric and nonparametric bootstrapping. Unlike other nonlinear modeling packages, this framework is designed to incorporate multistage survey sample designs common to nationally representative datasets. We illustrate the approach and evaluate its performance in specifying the correct number of knots under various conditions with an example using body mass index (BMI; kg/m2 and the complex multi-stage sampling design from the Third National Health and Nutrition Examination Survey to simulate binary mortality outcomes data having realistic nonlinear sample-weighted risk associations with BMI. BMI and mortality data provide a particularly apt example and area of application since BMI is commonly recorded in large health surveys with complex designs, often categorized for modeling, and nonlinearly related to mortality. When complex sample design considerations were ignored, our method was generally similar to or more accurate than two common model selection procedures, Schwarz’s Bayesian Information Criterion (BIC and Akaike’s Information Criterion (AIC, in terms of correctly selecting the correct number of knots. Our approach provided accurate knot selections when complex sampling weights were incorporated, while AIC and BIC were not effective under these conditions.

Linked and knotted beams of light, conservation of helicity and the flow of null electromagnetic fields

International Nuclear Information System (INIS)

Irvine, William T M

2010-01-01

Maxwell's equations allow for some remarkable solutions consisting of pulsed beams of light which have linked and knotted field lines. The preservation of the topological structure of the field lines in these solutions has previously been ascribed to the fact that the electric and magnetic helicities, a measure of the degree of linking and knotting between field lines, are conserved. Here we show that the elegant evolution of the field is due to the stricter condition that the electric and magnetic fields be everywhere orthogonal. The field lines then satisfy a 'frozen field' condition and evolve as if they were unbreakable filaments embedded in a fluid. The preservation of the orthogonality of the electric and magnetic field lines is guaranteed for null, shear-free fields such as the ones considered here by a theorem of Robinson. We calculate the flow field of a particular solution and find it to have the form of a Hopf fibration moving at the speed of light in a direction opposite to the propagation of the pulsed light beam, a familiar structure in this type of solution. The difference between smooth evolution of individual field lines and conservation of electric and magnetic helicities is illustrated by considering a further example in which the helicities are conserved, but the field lines are not everywhere orthogonal. The field line configuration at time t = 0 corresponds to a nested family of torus knots but unravels upon evolution.

Activated carbon-modified knotted reactor coupled to electrothermal atomic absorption spectrometry for sensitive determination of arsenic species in medicinal herbs and tea infusions

International Nuclear Information System (INIS)

Grijalba, Alexander Castro; Martinis, Estefanía M.; Lascalea, Gustavo E.; Wuilloud, Rodolfo G.

2015-01-01

A flow injection system based on a modified polytetrafluoroethylene (PTFE) knotted reactor (KR) was developed for arsenite [As(III)] and arsenate [As(V)] species preconcentration and determination by electrothermal atomic absorption spectrometry (ETAAS). Activated carbon (AC) was immobilized on the inner walls of a PTFE KR by a thermal treatment. A significant increase in analyte retention was obtained with the AC-modified KR (100%) as compared to the regular PTFE KR (25%). The preconcentration method involved the on-line formation of As(III)-ammonium pyrrolidinedithiocarbamate (As-APDC) complex, followed by its adsorption onto the inner walls of the AC-modified KR. After analyte retention, the complex was eluted with acetone directly into the graphite furnace of ETAAS. The parameters affecting the flow injection system were evaluated with a full central composite face centered design with three center points. Under optimum conditions, a preconcentration factor of 200 was obtained with 10 ml of sample. The detection limit was 4 ng L −1 and the relative standard deviation (RSD) for six replicate measurements at 0.2 μg L −1 of As were 4.3% and 4.7% for As(III) and As(V), respectively. The developed methodology was highly selective towards As(III), while As(V), monomethylarsonic acid [MMA(V)] and dimethylarsinic [DMA(V)] were not retained in the AC-modified KR. The proposed method was successfully applied for As speciation analysis in infusions originated from medicinal herbs and tea. - Highlights: • We report an efficient method for As speciation. • We have modified a knotted reactor with activated carbon for high sorption capacity. • We provide a simple procedure for surface modification of a PTFE knotted reactor. • We have selectively separated inorganic As species from complex matrix samples. • We have implemented a modified KR in a flow injection system coupled to ETAAS

Activated carbon-modified knotted reactor coupled to electrothermal atomic absorption spectrometry for sensitive determination of arsenic species in medicinal herbs and tea infusions

Energy Technology Data Exchange (ETDEWEB)

Grijalba, Alexander Castro; Martinis, Estefanía M. [Laboratory of Analytical Chemistry for Research and Development (QUIANID), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre J. Contreras 1300, (5500) Mendoza (Argentina); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires (Argentina); Lascalea, Gustavo E. [Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires (Argentina); Wuilloud, Rodolfo G., E-mail: rwuilloud@mendoza-conicet.gob.ar [Laboratory of Analytical Chemistry for Research and Development (QUIANID), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre J. Contreras 1300, (5500) Mendoza (Argentina); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires (Argentina)

2015-01-01

A flow injection system based on a modified polytetrafluoroethylene (PTFE) knotted reactor (KR) was developed for arsenite [As(III)] and arsenate [As(V)] species preconcentration and determination by electrothermal atomic absorption spectrometry (ETAAS). Activated carbon (AC) was immobilized on the inner walls of a PTFE KR by a thermal treatment. A significant increase in analyte retention was obtained with the AC-modified KR (100%) as compared to the regular PTFE KR (25%). The preconcentration method involved the on-line formation of As(III)-ammonium pyrrolidinedithiocarbamate (As-APDC) complex, followed by its adsorption onto the inner walls of the AC-modified KR. After analyte retention, the complex was eluted with acetone directly into the graphite furnace of ETAAS. The parameters affecting the flow injection system were evaluated with a full central composite face centered design with three center points. Under optimum conditions, a preconcentration factor of 200 was obtained with 10 ml of sample. The detection limit was 4 ng L{sup −1} and the relative standard deviation (RSD) for six replicate measurements at 0.2 μg L{sup −1} of As were 4.3% and 4.7% for As(III) and As(V), respectively. The developed methodology was highly selective towards As(III), while As(V), monomethylarsonic acid [MMA(V)] and dimethylarsinic [DMA(V)] were not retained in the AC-modified KR. The proposed method was successfully applied for As speciation analysis in infusions originated from medicinal herbs and tea. - Highlights: • We report an efficient method for As speciation. • We have modified a knotted reactor with activated carbon for high sorption capacity. • We provide a simple procedure for surface modification of a PTFE knotted reactor. • We have selectively separated inorganic As species from complex matrix samples. • We have implemented a modified KR in a flow injection system coupled to ETAAS.

Ab-interno scleral suture loop fixation with cow-hitch knot in posterior chamber intraocular lens decentration

Directory of Open Access Journals (Sweden)

Ertugrul Can

2016-01-01

Full Text Available Aim of Study: To describe a simplified ab-interno cow-hitch suture fixation technique for repositioning decentered posterior chamber intraocular lens (PC IOL. Materials and Methods: Two cases are presented with the surgical correction of decentered and subluxated IOL. Ab-interno scleral suture fixation technique with hitch-cow knot in the eye was performed with a ciliary sulcus guide instrument and 1 year follow-up was completed. Results: Both of the patients had well centered lenses postoperatively. Corrected distant and near visual acuities of the patients were improved. There was no significant postoperative complication. In the follow-up period of 1 year, no evidence of suture erosion was found. Conclusions: Ab-interno scleral suture loop fixation with hitch-cow knot in the eye was effective in repositioning decentered or subluxated PC IOLs with excellent postoperative centered lenses and visual outcomes.

Damage-associated responses of the host contribute to defence against cyst nematodes but not root-knot nematodes.

Science.gov (United States)

Shah, Syed Jehangir; Anjam, Muhammad Shahzad; Mendy, Badou; Anwer, Muhammad Arslan; Habash, Samer S; Lozano-Torres, Jose L; Grundler, Florian M W; Siddique, Shahid

2017-12-16

When nematodes invade and subsequently migrate within plant roots, they generate cell wall fragments (in the form of oligogalacturonides; OGs) that can act as damage-associated molecular patterns and activate host defence responses. However, the molecular mechanisms mediating damage responses in plant-nematode interactions remain unexplored. Here, we characterized the role of a group of cell wall receptor proteins in Arabidopsis, designated as polygalacturonase-inhibiting proteins (PGIPs), during infection with the cyst nematode Heterodera schachtii and the root-knot nematode Meloidogyne incognita. PGIPs are encoded by a family of two genes in Arabidopsis, and are involved in the formation of active OG elicitors. Our results show that PGIP gene expression is strongly induced in response to cyst nematode invasion of roots. Analyses of loss-of-function mutants and overexpression lines revealed that PGIP1 expression attenuates infection of host roots by cyst nematodes, but not root-knot nematodes. The PGIP1-mediated attenuation of cyst nematode infection involves the activation of plant camalexin and indole-glucosinolate pathways. These combined results provide new insights into the molecular mechanisms underlying plant damage perception and response pathways during infection by cyst and root-knot nematodes, and establishes the function of PGIP in plant resistance to cyst nematodes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Disciplinary Knots and Learning Problems in Waves Physics

Science.gov (United States)

Di Renzone, Simone; Frati, Serena; Montalbano, Vera

An investigation on student understanding of waves is performed during an optional laboratory realized in informal extracurricular way with few, interested and talented pupils. The background and smart intuitions of students rendered the learning path very dynamic and ambitious. The activities started by investigating the basic properties of waves by means of a Shive wave machine. In order to make quantitative observed phenomena, the students used a camcorder and series of measures were obtained from the captured images. By checking the resulting data, it arose some learning difficulties especially in activities related to the laboratory. This experience was the starting point for a further analysis on disciplinary knots and learning problems in the physics of waves in order to elaborate a teaching-learning proposal on this topic.

[Diversity of actinomycetes associated with root-knot nematode and their potential for nematode control].

Science.gov (United States)

Luo, Hong-li; Sun, Man-hong; Xie, Jian-ping; Liu, Zhi-heng; Huang, Ying

2006-08-01

Twenty actinomycetes were isolated from root-knot nematode eggs and females collected from 11 plant root samples infested by Meloidogyne spp.. The isolates were assigned to the genera Streptomyces, Nocardia and Pseudonocardia respectively, based on analysis of morphological characteristics, cell-wall DAPs and 16S rRNA gene sequences. 80% of them were streptomycetes. Biocontrol potential of the isolates against Meloidogyne hapla was evaluated in liquid culture in vitro. The average percentages of egg parasitism, egg hatching, and juvenile mortality were 54.1, 40.4 and 26.2, respectively. Three Streptomyces strains and one Nocardia strain with high pathogenicity in vitro were selected to determine their ability to reduce tomato root galls in greenhouse. The results demonstrated good biocontrol efficacy (31.4%-56.4%) of the strains.

High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

Directory of Open Access Journals (Sweden)

Soichi Inagaki

Full Text Available Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces

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Eveson J Paige

2006-08-01

Full Text Available Abstract Background Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (λ can be estimated by determining the rate of decline. Results The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean λpredator = 0.0106 per nucleotide; mean λprey = 0.0176 per nucleotide. This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples. Conclusion We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will

Three-dimensional printed knotted reactors enabling highly sensitive differentiation of silver nanoparticles and ions in aqueous environmental samples

Energy Technology Data Exchange (ETDEWEB)

Su, Cheng-Kuan, E-mail: chengkuan@ntou.edu.tw [Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, 20224, Taiwan, ROC (China); Hsieh, Meng-Hsuan [Department of Biomedical Engineering and Environmental Sciences, National Tsing-Hua University, Hsinchu, 30013, Taiwan, ROC (China); Sun, Yuh-Chang, E-mail: ycsun@mx.nthu.edu.tw [Department of Biomedical Engineering and Environmental Sciences, National Tsing-Hua University, Hsinchu, 30013, Taiwan, ROC (China)

2016-03-31

Whether silver nanoparticles (AgNPs) persist or release silver ions (Ag{sup +}) when discharged into a natural environment has remained an unresolved issue. In this study, we employed a low-cost stereolithographic three-dimensional printing (3DP) technology to fabricate the angle-defined knotted reactors (KRs) to construct a simple differentiation scheme for quantitative assessment of Ag{sup +} ions and AgNPs in municipal wastewater samples. We chose xanthan/phosphate-buffered saline as a dispersion medium for in situ stabilization of the two silver species, while also facilitating their extraction from complicated wastewater matrices. After method optimization, we measured extraction efficiencies of 54.5 and 32.3% for retaining Ag{sup +} ions and AgNPs, respectively, in the printed KR (768-turn), with detection limits (DLs) of 0.86 and 0.52 ng L{sup −1} when determining Ag{sup +} ions and AgNPs, respectively (sample run at pH 11 without a rinse solution), and 0.86 ng L{sup −1} when determining Ag{sup +} ions alone (sample run at pH 12 with a 1.5-mL rinse solution). The proposed scheme is tolerant of the wastewater matrix and provides more reliable differentiation between Ag{sup +}/AgNPs than does a conventional filtration method. The concept and applicability of adopting 3DP technology to renew traditional KR devices were evidently proven by means of these significantly improved analytical performance. Our analytical data suggested that the concentrations of Ag{sup +} ions and AgNPs in the tested industrial wastewater sample were both higher than those in domestic wastewater, implying that industrial activity might be a main source of environmental silver species, rather than domestic discharge from AgNP-containing products. - Highlights: • 3D printed knotted reactors are utilized to differentiate AgNPs and Ag{sup +} ions. • Xanthan/phosphate-buffered saline is used for stabilizing the two silver species. • Extraction efficiency up to 54.5% is

Topological Vortex and Knotted Dissipative Optical 3D Solitons Generated by 2D Vortex Solitons.

Science.gov (United States)

Veretenov, N A; Fedorov, S V; Rosanov, N N

2017-12-29

We predict a new class of three-dimensional (3D) topological dissipative optical one-component solitons in homogeneous laser media with fast saturable absorption. Their skeletons formed by vortex lines where the field vanishes are tangles, i.e., N_{c} knotted or unknotted, linked or unlinked closed lines and M unclosed lines that thread all the closed lines and end at the infinitely far soliton periphery. They are generated by embedding two-dimensional laser solitons or their complexes in 3D space after their rotation around an unclosed, infinite vortex line with topological charge M_{0} (N_{c}, M, and M_{0} are integers). With such structure propagation, the "hula-hoop" solitons form; their stability is confirmed numerically. For the solitons found, all vortex lines have unit topological charge: the number of closed lines N_{c}=1 and 2 (unknots, trefoils, and Solomon knots links); unclosed vortex lines are unknotted and unlinked, their number M=1, 2, and 3.

Highly multiplexed targeted DNA sequencing from single nuclei.

Science.gov (United States)

Leung, Marco L; Wang, Yong; Kim, Charissa; Gao, Ruli; Jiang, Jerry; Sei, Emi; Navin, Nicholas E

2016-02-01

Single-cell DNA sequencing methods are challenged by poor physical coverage, high technical error rates and low throughput. To address these issues, we developed a single-cell DNA sequencing protocol that combines flow-sorting of single nuclei, time-limited multiple-displacement amplification (MDA), low-input library preparation, DNA barcoding, targeted capture and next-generation sequencing (NGS). This approach represents a major improvement over our previous single nucleus sequencing (SNS) Nature Protocols paper in terms of generating higher-coverage data (>90%), thereby enabling the detection of genome-wide variants in single mammalian cells at base-pair resolution. Furthermore, by pooling 48-96 single-cell libraries together for targeted capture, this approach can be used to sequence many single-cell libraries in parallel in a single reaction. This protocol greatly reduces the cost of single-cell DNA sequencing, and it can be completed in 5-6 d by advanced users. This single-cell DNA sequencing protocol has broad applications for studying rare cells and complex populations in diverse fields of biological research and medicine.

Extraction of high quality DNA from seized Moroccan cannabis resin (Hashish.

Directory of Open Access Journals (Sweden)

Moulay Abdelaziz El Alaoui

Full Text Available The extraction and purification of nucleic acids is the first step in most molecular biology analysis techniques. The objective of this work is to obtain highly purified nucleic acids derived from Cannabis sativa resin seizure in order to conduct a DNA typing method for the individualization of cannabis resin samples. To obtain highly purified nucleic acids from cannabis resin (Hashish free from contaminants that cause inhibition of PCR reaction, we have tested two protocols: the CTAB protocol of Wagner and a CTAB protocol described by Somma (2004 adapted for difficult matrix. We obtained high quality genomic DNA from 8 cannabis resin seizures using the adapted protocol. DNA extracted by the Wagner CTAB protocol failed to give polymerase chain reaction (PCR amplification of tetrahydrocannabinolic acid (THCA synthase coding gene. However, the extracted DNA by the second protocol permits amplification of THCA synthase coding gene using different sets of primers as assessed by PCR. We describe here for the first time the possibility of DNA extraction from (Hashish resin derived from Cannabis sativa. This allows the use of DNA molecular tests under special forensic circumstances.

Microbiomes associated with infective stages of root-knot and lesion nematodes in soil.

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Ahmed Elhady

Full Text Available Endoparasitic root-knot (Meloidogyne spp. and lesion (Pratylenchus spp. nematodes cause considerable damage in agriculture. Before they invade roots to complete their life cycle, soil microbes can attach to their cuticle or surface coat and antagonize the nematode directly or by induction of host plant defenses. We investigated whether the nematode-associated microbiome in soil differs between infective stages of Meloidogyne incognita and Pratylenchus penetrans, and whether it is affected by variation in the composition of microbial communities among soils. Nematodes were incubated in suspensions of five organically and two integrated horticultural production soils, recovered by sieving and analyzed for attached bacteria and fungi after washing off loosely adhering microbes. Significant effects of the soil type and nematode species on nematode-associated fungi and bacteria were revealed as analyzed by community profiling using denaturing gradient gel electrophoresis. Attached microbes represented a small specific subset of the soil microbiome. Two organic soils had very similar bacterial and fungal community profiles, but one of them was strongly suppressive towards root-knot nematodes. They were selected for deep amplicon sequencing of bacterial 16S rRNA genes and fungal ITS. Significant differences among the microbiomes associated with the two species in both soils suggested specific surface epitopes. Among the 28 detected bacterial classes, Betaproteobacteria, Bacilli and Actinobacteria were the most abundant. The most frequently detected fungal genera were Malassezia, Aspergillus and Cladosporium. Attached microbiomes did not statistically differ between these two soils. However, Malassezia globosa and four fungal species of the family Plectosphaerellaceae, and the bacterium Neorhizobium galegae were strongly enriched on M. incognita in the suppressive soil. In conclusion, the highly specific attachment of microbes to infective stages of

Two high-mobility group box domains act together to underwind and kink DNA

Energy Technology Data Exchange (ETDEWEB)

Sánchez-Giraldo, R.; Acosta-Reyes, F. J. [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain); Malarkey, C. S. [University of Colorado School of Medicine, Aurora, CO 80045 (United States); Saperas, N. [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain); Churchill, M. E. A., E-mail: mair.churchill@ucdenver.edu [University of Colorado School of Medicine, Aurora, CO 80045 (United States); Campos, J. L., E-mail: mair.churchill@ucdenver.edu [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain)

2015-06-30

The crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment is reported at a resolution of 2 Å. A new mode of DNA recognition for HMG box proteins is found in which two box A domains bind in an unusual configuration generating a highly kinked DNA structure. High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1–DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.

Two high-mobility group box domains act together to underwind and kink DNA

International Nuclear Information System (INIS)

Sánchez-Giraldo, R.; Acosta-Reyes, F. J.; Malarkey, C. S.; Saperas, N.; Churchill, M. E. A.; Campos, J. L.

2015-01-01

The crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment is reported at a resolution of 2 Å. A new mode of DNA recognition for HMG box proteins is found in which two box A domains bind in an unusual configuration generating a highly kinked DNA structure. High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1–DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria.

Science.gov (United States)

Zhao, Meicheng; Zhi, Hui; Doust, Andrew N; Li, Wei; Wang, Yongfang; Li, Haiquan; Jia, Guanqing; Wang, Yongqiang; Zhang, Ning; Diao, Xianmin

2013-04-11

The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide. GISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus. Three novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC'C'. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The

Cutting the Gordian Knot of electrodeposition via controlled cathodic corrosion enabling the production of supported metal nanoparticles below 5 nm

OpenAIRE

Vanrenterghem, B.; Bele, M.; Zepeda, F.R.; Sala, M.; Hodnik, N.; Breugelmans, Tom

2018-01-01

Abstract: In the past decades, there has been an ongoing search for tailor-made active metal nanoparticles for the use as electrocatalysts. An upcoming versatile and green method for the synthesis of nanoparticles is electrodeposition. However, the state-of-the-art electrodeposited metal particle sizes are in the range of 50200 nm. Production of high surface area metallic electrocatalysts with small particle sizes is a serious limitation of electrodeposition, i.e., the Gordian Knot. In this a...

Directed PCR-free engineering of highly repetitive DNA sequences

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Preissler Steffen

2011-09-01

Full Text Available Abstract Background Highly repetitive nucleotide sequences are commonly found in nature e.g. in telomeres, microsatellite DNA, polyadenine (poly(A tails of eukaryotic messenger RNA as well as in several inherited human disorders linked to trinucleotide repeat expansions in the genome. Therefore, studying repetitive sequences is of biological, biotechnological and medical relevance. However, cloning of such repetitive DNA sequences is challenging because specific PCR-based amplification is hampered by the lack of unique primer binding sites resulting in unspecific products. Results For the PCR-free generation of repetitive DNA sequences we used antiparallel oligonucleotides flanked by restriction sites of Type IIS endonucleases. The arrangement of recognition sites allowed for stepwise and seamless elongation of repetitive sequences. This facilitated the assembly of repetitive DNA segments and open reading frames encoding polypeptides with periodic amino acid sequences of any desired length. By this strategy we cloned a series of polyglutamine encoding sequences as well as highly repetitive polyadenine tracts. Such repetitive sequences can be used for diverse biotechnological applications. As an example, the polyglutamine sequences were expressed as His6-SUMO fusion proteins in Escherichia coli cells to study their aggregation behavior in vitro. The His6-SUMO moiety enabled affinity purification of the polyglutamine proteins, increased their solubility, and allowed controlled induction of the aggregation process. We successfully purified the fusions proteins and provide an example for their applicability in filter retardation assays. Conclusion Our seamless cloning strategy is PCR-free and allows the directed and efficient generation of highly repetitive DNA sequences of defined lengths by simple standard cloning procedures.

Interference from adults forces young red knots to forage for longer and in dangerous places

NARCIS (Netherlands)

van den Hout, P.J.; van Gils, J.A.; Robin, F.; van der Geest, M.; Dekinga, A.; Piersma, T.

2014-01-01

In birds and mammals, juvenile and adult foragers are often found apart from each other. In this study, we found this is also true for red knots, Calidris canutus canutus, wintering on the intertidal flats of Banc d'Arguin, Mauritania. Not only did juveniles feed separately from adults, they also

Crystallization of Spätzle, a cystine-knot protein involved in embryonic development and innate immunity in Drosophila melanogaster

Energy Technology Data Exchange (ETDEWEB)

Hoffmann, Anita; Neumann, Piotr [Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Abteilung Physikalische Biotechnologie, Kurt-Mothes-Strasse 3, 06120 Halle (Saale) (Germany); Schierhorn, Angelika [Max-Planck-Institut für Proteinfaltung, Abteilung Massenspektrometrie, Kurt-Mothes-Strasse 3, 06120 Halle (Saale) (Germany); Stubbs, Milton T., E-mail: stubbs@biochemtech.uni-halle.de [Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Abteilung Physikalische Biotechnologie, Kurt-Mothes-Strasse 3, 06120 Halle (Saale) (Germany); Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg (Germany)

2008-08-01

Crystallization of the cystine-knot protein Spätzle occurred following serendipitous limited degradation of the pro-Spätzle propeptide during the crystallization experiment. The Spätzle protein is involved in both the definition of the dorsal–ventral axis during embryonic development and in the adult innate immune response. The disulfide-linked dimeric cystine-knot protein has been expressed as a proprotein in inclusion bodies in Escherichia coli and refolded in vitro by rapid dilution. Initial orthorhombic crystals that diffracted to 7 Å resolution were obtained after three months by the sitting-drop vapour-diffusion method. Optimization of the crystallization conditions resulted in orthorhombic crystals (space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 53.0, b = 59.2, c = 62.5 Å) that diffracted to 2.8 Å resolution in-house. The small volume of the asymmetric unit indicated that it was not possible for the crystals to contain the complete pro-Spätzle dimer. Mass spectrometry, N-terminal sequencing and Western-blot analysis revealed that the crystals contained the C-terminal disulfide-linked cystine-knot dimer. Comparison of various crystallization experiments indicated that degradation of the N-terminal prodomain was dependent on the buffer conditions.

Use of electroporation for high-molecular-weight DNA-mediated gene transfer.

Science.gov (United States)

Jastreboff, M M; Ito, E; Bertino, J R; Narayanan, R

1987-08-01

Electroporation was used to introduce high-molecular-weight DNA into murine hematopoietic cells and NIH3T3 cells. CCRF-CEM cells were stably transfected with SV2NEO plasmid and the genomic DNA from G-418-resistant clones (greater than 65 kb) was introduced into mouse bone marrow and NIH3T3 cells by electroporation. NEO sequences and expression were detected in the hematopoietic tissues of lethally irradiated mice, with 24% of individual spleen colonies expressing NEO. The frequency of genomic DNA transfer into NIH3T3 cells was 0.25 X 10(-3). Electroporation thus offers a powerful mode of gene transfer not only of cloned genes but also of high-molecular-weight DNA into cells.

Multiple-strand displacement and identification of single nucleotide polymorphisms as markers of genotypic variation of Pasteuria penetrans biotypes infecting root-knot nematodes.

Science.gov (United States)

Nong, Guang; Chow, Virginia; Schmidt, Liesbeth M; Dickson, Don W; Preston, James F

2007-08-01

Pasteuria species are endospore-forming obligate bacterial parasites of soil-inhabiting nematodes and water-inhabiting cladocerans, e.g. water fleas, and are closely related to Bacillus spp. by 16S rRNA gene sequence. As naturally occurring bacteria, biotypes of Pasteuria penetrans are attractive candidates for the biocontrol of various Meloidogyne spp. (root-knot nematodes). Failure to culture these bacteria outside their hosts has prevented isolation of genomic DNA in quantities sufficient for identification of genes associated with host recognition and virulence. We have applied multiple-strand displacement amplification (MDA) to generate DNA for comparative genomics of biotypes exhibiting different host preferences. Using the genome of Bacillus subtilis as a paradigm, MDA allowed quantitative detection and sequencing of 12 marker genes from 2000 cells. Meloidogyne spp. infected with P. penetrans P20 or B4 contained single nucleotide polymorphisms (SNPs) in the spoIIAB gene that did not change the amino acid sequence, or that substituted amino acids with similar chemical properties. Individual nematodes infected with P. penetrans P20 or B4 contained SNPs in the spoIIAB gene sequenced in MDA-generated products. Detection of SNPs in the spoIIAB gene in a nematode indicates infection by more than one genotype, supporting the need to sequence genomes of Pasteuria spp. derived from single spore isolates.

Intracorporeal knotting of a femoral nerve catheter

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Ghanem, Mohamed

2015-01-01

Full Text Available Peripheral nerve catheters are effective and well-established tools to provide postoperative analgesia to patients undergoing orthopedic surgery. The performance of these techniques is usually considered safe. However, placement of nerve catheters may be associated with a considerable number of side effects and major complications have repeatedly been published. In this work, we report on a patient who underwent total knee replacement with spinal anesthesia and preoperative insertion of femoral and sciatic nerve catheters for postoperative analgesia. During insertion of the femoral catheter, significant resistance was encountered upon retracting the catheter. This occurred due to knotting of the catheter. The catheter had to be removed by operative intervention which has to be considered a major complication. The postoperative course was uneventful. The principles for removal of entrapped peripheral catheters are not well established, may differ from those for neuroaxial catheters, and range from cautious manipulation up to surgical intervention.

Effects of temperature on the life-history traits of Sancassania (Caloglyphus) berlesei (Acari: Astigmatina: Acaridae) feeding on root-knot nematodes, Meloidogyne spp. (Nematoda: Meloidogynidae).

Science.gov (United States)

Abou El-Atta, Doaa Abd El-Maksoud; Ghazy, Noureldin Abuelfadl; Osman, Mohamed Ali

2014-11-01

Sancassania (Caloglyphus) berlesei (Michael) is a cosmopolitan and free-living mite that inhabits soil as well as laboratory colonies of insects and fungi and may have a role as a biocontrol agent of nematodes. In this study, we investigated the effects of temperature on the development, reproduction, and food consumption of S. berlesei fed egg masses of root-knot nematodes, Meloidogyne spp., an important group of agricultural pests. Mites were reared at 20, 25 or 30 °C in the dark. The mites could feed on the nematode egg masses, and their developmental time decreased at higher temperatures. Time from the egg to adult was similar in females and males reared at the same temperature. Adult females lived longer than males at 25 °C, but not at 20 or 30 °C. Generally, females showed a higher rate of food consumption than males. Females laid the largest number of eggs at 20 and 25 °C (199.7 and 189.8 eggs/female, respectively), but the intrinsic rate of natural increase was highest at 30 °C (r m = 0.29). In comparing our data with previous reports, we noted that S. berlesei that fed on egg masses of root-knot nematodes showed a longer developmental time and a lower reproductive rate than Sancassania mites that fed on other diets. Nonetheless, the relatively high value of r m (e.g., at 25 and 30 °C) suggests that this mite may have certain advantages as a biocontrol agent of root-knot nematodes.

Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets.

Science.gov (United States)

Rant, Ulrich; Arinaga, Kenji; Scherer, Simon; Pringsheim, Erika; Fujita, Shozo; Yokoyama, Naoki; Tornow, Marc; Abstreiter, Gerhard

2007-10-30

We report a method to detect label-free oligonucleotide targets. The conformation of surface-tethered probe nucleic acids is modulated by alternating electric fields, which cause the molecules to extend away from or fold onto the biased surface. Binding (hybridization) of targets to the single-stranded probes results in a pronounced enhancement of the layer-height modulation amplitude, monitored optically in real time. The method features an exceptional detection limit of <3 x 10(8) bound targets per cm(2) sensor area. Single base-pair mismatches in the sequences of DNA complements may readily be identified; moreover, binding kinetics and binding affinities can be determined with high accuracy. When driving the DNA to oscillate at frequencies in the kHz regime, distinct switching kinetics are revealed for single- and double-stranded DNA. Molecular dynamics are used to identify the binding state of molecules according to their characteristic kinetic fingerprints by using a chip-compatible detection format.

Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining.

Directory of Open Access Journals (Sweden)

Etienne G J Danchin

2013-10-01

Full Text Available Root-knot nematodes are globally the most aggressive and damaging plant-parasitic nematodes. Chemical nematicides have so far constituted the most efficient control measures against these agricultural pests. Because of their toxicity for the environment and danger for human health, these nematicides have now been banned from use. Consequently, new and more specific control means, safe for the environment and human health, are urgently needed to avoid worldwide proliferation of these devastating plant-parasites. Mining the genomes of root-knot nematodes through an evolutionary and comparative genomics approach, we identified and analyzed 15,952 nematode genes conserved in genomes of plant-damaging species but absent from non target genomes of chordates, plants, annelids, insect pollinators and mollusks. Functional annotation of the corresponding proteins revealed a relative abundance of putative transcription factors in this parasite-specific set compared to whole proteomes of root-knot nematodes. This may point to important and specific regulators of genes involved in parasitism. Because these nematodes are known to secrete effector proteins in planta, essential for parasitism, we searched and identified 993 such effector-like proteins absent from non-target species. Aiming at identifying novel targets for the development of future control methods, we biologically tested the effect of inactivation of the corresponding genes through RNA interference. A total of 15 novel effector-like proteins and one putative transcription factor compatible with the design of siRNAs were present as non-redundant genes and had transcriptional support in the model root-knot nematode Meloidogyne incognita. Infestation assays with siRNA-treated M. incognita on tomato plants showed significant and reproducible reduction of the infestation for 12 of the 16 tested genes compared to control nematodes. These 12 novel genes, showing efficient reduction of parasitism when

A direct method to solve optimal knots of B-spline curves: An application for non-uniform B-spline curves fitting.

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Van Than Dung

Full Text Available B-spline functions are widely used in many industrial applications such as computer graphic representations, computer aided design, computer aided manufacturing, computer numerical control, etc. Recently, there exist some demands, e.g. in reverse engineering (RE area, to employ B-spline curves for non-trivial cases that include curves with discontinuous points, cusps or turning points from the sampled data. The most challenging task in these cases is in the identification of the number of knots and their respective locations in non-uniform space in the most efficient computational cost. This paper presents a new strategy for fitting any forms of curve by B-spline functions via local algorithm. A new two-step method for fast knot calculation is proposed. In the first step, the data is split using a bisecting method with predetermined allowable error to obtain coarse knots. Secondly, the knots are optimized, for both locations and continuity levels, by employing a non-linear least squares technique. The B-spline function is, therefore, obtained by solving the ordinary least squares problem. The performance of the proposed method is validated by using various numerical experimental data, with and without simulated noise, which were generated by a B-spline function and deterministic parametric functions. This paper also discusses the benchmarking of the proposed method to the existing methods in literature. The proposed method is shown to be able to reconstruct B-spline functions from sampled data within acceptable tolerance. It is also shown that, the proposed method can be applied for fitting any types of curves ranging from smooth ones to discontinuous ones. In addition, the method does not require excessive computational cost, which allows it to be used in automatic reverse engineering applications.

Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens.

Science.gov (United States)

Lyons, Eli; Sheridan, Paul; Tremmel, Georg; Miyano, Satoru; Sugano, Sumio

2017-10-24

High-throughput screens allow for the identification of specific biomolecules with characteristics of interest. In barcoded screens, DNA barcodes are linked to target biomolecules in a manner allowing for the target molecules making up a library to be identified by sequencing the DNA barcodes using Next Generation Sequencing. To be useful in experimental settings, the DNA barcodes in a library must satisfy certain constraints related to GC content, homopolymer length, Hamming distance, and blacklisted subsequences. Here we report a novel framework to quickly generate large-scale libraries of DNA barcodes for use in high-throughput screens. We show that our framework dramatically reduces the computation time required to generate large-scale DNA barcode libraries, compared with a naїve approach to DNA barcode library generation. As a proof of concept, we demonstrate that our framework is able to generate a library consisting of one million DNA barcodes for use in a fragment antibody phage display screening experiment. We also report generating a general purpose one billion DNA barcode library, the largest such library yet reported in literature. Our results demonstrate the value of our novel large-scale DNA barcode library generation framework for use in high-throughput screening applications.

Colloidal silica films for high-capacity DNA arrays

Science.gov (United States)

Glazer, Marc Irving

The human genome project has greatly expanded the amount of genetic information available to researchers, but before this vast new source of data can be fully utilized, techniques for rapid, large-scale analysis of DNA and RNA must continue to develop. DNA arrays have emerged as a powerful new technology for analyzing genomic samples in a highly parallel format. The detection sensitivity of these arrays is dependent on the quantity and density of immobilized probe molecules. We have investigated substrates with a porous, "three-dimensional" surface layer as a means of increasing the surface area available for the synthesis of oligonucleotide probes, thereby increasing the number of available probes and the amount of detectable bound target. Porous colloidal silica films were created by two techniques. In the first approach, films were deposited by spin-coating silica colloid suspensions onto flat glass substrates, with the pores being formed by the natural voids between the solid particles (typically 23nm pores, 35% porosity). In the second approach, latex particles were co-deposited with the silica and then pyrolyzed, creating films with larger pores (36 nm), higher porosity (65%), and higher surface area. For 0.3 mum films, enhancements of eight to ten-fold and 12- to 14-fold were achieved with the pure silica films and the films "templated" with polymer latex, respectively. In gene expression assays for up to 7,000 genes using complex biological samples, the high-capacity films provided enhanced signals and performed equivalently or better than planar glass on all other functional measures, confirming that colloidal silica films are a promising platform for high-capacity DNA arrays. We have also investigated the kinetics of hybridization on planar glass and high-capacity substrates. Adsorption on planar arrays is similar to ideal Langmuir-type adsorption, although with an "overshoot" at high solution concentration. Hybridization on high-capacity films is

Average size of random polygons with fixed knot topology.

Science.gov (United States)

Matsuda, Hiroshi; Yao, Akihisa; Tsukahara, Hiroshi; Deguchi, Tetsuo; Furuta, Ko; Inami, Takeo

2003-07-01

We have evaluated by numerical simulation the average size R(K) of random polygons of fixed knot topology K=,3(1),3(1) musical sharp 4(1), and we have confirmed the scaling law R(2)(K) approximately N(2nu(K)) for the number N of polygonal nodes in a wide range; N=100-2200. The best fit gives 2nu(K) approximately 1.11-1.16 with good fitting curves in the whole range of N. The estimate of 2nu(K) is consistent with the exponent of self-avoiding polygons. In a limited range of N (N greater, similar 600), however, we have another fit with 2nu(K) approximately 1.01-1.07, which is close to the exponent of random polygons.

An optimized rapid bisulfite conversion method with high recovery of cell-free DNA.

Science.gov (United States)

Yi, Shaohua; Long, Fei; Cheng, Juanbo; Huang, Daixin

2017-12-19

Methylation analysis of cell-free DNA is a encouraging tool for tumor diagnosis, monitoring and prognosis. Sensitivity of methylation analysis is a very important matter due to the tiny amounts of cell-free DNA available in plasma. Most current methods of DNA methylation analysis are based on the difference of bisulfite-mediated deamination of cytosine between cytosine and 5-methylcytosine. However, the recovery of bisulfite-converted DNA based on current methods is very poor for the methylation analysis of cell-free DNA. We optimized a rapid method for the crucial steps of bisulfite conversion with high recovery of cell-free DNA. A rapid deamination step and alkaline desulfonation was combined with the purification of DNA on a silica column. The conversion efficiency and recovery of bisulfite-treated DNA was investigated by the droplet digital PCR. The optimization of the reaction results in complete cytosine conversion in 30 min at 70 °C and about 65% of recovery of bisulfite-treated cell-free DNA, which is higher than current methods. The method allows high recovery from low levels of bisulfite-treated cell-free DNA, enhancing the analysis sensitivity of methylation detection from cell-free DNA.

Study the Effect of Three Species of Medicinal Plants of the Mint Family on Pathogenicity and Damage Root Knot Nematode Meloidogyne javanica in Tomato

Directory of Open Access Journals (Sweden)

Maryam Fayaz

2017-03-01

Full Text Available Introduction: Root-knot nematodes (Meloidogyne spp. are important plant pathogens that make large damage to the crops. The activity of root-knot nematode and reaction of host plant results in the development of several knots on the root, which interrupts water and food absorption system of the plant. Among popular methods for controlling root-knot nematodes are physical methods (soil solarization and flooding, farming methods (crop rotation, weed removal, contaminated roots removal, fertilization, soil reinforcement, planting time adjustment, and use of resistant varieties, and chemical methods (disinfection with pesticide and foliar spray. Incomplete control, high cost and environmental problems (chemical compounds have directed some researchers toward to use non-chemical methods such as herbs and herbal products for the management nematodes. Mankind has used medicinal plants throughout the history in both direct and indirect ways. Today, medicinal plants have a considerable share of medical products. The nematicidal effect of many plants has been demonstrated and the use of plant products has been considered as a safe method to control root-knot nematode. This method is cheap and easy to use, does not cause environmental pollution, and is able to improve the soil in structural and nutritional terms. Organic plants possess a wide range of secondary metabolites such as phenyls, flavonoids, coinons, tanons, essences, alkaloids, saponins, and sterols. These substances are biodegradable owing to their natural origin and do not pollute the environment. Today, active plant compounds are given much attention because they are less durable and do not have the negative impact on mammals and non-target organisms. Plant products including essences and extracts are usually used to control plant diseases nematodes. Therefore, due to the favorable impact of plants in controlling Root-knot nematodes, In this study, the presence of several herbs (thyme, hyssop

Development of a sweet cherry pepper line with resistance to the southern root-knot nematode Meloidogyne incognita

Science.gov (United States)

The southern root-knot nematode (Meloidogyne incognita) is a major pathogen of pepper (Capsicum spp.), causing significant yield losses in heavily infected plants. The N-gene confers resistance to M. incognita, and has been successfully used to mitigate nematode damage in specific pepper varieties f...

Comparing root knot nematode (Meloidogyne spp.) effects on tomato (Solanum lycopersicum) and grapevine (Vitis spp.) metabolic profiles

Science.gov (United States)

Root knot nematodes (Meloidogyne spp., RKN) can negatively impact both herbaceous annual and woody perennial hosts. RKN infestations also may increase plant host susceptibility to other stresses such as those imposed by water deficits or various diseases. However, little is known about direct or ind...

High Efficiency Hydrodynamic DNA Fragmentation in a Bubbling System.

Science.gov (United States)

Li, Lanhui; Jin, Mingliang; Sun, Chenglong; Wang, Xiaoxue; Xie, Shuting; Zhou, Guofu; van den Berg, Albert; Eijkel, Jan C T; Shui, Lingling

2017-01-18

DNA fragmentation down to a precise fragment size is important for biomedical applications, disease determination, gene therapy and shotgun sequencing. In this work, a cheap, easy to operate and high efficiency DNA fragmentation method is demonstrated based on hydrodynamic shearing in a bubbling system. We expect that hydrodynamic forces generated during the bubbling process shear the DNA molecules, extending and breaking them at the points where shearing forces are larger than the strength of the phosphate backbone. Factors of applied pressure, bubbling time and temperature have been investigated. Genomic DNA could be fragmented down to controllable 1-10 Kbp fragment lengths with a yield of 75.30-91.60%. We demonstrate that the ends of the genomic DNAs generated from hydrodynamic shearing can be ligated by T4 ligase and the fragmented DNAs can be used as templates for polymerase chain reaction. Therefore, in the bubbling system, DNAs could be hydrodynamically sheared to achieve smaller pieces in dsDNAs available for further processes. It could potentially serve as a DNA sample pretreatment technique in the future.

From the root to the stem: interaction between the biocontrol root endophyte Pseudomonas fluorescens PICF7 and the pathogen Pseudomonas savastanoi NCPPB 3335 in olive knots

Science.gov (United States)

Maldonado-González, M Mercedes; Prieto, Pilar; Ramos, Cayo; Mercado-Blanco, Jesús

2013-01-01

Olive knot disease, caused by Pseudomonas savastanoi pv. savastanoi, is one of the most important biotic constraints for olive cultivation. Pseudomonas fluorescens PICF7, a natural colonizer of olive roots and effective biological control agent (BCA) against Verticillium wilt of olive, was examined as potential BCA against olive knot disease. Bioassays using in vitro-propagated olive plants were carried out to assess whether strain PICF7 controlled knot development either when co-inoculated with the pathogen in stems or when the BCA (in roots) and the pathogen (in stems) were spatially separated. Results showed that PICF7 was able to establish and persist in stem tissues upon artificial inoculation. While PICF7 was not able to suppress disease development, its presence transiently decreased pathogen population size, produced less necrotic tumours, and sharply altered the localization of the pathogen in the hyperplasic tissue, which may pose epidemiological consequences. Confocal laser scanning microscopy combined with fluorescent tagging of bacteria revealed that when PICF7 was absent the pathogen tended to be localized at the knot surface. However, presence of the BCA seemed to confine P. savastanoi at inner regions of the tumours. This approach has also enabled to prove that the pathogen can moved systemically beyond the hypertrophied tissue. PMID:23425069

Knots, topology and quantum field theories

International Nuclear Information System (INIS)

Lusanna, L.

1989-01-01

The title of the workshop, Knots, Topology and Quantum Field Theory, accurate reflected the topics discussed. There have been important developments in mathematical and quantum field theory in the past few years, which had a large impact on physicist thinking. It is historically unusual and pleasing that these developments are taking place as a result of an intense interaction between mathematical physicists and mathematician. On the one hand, topological concepts and methods are playing an increasingly important lead to novel mathematical concepts: for instance, the study of quantum groups open a new chapter in the deformation theory of Lie algebras. These developments at present will lead to new insights into the theory of elementary particles and their interactions. In essence, the talks dealt with three, broadly defined areas of theoretical physics. One was topological quantum field theories, the other the problem of quantum groups and the third one certain aspects of more traditional field theories, such as, for instance, quantum gravity. These topics, however, are interrelated and the general theme of the workshop defies rigid classification; this was evident from the cross references to be found in almo all the talks

DNA-dispersed graphene/NiO hybrid materials for highly sensitive non-enzymatic glucose sensor

International Nuclear Information System (INIS)

Lv Wei; Jin Fengmin; Guo Quangui; Yang Quanhong; Kang Feiyu

2012-01-01

Highlights: ► We investigated the potential of GNS/NiO/DNA hybrid used as a nonenzymatic sensor. ► DNA is a highly efficient disperse agent for GNS/NiO hybrid than ionic surfactants. ► GNS/NiO/DNA hybrid shows fast electron transfer in the electrochemical reaction. ► GNS/NiO/DNA hybrid shows good detection performance towards glucose. - Abstract: We demonstrate graphene nanosheet/NiO hybrids (GNS/NiO) as the active material for high-performance non-enzymatic glucose sensors. Such sensors are fabricated by DNA-dispersed GNS/NiO suspension deposited on glassy carbon electrodes. ss-DNA shows strong dispersing ability for the GNS/NiO hybrid materials resulting in stable water-dispersible GNS/NiO/DNA hybrids with fully separated layers. The GNS/NiO/DNA hybrids show enhanced electron transfer in the electrocatalytic reaction process, and accordingly, such hybrids modified electrodes show good sensing performance towards glucose and are characterized by large detection ranges, short response periods, low detection limit and high sensitivity and stability.

Quantum invariants of knots and 3-manifolds. 2. rev. ed.

International Nuclear Information System (INIS)

Turaev, Vladimir G.

2010-01-01

Due to the strong appeal and wide use of this monograph, it is now available in its second revised edition. The monograph gives a systematic treatment of 3-dimensional topological quantum field theories (TQFTs) based on the work of the author with N. Reshetikhin and O. Viro. This subject was inspired by the discovery of the Jones polynomial of knots and the Witten-Chern-Simons field theory. On the algebraic side, the study of 3-dimensional TQFTs has been influenced by the theory of braided categories and the theory of quantum groups. The book is divided into three parts. Part I presents a construction of 3-dimensional TQFTs and 2-dimensional modular functors from so-called modular categories. This gives a vast class of knot invariants and 3-manifold invariants as well as a class of linear representations of the mapping class groups of surfaces. In Part II the technique of 6j-symbols is used to define state sum invariants of 3-manifolds. Their relation to the TQFTs constructed in Part I is established via the theory of shadows. Part III provides constructions of modular categories, based on quantum groups and skein modules of tangles in the 3-space. This fundamental contribution to topological quantum field theory is accessible to graduate students in mathematics and physics with knowledge of basic algebra and topology. It is an indispensable source for everyone who wishes to enter the forefront of this fascinating area at the borderline of mathematics and physics. From the contents: - Invariants of graphs in Euclidean 3-space and of closed 3-manifolds - Foundations of topological quantum field theory - Three-dimensional topological quantum field theory - Two-dimensional modular functors - 6j-symbols - Simplicial state sums on 3-manifolds - Shadows of manifolds and state sums on shadows - Constructions of modular categories. (orig.)

Behavioural evidence for heat-load problems in Great Knots in tropical Australia fuelling for long-distance flight

NARCIS (Netherlands)

Battley, PF; Rogers, DI; Piersma, T; Koolhaas, A; Battley, Phil F.; Rogers, Danny I.

2003-01-01

Migratory shorebirds that live in the tropics prior to embarking on long (> 5000 km) flights may face heat-load problems. The behaviour of a large sandpiper, the Great Knot (Calidris tenuirostris), was studied in Roebuck Bay, north-west Australia, from February to April 2000. We determined the

RECONSTRUCTING DIET COMPOSITION ON THE BASIS OF FECES IN A MOLLUSK-EATING WADER, THE KNOT CALIDRIS-CANUTUS

NARCIS (Netherlands)

DEKINGA, A; PIERSMA, T

Methods are described to assess the molluscan diet of Knots feeding on intertidal flats in western Europe from their faecal output. The size distributions of two common bivalve prey, Macoma balthica and Cerastoderma edule, can be estimated from the heights of shell hinges retrieved from droppings.

Reconstructing diet composition on the basis of faeces in a mollusc-eating wader, the Knot Calidris canutus

NARCIS (Netherlands)

Dekinga, A.; Piersma, T.

1993-01-01

Methods are described to assess the molluscan diet of Knots feeding on intertidal flats in western Europe from their faecal output. The size distributions of two common bivalve prey, Macoma balthica and Cerastoderma edule, can be estimated from the heights of shell hinges retrieved from droppings.

Hanseniaspora nodinigri, a new yeast species found in black knots (Dibotryon morbosum) of Prunus virginiana.

Science.gov (United States)

Lachance, M A

1981-07-01

The new yeast species Hanseniaspora nodinigri is described to accommodate members of the genus Hanseniaspora that are unable to assimilate glucono-sigma-lactone and isolated from stromatal tissue of black knots (Dobotryon morbosum) of chokecherry, Prunus virginiana. The newly described taxon shows much resemblance, by other criteria, to H. vineae van der Walt et Tscheuschner and H. osmophila (Niehaus) Phaff, Miller et Shifrine.

Explicit Gaussian quadrature rules for C^1 cubic splines with symmetrically stretched knot sequence

KAUST Repository

Ait-Haddou, Rachid

2015-06-19

We provide explicit expressions for quadrature rules on the space of C^1 cubic splines with non-uniform, symmetrically stretched knot sequences. The quadrature nodes and weights are derived via an explicit recursion that avoids an intervention of any numerical solver and the rule is optimal, that is, it requires minimal number of nodes. Numerical experiments validating the theoretical results and the error estimates of the quadrature rules are also presented.

Coupling of MIC-3 overexpression with the chromosome 11 and 14 root-knot nematode (RKN) (Meloidogyne incognita) resistance QTLs provides insights into the regulation of the RKN resistance response in Upland cotton...

Science.gov (United States)

High levels of resistance to root-knot nematode (RKN) (Meloidogyne incognita) in Upland cotton (Gossypium hirsutum) is mediated by two major quantitative trait loci (QTL) located on chromosomes 11 and 14. We had previously determined that MIC-3 expression played a direct role in suppressing RKN egg...

New knotted solutions of Maxwell's equations

International Nuclear Information System (INIS)

Hoyos, Carlos; Sircar, Nilanjan; Sonnenschein, Jacob

2015-01-01

In this paper we have further developed the study of topologically non-trivial solutions of vacuum electrodynamics. We have discovered a novel method of generating such solutions by applying conformal transformations with complex parameters on known solutions expressed in terms of Bateman's variables. This has enabled us to obtain a wide class of solutions from the basic configuration, such as constant electromagnetic fields and plane-waves. We have introduced a covariant formulation of Bateman's construction and discussed the conserved charges associated with the conformal group as well as a set of four types of conserved helicities. We have also given a formulation in terms of quaternions. This led to a simple map between the electromagnetic knotted and linked solutions into flat connections of SU(2) gauge theory. We have computed the corresponding Chern–Simons charge in a class of solutions and the charge takes integer values. (paper)

High-throughput STR analysis for DNA database using direct PCR.

Science.gov (United States)

Sim, Jeong Eun; Park, Su Jeong; Lee, Han Chul; Kim, Se-Yong; Kim, Jong Yeol; Lee, Seung Hwan

2013-07-01

Since the Korean criminal DNA database was launched in 2010, we have focused on establishing an automated DNA database profiling system that analyzes short tandem repeat loci in a high-throughput and cost-effective manner. We established a DNA database profiling system without DNA purification using a direct PCR buffer system. The quality of direct PCR procedures was compared with that of conventional PCR system under their respective optimized conditions. The results revealed not only perfect concordance but also an excellent PCR success rate, good electropherogram quality, and an optimal intra/inter-loci peak height ratio. In particular, the proportion of DNA extraction required due to direct PCR failure could be minimized to <3%. In conclusion, the newly developed direct PCR system can be adopted for automated DNA database profiling systems to replace or supplement conventional PCR system in a time- and cost-saving manner. © 2013 American Academy of Forensic Sciences Published 2013. This article is a U.S. Government work and is in the public domain in the U.S.A.

High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center.

Science.gov (United States)

Baños-Mateos, Soledad; van Roon, Anne-Marie M; Lang, Ulla F; Maslen, Sarah L; Skehel, J Mark; Lamers, Meindert H

2017-10-11

High-fidelity DNA replication depends on a proofreading 3'-5' exonuclease that is associated with the replicative DNA polymerase. The replicative DNA polymerase DnaE1 from the major pathogen Mycobacterium tuberculosis (Mtb) uses its intrinsic PHP-exonuclease that is distinct from the canonical DEDD exonucleases found in the Escherichia coli and eukaryotic replisomes. The mechanism of the PHP-exonuclease is not known. Here, we present the crystal structure of the Mtb DnaE1 polymerase. The PHP-exonuclease has a trinuclear zinc center, coordinated by nine conserved residues. Cryo-EM analysis reveals the entry path of the primer strand in the PHP-exonuclease active site. Furthermore, the PHP-exonuclease shows a striking similarity to E. coli endonuclease IV, which provides clues regarding the mechanism of action. Altogether, this work provides important insights into the PHP-exonuclease and reveals unique properties that make it an attractive target for novel anti-mycobacterial drugs.The polymerase and histidinol phosphatase (PHP) domain in the DNA polymerase DnaE1 is essential for mycobacterial high-fidelity DNA replication. Here, the authors determine the DnaE1 crystal structure, which reveals the PHP-exonuclease mechanism that can be exploited for antibiotic development.

Analysis of JC virus DNA replication using a quantitative and high-throughput assay

International Nuclear Information System (INIS)

Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert; Gagnon, David; Gjoerup, Ole; Archambault, Jacques; Bullock, Peter A.

2014-01-01

Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication

Analysis of JC virus DNA replication using a quantitative and high-throughput assay

Energy Technology Data Exchange (ETDEWEB)

Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States); Gagnon, David [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Gjoerup, Ole [Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA 02111 (United States); Archambault, Jacques [Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7 (Canada); Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec (Canada); Bullock, Peter A., E-mail: Peter.Bullock@tufts.edu [Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111 (United States)

2014-11-15

Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. - Highlights: • Development of a high-throughput screening assay for JCV DNA replication using C33A cells. • Evidence that T-ag fails to accumulate in the nuclei of established glioma cell lines. • Evidence that NF-1 directly promotes JCV DNA replication in C33A cells. • Proof-of-concept that the HTS assay can be used to identify pharmacological inhibitor of JCV DNA replication.

Coastal Fishermen as Lifesavers While Sailing at High Speed: A Crossover Study

Directory of Open Access Journals (Sweden)

Ramón Fungueiriño-Suárez

2018-01-01

Full Text Available Purpose. Starting basic cardiopulmonary resuscitation (CPR early improves survival. Fishermen are the first bystanders while at work. Our objective was to test in a simulated scenario the CPR quality performed by fishermen while at port and while navigating at different speeds. Methods. Twenty coastal fishermen were asked to perform 2 minutes of CPR (chest compressions and mouth-to-mouth ventilations on a manikin, in three different scenarios: (A at port on land, (B on the boat floor sailing at 10 knots, and (C sailing at 20 knots. Data was recorded using quality CPR software, adjusted to current CPR international guidelines. Results. The quality of CPR (QCPR was significantly higher at port (43%±10 than sailing at 10 knots (30%±15; p=0.01 or at 20 knots (26%±12; p=0.001. The percentage of ventilation that achieved some lung insufflation was also significantly higher when CPR was done at port (77%±14 than while sailing at 10 knots (59%±18 or 20 knots (57%±21 (p=0.01. Conclusion. In the event of drowning or cardiac arrest on a small boat, fishermen should immediately start basic CPR and navigate at a relatively high speed to the nearest port if the sea conditions are safe.

Effects of Microhabitat, Flocking, Climate and Migratory Goal on Energy Expenditure in the Annual Cycle of Red Knots

NARCIS (Netherlands)

Wiersma, Popko; Piersma, Theunis

We quantify seasonal changes in the maintenance energy requirements of Red Knots (Calidris canutus islandica). This subspecies breeds on the tundra of northeast Canada and north Greenland, migrates through Iceland and spends the winter in the coastal regions of western Europe. Maintenance Metabolism

Influence of root exudates and soil on attachment of Pasteuria penetrans to root-knot nematode Meloidogyne arenaria

Science.gov (United States)

Pasteuria penetrans is a parasite of root-knot nematode (Meloidogyne spp.). Spores of P. penetrans attach to the cuticle of second stage juvenile (J2) and sterilize infected female. This study looked at different factors that influence spore attachment of P. penetrans to M. arenaria. Incubating J2 ...

Knot wormholes and the dimensional invariant of exceptional Lie groups and Stein space hierarchies

International Nuclear Information System (INIS)

Elokaby, Ayman

2009-01-01

The present short note points out a most interesting and quite unexpected connection between the number of distinct knot as a function of their crossing number and exceptional Lie groups and Stein space hierarchies. It is found that the crossing number 7 plays the role of threshold similar to 4 and 5 in E-infinity theory and for the 11 crossing the number of distinct knots is very close to 4α-bar 0 +1=548+1=549, where α-bar 0 =137 is the inverse integer electromagnetic fine structure constant. This is particularly intriguing in view of a similar relation pertinent to the 17 two and three Stein spaces where the total dimension is Σ 1 17 Stein=5α-bar 0 +1=685+1=686, as well as the sum of the eight exceptional Lie symmetry groups Σ i=1 8 |E i |=4α-bar 0 =548. The slight discrepancy of one is explained in both cases by the inclusion of El Naschie's transfinite corrections leading to Σ i=1 8 |E i |=(4)(137+k 0 )=548.328157 and Σ i=1 17 Stein=(5)(137+k 0 )=685.41097, where k o = φ 5 (1 - φ 5 ) and φ=(√(5)-1)/2.

Sustainable management of root-knot disease of tomato by neem cake and Glomus fasciculatum

Directory of Open Access Journals (Sweden)

Rose Rizvi

2015-12-01

Full Text Available A pot experiment was conducted during winter season of 2009–2010 in the department of Botany, AMU, Aligarh, India, to determine the nematicidal potential of organic matter, neem cake at third level of dose, and bioagent, Glomus fasciculatum in terms of various growth parameters of tomato, when inoculated individually as well as concomitantly with respect to root-knot development. Neem cake and G. fasciculatum showed potential for sustainable management while providing nutrient sources for proper plant growth. Disease intensity of root-knot nematode decreased while increasing the doses of neem cake along with the G. fasciculatum. Chlorophyll contents have been found to be increased in single and combined application as well. There is a progressive increase in growth parameters raised in soil amended with 10, 20, and 30 g neem cake/kg soil and inoculated with G. fasciculatum. Significant improvement in the plant growth was observed when G. fasciculatum and neem cake were inoculated simultaneously. Neem cake plus G. fasciculatum reduced the nematodes’ multiplication and root-galling, and increased the plant growth of tomato as compared to unamended and Meloidogyne incognita-inoculated plants. Mycorrhyzation and agronomic parameters were increased due to application of G. fasciculatum alone, but enhanced further when inoculated with neem cake.

High Efficiency Acetylcholinesterase Immobilization on DNA Aptamer Modified Surfaces

Directory of Open Access Journals (Sweden)

Orada Chumphukam

2014-04-01

Full Text Available We report here the in vitro selection of DNA aptamers for electric eel acetylcholinesterase (AChE. One selected aptamer sequence (R15/19 has a high affinity towards the enzyme (Kd = 157 ± 42 pM. Characterization of the aptamer showed its binding is not affected by low ionic strength (~20 mM, however significant reduction in affinity occurred at high ionic strength (~1.2 M. In addition, this aptamer does not inhibit the catalytic activity of AChE that we exploit through immobilization of the DNA on a streptavidin-coated surface. Subsequent immobilization of AChE by the aptamer results in a 4-fold higher catalytic activity when compared to adsorption directly on to plastic.

Type IIB Ileosigmoid knotting: a case report

Directory of Open Access Journals (Sweden)

Ajak Makor

2018-02-01

Full Text Available Ileosigmoid knotting is a rare cause of acute intestinal obstruction. It is more common in Africans and Asians than in white populations and it is more prevalent in males than in females with a ratio of 14:1. It is classified into four types (I, II, III and IV with further extra two subtypes of A and B where type A is the most common presentation. Preoperative diagnosis is a challenge to the frontline doctors in the accidents and emergency departments; especially with limited diagnostic tools. Ultrasonography may be misleading in most of the cases due to the similarity of the disease with other causes of acute abdomen, especially acute appendicitis. Clinical presentation of an unprecedented intestinal obstruction with constant upper to mid-abdominal quadrant pain associated with mild to moderate abdominal distension contrary to the severe abdominal distension in sigmoid volvulus are the hallmarks that can help the surgical team to reach an accurate and early diagnosis preoperatively to avoid the devastating ischemia and gangrene in case of delay.

Selection of DNA aptamers against epidermal growth factor receptor with high affinity and specificity

Energy Technology Data Exchange (ETDEWEB)

Wang, Deng-Liang [The First Clinical Medical College of Fujian Medical University, Fuzhou (China); Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou (China); Song, Yan-Ling; Zhu, Zhi; Li, Xi-Lan; Zou, Yuan [State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (China); Yang, Hai-Tao; Wang, Jiang-Jie [The First Clinical Medical College of Fujian Medical University, Fuzhou (China); Yao, Pei-Sen [Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou (China); Pan, Ru-Jun [The First Clinical Medical College of Fujian Medical University, Fuzhou (China); Yang, Chaoyong James, E-mail: cyyang@xmu.edu.cn [State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (China); Kang, De-Zhi, E-mail: kdzy99988@163.com [The First Clinical Medical College of Fujian Medical University, Fuzhou (China); Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou (China)

2014-10-31

Highlights: • This is the first report of DNA aptamer against EGFR in vitro. • Aptamer can bind targets with high affinity and selectivity. • DNA aptamers are more stable, cheap and efficient than RNA aptamers. • Our selected DNA aptamer against EGFR has high affinity with K{sub d} 56 ± 7.3 nM. • Our selected DNA aptamer against EGFR has high selectivity. - Abstract: Epidermal growth factor receptor (EGFR/HER1/c-ErbB1), is overexpressed in many solid cancers, such as epidermoid carcinomas, malignant gliomas, etc. EGFR plays roles in proliferation, invasion, angiogenesis and metastasis of malignant cancer cells and is the ideal antigen for clinical applications in cancer detection, imaging and therapy. Aptamers, the output of the systematic evolution of ligands by exponential enrichment (SELEX), are DNA/RNA oligonucleotides which can bind protein and other substances with specificity. RNA aptamers are undesirable due to their instability and high cost of production. Conversely, DNA aptamers have aroused researcher’s attention because they are easily synthesized, stable, selective, have high binding affinity and are cost-effective to produce. In this study, we have successfully identified DNA aptamers with high binding affinity and selectivity to EGFR. The aptamer named TuTu22 with K{sub d} 56 ± 7.3 nM was chosen from the identified DNA aptamers for further study. Flow cytometry analysis results indicated that the TuTu22 aptamer was able to specifically recognize a variety of cancer cells expressing EGFR but did not bind to the EGFR-negative cells. With all of the aforementioned advantages, the DNA aptamers reported here against cancer biomarker EGFR will facilitate the development of novel targeted cancer detection, imaging and therapy.

Selection of DNA aptamers against epidermal growth factor receptor with high affinity and specificity

International Nuclear Information System (INIS)

Wang, Deng-Liang; Song, Yan-Ling; Zhu, Zhi; Li, Xi-Lan; Zou, Yuan; Yang, Hai-Tao; Wang, Jiang-Jie; Yao, Pei-Sen; Pan, Ru-Jun; Yang, Chaoyong James; Kang, De-Zhi

2014-01-01

Highlights: • This is the first report of DNA aptamer against EGFR in vitro. • Aptamer can bind targets with high affinity and selectivity. • DNA aptamers are more stable, cheap and efficient than RNA aptamers. • Our selected DNA aptamer against EGFR has high affinity with K d 56 ± 7.3 nM. • Our selected DNA aptamer against EGFR has high selectivity. - Abstract: Epidermal growth factor receptor (EGFR/HER1/c-ErbB1), is overexpressed in many solid cancers, such as epidermoid carcinomas, malignant gliomas, etc. EGFR plays roles in proliferation, invasion, angiogenesis and metastasis of malignant cancer cells and is the ideal antigen for clinical applications in cancer detection, imaging and therapy. Aptamers, the output of the systematic evolution of ligands by exponential enrichment (SELEX), are DNA/RNA oligonucleotides which can bind protein and other substances with specificity. RNA aptamers are undesirable due to their instability and high cost of production. Conversely, DNA aptamers have aroused researcher’s attention because they are easily synthesized, stable, selective, have high binding affinity and are cost-effective to produce. In this study, we have successfully identified DNA aptamers with high binding affinity and selectivity to EGFR. The aptamer named TuTu22 with K d 56 ± 7.3 nM was chosen from the identified DNA aptamers for further study. Flow cytometry analysis results indicated that the TuTu22 aptamer was able to specifically recognize a variety of cancer cells expressing EGFR but did not bind to the EGFR-negative cells. With all of the aforementioned advantages, the DNA aptamers reported here against cancer biomarker EGFR will facilitate the development of novel targeted cancer detection, imaging and therapy

A farmer friendly and economic IPM strategy to combat root-knot nematodes infesting lentil

OpenAIRE

Rose Rizvi; Rizwan Ali Ansari; Gulshan Zehra; Irshad Mahmood

2015-01-01

An experiment was conducted to assess the effect of Rhizobium sp., waste tea leaves, eggshell powder, and composted cow dung manure on the root-knot nematode, Meloidogyne incognita, on lentil in Botany department AMU, Aligarh, India. When used alone, composted cow dung was better in reducing galling and nematode multiplication and improving lentil growth followed by eggshell powder, Rhizobium sp., and waste tea leaves. Significant result in the integrated management of M. incognita was obtain...

Rapid population decline in red knots : fitness consequences of decreased refuelling rates and late arrival in Delaware Bay

NARCIS (Netherlands)

Baker, AJ; Gonzalez, PM; Piersma, T; Niles, LJ; do Nascimento, IDS; Atkinson, PW; Clark, NA; Minton, CDT; Peck, MK; Aarts, G

2004-01-01

Most populations of migrant shorebirds around the world are in serious decline, suggesting that vital condition-dependent rates such as fecundity and annual survival are being affected globally. A striking example is the red knot (Calidris canutus rufa) population wintering in Tierra del Fuego,

Self-Assembly DNA Polyplex Vaccine inside Dissolving Microneedles for High-Potency Intradermal Vaccination

Science.gov (United States)

Liao, Jing-Fong; Lee, Jin-Ching; Lin, Chun-Kuang; Wei, Kuo-Chen; Chen, Pin-Yuan; Yang, Hung-Wei

2017-01-01

The strong immunogenicity induction is the powerful weapon to prevent the virus infections. This study demonstrated that one-step synthesis of DNA polyplex vaccine in microneedle (MN) patches can induce high immunogenicity through intradermal vaccination and increase the vaccine stability for storage outside the cold chain. More negative charged DNA vaccine was entrapped into the needle region of MNs followed by DNA polyplex formation with branched polyethylenimine (bPEI) pre-coated in the cavities of polydimethylsiloxane (PDMS) molds that can deliver more DNA vaccine to immune-cell rich epidermis with high transfection efficiency. Our data in this study support the safety and immunogenicity of the MN-based vaccine; the MN patch delivery system induced an immune response 3.5-fold as strong as seen with conventional intramuscular administration; the DNA polyplex formulation provided excellent vaccine stability at high temperature (could be stored at 45ºC for at least 4 months); the DNA vaccine is expected to be manufactured at low cost and not generate sharps waste. We think this study is significant to public health because there is a pressing need for an effective vaccination in developing countries. PMID:28819449

Quandles and topological pairs symmetry, knots, and cohomology

CERN Document Server

Nosaka, Takefumi

2017-01-01

This book surveys quandle theory, starting from basic motivations and going on to introduce recent developments of quandles with topological applications and related topics. The book is written from topological aspects, but it illustrates how esteemed quandle theory is in mathematics, and it constitutes a crash course for studying quandles. More precisely, this work emphasizes the fresh perspective that quandle theory can be useful for the study of low-dimensional topology (e.g., knot theory) and relative objects with symmetry. The direction of research is summarized as “We shall thoroughly (re)interpret the previous studies of relative symmetry in terms of the quandle”. The perspectives contained herein can be summarized by the following topics. The first is on relative objects G/H, where G and H are groups, e.g., polyhedrons, reflection, and symmetric spaces. Next, central extensions of groups are discussed, e.g., spin structures, K2 groups, and some geometric anomalies. The third topic is a method to s...

Effect of Emamectin Benzoate on Root-Knot Nematodes and Tomato Yield.

Science.gov (United States)

Cheng, Xingkai; Liu, Xiumei; Wang, Hongyan; Ji, Xiaoxue; Wang, Kaiyun; Wei, Min; Qiao, Kang

2015-01-01

Southern root-knot nematode (Meloidogyne incognita) is an obligate, sedentary endoparasite of more than 3000 plant species, that causes heavy economic losses and limit the development of protected agriculture of China. As a biological pesticide, emamectin benzoate has effectively prevented lepidopteran pests; however, its efficacy to control M. incognita remains unknown. The purpose of the present study was to test soil application of emamectin benzoate for management of M. incognita in laboratory, greenhouse and field trials. Laboratory results showed that emamectin benzoate exhibited high toxicity to M. incognita, with LC50 and LC90 values 3.59 and 18.20 mg L(-1), respectively. In greenhouse tests, emamectin benzoate soil application offered good efficacy against M. incognita while maintaining excellent plant growth. In field trials, emamectin benzoate provided control efficacy against M. incognita and resulted in increased tomato yields. Compared with the untreated control, there was a 36.5% to 81.3% yield increase obtained from all treatments and the highest yield was received from the highest rate of emamectin benzoate. The results confirmed that emamectin benzoate has enormous potential for the control of M. incognita in tomato production in China.

Effect of Emamectin Benzoate on Root-Knot Nematodes and Tomato Yield.

Directory of Open Access Journals (Sweden)

Xingkai Cheng

Full Text Available Southern root-knot nematode (Meloidogyne incognita is an obligate, sedentary endoparasite of more than 3000 plant species, that causes heavy economic losses and limit the development of protected agriculture of China. As a biological pesticide, emamectin benzoate has effectively prevented lepidopteran pests; however, its efficacy to control M. incognita remains unknown. The purpose of the present study was to test soil application of emamectin benzoate for management of M. incognita in laboratory, greenhouse and field trials. Laboratory results showed that emamectin benzoate exhibited high toxicity to M. incognita, with LC50 and LC90 values 3.59 and 18.20 mg L(-1, respectively. In greenhouse tests, emamectin benzoate soil application offered good efficacy against M. incognita while maintaining excellent plant growth. In field trials, emamectin benzoate provided control efficacy against M. incognita and resulted in increased tomato yields. Compared with the untreated control, there was a 36.5% to 81.3% yield increase obtained from all treatments and the highest yield was received from the highest rate of emamectin benzoate. The results confirmed that emamectin benzoate has enormous potential for the control of M. incognita in tomato production in China.

Effect of castor bean (Ricinus communis L.) aqueous extracts on the performance of root-knot nematodes (Meloidogyne spp.) on tomato (Solanum lycopersicum L.)

International Nuclear Information System (INIS)

Adomako, J.; Kwoseh, C. K.

2013-01-01

The increased concern for environmental and health hazards have called for a reduction in the use of synthetic nematicides for nematode control. Experiments were, therefore, conducted to ascertain the nematicidal potential of castor bean's crude extract and its five lower concentrations with water as control. In the in vitro studies, crude castor bean aqueous extract and 10, 20, 30 and 40% different concentrations with 100 root-knot nematode eggs or juveniles in separate Petri dishes showed that all the different concentrations had toxic effects on eggs and juveniles of root-knot nematode. Egg hatch inhibition and juvenile mortality increased with increased concentration of the extracts. With an increase in exposure time, juvenile mortality increased. In potted plant studies, crude castor bean aqueous extracts and its lower concentrations of 20, 40 and 60% caused significant improvement in plant growth measures such as height and fresh shoot weight over the water blank control. The crude castor bean extract was nematotoxic to root -knot nematodes in vitro and in potted-tomato plants, but this was not demonstrated in field studies. Further work needs to be done before a firm recommendation can be made. (au)

Highly sensitive polymerase chain reaction-free quantum dot-based quantification of forensic genomic DNA

International Nuclear Information System (INIS)

Tak, Yu Kyung; Kim, Won Young; Kim, Min Jung; Han, Eunyoung; Han, Myun Soo; Kim, Jong Jin; Kim, Wook; Lee, Jong Eun; Song, Joon Myong

2012-01-01

Highlights: ► Genomic DNA quantification were performed using a quantum dot-labeled Alu sequence. ► This probe provided PCR-free determination of human genomic DNA. ► Qdot-labeled Alu probe-hybridized genomic DNAs had a 2.5-femtogram detection limit. ► Qdot-labeled Alu sequence was used to assess DNA samples for human identification. - Abstract: Forensic DNA samples can degrade easily due to exposure to light and moisture at the crime scene. In addition, the amount of DNA acquired at a criminal site is inherently limited. This limited amount of human DNA has to be quantified accurately after the process of DNA extraction. The accurately quantified extracted genomic DNA is then used as a DNA template in polymerase chain reaction (PCR) amplification for short tandem repeat (STR) human identification. Accordingly, highly sensitive and human-specific quantification of forensic DNA samples is an essential issue in forensic study. In this work, a quantum dot (Qdot)-labeled Alu sequence was developed as a probe to simultaneously satisfy both the high sensitivity and human genome selectivity for quantification of forensic DNA samples. This probe provided PCR-free determination of human genomic DNA and had a 2.5-femtogram detection limit due to the strong emission and photostability of the Qdot. The Qdot-labeled Alu sequence has been used successfully to assess 18 different forensic DNA samples for STR human identification.

Exploitation of FTA cartridges for the sampling, long-term storage, and DNA-based analyses of plant-parasitic nematodes.

Science.gov (United States)

Marek, Martin; Zouhar, Miloslav; Douda, Ondřej; Maňasová, Marie; Ryšánek, Pavel

2014-03-01

The use of DNA-based analyses in molecular plant nematology research has dramatically increased over recent decades. Therefore, the development and adaptation of simple, robust, and cost-effective DNA purification procedures are required to address these contemporary challenges. The solid-phase-based approach developed by Flinders Technology Associates (FTA) has been shown to be a powerful technology for the preparation of DNA from different biological materials, including blood, saliva, plant tissues, and various human and plant microbial pathogens. In this work, we demonstrate, for the first time, that this FTA-based technology is a valuable, low-cost, and time-saving approach for the sampling, long-term archiving, and molecular analysis of plant-parasitic nematodes. Despite the complex structure and anatomical organization of the multicellular bodies of nematodes, we report the successful and reliable DNA-based analysis of nematode high-copy and low-copy genes using the FTA technology. This was achieved by applying nematodes to the FTA cards either in the form of a suspension of individuals, as intact or pestle-crushed nematodes, or by the direct mechanical printing of nematode-infested plant tissues. We further demonstrate that the FTA method is also suitable for the so-called "one-nematode-assay", in which the target DNA is typically analyzed from a single individual nematode. More surprisingly, a time-course experiment showed that nematode DNA can be detected specifically in the FTA-captured samples many years after initial sampling occurs. Collectively, our data clearly demonstrate the applicability and the robustness of this FTA-based approach for molecular research and diagnostics concerning phytonematodes; this research includes economically important species such as the stem nematode (Ditylenchus dipsaci), the sugar beet nematode (Heterodera schachtii), and the Northern root-knot nematode (Meloidogyne hapla).

High quality DNA from human papillomavirus (HPV for PCR/RFLPs

Directory of Open Access Journals (Sweden)

Denise Wanderlei-Silva

2005-01-01

Full Text Available The analysis of DNA in clinical samples for a secure diagnostic has become indispensable nowadays. Techniques approaching isolation of high molecular weigth DNA of HPV could lead to efficient amplification and early clinical diagnosis of the virus DNA by PCR (polymerase chain reaction. We describe a fast, non-toxical, efficient and cheap method for DNA isolation of human papilloma virus (HPV from cervical smears using guanidine (DNAzol solution. A 450 bp DNA band correponding to the late region (L1 of the virus genome was detected by PCR, showing that the DNAzol extraction soluction generated a good viral DNA yield. The electrophoretic pattern after digestion with restriction endonucleases (RFLPs/PCR revealed the predominance of HPV-16 and HPV-33 in the samples from the State of Alagoas, Brazil.A detecção de DNA em amostras clínicas visando um diagnóstico mais seguro vem se tornando uma prática comum em laboratórios de análise clínica. Metodologias que objetivem o isolamento de DNA de alto peso molecular de HPV podem levar a uma amplificação precisa e diagnose precoce do DNA do vírus por PCR (reação de polimerase em cadeia. Nós descrevemos um método para o isolamento do DNA do vírus do papiloma humano de amostras cervicais utilizando o detergente guanidina (solução DNAzol. O método foi rápido, não-tóxico e eficiente. Uma banda de DNA de 450 pb correspondente à região tardia (L1 do genoma viral foi detectada por PCR, mostrando que a extração com DNAzol gerou quantidade suficiente de DNA para análise. O padrão eletroforético, após digestão com endonucleases de restrição (RFLPs/PCR, revelou predominância de HPV 16 e HPV-33 nas amostras no Estado de Alagoas, Brasil.

Persistent DNA damage after high dose in vivo gamma exposure of minipig skin.

Directory of Open Access Journals (Sweden)

Emad A Ahmed

Full Text Available Exposure to high doses of ionizing radiation (IR can lead to localized radiation injury of the skin and exposed cells suffer dsDNA breaks that may elicit cell death or stochastic changes. Little is known about the DNA damage response after high-dose exposure of the skin. Here, we investigate the cellular and DNA damage response in acutely irradiated minipig skin.IR-induced DNA damage, repair and cellular survival were studied in 15 cm(2 of minipig skin exposed in vivo to ~50 Co-60 γ rays. Skin biopsies of control and 4 h up to 96 days post exposure were investigated for radiation-induced foci (RIF formation using γ-H2AX, 53BP1, and active ATM-p immunofluorescence. High-dose IR induced massive γ-H2AX phosphorylation and high 53BP1 RIF numbers 4 h, 20 h after IR. As time progressed RIF numbers dropped to a low of 3-fold elevated at all subsequent time points. Replicating basal cells (Ki67+ were reduced 3 days post IR followed by increased proliferation and recovery of epidermal cellularity after 28 days.Acute high dose irradiation of minipig epidermis impaired stem cell replication and induced elevated apoptosis from 3 days onward. DNA repair cleared the high numbers of DBSs in skin cells, while RIFs that persisted in <1% cells marked complex and potentially lethal DNA damage up to several weeks after exposure. An elevated frequency of keratinocytes with persistent RIFs may thus serve as indicator of previous acute radiation exposure, which may be useful in the follow up of nuclear or radiological accident scenarios.

Interaction of a non-histone chromatin protein (high-mobility group protein 2) with DNA

International Nuclear Information System (INIS)

Goodwin, G.H.; Shooter, K.V.; Johns, E.W.

1975-01-01

The interaction with DNA of the calf thymus chromatin non-histone protein termed the high-mobility group protein 2 has been studied by sedimentation analysis in the ultracentrifuge and by measuring the binding of the 125 I-labelled protein to DNA. The results have been compared with those obtained previously by us [Eur. J. Biochem. (1974) 47, 263-270] for the interaction of high-mobility group protein 1 with DNA. Although the binding parameters are similar for these two proteins, high-mobility group protein 2 differs from high-mobility group protein 1 in that the former appears to change the shape of the DNA to a more compact form. The molecular weight of high-mobility group protein 2 has been determined by equilibrium sedimentation and a mean value of 26,000 was obtained. A low level of nuclease activity detected in one preparation of high-mobility group protein 2 has been investigated. (orig.) [de

Comparison of extra-corporeal knot-tying suture and metallic endo-clips in laparoscopic appendiceal stump closure in uncomplicated acute appendicitis

Directory of Open Access Journals (Sweden)

M. Nadeem

2016-01-01

Conclusion: The use of metallic endoclip for appendix stump closure is safe and less time consuming but costs higher. Because of the simplicity of the technique it's a useful alternative to the extracorporeal knotting especially for learners.

High-Resolution X-Ray Spectroscopy of Galactic Supernova Remnants

Directory of Open Access Journals (Sweden)

Satoru Katsuda

2014-12-01

Full Text Available High-resolution X-ray spectroscopy of Galactic supernova remnants (SNRs, based on grating spectrometers onboard XMM-Newton and Chandra, has been revealing a variety of new astrophysical phenomena. Broadened oxygen lines for a northwestern compact knot in SN 1006 clearly show a high oxygen temperature of ~300 keV. The high temperature together with a lower electron temperature (kTe ~ 1 keV can be reasonably interpreted as temperature non-equilibration between electrons and oxygen behind a collisionless shock. An ejecta knot in the Puppis A SNR shows blueshifted line emission by ~ 1500kms-1. The line widths are fairly narrow in contrast to the SN 1006's knot; an upper limit of 0.9 eV is obtained for O VIII Lyα, which translates to an oxygen temperature of kTO < 30 keV. The low temperature suggests that the knot was heated by a reverse shock whose velocity is 4 times slower than that of a forward shock. Anomalous intensity ratios in O VII Heα lines, i.e., a stronger forbidden line than a resonance line, is found in a cloud-shock interaction region in Puppis A. The line ratio can be best explained by the charge-exchange emission that should arise at interfaces between the cold/warm clouds and the hot plasma. There are several other targets for which we plan to analyze high-quality grating data prior to the operation of the soft X-ray spectrometer onboard Astro-H.

PCR cycles above routine numbers do not compromise high-throughput DNA barcoding results.

Science.gov (United States)

Vierna, J; Doña, J; Vizcaíno, A; Serrano, D; Jovani, R

2017-10-01

High-throughput DNA barcoding has become essential in ecology and evolution, but some technical questions still remain. Increasing the number of PCR cycles above the routine 20-30 cycles is a common practice when working with old-type specimens, which provide little amounts of DNA, or when facing annealing issues with the primers. However, increasing the number of cycles can raise the number of artificial mutations due to polymerase errors. In this work, we sequenced 20 COI libraries in the Illumina MiSeq platform. Libraries were prepared with 40, 45, 50, 55, and 60 PCR cycles from four individuals belonging to four species of four genera of cephalopods. We found no relationship between the number of PCR cycles and the number of mutations despite using a nonproofreading polymerase. Moreover, even when using a high number of PCR cycles, the resulting number of mutations was low enough not to be an issue in the context of high-throughput DNA barcoding (but may still remain an issue in DNA metabarcoding due to chimera formation). We conclude that the common practice of increasing the number of PCR cycles should not negatively impact the outcome of a high-throughput DNA barcoding study in terms of the occurrence of point mutations.

Cost reduction in the cold: heat generated by terrestrial locomotion partly substitutes for thermoregulation costs in Knot Calidris canutus

NARCIS (Netherlands)

Bruinzeel, L.W.; Piersma, T.

1998-01-01

To test whether heat generated during locomotion substitutes for the thermoregulation cost, oxygen consumption of four post-absorptive temperate-wintering Knot Calidris canutus was measured at air temperatures of 25 degrees C (thermoneutral) and 10 degrees C (c. 10 degrees below the lower critical

Transfer validity of laparoscopic knot-tying training on a VR simulator to a realistic environment : A randomized controlled trial

NARCIS (Netherlands)

Verdaasdonk, E.G.G.; Dankelman, J.; Lange, J.F.; Stassen, L.P.S.

2007-01-01

Background- Laparoscopic suturing is one of the most difficult tasks in endoscopic surgery, requiring extensive training. The aim of this study was to determine the transfer validity of knot-tying training on a virtual-reality (VR) simulator to a realistic laparoscopic environment. Methods- Twenty

Association between high risk papillomavirus DNA and nitric oxide release in the human uterine cervix.

Science.gov (United States)

Rahkola, Paivi; Mikkola, Tomi S; Ylikorkala, Olavi; Vaisanen-Tommiska, Mervi

2009-08-01

Local cervical factors may determine the outcome of human papillomavirus (HPV) infection. Nitric oxide (NO) may be one such factor, since it is produced by uterine cervical cells and it takes part in both immunological and carcinogenic reactions. We studied the association between the presence of cervical high risk (hr) HPV DNA and NO in the cervical canal in women. High risk HPV DNA status was assessed from 328 women by using a specific DNA test and the release of cervical NO was assessed as nitrate/nitrite in cervical fluid. Cervical NO was then compared between women showing different status of hr HPV DNA and different cytological and histological findings. High risk HPV DNA was present in 175/328 (53%) women. The cervical NO release in women with hr HPV DNA was 90% higher compared to hr HPV DNA negative women (poral contraception, intrauterine devices, or signs of bacterial vaginosis or candida infection. Cytologically healthy epithelium and epithelium with mild cytological or histological changes showed elevated NO release if hr HPV DNA was present. The presence of hr HPV DNA is associated with an increased release of NO in the human uterine cervix. The clinical significance of this phenomenon remains open.

Commercial Biological Control Agents Targeted Against Plant-Parasitic Root-knot Nematodes

Directory of Open Access Journals (Sweden)

Marie-Stéphane Tranier

2014-12-01

Full Text Available Root-knot nematodes are microscopic round worms, which cause severe agricultural losses. Their attacks affect the productivity by reducing the amount and the caliber of the fruits. Chemical control is widely used, but biological control appears to be a better solution, mainly using microorganisms to reduce the quantity of pests infecting crops. Biological control is developing gradually, and with time, more products are being marketed worldwide. They can be formulated with bacteria, viruses or with filamentous fungi, which can destroy and feed on phytoparasitic nematodes. To be used by the farmers, biopesticides must be legalized by the states, which has led to the establishment of a legal framework for their use, devised by various governmental organizations.

Two efficient methods for isolation of high-quality genomic DNA from entomopathogenic fungi.

Science.gov (United States)

Serna-Domínguez, María G; Andrade-Michel, Gilda Y; Arredondo-Bernal, Hugo C; Gallou, Adrien

2018-03-27

Conventional and commercial methods for isolation of nucleic acids are available for fungal samples including entomopathogenic fungi (EPF). However, there is not a unique optimal method for all organisms. The cell wall structure and the wide range of secondary metabolites of EPF can broadly interfere with the efficiency of the DNA extraction protocol. This study compares three commercial protocols: DNeasy® Plant Mini Kit (Qiagen), Wizard® Genomic DNA Purification Kit (Promega), and Axygen™ Multisource Genomic DNA Miniprep Kit (Axygen) and three conventional methods based on different buffers: SDS, CTAB/PVPP, and CTAB/β-mercaptoethanol versus three cell lysis procedures: liquid nitrogen homogenization and two bead-beating materials (i.e., tungsten-carbide and stainless-steel) for four representative species of EPF (i.e., Beauveria bassiana, Hirsutella citriformis, Isaria javanica, and Metarhizium anisopliae). Liquid nitrogen homogenization combined with DNeasy® Plant Mini Kit (i.e., QN) or SDS buffer (i.e., SN) significantly improved the yield with a good purity (~1.8) and high integrity (>20,000 bp) of genomic DNA in contrast with other methods, also, these results were better when compared with the two bead-beating materials. The purified DNA was evaluated by PCR-based techniques: amplification of translation elongation factor 1-α (TEF) and two highly sensitive molecular markers (i.e., ISSR and AFLP) with reliable and reproducible results. Despite a variation in yield, purity, and integrity of extracted DNA across the four species of EPF with the different DNA extraction methods, the SN and QN protocols maintained a high-quality of DNA which is required for downstream molecular applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Protection of olive planting stocks against parasitism of root-knot nematodes by arbuscular mycorrhizal fungi

OpenAIRE

Castillo, Pablo; Nico, Andrés I.; Azcón González de Aguilar, Concepción; Río Rincón, C. del; Calvet, Cinta; Jiménez-Díaz, Rafael M.

2006-01-01

The effects were investigated, under controlled conditions, of single and joint inoculation of olive planting stocks cvs Arbequina and Picual with the arbuscular mycorrhizal fungi (AMF) Glomus intraradices, Glomus mosseae or Glomus viscosum, and the root-knot nematodes Meloidogyne incognita and Meloidogyne javanica, on plant performance and nematode infection. Establishment of the fungal symbiosis significantly increased growth of olive plants by 88·9% within a range of 11·9–214·0%, ...

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Directory of Open Access Journals (Sweden)

Jason D Thompson

Full Text Available Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Science.gov (United States)

Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta; Pel, Joel; Marziali, Andre

2012-01-01

Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

Synthetic LNA/DNA nano-scaffolds for highly efficient diagnostics of nucleic acids and autoimmune antibodies

DEFF Research Database (Denmark)

Astakhova, Irina Kira

2014-01-01

) strands and a series of fluorescent azides. The multiply labeled fluorescent LNA/DNA probes prepared herein generally display high binding affinity to complementary DNA/RNA, high quantum yields and, hence, high fluorescence brightness values. With the novel fluorescent probes, specific sensing...

Analysis of JC virus DNA replication using a quantitative and high-throughput assay

Science.gov (United States)

Shin, Jong; Phelan, Paul J.; Chhum, Panharith; Bashkenova, Nazym; Yim, Sung; Parker, Robert; Gagnon, David; Gjoerup, Ole; Archambault, Jacques; Bullock, Peter A.

2015-01-01

Progressive Multifocal Leukoencephalopathy (PML) is caused by lytic replication of JC virus (JCV) in specific cells of the central nervous system. Like other polyomaviruses, JCV encodes a large T-antigen helicase needed for replication of the viral DNA. Here, we report the development of a luciferase-based, quantitative and high-throughput assay of JCV DNA replication in C33A cells, which, unlike the glial cell lines Hs 683 and U87, accumulate high levels of nuclear T-ag needed for robust replication. Using this assay, we investigated the requirement for different domains of T-ag, and for specific sequences within and flanking the viral origin, in JCV DNA replication. Beyond providing validation of the assay, these studies revealed an important stimulatory role of the transcription factor NF1 in JCV DNA replication. Finally, we show that the assay can be used for inhibitor testing, highlighting its value for the identification of antiviral drugs targeting JCV DNA replication. PMID:25155200

Usos del nudo. Efectos de nominación en el autismo. (Uses of the Knot. Effects of Naming in Autism.

Directory of Open Access Journals (Sweden)

Marcela Beatriz Piaggi

2016-07-01

Full Text Available Resumen Este texto forma parte del estado de trabajo de la tesis de maestría en Psicoanálisis que actualmente estamos desarrollando en la Facultad de Psicología de la Universidad de Buenos Aires. Uno de los aportes más interesantes será interrogarnos sobre el uso de los nudos en la clínica del autismo. Tomaremos como eje de la enseñanza de Lacan los años 1974-1976, donde aborda el nudo borromeo en el del pasaje del nudo triádico al tetrádico con la función de nominación, punto de partida para llegar con la lógica de los nudos al autismo caracterizado por la forclusión del agujero. Será central desarrollar el concepto de nominación como efectos para comprender el planteo del escrito. Palabras claves: Autismo- nudos- escritura-nominación- agujeros- sinthome. Abstract This paper is part of an ongoing thesis of the Master's Degree at the Faculty of Psychology of the University of Buenos Aires. The reflection on the use of the knots in the autism clinic is one of the most interesting contributions of this work. Lacan's teaching between 1974-1976 is the base of this study, in which he addresses the Borromean knot in the passage from the triadic to the tetradic knot with the naming function as starting point, to arrive with the logic of knots to autism, characterized by the foreclosure of the gap. The development of the concept of naming as effects is essential to understand the approach of this paper. Keywords: autism- knots- writing-naming- gaps- sinthome. Résumé Ce texte fait partie de l'avancement d’un travail de recherche pour l'obtention du Master en psychanalyse de la faculté de psychologie de l'Université de Buenos Aires. La réflexion sur l'usage des nœuds dans la pratique clinique de l'autisme est l'une des contributions les plus intéressantes de ce travail. Les enseignements de Lacan des années 1974-1976 sont la base de cette étude, enseignements où il aborde le Nœud borroméen dans le passage du nœud triadique

High-resolution DNA content analysis of microbiopsy samples in oral lichen planus.

Science.gov (United States)

Pentenero, M; Monticone, M; Marino, R; Aiello, C; Marchitto, G; Malacarne, D; Giaretti, W; Gandolfo, S; Castagnola, P

2017-04-01

DNA aneuploidy has been reported to be a predictor of poor prognosis in both premalignant and malignant lesions. In oral lichen planus (OLP), this hypothesis remains to be proved. This study aimed to determine the rate of occurrence of DNA aneuploidy in patients with OLP by high-resolution DNA flow cytometry. Patients with OLP were consecutively enrolled. Tissue samples were subdivided for formalin fixation and routine histological assessment and for immediate storage at -20°C for later DNA ploidy analysis, which was performed by DAPI staining of the extracted nuclei and excitation with a UV lamp. The DNA aneuploid sublines were characterized by the DNA Index. A DNA aneuploid status was observed in two of 77 patients with OLP (2.6%). When considering the clinical aspect of the OLP lesions, both DNA aneuploid cases had a reticular clinical aspect. DNA aneuploidy is an uncommon event in OLP and less frequent compared to other non-dysplastic and non-OLP oral potentially malignant disorders. The extremely low rate of DNA aneuploidy could represent an occasional finding or reflect the low rate of malignant transformation observed in patients with OLP even if the real prognostic value of DNA ploidy analysis in patients with OLP remains to be confirmed. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A high-throughput and quantitative method to assess the mutagenic potential of translesion DNA synthesis

Science.gov (United States)

Taggart, David J.; Camerlengo, Terry L.; Harrison, Jason K.; Sherrer, Shanen M.; Kshetry, Ajay K.; Taylor, John-Stephen; Huang, Kun; Suo, Zucai

2013-01-01

Cellular genomes are constantly damaged by endogenous and exogenous agents that covalently and structurally modify DNA to produce DNA lesions. Although most lesions are mended by various DNA repair pathways in vivo, a significant number of damage sites persist during genomic replication. Our understanding of the mutagenic outcomes derived from these unrepaired DNA lesions has been hindered by the low throughput of existing sequencing methods. Therefore, we have developed a cost-effective high-throughput short oligonucleotide sequencing assay that uses next-generation DNA sequencing technology for the assessment of the mutagenic profiles of translesion DNA synthesis catalyzed by any error-prone DNA polymerase. The vast amount of sequencing data produced were aligned and quantified by using our novel software. As an example, the high-throughput short oligonucleotide sequencing assay was used to analyze the types and frequencies of mutations upstream, downstream and at a site-specifically placed cis–syn thymidine–thymidine dimer generated individually by three lesion-bypass human Y-family DNA polymerases. PMID:23470999

Isolation and characterization of high affinity aptamers against DNA polymerase iota.

Science.gov (United States)

Lakhin, Andrei V; Kazakov, Andrei A; Makarova, Alena V; Pavlov, Yuri I; Efremova, Anna S; Shram, Stanislav I; Tarantul, Viacheslav Z; Gening, Leonid V

2012-02-01

Human DNA-polymerase iota (Pol ι) is an extremely error-prone enzyme and the fidelity depends on the sequence context of the template. Using the in vitro systematic evolution of ligands by exponential enrichment (SELEX) procedure, we obtained an oligoribonucleotide with a high affinity to human Pol ι, named aptamer IKL5. We determined its dissociation constant with homogenous preparation of Pol ι and predicted its putative secondary structure. The aptamer IKL5 specifically inhibits DNA-polymerase activity of the purified enzyme Pol ι, but did not inhibit the DNA-polymerase activities of human DNA polymerases beta and kappa. IKL5 suppressed the error-prone DNA-polymerase activity of Pol ι also in cellular extracts of the tumor cell line SKOV-3. The aptamer IKL5 is useful for studies of the biological role of Pol ι and as a potential drug to suppress the increase of the activity of this enzyme in malignant cells.

High-Resolution Melting (HRM) of Hypervariable Mitochondrial DNA Regions for Forensic Science.

Science.gov (United States)

Dos Santos Rocha, Alípio; de Amorim, Isis Salviano Soares; Simão, Tatiana de Almeida; da Fonseca, Adenilson de Souza; Garrido, Rodrigo Grazinoli; Mencalha, Andre Luiz

2018-03-01

Forensic strategies commonly are proceeding by analysis of short tandem repeats (STRs); however, new additional strategies have been proposed for forensic science. Thus, this article standardized the high-resolution melting (HRM) of DNA for forensic analyzes. For HRM, mitochondrial DNA (mtDNA) from eight individuals were extracted from mucosa swabs by DNAzol reagent, samples were amplified by PCR and submitted to HRM analysis to identify differences in hypervariable (HV) regions I and II. To confirm HRM, all PCR products were DNA sequencing. The data suggest that is possible discriminate DNA from different samples by HRM curves. Also, uncommon dual-dissociation was identified in a single PCR product, increasing HRM analyzes by evaluation of melting peaks. Thus, HRM is accurate and useful to screening small differences in HVI and HVII regions from mtDNA and increase the efficiency of laboratory routines based on forensic genetics. © 2017 American Academy of Forensic Sciences.

Highly Sensitive DNA Sensor Based on Upconversion Nanoparticles and Graphene Oxide.

Science.gov (United States)

Alonso-Cristobal, P; Vilela, P; El-Sagheer, A; Lopez-Cabarcos, E; Brown, T; Muskens, O L; Rubio-Retama, J; Kanaras, A G

2015-06-17

In this work we demonstrate a DNA biosensor based on fluorescence resonance energy transfer (FRET) between NaYF4:Yb,Er nanoparticles and graphene oxide (GO). Monodisperse NaYF4:Yb,Er nanoparticles with a mean diameter of 29.1 ± 2.2 nm were synthesized and coated with a SiO2 shell of 11 nm, which allowed the attachment of single strands of DNA. When these DNA-functionalized NaYF4:Yb,Er@SiO2 nanoparticles were in the proximity of the GO surface, the π-π stacking interaction between the nucleobases of the DNA and the sp(2) carbons of the GO induced a FRET fluorescence quenching due to the overlap of the fluorescence emission of the NaYF4:Yb,Er@SiO2 and the absorption spectrum of GO. By contrast, in the presence of the complementary DNA strands, the hybridization leads to double-stranded DNA that does not interact with the GO surface, and thus the NaYF4:Yb,Er@SiO2 nanoparticles remain unquenched and fluorescent. The high sensitivity and specificity of this sensor introduces a new method for the detection of DNA with a detection limit of 5 pM.

Cell proliferation and apoptosis in the primary enamel knot measured by flow cytometry of laser microdissected samples

Czech Academy of Sciences Publication Activity Database

Matalová, Eva; Dubská, L.; Fleischmannová, Jana; Chlastáková, Ivana; Janečková, Eva; Tucker, A. S.

2010-01-01

Roč. 55, č. 8 (2010), s. 570-575 ISSN 0003-9969 R&D Projects: GA AV ČR KJB500450802; GA AV ČR IAA600450904; GA ČR GA203/08/1680 Institutional research plan: CEZ:AV0Z50450515 Keywords : Laser capture microdissection * Flow cytometry * Primary enamel knot Subject RIV: EA - Cell Biology Impact factor: 1.463, year: 2010

OH+ emission from cometary knots in planetary nebulae

Science.gov (United States)

Priestley, F. D.; Barlow, M. J.

2018-05-01

We model the molecular emission from cometary knots in planetary nebulae (PNe) using a combination of photoionization and photodissociation region (PDR) codes, for a range of central star properties and gas densities. Without the inclusion of ionizing extreme ultraviolet (EUV) radiation, our models require central star temperatures T* to be near the upper limit of the range investigated in order to match observed H2 and OH+ surface brightnesses consistent with observations - with the addition of EUV flux, our models reproduce observed OH+ surface brightnesses for T* ≥ 100 kK. For T* non-detection of this molecule in PNe with such central star temperatures. Our predicted level of H2 emission is somewhat weaker than commonly observed in PNe, which may be resolved by the inclusion of shock heating or fluorescence due to UV photons. Some of our models also predict ArH+ and HeH+ rotational line emission above detection thresholds, despite neither molecule having been detected in PNe, although the inclusion of photodissociation by EUV photons, which is neglected by our models, would be expected to reduce their detectability.

Fuelling and moult in Red Knots before northward departure: a visual evaluation of differences between ages, sexes and subspecies

NARCIS (Netherlands)

Verhoeven, M.A.; Van Eerbeek, J.; Hassell, C.J.; Piersma, T.

2016-01-01

The departure of migratory birds from their non-breeding grounds is thought to be driven by the phenologyof their breeding destination. In north-west Australia, two plumage morphs of Red Knot (Calidris canutus) prepare for a5500-km journey to Yellow Sea staging areas. These morphs are recognised as

A Robust Highly Aligned DNA Nanowire Array-Enabled Lithography for Graphene Nanoribbon Transistors.

Science.gov (United States)

Kang, Seok Hee; Hwang, Wan Sik; Lin, Zhiqun; Kwon, Se Hun; Hong, Suck Won

2015-12-09

Because of its excellent charge carrier mobility at the Dirac point, graphene possesses exceptional properties for high-performance devices. Of particular interest is the potential use of graphene nanoribbons or graphene nanomesh for field-effect transistors. Herein, highly aligned DNA nanowire arrays were crafted by flow-assisted self-assembly of a drop of DNA aqueous solution on a flat polymer substrate. Subsequently, they were exploited as "ink" and transfer-printed on chemical vapor deposited (CVD)-grown graphene substrate. The oriented DNA nanowires served as the lithographic resist for selective removal of graphene, forming highly aligned graphene nanoribbons. Intriguingly, these graphene nanoribbons can be readily produced over a large area (i.e., millimeter scale) with a high degree of feature-size controllability and a low level of defects, rendering the fabrication of flexible two terminal devices and field-effect transistors.

Minilaparoscopic varicocelectomy with preservation of testicular artery and lymphatic vessels by using intracorporeal knot-tying technique: five-year experience.

Science.gov (United States)

Chung, Shiu-Dong; Wu, Chia-Chang; Lin, Victor Chia-Hsiang; Ho, Chen-Hsun; Yang, Stephen Shei Dei; Tsai, Yao-Chou

2011-08-01

In this study we present our experience using minilaparoscopic intracorporeal knot tying to ligate internal spermatic veins (ISV) while sparing the spermatic artery and lymphatics. Minilaparoscopic varicocelectomies were performed in 87 patients between January 2004 and January 2009. All varicoceles were detected clinically according to the World Health Organization (WHO) classification and confirmed by scrotal color Doppler ultrasonography. The surgical indications were scrotal symptoms in 71, infertility in 16, and both conditions in 2. Three 3.5 mm minilaparoscopic ports were used for the operation. The ISVs were dissected and then ligated with intracorporeal knot-tying. The testicular artery and lymphatic vessels were carefully preserved to minimize procedure-related complications. Unilateral laparoscopic varicocelectomy was performed in 21 (24.2%) patients and bilateral in 66 (75.8%). Mean operative time was 71.1 ± 29.2 and 46.8 ± 12.6 min for bilateral and unilateral varicocelectomies, respectively. All patients were discharged within 24 h after surgery. Neither immediate major nor late procedure-related complications were noted. Of the 71 patients with scrotal symptoms, the symptoms completely subsided in 55 (77.5%) and partially subsided in 10 (14.1%). Only one (1.2%) recurrent varicocele was detected within a mean follow-up of 21 months (range = 3-42). Neither hydrocele formation nor testicular atrophy was found during the follow-up period. Our 5-year experience revealed that minilaparoscopic varicocelectomy with sparing of artery and lymphatic vessels could safely and effectively ligate all spermatic veins and preserve spermatic arteries and lymphatic channels without leading to a high varicocele persistence or recurrence.

Binary self-assembly of highly symmetric DNA nanocages via sticky-end engineering

Institute of Scientific and Technical Information of China (English)

Xiao-Rong Wu; Chen-Wei Wu; Fei Ding; Cheng Tian; Wen Jiang; Cheng-De Mao; Chuan Zhang

2017-01-01

Discrete and symmetric three-dimensional (3D) DNA nanocages have been revoked as excellent candidates for various applications,such as guest component encapsulation and organization (e.g.dye molecules,proteins,inorganic nanoparticles,etc.) to construct new materials and devices.To date,a large variety of DNA nanocages has been synthesized through assembling small individual DNA motifs into predesigned structures in a bottom-up fashion.Most of them rely on the assembly using multiple copies of single type of motifs and a few sophisticated nanostructures have been engineered by co-assembling multi-types of DNA tiles simultaneously.However,the availability of complex DNA nanocages is still limited.Herein,we demonstrate that highly symmetric DNA nanocages consisted of binary DNA pointstar motifs can be easily assembled by deliberately engineering the sticky-end interaction between the component building blocks.As such,DNA nanocages with new geometries,including elongated tetrahedron (E-TET),rhombic dodecahedron (R-DOD),and rhombic triacontahedron (R-TRI) are successfully synthesized.Moreover,their design principle,assembly process,and structural features are revealed by polyacryalmide gel electrophoresis (PAGE),atomic force microscope (AFM) imaging,and cryogenic transmission electron microscope imaging (cryo-TEM) associated with single particle reconstruction.

Sequence of a cDNA encoding turtle high mobility group 1 protein.

Science.gov (United States)

Zheng, Jifang; Hu, Bi; Wu, Duansheng

2005-07-01

In order to understand sequence information about turtle HMG1 gene, a cDNA encoding HMG1 protein of the Chinese soft-shell turtle (Pelodiscus sinensis) was amplified by RT-PCR from kidney total RNA, and was cloned, sequenced and analyzed. The results revealed that the open reading frame (ORF) of turtle HMG1 cDNA is 606 bp long. The ORF codifies 202 amino acid residues, from which two DNA-binding domains and one polyacidic region are derived. The DNA-binding domains share higher amino acid identity with homologues sequences of chicken (96.5%) and mammalian (74%) than homologues sequence of rainbow trout (67%). The polyacidic region shows 84.6% amino acid homology with the equivalent region of chicken HMG1 cDNA. Turtle HMG1 protein contains 3 Cys residues located at completely conserved positions. Conservation in sequence and structure suggests that the functions of turtle HMG1 cDNA may be highly conserved during evolution. To our knowledge, this is the first report of HMG1 cDNA sequence in any reptilian.

The Potential of veticillium Chlamydosporium and Pasteuria Penetrans for the Management of Root-Knot Namatode on Smallholder Tomato Farms in Kenya

International Nuclear Information System (INIS)

Karanja, D.K

2002-01-01

Root-knot nematode (meloidogyne spp.) is a seriously pest problem in smallholder tomato farms in Kenya. Awareness of the toxicity effects and increasing costs of chemical control of root-knot nematodes has led to demand for alternative nematode management strategies, including use of potential biological control agents. The use of Verticillium chlamydosporium and Pasteuria penetrans, as biocontrol agents (BCA's) in tomato nursery beds has been evaluated and the results presented. The biocontrol agents significantly lowered the number of nematodes in roots of tomato seedlings, four weeks after seeding. Alternative treatments: Crotalaria, Dazomet 98% (Basamid granular) and trash burning, significantly reduced the number of second stage juveniles in soil. Transplanting of seedlings, from BCA treatment, to a nematode infested field reduced the number of egg masses at the end of harvesting period but did not result in a significant increase in tomato yield

The Potential of veticillium Chlamydosporium and Pasteuria Penetrans for the Management of Root-Knot Namatode on Smallholder Tomato Farms in Kenya

Energy Technology Data Exchange (ETDEWEB)

Karanja, D K

2002-07-01

Root-knot nematode (meloidogyne spp.) is a seriously pest problem in smallholder tomato farms in Kenya. Awareness of the toxicity effects and increasing costs of chemical control of root-knot nematodes has led to demand for alternative nematode management strategies, including use of potential biological control agents. The use of Verticillium chlamydosporium and Pasteuria penetrans, as biocontrol agents (BCA's) in tomato nursery beds has been evaluated and the results presented. The biocontrol agents significantly lowered the number of nematodes in roots of tomato seedlings, four weeks after seeding. Alternative treatments: Crotalaria, Dazomet 98% (Basamid granular) and trash burning, significantly reduced the number of second stage juveniles in soil. Transplanting of seedlings, from BCA treatment, to a nematode infested field reduced the number of egg masses at the end of harvesting period but did not result in a significant increase in tomato yield.

Polypyrrole–gold nanoparticle composites for highly sensitive DNA detection

International Nuclear Information System (INIS)

Spain, Elaine; Keyes, Tia E.; Forster, Robert J.

2013-01-01

DNA capture surfaces represent a powerful approach to developing highly sensitive sensors for identifying the cause of infection. Electrochemically deposited polypyrrole, PPy, films have been functionalized with electrodeposited gold nanoparticles to give a nanocomposite material, PPy–AuNP. Thiolated capture strand DNA, that is complementary to the sequence from the pathogen Staphylococcus aureus that causes mammary gland inflammation, was then immobilized onto the gold nanoparticles and any of the underlying gold electrode that is exposed. A probe strand, labelled with horse radish peroxidase, HRP, was then hybridized to the target. The concentration of the target was determined by measuring the current generated by reducing benzoquinone produced by the HRP label. Semi-log plots of the pathogen DNA concentration vs. faradaic current are linear from 150 pM to 1 μM and pM concentrations can be detected without the need for molecular, e.g., PCR or NASBA, amplification. The nanocomposite also exhibits excellent selectivity and single base mismatches in a 30 mer sequence can be detected

Pioglitazone retrieves hepatic antioxidant DNA repair in a mice model of high fat diet

Directory of Open Access Journals (Sweden)

Yang Ching-Hsiu

2008-09-01

Full Text Available Abstract Background Pioglitazone was reported to improve hepatic steatosis and necroinflammation in human studies. To investigate whether the hepato-protective effect of pioglitazone was associated with an improvement of antioxidant defense mechanism, oxidative DNA damage and repair activity were determined in a high fat diet model. Male C57BL/6 mice were respectively fed with a 30% fat diet, the same diet with pioglitazone 100 mg/kg/day, or a chow diet as control for 8 weeks. Tissue oxidative stress was indicated by malondialdehyde concentration. Oxidative DNA damage was detected by immunohistochemical 8-oxoG staining. Enzymatic antioxidant defense was detected by the real-time PCR of superoxide dismutase (Sod1, Sod2 and DNA glycosylase (Ogg1, MutY. Oxidative DNA repair was detected by immunohistochemical staining and western blotting of OGG1 expression. Results Our results show that hepatic steatosis was induced by a high-fat diet and improved by adding pioglitazone. Malondialdehyde concentration and 8-oxoG staining were strongly increased in the high-fat diet group, but attenuated by pioglitazone. Gene expressions of antioxidant defense mechanism: Sod1, Sod2, Ogg1 and MutY significantly decreased in the high-fat diet group but reversed by pioglitazone co-administration. Conclusion The attenuation of hepatic oxidative DNA damage by pioglitazone in a high-fat diet may be mediated by up-regulation of the antioxidant defense mechanism and oxidative DNA repair activity. The diminution of oxidative damage may explain the clinical benefit of pioglitazone treatment in patients with non-alcoholic fatty liver disease.

Pioglitazone retrieves hepatic antioxidant DNA repair in a mice model of high fat diet

Science.gov (United States)

Hsiao, Pi-Jung; Hsieh, Tusty-Jiuan; Kuo, Kung-Kai; Hung, Wei-Wen; Tsai, Kun-Bow; Yang, Ching-Hsiu; Yu, Ming-Lung; Shin, Shyi-Jang

2008-01-01

Background Pioglitazone was reported to improve hepatic steatosis and necroinflammation in human studies. To investigate whether the hepato-protective effect of pioglitazone was associated with an improvement of antioxidant defense mechanism, oxidative DNA damage and repair activity were determined in a high fat diet model. Male C57BL/6 mice were respectively fed with a 30% fat diet, the same diet with pioglitazone 100 mg/kg/day, or a chow diet as control for 8 weeks. Tissue oxidative stress was indicated by malondialdehyde concentration. Oxidative DNA damage was detected by immunohistochemical 8-oxoG staining. Enzymatic antioxidant defense was detected by the real-time PCR of superoxide dismutase (Sod1, Sod2) and DNA glycosylase (Ogg1, MutY). Oxidative DNA repair was detected by immunohistochemical staining and western blotting of OGG1 expression. Results Our results show that hepatic steatosis was induced by a high-fat diet and improved by adding pioglitazone. Malondialdehyde concentration and 8-oxoG staining were strongly increased in the high-fat diet group, but attenuated by pioglitazone. Gene expressions of antioxidant defense mechanism: Sod1, Sod2, Ogg1 and MutY significantly decreased in the high-fat diet group but reversed by pioglitazone co-administration. Conclusion The attenuation of hepatic oxidative DNA damage by pioglitazone in a high-fat diet may be mediated by up-regulation of the antioxidant defense mechanism and oxidative DNA repair activity. The diminution of oxidative damage may explain the clinical benefit of pioglitazone treatment in patients with non-alcoholic fatty liver disease. PMID:18822121

Description of Meloidogyne minor n.sp. (Nematoda: Meloidogynidae), a root-knot nematode associated with yellow patch disease in golf courses

NARCIS (Netherlands)

Karssen, G.; Bolk, R.J.; Aelst, van A.C.; Beld, van den I.; Kox, L.F.F.; Korthals, G.W.; Molendijk, L.P.G.; Zijlstra, C.; Hoof, van R.A.; Cook, R.

2004-01-01

A relatively small root-knot nematode, Meloidogyne minor n. sp., is described and illustrated from tomato from the Netherlands. This new species is characterised by the following features: female with dorsally curved stylet, 14 Pm long, with transversely ovoid knobs slightly sloping backwards from

Pathways of DNA unlinking: A story of stepwise simplification.

Science.gov (United States)

Stolz, Robert; Yoshida, Masaaki; Brasher, Reuben; Flanner, Michelle; Ishihara, Kai; Sherratt, David J; Shimokawa, Koya; Vazquez, Mariel

2017-09-29

In Escherichia coli DNA replication yields interlinked chromosomes. Controlling topological changes associated with replication and returning the newly replicated chromosomes to an unlinked monomeric state is essential to cell survival. In the absence of the topoisomerase topoIV, the site-specific recombination complex XerCD- dif-FtsK can remove replication links by local reconnection. We previously showed mathematically that there is a unique minimal pathway of unlinking replication links by reconnection while stepwise reducing the topological complexity. However, the possibility that reconnection preserves or increases topological complexity is biologically plausible. In this case, are there other unlinking pathways? Which is the most probable? We consider these questions in an analytical and numerical study of minimal unlinking pathways. We use a Markov Chain Monte Carlo algorithm with Multiple Markov Chain sampling to model local reconnection on 491 different substrate topologies, 166 knots and 325 links, and distinguish between pathways connecting a total of 881 different topologies. We conclude that the minimal pathway of unlinking replication links that was found under more stringent assumptions is the most probable. We also present exact results on unlinking a 6-crossing replication link. These results point to a general process of topology simplification by local reconnection, with applications going beyond DNA.

Visualization of DNA in highly processed botanical materials.

Science.gov (United States)

Lu, Zhengfei; Rubinsky, Maria; Babajanian, Silva; Zhang, Yanjun; Chang, Peter; Swanson, Gary

2018-04-15

DNA-based methods have been gaining recognition as a tool for botanical authentication in herbal medicine; however, their application in processed botanical materials is challenging due to the low quality and quantity of DNA left after extensive manufacturing processes. The low amount of DNA recovered from processed materials, especially extracts, is "invisible" by current technology, which has casted doubt on the presence of amplifiable botanical DNA. A method using adapter-ligation and PCR amplification was successfully applied to visualize the "invisible" DNA in botanical extracts. The size of the "invisible" DNA fragments in botanical extracts was around 20-220 bp compared to fragments of around 600 bp for the more easily visualized DNA in botanical powders. This technique is the first to allow characterization and visualization of small fragments of DNA in processed botanical materials and will provide key information to guide the development of appropriate DNA-based botanical authentication methods in the future. Copyright © 2017 Elsevier Ltd. All rights reserved.

Arbuscular mycorrhizal fungi affect both penetration and further life stage development of root-knot nematodes in tomato.

Science.gov (United States)

Vos, Christine; Geerinckx, Katleen; Mkandawire, Rachel; Panis, Bart; De Waele, Dirk; Elsen, Annemie

2012-02-01

The root-knot nematode Meloidogyne incognita poses a worldwide threat to agriculture, with an increasing demand for alternative control options since most common nematicides are being withdrawn due to environmental concerns. The biocontrol potential of arbuscular mycorrhizal fungi (AMF) against plant-parasitic nematodes has been demonstrated, but the modes of action remain to be unraveled. In this study, M. incognita penetration of second-stage juveniles at 4, 8 and 12 days after inoculation was compared in tomato roots (Solanum lycopersicum cv. Marmande) pre-colonized or not by the AMF Glomus mosseae. Further life stage development of the juveniles was also observed in both control and mycorrhizal roots at 12 days, 3 weeks and 4 weeks after inoculation by means of acid fuchsin staining. Penetration was significantly lower in mycorrhizal roots, with a reduction up to 32%. Significantly lower numbers of third- and fourth-stage juveniles and females accumulated in mycorrhizal roots, at a slower rate than in control roots. The results show for the first time that G. mosseae continuously suppresses root-knot nematodes throughout their entire early infection phase of root penetration and subsequent life stage development.

High Performance Systolic Array Core Architecture Design for DNA Sequencer

Directory of Open Access Journals (Sweden)

Saiful Nurdin Dayana

2018-01-01

Full Text Available This paper presents a high performance systolic array (SA core architecture design for Deoxyribonucleic Acid (DNA sequencer. The core implements the affine gap penalty score Smith-Waterman (SW algorithm. This time-consuming local alignment algorithm guarantees optimal alignment between DNA sequences, but it requires quadratic computation time when performed on standard desktop computers. The use of linear SA decreases the time complexity from quadratic to linear. In addition, with the exponential growth of DNA databases, the SA architecture is used to overcome the timing issue. In this work, the SW algorithm has been captured using Verilog Hardware Description Language (HDL and simulated using Xilinx ISIM simulator. The proposed design has been implemented in Xilinx Virtex -6 Field Programmable Gate Array (FPGA and improved in the core area by 90% reduction.

Soil amendment with halophytes induces physiological changes and reduces root-knot infection in eggplant and okra

Directory of Open Access Journals (Sweden)

Waseem M. ABBASI

2011-01-01

Full Text Available Root-knot nematode, Meloidogyne javanica (Treub Chitwood is a soil-borne plant pathogen of roots. Nematode infection results in altered plant growth and physicochemical processes due to gall formation. Many plants contain unique biochemicals that have biocidal properties and offer a potential novel approach to suppress the nematode populations in soil and improve growth of crop plants. In the present study effect of some indigenous halophytic plant species (Tamarix indica Willd, Suaeda fruticosa Forssk and Salsola imbricata (Schultz Dandy were tested against M. javanica. Tested halophytes significantly (P<0.001 reduced egg hatching and caused mortality of second stage juveniles (J2 in vitro. These halophytes when incorporated in soil (0.3, 0.5 and 1% w/w markedly increased growth of eggplant (Solanum melongena L. cv. Black beauty and okra (Abelmoschus esculentus [L.] Moench. cv. Arka anamika and provided control of root-knot infection at higher doses (0.5 and 1%. Amended eggplants and okra showed significant (P<0.001 increase in chlorophylls and decrease in chlorophyll a/b ratio. Protein concentration in leaves of both the plants were increased with 1% amendment of S. fruticosa and S. imbricata. While nucleic acid concentrations were varied with different treatments.  

The temporal outcomes of open versus arthroscopic knotted and knotless rotator cuff repair over 5 years

Science.gov (United States)

Lucena, Thomas R; Lam, Patrick H; Millar, Neal L

2015-01-01

Background The present study aimed to determine how repair technique influenced structural and clinical outcomes at 5 years post-surgery. Methods Three cohorts of patients had repair of a symptomatic rotator cuff tear using (i) an open double-row mattress repair technique (n = 25); (ii) arthroscopic single-row simple suture knotted technique (n = 25); or (iii) arthroscopic single-row inverted mattress knotless technique (n = 36) by one surgeon. Standardized patient- and examiner-determined outcomes were obtained pre-operatively and postoperatively with a validated protocol, ultrasound were also performed at the same time. Results Retear occurred more often after open repair (48%) at 5 years than after arthroscopic knotted (33%) and arthroscopic knotless (26%) repair. Retear was associated with increasing age, pre-operative tear size and weaker pre-operative and 5 years postoperative cuff strength. Between 2 years and 5 years, the open repair group experienced an increase in the frequency of pain during activity, as well as in the difficulty experienced and the severity of pain during overhead activities (p repair group. Conclusions At 5-year follow-up, arthroscopic rotator cuff repair techniques resulted in fewer retears and better outcomes compared to an open double-row technique. PMID:27582985

High-resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous base stacking at junctions

International Nuclear Information System (INIS)

Chou, Shanho; Flynn, P.; Wang, A.; Reid, B.

1991-01-01

Two symmetrical DNA-RNA-DNA duplex chimeras, d(CGCG)r(AAUU)d(CGCG) (designated rAAUU) and d(CGCG)r(UAUA)d(CGCG) (designated rUAUA), and a nonsymmetrical chimeric duplex, d(CGTT)r(AUAA)d(TGCG)/d(CGCA)r(UUAU)d(AACG) (designated rAUAA), as well as their pure DNA analogues, containing dU instead of T, have been synthesized by solid-phase phosphoramidite methods and studied by high-resolution NMR techniques. The 1D imino proton NOE spectra of these d-r-d chimeras indicate normal Watson-Crick hydrogen bonding and base stacking at the junction region. Preliminary qualitative NOESY, COSY, and chemical shift data suggest that the internal RNA segment contains C3'-endo (A-type) sugar conformations except for the first RNA residues (position 5 and 17) following the 3' end of the DNA block, which, unlike the other six ribonucleotides, exhibit detectable H1'-H2' J coupling. The nucleosides of the two flanking DNA segments appear to adopt a fairly normal C2'-endo B-DNA conformation except at the junction with the RNA blocks (residues 4 and 16), where the last DNA residue appears to adopt an intermediate sugar conformation. The data indicate that A-type and B-type conformations can coexist in a single short continuous nucleic acid duplex, but these results differ somewhat from previous theoretical model studies

Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts.

Science.gov (United States)

Trofimova, Irina; Krasikova, Alla

2016-12-01

Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.

Knot invariants and universal R-matrices from perturbative Chern-Simon theory in the almost axial gauge

International Nuclear Information System (INIS)

Van de Wetering, J.F.W.H.

1992-01-01

Using perturbative Chern-Simons theory in the almost axial gauge on the euclidean manifold S 1 xR 2 , we give a prescription for the computation of knot invariants. The method gives the correct expectation value of the unknot to all orders in perturbation theory and gives the correct answer for the spectral-parameter-dependent universal R-matrix to second order. All results are derived for a general semi-simple Lie algebra. (orig.)

Control of Pathogenicity Root-Knot Nematode (Meloidogyne Javanica by Earthworm Eisenia Feoetida-Based Products in Greenhouse

Directory of Open Access Journals (Sweden)

M. Rostami

2016-06-01

Full Text Available Introduction: Biocontrol of nematode agents in order to decrease the hazardous impacts of chemical pesticide application including problems of public health and environmental pollution is apriority. In this study, solid (Vermicompost and liquid products (Liquid Vermicompost, Vermiwash and Coelomic fluidof the earthworm species Eisenia fetida were tested against root-knot nematode, Meloidogyne javanica in greenhouse conditions. Materials and Methods: In this study, Solid (Vermicompost and Liquid products(Wormtea, Vermiwash, Coelomic fluid erthworms (Eisenia foetida were tested against Meloidogyne javanica and also the effect of Vermicompost was evaluated on Pathogenicity of various nematode initial inoculum in two stage greenhouse conditions. Earthworm-based products (Vermicompost, Wormtea, Vermiwash and Coelomic fluid were added to tomato pots. Various treatments of liquid as well as solid products and their combination were used in the greenhouse trial. The first Stage greenhouse experiment- Tomato seeds grown in 2 kg sterilized soil. In the treatments having Vermicompost, pots incorporated with 200 gr of this compost homogeneously mixed with soil. After plants reached at two leaf stage, to study the effects of liquid products (Wormtea, Vermiwash, and Coelomic fluid they added to the pots (500cc along with the irrigation water every week and after of 4 leaf stage, 5000 nematode eggs and larva inoculated to the tomato host plants. 90 days after nematode inoculation, plant and nematode growth indices separately measured and compared. The experiment conducted based on completely randomized design having four replicates. The second stage greenhouse experiment- Tomato seeds grown in 2 kg sterilized soil. In the treatments, pots incorporated with 200 gr of this compost homogeneously mixed with soil. After of 4 leaf stage, 0,1000,2000,4000 and 10000 nematode eggs and larva inoculated to the tomato host plants. 90 days after nematode inoculation, plant

Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin

Directory of Open Access Journals (Sweden)

Mayra Eduardoff

2017-09-01

Full Text Available The analysis of mitochondrial DNA (mtDNA has proven useful in forensic genetics and ancient DNA (aDNA studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR is commonly sequenced using established Sanger-type Sequencing (STS protocols involving fragment sizes down to approximately 150 base pairs (bp. Recent developments include Massively Parallel Sequencing (MPS of (multiplex PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less, and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples, and tested challenging forensic samples (n = 2 as well as compromised solid tissue samples (n = 15 up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS

Targeted DNA Methylation Analysis by High Throughput Sequencing in Porcine Peri-attachment Embryos

OpenAIRE

MORRILL, Benson H.; COX, Lindsay; WARD, Anika; HEYWOOD, Sierra; PRATHER, Randall S.; ISOM, S. Clay

2013-01-01

Abstract The purpose of this experiment was to implement and evaluate the effectiveness of a next-generation sequencing-based method for DNA methylation analysis in porcine embryonic samples. Fourteen discrete genomic regions were amplified by PCR using bisulfite-converted genomic DNA derived from day 14 in vivo-derived (IVV) and parthenogenetic (PA) porcine embryos as template DNA. Resulting PCR products were subjected to high-throughput sequencing using the Illumina Genome Analyzer IIx plat...

76 FR 304 - Endangered and Threatened Wildlife and Plants; 90-Day Finding on a Petition To List the Red Knot...

Science.gov (United States)

2011-01-04

... breeding areas, in addition to having morphological and behavioral character differences. The Service and... subspecies' ability to build up adequate nutrient and energy stores to complete their long migrations... both market and sport (Harrington 2001, p. 22). Hunting of red knots is no longer allowed in the United...

Where waders may parallel penguins : Spontaneous increase in locomotor activity triggered by fat depletion in a voluntarily fasting Knot

NARCIS (Netherlands)

Piersma, T.; Poot, M.

1993-01-01

A Knot Calidris canutus, kept with four conspecifics on an enclosed artificial outdoor tidal flat in The Netherlands, refused to feed on the available bivalve prey for a period of 18 days and thereby decreased in mass from 209 g to 107 g, at which point the bird resumed feeding on the then freely

Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies.

Science.gov (United States)

Taubert, Martin; Grob, Carolina; Howat, Alexandra M; Burns, Oliver J; Chen, Yin; Neufeld, Josh D; Murrell, J Colin

2016-01-01

Methylotrophs are microorganisms ubiquitous in the environment that can metabolize one-carbon (C1) compounds as carbon and/or energy sources. The activity of these prokaryotes impacts biogeochemical cycles within their respective habitats and can determine whether these habitats act as sources or sinks of C1 compounds. Due to the high importance of C1 compounds, not only in biogeochemical cycles, but also for climatic processes, it is vital to understand the contributions of these microorganisms to carbon cycling in different environments. One of the most challenging questions when investigating methylotrophs, but also in environmental microbiology in general, is which species contribute to the environmental processes of interest, or "who does what, where and when?" Metabolic labeling with C1 compounds substituted with (13)C, a technique called stable isotope probing, is a key method to trace carbon fluxes within methylotrophic communities. The incorporation of (13)C into the biomass of active methylotrophs leads to an increase in the molecular mass of their biomolecules. For DNA-based stable isotope probing (DNA-SIP), labeled and unlabeled DNA is separated by isopycnic ultracentrifugation. The ability to specifically analyze DNA of active methylotrophs from a complex background community by high-throughput sequencing techniques, i.e. targeted metagenomics, is the hallmark strength of DNA-SIP for elucidating ecosystem functioning, and a protocol is detailed in this chapter.

Foraging conditions 'at the end of the world' in the context of long-distance migration and population declines in red knots

NARCIS (Netherlands)

Escudero, Graciela; Navedo, Juan G.; Piersma, Theunis; De Goeij, Petra; Edelaar, Pim

The long-distance migrant red knot (Calidris canutus ssp. rufa Scolopacidae) alternates between the northern and southern ends of the New World, one of the longest yearly migrations of any bird and paradoxically overflying apparently suitable habitat at lower latitudes. This subspecies is sharply

Foraging conditions 'at the end of the world' in the context of long-distance migration and population declines in red knots

NARCIS (Netherlands)

Escudero, G.; Navedo, J.G.; Piersma, T.; de Goeij, P.; Edelaar, P.

2012-01-01

The long-distance migrant red knot (Calidris canutus ssp. rufa Scolopacidae) alternates between the northern and southern ends of the New World, one of the longest yearly migrations of any bird and paradoxically overflying apparently suitable habitat at lower latitudes. This subspecies is sharply

Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity.

Science.gov (United States)

Boessenkool, Sanne; McGlynn, Gayle; Epp, Laura S; Taylor, David; Pimentel, Manuel; Gizaw, Abel; Nemomissa, Sileshi; Brochmann, Christian; Popp, Magnus

2014-04-01

Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited. © 2013 Society for Conservation Biology.

A DNA fingerprinting procedure for ultra high-throughput genetic analysis of insects.

Science.gov (United States)

Schlipalius, D I; Waldron, J; Carroll, B J; Collins, P J; Ebert, P R

2001-12-01

Existing procedures for the generation of polymorphic DNA markers are not optimal for insect studies in which the organisms are often tiny and background molecular information is often non-existent. We have used a new high throughput DNA marker generation protocol called randomly amplified DNA fingerprints (RAF) to analyse the genetic variability in three separate strains of the stored grain pest, Rhyzopertha dominica. This protocol is quick, robust and reliable even though it requires minimal sample preparation, minute amounts of DNA and no prior molecular analysis of the organism. Arbitrarily selected oligonucleotide primers routinely produced approximately 50 scoreable polymorphic DNA markers, between individuals of three independent field isolates of R. dominica. Multivariate cluster analysis using forty-nine arbitrarily selected polymorphisms generated from a single primer reliably separated individuals into three clades corresponding to their geographical origin. The resulting clades were quite distinct, with an average genetic difference of 37.5 +/- 6.0% between clades and of 21.0 +/- 7.1% between individuals within clades. As a prelude to future gene mapping efforts, we have also assessed the performance of RAF under conditions commonly used in gene mapping. In this analysis, fingerprints from pooled DNA samples accurately and reproducibly reflected RAF profiles obtained from individual DNA samples that had been combined to create the bulked samples.

Measurement of spontaneous DNA damage and DNA repair capacity in healthy adult individuals from high and normal level natural radiation areas of Kerala, India

International Nuclear Information System (INIS)

Vivek Kumar, P.R.; Jaikrishan, G.; Das, Birajalaxmi

2014-01-01

Inhabitants of the south west coastal areas of Kerala receive high level natural radiation due to the presence of monazite ( 232 Th) in the beach sand. This provides a unique opportunity to investigate the biological effects of high level natural radiation on humans. This study evaluate basal DNA damage in 149 healthy adult male subjects (104 from high level natural radiation areas (HLNRA, > 1mSv year -1 ) and 45 from normal level natural radiation area (NLNRA, d''1mSv year -1 ) by the alkaline comet assay. Oxidative DNA damage (ENDO III, FPG and hOGG1-sensitive sites) was measured by the enzyme modified comet assay. Induction and rejoining of DNA strand breaks was measured after irradiating peripheral blood lymphocytes with 2 Gy or 4 Gy gamma radiation. Basal damage due to age and residential area of the donors showed significant interaction (P=0.001), when all subjects were analyzed using a general linear model (GLM). In subgroup analysis, basal damage increased with age in subjects from the NLNRA (P=0.007), while a significant negative correlation (P=0.01) was observed in subjects from HLNRA. Oxidative DNA damage was not influenced by age, smoking habit or residential area in the entire sample. Subjects of high dose group from HLNRA (>5.75 mSv/y, N=34) showed a significant reduction in the induction of DNA damage after 2 Gy (P=0.03) and 4 Gy (P=0.05) compared to subjects form NLNRA. The study showed increased rejoining of DNA strand breaks in subjects from HLNRA when measured at 7 minutes after irradiation (P=0.04). In this pilot study, a low basal damage in elderly subjects from HLNRA and a reduced induction of DNA damage after 2 Gy and 4 Gy irradiation in high dose group subjects from HLNRA might suggest a possible role of chronic low dose natural radiation on the induction of an in vivo radio adaptive response. However, our findings need more validation in a larger study population. (author)

Novel PVA-DNA nanoparticles prepared by ultra high pressure technology for gene delivery

International Nuclear Information System (INIS)

Kimura, Tsuyoshi; Okuno, Akira; Miyazaki, Kozo; Furuzono, Tsutomu; Ohya, Yuichi; Ouchi, Tatsuro; Mutsuo, Shingo; Yoshizawa, Hidekazu; Kitamura, Yoshiro; Fujisato, Toshiyta; Kishida, Akio

2004-01-01

Polyvinyl alcohol (PVA)-DNA nanoparticles have been developed by ultra high pressure (UHP) technology. Mixture solutions of DNA and PVA having various molecular weights (Mw) and degree of saponifications (DS) were treated under 10,000 atmospheres (981 MPa) condition at 40 deg. C for 10 min. Agarose gel electrophoresis and scanning electron microscope observation revealed that the PVA-DNA nanoparticles with average diameter of about 200 nm were formed. Using PVA of higher Mw and degree of saponifications, the amount of nanoparticles formed increased. The driving force of nanoparticle formation was the hydrogen bonding between DNA and PVA. In order to apply the PVA-DNA nanoparticles for gene delivery, the cytotoxicity and the cellular uptake of them were investigated using Raw264 cell lines. The cell viability was not influenced whether the presence of the PVA-DNA nanoparticles. Further, the nanoparticles internalized into cells were observed by fluorescent microscope. These results indicates that the PVA-DNA nanoparticles prepared by UHP technology showed be useful as drug carrier, especially for gene delivery

Nematicidal potential of aqueous extract of Hyptis suaveolens in the management of root-knot nematode, Meloidogyne incognita of some cowpea cultivars

Directory of Open Access Journals (Sweden)

S. A. Abolusoro

2016-01-01

Full Text Available Studies were conducted under field and screenhouse conditions to investigate the potentials of crude aqueous leaf extract of Hyptis suaveolens in the management of the root-knot nematode Meloidogyne incognita of three cowpea varieties (Sampea 9, 10 and 11. A Randomized Complete Block Design was used in the field while a completely randomized design was used for the screenhouse trials. Results showed that the treatment significantly (p < 0.05 improved the growth and yield of the three varieties and also reduced soil nematode population and root galls. It was also observed that all the three varieties were susceptible to the root-knot nematode infestation but Sampea 10 recorded higher yield that were significant in the pot trials. Phytochemical screening revealed the presence of saponins, alkaloids, flavonoids and steroids in the leaves of H. suaveolens. For higher yield of the evaluated cowpea varieties in a nematode endemic zone, aqueous leaf extract of H. suaveolens is being recommended for infested soil treatment.

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

Science.gov (United States)

Adalsteinsson, Viktor A; Ha, Gavin; Freeman, Samuel S; Choudhury, Atish D; Stover, Daniel G; Parsons, Heather A; Gydush, Gregory; Reed, Sarah C; Rotem, Denisse; Rhoades, Justin; Loginov, Denis; Livitz, Dimitri; Rosebrock, Daniel; Leshchiner, Ignaty; Kim, Jaegil; Stewart, Chip; Rosenberg, Mara; Francis, Joshua M; Zhang, Cheng-Zhong; Cohen, Ofir; Oh, Coyin; Ding, Huiming; Polak, Paz; Lloyd, Max; Mahmud, Sairah; Helvie, Karla; Merrill, Margaret S; Santiago, Rebecca A; O'Connor, Edward P; Jeong, Seong H; Leeson, Rachel; Barry, Rachel M; Kramkowski, Joseph F; Zhang, Zhenwei; Polacek, Laura; Lohr, Jens G; Schleicher, Molly; Lipscomb, Emily; Saltzman, Andrea; Oliver, Nelly M; Marini, Lori; Waks, Adrienne G; Harshman, Lauren C; Tolaney, Sara M; Van Allen, Eliezer M; Winer, Eric P; Lin, Nancy U; Nakabayashi, Mari; Taplin, Mary-Ellen; Johannessen, Cory M; Garraway, Levi A; Golub, Todd R; Boehm, Jesse S; Wagle, Nikhil; Getz, Gad; Love, J Christopher; Meyerson, Matthew

2017-11-06

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.

Functional role of a highly repetitive DNA sequence in anchorage of the mouse genome.

Science.gov (United States)

Neuer-Nitsche, B; Lu, X N; Werner, D

1988-09-12

The major portion of the eukaryotic genome consists of various categories of repetitive DNA sequences which have been studied with respect to their base compositions, organizations, copy numbers, transcription and species specificities; their biological roles, however, are still unclear. A novel quality of a highly repetitive mouse DNA sequence is described which points to a functional role: All copies (approximately 50,000 per haploid genome) of this DNA sequence reside on genomic Alu I DNA fragments each associated with nuclear polypeptides that are not released from DNA by proteinase K, SDS and phenol extraction. By this quality the repetitive DNA sequence is classified as a member of the sub-set of DNA sequences involved in tight DNA-polypeptide complexes which have been previously shown to be components of the subnuclear structure termed 'nuclear matrix'. From these results it has to be concluded that the repetitive DNA sequence characterized in this report represents or comprises a signal for a large number of site specific attachment points of the mouse genome in the nuclear matrix.

Charge reversible gold nanoparticles for high efficient absorption and desorption of DNA

Energy Technology Data Exchange (ETDEWEB)

Wang Can; Zhuang Jiaqi; Jiang Shan; Li Jun; Yang Wensheng, E-mail: wsyang@jlu.edu.cn [Jilin University, State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry (China)

2012-10-15

Mercaptoundecylamine and mercaptoundecanoic acid co-modified Au nanoparticles were prepared by two-step ligand exchange of 6-mercaptohexanoic acid modified gold nanoparticles. Such particles terminated by appropriate ratios of the amine and carboxyl groups (R{sub N/C}) were identified to show reversible charge on their surface, which were switchable by pH of the solution. The isoelectric point (IEP) of the particles is tunable by changing the ratios of the amine and carboxyl groups on the particle surfaces. The particles can absorb DNA effectively at pH lower than the IEP driven by the direct electrostatic interactions between DNA and the particle surface. When pH of the solutions was elevated to be higher than the IEP, the absorbed DNA can be released almost completely due to the electrostatic repulsion between the particle surface and DNA. With appropriate R{sub N/C} ratios of 0.8, the absorption and desorption efficiencies of DNA were 97 and 98%, respectively, corresponding an extraction efficiency of 95 %. Such particles with reversible surface charges allow the high efficient extraction of DNA by simply changing pH instead of by changing salt concentration in the conventional salt bridge method.Graphical Abstract.

Economic design in a long-distance migrating molluscivore: how fast-fuelling red knots in Bohai Bay, China, get away with small gizzards

NARCIS (Netherlands)

Yang, H.-Y.; Ma, Z.-J.; Hua, N.; van Gils, J.A.; Zhang, Z.-W.; Piersma, T.

2013-01-01

We carried out an observational and experimental study to decipher how resource characteristics, in interaction with the predator's phenotype, constrain a fitness-determining performance measure, i.e. refuelling in a migrant bird. Two subspecies of red knot (Calidris canutus rogersi and C. c.

No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation

Directory of Open Access Journals (Sweden)

Hellberg Michael E

2006-03-01

Full Text Available Abstract Background The mitochondrial DNA (mtDNA of most animals evolves more rapidly than nuclear DNA, and often shows higher levels of intraspecific polymorphism and population subdivision. The mtDNA of anthozoans (corals, sea fans, and their kin, by contrast, appears to evolve slowly. Slow mtDNA evolution has been reported for several anthozoans, however this slow pace has been difficult to put in phylogenetic context without parallel surveys of nuclear variation or calibrated rates of synonymous substitution that could permit quantitative rate comparisons across taxa. Here, I survey variation in the coding region of a mitochondrial gene from a coral species (Balanophyllia elegans known to possess high levels of nuclear gene variation, and estimate synonymous rates of mtDNA substitution by comparison to another coral (Tubastrea coccinea. Results The mtDNA surveyed (630 bp of cytochrome oxidase subunit I was invariant among individuals sampled from 18 populations spanning 3000 km of the range of B. elegans, despite high levels of variation and population subdivision for allozymes over these same populations. The synonymous substitution rate between B. elegans and T. coccinea (0.05%/site/106 years is similar to that in most plants, but 50–100 times lower than rates typical for most animals. In addition, while substitutions to mtDNA in most animals exhibit a strong bias toward transitions, mtDNA from these corals does not. Conclusion Slow rates of mitochondrial nucleotide substitution result in low levels of intraspecific mtDNA variation in corals, even when nuclear loci vary. Slow mtDNA evolution appears to be the basal condition among eukaryotes. mtDNA substitution rates switch from slow to fast abruptly and unidirectionally. This switch may stem from the loss of just one or a few mitochondrion-specific DNA repair or replication genes.

mtDNA point and length heteroplasmy in high- and low radiation areas of Kerala

International Nuclear Information System (INIS)

Forster, L.; Forster, P.; Gurney, S.M.; Spencer, M.; Huang, C.; Röhl, A.; Brinkmann, B.

2010-01-01

A coastal peninsula in Kerala (India) contains the world's highest level of natural radioactivity in a densely populated area, offering an opportunity to characterize radiation-associated DNA mutations. Here, we focus on mitochondrial DNA (mtDNA) mutations, which are passed exclusively from the mother to her children. To analyse point mutations, we sampled 248 pedigrees (988 individuals) in the high-radiation peninsula and in nearby low-radiation islands as a control population. Then, in an extended sample of 1,172 mtDNA sequences (containing some non-Indians for comparison), we also analysed length mutations, which in mtDNA can lead to the phenomenon of length heteroplasmy, i.e. the existence of different DNA types in the same cell. We wished to find out how fast mtDNA mutates between generations, and whether the mutation rate is increased in radioactive conditions compared to the low-irradiation sample

Oxidative DNA damage and repair in skeletal muscle of humans exposed to high-altitude hypoxia

International Nuclear Information System (INIS)

Lundby, Carsten; Pilegaard, Henriette; Hall, Gerrit van; Sander, Mikael; Calbet, Jose; Loft, Steffen; Moeller, Peter

2003-01-01

Recent research suggests that high-altitude hypoxia may serve as a model for prolonged oxidative stress in healthy humans. In this study, we investigated the consequences of prolonged high-altitude hypoxia on the basal level of oxidative damage to nuclear DNA in muscle cells, a major oxygen-consuming tissue. Muscle biopsies from seven healthy humans were obtained at sea level and after 2 and 8 weeks of hypoxia at 4100 m.a.s.l. We found increased levels of strand breaks and endonuclease III-sensitive sites after 2 weeks of hypoxia, whereas oxidative DNA damage detected by formamidopyrimidine DNA glycosylase (FPG) protein was unaltered. The expression of 8-oxoguanine DNA glycosylase 1 (OGG1), determined by quantitative RT-PCR of mRNA levels did not significantly change during high-altitude hypoxia, although the data could not exclude a minor upregulation. The expression of heme oxygenase-1 (HO-1) was unaltered by prolonged hypoxia, in accordance with the notion that HO-1 is an acute stress response protein. In conclusion, our data indicate high-altitude hypoxia may serve as a good model for oxidative stress and that antioxidant genes are not upregulated in muscle tissue by prolonged hypoxia despite increased generation of oxidative DNA damage

On knottings in the physical Hilbert space of LQG as given by the EPRL model

International Nuclear Information System (INIS)

Bahr, Benjamin

2011-01-01

We consider the EPRL spin foam amplitude for arbitrary embedded two-complexes. Choosing a definition of the face- and edge amplitudes which lead to spin foam amplitudes invariant under trivial subdivisions, we investigate invariance properties of the amplitude under consistent deformations, which are deformations of the embedded two-complex where faces are allowed to pass through each other in a controlled way. Using this surprising invariance, we are able to show that the physical Hilbert space, as defined by the sum over all spin foams, contains no information about knotting classes of graphs anymore.

ANNUAL AND SEASONAL-VARIATION IN THE FOOD-SUPPLY HARVESTABLE BY KNOT CALIDRIS-CANUTUS STAGING IN THE WADDEN SEA IN LATE SUMMER

NARCIS (Netherlands)

ZWARTS, L; BLOMERT, AM; WANINK, JH

The biomass of the macrobenthic animals living in intertidal flats of the Wadden Sea varies annually and seasonally. However, the variation in prey biomass harvestable by wading birds such as knot Calidris canutus, which feed mainly on the middle range of their prey size classes, is even larger. The

Management of High-Throughput DNA Sequencing Projects: Alpheus.

Science.gov (United States)

Miller, Neil A; Kingsmore, Stephen F; Farmer, Andrew; Langley, Raymond J; Mudge, Joann; Crow, John A; Gonzalez, Alvaro J; Schilkey, Faye D; Kim, Ryan J; van Velkinburgh, Jennifer; May, Gregory D; Black, C Forrest; Myers, M Kathy; Utsey, John P; Frost, Nicholas S; Sugarbaker, David J; Bueno, Raphael; Gullans, Stephen R; Baxter, Susan M; Day, Steve W; Retzel, Ernest F

2008-12-26

High-throughput DNA sequencing has enabled systems biology to begin to address areas in health, agricultural and basic biological research. Concomitant with the opportunities is an absolute necessity to manage significant volumes of high-dimensional and inter-related data and analysis. Alpheus is an analysis pipeline, database and visualization software for use with massively parallel DNA sequencing technologies that feature multi-gigabase throughput characterized by relatively short reads, such as Illumina-Solexa (sequencing-by-synthesis), Roche-454 (pyrosequencing) and Applied Biosystem's SOLiD (sequencing-by-ligation). Alpheus enables alignment to reference sequence(s), detection of variants and enumeration of sequence abundance, including expression levels in transcriptome sequence. Alpheus is able to detect several types of variants, including non-synonymous and synonymous single nucleotide polymorphisms (SNPs), insertions/deletions (indels), premature stop codons, and splice isoforms. Variant detection is aided by the ability to filter variant calls based on consistency, expected allele frequency, sequence quality, coverage, and variant type in order to minimize false positives while maximizing the identification of true positives. Alpheus also enables comparisons of genes with variants between cases and controls or bulk segregant pools. Sequence-based differential expression comparisons can be developed, with data export to SAS JMP Genomics for statistical analysis.

Bacterial natural transformation by highly fragmented and damaged DNA

DEFF Research Database (Denmark)

Overballe-Petersen, Søren; Harms, Klaus; Orlando, Ludovic Antoine Alexandre

2013-01-01

for microbes, but not as potential substrate for bacterial evolution. Here, we show that fragmented DNA molecules (≥20 bp) that additionally may contain abasic sites, cross-links, or miscoding lesions are acquired by the environmental bacterium Acinetobacter baylyi through natural transformation. With uptake......DNA molecules are continuously released through decomposition of organic matter and are ubiquitous in most environments. Such DNA becomes fragmented and damaged (often DNA is recognized as nutrient source...... of DNA from a 43,000-y-old woolly mammoth bone, we further demonstrate that such natural transformation events include ancient DNA molecules. We find that the DNA recombination is RecA recombinase independent and is directly linked to DNA replication. We show that the adjacent nucleotide variations...

Rapid isolation of high molecular weight DNA from single dried ...

African Journals Online (AJOL)

ANAND

For studying genetic diversity in populations of predatory coccinellid, Cryptolaemus montrouzieri. Mulsant (Coccinellidae: Coleoptera), our attempts to isolate high quality DNA from individual adult beetle using several previously reported protocols and even modifications were quite unsuccessful as the insect size was small ...

DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

Directory of Open Access Journals (Sweden)

Masudur Rahman

2016-10-01

Full Text Available Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material.

DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

Science.gov (United States)

Rahman, Masudur; Neff, David; Green, Nathaniel; Norton, Michael L.

2016-01-01

Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material. PMID:28335324

Footprint Contact Area and Interface Pressure Comparison Between the Knotless and Knot-Tying Transosseous-Equivalent Technique for Rotator Cuff Repair.

Science.gov (United States)

Kim, Sung-Jae; Kim, Sung-Hwan; Moon, Hyun-Soo; Chun, Yong-Min

2016-01-01

To quantify and compare the footprint contact area and interface pressure on the greater tuberosity between knotless and knot-tying transosseous-equivalent (TOE) repair using pressure-sensitive film. We used 11 pairs of fresh-frozen cadaveric shoulders (22 specimens), in which rotator cuff tears were created before repair. Each pair was randomized to either conventional medial knot-tying TOE repair (group A) or medial knotless TOE repair using the modified Mason-Allen technique (group B). Pressure-sensitive film was used to quantify the pressurized contact area and interface pressure between the greater tuberosity and supraspinatus tendon. The mean pressurized contact area was 33.2 ± 2.5 mm(2) for group A and 28.4 ± 2.4 mm(2) for group B. There was a significant difference between groups (P = .005). Although the overall contact configuration of both groups was similar and showed an M shape, group A showed a greater pressurized configuration around the medial row. The mean interface pressure was 0.20 ± 0.02 MPa for group A and 0.17 ± 0.02 MPa for group B. There was a significant difference between groups (P = .001). Contrary to our hypothesis, in this time-zero study, medial knotless TOE repair using a modified Mason-Allen suture produced a significantly inferior footprint contact area and interface pressure compared with conventional medial knot-tying TOE repair. Even though we found a statistically significant difference between the 2 repair methods, it is still unknown if this statistical difference seen in our study has any clinical and radiologic significance. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Quality of human spermatozoa: relationship between high-magnification sperm morphology and DNA integrity.

Science.gov (United States)

Maettner, R; Sterzik, K; Isachenko, V; Strehler, E; Rahimi, G; Alabart, J L; Sánchez, R; Mallmann, P; Isachenko, E

2014-06-01

The aim of this work is to establish the relationship between the morphology of Intracytoplasmic Morphologically Selected Sperm Injection (IMSI)-selected spermatozoa and their DNA integrity. The 45 ejaculates were randomly distributed into three treatment groups: normozoospermic, oligoasthenozoospermic and oligoasthenotheratozoospermic samples. The evaluation of DNA integrity was performed using the sperm chromatin dispersion test. It was established that DNA integrity of spermatozoa is strongly dependent on ejaculate quality (P count of spermatozoa with nonfragmented DNA in normozoospermic samples was high and independent from IMSI-morphological classes (Class 1 versus Class 3, respectively) (P > 0.1). With decreased ejaculate quality, the percentage of spermatozoa with nonfragmented DNA decreased significantly (P < 0.05) independent from morphological class. Nevertheless, the rate of IMSI-selected spermatozoa with fragmented DNA within of Class 1 in normozoospermic (Group 1), in oligoasthenozoospermic (Group 2) and in oligoasthenotheratozoospermic (Group 3) samples was 21.1%, 31.8% and 54.1%, respectively. In conclusion, there is a direct relationship between morphological parameters of spermatozoa and their DNA integrity. However, the IMSI technique alone is not enough for the selection of spermatozoa with intact nuclei. © 2013 Blackwell Verlag GmbH.

Role of the low-affinity glucocorticoid receptor in the regulation of behavior and energy metabolism in the migratory red knot Calidris canutus islandica

NARCIS (Netherlands)

Landys, MM; Piersma, T; Ramenofsky, M; Wingfield, JC; Wingfield, John C.

2004-01-01

Plasma corticosterone increases in association with migratory flight in the red knot Calidris canutus islandica, suggesting that corticosterone may promote migratory activity and/or energy mobilization in this species. This hypothesis is supported by general effects of glucocorticoids, which include

Selection of DNA aptamers against epidermal growth factor receptor with high affinity and specificity.

Science.gov (United States)

Wang, Deng-Liang; Song, Yan-Ling; Zhu, Zhi; Li, Xi-Lan; Zou, Yuan; Yang, Hai-Tao; Wang, Jiang-Jie; Yao, Pei-Sen; Pan, Ru-Jun; Yang, Chaoyong James; Kang, De-Zhi

2014-10-31

Epidermal growth factor receptor (EGFR/HER1/c-ErbB1), is overexpressed in many solid cancers, such as epidermoid carcinomas, malignant gliomas, etc. EGFR plays roles in proliferation, invasion, angiogenesis and metastasis of malignant cancer cells and is the ideal antigen for clinical applications in cancer detection, imaging and therapy. Aptamers, the output of the systematic evolution of ligands by exponential enrichment (SELEX), are DNA/RNA oligonucleotides which can bind protein and other substances with specificity. RNA aptamers are undesirable due to their instability and high cost of production. Conversely, DNA aptamers have aroused researcher's attention because they are easily synthesized, stable, selective, have high binding affinity and are cost-effective to produce. In this study, we have successfully identified DNA aptamers with high binding affinity and selectivity to EGFR. The aptamer named TuTu22 with Kd 56±7.3nM was chosen from the identified DNA aptamers for further study. Flow cytometry analysis results indicated that the TuTu22 aptamer was able to specifically recognize a variety of cancer cells expressing EGFR but did not bind to the EGFR-negative cells. With all of the aforementioned advantages, the DNA aptamers reported here against cancer biomarker EGFR will facilitate the development of novel targeted cancer detection, imaging and therapy. Copyright © 2014 Elsevier Inc. All rights reserved.

Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques.

OpenAIRE

Aljanabi, S M; Martinez, I

1997-01-01

A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification. The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even i...

Turning Maneuver Limitations Imposed by Sudden Strut Side Ventilation on a 200-Ton 80-Knot Hydrofoil Craft

Science.gov (United States)

1975-05-01

ventilated, but never supercavitating , for speeds up to 80 knots. In particular, choking of the air flow to the foil vent was not con- sidered. If this...4Conolly, A.C., "Experimental Investigations of Supercavitating Hydrofoils with Flaps," General Dynamics/Convair Report GD/C-63-210 (Dec 1963). 10 THE SIX...Dec 1966). 4. Conolly, A.C., "Experimenta, Investigations of Supercavitating Hydro- foils with Flaps," General Dynamics/Convair Report GD/C-63-210 (Dec

Interspersion of highly repetitive DNA with single copy DNA in the genome of the red crab, Geryon quinquedens

Energy Technology Data Exchange (ETDEWEB)

Christie, N.T. (Univ. of Tennessee, Oak Ridge); Skinner, D.M.

1979-02-01

Kinetic analysis of the reassociation of 420 nucleotide (NT) long fragments has shown that essentially all of the repetitive sequences of the DNA of the red crab Geryon quinquedens are highly repetitive. There are negligible amounts of low and intermediate repetitive DNAs. Though atypical of most eukaryotes, this pattern has been observed in al other brachyurans (true crabs) studied. The major repetitive component is subdivided into short runs of 300 NT and longer runs of greater than 1200 NT while the minor component has an average sequence length of 400 NT. Both components reassociate at rates commonly observed for satellite DNAs. Unique among eukaryotes the organization of the genome includes single copy DNA contiguous to short runs (300 NT) of both repetitive components. Although patent satellites are not present, subsets of the repetitive DNA have been isolated by either restriction endonuclease digestion or by centrifugation in Ag/sup +/ or Hg/sup 2 +//Cs/sub 2/SO/sub 4/ density gradients.

Improving the Efficiency of a High Speed Catamaran Through the Replacement of the Propulsion System

Directory of Open Access Journals (Sweden)

German de Melo Rodriguez

2015-12-01

Full Text Available The high speed vessels are primarily designed for short distances services as public transport of passengers and vehicles. The range of high speed, according to the Code of high-speed vessels begins at 20 knots, which depends on the cruise speed you desire for your vessel; you will have to use the most appropriate type of propellant. In general, in the past 20 years, they have been building high-speed vessels with speeds above 33 knots, which meant installing water jet propellants coupled to powerful engines and therefore of high consumption of fuel, increasing operating costs and causing increased air pollution. Although the prices of fuel have been reduced to half, due to the sharp fall in oil prices, the consumption of fuel and the air pollution remains high at these speeds and powers used, in addition to that the reduction of the time spent on each trip is not excessive, mainly in short routes that are less than an hour . This article is about adapting a ship of high-speed service, with a maximum speed in tests of 34 knots and to reduce its operating costs (fuel, maintenance, etc. and make it economically viable; before the transformation, this vessel was operating with a service speed of 22 knots, and with a consumption per mile of 135 litters of MGO. The transformation process has consisted by: – Replacement of the two original water jet with four shaft lines with fix pitch propeller. – Replacement of the two original main engines (2 x 6500 kW = 13000 kW by four engines (4 x 1380kW = 5.520 kW. – Changing the underwater hull shape to fit the new propellers and maximize its efficiency. – Relocation of auxiliary engines, to achieve the most efficient trim. – Installation of two lateral propellers to improve maneuverability and shorten the total time of journey. After the reform and the return to service of the vessel with a service speed of over 22 knots, it has been verified that the consumption per mile is of 45 litters MGO

Methods for High-throughput Characterisation of Environmental DNA

DEFF Research Database (Denmark)

Andersen, Kenneth

This PhD thesis examines the potential of describing biodiversity of green plants (Viridiplantae), birds (Aves) and mammals (Mammalia), in the context of next-generation sequencing, from the DNA that all organisms segregate into the environment (eDNA). The research is based on case studies...... of species assemblages described by eDNA recovered from contemporary surface soil and Holocene sediment sequences, to assess the accuracy and limitations of the approach. Biodiversity incorporates two aspects of ecological communities, including both the taxonomic richness and abundance of individual taxa...... inhibition. In chapter four, alternative DNA extraction protocols and pipelines for characterising plant eDNA are tested on samples from contrasting environments including modern, Holocene and Pleistocene sediment samples. These results are compared to pollen and macrofossil records described from earlier...

Decondensation behavior of DNA chains induced by multivalent cations at high salt concentrations: Molecular dynamics simulations and experiments

International Nuclear Information System (INIS)

Jiang Yang-Wei; Zhang Lin-Xi; Ran Shi-Yong; He Lin-Li; Wang Xiang-Hong

2015-01-01

Using molecular dynamics simulations and atomic force microscopy (AFM), we study the decondensation process of DNA chains induced by multivalent cations at high salt concentrations in the presence of short cationic chains in solutions. The typical simulation conformations of DNA chains with varying salt concentrations for multivalent cations imply that the concentration of salt cations and the valence of multivalent cations have a strong influence on the process of DNA decondensation. The DNA chains are condensed in the absence of salt or at low salt concentrations, and the compacted conformations of DNA chains become loose when a number of cations and anions are added into the solution. It is explicitly demonstrated that cations can overcompensate the bare charge of the DNA chains and weaken the attraction interactions between the DNA chains and short cationic chains at high salt concentrations. The condensation-decondensation transitions of DNA are also experimentally observed in mixing spermidine with λ-phage DNA at different concentrations of NaCl/MgCl 2 solutions. (paper)

Tomato transgenic plants expressing hairpin construct of a nematode protease gene conferred enhanced resistance to root-knot nematodes

Directory of Open Access Journals (Sweden)

Tushar Kanti Dutta

2015-04-01

Full Text Available Root-knot nematodes (Meloidogyne incognita cause substantial yield losses in vegetables worldwide, and are difficult to manage. Continuous withdrawal of environmentally-harmful nematicides from the global market warrants the need for novel nematode management strategies. Utility of host-delivered RNAi has been demonstrated in several plants (Arabidopsis, tobacco and soybean that exhibited resistance against root-knot and cyst nematodes. Herein, a M. incognita-specific protease gene, cathepsin L cysteine proteinase (Mi-cpl-1, was targeted to generate tomato transgenic lines to evaluate the genetically modified nematode resistance. In vitro knockdown of Mi-cpl-1 gene led to the reduced attraction and penetration of M. incognita in tomato, suggesting the involvement of Mi-cpl-1 in nematode parasitism. Transgenic expression of the RNAi construct of Mi-cpl-1 gene resulted in 60-80% reduction in infection and multiplication of M. incognita in tomato. Evidence for in vitro and in vivo silencing of Mi-cpl-1 was confirmed by expression analysis using quantitative PCR. Our study demonstrates that Mi-cpl-1 plays crucial role during plant-nematode interaction and plant-mediated downregulation of this gene elicits detrimental effect on M. incognita development, reinforcing the potential of RNAi technology for management of phytonematodes in crop plants.

A Microneedle Functionalized with Polyethyleneimine and Nanotubes for Highly Sensitive, Label-Free Quantification of DNA

OpenAIRE

Saadat-Moghaddam, Darius; Kim, Jong-Hoon

2017-01-01

The accurate measure of DNA concentration is necessary for many DNA-based biological applications. However, the current methods are limited in terms of sensitivity, reproducibility, human error, and contamination. Here, we present a microneedle functionalized with polyethyleneimine (PEI) and single-walled carbon nanotubes (SWCNTs) for the highly sensitive quantification of DNA. The microneedle was fabricated using ultraviolet (UV) lithography and anisotropic etching, and then functionalized w...

Non-Gaussian Distribution of DNA Barcode Extension In Nanochannels Using High-throughput Imaging

Science.gov (United States)

Sheats, Julian; Reinhart, Wesley; Reifenberger, Jeff; Gupta, Damini; Muralidhar, Abhiram; Cao, Han; Dorfman, Kevin

2015-03-01

We present experimental data for the extension of internal segments of highly confined DNA using a high-­throughput experimental setup. Barcode­-labeled E. coli genomic DNA molecules were imaged at a high areal density in square nanochannels with sizes ranging from 40 nm to 51 nm in width. Over 25,000 molecules were used to obtain more than 1,000,000 measurements for genomic distances between 2,500 bp and 100,000 bp. The distribution of extensions has positive excess kurtosis and is skew­ left due to weak backfolding in the channel. As a result, the two Odijk theories for the chain extension and variance bracket the experimental data. We compared to predictions of a harmonic approximation for the confinement free energy and show that it produces a substantial error in the variance. These results suggest an inherent error associated with any statistical analysis of barcoded DNA that relies on harmonic models for chain extension. Present address: Department of Chemical and Biological Engineering, Princeton University.

Highly sensitive DNA sensors based on cerium oxide nanorods

Science.gov (United States)

Nguyet, Nguyen Thi; Hai Yen, Le Thi; Van Thu, Vu; lan, Hoang; Trung, Tran; Vuong, Pham Hung; Tam, Phuong Dinh

2018-04-01

In this work, a CeO2 nanorod (NR)-based electrochemical DNA sensor was developed to identify Salmonella that causes food-borne infections. CeO2 NRs were synthesized without templates via a simple and unexpensive hydrothermal approach at 170 °C for 12 h by using CeO(NO3)3·6H2O as a Ce source. The DNA probe was immobilized onto the CeO2 NR-modified electrode through covalent attachment. The characteristics of the hybridized DNA were analyzed through electrochemical impedance spectroscopy (EIS) with [Fe(CN)6]3-/4- as a redox probe. Experimental results showed that electron transfer resistance (Ret) increased after the DNA probe was attached to the electrode surface and increased further after the DNA probe hybridized with its complementary sequence. A linear response of Ret to the target DNA concentration was found from 0.01 μM to 2 μM. The detection limit and sensitivity of the DNA sensor were 0.01 μM and 3362.1 Ω μM-1 cm-2, respectively. Various parameters, such as pH value, ionic strength, DNA probe concentration, and hybridization time, influencing DNA sensor responses were also investigated.

Disruption of prefoldin-2 protein synthesis in root-knot nematodes via host-mediated gene silencing efficiently reduces nematode numbers and thus protects plants.

Science.gov (United States)

Ajjappala, Hemavathi; Chung, Ha Young; Sim, Joon-Soo; Choi, Inchan; Hahn, Bum-Soo

2015-03-01

The aim of this study is to demonstrate the feasibility of down-regulating endogeneous prefoldin-2 root-knot nematode transcripts by expressing dsRNA with sequence identity to the nematode gene in tobacco roots under the influence of strong Arabidopsis ubiquitin (UBQ1) promoter. Root-knot nematodes (RKNs) are sedentary endoparasites infecting a wide range of plant species. They parasitise the root system, thereby disrupting water and nutrient uptake and causing major reductions in crop yields. The most reliable means of controlling RKNs is via the use of soil fumigants such as methyl bromide. With the emergence of RNA interference (RNAi) technology, which permits host-mediated nematode gene silencing, a new strategy to control plant pathogens has become available. In the present study, we investigated host-induced RNAi gene silencing of prefoldin-2 in transgenic Nicotiana benthamiana. Reductions in prefoldin-2 mRNA transcript levels were observed when nematodes were soaked in a dsRNA solution in vitro. Furthermore, nematode reproduction was suppressed in RNAi transgenic lines, as evident by reductions in the numbers of root knots (by 34-60 % in independent RNAi lines) and egg masses (by 33-58 %). Endogenous expression of prefoldin-2, analysed via real-time polymerase chain reaction and Western blotting, revealed that the gene was strongly expressed in the pre-parasitic J2 stage. Our observations demonstrate the relevance and potential importance of targeting the prefoldin gene during the nematode life cycle. The work also suggests that further improvements in silencing efficiency in economically important crops can be accomplished using RNAi directed against plant-parasitic nematodes.

Selective automation and skill transfer in medical robotics: a demonstration on surgical knot-tying.

Science.gov (United States)

Knoll, Alois; Mayer, Hermann; Staub, Christoph; Bauernschmitt, Robert

2012-12-01

Transferring non-trivial human manipulation skills to robot systems is a challenging task. There have been a number of attempts to design research systems for skill transfer, but the level of the complexity of the actual skills transferable to the robot was rather limited, and delicate operations requiring a high dexterity and long action sequences with many sub-operations were impossible to transfer. A novel approach to human-machine skill transfer for multi-arm robot systems is presented. The methodology capitalizes on the metaphor of 'scaffolded learning', which has gained widespread acceptance in psychology. The main idea is to formalize the superior knowledge of a teacher in a certain way to generate support for a trainee. In our case, the scaffolding is constituted by abstract patterns, which facilitate the structuring and segmentation of information during 'learning by demonstration'. The actual skill generalization is then based on simulating fluid dynamics. The approach has been successfully evaluated in the medical domain for the delicate task of automated knot-tying for suturing with standard surgical instruments and a realistic minimally invasive robotic surgery system. Copyright © 2012 John Wiley & Sons, Ltd.

Excessive counterion condensation on immobilized ssDNA in solutions of high ionic strength.

Science.gov (United States)

Rant, Ulrich; Arinaga, Kenji; Fujiwara, Tsuyoshi; Fujita, Shozo; Tornow, Marc; Yokoyama, Naoki; Abstreiter, Gerhard

2003-12-01

We present experiments on the bias-induced release of immobilized, single-stranded (ss) 24-mer oligonucleotides from Au-surfaces into electrolyte solutions of varying ionic strength. Desorption is evidenced by fluorescence measurements of dye-labeled ssDNA. Electrostatic interactions between adsorbed ssDNA and the Au-surface are investigated with respect to 1), a variation of the bias potential applied to the Au-electrode; and 2), the screening effect of the electrolyte solution. For the latter, the concentration of monovalent salt in solution is varied from 3 to 1600 mM. We find that the strength of electric interaction is predominantly determined by the effective charge of the ssDNA itself and that the release of DNA mainly occurs before the electrochemical double layer has been established at the electrolyte/Au interface. In agreement with Manning's condensation theory, the measured desorption efficiency (etarel) stays constant over a wide range of salt concentrations; however, as the Debye length is reduced below a value comparable to the axial charge spacing of the DNA, etarel decreases substantially. We assign this effect to excessive counterion condensation on the DNA in solutions of high ionic strength. In addition, the relative translational diffusion coefficient of ssDNA in solution is evaluated for different salt concentrations.

Hybridization chain reaction amplification for highly sensitive fluorescence detection of DNA with dextran coated microarrays.

Science.gov (United States)

Chao, Jie; Li, Zhenhua; Li, Jing; Peng, Hongzhen; Su, Shao; Li, Qian; Zhu, Changfeng; Zuo, Xiaolei; Song, Shiping; Wang, Lianhui; Wang, Lihua

2016-07-15

Microarrays of biomolecules hold great promise in the fields of genomics, proteomics, and clinical assays on account of their remarkably parallel and high-throughput assay capability. However, the fluorescence detection used in most conventional DNA microarrays is still limited by sensitivity. In this study, we have demonstrated a novel universal and highly sensitive platform for fluorescent detection of sequence specific DNA at the femtomolar level by combining dextran-coated microarrays with hybridization chain reaction (HCR) signal amplification. Three-dimensional dextran matrix was covalently coated on glass surface as the scaffold to immobilize DNA recognition probes to increase the surface binding capacity and accessibility. DNA nanowire tentacles were formed on the matrix surface for efficient signal amplification by capturing multiple fluorescent molecules in a highly ordered way. By quantifying microscopic fluorescent signals, the synergetic effects of dextran and HCR greatly improved sensitivity of DNA microarrays, with a detection limit of 10fM (1×10(5) molecules). This detection assay could recognize one-base mismatch with fluorescence signals dropped down to ~20%. This cost-effective microarray platform also worked well with samples in serum and thus shows great potential for clinical diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.