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Sample records for field slab gel

  1. Optimization of separation and detection schemes for DNA with pulsed field slab gel and capillary electrophoresis

    SciTech Connect

    McGregor, David A.

    1993-07-01

    The purpose of the Human Genome Project is outlined followed by a discussion of electrophoresis in slab gels and capillaries and its application to deoxyribonucleic acid (DNA). Techniques used to modify electroosmotic flow in capillaries are addressed. Several separation and detection schemes for DNA via gel and capillary electrophoresis are described. Emphasis is placed on the elucidation of DNA fragment size in real time and shortening separation times to approximate real time monitoring. The migration of DNA fragment bands through a slab gel can be monitored by UV absorption at 254 nm and imaged by a charge coupled device (CCD) camera. Background correction and immediate viewing of band positions to interactively change the field program in pulsed-field gel electrophoresis are possible throughout the separation. The use of absorption removes the need for staining or radioisotope labeling thereby simplifying sample preparation and reducing hazardous waste generation. This leaves the DNA in its native state and further analysis can be performed without de-staining. The optimization of several parameters considerably reduces total analysis time. DNA from 2 kb to 850 kb can be separated in 3 hours on a 7 cm gel with interactive control of the pulse time, which is 10 times faster than the use of a constant field program. The separation of ΦX174RF DNA-HaeIII fragments is studied in a 0.5% methyl cellulose polymer solution as a function of temperature and applied voltage. The migration times decreased with both increasing temperature and increasing field strength, as expected. The relative migration rates of the fragments do not change with temperature but are affected by the applied field. Conditions were established for the separation of the 271/281 bp fragments, even without the addition of intercalating agents. At 700 V/cm and 20°C, all fragments are separated in less than 4 minutes with an average plate number of 2.5 million per meter.

  2. Hybrid slab-microchannel gel electrophoresis system

    DOEpatents

    Balch, Joseph W.; Carrano, Anthony V.; Davidson, James C.; Koo, Jackson C.

    1998-01-01

    A hybrid slab-microchannel gel electrophoresis system. The hybrid system permits the fabrication of isolated microchannels for biomolecule separations without imposing the constraint of a totally sealed system. The hybrid system is reusable and ultimately much simpler and less costly to manufacture than a closed channel plate system. The hybrid system incorporates a microslab portion of the separation medium above the microchannels, thus at least substantially reducing the possibility of non-uniform field distribution and breakdown due to uncontrollable leakage. A microslab of the sieving matrix is built into the system by using plastic spacer materials and is used to uniformly couple the top plate with the bottom microchannel plate.

  3. A Simple Vertical Slab Gel Electrophoresis Apparatus.

    ERIC Educational Resources Information Center

    Carter, J. B.; And Others

    1983-01-01

    Describes an inexpensive, easily constructed, and safe vertical slab gel kit used routinely for sodium dodecyl sulphate-polyacrylamide gel electrophoresis research and student experiments. Five kits are run from a single transformer. Because toxic solutions are used, students are given plastic gloves and closely supervised during laboratory…

  4. A Simple Vertical Slab Gel Electrophoresis Apparatus.

    ERIC Educational Resources Information Center

    Carter, J. B.; And Others

    1983-01-01

    Describes an inexpensive, easily constructed, and safe vertical slab gel kit used routinely for sodium dodecyl sulphate-polyacrylamide gel electrophoresis research and student experiments. Five kits are run from a single transformer. Because toxic solutions are used, students are given plastic gloves and closely supervised during laboratory…

  5. Hybrid slab-microchannel gel electrophoresis system

    DOEpatents

    Balch, J.W.; Carrano, A.V.; Davidson, J.C.; Koo, J.C.

    1998-05-05

    A hybrid slab-microchannel gel electrophoresis system is described. The hybrid system permits the fabrication of isolated microchannels for biomolecule separations without imposing the constraint of a totally sealed system. The hybrid system is reusable and ultimately much simpler and less costly to manufacture than a closed channel plate system. The hybrid system incorporates a microslab portion of the separation medium above the microchannels, thus at least substantially reducing the possibility of non-uniform field distribution and breakdown due to uncontrollable leakage. A microslab of the sieving matrix is built into the system by using plastic spacer materials and is used to uniformly couple the top plate with the bottom microchannel plate. 4 figs.

  6. System for loading slab-gel holders for electrophoresis separation

    DOEpatents

    Anderson, Norman G.; Anderson, Norman L.

    1979-01-01

    A slab-gel loading system includes a prismatic chamber for filling a plurality of slab-gel holders simultaneously. Each slab-gel holder comprises a pair of spaced apart plates defining an intermediate volume for gel containment. The holders are vertically positioned in the chamber with their major surfaces parallel to the chamber end walls. A liquid inlet is provided at the corner between the bottom and a side wall of the chamber for distributing a polymerizable monomer solution or a coagulable colloidal solution into each of the holders. The chamber is rotatably supported so that filling can begin with the corner having the liquid inlet directed downwardly such that the solution is gently funneled upwardly, without mixing, along the diverging side and bottom surfaces. As filling proceeds, the chamber is gradually rotated to position the bottom wall in a horizontal mode. The liquid filling means includes a plastic envelope with a septum dividing it into two compartments for intermixing two solutions of different density and thereby providing a liquid flow having a density gradient. The resulting gels have a density gradient between opposite edges for subsequent use in electrophoresis separations.

  7. Pulse Field Gel Electrophoresis

    PubMed Central

    Sharma-Kuinkel, Batu K.; Rude, Thomas H.; Fowler, Vance G.

    2015-01-01

    Pulse Field Gel Electrophoresis (PFGE) is a powerful genotyping technique used for the separation of large DNA molecules (entire genomic DNA) after digesting it with unique restriction enzymes and applying to a gel matrix under the electric field that periodically changes direction. PFGE is a variation of agarose gel electrophoresis that permits analysis of bacterial DNA fragments over an order of magnitude larger than that with conventional restriction enzyme analysis. It provides a good representation of the entire bacterial chromosome in a single gel with a highly reproducible restriction profile, providing clearly distinct and well-resolved DNA fragments. PMID:25682374

  8. Pulse Field Gel Electrophoresis.

    PubMed

    Sharma-Kuinkel, Batu K; Rude, Thomas H; Fowler, Vance G

    2016-01-01

    Pulse Field Gel Electrophoresis (PFGE) is a powerful genotyping technique used for the separation of large DNA molecules (entire genomic DNA) after digesting it with unique restriction enzymes and applying to a gel matrix under the electric field that periodically changes direction. PFGE is a variation of agarose gel electrophoresis that permits analysis of bacterial DNA fragments over an order of magnitude larger than that with conventional restriction enzyme analysis. It provides a good representation of the entire bacterial chromosome in a single gel with a highly reproducible restriction profile, providing clearly distinct and well-resolved DNA fragments.

  9. A method for horizontal polyacrylamide slab gel electrophoresis.

    PubMed

    Bellomy, G R; Record, M T

    1989-01-01

    We present a simplified method of preparation of polyacrylamide gels which is totally analogous to the procedure now widely used to pour and run horizontal agarose gels. The acrylamide is poured into an open air gel mold consisting of a glass plate with a masking tape border and a comb. It is subsequently run in a submarine horizontal electrophoresis apparatus. The electrophoretic mobility and resolution of DNA fragments obtained in such gels are identical to results obtained with gels poured and run in the vertical configuration. Numerous advantages of horizontal polyacrylamide gel electrophoresis are discussed.

  10. Shotgun electroelution: a proteomic tool for simultaneous sample elution from whole SDS-polyacrylamide gel slabs.

    PubMed

    Antal, József; Bányász, Borbála; Buzás, Zsuzsanna

    2007-02-01

    A high-throughput device has been constructed which allows parallel electroelution of separated SDS-protein bands directly from intact unsectioned polyacrylamide gel slabs as well as single electroelution of certain protein spots into a 384-well standard flat-bottom multiwell plate. The prototype provides complete, quick elution for proteomics from 1-D or from 2-D gels without gel sectioning. Since the elution chamber matrix requires no assembly, sample handling can be easily carried out by existing robotic workstations. The current design is a good candidate for automation of spot elution since there are no moving liquid containing components in the apparatus. Eight SDS-proteins were eluted in test runs and an average 70% sample recovery was achieved by re-electrophoresis of the electro-eluates.

  11. A rapid 3% polyacrylamide slab gel electrophoresis method for high through put screening of LDL phenotype

    PubMed Central

    Singh, Yogendra; Lakshmy, Ramakrishnan; Gupta, Ruby; Kranthi, Vemparala

    2008-01-01

    Background Small dense LDL is reported to be associated with increased coronary artery disease risk by various epidemiological studies. The gold standard for separation and identification of LDL subtypes in plasma is ultracentrifugation which is a lengthy procedure and difficult to perform. Various other methods like NMR, HPLC, gradient gel electrophoresis (GGE) have been reported for LDL sub fractionation all of which require specialized equipments and expertise. We report here a high throughput 3% polyacrylamide slab gel electrophoresis method (PASGE) for sub fractionation of LDL which was compared with GGE, a commonly used method for LDL sub fractionation. Results The 3% PASGE method compared well with the GGE method There was a good correlation between LDL particle diameter identified by the PASGE and GGE (Pearson correlation coefficient = 0.950). A 100% concordance was found when samples were classified as per LDL phenotypes in subjects with A and B phenotype by the two methods with the concordance being 66% in subjects with intermediate (I) phenotype. The electrophoresis apparatus was optimized and designed for running twenty eight samples at a time compared to twelve to fourteen by the conventional PASGE and eight to twelve by disc electrophoresis. Conclusion The rapid 3% polyacrylamide slab gel electrphoresis method developed is simple to perform, cost-effective and can be used for the identification LDL sub fractionation and phenotyping in large epidemiological studies. PMID:19036141

  12. Ion trap electric field measurements using slab coupled optical sensors

    NASA Astrophysics Data System (ADS)

    Shumway, L.; Chadderdon, S.; Powell, A.; Li, A.; Austin, D.; Hawkins, A.; Selfridge, R.; Schultz, S.

    2014-03-01

    Ion traps are widely used in the field of mass spectrometry. These devices use high electric fields to mass-selectively trap, eject, and count the particles of a material, producing a mass spectrum of the given material. Because of their usefulness, technology pushes for smaller, more portable ion traps for field use. Making internal ion trap field measurements not yet feasible because current electric field sensors are often too bulky or their metallic composition perturbs field measurements. Using slab coupled optical sensor (SCOS) technology, we are able to build sensors that are compatible with the spacing constraints of the ion trap. These sensors are created by attaching a nonlinear crystal slab waveguide to an optical fiber. When a laser propagates through the fiber, certain wavelengths of light couple out of the fiber via the crystal and create "resonances" in the output light spectrum. These resonances shift in proportion to a given applied electric field, and by measuring that shift, we can approximate the electric field. Developing a sensor that can effectively characterize the electric fields within an ion trap will greatly assist in ion trap design, fabrication, and troubleshooting techniques.

  13. Flow field predictions for a slab delta wing at incidence

    NASA Technical Reports Server (NTRS)

    Conti, R. J.; Thomas, P. D.; Chou, Y. S.

    1972-01-01

    Theoretical results are presented for the structure of the hypersonic flow field of a blunt slab delta wing at moderately high angle of attack. Special attention is devoted to the interaction between the boundary layer and the inviscid entropy layer. The results are compared with experimental data. The three-dimensional inviscid flow is computed numerically by a marching finite difference method. Attention is concentrated on the windward side of the delta wing, where detailed comparisons are made with the data for shock shape and surface pressure distributions. Surface streamlines are generated, and used in the boundary layer analysis. The three-dimensional laminar boundary layer is computed numerically using a specially-developed technique based on small cross-flow in streamline coordinates. In the rear sections of the wing the boundary layer decreases drastically in the spanwise direction, so that it is still submerged in the entropy layer at the centerline, but surpasses it near the leading edge. Predicted heat transfer distributions are compared with experimental data.

  14. Slab stress field in the Hellenic subduction zone as inferred from intermediate depth earthquakes

    NASA Astrophysics Data System (ADS)

    Rontogianni, S.; Konstantinou, K.; Melis, N. S.; Evangelidis, C.

    2010-12-01

    In this study we investigate the stress regime of the subducting slab beneath the Hellenic Arc aiming to answer two fundamental questions; a) How does the slab deformation vary horizontally and vertically along this large curvature arc? b) Which are the mechanisms inferred from global observations that can explain this deformation and have not been identified previously due to dataset limitations. The data are selected from various seismic networks, global and local seismic catalogues and the newly established Hellenic broadband seismic network (http://bbnet.gein.noa.gr/). An updated view of the geometry of the Hellenic Wadati-Benioff zone (WBZ) is gained by the spatial distribution of intermediate depth earthquakes (40 km≤ depth ≤ 180km). Stress tensor inversion is performed on 100 fault plane solutions of intermediate depth earthquakes after quality control has been applied. The stress field parameters are determined along the arc for several depth ranges. The slab is divided into four subsets, each containing enough focal mechanisms for stress inversion to be performed successfully. The Peloponnese segment shows for depths 50-80 km σ1 almost normal to the slab and σ3 steeper than the slab dip that might indicate suction force-the component of the slab pull force that is unbalanced by the subduction resistance. The Kithira-Western Crete segment shows for depths 50-100 km a biaxial deviatoric compression or a state of confined compression with the σ1 along strike. The stress regime in this section of the slab might be related to its complex shape and geometry (width, curvature) reflecting changes in the slab dip between the Peloponnese-Kithira strait and the Crete region as has also been identified by teleseimic receiver functions. The third segment below Crete shows σ1 along strike and σ3 almost subvertical to slab direction. The stress field for the forth segment below Karpathos and Rhodos has been divided into two depth ranges. The shallow subset (50

  15. Numerical calculation of superheating magnetic fields and currents for superconducting slabs

    NASA Astrophysics Data System (ADS)

    Landau, I. L.; Rinderer, L.

    1995-08-01

    Numerical calculations of superheating magnetic fields and superheating currents for superconducting slabs for a wide range of the sample thickness are presented. The calculations were made for low values of Ginzburg-Landau parameter κ, i.e., for type-1 superconductors. We propose also experimental procedures to measure superheating fields and currents in films and bulk samples.

  16. Stress field evolution above the Peruvian flat-slab (Cordillera Blanca, northern Peru)

    NASA Astrophysics Data System (ADS)

    Margirier, A.; Audin, L.; Robert, X.; Pêcher, A.; Schwartz, S.

    2017-08-01

    In subduction settings, the tectonic regime of the overriding plate is closely related to the geometry of the subducting plate. Flat-slab segments are supposed to increase coupling at the plate interface in the Andes, resulting in an increase and eastward migration of the shortening in the overriding plate. Above the Peruvian flat-slab, a 200 km-long normal fault trend parallel to the range and delimits the western flank of the Cordillera Blanca. In a context of flat subduction, expected to produce shortening, the presence of the Cordillera Blanca normal fault (CBNF) is surprising. We performed a systematic inversion of striated fault planes in the Cordillera Blanca region to better characterize the stress field above the Peruvian flat-slab. It evidences the succession of different tectonic regimes. NE-SW extension is predominant in most of the sites indicating a regional extension. We suggest that the Peruvian flat-slab trigger extension in the Western Cordillera while the shortening migrated eastward. Finally, we propose that flat-slab segments do not increase the coupling at the trench neither the shortening in the overriding plate but only favor shortening migration backward. However, the stress field of the overriding plate arises from the evolution of plate interface properties through time due to bathymetric anomaly migration.

  17. Effect of an electric field on the bifurcation of a biaxially stretched incompressible slab rubber.

    PubMed

    Díaz-Calleja, R; Sanchis, M J; Riande, E

    2009-12-01

    This paper describes the effect of an electrical field on the bifurcation phenomenon that appears in a biaxially stretched slab of Mooney-Rivlin material (M. Mooney, J. Appl. Phys. 11, 582 (1940)) subjected to equal dead loads. The main conclusion of the analysis is that the stretch ratio at which the bifurcation phenomenon appears crucially depends on the configuration of the system rubber slab-electrodes. The theoretical foundations of the present study are based on a recent formulation on this subject carried out by Dorfmann and Ogden (A. Dorfmann, R.W. Ogden, Acta Mech. 174, 167 (2005); J. Elasticity 82, 99 (2006)).

  18. Sub-slab pressure field extension in schools and other large buildings

    NASA Astrophysics Data System (ADS)

    Harris, D. B.; Craig, A. B.; Leovic, K. W.

    1991-09-01

    The experiences of EPA are discussed in using pressure field extension (PFE) to design active subslab depressurization (ASD) systems to reduce radon levels in old and new schools, including instances where the data collected resulted in the installation of smaller systems than expected and selection of high vacuum fans instead of normal mitigation fans. A central collection system for use under very large slabs is discussed and PFE data are given for a hospital under construction. The most direct method of projecting or measuring the performance of an ASD system is to measure the strength and extent of the pressure field established under the slab. The PFE can be determined (during diagnostics) to help design an ASD system and (following installation) to ascertain system performance. In schools and other large buildings, these data are invaluable to provide a system that will mitigate the building without undue cost escalation.

  19. Acoustic field enhancement and subwavelength imaging by coupling to slab waveguide modes

    NASA Astrophysics Data System (ADS)

    Christensen, J.; García de Abajo, F. J.

    2010-10-01

    We present a theoretical study on the amplification of evanescent sound waves produced by coupling to trapped modes hosted by a fluidic planar waveguide. Total internal reflection at interfaces of different refractive indexes can be frustrated by the introduction of a slow slab waveguide which is leading to a gigantic field enhancement, useful for sensitive transducers and acoustic shock lithotripsy. The mechanism behind the evanescent field coupling that is also known as tunnelling barrier penetration in quantum mechanics is here adopted for its use in an acoustic superlens. The higher spatial harmonics produced by a subwavelength object can couple to trapped modes of the slow waveguide and be reproduced as an image at a distant plane. We suggest a practical implementation of these ideas by means of a silicone rubber slab containing positive acoustic wave propagation parameters.

  20. Effects of magnetic field on the interaction between terahertz wave and non-uniform plasma slab

    SciTech Connect

    Tian, Yuan; Han, YiPing; Guo, LiXin; Ai, Xia

    2015-10-15

    In this paper, the interaction between terahertz electromagnetic wave and a non-uniform magnetized plasma slab is investigated. Different from most of the published literatures, the plasma employed in this work is inhomogeneous in both collision frequency and electron density. Profiles are introduced to describe the non-uniformity of the plasma slab. At the same time, magnetic field is applied to the background of the plasma slab. It came out with an interesting phenomenon that there would be a valley in the absorption band as the plasma's electromagnetic characteristic is affected by the magnetic field. In addition, the valley located just near the middle of the absorption peak. The cause of the valley's appearance is inferred in this paper. And the influences of the variables, such as magnetic field strength, electron density, and collision frequency, are discussed in detail. The objective of this work is also pointed out, such as the applications in flight communication, stealth, emissivity, plasma diagnose, and other areas of plasma.

  1. Nonstationary Axisymmetric Temperature Field in a Two-Layer Slab Under Mixed Heating Conditions

    NASA Astrophysics Data System (ADS)

    Turchin, I. N.; Timar, I.; Kolodii, Yu. A.

    2015-09-01

    With the use of the Laguerre and Hankel integral transforms, the solution of a two-dimensional initial-boundary-value heat conduction problem for a two-layer slab under mixed boundary conditions is constructed: one of the surfaces is heated by a heat flux distributed axisymmetrically in a circle of radius R and is cooled by the Newton law outside this circle. The solution of the problem is reduced to a sequence of infinite quasi-regular systems of algebraic equations. The results of numerical analysis of the temperature field in the two-layer slab made from an aluminum alloy and ceramicsare presented depending on the relative geometric properties of the components and cooling intensity.

  2. Ion Trap Electric Field Characterization Using Slab Coupled Optical Fiber Sensors

    NASA Astrophysics Data System (ADS)

    Chadderdon, Spencer; Shumway, LeGrand; Powell, Andrew; Li, Ailin; Austin, Daniel E.; Hawkins, Aaron R.; Selfridge, Richard H.; Schultz, Stephen M.

    2014-09-01

    This paper presents a method for characterizing electric field profiles of radio frequency (rf) quadrupole ion trap structures using sensors based on slab coupled optical-fiber sensor (SCOS) technology. The all-dielectric and virtually optical fiber-sized SCOS fits within the compact environment required for ion traps and is able to distinguish electric field orientation and amplitude with minimal perturbation. Measurement of the fields offers insight into the functionality of traps, which may not be obtainable solely by performing simulations. The SCOS accurately mapped the well-known field profiles within a commercially available three-dimensional quadrupole ion trap (Paul trap). The results of this test allowed the SCOS to map the more complicated fields within the coaxial ion trap with a high degree of confidence as to the accuracy of the measurement. [Figure not available: see fulltext.

  3. Self-consistent solution for a collisionless plasma slab in motion across a magnetic field

    SciTech Connect

    Echim, Marius M.; Lemaire, Joseph F.; Roth, Michel

    2005-07-15

    The problem of the dynamics of a plasma slab moving across a magnetic field is treated in the framework of the kinetic theory. A velocity distribution function (VDF) is found for each plasma species, electrons and protons, in terms of the constants of motion defined by the geometry of the problem. The zero- and first-order moments of the VDF are introduced into the right-hand side term of Maxwell's equations to compute the electric and magnetic vector potentials and corresponding fields. The solutions are found numerically. We obtain a region of plasma convection--the slab proper--where the plasma moves with a uniform velocity, V{sub x}=V{sub 0}=(ExB/B{sup 2}){sub x}. At the core margins two plasma 'wings' are formed, each being the result of a pair of interpenetrated boundary layers with different transition lengths. Inside these wings, the plasma velocity is not uniform, V{sub x}{ne}(ExB/B{sup 2}){sub x}. It decreases from the maximum value obtained in the core to a minimum value in the central region of the wings where a flow reversal is found with the plasma convecting in the opposite direction to the core motion. There is also an asymmetry of the velocity gradient at the borders of the core, which results in a corresponding asymmetry in the thickness of the wings. Furthermore, it is found that the reversed plasma flow in the thinner wing is larger than that in the broader wing. For a fixed direction of the magnetic field the two plasma wings interchange position with respect to the center of the slab when the plasma bulk velocity reverses sign.

  4. Electric-field sensors utilizing coupling between a D-fiber and an electro-optic polymer slab.

    PubMed

    Chadderdon, Spencer; Gibson, Richard; Selfridge, Richard H; Schultz, Stephen M; Wang, Wen C; Forber, Richard; Luo, Jingdong; Jen, Alex K-Y

    2011-07-10

    This paper provides a detailed analysis of electric field sensing using a slab-coupled optical fiber sensor (SCOS). This analysis explains that the best material for the slab waveguide is an inorganic material because of the low RF permittivity combined with the high electro-optic coefficient. The paper also describes the fabrication and testing of a SCOS using an AJL chromophore in amorphous polycarbonate. The high uniform polymer slab waveguide is fabricated using a hot embossing process to create a slab with a thickness of 50 μm. The fabricated polymer SCOS was characterized to have a resonance slope of ΔP/Δλ=6.83E5 W/m and a resonance shift of Δλ/E=1.47E-16 m(2)/V.

  5. Large field enhancement obtained by combining Fabry–Perot resonance and Rayleigh anomaly in photonic crystal slabs

    NASA Astrophysics Data System (ADS)

    Dossou, Kokou B.

    2017-04-01

    By applying the properties of Fabry–Perot resonance and Rayleigh anomaly, we have shown that a photonic crystal slab can scatter the light from an incident plane wave into a diffracted light with a very large reflection or transmission coefficient. The enhanced field is either a propagating diffracted wave (with a grazing angle of diffraction) or a weakly evanescent diffracted wave, so it can be particularly useful for applications requiring an enhanced propagating field (or an enhanced field with a low attenuation). An efficient effective medium technique is developed for the design of the resonant photonic crystal slabs. Numerical simulations have shown that photonic crystal slabs with low index contrast, such as the ones found in the cell wall of diatoms, can enhance the intensity of the incident light by four orders of magnitude.

  6. Magnification of subwavelength field distributions at microwave frequencies using a wire medium slab operating in the canalization regime

    NASA Astrophysics Data System (ADS)

    Ikonen, Pekka; Simovski, Constantin; Tretyakov, Sergei; Belov, Pavel; Hao, Yang

    2007-09-01

    Authors demonstrate numerically the magnification of subwavelength field pattern using a wire medium slab operating in the canalization regime. The magnifying slab is implemented by radially enlarging the distance between adjacent wires, and the operational frequency is tuned to coincide with the Fabry-Pérot resonance condition. The near-field pattern of a complex-shaped source is canalized over an electrical distance corresponding roughly to three wavelengths (3λ), and the pattern details are magnified by a factor of 3. The performance is also studied at several frequencies deviating from the one of the Fabry-Pérot resonance.

  7. Stress distribution calculations through a snow slab of varying elastic modulus; comparison with stability evaluation in the field

    NASA Astrophysics Data System (ADS)

    Swinkels, Laura; Borstad, Chris

    2017-04-01

    Field observations are the main tools for assessing the snow stability concerning dry snow slab avalanche release. Often, theoretical studies cannot directly be translated into useful information for avalanche recreationists and forecasters in the field, and vice versa; field observations are not always objective and quantifiable for theoretical studies. Moreover, numerical models often simplify the snowpack and generally use an isotropic single layer slab which is not representative of the real-life situation. The aim of this study is to investigate the stress distribution in a snowpack with an elastic modulus that continuously varies with depth. The focus lies on the difference between a slab with a gradient in hardness and a slab with isotropic hardness and the effect on the calculated maximum stress and the stability evaluation in the field. Approximately 20 different snow pits were evaluated in the mountains around Tromsø, Norway and Longyearbyen, Svalbard. In addition to the standard snowpack observations, the hardness was measured using a thin-blade gauge. Extended column tests were executed for stability evaluation. Measurements from the field were used as input for stress calculations for each snow pit using a line load solution for a sloping half space with a non-homogeneous elastic modulus. The hardness measurements were used to calculate the elastic modulus and a power law relation was fit through the modulus in the slab. The calculated shear stress was compared to the estimated stability and character of the specific snowpack The results show that the approach used for this study improves the calculation of stress at a given depth, although many assumptions and simplifications were still needed. Comparison with the snow profiles indicate that calculated stresses correlate well with the observed snowpack properties and stability. The calculated shear stresses can be introduced in the standard stability index and give a better indication for the

  8. Pulsed-field gel electrophoresis of bacterial chromosomes.

    PubMed

    Mawer, Julia S P; Leach, David R F

    2013-01-01

    The separation of fragments of DNA by agarose gel electrophoresis is integral to laboratory life. Nevertheless, standard agarose gel electrophoresis cannot resolve fragments bigger than 50 kb. Pulsed-field gel electrophoresis is a technique that has been developed to overcome the limitations of standard agarose gel electrophoresis. Entire linear eukaryotic chromosomes, or large fragments of a chromosome that have been generated by the action of rare-cutting restriction endonucleases, can be separated using this technique. As a result, pulsed-field gel electrophoresis has many applications, from karyotype analysis of microbial genomes, to the analysis of chromosomal strand breaks and their repair intermediates, to the study of DNA replication and the identification of origins of replication. This chapter presents a detailed protocol for the preparation of Escherichia coli chromosomal DNA that has been embedded in agarose plugs, digested with the rare-cutting endonuclease NotI, and separated by contour-clamped homogeneous field electrophoresis. The principles in this protocol can be applied to the separation of all fragments of DNA whose size range is between 40 kb and 1 Mb.

  9. Tunable Lamb wave band gaps in two-dimensional magnetoelastic phononic crystal slabs by an applied external magnetostatic field.

    PubMed

    Zhou, Changjiang; Sai, Yi; Chen, Jiujiu

    2016-09-01

    This paper theoretically investigates the band gaps of Lamb mode waves in two-dimensional magnetoelastic phononic crystal slabs by an applied external magnetostatic field. With the assumption of uniformly oriented magnetization, an equivalent piezomagnetic material model is used. The effects of magnetostatic field on phononic crystals are considered carefully in this model. The numerical results indicate that the width of the first band gap is significantly changed by applying the external magnetic field with different amplitude, and the ratio between the maximum and minimum gap widths reaches 228%. Further calculations demonstrate that the orientation of the magnetic field obviously affects the width and location of the first band gap. The contactless tunability of the proposed phononic crystal slabs shows many potential applications of vibration isolation in engineering. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Quantization of the electromagnetic field at the presence of two dielectric slabs and application to the Casimir effect

    NASA Astrophysics Data System (ADS)

    Falinejad, Hossein

    2017-06-01

    The three dimensional formalism of the Green function method of the electro-magnetic field quantization is extended to quantize the electromagnetic field, at the presence of two dispersive and dissipative dielectric slabs. It is shown that the system decomposes into a singlet and a doublet parts. The singlet system corresponds to the normal polarization state of the electric field and the doublet system corresponds to the sum of parallel and longitudinal polarization states. Each part is quantized separately and vector potential operator of the each part is derived in terms of rightward and leftwards annihilation and creation operators. By using the assuming commutation properties of the noise current density, the equal time canonical commutation relations between the vector potential operator and its conjugate generalized momentum are verified for each part. Finally as an application, the explicit form of field operators are used to obtain an expression for the Casimir force between the two slabs via Maxwell stress tensor.

  11. Bistable near field and bistable transmittance in 2D composite slab consisting of nonlocal core-Kerr shell inclusions.

    PubMed

    Huang, Yang; Wu, Ya Min; Gao, Lei

    2017-01-23

    We carry out a theoretical study on optical bistability of near field intensity and transmittance in two-dimensional nonlinear composite slab. This kind of 2D composite is composed of nonlocal metal/Kerr-type dielectric core-shell inclusions randomly embedded in the host medium, and we derivate the nonlinear relation between the field intensity in the shell of inclusions and the incident field intensity with self-consistent mean field approximation. Numerical demonstration has been performed to show the viable parameter space for the bistable near field. We show that nonlocality can provide broader region in geometric parameter space for bistable near field as well as bistable transmittance of the nonlocal composite slab compared to local case. Furthermore, we investigate the bistable transmittance in wavelength spectrum, and find that besides the input intensity, the wavelength operation could as well make the transmittance jump from a high value to a low one. This kind of self-tunable nano-composite slab might have potential application in optical switching devices.

  12. Protein Crystal Growth in Gels and Stationary Magnetic Fields

    SciTech Connect

    Moreno,A.; Quiroz-Garcia, B.; Yokaichiya, F.; Stojanoff, V.; Rudolph, P.

    2007-01-01

    Thaumatin, lysozyme, and ferritin single crystals were grown in solutions and gels without and with surrounding strong stationary magnetic fields. The crystal size, number and alignment in dependence on the induction force were analyzed. The crystal quality, like mosaicity, as function of the magnetic force is discussed by using synchrotron X-ray diffraction analysis.

  13. Pulsed-field gel electrophoresis typing of Staphylococcus aureus isolates

    USDA-ARS?s Scientific Manuscript database

    Pulsed-field gel electrophoresis (PFGE) is the most applied and effective genetic typing method for epidemiological studies and investigation of foodborne outbreaks caused by different pathogens, including Staphylococcus aureus. The technique relies on analysis of large DNA fragments generated by th...

  14. Fricke dosimeter gel measurements of the profiles of shielded fields.

    PubMed

    Pirani, Luis F; Moreira, Marcos V; Costa, Jhonatha J L; Oliveira, Lucas N; Caldas, Linda V E; de Almeida, Adelaide

    2013-12-01

    In radiation therapy, the shielding of normal tissue can be made using Cerrobend® blocks or a multileaf collimator. In this work, profiles of shielded fields collimated by Cerrobend blocks were obtained through the Fricke Xylenol Gel (FXG) dosimeter irradiated with 6 MV photon beams. The results show that the FXG system can be used in profile measurements of small fields in radiotherapy. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Sub-slab pressure-field extension in schools and other large buildings. Rept. for 1988-91

    SciTech Connect

    Harris, D.B.; Craig, A.B.; Leovic, K.W.

    1991-01-01

    The paper discusses EPA's experiences using pressure field extension (PFE) to design active subslab depressurization (ASD) systems to reduce radon levels in old and new schools, including instances where the data collected resulted in the installation of smaller systems than expected and selection of high vacuum fans instead of 'normal' mitigation fans. A central collection system for use under very large slabs is discussed and PFE data are given for a hospital under construction. The most direct method of projecting or measuring the performance of an ASD system is to measure the strength and extent of the pressure field established under the slab. The PFE can be determined (during diagnostics) to help design an ASD system and (following installation) to ascertain system performance. In schools and other large buildings, these data are invaluable to provide a system that will mitigate the building without undue cost escalation.

  16. Detection of undeclared animal by-products in commercial canine canned foods: Comparative analyses by ELISA and PCR-RFLP coupled with slab gel electrophoresis or capillary gel electrophoresis.

    PubMed

    Hsieh, Ming-Kun; Shih, Pei-Yin; Wei, Chia-Fong; Vickroy, Thomas W; Chou, Chi-Chung

    2016-03-30

    The potential presence of undeclared animal by-products in pet foods is not subject to routine examination. Previously published methods for species-based identification of animal by-products have not been used routinely owing to inconsistent results. The present study evaluated the utility of several approaches for accurate identification of animal by-products in 11 commercial brands of canine canned foods. Canine canned foods from several countries were analysed by ELISA, PCR-RFLP coupled with slab-gel electrophoresis (SGE) and capillary gel electrophoresis (CGE) to test for evidence of by-products derived from cattle, chicken, sheep or pig. While CGE-based analysis detected all (24) animal-derived by-products that were reported for the 11 test samples, SGE and ELISA detected only 22/24 (92%) and 14/24 (58%) of labelled by-products, respectively. In addition, undeclared animal by-products were found using all three analytical approaches with CGE detecting more positives (19) than SGE (17) or ELISA (5). Significant disparities were evident between the labelled contents and the detected content of animal by-products. CGE-based testing for PCR products appears to provide greater sensitivity and accuracy than either SGE or ELISA-based methods. As testing of commercial products becomes more reliable and mainstream, manufacturers will need to develop more thorough and accurate labelling protocols. © 2015 Society of Chemical Industry.

  17. Pulsed field gel electrophoresis on frozen tumour tissue sections.

    PubMed Central

    Boultwood, J.; Kaklamanis, L.; Gatter, K. C.; Wainscoat, J. S.

    1992-01-01

    The application of pulsed field gel electrophoresis (PFGE) to the molecular genetic analysis of solid tumours has been restricted by the requirement for whole single cells as a DNA source. A simple technique which allows for the direct analysis of histologically characterised solid tumour material by pulsed field gel electrophoresis was developed. Single frozen tissue sections obtained from colonic carcinoma specimens were embedded without further manipulation in molten, low melting temperature agarose. The tumour DNA contained within the agarose plug was subjected to restriction enzyme digestion and PFGE. Sufficient high molecular weight DNA is yielded by this method to obtain a hybridisation signal with a single copy probe. Histological examination of adjacent tissue sections may also be carried out, permitting correlation between molecular analysis and tumour histology. Images PMID:1401187

  18. Frequency-selective near-field radiative heat transfer between photonic crystal slabs: a computational approach for arbitrary geometries and materials.

    PubMed

    Rodriguez, Alejandro W; Ilic, Ognjen; Bermel, Peter; Celanovic, Ivan; Joannopoulos, John D; Soljačić, Marin; Johnson, Steven G

    2011-09-09

    We demonstrate the possibility of achieving enhanced frequency-selective near-field radiative heat transfer between patterned (photonic-crystal) slabs at designable frequencies and separations, exploiting a general numerical approach for computing heat transfer in arbitrary geometries and materials based on the finite-difference time-domain method. Our simulations reveal a tradeoff between selectivity and near-field enhancement as the slab-slab separation decreases, with the patterned heat transfer eventually reducing to the unpatterned result multiplied by a fill factor (described by a standard proximity approximation). We also find that heat transfer can be further enhanced at selective frequencies when the slabs are brought into a glide-symmetric configuration, a consequence of the degeneracies associated with the nonsymmorphic symmetry group.

  19. Linear polarization of resonance lines in the absence of magnetic fields. I - Slabs of finite optical thickness

    NASA Astrophysics Data System (ADS)

    Faurobert, M.

    1987-05-01

    Effects of partial frequency redistribution on resonance polarization of spectral lines in the absence of magnetic fields are studied for resonance lines formed in finite slabs. The emphasis is on testing the validity (for polarization calculations) of various approximate forms of the so-called RII frequency redistribution function which describes the formation of resonance lines formed in dilute media. Polarization profiles obtained with the angle-dependent RII are compared to profiles calculated with the angle-averaged form of RII and its approximate versions proposed by Kneer and Ayres. A comparison with complete frequency redistribution polarization profiles is also presented.

  20. ELECTROMAGNETISM, OPTICS, ACOUSTICS, HEAT TRANSFER, CLASSICAL MECHANICS, AND FLUID DYNAMICS: Analysis on Far-Field of Slab Waveguide and Its Gaussian Approximation

    NASA Astrophysics Data System (ADS)

    Li, Lian-Huang; Guo, Fu-Yuan; Peng, Yu-Jia; Tang, Xiao-Shan; Gao, Rui

    2010-02-01

    This paper researches end diffraction of slab waveguide and then matching efficiency between the far-field and its Gaussian approximate field is analyzed leads to a new definition of divergence half-angle. Finally, why the far-field can be approximated by a Gaussian function is presented according to characteristic of beam propagation factor.

  1. Field lines and magnetic surfaces in a two-component slab/2D model of interplanetary magnetic fluctuations

    NASA Technical Reports Server (NTRS)

    Matthaeus, W. H.; Pontius, D. H., Jr.; Gray, P. C.; Bieber, J. W.

    1995-01-01

    A two-component model for the spectrum of interplanetary magnetic fluctuations was proposed on the basis of ISEE observations, and has found an intriguing level of application in other solar wind studies. The model fluctuations consist of a fraction of 'slab' fluctuations, varying only in the direction parallel to the locally uniform mean magnetic field B(0) and a complement of 2D (two-dimensional) fluctuations that vary in the directions transverse to B(0). We have developed an spectral method computational algorithm for computing the magnetic flux surfaces (flux tubes) associated with the composite model, based upon a precise analogy with equations for ideal transport of a passive scalar in planar two dimensional geometry. Visualization of various composite models will be presented, including the 80 percent 2D/ 20 percent slab model with delta B/B(0) approximately equals 1 and a minus 5/3 spectral law, that is thought to approximately represent a snapshot of solar wind turbulence. Characteristically, the visualizations show that flux tubes, even when defined as regular on some plane, shred and disperse rapidly as they are viewed along the parallel direction. This diffusive process, which generalizes the standard picture of field line random walk, will be discussed in detail. Evidently, the traditional picture that flux tubes randomize like strands of spaghetti with a uniform tangle along the axial direction is in need of modification.

  2. Present-day stress field on the South American slab underneath the Sandwich Plate (Southern Atlantic Ocean)

    NASA Astrophysics Data System (ADS)

    Giner-Robles, J. L.; Pérez-López, R.; Álvarez-Gómez, J. A.; Martínez-Díaz, J. J.; Rodríguez-Pascua, M. A.

    2009-04-01

    This work confirms the present-day principal stress orientation on the South Sandwich Plate (SSP) from the analysis of 331 earthquake focal mechanisms (Harvard catalog, HCMT). Principal stress orientation was deduced from earthquake focal mechanisms, examined by fault population analysis methods. The SSP plate is composed by oceanic crust limits an elliptical trench to the east (South Sandwich Trench), a ridge to the west and transforms faults towards the northern and southern boundaries. Within the trench region, the maximum horizontal shortening direction (SHMAX) rotates in trend in a clockwise direction, from NNE, in the northern boundary, to SSE in the southern boundary. Therefore, and keeping in mind the gradual rotation of SHMAX along the trench, three different areas were defined according to the prevailing focal mechanism type: (1) the North Zone, with SHMAX oriented N060°E and reverse and strike-slip focal mechanisms; (2) the Central Zone, with only reverse focal mechanism and SHMAX striking N080°E; (3) the South Zone, with SHMAX oriented N110°E and reverse and strike-slip focal geometry. Furthermore, the accommodation of the strain field in the Northern Zone of the South Sandwich Plate generates a subduction decoupling of the slab at, approximately, 70 km depth. In contrast, the South Zone slab exhibits a gradual stress and strain magnitude decreasing in depth. Finally, we define a sinistral strike-slip parallel to the southern boundary between the South Sandwich Plate and the Antarctic Plate, the South Sandwich Fault Zone.

  3. Friction Control of a Gel by Electric Field in Ionic Surfactant Solution

    NASA Astrophysics Data System (ADS)

    Masakazu Takata,; Tetsuo Yamaguchi,; Masao Doi,

    2010-06-01

    We observed that the frictional force between acrylamide gel and silicon dioxide substrate is reduced upon application of electric voltage if the gel is swollen with anionic surfactant (sodium dodecyl sulfate). The effect was not seen in cationic surfactant. We conjecture that the reduction is due to formation of a lubrication layer by electric field at the gel/solid interface.

  4. The textural properties and microstructure of konjac glucomannan - tungsten gels induced by DC electric fields.

    PubMed

    Wang, Lixia; Zhuang, Yuanhong; Li, Jingliang; Pang, Jie; Liu, Xiangyang

    2016-12-01

    Konjac glucomannan - tungsten (KGM-T) gels were successfully prepared under DC electric fields, in the presence of sodium tungstate. The textural properties and microstructure of the gels were investigated by Texture Analyzer, Rheometer and SEM. Based on the response surface methodology (RSM) results, the optimum conditions for KGM-T gel springiness is 0.32% sodium tungstate concentration, 0.54% KGM concentration, 24.66V voltage and 12.37min treatment time. Under these conditions, the maximum springiness value of KGM-T gel is 1.21mm. Steady flow measurement indicated that KGM-T gel showed characteristic non-Newtonian pseudoplastic behaviour, with low flow behaviour indexes in the shear thinning region. SEM demonstrated the porosity of the freeze-dried samples. These findings may pave the way to use DC electric fields for the design and development of KGM gels and to apply KGM gels for practical applications.

  5. Analysis of strains of Campylobacter fetus by pulsed-field gel electrophoresis.

    PubMed Central

    Fujita, M; Fujimoto, S; Morooka, T; Amako, K

    1995-01-01

    Campylobacter fetus chromosomal DNA from 21 strains was analyzed by pulsed-field gel electrophoresis. The fingerprint patterns generated with SmaI and SalI were distinctive. Using the profiles obtained by pulsed-field gel electrophoresis, we established the phylogenetic dendrogram of C. fetus to identify the genetic relationship of the strains. PMID:7650215

  6. Quantification of Vapor Intrusion Pathways into a Slab-on-Ground Building: an Integration of Mathematical Modeling and Field Experiments

    NASA Astrophysics Data System (ADS)

    Li, Y.; Akbariyeh, S.; Patterson, B.

    2014-12-01

    Vapor intrusion of volatile organic compounds into buildings can be a significant source of human exposure to hazardous materials. Field assessment is essential to evaluate the vapor intrusion pathways, which has been recognized to be challenging due to the heterogeneity of sites and uncontrolled site environments. Modeling of vapor intrusion processes can predict subsurface vapor and oxygen concentrations and indoor air concentration under various environmental site conditions. However, detailed experimental quantification for model validation is typically unavailable. In this work, we report our efforts to quantifying vapor intrusion pathways into a slab-on-ground building by integrating mathematical modeling with well-controlled field measurements under three different pressure and ventilation site conditions. Comparisons between modeling and field measurements include indoor air concentration, contaminant and oxygen distribution profile beneath and inside the building, diffusive and advective flux under different pressure and air vitalization conditions. In addition to typically identified key factors influencing vapor intrusion (e.g. the building construction, the properties of compounds, and depth to the source), we found several additional parameters, such as anisotropic property of surface soil, locations of crack, and dependency of reaction rates on oxygen concentration, are critical to evaluate vapor intrusion pathways.

  7. Electromagnetic eigenstates and the field of an oscillating point electric dipole in a flat-slab composite structure

    NASA Astrophysics Data System (ADS)

    Farhi, Asaf; Bergman, David J.

    2016-06-01

    An exact calculation of the local electric field E (r ) is described for the case of a time-dependent point electric dipole p e-i ω t in the top layer of an ɛ2, ɛ1, ɛ2 three parallel slabs composite structure, where the ɛ1 layer has a finite thickness 2 d but the ɛ2 layers are infinitely thick. For this purpose we first calculate all the eigenstates of the full Maxwell equations for the case where μ =1 everywhere in the system. The eigenvalues appear as special, nonphysical values of ɛ1 when ɛ2 is given. These eigenstates are then used to develop an exact expansion for the physical values of E (r ) in the system characterized by physical values of ɛ1(ω ) and ɛ2(ω ) . Results are compared with those of a previous calculation of the local field of a time-dependent point charge in the quasistatic regime. Numerical results are shown for the local electric field in practically important configurations where attaining an optical image with subwavelength resolution has practical significance.

  8. Effect of gel structure of matrix orientation in pulsed alternating electric fields

    SciTech Connect

    Stellwagen, N.C.; Stellwagen, J.

    1993-12-31

    Four polymeric gels with different structures, LE agarose, HEEO agarose, beta-carrageenan, and polyacrylamide, were studied by transient electric birefringence to determine the importance of various structural features on the orientation of the gels in pulsed alternating electric fields. The birefrigence relaxation times observed for agarose gels in low voltage electric fields suggest that long fibers and/or domains, ranging up to tens of microns in size, are oriented by the electric field. The sign of the birefringence reverses when the direction of the electric field is reversed, suggesting that the oriented domains change their direction of orientation from parallel to perpendicular (or vice versa) when the polarity of the electric field is reversed. These anamalous orientation effects are observed with both types of agarose gels, but not with beta-carrageenan or polyacrylamide gels, suggesting that the alternating D,L galactose residues in the agarose backbone are responsible for the anomalies.

  9. Absolute dose verifications in small photon fields using BANGTM gel

    NASA Astrophysics Data System (ADS)

    Scheib, S. G.; Schenkel, Y.; Gianolini, S.

    2004-01-01

    Polymer gel dosimeters change their magnetic resonance (MR) and optical properties with the absorbed dose when irradiated and are suitable for narrow photon beam dosimetry in radiosurgery. Such dosimeters enable relative and absolute 3D dose verifications in order to check the entire treatment chain from imaging to dose application during commissioning and quality assurance. For absolute 3D dose verifications in radiosurgery using Gamma Knife B, commercially available BANGTM Gels (BANG 25 Gy and BANG 3 Gy) together with dedicated phantoms were chosen in order to determine the potential of absolute gel dosimetry in radiosurgery.

  10. Increase in local protein concentration by field-inversion gel electrophoresis.

    PubMed

    Tsai, Henghang; Leung, Hon-Chiu Eastwood

    2012-01-01

    Proteins that migrate through cross-linked polyacrylamide gels (PAGs) under the influence of a constant electric field experience negative factors, such as diffusion and nonspecific trapping in the gel matrix. These negative factors reduce protein concentrations within a defined gel volume with increasing migration distance and, therefore, decrease protein recovery efficiency. Here, we describe the enhancement of protein separation efficiency up to twofold in conventional one-dimensional PAG electrophoresis (1D PAGE), two-dimensional (2D) PAGE, and native PAGE by implementing pulses of inverted electric field during gel electrophoresis.

  11. High electric field measurement with slab coupled optical sensors using nonlinear calibration

    NASA Astrophysics Data System (ADS)

    Stan, Nikola; Shumway, Legrand; Seng, Frederick; King, Rex; Selfridge, Richard; Schultz, Stephen

    2015-05-01

    We describe the application of SCOS technology in non-intrusive, directional and spatially localized measurements of high electric fields. When measuring electric fields above a certain threshold, SCOS measurement sensitivity starts varying to a great extent and the linear approximation that assumes sensitivity to be constant breaks down. This means that a comprehensive nonlinear calibration method is required for accurate calibration of both low and high electric fields, while linear calibration can only be accurately applied for low fields. Nonlinear calibration method relies on the knowledge of the variability of sensitivity, while linear calibration relies on approximation of sensitivity with a constant value, which breaks down for high fields. We analyze and compare the two calibration methods by applying them to a same set of measurements. We measure electric field pulses with magnitudes from 1 MV/m to 8.2 MV/m, with sub-300 ns rise time and fall-off time constant of 60 μs. We show that the nonlinear calibration very accurately predicts all measured fields, both high and low, while the linear calibration becomes increasingly inaccurate for fields above 1 MV/m.

  12. Time-varied magnetic field enhances transport of magnetic nanoparticles in viscous gel.

    PubMed

    MacDonald, Cristin; Friedman, Gary; Alamia, John; Barbee, Kenneth; Polyak, Boris

    2010-01-01

    The potential of magnetic nanoparticles (MNPs) to deliver various forms of therapy has not been fully realized, in part due to difficulties in transporting the carriers through soft tissue to different target sites. The aim of this study was to demonstrate that transport of MNPs through a viscous gel can be controlled by a combined AC (time-varying) magnetic field and static field gradient. MNP velocity and transport efficiency were measured in a viscous gel at various settings of magnetic field and magnetite loadings. Combined application of an AC magnetic field with the static field gradient resulted in a nearly 30-fold increase in MNP transport efficiency in viscous gel for 30% (w/w) magnetite-loaded particles as compared with static field conditions. The 'oscillating' effect of an AC magnetic field greatly improves the ability to transport MNPs within soft media by decreasing the effective viscosity of the gel.

  13. Resolution of high molecular weight proteins in dependence on electric field strength in polyacrylamide gel electrophoresis.

    PubMed

    Starita-Geribaldi, M; Houri, A

    1997-01-01

    Resolution of high molecular weight proteins, in the upper region of polyacrylamide gels, was studied in relation to the type of electric field. Separations by constant field gel electrophoresis (CFGE) were compared to those in pulsed oscillatory high-performance electrophoresis (POPE), a novel technique which allows electrophoresis at high field strengths owing to a novel local field distribution. This distribution contributes to structural and mechanical stability of the gel with resultant well-reproducible separation, enhanced resolution, and higher absolute mobility of proteins in POPE.

  14. Polymer slab waveguides for the optical detection of nanoparticles in evanescent field based biosensors

    NASA Astrophysics Data System (ADS)

    Teigell Beneitez, Nuria; Missinne, Jeroen; Schleipen, Jean; Orsel, Joke; Prins, Menno W. J.; Van Steenberge, Geert

    2014-02-01

    We present a polymer optical waveguide integration technology for the detection of nanoparticles in an evanescent field based biosensor. In the proposed biosensor concept, super-paramagnetic nanoparticles are used as optical contrast labels. The nanoparticles capture target molecules from a sample fluid and bind to the sensor surface with biological specificity. The surface-bound nanoparticles are then detected using frustration of an evanescent field. In the current paper we elaborate on the polymer waveguides which are used to generate a well-defined optical field for nanoparticle detection.

  15. Full-field dye concentration measurement within saturated/unsaturated thin slabs of porous media

    SciTech Connect

    Norton, D.L.; Glass, R.J.

    1992-12-31

    This paper presents a full-field dye concentration measurement technique that extends our experimental capabilities to the measurement of transient dye concentration fields within steady state flow fields under unsaturated or saturated conditions. Simple light absorption theory provides a basis for translating images into high resolution dye concentration fields. A series of dye pulse experiments that demonstrate the combined use of the full-field saturation and dye concentration techniques was conducted at four different degrees of saturation. Each of these experimental sequences was evaluated with respect to mass balance, the results being within 5% of the known dye mass input. An image windowing technique allowed us to see increased dispersion due to decreasing moisture content, tailing of concentration at the rear of the dye pulse and slight velocity changes of the dispersive front due to changes in moisture content. The exceptional resolution of dye concentration in space and time provided by this laboratory technique allows systematic experimentation for examining basic processes affecting solute transport within saturated/unsaturated porous media. Future challenges for this work will be to use these techniques to analyze more complex systems involving heterogeneities, scaling laws, and detailed investigations of the relationship between transverse and longitudinal dispersion in unsaturated media.

  16. Feasibility of 3D printed air slab diode caps for small field dosimetry.

    PubMed

    Perrett, Benjamin; Charles, Paul; Markwell, Tim; Kairn, Tanya; Crowe, Scott

    2017-07-31

    Commercial diode detectors used for small field dosimetry introduce a field-size-dependent over-response relative to an ideal, water-equivalent dosimeter due to high density components in the body of the detector. An air gap above the detector introduces a field-size-dependent under-response, and can be used to offset the field-size-dependent detector over-response. Other groups have reported experimental validation of caps containing air gaps for use with several types of diodes in small fields. This paper examines two designs for 3D printed diode air caps for the stereotactic field diode (SFD)-a cap containing a sealed air cavity, and a cap with an air cavity at the face of the SFD. Monte Carlo simulations of both designs were performed to determine dimensions for an air cavity to introduce the desired dosimetric correction. Various parameter changes were also simulated to estimate the dosimetric uncertainties introduced by 3D printing. Cap layer dimensions, cap density changes due to 3D printing, and unwanted air gaps were considered. For the sealed design the optimal air gap size for water-equivalent cap material was 0.6 mm, which increased to 1.0 mm when acrylonitrile butadiene styrene in the cap was simulated. The unsealed design had less variation, a 0.4 mm air gap is optimal in both situations. Unwanted air pockets in the bore of the cap and density changes introduced by the 3D printing process can potentially introduce significant dosimetric effects. These effects may be limited by using fine print resolutions and minimising the volume of cap material.

  17. Electronic structure and its external electric field modulation of PbPdO2 ultrathin slabs with (002) and (211) preferred orientations.

    PubMed

    Yang, Yanmin; Zhong, Kehua; Xu, Guigui; Zhang, Jian-Min; Huang, Zhigao

    2017-07-31

    The Electronic structure of PbPdO2 with (002) and (211) preferred orientations were investigated using first-principles calculation. The calculated results indicate that, (002) and (211) orientations exhibit different electric field dependence of band-gap and carrier concentration. The small band gap and more sensitive electric field modulation of band gap were found in (002) orientation. Moreover, the electric field modulation of the resistivity up to 3-4 orders of magnitude is also observed in (002) slab, which reveals that origin of colossal electroresistance. Lastly, electric field modulation of band gap is well explained. This work should be significant for repeating the colossal electroresistance.

  18. Diode end-pumped high-power Q-switched double Nd:YAG slab laser and its efficient near-field second-harmonic generation.

    PubMed

    Zhu, Peng; Li, Daijun; Qi, Bingsong; Schell, Alexander; Shi, Peng; Haas, Claus; Fu, Shaojun; Wu, Nianle; Du, Keming

    2008-10-01

    We reported on an all-solid-state double Nd:YAG slab laser. The laser was based on two diode end-pumped Nd:YAG slabs and a stable-unstable hybrid resonator. A cw output of 189 W and an average Q-switched output of 169 W at 10 kHz with an M(2) factor of 1.5 in the slow direction and 1.7 in the fast direction were obtained. We demonstrated efficient near-field frequency doubling by imaging the one-dimensional top-hat near-field to a lithium triborate frequency doubler. We obtained 93 W green light at 10 kHz with a pulse width of 10.7 ns. The efficiency of second-harmonic generation was up to 57%.

  19. Evanescent field enhancement due to plasmonic resonances of a metamaterial slab.

    PubMed

    Chiu, K P; Kao, T S; Tsai, D P

    2008-02-01

    The characteristics of plasmonic resonance in a dielectric-sandwiched metamaterial film at visible wavelengths of 650 and 568 nm have been investigated (for both p- and s-polarized light). Our calculated results demonstrate that each mode of plasmonic resonance has maximum resonance strength at a particular film thickness of the metamaterial. We also demonstrated that the effect of evanescent field enhancement is due to plasmonic resonances of the sandwiched metamaterial system. And the stronger the plasmonic resonance strength the larger the evanescent field is enhanced at the interfaces of the metamaterial film. Also we see that the plasmonic resonances in a sandwiched metamaterial are influenced not only by the materials that constitute the interfaces but also by the thickness of surrounding dielectrics or distance between evanescent light source and metamaterial film. Finally, our results show that there might be an effective light propagation length that will let the coupling efficiency between evanescent light source and SPs resonance become a maximum. These properties of plasmonic resonances to structure parameters of metamaterial film and its surrounding dielectrics provide a useful way to control the optical responses of an optoelectronic device when the wavelength of light source is fixed. That is, by suitably choosing light polarizations, thickness of the metamaterial thin film or the surrounding dielectrics and the position of evanescent light source, it is possible to modulate the plasmonic resonance wavenumber or resonance strength of the system. Therefore, the optical responses of the system can be modulated. Our results will be helpful for the structure design to control the behaviours of coupled plasmonic resonances and consequently the optical properties of the dielectric-sandwiched metamaterial film.

  20. Slab reformer

    DOEpatents

    Spurrier, Francis R.; DeZubay, Egon A.; Murray, Alexander P.; Vidt, Edward J.

    1985-03-12

    Slab-shaped high efficiency catalytic reformer configurations particularly useful for generation of fuels to be used in fuel cell based generation systems. A plurality of structures forming a generally rectangular peripheral envelope are spaced about one another to form annular regions, an interior annular region containing a catalytic bed and being regeneratively heated on one side by a hot combustion gas and on the other side by the gaseous products of the reformation. An integrally mounted combustor is cooled by impingement of incoming oxidant.

  1. Slab reformer

    DOEpatents

    Spurrier, Francis R.; DeZubay, Egon A.; Murray, Alexander P.; Vidt, Edward J.

    1984-02-07

    Slab-shaped high efficiency catalytic reformer configurations particularly useful for generation of fuels to be used in fuel cell based generation systems. A plurality of structures forming a generally rectangular peripheral envelope are spaced about one another to form annular regions, an interior annular region containing a catalytic bed and being regeneratively heated on one side by a hot comubstion gas and on the other side by the gaseous products of the reformation. An integrally mounted combustor is cooled by impingement of incoming oxidant.

  2. Slab reformer

    DOEpatents

    Spurrier, F.R.; DeZubay, E.A.; Murray, A.P.; Vidt, E.J.

    1984-02-07

    Slab-shaped high efficiency catalytic reformer configurations are disclosed particularly useful for generation of fuels to be used in fuel cell based generation systems. A plurality of structures forming a generally rectangular peripheral envelope are spaced about one another to form annular regions, an interior annular region containing a catalytic bed and being regeneratively heated on one side by a hot combustion gas and on the other side by the gaseous products of the reformation. An integrally mounted combustor is cooled by impingement of incoming oxidant. 14 figs.

  3. Slab reformer

    NASA Technical Reports Server (NTRS)

    Spurrier, Francis R. (Inventor); DeZubay, Egon A. (Inventor); Murray, Alexander P. (Inventor); Vidt, Edward J. (Inventor)

    1984-01-01

    Slab-shaped high efficiency catalytic reformer configurations particularly useful for generation of fuels to be used in fuel cell based generation systems. A plurality of structures forming a generally rectangular peripheral envelope are spaced about one another to form annular regions, an interior annular region containing a catalytic bed and being regeneratively heated on one side by a hot comubstion gas and on the other side by the gaseous products of the reformation. An integrally mounted combustor is cooled by impingement of incoming oxidant.

  4. Slab reformer

    NASA Technical Reports Server (NTRS)

    Spurrier, Francis R. (Inventor); DeZubay, Egon A. (Inventor); Murray, Alexander P. (Inventor); Vidt, Edward J. (Inventor)

    1985-01-01

    Slab-shaped high efficiency catalytic reformer configurations particularly useful for generation of fuels to be used in fuel cell based generation systems. A plurality of structures forming a generally rectangular peripheral envelope are spaced about one another to form annular regions, an interior annular region containing a catalytic bed and being regeneratively heated on one side by a hot combustion gas and on the other side by the gaseous products of the reformation. An integrally mounted combustor is cooled by impingement of incoming oxidant.

  5. Electric-field-induced response of a droplet embedded in a polyelectrolyte gel

    NASA Astrophysics Data System (ADS)

    Mohammadi, Aliasghar

    2013-08-01

    The electric-field induced response of a droplet embedded in a quenched polyelectrolyte gel is calculated theoretically. The response comprises the droplet translation and the electric-field induced flow fields within the droplet. The gel is modeled as a soft, and electrically charged porous solid saturated with a salted Newtonian fluid. The droplet is considered an incompressible Newtonian fluid with no free charge. An analytical solution, using the perturbation methodology and linear superposition, is obtained for the leading-order steady response to a DC electric-field. The fluid within the droplet is driven due to hydrodynamic coupling with the electroosmotic flow. The fluid velocity within the droplet is linearly proportional to the electroosmotic flow. Moreover, the microrheological response function of a droplet within a polyelectrolyte gel is also provided, highlighting the importance of boundary conditions at the droplet-gel interface on microrheological measurements.

  6. Prediction of electric field frequency correlations for randomly scattering slabs in the nondiffusive regime with the scalar Bethe-Salpeter equation.

    PubMed

    Gaind, Vaibhav; San, Aung K; Lin, Dergan; Webb, Kevin J

    2014-01-01

    We show that a scalar Bethe-Salpeter equation model captures the measured copolarized electric field frequency correlation magnitude for randomly scattering slabs in the weakly scattering, nondiffusive regime. Consequently, the model could be used to form images of tissue on the millimeter and submillimeter length scale, and for environmental sensing with comparable scatter, as dictated by the optical scattering length in relation to the scattering domain size.

  7. Investigating DNA Migration in Pulsed Fields Using a Miniaturized Field Inversion Gel Electrophoresis System

    PubMed Central

    Chen, Xiaojia; Ugaz, Victor M.

    2010-01-01

    Pulsed field gel electrophoresis (PFGE) is a well-established technique for fractionation of DNA fragments ranging from kilobases to megabases in length. But many of these separations require an undesirable combination of long experiment times (often approaching tens of hours) and application of high voltages (often approaching tens of kV). Here we present a simple miniaturized field inversion gel electrophoresis (FIGE) apparatus capable of separating DNA fragments up to 32.5 kb in length within 3 hours using a modest applied potential of 20 V. The device is small enough to be imaged under a fluorescence microscope, permitting the migrating DNA bands to be observed during the course of the separation run. We use this capability to investigate how separation performance is affected by parameters including the ratio of forward and backward voltage, pulse time, and temperature. We also characterize the dependence of DNA mobility on fragment size N, and observe a scaling in the vicinity of N−0.5 over the size range investigated. The high speed, low power consumption, and simple design of this system may help enable future studies of DNA migration in PFGE to be performed quickly and inexpensively. PMID:19053074

  8. Rheological properties and formation mechanism of DC electric fields induced konjac glucomannan-tungsten gels.

    PubMed

    Wang, Lixia; Jiang, Yaoping; Lin, Youhui; Pang, Jie; Liu, Xiang Yang

    2016-05-20

    Konjac glucomannan-tungsten (KGM-T) hydrogel of electrochemical reversibility was successfully produced under DC electric fields in the presence of sodium tungstate. The structure and the effects of sodium tungstate concentration, KGM concentration, voltage and electric processing time on the rheological properties of the gels were investigated. pH experiments showed that KGM sol containing Na2WO4·2H2O in the vicinity of the positive electrode became acidic and the negative electrode basic after the application of DC electric fields. Under acid conditions, WO4(2-) ions transformed into isopoly-tungstic acid ions. FTIR and Raman studies indicated that isopoly-tungstic acid ions absorbed on KGM molecular chain and cross-linked with -OH groups at C-6 position on sugar units of KGM. Frequency sweep data showed with increasing sodium tungstate concentration, voltage, and electric processing time, the viscoelastic moduli, i.e., the storage and the loss moduli of the gel increased, whereas an increase in KGM concentration led to a decrease in gel viscoelastic moduli. The temperature sweep measurements indicated the obtained gel exhibited high thermal stability. Finally, the mechanism of gel formation was proposed. Our work may pave the way to use DC electric fields for the design and development of KGM gels as well as polysaccharide gels. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. IMPROVED APPROACHES TO DESIGN OF POLYMER GEL TREATMENTS IN MATURE OIL FIELDS: FIELD DEMONSTRATION IN DICKMAN FIELD, NESS COUNTY, KANSAS

    SciTech Connect

    Ronald Fowler

    2004-11-30

    This report describes the results of the one-year project entitled ''Improved Approaches to Design of Polymer Gel Treatments in Mature Oil Fields: Field Demonstration in Dickman Field, Ness County, Kansas''. The project was a 12-month collaboration of Grand Mesa Operating Company (a small independent), TIORCO Inc. (a company focused on improved recovery technology) and the University of Kansas. The study undertook tasks to determine an optimum polymer gel treatment design in Mississippian reservoirs, demonstrate application, and evaluate the success of the program. The project investigated geologic and engineering parameters and cost-effective technologies required for design and implementation of effective polymer gel treatment programs in the Mississippian reservoir in the Midcontinent. The majority of Mississippian production in Kansas occurs at or near the top of the Mississippian section just below the regional sub-Pennsylvanian unconformity and karst surface. Dickman Field with the extremely high water cuts and low recovery factors is typical of Mississippian reservoirs. Producibility problems in these reservoirs include inadequate reservoir characterization, drilling and completion design problems, and most significantly extremely high water cuts and low recovery factors that place continued operations at or near their economic limits. Geologic, geophysical and engineering data were integrated to provide a technical foundation for candidate selection and treatment design. Data includes core, engineering data, and 3D seismic data. Based on technical and economic considerations a well was selected for gel-polymer treatment (Grand Mesa Operating Company Tilley No.2). The treatment was not successful due to the small amount of polymer that could be injected. Data from the initial well and other candidates in the demonstration area was analyzed using geologic, geophysical and engineering data. Based on the results of the treatment and the integrated reservoir

  10. Solubility of NaCl in water and its melting point by molecular dynamics in the slab geometry and a new BK3-compatible force field

    NASA Astrophysics Data System (ADS)

    Kolafa, Jiří

    2016-11-01

    Saturated concentration of rock salt in water is determined by a simulation of brine in contact with a crystal in the slab geometry. The NaCl crystals are rotated to expose facets with higher Miller indices than [001] to brine. The rock salt melting point is obtained by both the standard and adiabatic simulations in the slab geometry with attention paid to finite size effects as well as to a possible influence of facets with higher Miller indices and applied stress. Two force fields are used, the Lennard-Jones-based model by Young and Cheatham with SPC/E water and the Kiss and Baranyai polarizable model with BK3 water. The latter model is refitted to thermomechanical properties of crystal NaCl leading to better values of solubility and the melting point.

  11. Solubility of NaCl in water and its melting point by molecular dynamics in the slab geometry and a new BK3-compatible force field.

    PubMed

    Kolafa, Jiří

    2016-11-28

    Saturated concentration of rock salt in water is determined by a simulation of brine in contact with a crystal in the slab geometry. The NaCl crystals are rotated to expose facets with higher Miller indices than [001] to brine. The rock salt melting point is obtained by both the standard and adiabatic simulations in the slab geometry with attention paid to finite size effects as well as to a possible influence of facets with higher Miller indices and applied stress. Two force fields are used, the Lennard-Jones-based model by Young and Cheatham with SPC/E water and the Kiss and Baranyai polarizable model with BK3 water. The latter model is refitted to thermomechanical properties of crystal NaCl leading to better values of solubility and the melting point.

  12. Molecular stretching of long DNA in agarose gel using alternating current electric fields.

    PubMed Central

    Kaji, Noritada; Ueda, Masanori; Baba, Yoshinobu

    2002-01-01

    We demonstrate a novel method for stretching a long DNA molecule in agarose gel with alternating current (AC) electric fields. The molecular motion of a long DNA (T4 DNA; 165.6 kb) in agarose gel was studied using fluorescence microscopy. The effects of a wide range of field frequencies, field strengths, and gel concentrations were investigated. Stretching was only observed in the AC field when a frequency of approximately 10 Hz was used. The maximal length of the stretched DNA had the longest value when a field strength of 200 to 400 V/cm was used. Stretching was not sensitive to a range of agarose gel concentrations from 0.5 to 3%. Together, these experiments indicate that the optimal conditions for stretching long DNA in an AC electric field are a frequency of 10 Hz with a field strength of 200 V/cm and a gel concentration of 1% agarose. Using these conditions, we were able to successfully stretch Saccharomyces cerevisiae chromosomal DNA molecules (225-2,200 kb). These results may aid in the development of a novel method to stretch much longer DNA, such as human chromosomal DNA, and may contribute to the analysis of a single chromosomal DNA from a single cell. PMID:11751320

  13. Microchip gel electrophoresis with programmed field strength gradients for ultra-fast detection of canine T-cell lymphoma in dogs.

    PubMed

    Suresh, Kumar K; Lee, Mi-Jin; Park, Jinho; Kang, Seong Ho

    2008-03-15

    This paper describes the applicability of microchip gel electrophoresis using a programmed field strength gradients (MGE-PFSG) method coupled with a polymerase chain reaction (PCR) for the ultra-fast diagnosis of canine T-cell lymphoma. The variable region in the T-cell receptor gamma (TCRgamma) gene from a T-cell lymphoma was used in PCR amplification. The contributions of the various parameters, including the effects of the molecular weight, concentration of the sieving matrix and field strength in MGE, were examined. 0.5% poly (ethyleneoxide) (PEO, M(r) 8000000) was used as the sieving matrix for the ultra-rapid separation of the amplified-PCR products (90 and 130-bp DNA fragments) from the PFSG at an effective length of 20mm in a glass microchip. The PCR products (90 and 130-bp DNA) of the T-cell lymphoma were analyzed within 41.7+/-0.1s, 15.5+/-0.2s and only 7.0+/-0.1s using a low-constant field strength, high-constant field strength and the PFSG, respectively. When 11 clinical samples were analyzed using the MGE-PFSG method, there was a 100% correlation with those obtained using conventional slab gel electrophoresis. The ultra-fast detection and rapid separation capabilities of MGE-PFSG make it an efficient tool for diagnosing T-cell lymphoma in clinical samples with high sensitivity.

  14. Subducted Farallon Plate Carries Water for Hydration Above the Flat Slab and Deep into the Mantle: Evidence from the Navajo Volcanic Field HP and UHP Xenolith Suite

    NASA Astrophysics Data System (ADS)

    Schulze, D. J.; Helmstaedt, H. H.; Davis, D.

    2014-12-01

    Xenoliths in the Navajo Volcanic Field diatremes include HP-LT and UHP metamorphic eclogites (with lawsonite, phengite, coesite, zircon), exotic hydrous Cr-omphacitites (with guyanaite - CrOOH, carmichaelite, eskolaite, tawmawite, redledgeite) and hydrous and anhydrous peridotite, pyroxenite and lower crustal rocks. The eclogites (primarily dated at 30-80 Ma), omphacitites (30 Ma) and some of the (serpentinized) peridotites were derived from the subducted Farallon Plate (and possibly near-trench mantle wedge material accompanying the slab) from the flat slab by the diatremes at 30 Ma, approximately 700 km from the trench. Dehydration reactions in this assemblage (primarily prograde metamorphism of serpentinite yielding peridotite but also breakdown of guyanaite to eskolaite + water) provided water that hydrated overlying mantle materials (garnet and spinel peridotite to antigorite/chlorite serpentinite, garnet pyroxenite to chlorite-bearing eclogite, garnet and spinel pyroxenite to pargasite + chlorite). The accompanying volume expansion contributed to uplift of the Colorado Plateau, as originally suggested by Hess (1955). Phengite and possibly lawsonite remained stable and continued to carry water to greater depths. Guyanaite is stable to over 13.5 GPa and can transport water at least into the transition zone and thus may be a vehicle for hydrating ringwoodite in the transition zone (the present location of the Farallon slab). It is not known to how deep other hydrous minerals in these assemblages are stable (e.g., carmichaelite, redledgeite, tawmawite) but they, too, have potential for carrying water deep into the mantle.

  15. Small-Field Measurements of 3D Polymer Gel Dosimeters through Optical Computed Tomography

    PubMed Central

    Shih, Cheng-Ting; Lee, Yao-Ting; Wu, Shin-Hua; Yao, Chun-Hsu; Hsieh, Bor-Tsung

    2016-01-01

    With advances in therapeutic instruments and techniques, three-dimensional dose delivery has been widely used in radiotherapy. The verification of dose distribution in a small field becomes critical because of the obvious dose gradient within the field. The study investigates the dose distributions of various field sizes by using NIPAM polymer gel dosimeter. The dosimeter consists of 5% gelatin, 5% monomers, 3% cross linkers, and 5 mM THPC. After irradiation, a 24 to 96 hour delay was applied, and the gel dosimeters were read by a cone beam optical computed tomography (optical CT) scanner. The dose distributions measured by the NIPAM gel dosimeter were compared to the outputs of the treatment planning system using gamma evaluation. For the criteria of 3%/3 mm, the pass rates for 5 × 5, 3 × 3, 2 × 2, 1 × 1, and 0.5 × 0.5 cm2 were as high as 91.7%, 90.7%, 88.2%, 74.8%, and 37.3%, respectively. For the criteria of 5%/5 mm, the gamma pass rates of the 5 × 5, 3 × 3, and 2 × 2 cm2 fields were over 99%. The NIPAM gel dosimeter provides high chemical stability. With cone-beam optical CT readouts, the NIPAM polymer gel dosimeter has potential for clinical dose verification of small-field irradiation. PMID:26974434

  16. Model and computer simulations of the motion of DNA molecules during pulse field gel electrophoresis

    SciTech Connect

    Smith, S.B.; Bustamante, C. ); Heller, C. )

    1991-05-28

    A model is presented for the motion of individual molecules of DNA undergoing pulse field gel electrophoresis (PFGE). The molecule is represented by a chain of charged beads connected by entropic springs, and the gel is represented by a segmented tube surrounding the beads. This model differs from earlier reptation/tube models in that the tube is allowed to leak in certain places and the chain can double over and flow out of the side of the tube in kinks. It is found that these kinks often lead to the formation of U shapes, which are a major source of retardation in PFGE. The results of computer simulations using this model are compared with real DNA experimental results for the following cases: steady field motion as seen in fluorescence microscopy, mobility in steady fields, mobility in transverse field alternation gel electrophoresis (TFAGE), mobility in field inversion gel electrophoresis (FIGE), and linear dichroism (LD) of DNA in agarose gels during PFGE. Good agreement between the simulations and the experimental results is obtained.

  17. Pulsed field electrophoresis for the separation of protein-sodium dodecyl sulfate-complexes in polyacrylamide gels.

    PubMed

    Houri, A; Starita-Geribaldi, M

    1994-01-01

    Polyacrylamide gel electrophoresis of proteins was studied using a pulsed-current mode. A new "local field" distribution was used to correct the gel patterns and optimize migration. A corrective field was applied at fixed 2 s intervals to a constant field, inducing a complex relaxation mechanism. Calculated variations in the local field directions decreased the electric strain on the gel during the run, with resultant optimum gel structure. The relaxation mechanism was found to enhance the absolute mobility of proteins with shorter running times compared to constant field gel electrophoresis (CFGE) and other pulsed field techniques. The enhancement of molecular mobility was explored by transverse pore gradient gel electrophoresis. Ferguson curves which exhibited a convex shape in CFGE were linearized by the new pulsed-field method named pulsed oscillatory high-performance electrophoresis (POPE).

  18. The effects of fully implicit coupling on heat conduction between a flow field and conduction between a flow field and conduction slab in TRAC-PF1

    SciTech Connect

    Wang, L.C.; Baratta, A.J.; Mahaffy, J.H. )

    1990-01-01

    Numerical techniques used in thermal-hydraulic computer analysis codes must be fast to enable modeling of complex transients and accurate to provide a high degree of fidelity. In an attempt to satisfy these conflicting requirements, the best-estimate code TRAC-PF1 uses a semi-implicit technique to couple heat transfer between a flow field and a conduction slab. To test the accuracy of the current semi-implicit method used in TRAC-PF1, a series of simple tube experiments were modeled with TRAC-PF1 version 3.9B. To overcome identified problems, fully implicit techniques were developed and incorporated into TRAC-PF1. The new methods treat the heat transfer coefficient and wall temperature in the energy source term of both the convection and the conduction equation implicitly. One method uses a linear extrapolation and the other a nonlinear iterative technique. In general, both methods produced higher wall temperature and a lattice quench in better agreement with the experimental data. These methods also eliminated the double-valued results obtained for the other experiments. In general, these techniques have given more accurate results and saved computer time in the film boiling heat transfer regime.

  19. Instability in the dynamics of long DNA undergoing gel electrophoresis in a strong field

    NASA Astrophysics Data System (ADS)

    Semenov, A. N.; Subbotin, A. V.

    1995-05-01

    We present a model describing reptation motion of a long DNA chain undergoing gel electrophoresis. Internal modes of the chain in an effective tube are associated with lateral loops (hernias), and the effect of the field on these lateral loops is analyzed. An equation describing reptation dynamics of the chain is derived. It is shown for fields exceeding some critical value that stationary reptation motion becomes unstable. Mobility of the chain in the weak fields is also calculated.

  20. Relationship Between Far Field Stresses, Fluid Flow and High-Pressure Deserpentinization in Subducting Slabs: a Case Study From the Almirez Ultramafic Massif

    NASA Astrophysics Data System (ADS)

    Dilissen, Nicole; Hidas, Károly; Garrido, Carlos J.; López Sánchez-Vizcaíno, Vicente; Kahl, Wolf-Achim; Padrón-Navarta, José Alberto; Jesús Román-Alpiste, Manuel

    2017-04-01

    Serpentinite dehydration during prograde metamorphism plays a crucial role in subduction dynamics. Observations from exhumed paleo-subduction metamorphic terranes suggest that the discharge of deserpentinization fluids from the subducting slab takes place along different pathways and mechanisms [e.g. 1-3]. Analysis of intermediate-depth focal solutions in active subduction zones indicates that slabs are subjected to different principal stress fields characterized primarily by downdip compression and downdip tension [4]. Although it is well known that far field stresses play a crucial role on fluid flow channeling, their potential impact on the kinetics of serpentinite dehydration and subsequent fluid escape in subducting slabs is still poorly understood. Here, we present a detailed structural and microstructural study to investigate the relationships between far field stresses, fluid flow and high-pressure deserpentinization in the Almirez ultramafic massif (Betic Cordillera, SE Spain) [1, 2]. This massif preserves the high-pressure breakdown of antigorite (Atg-) serpentinite to prograde chlorite (Chl-) harzburgite, which are separated by a sharp isograd [2, 5]. The Chl-harzburgite reaction products show either a granofels or spinifex-like texture indicating crystallization under different overstepping of the Atg-out reaction. The two different textural types of Chl-harzburgite occur below the Atg-out isograd as alternating, meter-wide lenses with either a granofels or spinifex texture. From field measurements, we infer that during antigorite dehydration the minimum compressive stress was subnormal to the dehydration front and the paleo-slab surface. This stress field is consistent with subduction zones with slabs under downdip compression at intermediate depths [4]. The detailed microstructural study —combining µ-CT and EBSD-SEM [6]— of Chl-harzburgite across a c. 15 m wide lens reveals that the SPO and CPO of olivines with contrasting textures are strongly

  1. Preface: Deep Slab and Mantle Dynamics

    NASA Astrophysics Data System (ADS)

    Suetsugu, Daisuke; Bina, Craig R.; Inoue, Toru; Wiens, Douglas A.

    2010-11-01

    We are pleased to publish this special issue of the journal Physics of the Earth and Planetary Interiors entitled "Deep Slab and Mantle Dynamics". This issue is an outgrowth of the international symposium "Deep Slab and Mantle Dynamics", which was held on February 25-27, 2009, in Kyoto, Japan. This symposium was organized by the "Stagnant Slab Project" (SSP) research group to present the results of the 5-year project and to facilitate intensive discussion with well-known international researchers in related fields. The SSP and the symposium were supported by a Grant-in-Aid for Scientific Research (16075101) from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government. In the symposium, key issues discussed by participants included: transportation of water into the deep mantle and its role in slab-related dynamics; observational and experimental constraints on deep slab properties and the slab environment; modeling of slab stagnation to constrain its mechanisms in comparison with observational and experimental data; observational, experimental and modeling constraints on the fate of stagnant slabs; eventual accumulation of stagnant slabs on the core-mantle boundary and its geodynamic implications. This special issue is a collection of papers presented in the symposium and other papers related to the subject of the symposium. The collected papers provide an overview of the wide range of multidisciplinary studies of mantle dynamics, particularly in the context of subduction, stagnation, and the fate of deep slabs.

  2. Pulsed electric field assisted sol-gel preparation of TiO2 nanoparticles

    NASA Astrophysics Data System (ADS)

    Mani, Rajaboopathi; Han, Bing; Louhi-Kultanen, Marjatta

    2016-10-01

    This work studies the effect of a pulsed electric field (PEF) on the precipitation and properties of TiO2 nanoparticles. TiO2 nanoparticles were prepared using pulsed DC electric field assisted sol-gel method. The duration of the PEF treatment was varied to investigate its effect on the particle size of TiO2 nanoparticles. The nanoparticles were characterized by X-ray powder diffraction (XRD), Raman spectroscopy, UV diffuse reflectance spectroscopy (UV-DRS) and transmission electron microscopy (TEM). It was found that TiO2 particles prepared with pulsed electric field assisted sol-gel method had enhanced average crystallite size due to the effect of the pulsed electric field on primary nucleation. The effect of electric field on nanoparticle preparation is interesting which can be used to control the grain and crystallite size of nanoparticle.

  3. Strong Plate, Weak Slab Dichotomy

    NASA Astrophysics Data System (ADS)

    Petersen, R. I.; Stegman, D. R.; Tackley, P.

    2015-12-01

    Models of mantle convection on Earth produce styles of convection that are not observed on Earth.Moreover non-Earth-like modes, such as two-sided downwellings, are the de facto mode of convection in such models.To recreate Earth style subduction, i.e. one-sided asymmetric recycling of the lithosphere, proper treatment of the plates and plate interface are required. Previous work has identified several model features that promote subduction. A free surface or pseudo-free surface and a layer of material with a relatively low strength material (weak crust) allow downgoing plates to bend and slide past overriding without creating undue stress at the plate interface. (Crameri, et al. 2012, GRL)A low viscosity mantle wedge, possibly a result of slab dehydration, decouples the plates in the system. (Gerya et al. 2007, Geo)Plates must be composed of material which, in the case of the overriding plate, are is strong enough to resist bending stresses imposed by the subducting plate and yet, as in the case of the subducting plate, be weak enough to bend and subduct when pulled by the already subducted slab. (Petersen et al. 2015, PEPI) Though strong surface plates are required for subduction such plates may present a problem when they encounter the lower mantle.As the subducting slab approaches the higher viscosity, lower mantle stresses are imposed on the tip.Strong slabs transmit this stress to the surface.There the stress field at the plate interface is modified and potentially modifies the style of convection. In addition to modifying the stress at the plate interface, the strength of the slab affects the morphology of the slab at the base of the upper mantle. (Stegman, et al 2010, Tectonophysics)Slabs that maintain a sufficient portion of their strength after being bent require high stresses to unbend or otherwise change their shape.On the other hand slabs that are weakened though the bending process are more amenable to changes in morphology. We present the results of

  4. Three-dimensional dosimetry of small megavoltage radiation fields using radiochromic gels and optical CT scanning.

    PubMed

    Babic, Steven; McNiven, Andrea; Battista, Jerry; Jordan, Kevin

    2009-04-21

    The dosimetry of small fields as used in stereotactic radiotherapy, radiosurgery and intensity-modulated radiation therapy can be challenging and inaccurate due to partial volume averaging effects and possible disruption of charged particle equilibrium. Consequently, there exists a need for an integrating, tissue equivalent dosimeter with high spatial resolution to avoid perturbing the radiation beam and artificially broadening the measured beam penumbra. In this work, radiochromic ferrous xylenol-orange (FX) and leuco crystal violet (LCV) micelle gels were used to measure relative dose factors (RDFs), percent depth dose profiles and relative lateral beam profiles of 6 MV x-ray pencil beams of diameter 28.1, 9.8 and 4.9 mm. The pencil beams were produced via stereotactic collimators mounted on a Varian 2100 EX linear accelerator. The gels were read using optical computed tomography (CT). Data sets were compared quantitatively with dosimetric measurements made with radiographic (Kodak EDR2) and radiochromic (GAFChromic EBT) film, respectively. Using a fast cone-beam optical CT scanner (Vista), corrections for diffusion in the FX gel data yielded RDFs that were comparable to those obtained by minimally diffusing LCV gels. Considering EBT film-measured RDF data as reference, cone-beam CT-scanned LCV gel data, corrected for scattered stray light, were found to be in agreement within 0.5% and -0.6% for the 9.8 and 4.9 mm diameter fields, respectively. The validity of the scattered stray light correction was confirmed by general agreement with RDF data obtained from the same LCV gel read out with a laser CT scanner that is less prone to the acceptance of scattered stray light. Percent depth dose profiles and lateral beam profiles were found to agree within experimental error for the FX gel (corrected for diffusion), LCV gel (corrected for scattered stray light), and EBT and EDR2 films. The results from this study reveal that a three-dimensional dosimetry method utilizing

  5. A self-consistent mean-field model for polyelectrolyte gels.

    PubMed

    Rud, Oleg; Richter, Tobias; Borisov, Oleg; Holm, Christian; Košovan, Peter

    2017-03-01

    We present a novel approach to modeling polyelectrolyte gels, exploiting the analogy between star-branched polymers and polymer networks as a computationally inexpensive yet reliable alternative to full-scale simulations. In the numerical mean-field model of a star-like polymer we modify the boundary conditions to represent an infinite network. We validate the predictions of our new model against a coarse-grained simulation model. We also validate it against a phenomenological analytical model which has been previously shown to agree with simulations in a limited range of parameters. The mean-field model explicitly considers local density gradients and agrees with the simulation results in a broad range of parameters, beyond that of the analytical model. Finally, we use the mean-field model for predictions of the swelling behaviour of weak polyelectrolyte gels under different pH conditions. We demonstrate that the local density gradients are important and that the ionization of the weak polyelectrolyte gel is significantly suppressed. Under the studied conditions the effective pKA is about one unit higher than that of the free monomer. This shift in the effective pKA stems from the different pH values inside and outside the gel.

  6. MAGAT gel dosimetry for its application in small field treatment techniques

    NASA Astrophysics Data System (ADS)

    Gopishankar, N.; Vivekanandhan, S.; Kale, S. S.; Rath, G. K.; Senthil Kumaran, S.; Thulkar, Sanjay; Subramani, V.; Laviraj, M. A.; Bisht, R. K.; Mahapatra, A. K.

    2010-11-01

    Purpose of this work is to present the role of in-house manufactured MAGAT gel for treatment verification in small field dosimetric techniques such as Gammaknife (GK) and intensity-modulated radiation therapy (IMRT). Magnetic resonance imaging (MRI) is one of the most extensively used imaging technique for polymer gel dosimetry hence we used this method for gel evaluation. Different MR scanners and MRI sequences were used in this study for obtaining calibration plot between R2 and absorbed dose. An experimental plan was created for Gammaknife and IMRT. The prepared gel was filled in spherical glass phantom and in-house designed human head shape phantom for verification purpose. We used 8 TE values for all the imaging sequences for two reasons. Firstly it is sufficient enough to give good signal to noise ratio. Second considering the enormous scanning time involved in multiple spin echo sequence. MATLAB based in-house programs were used for R2 estimation and dose comparison. The isodose comparison with MAGAT gel showed reasonable agreement for both Gammaknife and IMRT techniques.

  7. Dynamics of slab detachment

    NASA Astrophysics Data System (ADS)

    Duretz, T.; Schmalholz, S. M.; Gerya, T. V.

    2012-04-01

    Our study investigates the dynamics of slab detachment and evaluates the amount of time necessary for slabs to detach. We combine both the results of two-dimensional numerical modeling with the prediction of a one-dimensional analytical solution for viscous necking under gravity. This tidy suggest that the dominant deformation mechanisms leading to slab detachment is viscous necking, independently of the depth of slab detachment. Localised simple shear may also occur when the slab dip is moderate, especially in the colder parts of the slab. Brittle fracturing, or breaking, plays a minor role during the slab detachment process. 2D thermo-mechanical simulations indicate that the duration of slab detachment is short (< 4 Ma) and can occur in less than 0.5 Ma. No simple correlation between the slab detachment depth and duration was found. Our results suggest that deep slab detachments (> 250 km) can also occur within a short time (< 1 Ma). On the other hand, slab detachments taking place between 35 and 250 km depth may last less than 2 Ma. This aspect has implications for geodynamic interpretations using slab detachment as explanation for processes such as melting, exhumation or surface uplift.

  8. A dosimetric study of small photon fields using polymer gel and Gafchromic EBT films

    SciTech Connect

    Hassani, Hossein; Nedaie, Hassan Ali; Zahmatkesh, Mohammad Hassan; Shirani, Kaveh

    2014-04-01

    The use of small field sizes is increasingly becoming important in radiotherapy particularly since the introduction of stereotactic radiosurgery and intensity-modulated radiation therapy techniques. The reliable measurement of delivered dose from such fields with conventional dosimeters, such as ionization chambers, is a challenging task. In this work, methacrylic and ascorbic acid in gelatin initiated by copper polymer gel dosimeters are employed to measure dose in 3 dimensions. Field sizes of 5 × 5 mm{sup 2}, 10 × 10 mm{sup 2}, 20 × 20 mm{sup 2}, and 30 × 30 mm{sup 2} are investigated for a 6-MV x-rays. The results show an agreement with Gafchromic film, with some variation in measured doses near the edge of the fields, where the film data decrease more rapidly than the other methods. Dose penumbra widths obtained with gel dosimeters and Gafchormic film were generally in agreement with each other. The results of this work indicate that polymer gel dosimetry could be invaluable for the quantification of the 3-dimensional dose distribution in small field size.

  9. Trapping and breaking of in vivo nicked DNA during pulsed field gel electrophoresis.

    PubMed

    Khan, Sharik R; Kuzminov, Andrei

    2013-12-15

    Pulsed field gel electrophoresis (PFGE) offers a high-resolution approach to quantify chromosomal fragmentation in bacteria, measured as percentage of chromosomal DNA entering the gel. The degree of separation in pulsed field gel (PFG) depends on the size of DNA as well as various conditions of electrophoresis such as electric field strength, time of electrophoresis, switch time, and buffer composition. Here we describe a new parameter, the structural integrity of the sample DNA itself, that influences its migration through PFGs. We show that subchromosomal fragments containing both spontaneous and DNA damage-induced nicks are prone to breakage during PFGE. Such breakage at single-strand interruptions results in artifactual decrease in molecular weight of linear DNA making accurate determination of the number of double-strand breaks difficult. Although breakage of nicked subchromosomal fragments is field strength independent, some high-molecular-weight subchromosomal fragments are also trapped within wells under the standard PFGE conditions. This trapping can be minimized by lowering the field strength and increasing the time of electrophoresis. We discuss how breakage of nicked DNA may be mechanistically linked to trapping. Our results suggest how to optimize conditions for PFGE when quantifying chromosomal fragmentation induced by DNA damage.

  10. Transport in polymer-gel composites: theoretical methodology and response to an electric field

    NASA Astrophysics Data System (ADS)

    Hill, Reghan J.

    2006-03-01

    A theoretical model of electromigrative, diffusive and convective transport in polymer-gel composites is presented. Bulk properties are derived from the standard electrokinetic model with an impenetrable charged sphere embedded in an electrolyte-saturated Brinkman medium. Because the microstructure can be carefully controlled, these materials are promising candidates for enhanced gel-electrophoresis, chemical sensing, drug delivery, and microfluidic pumping technologies. The methodology provides solutions for situations where perturbations from equilibrium are induced by gradients of electrostatic potential, concentration and pressure. While the volume fraction of the inclusions should be small, Maxwell's well-known theory of conduction suggests that the model may also be accurate at moderate volume fractions. In this work, the theory is used to compute ion fluxes, electrical current density, and convective flow driven by an electric field applied to an homogeneous composite. The electric-field-induced (electro-osmotic) flow is a sensitive indicator of the inclusion zeta-potential and size, electrolyte concentration, and Darcy permeability of the gel, while the electrical conductivity is usually independent of the polymer gel and is relatively insensitive to characteristics of the inclusions and electrolyte.

  11. Differentiation of human and animal strains of Streptococcus dysgalactiae by pulsed-field gel electrophoresis.

    PubMed

    Bert, F; Branger, C; Poutrel, B; Lambert-Zechovsky, N

    1997-05-01

    The genetic diversity among 54 human isolates and 33 animal isolates belonging to the species Streptococcus dysgalactiae (20 alpha-haemolytic Streptococcus dysgalactiae, 23 Streptococcus equisimilis, 43 group G streptococci and one group L streptococcus) was evaluated by macrorestriction analysis of chromosomal DNA with SmaI and resolution by pulsed-field gel electrophoresis. This technique revealed a high degree of intraspecies polymorphism, leading to the differentiation of 80 distinct banding patterns, and identified the presence of two major clusters, one containing isolates of human origin and the other isolates of animal origin. These results suggest than human and animal isolates of S.dysgalactiae are genetically distinct, and support the recent proposal of the subspecies S. dysgalactiae subsp. equisimilis for human isolates. The heterogeneity revealed within isolates from the same host type indicates that pulsed-field gel electrophoresis is a powerful epidemiological tool for studying S. dysgalactiae infections.

  12. Salmonella enterica Pulsed-Field Gel Electrophoresis Clusters, Minnesota, USA, 2001–2007

    PubMed Central

    Hedberg, Craig W.; Meyer, Stephanie; Boxrud, David J.; Smith, Kirk E.

    2010-01-01

    We determined characteristics of Salmonella enterica pulsed-field gel electrophoresis clusters that predict their being solved (i.e., that result in identification of a confirmed outbreak). Clusters were investigated by the Minnesota Department of Health by using a dynamic iterative model. During 2001–2007, a total of 43 (12.5%) of 344 clusters were solved. Clusters of >4 isolates were more likely to be solved than clusters of 2 isolates. Clusters in which the first 3 case isolates were received at the Minnesota Department of Health within 7 days were more likely to be solved than were clusters in which the first 3 case isolates were received over a period >14 days. If resources do not permit investigation of all S. enterica pulsed-field gel electrophoresis clusters, investigation of clusters of >4 cases and clusters in which the first 3 case isolates were received at a public health laboratory within 7 days may improve outbreak investigations. PMID:21029524

  13. Molecular characterization of Clostridium tetani strains by pulsed-field gel electrophoresis and colony PCR.

    PubMed

    Plourde-Owobi, Lucile; Seguin, Delphine; Baudin, Marie-Anne; Moste, Catherine; Rokbi, Bachra

    2005-09-01

    Pulsed-field gel electrophoresis and PCR were applied for the first time to the molecular characterization of Clostridium tetani. Among five strains tested, one (CN1339) turned out to contain a mixture of two genetically different clones and two (D11 and G761) to contain bacteria differing by the presence or absence of the 74-kb plasmid harboring the tetX gene.

  14. Molecular Characterization of Clostridium tetani Strains by Pulsed-Field Gel Electrophoresis and Colony PCR

    PubMed Central

    Plourde-Owobi, Lucile; Seguin, Delphine; Baudin, Marie-Anne; Moste, Catherine; Rokbi, Bachra

    2005-01-01

    Pulsed-field gel electrophoresis and PCR were applied for the first time to the molecular characterization of Clostridium tetani. Among five strains tested, one (CN1339) turned out to contain a mixture of two genetically different clones and two (D11 and G761) to contain bacteria differing by the presence or absence of the 74-kb plasmid harboring the tetX gene. PMID:16151158

  15. Slab-derived metasomatism in the Carpathian-Pannonian mantle revealed by investigations of mantle xenoliths from the Bakony-Balaton Highland Volcanic Field

    NASA Astrophysics Data System (ADS)

    Créon, Laura; Delpech, Guillaume; Rouchon, Virgile; Guyot, François

    2017-08-01

    A suite of fifteen peridotite xenoliths from the Bakony-Balaton Highland Volcanic Field (BBHVF, Pannonian Basin, Central Europe) that show abundant petrographic evidence of fluid and melt percolation were studied in order to decipher the formation of their melt pockets and veins. The suite mainly consists of ;fertile; lherzolites (5.8-19.9 vol.% clinopyroxene) and a few harzburgites (1.9-5.4 vol.% clinopyroxene) from well-known localities (Szentbékkálla, Szigliget) and two previously unreported localities (Füzes-tó and Mindszentkálla). Major and trace element data indicate that most of the peridotites record variable degrees of partial melt extraction, up to > 15% for the harzburgites. Subsequently, the xenoliths experienced at least two stages of metasomatic modification. The first stage was associated with percolation of a volatile-bearing silicate melt and resulted in crystallization of amphibole, enrichment in the most incompatible trace elements (Ba, Th, U, Sr), and development of negative Nb-Ta anomalies in clinopyroxene. The second and last metasomatic event, widespread beneath the BBHVF, is associated with the formation of silicate melt pockets, physically connected to a network of melt veins, with large and abundant CO2 vesicles. The glass in these veins has sub-alkaline trachy-andesitic composition and displays an OIB-like trace element signature. Its composition attests to the migration through a supra-subduction zone mantle wedge of silicic melt highly enriched in volatiles (CO2, H2O, Cl, F), LILE, REE and HFSE and consistent with compositions of natural and experimental examples of slab melting-derived magma. In the present case, however, melt was likely derived from melting of oceanic crust and carbonated sediments under conditions where Nb-rich mineral phases were not stable in the residue. A likely scenario for the origin such melts involves melting after subduction ceased as the slab thermally equilibrated with the asthenosphere. Melt

  16. DNA electrophoresis in agarose gels: effects of field and gel concentration on the exponential dependence of reciprocal mobility on DNA length.

    PubMed

    Rill, Randolph L; Beheshti, Afshin; Van Winkle, David H

    2002-08-01

    Electrophoretic mobilities of DNA molecules ranging in length from 200 to 48 502 base pairs (bp) were measured in agarose gels with concentrations T = 0.5% to 1.3% at electric fields from E = 0.71 to 5.0 V/cm. This broad data set determines a range of conditions over which the new interpolation equation nu(L) = (beta+alpha(1+exp(-L/gamma))(-1) can be used to relate mobility to length with high accuracy. Mobility data were fit with chi(2) > 0.999 for all gel concentrations and fields ranging from 2.5 to 5 V/cm, and for lower fields at low gel concentrations. Analyses using so-called reptation plots (Rousseau, J., Drouin, G., Slater, G. W., Phys. Rev. Lett. 1997, 79, 1945-1948) indicate that this simple exponential relation is obeyed well when there is a smooth transition from the Ogston sieving regime to the reptation regime with increasing DNA length. Deviations from this equation occur when DNA migration is hindered, apparently by entropic-trapping, which is favored at low fields and high gel concentrations in the ranges examined.

  17. Topological susceptibility from slabs

    NASA Astrophysics Data System (ADS)

    Bietenholz, Wolfgang; de Forcrand, Philippe; Gerber, Urs

    2015-12-01

    In quantum field theories with topological sectors, a non-perturbative quantity of interest is the topological susceptibility χ t. In principle it seems straightforward to measure χ t by means of Monte Carlo simulations. However, for local update algorithms and fine lattice spacings, this tends to be difficult, since the Monte Carlo history rarely changes the topological sector. Here we test a method to measure χ t even if data from only one sector are available. It is based on the topological charges in sub-volumes, which we denote as slabs. Assuming a Gaussian distribution of these charges, this method enables the evaluation of χ t, as we demonstrate with numerical results for non-linear σ-models.

  18. Use of conductive gels for electric field homogenization increases the antitumor efficacy of electroporation therapies

    NASA Astrophysics Data System (ADS)

    Ivorra, Antoni; Al-Sakere, Bassim; Rubinsky, Boris; Mir, Lluis M.

    2008-11-01

    Electroporation is used in tissue for gene therapy, drug therapy and minimally invasive tissue ablation. The electrical field that develops during the application of the high voltage pulses needs to be precisely controlled. In the region to be treated, it is desirable to generate a homogeneous electric field magnitude between two specific thresholds whereas in other regions the field magnitude should be as low as possible. In the case of irregularly shaped tissue structures, such as bulky tumors, electric field homogeneity is almost impossible to be achieved with current electrode arrangements. We propose the use of conductive gels, matched to the conductivity of the tissues, to fill dead spaces between plate electrodes gripping the tissue so that the electric field distribution becomes less heterogeneous. Here it is shown that this technique indeed improves the antitumor efficacy of electrochemotherapy in sarcomas implanted in mice. Furthermore, we analyze, through finite element method simulations, how relevant the conductivity mismatches are. We found that conductivity mismatching errors are surprisingly well tolerated by the technique. Gels with conductivities ranging from 5 mS cm-1 to 10 mS cm-1 will be a proper solution for most cases.

  19. Interlaboratory Agreement of Pulsed-Field Gel Electrophoresis Identification of Leptospira Serovars

    PubMed Central

    Mende, Katrin; Galloway, Renee L.; Becker, Sara J.; Beckius, Miriam L.; Murray, Clinton K.; Hospenthal, Duane R.

    2013-01-01

    Leptospirosis may be caused by > 250 Leptospira serovars. Serovar classification is a complex task that most laboratories cannot perform. We assessed the interlaboratory reproducibility of a pulsed-field gel electrophoresis (PFGE) identification technique developed by the Centers for Disease Control and Prevention (CDC). Blinded exchange of 93 Leptospiraceae strains occurred between San Antonio Military Medical Center (SAMMC) and the CDC. PFGE was performed and gel images were analyzed and compared with patterns present in each laboratory's database (CDC database: > 800 strain patterns; SAMMC database: > 300 strain patterns). Overall, 93.7% (74 of 79) of strains present in each receiving laboratory's database were correctly identified. Five isolates were misidentified, and two isolates did not match serovar PFGE patterns in the receiving laboratory's database. Patterns for these seven isolates were identical between laboratories; four serovars represented misidentified reference strains. The PFGE methodology studied showed excellent interlaboratory reproducibility, enabling standardization and data sharing between laboratories. PMID:23817329

  20. Interlaboratory agreement of pulsed-field gel electrophoresis identification of Leptospira serovars.

    PubMed

    Mende, Katrin; Galloway, Renee L; Becker, Sara J; Beckius, Miriam L; Murray, Clinton K; Hospenthal, Duane R

    2013-08-01

    Leptospirosis may be caused by > 250 Leptospira serovars. Serovar classification is a complex task that most laboratories cannot perform. We assessed the interlaboratory reproducibility of a pulsed-field gel electrophoresis (PFGE) identification technique developed by the Centers for Disease Control and Prevention (CDC). Blinded exchange of 93 Leptospiraceae strains occurred between San Antonio Military Medical Center (SAMMC) and the CDC. PFGE was performed and gel images were analyzed and compared with patterns present in each laboratory's database (CDC database: > 800 strain patterns; SAMMC database: > 300 strain patterns). Overall, 93.7% (74 of 79) of strains present in each receiving laboratory's database were correctly identified. Five isolates were misidentified, and two isolates did not match serovar PFGE patterns in the receiving laboratory's database. Patterns for these seven isolates were identical between laboratories; four serovars represented misidentified reference strains. The PFGE methodology studied showed excellent interlaboratory reproducibility, enabling standardization and data sharing between laboratories.

  1. Equilibrium intermediate-state patterns in a type-I superconducting slab in an arbitrarily oriented applied magnetic field

    DOE PAGES

    Clem, John; Prozorov, Ruslan; Wijngaarden, Rinke J.

    2013-09-04

    The equilibrium topology of superconducting and normal domains in flat type-I superconductors is investigated. Important improvements with respect to previous work are that (1) the energy of the external magnetic field, as deformed by the presence of superconducting domains, is calculated in the same way for three different topologies and (2) calculations are made for arbitrary orientation of the applied field. A phase diagram is presented for the minimum-energy topology as a function of applied field magnitude and angle. For small (large) applied fields, normal (superconducting) tubes are found, while for intermediate fields, parallel domains have a lower energy. Themore » range of field magnitudes for which the superconducting-tubes structure is favored shrinks when the field is more in-plane oriented.« less

  2. Equilibrium intermediate-state patterns in a type-I superconducting slab in an arbitrarily oriented applied magnetic field

    SciTech Connect

    Clem, John; Prozorov, Ruslan; Wijngaarden, Rinke J.

    2013-09-04

    The equilibrium topology of superconducting and normal domains in flat type-I superconductors is investigated. Important improvements with respect to previous work are that (1) the energy of the external magnetic field, as deformed by the presence of superconducting domains, is calculated in the same way for three different topologies and (2) calculations are made for arbitrary orientation of the applied field. A phase diagram is presented for the minimum-energy topology as a function of applied field magnitude and angle. For small (large) applied fields, normal (superconducting) tubes are found, while for intermediate fields, parallel domains have a lower energy. The range of field magnitudes for which the superconducting-tubes structure is favored shrinks when the field is more in-plane oriented.

  3. Strong Static Magnetic Fields Increase the Gel Signal in Partially Hydrated DPPC/DMPC Membranes.

    PubMed

    Tang, Jennifer; Alsop, Richard J; Schmalzl, Karin; Epand, Richard M; Rheinstädter, Maikel C

    2015-09-29

    NIt was recently reported that static magnetic fields increase lipid order in the hydrophobic membrane core of dehydrated native plant plasma membranes [Poinapen, Soft Matter 9:6804-6813, 2013]. As plasma membranes are multicomponent, highly complex structures, in order to elucidate the origin of this effect, we prepared model membranes consisting of a lipid species with low and high melting temperature. By controlling the temperature, bilayers coexisting of small gel and fluid domains were prepared as a basic model for the plasma membrane core. We studied molecular order in mixed lipid membranes made of dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) using neutron diffraction in the presence of strong static magnetic fields up to 3.5 T. The contribution of the hydrophobic membrane core was highlighted through deuterium labeling the lipid acyl chains. There was no observable effect on lipid organization in fluid or gel domains at high hydration of the membranes. However, lipid order was found to be enhanced at a reduced relative humidity of 43%: a magnetic field of 3.5 T led to an increase of the gel signal in the diffraction patterns of 5%. While all biological materials have weak diamagnetic properties, the corresponding energy is too small to compete against thermal disorder or viscous effects in the case of lipid molecules. We tentatively propose that the interaction between the fatty acid chains' electric moment and the external magnetic field is driving the lipid tails in the hydrophobic membrane core into a better ordered state.

  4. A model for the separation of large DNA molecules by crossed field gel electrophoresis.

    PubMed

    Southern, E M; Anand, R; Brown, W R; Fletcher, D S

    1987-08-11

    The idea that large DNA molecules adopt a stretched conformation as they pass through gels suggests a simple mechanism for the separation of DNA by crossed field electrophoresis: at each change in field direction a DNA molecule takes off in the new direction of the field by a movement which is led by what was formerly its back end. The effect of this ratcheting motion is to subtract from the DNA molecule's forward movement, at each step, an amount which is proportional to its length. We find that this model explains most of the features of the separation, and we describe experiments, using a novel electrophoresis apparatus, which support the model. The apparatus turns the gel between two preset orientations in a uniform electric field at preset time intervals. This separation method has the practical advantage over some others that the DNA molecules follow straight tracks. A further advantage is that the parameters which determine the separation are readily predicted from the simple theory describing their motion.

  5. Laboratory and field evaluation of an indoxacarb gel bait against two cockroach species (Dictyoptera: Blattellidae, Blattidae) in Lagos, Nigeria.

    PubMed

    Anikwe, Joseph Chuks; Adetoro, Fouad Abidemi; Anogwih, Joy Anuri; Makanjuola, Winifred Ayinke; Kemabonta, Kehinde Abike; Akinwande, Kayode Lawrence

    2014-08-01

    Indoxacarb gel bait was evaluated for its efficacy in the laboratory and field against American cockroaches, Periplaneta americana (L.), and German cockroaches, Blattella germanica (L.). Advion 0.6% indoxacarb gel bait was toxic to both P. americana and B. germanica. There were no significant differences in the LT50 (h) values for treatment levels of 0.25 g, 0.5 g, and 1.0 g gel applied against P. americana, whereas gel applied at 0.5 g to B. germanica had a significantly greater LT50 (h) in the laboratory than the gel treatments on P. americana. The LT50 for both cockroach species ranged from 40.65 to 145.60 h. There was no control mortality in the laboratory bioassays. In the field, 55 houses were treated with 0.5 g of 6-8 spots of indoxacarb gel bait per kitchen of two or three bedroom bungalows from three Local Government Areas of Lagos State, comprising Surulere (22), Alimosho (12), and Shomolu (21). Mean reduction in cockroach populations varied from location to location based on the level of infestations. Percentage reductions in the indoxacarb gel-treated units ranged from 3.5% at 1 d after treatment to 99.8% at 14 d at Surulere, while reductions ranged from 8.9% at 1 d after treatment to 99.7% at 14 d at Shomolu; a similar trend was observed for Alimosho. Indoxacarb gel bait was highly effective in the control of cockroaches.

  6. Direct observation by laser scanning confocal microscopy of microstructure and phase migration of PVC gels in an applied electric field.

    PubMed

    Xia, Hong; Ueki, Takamitsu; Hirai, Toshihiro

    2011-02-01

    The fluorescent probe lucigenin was incorporated in poly(vinyl chloride) (PVC) gels, and laser scanning confocal microscopy (LSCM) was used to clarify the internal structures of the gels. From the two-dimensional and three-dimensional information by LSCM, we first observed the internal structure of the PVC gel at a wet status, where the PVC gels comprised a polymer-rich phase and a polymer-poor phase uniformly with a three-dimensional network structure. After an electric field was applied, an effect of the electric field resulted in the change of internal structure in the gels. The polymer-poor phase moved from the cathode to the anode and the polymer-rich phase formed linelike arrangement between electrodes due to the attraction force. On the other hand, the freeze-dried PVC gels with/without in-situ dc voltage casting were particularly fabricated to confirm above results by the field emission scanning electron microscopy (FE-SEM). It was found that many craters remained on the surface of the gel near the anode due to sublimation in freeze-drying. This phenomenon did not appear on the surface near the cathode. The results of in-situ dc voltage casting also suggested that a substantial amount of polymer-poor phase was moved and fixed at the anode. Thus, results of both LSCM and in-situ dc voltage casting corresponded to the effect of electric field on PVC gels and provided a convincing evidence for the interpretation of the deformation mechanism of PVC gel actuators by an applied electric field.

  7. Early Earth slab stagnation

    NASA Astrophysics Data System (ADS)

    Agrusta, R.; Van Hunen, J.

    2016-12-01

    At present day, the Earth's mantle exhibits a combination of stagnant and penetrating slabs within the transition zone, indicating a intermittent convection mode between layered and whole-mantle convection. Isoviscous thermal convection calculations show that in a hotter Earth, the natural mode of convection was dominated by double-layered convection, which may imply that slabs were more prone to stagnate in the transition zone. Today, slab penetration is to a large extent controlled by trench mobility for a plausible range of lower mantle viscosity and Clapeyron slope of the mantle phase transitions. Trench mobility is, in turn, governed by slab strength and density and upper plate forcing. In this study, we systematically investigate the slab-transition zone internation in the Early Earth, using 2D self-consistent numerical subduction models. Early Earth's higher mantle temperature facilitates decoupling between the plates and the underlying asthenosphere, and may result in slab sinking almost without trench retreat. Such behaviour together with a low resistance of a weak lower mantle may allow slabs to penetrate. The ability of slab to sink into the lower mantle throughout Earth's history may have important implications for Earth's evolution: it would provide efficient mass and heat flux through the transition zone therefore provide an efficient way to cool and mix the Earth's mantle.

  8. Trapping and breaking of in vivo nicked DNA during pulsed-field gel electrophoresis

    PubMed Central

    Khan, Sharik R.; Kuzminov, Andrei

    2013-01-01

    Pulsed field gel electrophoresis (PFGE) offers a high-resolution approach to quantify chromosomal fragmentation in bacteria, measured as percent of chromosomal DNA entering the gel. The degree of separation in PFG depends upon the size of DNA, as well as various conditions of electrophoresis, such as electric field strength (FS), time of electrophoresis, switch time and buffer composition. Here we describe a new parameter, the structural integrity of the sample DNA itself, that influences its migration through PFGs. We show that sub-chromosomal fragments containing both spontaneous and DNA damage-induced nicks are prone to breakage during PFGE. Such breakage at single strand interruptions results in artefactual decrease in molecular weight of linear DNA making accurate determination of the number of double strand breaks difficult. While breakage of nicked sub-chromosomal fragments is FS-independent, some high molecular weight sub-chromosomal fragments are also trapped within wells under the standard PFGE conditions. This trapping can be minimized by lowering the field strength and increasing the time of electrophoresis. We discuss how breakage of nicked DNA may be mechanistically linked to trapping. Our results suggest how to optimize conditions for PFGE when quantifying chromosomal fragmentation induced by DNA damage. PMID:23770235

  9. Interaction of electromagnetic fields with chondrocytes in gel culture. Final report, February-August 1989

    SciTech Connect

    Grodzinsky, A.J.; Gluzband, Y.A.; Buschmann, M.D.

    1990-02-01

    The research accomplished during this project period focused on control experiments designed to establish whether cartilage cells from normal cartilage will continue to synthesize and accumulate normal extracellular matrix in agarose gel culture. This information is essential to properly design experiments to qualify changes in chondrocyte biosynthesis due to applied electromagnetic fields. The results suggest that both normal chondrocytes and swarm rat chondrosarcoma cells in agarose culture can continue to synthesize matrix macromolecules at a rate similar to or slightly higher than that in normal cartilage; also, that chondrocytes in agarose can successfully mediate assembly and accumulation of normal, mechanically functional extracellular matrix.

  10. Genetic profiling of Klebsiella pneumoniae: comparison of pulsed field gel electrophoresis and random amplified polymorphic DNA

    PubMed Central

    Ashayeri-Panah, Mitra; Eftekhar, Fereshteh; Ghamsari, Maryam Mobarak; Parvin, Mahmood; Feizabadi, Mohammad Mehdi

    2013-01-01

    In this study, the discriminatory power of pulsed field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD) methods for subtyping of 54 clinical isolates of Klebsiella pneumoniae were compared. All isolates were typeable by RAPD, while 3.6% of them were not typeable by PFGE. The repeatability of both typing methods were 100% with satisfying reproducibility (≥ 95%). Although the discriminatory power of PFGE was greater than RAPD, both methods showed sufficient discriminatory power (DI > 0.95) which reflects the heterogeneity among the K. pneumoniae isolates. An optimized RAPD protocol is less technically demanding and time consuming that makes it a reliable typing method and competitive with PFGE. PMID:24516423

  11. Molecular subtyping of Clostridium botulinum by pulsed-field gel electrophoresis.

    PubMed

    Lúquez, Carolina; Joseph, Lavin A; Maslanka, Susan E

    2015-01-01

    Pulsed-field gel electrophoresis (PFGE) has been extensively used to estimate the genetic diversity of Clostridium botulinum. In addition, PFGE is the standard method for investigating foodborne outbreaks associated with various enteric pathogens, including C. botulinum. PFGE can be used to exclude a suspected but not confirmed food source when the patterns of the food and clinical isolates are different. Indistinguishable PFGE patterns may also be useful for linking isolates between patients or to a food source, but results must be interpreted within an epidemiological context to ensure isolates are truly related. Here, we describe a standardized laboratory protocol for molecular subtyping of C. botulinum by PFGE.

  12. An exactly solvable Ogston model of gel electrophoresis: X. Application to high-field separation techniques.

    PubMed

    Gauthier, Michel G; Slater, Gary W

    2003-01-01

    Recently, we generalized our lattice model of gel electrophoresis to study the net velocity of particles being pulled by a high-intensity electric field through an arbitrary distribution of immobile obstacles (Gauthier, M. G., Slater, G. W., J. Chem. Phys. 2002, 117, 6745-6756). In this article, we show how the high-field version of our model can be used to compare the velocity of particles with different electric charges and/or physical sizes. We then investigate specific two-dimensional distributions of obstacles that can be used to separate particles, e.g., in a microfluidic device. More precisely, we compare the velocity of differently charged or sized analytes in sieving, trapping and deflecting systems to model various electrophoretic separation techniques. In particular, we study the nonlinear effects present in ratchet systems and how they can be combined with time-asymmetric pulsed fields to provide new modes of separation.

  13. XPCS study of dynamic correlation in polyurethane gel-carbonyl iron composite under magnetic field

    NASA Astrophysics Data System (ADS)

    Grigoriew, Helena; Wiegart, Lutz; Boczkowska, Anna; Mirkowska, Monika

    2010-10-01

    An X-ray photon correlation spectroscopy (XPCS) study of composite-type material consisting of polyurethane gel and carbonyl iron micrometric spheres was performed under magnetic fields of 0, 300 and 600 mT. The onion-like spheres structure was destroyed during the composite processing. The following conclusions were obtained from the study: -The polyurethane matrix is preferred as a source for the observed dynamic effects. -Below 300mT the material dynamics in direction of the outer magnetic field are very clear. -For 600 mT the dependence of the dynamics on magnetic field direction disappears, but the correlation rate is much higher. These findings may be caused by a disturbance of the polymer mesostructure by larger strain leading to its cross-linking.

  14. Model and field studies of the degradation of cross-linked polyacrylamide gels used during the revegetation of slate waste.

    PubMed

    Holliman, Peter J; Clark, Jennifer A; Williamson, Julie C; Jones, Davey L

    2005-01-05

    Cross-linked polyacrylamide gels are increasingly being used in environmental restoration schemes and horticulture as a means of enhancing water supply to plants. However, the environmental impact of cross-linked polyacrylamide gel deployment in soil remains poorly understood. This study assessed the chemical, physical and biological properties of new and field-conditioned cross-linked polyacrylamide gels. Both monomeric acrylamide (11 microg l(-1)) and acrylic acid (285 microg l(-1)) were observed in new gel; however, the levels of monomers in field-conditioned gels (1-6 years old) were very low (acrylamide <1 microg l(-1); acrylic acid <7 microg l(-1)). Generally, freeze-thaw processes and exposure to UV radiation had little effect on gel acrylic acid and acrylamide concentrations. However, elevated temperatures (35 degrees C) caused a significant release of up to 144 mug l(-1) of acrylamide and 453 microg l(-1) of acrylic acid in new gel and up to 25 microg l(-1) of acrylamide and 157 microg l(-1) of acrylic acid in field-conditioned gels. In contrast, gel water holding capacity was highly dependent upon environmental conditions (UV exposure and freeze/thaw cycles produced the greatest loss of water holding in new gels) and gel age. Optical microscopy revealed that after placement in the field the gels became increasingly colonised over time by fungi and bacteria. In enrichment cultures, we were unable, however, to demonstrate microbial growth when cross-linked polyacrylamide was used as the sole nitrogen source. In summary, under a range of conditions cross-linked polyacrylamide did not release acrylamide above legally permitted limits, with the exception of gel subjected to elevated temperatures. However, their capacity for holding water decreased sharply within 18 months. We therefore conclude that cross-linked polyacrylamide placed in soil is relatively stable with respect to the production of potentially toxic acrylamide, a species with a short half

  15. Biochemical Identification of the Two Races of Radopholus similis by Polyacrylamide Gel Electrophoresis.

    PubMed

    Huettel, R N; Dickson, D W; Kaplan, D T

    1983-07-01

    Analysis of proteins of the banana and citrus race of Radopholus similis was carried out by several different types of polyacrylamide gel electrophoresis. These included standard slab gel, SDS slab gel, gradient slab gel, and two-ditnensional slab gel electrophoresis. A major band difference was detected between the two races by slab gel electrophoresis. However, several other poorly resolved but consistent hands of high molecular weight proteins near the gel origin also were considered as diagnostic. Resolution of protein bands was greatly improved by SDS and gradient slab gel electrophoresis, but no differences could be detected among the proteins resolved between the two rares with these techniques. Two-dimensional gels revealed a large number of proteins, but background staining obscured them hindering interpretation. When nematode races were reared on three different host plants, no differences in protein patterns were detected between them, indicating host preferences does not play a role in determining the types proteins occurring in these nematodes.

  16. Conformational Entropy Mechanism for Periodic Motion of DNA under Constant-Field Gel Electrophoresis

    NASA Astrophysics Data System (ADS)

    Azuma, Ryuzo; Takayama, Hajime

    2006-06-01

    Entropic elasticity of a single charged polymer undergoing gel electrophoresis is a fundamental theme of polymer statistical physics since the discovery of “periodic” behavior in constant field gel electrophoresis (CFGE). In the present work we address the problem numerically by two steps. In the first step, we carry out Brownian dynamics (BD) simulations on CFGE by solving semi-microscopic Langevin equations of a polymer consisting of beads separated by a mean distance much smaller than the Kuhn length. Results are analyzed based on coarse-graining over the Kuhn length scale. We show the averaged elongation-contraction motion involves asymmetric V-shaped configurations whose shorter arm length depends on the field and the temperature consistently with what is expected when the BD chain is described by the freely-jointed chain (FJC) model with a suitable Kuhn length. To our knowledge, this is the first numerical confirmation of the FJC model itself from a submicroscopic description of polymer motion. The saturation of chain mobility in high fields agrees well with the nonlinear dependence of this shorter arm length on the field. In the second step, we discuss the periodic elongation-contraction motion of the coarse-grained chain by such a simplified model as a one-dimensional chain consisting of beads, elastic strings, and obstacles. The results from these two chain models indicate that the periodic elongation-contraction motion of DNA under CFGE is self-organized by a balance between the field force and the conformational entropic force.

  17. Intra-species chromosome-length polymorphism in Geotrichum candidum revealed by pulsed field gel electrophoresis.

    PubMed

    Gente, Stéphanie; Desmasures, Nathalie; Jacopin, Cyril; Plessis, Ghislaine; Beliard, Martine; Panoff, Jean-Michel; Guéguen, Micheline

    2002-06-05

    Geotrichum candidum is an ascomycetous anamorph yeast-like fungus found in various habitats. It is a component of the natural flora of milk and is used as a maturing agent for both soft and hard cheeses. This microorganism displays phenotypic variability and may act as an opportunist pathogen, causing geotrichosis. Cytological analysis of G. candidum strain ATCC 204307 showed this strain to have eight chromosomes. We prepared chromosomal DNA from 13 strains of G. candidum differing in habitat and morphotype. We used pulsed field gel electrophoresis (PFGE) in two sets of conditions to determine the size of the chromosomal DNA molecules. The strains investigated had five to eight chromosomes, 0.6 to 4.5 Mb in size. We estimated genome size in these 13 strains to be between 11 and 19 Mb. Pulsed-field gel electrophoresis profiles showed a high degree of polymorphism, indicating considerable variability between strains. Genome size and the presence of large chromosomes appeared to be correlated with morphotype. Strains with a mold-like or intermediate morphotype tended to have larger genomes than strains with a yeast-like morphotype did.

  18. 5 × 5 cm2 silicon photonic crystal slabs on glass and plastic foil exhibiting broadband absorption and high-intensity near-fields

    PubMed Central

    Becker, C.; Wyss, P.; Eisenhauer, D.; Probst, J.; Preidel, V.; Hammerschmidt, M.; Burger, S.

    2014-01-01

    Crystalline silicon photonic crystal slabs are widely used in various photonics applications. So far, the commercial success of such structures is still limited owing to the lack of cost-effective fabrication processes enabling large nanopatterned areas (≫ 1 cm2). We present a simple method for producing crystalline silicon nanohole arrays of up to 5 × 5 cm2 size with lattice pitches between 600 and 1000 nm on glass and flexible plastic substrates. Exclusively up-scalable, fast fabrication processes are applied such as nanoimprint-lithography and silicon evaporation. The broadband light trapping efficiency of the arrays is among the best values reported for large-area experimental crystalline silicon nanostructures. Further, measured photonic crystal resonance modes are in good accordance with light scattering simulations predicting strong near-field intensity enhancements greater than 500. Hence, the large-area silicon nanohole arrays might become a promising platform for ultrathin solar cells on lightweight substrates, high-sensitive optical biosensors, and nonlinear optics. PMID:25073935

  19. 5 × 5 cm² silicon photonic crystal slabs on glass and plastic foil exhibiting broadband absorption and high-intensity near-fields.

    PubMed

    Becker, C; Wyss, P; Eisenhauer, D; Probst, J; Preidel, V; Hammerschmidt, M; Burger, S

    2014-07-30

    Crystalline silicon photonic crystal slabs are widely used in various photonics applications. So far, the commercial success of such structures is still limited owing to the lack of cost-effective fabrication processes enabling large nanopatterned areas (≫ 1 cm(2)). We present a simple method for producing crystalline silicon nanohole arrays of up to 5 × 5 cm(2) size with lattice pitches between 600 and 1000 nm on glass and flexible plastic substrates. Exclusively up-scalable, fast fabrication processes are applied such as nanoimprint-lithography and silicon evaporation. The broadband light trapping efficiency of the arrays is among the best values reported for large-area experimental crystalline silicon nanostructures. Further, measured photonic crystal resonance modes are in good accordance with light scattering simulations predicting strong near-field intensity enhancements greater than 500. Hence, the large-area silicon nanohole arrays might become a promising platform for ultrathin solar cells on lightweight substrates, high-sensitive optical biosensors, and nonlinear optics.

  20. Theory of gel electrophoresis in high fields: Evolution of a population of hernias

    NASA Astrophysics Data System (ADS)

    Long, Didier; Viovy, Jean-Louis

    1997-02-01

    We consider long polyelectrolytes that are initially at rest in a gel and suddenly submitted to a strong electric field. The evolution of the conformation regime is described up to the final disengagement from the initial tube. Just after the field has been applied, the chain adopts a comb-like conformation with several “hernias”, which evolve in competition with each other. As long as the conformation has many hernias, the distribution of their size follows a self-similar law, first described by Deutsch. The number of hernias decreases, and ultimately the chain disengages from its initial tube. Various predictions for the conformation of the chain in this last stage and for time constants are proposed. In particular, the disengagement times are found to follow a self-similar law in the size of the chains.

  1. Dc to ac field conversion due to leaky-wave excitation in a plasma slab behind an ionization front

    NASA Astrophysics Data System (ADS)

    Kostin, V. A.; Vvedenskii, N. V.

    2015-03-01

    We present a way for generating coherent tunable electromagnetic radiation through dc to ac field conversion by an ionization front. The conversion is caused by the excitation of leaky waves behind the transversely limited ionization front propagating in a uniform electrostatic field. This differs significantly from the well-known dc-to-ac-radiation-converter models which consider Doppler-like frequency conversion by a transversely unlimited ionization front propagating in a spatially periodic electric field. We explore the dispersion properties and excitation of these leaky waves radiated through the transverse plasma boundary at the Cherenkov angle to the direction of propagation of a superluminal ionization front as dependent on the parameters of the plasma produced and on the speed of the ionization front. It is shown that not only the center frequency but also the duration and waveform of the generated pulse may significantly depend on the speed of the ionization front. The results indicate the possibility of using such converters based on planar photoconductive antennas to create sources of microwave and terahertz radiation with controllable waveforms that are transformed from video to radio pulse when the angle of incident ionizing radiation is tuned.

  2. Effects of change in slab geometry on the mantle flow and slab fabric in Southern Peru

    NASA Astrophysics Data System (ADS)

    Knezevic Antonijevic, Sanja; Wagner, Lara S.; Beck, Susan L.; Long, Maureen D.; Zandt, George; Tavera, Hernando

    2016-10-01

    The effects of complex slab geometries on the surrounding mantle flow field are still poorly understood. Here we combine shear wave velocity structure with Rayleigh wave phase anisotropy to examine these effects in southern Peru, where the slab changes its geometry from steep to flat. To the south, where the slab subducts steeply, we find trench-parallel anisotropy beneath the active volcanic arc that we attribute to the mantle wedge and/or upper portions of the subducting plate. Farther north, beneath the easternmost corner of the flat slab, we observe a pronounced low-velocity anomaly. This anomaly is caused either by the presence of volatiles and/or flux melting that could result from southward directed, volatile-rich subslab mantle flow or by increased temperature and/or decompression melting due to small-scale vertical flow. We also find evidence for mantle flow through the tear north of the subducting Nazca Ridge. Finally, we observe anisotropy patterns associated with the fast velocity anomalies that reveal along strike variations in the slab's internal deformation. The change in slab geometry from steep to flat contorts the subducting plate south of the Nazca Ridge causing an alteration of the slab petrofabric. In contrast, the torn slab to the north still preserves the primary (fossilized) petrofabric first established shortly after plate formation.

  3. Mixing characterization in a slab tank

    SciTech Connect

    Stoots, C.M.; Gavlak, A.M.; Calabrese, R.V.; Kyser, E.A.; Tatterson, G.B.

    1989-01-01

    Due to safety requirements, slab tanks are often used to process radioactive materials. The configuration is that of a slit or a tank of rectangular cross section with very low aspect ratio. Due to its nonconventional geometry, very little is known about the slab tank mixing environment. To better understand it, experiments have been performed in a full scale standard configuration equipped with two stirrer shafts, each containing several axial impellers. To characterize the velocity field, mean and RMS turbulent velocities have been measured at several impeller speeds with a two-component Laser Doppler Anemometer (LDA). The LDA data have been supplemented with flow visualization, circulation time, and mixing time studies. Since the slab tank is often used as a precipitator, solids suspension studies have also been performed. The results of the various experiments will be presented and will be interpreted to elucidate slab tank dynamics. The implication to mixing efficiency will also be discussed.

  4. Deepest hypocentral distributions associated with stagnant slabs and penetrated slabs

    NASA Astrophysics Data System (ADS)

    Fukao, Y.; Obayashi, M.

    2013-12-01

    We constructed a new P-wave tomographic model of the mantle, GAP_P4, using more than ten millions of travel time data, including waveform-based differential travel times from ocean bottoms, to all of which the finite frequency kernels were applied in the inversion. Based on this model, we made a systematic survey for subducted slab images around the Circum Pacific. This survey revealed a progressive lateral variation of slab configuration along arc(s), where a subducted slab is in general in one or two of the following four stages: I. slab stagnant above the 660, II. slab penetrating the 660, III. slab trapped in the uppermost lower mantle (660 to ˜1000 km in depth), and IV. slab descending well into the deep lower mantle. The majority of the slab images are either at stage I or III. We interpret I to IV as the successive stages of slab subduction through the transition region with the 660 at the middle. There is a remarkable correlation of the slab configuration with the deepest shock hypocentral distribution. Subhorizontal distributions of deepest shocks are associated with stagnant slabs in the transition zone (slabs at stage I). Their focal depths are limited to shallower than ˜620 km. Steeply dipping deepest shock distributions are associated with penetrating slabs across the 660-km discontinuity or trapped slabs below it (slabs at stages II and III). Their focal depths extend well beyond ˜620 km. There are no cases of association of either a stagnant slab (at stage I) with subvertical distribution of deepest shocks or a trapped slab (at stage II or III) with their subhorizontal distribution. Only steeply dipping slabs appear to penetrate the 660 to be trapped in the uppermost lower mantle. The along-arc variations of stagnant-slab configuration and deepest shock distribution beneath the Bonin arc indicate a process of how the slab begins to penetrate the 660-km discontinuity after the slab stagnation. Those beneath the Java arc and Kermadec arc commonly

  5. Use of pulsed-field gel electrophoresis to measure DNA damage and repair

    SciTech Connect

    Scicchitano, D.A. New York Univ., New York )

    1991-03-11

    A method is described here for the analysis of single-strand break formation and repair in genomic DNA. The procedure involves exposing cells to a DNA-damaging agent, allowing time for recovery, and embedding the cells in agarose. After lysis and digestion with a protease, the DNA, which remains in the agarose plug, is denatured with glyoxal and separated by pulsed-field gel electrophoresis. The DNA in the gel is then transferred to a support membrane and quantitated with a radioanalytic imaging system to determine the average size of the DNA at each time point of recovery. The results indicate that the repair of methyl-induced breaks in total genomic DNA is approximately 80% complete in 48 hr in CHO B11 and ARL 14 cells exposed to dimethyl sulfate. These results are in agreement with those obtained by using other techniques like alkaline sucrose sedimentation. The method developed and described here has several advantages over existing techniques for repair measurements: It can be used to monitor genotoxic agents that nick DNA, to study the removal of breaks from genomic DNA, and to test for repair of damage in specific domains of chromatin that would be too large to examine by conventional electrophoresis.

  6. Pulsed-field gel electrophoresis analysis of multicellular DNA double-strand break damage and repair.

    PubMed

    Joshi, Nina; Grant, Stephen G

    2014-01-01

    This assay quantifies the extent of double-strand break (DSB) DNA damage in cell populations embedded in agarose and analyzed for migratory DNA using pulsed-field gel electrophoresis with ethidium bromide staining. The assay can measure preexisting damage as well as induction of DSB by chemical (e.g., bleomycin), physical (e.g., X-irradiation), or biological (e.g., restriction enzymes) agents. By incubating the cells under physiological conditions prior to processing, the cells can be allowed to repair DSB, primarily via the process of nonhomologous end joining. The amount of repair, corresponding to the repair capacity of the treated cells, is then quantified by determining the ratio of the fractions of activity released in the lanes in comparison to the total amount of DNA fragmentation following determination of an optimal exposure for maximum initial fragmentation. Repair kinetics can also be analyzed through a time-course regimen.

  7. Characterization of Listeria monocytogenes isolates from cattle and ground beef by pulsed-field gel electrophoresis.

    PubMed

    Foerster, Claudia; Vidal, Lorena; Troncoso, Miriam; Figueroa, Guillermo

    2012-01-01

    The aims of this study were to determine the occurrence of Listeria monocytogenes in cattle feces and ground beef, to characterize these strains by pulsed-field gel electrophoresis and to compare them to three listeria strains found in humans. Cattle from different origins (n = 250) and ground beef obtained from supermarkets (n = 40) were sampled. The results show low occurrence in cattle feces (0.4 %) but a higher presence in ground beef (37 %). An important part of the ground beef strains (80 %) had > 95 % similarity with a strain isolated from a human sporadic case and the ATCC 19115 used as control. The strain isolated from cattle feces had 93 % similarity to clone 009, previously associated with a listeriosis outbreak related to cheese. Cattle and ground beef can harbor virulent L. monocytogenes strains. Further studies in animals and animal products are needed to improve listeriosis control.

  8. Molecular Typing by Pulsed-Field Gel Electrophoresis of Spanish Animal and Human Listeria monocytogenes Isolates

    PubMed Central

    Vela, A. I.; Fernandez-Garayzabal, J. F.; Vazquez, J. A.; Latre, M. V.; Blanco, M. M.; Moreno, M. A.; de la Fuente, L.; Marco, J.; Franco, C.; Cepeda, A.; Rodriguez Moure, A. A.; Suarez, G.; Dominguez, L.

    2001-01-01

    A total of 153 strains of Listeria monocytogenes isolated from different sources (72 from sheep, 12 from cattle, 18 from feedstuffs, and 51 from humans) in Spain from 1989 to 2000 were characterized by pulsed-field gel electrophoresis. The strains of L. monocytogenes displayed 55 pulsotypes. The 84 animal, 51 human, and 18 feedstuff strains displayed 31, 29, and 7 different pulsotypes, respectively, indicating a great genetic diversity among the Spanish L. monocytogenes isolates studied. L. monocytogenes isolates from clinical samples and feedstuffs consumed by the diseased animals were analyzed in 21 flocks. In most cases, clinical strains from different animals of the same flock had identical pulsotypes, confirming the existence of a listeriosis outbreak. L. monocytogenes strains with pulsotypes identical to those of clinical strains were isolated from silage, potatoes, and maize stalks. This is the first study wherein potatoes and maize stalks are epidemiologically linked with clinical listeriosis. PMID:11722943

  9. Evaluation of Pulsed-Field Gel Electrophoresis Profiles for Identification of Salmonella Serotypes▿ †

    PubMed Central

    Zou, Wen; Lin, Wei-Jiun; Foley, Steven L.; Chen, Chun-Houh; Nayak, Rajesh; Chen, James J.

    2010-01-01

    Pulsed-field gel electrophoresis (PFGE) is a standard typing method for isolates from Salmonella outbreaks and epidemiological investigations. Eight hundred sixty-six Salmonella enterica isolates from eight serotypes, including Heidelberg (n = 323), Javiana (n = 200), Typhimurium (n = 163), Newport (n = 93), Enteritidis (n = 45), Dublin (n = 25), Pullorum (n = 9), and Choleraesuis (n = 8), were subjected to PFGE, and their profiles were analyzed by random forest classification and compared to conventional hierarchical cluster analysis to determine potential predictive relationships between PFGE banding patterns and particular serotypes. Cluster analysis displayed only the underlying similarities and relationships of the isolates from the eight serotypes. However, for serotype prediction of a nonserotyped Salmonella isolate from its PFGE pattern, random forest classification provided better accuracy than conventional cluster analysis. Discriminatory DNA band class markers were identified for distinguishing Salmonella serotype Heidelberg, Javiana, Typhimurium, and Newport isolates. PMID:20631109

  10. Molecular analysis of chromosomal rearrangements using pulsed field gel electrophoresis and somatic cell hybrids

    SciTech Connect

    Davis, L.M. )

    1991-01-01

    Many human genetic diseases, including some cancers, are characterized by consistent chromosome abnormalities, such as deletions and translocations. Analyses of these mutations often prove crucial to the eventual cloning and characterization of the gene(s) responsible for the disease. Two methods for analyzing these chromosome abnormalities have been developed in recent years: somatic cell hybridization and pulsed field gel electrophoresis (PFGE). Somatic cell hybridization is a technique for segregating an aberrant chromosome from its normal homologue in a cell derived from an unrelated species, which is usually a rodent. Demonstrations of these analytic techniques are presented, using as an example chromosomal abnormalities involving human chromosome band 11p13, the locus for the Wilms' tumor, aniridia, genitourinary abnormality, and mental retardation (WAGR) syndrome.

  11. Campylobacter coli pulsed field gel electrophoresis genotypic diversity among sows and piglets in a farrowing barn.

    PubMed

    Hume, Michael E; Droleskey, Robert E; Sheffield, Cynthia L; Harvey, Roger B

    2002-08-01

    Genotypes of Campylobacter coli isolates from feces of three sows and rectal swabs of 17 piglets were examined by pulsed field gel electrophoresis (PFGE). All of the animals originated from a single farrowing barn of a farrow-to-finish swine operation. Five Campylobacter colonies were picked from a single agar plate for each sample after broth enrichment and growth on Campy-Cefex agar. Genotypes were examined by PFGE after genomic DNA digestion with SmaI and SacII restriction endonucleases. Twenty SmaI genotypes and 12 SacII genotypes were detected among 99 Campylobacter coli isolates. There was no pattern of shared genotypes between sows and their respective piglets, nor between littermates. Results indicate that a high number of Campylobacter genotypes may coexist in related pigs from a single housing facility.

  12. Megabase-scale mapping of the HLA gene complex by pulsed field gel electrophoresis

    SciTech Connect

    Lawrance, S.K.; Smith, C.L.; Srivastava, R.; Cantor, C.R.; Weissman, S.M.

    1987-03-13

    In the study of the genetic structure of mammalian chromosomes, there exists a resolution gap between molecular cloning experiments and meiotic linkage analyses. This gap has discouraged attempts to construct full-scale genetic maps of mammalian chromosomes. The organization of the human major histocompatibility complex was examined within this range by pulsed field gel electrophoresis. The data obtained indicate that the complex spans over 3000 kilobases and enable the construction of a megabase-scale molecular map. These results indicate that the techniques employed in DNA extraction, enzymatic digestion, electrophoresis, and hybridization are suitable for the efficient analysis of megabase regions of mammalian chromosomes and effectively bridge the resolution gap between molecular cloning and classical genetics.

  13. Mapping of Escherichia Coli Chromosomal Tn5 and F Insertions by Pulsed Field Gel Electrophoresis

    PubMed Central

    Smith, C. L.; Kolodner, R. D.

    1988-01-01

    A low resolution Not I physical map of Escherichia coli was recently constructed. In this report we demonstrated that this map can be used to map Tn5 and F insertions physically. The transposon, Tn5, contains Not I recognition sequences in its IS50 sequences. F plasmid contains an unmapped Not I site. Hence, the location of Tn5 and F in the chromosome can be mapped by identifying the location of the introduced Not I sites using pulsed field gel electrophoresis. The physical mapping of genetically mapped Tn5 insertions confirm the previously constructed Not I map and helps align the E. coli physical and genetic maps. The use of Tn5 can assist the construction of both physical and genetic maps for microorganisms lacking such maps. Variations on this approach will facilitate physical mapping with a wide variety of organisms, enzymes, and genetic elements. PMID:2840334

  14. Pulsed-field gel electrophoresis patterns of Escherichia coli O157 isolates from Kansas feedlots.

    PubMed

    Sargeant, J M; Shi, X; Sanderson, M W; Renter, D G; Nagaraja, T G

    2006-01-01

    This study investigated the prevalence and distribution of Escherichia coli O157 genetic types within and among feedlots using pulsed-field gel electrophoresis to separate XbaI-digested DNA. The study population consisted of 300 pens of cattle in 30 feedlots in Kansas that were sampled (feces, water, and water sediment) within a month of being shipped for slaughter. The prevalence of E. coli O157 was 8.5% in feces, 3.1% in water, and 4.5% in water sediment samples. A total of 424 E. coli O157 isolates were characterized by pulsed-field gel electrophoresis, and 139 subtypes (100% Dice similarity with no band differences) were identified. The majority of subtypes (70/139) was identified only once, but nine were identified 10 or more times. Identical subtypes were recovered from both feces and water tanks in 10 feedlots. The majority of subtypes were identified in only one feedlot, and the number of subtypes ranged from one to 23 within a feedlot and from one to seven within a pen. There were 10 feedlots with at least 15 positive samples. In these 10 feedlots, the most common subtype accounted for 16.9-78.6% of the isolates. Common subtypes differed among feedlots. In eight of the 10 feedlots, the most common subtype was identified in multiple pens. The results support a complex ecology for E. coli O157 in feedlot operations, with factors associated with exposure and transmission likely acting at a common level for multiple feedlots, within feedlots, and within pens of cattle.

  15. Motion of megabase deoxyribonucleic acid during field-inversion gel electrophoresis: Investigation by nonlocal Monte Carlo

    NASA Astrophysics Data System (ADS)

    Duke, T. A. J.; Viovy, J. L.

    1992-06-01

    We give a detailed description of a new Monte Carlo method for the simulation of the forced dynamics of long chain polymers in a constrictive environment. The model is based on the reptation theory but admits, in addition, the possibility that loops of the chain (``hernias'') may escape laterally out of the tube. A discrete representation of the molecule, in which individual chain segments are either taut or slack, permits the extensional mode of the molecule within the tube to be taken into consideration. The dynamics is modeled by the nonlocal hopping of ``defects'' (regions of slack) along the chain, with Monte Carlo rules based on the stochastic equations of motion of the taut portions of the molecule. We use the technique to investigate the motion of long deoxyribonucleic acid (DNA) molecules, containing millions of base pairs, during field-inversion gel electrophoresis. For the pulse ratios most commonly used in practice, we find that the separation patterns display two regions of band-inversion. This anomalous behavior is linked to the strong transient response of the molecules when the field is reversed; sudden field inversion induces the formation of a chain configuration shaped like an extended V after an interval of time that increases linearly with the chain length. The DNA molecules that have the minimum and the maximum migration speeds are those whose transient response times are approximately equal to the forward and the reverse pulse time, respectively.

  16. Separation of chromosomal DNA molecules from C.albicans by pulsed field gel electrophoresis.

    PubMed Central

    Snell, R G; Wilkins, R J

    1986-01-01

    Modifications have been made to standard pulse field gel electrophoresis (PFGE) systems to enable very large DNA molecules to be resolved. The single most important modification was to elevate the temperature of electrophoresis to 35 degrees C. This enabled the largest Saccharomyces cerevisiae chromosome to be reproducibly resolved. More impressively, it enabled the DNA of Candida albicans to be clearly resolved into six bands, a feat which was very difficult at lower temperatures. Even so, optimal resolution could only be obtained by carefully adjusting field voltages and switching times. The DNA from the two largest C. albicans chromosomes, which was estimated to be at least 5-10Mbp in size, ran somewhat anomalously, giving fuzzy bands which did not migrate in the direction of the average electric field. That the highest molecular weight band was a distinct chromosome was demonstrated by specific hybridisation to the C. albicans ADE2 gene probe. With further fine tuning, the PFGE system described here should be capable of resolving DNA from the smallest human chromosomes. Images PMID:3520483

  17. DNA electrophoresis in agarose gels: Effects of electric field and gel concentration on the exponential dependence of reciprocal mobility on DNA length

    NASA Astrophysics Data System (ADS)

    Beheshti, Afshin; van Winkle, David; Randolph, Rill

    2002-03-01

    Electrophoresis was performed on double stranded DNA fragments ranging in length from 200 bp to 48502 bp at agarose gel concentrations T = 0.5% - 1.5% and electric fields E = 0.71 V/cm to 5 V/cm. A wide range of electric fields and gel concentrations were used to find what range of conditions work with the new interpolation equation, 1/μ(L) = 1/μl - (1/μl - 1/μ_s)e^-L/γ. The equation fit extremely well (\\chi^2 >= 0.999) to data with E = 2.5 V/cm to 5 V/cm and for lower fields (E < 2.5 V/cm) at low gel concentrations (T = 0.5% and 0.7%). This exponential relation seemed to hold when there is a smooth transition from the Ogston sieving regime to the reptation regime when looking at the “reptation plots” (plotting 3μL/μo vs. L) (Rousseau, J., Drouin, G., and Slater, G. W., Phys Rev Lett. 1997, 79, 1945-1948). For separations of single-stranded DNA in polyacrylamide, similar reptation plots have a region with a negative slope between the Ogston sieving regime and the reptation regime which has been interpreted as the signature of entropic trapping. When separating double-stranded DNA in agarose it was observed that fits deviate from the data when three different slopes are observed in the reptation plots. Failure of the simple exponential relationship between reciprocal mobility and DNA length appears to be the consequence of entropic trapping.

  18. Cordilleran slab windows

    SciTech Connect

    Thorkelson, D.J.; Taylor, R.P. )

    1989-09-01

    The geometry and geologic implications of subducted spreading ridges are topics that have bedeviled earth scientists ever since the recognition of plate tectonics. As a consequence of subduction of the Kula-Farallon and East Pacific rises, slab windows formed and migrated beneath the North American Cordillera. The probable shape and extent of these windows, which represent the asthenosphere-filled gaps between two separating, subducting oceanic plates, are depicted from the Late Cretaceous to the present. Possible effects of the existence and migration of slab windows on the Cordillera at various times include cessation of arc volcanism and replacement by rift or plate-edge volcanism; lithospheric uplift, attenuation, and extension; and increased intensity of compressional tectonism. Eocene extensional tectonism and alkaline magmatism in southern British Columbia and the northwestern United States were facilitated by slab-window development.

  19. Genetic fingerprinting of Brevibacterium linens by pulsed-field gel electrophoresis and ribotyping.

    PubMed

    Lima, P T; Correia, A M

    2000-07-01

    Members of Brevibacterium linens display physiological features that are relevant for cheese production. The genomes of five B. linens strains deposited on culture collections were compared by examining large restriction fragments on pulsed-field gel electrophoresis and detection of polymorphism at the level of 16S rRNA genes. Pulsed-field analysis with the endonucleases DraI and AsnI showed a characteristic restriction profile for each strain and allowed the calculation of genome sizes ranging between 3.2 and 3.9 Mbp. No linear genomic elements were detected. Polymorphisms at the level of 16S rRNA genes were revealed by hybridization with an oligonucleotide probe complementary to a universal domain of the 16S genes. An EcoRI fragment of 1.4 kb was identified as common to all strains under study. According to the number of positive bands detected by the probe, at least four rRNA operons must be present on the genome of the B. linens strains here studied.

  20. Enhanced field-dependent conductivity of magnetorheological gels with low-doped carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Qu, Hang; Yu, Miao; Fu, Jie; Yang, Pingan; Liu, Yuxuan

    2017-10-01

    Magnetorheological gels (MRG) exhibit field-dependent conductivity and controllable mechanical properties. In order to extend their application field, filling a large number of traditional conductive materials is the most common means to enhance the poor conductivity of MRG. In this study, the conductivity of MRG is improved by low-doped carbon nanotubes (CNTs). The influence of CNTs on the magnetoresistance of MRG is discussed from two aspects—the improvement in electrical conductivity and the magnetic sensitivity of conductivity variation. The percolation threshold of CNTs in MRG should be between 1 wt% and 2 wt%. The conductivity of a 4 wt% CNT-doped sample increases more than 28 000 times compared with pure MRG. However, there is a cliff-like drop for the range and rate of conductivity variation when the doping amount of CNTs is between 3 wt% and 4 wt%. Therefore, it is concluded that the optimal mass fraction of CNTs is 3%, which can maintain a suitable variation range and a strong conductivity. Compared with pure MRG, its conductivity increases by at least two orders of magnitude. Finally, a sketch of particle motion simulation is developed to understand the improving mechanism and the effect of CNTs.

  1. Application of multiplex PCR, pulsed-field gel electrophoresis (PFGE), and BOX-PCR for molecular analysis of enterococci

    USDA-ARS?s Scientific Manuscript database

    The objective of the study was to use band-based molecular methods including BOX-PCR (Polymerase Chain Reaction) and Pulsed-Field Gel Electrophoresis (PFGE) to determine if genetically related enterococci were found among different stores, food types, or years. Enterococci were also characterized f...

  2. Genetic diversity demonstrated by pulsed field gel electrophoresis of Salmonella enterica isolates obtained from diverse sources in Mexico

    USDA-ARS?s Scientific Manuscript database

    This study was conducted to determine the genetic diversity of Salmonella isolates recovered from a variety of sources using pulsed-field gel electrophoresis (PFGE) to assess their possible relatedness. Salmonella was isolated from ca. 52% of samples from a pepper var. Bell production system. A to...

  3. Sample collection system for gel electrophoresis

    DOEpatents

    Olivares, Jose A.; Stark, Peter C.; Dunbar, John M.; Hill, Karen K.; Kuske, Cheryl R.; Roybal, Gustavo

    2004-09-21

    An automatic sample collection system for use with an electrophoretic slab gel system is presented. The collection system can be used with a slab gel have one or more lanes. A detector is used to detect particle bands on the slab gel within a detection zone. Such detectors may use a laser to excite fluorescently labeled particles. The fluorescent light emitted from the excited particles is transmitted to low-level light detection electronics. Upon the detection of a particle of interest within the detection zone, a syringe pump is activated, sending a stream of buffer solution across the lane of the slab gel. The buffer solution collects the sample of interest and carries it through a collection port into a sample collection vial.

  4. The Propagation of Electromagnetic Waves in Thin Dielectric Slabs.

    DTIC Science & Technology

    1988-05-01

    Continue on reverse if recessary, and identify by block number) This report precents the solutions of Maxwell’s equations for the TE and TM modes of...field versus distance from slab center for two even and two odd TM modes .... 25 5. Electric field for TE even mode and magnetic field for TM even mode...34 vi1and/or ’it Special 6MEN Figures 6. Electric field versus distance from slab center for a slab of 0.35 [ tm thickness and dielectric coefficients of

  5. Slab Leaf Bowls

    ERIC Educational Resources Information Center

    Suitor, Cheryl

    2012-01-01

    In science class, fourth graders investigate the structure of plants and leaves from trees and how the process of photosynthesis turns sunlight into sugar proteins. In this article, the author fuses art and science for a creative and successful clay slab project in her elementary art classroom. (Contains 1 online resource.)

  6. Slab Leaf Bowls

    ERIC Educational Resources Information Center

    Suitor, Cheryl

    2012-01-01

    In science class, fourth graders investigate the structure of plants and leaves from trees and how the process of photosynthesis turns sunlight into sugar proteins. In this article, the author fuses art and science for a creative and successful clay slab project in her elementary art classroom. (Contains 1 online resource.)

  7. Prediction System for Rapid Identification of Salmonella Serotypes Based on Pulsed-Field Gel Electrophoresis Fingerprints

    PubMed Central

    Lin, Wei-Jiun; Hise, Kelley B.; Chen, Hung-Chia; Keys, Christine; Chen, James J.

    2012-01-01

    A classification model is presented for rapid identification of Salmonella serotypes based on pulsed-field gel electrophoresis (PFGE) fingerprints. The classification model was developed using random forest and support vector machine algorithms and was then applied to a database of 45,923 PFGE patterns, randomly selected from all submissions to CDC PulseNet from 2005 to 2010. The patterns selected included the top 20 most frequent serotypes and 12 less frequent serotypes from various sources. The prediction accuracies for the 32 serotypes ranged from 68.8% to 99.9%, with an overall accuracy of 96.0% for the random forest classification, and ranged from 67.8% to 100.0%, with an overall accuracy of 96.1% for the support vector machine classification. The prediction system improves reliability and accuracy and provides a new tool for early and fast screening and source tracking of outbreak isolates. It is especially useful to get serotype information before the conventional methods are done. Additionally, this system also works well for isolates that are serotyped as “unknown” by conventional methods, and it is useful for a laboratory where standard serotyping is not available. PMID:22378901

  8. The limitations of pulsed-field gel electrophoresis for analysis of Yersinia enterocolitica isolates.

    PubMed

    Gilpin, B J; Robson, B; Lin, S; Hudson, J A; Weaver, L; Dufour, M; Strydom, H

    2014-09-01

    This study describes the analysis of 432 isolates of Yersinia enterocolitica by pulsed-field gel electrophoresis (PFGE). PFGE had a high level of discrimination with biotype 1A isolates (Simpson's Diversity Index 0.997), but with the clinically important biotypes 2, 3 and 4, the discriminatory ability of PFGE was so low as to severely limit its usefulness (DI <0.6). For biotypes 2, 3 and 4, 79% or more of isolates of each biotype were of just three different PFGE profiles. Because of this, four known outbreaks of yersiniosis would not have been identified by PFGE analysis. However, a previously unrecognized potential outbreak of yersiniosis caused by biotype 4 isolates was identified on the basis of a rare PFGE genotype with spatial and temporal clustering. We conclude that PFGE has a very limited application to the genotyping of Y. enterocolitica biotypes 2, 3 and 4, and inferences based on finding indistinguishable PFGE profiles among cases or between cases and sources need to be substantiated using alternative typing tools, or strong epidemiological evidence.

  9. Pulsed-field gel electrophoresis and ribotype profiles of clinical and environmental Vibrio vulnificus isolates.

    PubMed Central

    Tamplin, M L; Jackson, J K; Buchrieser, C; Murphree, R L; Portier, K M; Gangar, V; Miller, L G; Kaspar, C W

    1996-01-01

    Vibrio vulnificus belongs to the autochthonous bacterial flora of warm estuarine waters. It can cause life-threatening extraintestinal disease in persons who have underlying illness and who consume raw shellfish or contact wounds with estuarine water. Currently, very little is known about genetic diversity within this species. In this report, we describe high-level variation in restriction fragment length polymorphism profiles among 53 clinical and 78 environmental isolates, as determined by pulsed-field gel electrophoresis. In contrast, ribotype profiles showed greater similarity. When combined ribotype profiles of clinical and environmental isolates were analyzed, four predominant clusters were observed. Interestingly, a low number (16%) of clinical isolates were found in cluster C, compared with clusters A, B, and D (range, 50 to 83%). In addition, 83% of all Hawaiian isolates were located in a single cluster, indicating a possible relationship between geography and genotype. We also report that spontaneous translucent colonial morphotypes were distinct by both restriction fragment length polymorphism and biochemical profiles, compared with opaque parent strains. PMID:8837412

  10. Epidemiological Validation of Pulsed-Field Gel Electrophoresis Patterns for Methicillin-Resistant Staphylococcus aureus

    PubMed Central

    Blanc, D. S.; Struelens, M. J.; Deplano, A.; De Ryck, R.; Hauser, P. M.; Petignat, C.; Francioli, P.

    2001-01-01

    To determine the stability of pulsed-field gel electrophoresis (PFGE) patterns of methicillin-resistant Staphylococcus aureus in the nosocomial setting, we analyzed isolates from long-term carriers (>1 month) and from patients involved in well-defined nosocomial epidemics. The number of fragment differences between the first isolate and subsequent isolates in long-term carriers showed a bimodal distribution, with one group having 0 to 6 fragment differences and the other group having 14 to 24 fragment differences. The PFGE patterns of isolates involved in epidemics also presented a similar bimodal distribution of the number of fragment differences. Typing these isolates with another molecular method (inter-IS256 PCR) showed that isolates of the first group (i.e., with 1 to 6 fragment differences) were clonally related, whereas the second group (with 14 to 24 fragment differences) could be considered genetically different. Among long-term carriers with clonally related isolates, 74 of 84 (88%) of consecutive isolates showed indistinguishable patterns, whereas 10 of 84 (12%) showed related patterns differing by one to six fragments. Moreover, the frequency of apparition of related patterns is higher when the time between the first and the subsequent isolate is longer. During seven nosocomial epidemics lasting from 1 to 15 months, only 2 of 120 isolates (1.7%) showed a pattern which was different, although related, from the predominant one involved in each of these outbreaks. PMID:11574553

  11. Typing of Methicillin Resistant Staphylococcus Aureus Using DNA Fingerprints by Pulsed-field Gel Electrophoresis

    PubMed Central

    Rebic, Velma; Budimir, Ana; Aljicevic, Mufida; Bektas, Sabaheta; Vranic, Sabina Mahmutovic; Rebic, Damir

    2016-01-01

    Background: Methicillin resistant Staphylococcus aureus (MRSA) is responsible for a wide spectrum of nosocomial and community associated infections worldwide. The aim of this study was to analyze MRSA strains from the general population in Canton Sarajevo, B&H. Methods: Our investigation including either phenotypic and genotypic markers such as antimicrobial resistance, pulsed-field gel electrophoresis (PFGE), SCC typing, and Panton-Valentine leukocidin (PVL) detection. Results: Antimicrobial susceptibility: all MRSA isolates were resistant to the β-lactam antibiotics tested, and all isolates were susceptible trimethoprim sulphamethoxazole, rifampicin, fusidic acid, linezolid and vancomycin. Sixty-eight per cent of the MRSA isolates were resistant to erythromycin, 5% to clindamycin, 5% to gentamicin and 4% to ciprofloxacin. After the PFGE analysis, the isolates were grouped into five similarity groups: A-E. The largest number of isolates belonged to one of two groups: C: 60 (60%) and D: 27 (27%). In both groups C and D, SCCmec type IV was predominant (60% and 88, 8%, respectively). A total of 24% of the isolates had positive expression of PVL genes, while 76% showed a statistically significantly greater negative expression of PVL genes. Conclusion: SCCmec type IV, together with the susceptibility profile and PFGE grouping, is considered to be typical of CA-MRSA PMID:27708486

  12. Application of pulsed-field gel electrophoresis to identify potential outbreaks of campylobacteriosis in New Zealand.

    PubMed

    Gilpin, Brent; Cornelius, Angela; Robson, Beth; Boxall, Naomi; Ferguson, Alan; Nicol, Carolyn; Henderson, Tom

    2006-02-01

    Since 2002, New Zealand's incidence of campylobacteriosis has exceeded 300 cases per 100,000 people per annum. To evaluate genetic variation in human isolates, 183 Campylobacter isolates were collected from a single clinical laboratory in Christchurch: 77 during an 8-week period in spring, and the rest 3 months later over a second 8-week period in autumn. Isolates were identified to the species level and subtyped using Penner serotyping (Campylobacter jejuni only) and pulsed-field gel electrophoresis (PFGE) using both SmaI and KpnI. Approximately two-thirds of the isolates could be grouped into clusters of between 2 and 26 isolates with indistinguishable SmaI and KpnI patterns. Less than 10% of the isolates were of the same type between the two sampling periods. The epidemiological relevance of the PFGE clusters was supported by temporal clustering, some spatial clustering, and some statistically significant demographic similarities among cases in a cluster. Conversely, patient cases yielding isolates which did not cluster with isolates from other cases were more likely to report recent overseas travel and less likely to live within larger urban centers. To identify whether these clusters actually represent common-source outbreaks, however, would require the detailed, rapid, and reiterative epidemiological investigation of cases within a PFGE cluster. The combined and timely application of subtyping and epidemiological investigation would appear to be a promising strategy for understanding campylobacteriosis in New Zealand.

  13. Molecular Analysis of Mycobacterium avium Isolates by Using Pulsed-Field Gel Electrophoresis and PCR

    PubMed Central

    Pestel-Caron, Martine; Graff, Gabriel; Berthelot, Gilles; Pons, Jean-Louis; Lemeland, Jean-François

    1999-01-01

    Genetic relationships among 46 isolates of Mycobacterium avium recovered from 37 patients in a 2,500-bed hospital from 1993 to 1998 were assessed by pulsed-field gel electrophoresis (PFGE) and PCR amplification of genomic sequences located between the repetitive elements IS1245 and IS1311. Each technique enabled the identification of 27 to 32 different patterns among the 46 isolates, confirming that the genetic heterogeneity of M. avium strains is high in a given community. Furthermore, this retrospective analysis of sporadic isolates allowed us (i) to suggest the existence of two remanent strains in our region, (ii) to raise the question of the possibility of nosocomial acquisition of M. avium strains, and (iii) to document laboratory contamination. The methods applied in the present study were found to be useful for the typing of M. avium isolates. In general, both methods yielded similar results for both related and unrelated isolates. However, the isolates in five of the six PCR clusters were distributed among two to three PFGE patterns, suggesting that this PCR-based method may have limitations for the analysis of strains with low insertion sequence copy numbers or for resolution of extended epidemiologic relationships. PMID:10405383

  14. Genetic variability among Chlamydia trachomatis reference and clinical strains analyzed by pulsed-field gel electrophoresis.

    PubMed Central

    Rodriguez, P; Allardet-Servent, A; de Barbeyrac, B; Ramuz, M; Bebear, C

    1994-01-01

    Pulsed-field gel electrophoresis (PFGE) was applied to Chlamydia trachomatis reference strains representing each of the 18 serovars and to 29 clinical isolates from genital specimens collected in Bordeaux, France, or Malmö, Sweden. Comparison of the fingerprint patterns of the reference strains revealed a high level of polymorphism of the total DNA when SmaI was used (14 profiles), whereas the other enzymes, Sse8387I and ApaI, showed fewer differences. Some serovars, considered to be closely related on the basis of their antigenic determinants located on the major outer membrane protein (MOMP), such as D and Da or I and Ia, were shown to be different after PFGE of their genomic DNAs. However, serovars B and Ba and serovars L2 and L2a had identical patterns after analysis with the three endonucleases. When applied to clinical isolates, which were typed by restriction fragment length polymorphism analysis of the MOMP gene, PFGE allowed the detection of intragenotype polymorphisms and showed the identity of two strains successively isolated from the same patient. This technique seems to be an efficient tool for epidemiological studies when used in addition to serotyping or genotyping by restriction fragment length polymorphism analysis of the MOMP gene. Images PMID:7883878

  15. Multilocus Sequence Typing Compared to Pulsed-Field Gel Electrophoresis for Molecular Typing of Pseudomonas aeruginosa▿

    PubMed Central

    Johnson, Jennifer K.; Arduino, Sonia M.; Stine, O. Colin; Johnson, Judith A.; Harris, Anthony D.

    2007-01-01

    For hospital epidemiologists, determining a system of typing that is discriminatory is essential for measuring the effectiveness of infection control measures. In situations in which the incidence of resistant Pseudomonas aeruginosa is increasing, the ability to discern whether it is due to patient-to-patient transmission versus an increase in patient endogenous strains is often made on the basis of molecular typing. The present study compared the discriminatory abilities of pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) for 90 P. aeruginosa isolates obtained from cultures of perirectal surveillance swabs from patients in an intensive care unit. PFGE identified 85 distinct types and 76 distinct groups when similarity cutoffs of 100% and 87%, respectively, were used. By comparison, MLST identified 60 sequence types that could be clustered into 11 clonal complexes and 32 singletons. By using the Simpson index of diversity (D), PFGE had a greater discriminatory ability than MLST for P. aeruginosa isolates (D values, 0.999 versus 0.975, respectively). Thus, while MLST was better for detecting genetic relatedness, we determined that PFGE was more discriminatory than MLST for determining genetic differences in P. aeruginosa. PMID:17881548

  16. Characterization of Erwinia amylovora strains from Bulgaria by pulsed-field gel electrophoresis.

    PubMed

    Atanasova, Iliana; Urshev, Zoltan; Hristova, Petya; Bogatzevska, Nevena; Moncheva, Penka

    2012-01-01

    The aim of this study was to characterize genetically Bulgarian Erwinia amylovora strains using pulsed-field gel electrophoresis (PFGE) analysis. Fifty E. amylovora strains isolated from different hosts, locations, as well as in different years were analysed by PFGE after XbaI, SpeI, and XhoI digestion of the genomic DNA. The strains were distributed into four groups according to their XbaI-generated profile. About 82% of the strains displayed a PFGE profile identical to that of type Pt2. Three strains belonged to the Central Europe Pt1 type. Two new PFGE profiles, not reported so far, were established--one for a strain isolated from Malus domestica and another for all Fragaria spp. strains. The same grouping of the strains was obtained after analysis of the SpeI digestion patterns. On the basis of PFGE profiles, after XbaI and SpeI digestion, a genetic differentiation between the strains associated with subfamily Maloideae and subfamily Rosoideae was revealed. The presence of more than one PFGE profile in the population of E. amylovora in Bulgaria suggests a multiple source of inoculum.

  17. High-frequency alternating-crossed-field gel electrophoresis with neutral or slightly charged interpenetrating networks to improve DNA separation.

    PubMed

    Boyd, B M; Prausnitz, J M; Blanch, H W

    1998-12-01

    Toward improving DNA separations, this work reports the effects of high-frequency square-wave AC fields superimposed perpendicular to the direct current (DC) separation field on DNA migration in both polyacrylamide-based interpenetrating networks (IPNs) and in agarose networks. Compared to standard polyacrylamide gels, IPNs allow the separation of larger DNA (9000 bp vs. 5000 bp at 5 V/cm). In novel polyacrylamide-based IPNs, an alternating current (AC) field of 5 Hz increased the maximum DNA size separable. This effect was extended to larger DNA sizes with increasing electric-field strength up to and apparently beyond the power supply-limited maximum electric-field strength of 48 V/cm. The orthogonal AC field also increased mobility. These two results combine to yield a reduction in separation time of up to a factor of 20 in novel polyacrylamide-based IPNs. When negatively charged acrylic-acid groups were incorporated into the IPNs, the use of the AC field changed the DNA-network interaction, which altered the size dependence of DNA mobility. In agarose gels, an AC field of 50 Hz increased the size range separable; however, there was no increase in DNA mobility. There was no change in size dependence of mobility in an AC field when the number of charged groups in the agarose network was increased. Based on results in the literature, possible mechanisms were examined for the effects of the AC field on DNA separation.

  18. Characterization of Mannheimia haemolytica in beef calves via nasopharyngeal culture and pulsed-field gel electrophoresis.

    PubMed

    Capik, Sarah F; White, Brad J; Lubbers, Brian V; Apley, Michael D; Mosier, Derek A; Larson, Robert L; Murray, Robert W

    2015-09-01

    Mannheimia haemolytica is a major bacterial component of bovine respiratory disease (BRD); unfortunately, very little is known about M. haemolytica transmission dynamics among cattle. Identifying potential variation in M. haemolytica populations over time and induction of nasopharyngeal colonization and subsequent shedding are 2 areas where knowledge is lacking. In our study, 2 separate loads of 20 mixed-origin, male calves were purchased through an order buyer on different dates. Deep nasopharyngeal cultures (NPC) were performed on all calves on arrival and, if M. haemolytica-negative, a second screening culture was obtained. Calves that were negative on 2 initial NPCs (NEG; n = 4) were subsequently challenged with a previously isolated field strain of M. haemolytica in both the upper and lower respiratory tract, individually housed, and then monitored for M. haemolytica shedding via NPCs at 0.5, 1, 3, 5, 7, and 9 days postchallenge. Naturally M. haemolytica-positive calves (2 per load) were kept for additional daily cultures (POS; n = 4). Individual calf M. haemolytica status for both the POS and NEG groups was inconsistent between study days. Additionally, pulsed-field gel electrophoresis performed on isolates from the positive cultures showed that the NEG calves did not shed the M. haemolytica challenge strain, but rather 2 distinct clusters of M. haemolytica were shared among POS and NEG calves regardless of their initial status. Although sample sizes were small, these findings illustrate how variable the results of a single nasopharyngeal swab can be and the challenges of using an individual culture to truly represent animal M. haemolytica status.

  19. Population Dynamics of Chesapeake Bay Virioplankton: Total-Community Analysis by Pulsed-Field Gel Electrophoresis†

    PubMed Central

    Wommack, K. Eric; Ravel, Jacques; Hill, Russell T.; Chun, Jongsik; Colwell, Rita R.

    1999-01-01

    Recognition of viruses as the most abundant component of aquatic microbial communities has stimulated investigations of the impact of viruses on bacterio- and phytoplankton host communities. From results of field studies to date, it is concluded that in most aquatic environments, a reduction in the number of bacteria on a daily basis is caused by viral infection. However, the modest amount of in situ virus-mediated mortality may be less significant than viral infection serving to maintain clonal diversity in the host communities directly, through gene transmission (i.e., transduction), and indirectly, by elimination of numerically dominant host species. If the latter mechanism for controlling community diversity prevails, then the overall structure of aquatic viral communities would be expected to change as well over short seasonal and spatial scales. To determine whether this occurs, pulsed-field gel electrophoresis (PFGE) was used to monitor the population dynamics of Chesapeake Bay virioplankton for an annual cycle (1 year). Virioplankton in water samples collected at six stations along a transect running the length of the bay were concentrated 100-fold by ultrafiltration. Viruses were further concentrated by ultracentrifugation, and the concentrated samples were embedded in agarose. PFGE analysis of virus DNA in the agarose plugs yielded several distinct bands, ranging from 50 to 300 kb. Principal-component and cluster analyses of the virus PFGE fingerprints indicated that changes in virioplankton community structure were correlated with time, geographical location, and extent of water column stratification. From the results of this study, it is concluded that, based on the dynamic nature of the Chesapeake Bay virioplankton community structure, the clonal diversity of bacterio- and phytoplankton host communities is an important component of the virus community. PMID:9872784

  20. Magnetohydrodynamic Waves in an Asymmetric Magnetic Slab

    NASA Astrophysics Data System (ADS)

    Allcock, Matthew; Erdélyi, Robert

    2017-02-01

    Analytical models of solar atmospheric magnetic structures have been crucial for our understanding of magnetohydrodynamic (MHD) wave behaviour and in the development of the field of solar magneto-seismology. Here, an analytical approach is used to derive the dispersion relation for MHD waves in a magnetic slab of homogeneous plasma enclosed on its two sides by non-magnetic, semi-infinite plasma with different densities and temperatures. This generalises the classic magnetic slab model, which is symmetric about the slab. The dispersion relation, unlike that governing a symmetric slab, cannot be decoupled into the well-known sausage and kink modes, i.e. the modes have mixed properties. The eigenmodes of an asymmetric magnetic slab are better labelled as quasi-sausage and quasi-kink modes. Given that the solar atmosphere is highly inhomogeneous, this has implications for MHD mode identification in a range of solar structures. A parametric analysis of how the mode properties (in particular the phase speed, eigenfrequencies, and amplitudes) vary in terms of the introduced asymmetry is conducted. In particular, avoided crossings occur between quasi-sausage and quasi-kink surface modes, allowing modes to adopt different properties for different parameters in the external region.

  1. Exact image theory for the slab problem

    NASA Technical Reports Server (NTRS)

    Lindell, I. V.

    1988-01-01

    Exact image theory, recently introduced for the exact solution of problems involving homogeneous half spaces and microstrip-like geometries, is developed here for the problem of homogeneous slab of isotropic dielectric and/or magnetic material in free space. Expressions for image sources, creating the exact reflected and transmitted fields, are given and their numerical evaluation is demonstrated. Nonradiating modes, guided by the slab and responsible for the loss of convergence of the image functions, are considered and extracted. The theory can be applied, for example, in an analysis of finite ground planes in microstrip antenna structures.

  2. High-Frequency Alternating-Crossed-Field Gel Electrophoresis WithNeutral or Slightly Charged Interpenetrating Networks to Improve DNASeparation

    SciTech Connect

    Boyd, B.; Prausnitz, J.; Blanch, H.

    1998-07-01

    Toward improving DNA separations, this work reports theeffects of high-frequency square-wave AC fields superimposedperpendicular to the direct current (DC) separation field on DNAmigration in both polyacrylamide-based interpenetrating networks (IPNs)and in agarose networks. Compared to standard polyacrylamide gels, IPNsallow the separation of larger DNA (9000 bp vs. 5000 bp at 5 V/cm). Innovel polyacrylamide-based IPNs, an alternating current (AC) field of 5Hz increased the maximum DNA size separable. This effect was extended tolarger DNA sizes with increasing electric-field strength up to andapparently beyond the power supply-limited maximum electric-fieldstrength of 48 V/cm. The orthogonal AC field also increased mobility.These two results combine to yield a reduction in separation time of upto a factor of 20 in novel polyacrylamide-based IPNs. When negativelycharged acrylic-acid groups were incorporated into the IPNs, the use ofthe AC field changed the DNA-network interaction, which altered the sizedependence of DNA mobility. In agarose gels, an AC field of 50 Hzincreased the size range separable; however, there was no increase in DNAmobility. There was no change in size dependence of mobility in an ACfield when the number of charged groups in the agarose network wasincreased. Based on results in the literature, possible mechanisms wereexamined for the effects of the AC field on DNA separation.

  3. Diversity of Proteolytic Clostridium botulinum Strains, Determined by a Pulsed-Field Gel Electrophoresis Approach

    PubMed Central

    Nevas, Mari; Lindström, Miia; Hielm, Sebastian; Björkroth, K. Johanna; Peck, Michael W.; Korkeala, Hannu

    2005-01-01

    Pulsed-field gel electrophoresis (PFGE) was applied to the study of the similarity of 55 strains of proteolytic Clostridium botulinum (C. botulinum group I) types A, AB, B, and F. Rare-cutting restriction enzymes ApaI, AscI, MluI, NruI, PmeI, RsrII, SacII, SmaI, and XhoI were tested for their suitability for the cleavage of DNA of five proteolytic C. botulinum strains. Of these enzymes, SacII, followed by SmaI and XhoI, produced the most convenient number of fragments for genetic typing and were selected for analysis of the 55 strains. The proteolytic C. botulinum species was found to be heterogeneous. In the majority of cases, PFGE enabled discrimination between individual strains of proteolytic C. botulinum types A and B. The different toxin types were discriminated at an 86% similarity level with both SacII and SmaI and at an 83% similarity level with XhoI. Despite the high heterogeneity, three clusters at a 95% similarity level consisting of more than three strains of different origin were noted. The strains of types A and B showed higher diversity than the type F organisms which formed a single cluster. According to this survey, PFGE is to be considered a useful tool for molecular epidemiological analysis of proteolytic C. botulinum types A and B. However, epidemiological conclusions based on PFGE data only should be made with discretion, since highly similar PFGE patterns were noticed, especially within the type B strains. PMID:15746333

  4. Diversity of proteolytic Clostridium botulinum strains, determined by a pulsed-field gel electrophoresis approach.

    PubMed

    Nevas, Mari; Lindström, Miia; Hielm, Sebastian; Björkroth, K Johanna; Peck, Michael W; Korkeala, Hannu

    2005-03-01

    Pulsed-field gel electrophoresis (PFGE) was applied to the study of the similarity of 55 strains of proteolytic Clostridium botulinum (C. botulinum group I) types A, AB, B, and F. Rare-cutting restriction enzymes ApaI, AscI, MluI, NruI, PmeI, RsrII, SacII, SmaI, and XhoI were tested for their suitability for the cleavage of DNA of five proteolytic C. botulinum strains. Of these enzymes, SacII, followed by SmaI and XhoI, produced the most convenient number of fragments for genetic typing and were selected for analysis of the 55 strains. The proteolytic C. botulinum species was found to be heterogeneous. In the majority of cases, PFGE enabled discrimination between individual strains of proteolytic C. botulinum types A and B. The different toxin types were discriminated at an 86% similarity level with both SacII and SmaI and at an 83% similarity level with XhoI. Despite the high heterogeneity, three clusters at a 95% similarity level consisting of more than three strains of different origin were noted. The strains of types A and B showed higher diversity than the type F organisms which formed a single cluster. According to this survey, PFGE is to be considered a useful tool for molecular epidemiological analysis of proteolytic C. botulinum types A and B. However, epidemiological conclusions based on PFGE data only should be made with discretion, since highly similar PFGE patterns were noticed, especially within the type B strains.

  5. [Analysis of thermostable direct hemolysin-producing Vibrio parahaemolyticus by pulsed-field gel electrophoresis].

    PubMed

    Kubota, T

    1999-10-01

    We investigated the source of thermostable direct hemolysin-producing Vibrio parahaemolticus infection (positive strains) that causes Vibrio parahaemolticus food poisoning. We investigated the coincidence rate of serotypes isolated from samples of sea water used to store clams in 1998 in Shizuoka Prefecture, and those isolated from patients who developed symptoms of food poisoning in the same year. Furthermore, using isolated types 03:K6 and 04:K68, We treated the chromosomal DNA with a restriction endonuclease Sfi I and compared the digestion patterns by pulsed-field gel electrophoresis (PFGE). (1) Of 225 samples of sea water used to store clams, the thermostable direct hemolysin gene was detected in 23 samples by the PCR method. Among these 23 samples, 10 positive strains were detected in five samples. The serotypes of these productive strains were 03:K6 (four isolates), 03:K37 (two isolates), 04:K8 (one isolate), 04:K9 (two isolates) and 04:K68 (one isolate). (2) The five serotypes isolated from the sea water samples were consistent with those of 17 of 17 cases (100%) of which serotypes could be confirmed by this institute and 94 of 100 strains (94%) isolated in a large scale outbreak of food poisoning that occurred in the same year. (3) Using types 03:K6 and 04:K68 isolated from sea water samples and patients, chromosomal DNA were compared among the isolates by PFGE. As a result, of 28 isolates examined, 26 isolates showed a similar electrophoretic migration pattern between the sources and serotypes. The etiologic strains for Vibrio parahaemolyticus food poisoning appear to have been derived from the environment. Regarding the findings that types 03:K6 and 04:K68 showed a similar electrophoretic migration pattern, these types can be considered to belong to the same PFGE type.

  6. Multilocus Sequence Typing Scheme versus Pulsed-Field Gel Electrophoresis for Typing Mycobacterium abscessus Isolates

    PubMed Central

    Machado, Gabriel Esquitini; Matsumoto, Cristianne Kayoko; Chimara, Erica; Duarte, Rafael da Silva; de Freitas, Denise; Palaci, Moises; Hadad, David Jamil; Lima, Karla Valéria Batista; Lopes, Maria Luiza; Ramos, Jesus Pais; Campos, Carlos Eduardo; Caldas, Paulo César; Heym, Beate

    2014-01-01

    Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus. PMID:24899019

  7. Piled-Slab Searches

    DTIC Science & Technology

    2006-12-01

    tinuously as one moves away from the origin (Figure 1). Because such a search is both strategically optimal and locally random, we will refer to it as SOLR ...approximating the inverted cup with a solid composed of n piled slabs. The resulting detection proba- bility will, of course, be smaller than the SOLR ...total effort density in the annulus between Ri−1 and Ri (Figure 2). The total Figure 1. The inverted SOLR cup has the greatest search effort density at

  8. Carbon dioxide slab laser

    SciTech Connect

    Tulip, J.

    1988-01-12

    A gas slab laser is described comprising: first and second elongated electrodes each including a planar light reflecting surface disposed so as to form a light guide only in a plane perpendicular to the planar surface and to define a gas discharge gap therebetween; a laser gas disposed in the gap; and means for applying a radio frequency current between the first and second electrodes to establish a laser-exciting discharge in the laser gas.

  9. First clinical isolates of Cronobacter spp. (Enterobacter sakazakii) in Argentina: characterization and subtyping by pulsed-field gel electrophoresis.

    PubMed

    Asato, Valeria C; Vilches, Viviana E; Pineda, María G; Casanueva, Enrique; Cane, Alejandro; Moroni, Mirian P; Brengi, Silvina P; Pichel, Mariana G

    2013-01-01

    Cronobacter species are opportunistic pathogens associated with severe infections in neonates and immunocompromised infants. From January 2009 through September 2010, two cases of neonatal infections associated with Cronobacter malonaticus and one case associated with Cronobacter sakazakii, two of them fatal, were reported in the same hospital. These are the first clinical isolates of Cronobacter spp. in Argentina. The objective of this work was to characterize and subtype clinical isolates of Cronobacter spp. in neonate patients, as well as to establish the genetic relationship between these isolates and the foodborne isolates previously identified in the country. Pulsed-field gel electrophoresis analysis showed a genetic relationship between the C. malonaticus isolates from two patients. Different results were found when the pulsed-field gel electrophoresis patterns of clinical isolates were compared with those deposited in the National Database of Cronobacter spp.

  10. Interaction of an ion bunch with a plasma slab

    SciTech Connect

    Krasovitskiy, V. B.; Turikov, V. A.

    2016-11-15

    Charge neutralization of a short ion bunch passing through a plasma slab is studied by means of numerical simulation. It is shown that a fraction of plasma electrons are trapped by the bunch under the action of the collective charge separation field. The accelerated electrons generated in this process excite beam−plasma instability, thereby violating the trapping conditions. The process of electron trapping is also strongly affected by the high-frequency electric field caused by plasma oscillations at the slab boundaries. It is examined how the degree of charge neutralization depends on the parameters of the bunch and plasma slab.

  11. On the parametric transparency of a magnetized plasma slab

    NASA Astrophysics Data System (ADS)

    Gradov, O. M.; Stenflo, L.

    1981-06-01

    A mechanism is proposed for the nonlinear transparency of a dense magnetized plasma slab to electromagnetic radiation. The mechanism is based on the parametric excitation of surface waves in a cold magnetized plasma slab. It is shown that a significant proportion of incident radiation will be able to penetrate the slab due to saturation caused by the nonlinear resonant absorption of the surface waves generated. The mechanism also predicts the presence of transmitted radiation at a frequency less than that of the incident radiation in a direction parallel to the incident pump-wave electric field, the external constant magnetic field and the plasma layer.

  12. The use of biphasic linear ramped pulsed field gel electrophoresis to quantify DNA damage based on fragment size distribution

    SciTech Connect

    Lawrence, T.S.; Normolle, D.P.; Davis, M.A.; Maybaum, J.

    1993-10-20

    The development of biphasic linear pulse ramping gel electrophoresis has permitted resolution of DNA fragments from 200 Kbp to 6 Mbp in a single gel. We used this technique to measure radiation-induced DNA damage based on fragment size. Human colon cancer cells (HT29 and LS174T) and Chinese hamster ovary cells were embedded in agarose, deproteinized, irradiated with 5-80 Gy, and assessed for DNA double strand breakage using pulsed field gel electrophoresis. The frequency of DNA double strand breakage determined using a previously published method was compared to the breakage frequency calculated using the fragment size distribution. Both methods produced similar estimates for breakage frequency of approximately 5 {times} 10{sup {minus}9} breaks Gy{sup {minus}1} bp{sup {minus}1}. These findings suggest that biphasic linear pulse ramping gel electrophoresis can yield a quantitative estimate of DNA fragment distribution resulting from irradiation. The ability to quantify the distribution of DNA fragment sizes produced by irradiation should yield information concerning the mechanisms of both DNA double strand break induction and repair. 16 refs., 5 figs.

  13. Slab-geometry Nd:glass laser performance studies

    NASA Technical Reports Server (NTRS)

    Eggleston, J. M.; Kane, T. J.; Byer, R. L.; Unternahrer, J.

    1982-01-01

    It is noted that slab-geometry solid-state lasers potentially provide significant performance improvements relative to conventional rod-geometry lasers. Experimental measurements that use an Nd:glass test-bed slab laser are presented. A comparison is made between the results and computer-model predictions of the slab-geometry approach. The computer model calculates and displays the temperature and stress fields in the slab, and on the basis of these predicts birefringence and index-of-refraction distributions. The effect that these distributions have on optical propagation is determined in a polarization-sensitive ray-tracing section of the model. Calculations are also made of stress-induced surface curvature and the resulting focusing effects. The measurements are found to be in good agreement with the computer-model predictions. It is concluded that the slab configuration offers significant laser-performance advantages in comparison with the traditional rod-laser geometry.

  14. Slab-geometry Nd:glass laser performance studies

    NASA Technical Reports Server (NTRS)

    Eggleston, J. M.; Kane, T. J.; Byer, R. L.; Unternahrer, J.

    1982-01-01

    It is noted that slab-geometry solid-state lasers potentially provide significant performance improvements relative to conventional rod-geometry lasers. Experimental measurements that use an Nd:glass test-bed slab laser are presented. A comparison is made between the results and computer-model predictions of the slab-geometry approach. The computer model calculates and displays the temperature and stress fields in the slab, and on the basis of these predicts birefringence and index-of-refraction distributions. The effect that these distributions have on optical propagation is determined in a polarization-sensitive ray-tracing section of the model. Calculations are also made of stress-induced surface curvature and the resulting focusing effects. The measurements are found to be in good agreement with the computer-model predictions. It is concluded that the slab configuration offers significant laser-performance advantages in comparison with the traditional rod-laser geometry.

  15. Electromagnetic Tunneling and Resonances in Pseudochiral Omega Slabs.

    PubMed

    Razzaz, Faroq; Alkanhal, Majeed A S

    2017-02-06

    This paper presents theoretical investigation of the electromagnetic wave tunneling and anomalous transmission around the trapped modes in a pseudochiral omega slab. The dispersion relation, the conditions of the trapped modes, and the evanescent wave coupling and tunneling in two different reciprocal pseudochiral omega slab structures are derived. The Berreman's matrix method is applied to obtain the transmission coefficients across the pseudochiral omega slab. When the structure is perturbed, a resonance phenomenon is detected around the trapped modes. This resonance results in transmission anomalies (total transmission and total reflection) and dramatic field amplifications around the trapped modes. The number of the discrete trapped modes and then the resonance frequencies are prescribed by the parameters of the pseudochiral omega slab such as the value of the omega parameter and its orientation and the slab thickness.

  16. Electromagnetic Tunneling and Resonances in Pseudochiral Omega Slabs

    PubMed Central

    Razzaz, Faroq; Alkanhal, Majeed A. S.

    2017-01-01

    This paper presents theoretical investigation of the electromagnetic wave tunneling and anomalous transmission around the trapped modes in a pseudochiral omega slab. The dispersion relation, the conditions of the trapped modes, and the evanescent wave coupling and tunneling in two different reciprocal pseudochiral omega slab structures are derived. The Berreman’s matrix method is applied to obtain the transmission coefficients across the pseudochiral omega slab. When the structure is perturbed, a resonance phenomenon is detected around the trapped modes. This resonance results in transmission anomalies (total transmission and total reflection) and dramatic field amplifications around the trapped modes. The number of the discrete trapped modes and then the resonance frequencies are prescribed by the parameters of the pseudochiral omega slab such as the value of the omega parameter and its orientation and the slab thickness. PMID:28165058

  17. Interior view of groundfloor porch showing exposed concrete floor slab ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Interior view of ground-floor porch showing exposed concrete floor slab system, facing west. - Albrook Air Force Station, Field Officer's Quarters, West side of Dargue Avenue Circle, Balboa, Former Panama Canal Zone, CZ

  18. Pulsed field gel electrophoresis analysis of Vibrio cholerae isolates in southern Thailand.

    PubMed

    Kondo, Sumalee; Trakulsomboon, Suwanna; Trakoolsomboon, Suwanna; Smittipat, Nat; Juthayothin, Tada; Palittapongarnpim, Prasit

    2010-03-01

    Forty isolates of V. cholorae O1, O139 and non-O1/non-O139 collected from outbreaks in Songkhla and Phuket Provinces of southern Thailand during 1999-2001 and sporadic cases from different regions of Thailand during 1993-2002 were characterized using pulsed field gel electrophoresis (PFGE). Digestion of chromosomal DNA of the V cholerae isolates with restriction endonuclease NotI, followed by PFGE, generated 10 distinct restriction endonuclease analysis patterns consisting of 8 to 13 bands, ranging in size from 78 to 394 kb. PFGE patterns of O1 Inaba strains from the outbreak in Songkhla were identical (P1) except one isolate (P3). The O1 Inaba outbreak strains from Phuket in the same period belonged to P2 pattern, whereas the O1 Ogawa strain from the outbreak in Phuket isolated in 1999 was of P7 pattern. These patterns of O1 Inaba and Ogawa strains were slightly different suggesting that the isolates were epidemiologically related and therefore the outbreaks were likely due to the same V cholerae clone. Isolates of V cholerae O1 Inaba from sporadic cases in the neighboring area (e.g., Pattani Province) in a similar period of time of the outbreak in Songkhla Province had very similar patterns, with only one single band different from those of the outbreak isolates. This indicates that the Inaba strains isolated from Songkhla Province during the 2001 cholera outbreak belonging to P1 pattern had not spread to other regions in 2001 and 2002. On the otherhand, the sporadic isolates collected from other regions of Thailand were quite distinct from the outbreak isolates in Songkhla Province, especially those from Chaiyaphum and Chaing Mai Provinces, which belonged to P5 and P6 pattern, respectively. Isolates of V cholerae O139 and non-O1/non-O139 gave different patterns from that of V. cholerae O1. This study shows that the PFGE technique is markedly advantageous in distinguishing strains of V cholerae isolates leading to insightful detailed charateristics of these

  19. Determination of the Genetic Diversity of Different Bioluminescent Bacteria by Pulsed-Field Gel Electrophoresis (PFGE)

    PubMed Central

    Ersoy Omeroglu, Esra

    2015-01-01

    Background: There are 4 different genera (i.e. Vibrio, Aliivibrio, Photobacterium, and Shewanella) in the new classification of bioluminescent bacteria. The mechanism of bioluminescence has yet to be fully elucidated. Therefore, the determination of physiological and genetic characteristics of bioluminescent bacteria isolated from different sources is very important. Pulsed-Field Gel Electrophoresis (PFGE) has the highest discriminatory power among the different molecular typing methods for the investigation of the clonal relationships between bacteria. For the PFGE analysis of bioluminescent bacteria, the NotI-HF™ is the method of choice among the restriction enzymes. Objectives: The present study aimed to determine genetic relatedness via PFGE in 41 bioluminescent bacteria (belonging to 10 different species) isolated and identified from various marine sources. Materials and Methods: Different bioluminescent bacteria (i.e. Vibrio gigantis, V. azureus, V. harveyi, V. lentus, V. crassostreae, V. orientalis, Aliivibrio logei, A. fischeri, Shewanella woodyi, and Photobacterium kishitanii) were analyzed by PFGE using the NotI-HF™ restriction enzyme. The whole DNA of the strains embedded into the agarose plugs was digested with enzyme at 37°C for 30 minutes. CHEF-Mapper PFGE system was used for electrophoresis and band profile of the strains for the NotI-HF™ restriction enzyme were analyzed by Bio-Profil-1D++ software (Vilber Lourmat) at 10% homology coefficient. Results: Although all experiments were performed three times, four of forty-one bioluminescent strains (V. gigantis E-16, H-16 and S3W46 strains and A. fischeri E-4 strain) could not be typed by PFGE technique with NotI-HF™ enzyme. While only two strains (V. crassostreae H-12 and H-19 strains) were exhibiting same band pattern profiles (100% genome homology), thirty-six different PFGE band patterns were obtained. Pattern homologies changed between 66% - 92%, 73% - 83% and 49% - 100% for V. gigantis, V

  20. Molecular Typing of Vibrio cholerae O1 Isolates from Thailand by Pulsed-field Gel Electrophoresis

    PubMed Central

    Tapchaisri, Pramuan; Na-Ubol, Mathukorn; Tiyasuttipan, Watcharee; Chaiyaroj, Sansanee C.; Yamasaki, Shinji; Wongsaroj, Thitima; Hayashi, Hideo; Nair, G. Balakrish; Chongsa-Nguan, Manas; Kurazono, Hisao; Chaicumpa, Wanpen

    2008-01-01

    The aim of the present study was to genotypically characterize Vibrio cholerae strains isolated from cholera patients in various provinces of Thailand. Two hundred and forty V. cholerae O1 strains, isolated from patients with cholera during two outbreaks, i.e. March 1999–April 2000 and December 2001–February 2002, in Thailand, were genotypically characterized by NotI digestion and pulsed-field gel electrophoresis (PFGE). In total, 17 PFGE banding patterns were found and grouped into four Dice-coefficient clusters (PF-I to PF-IV). The patterns of V. cholerae O1, El Tor reference strains from Australia, Peru, Romania, and the United States were different from the patterns of reference isolates from Asian countries, such as Bangladesh, India, and Thailand, indicating a close genetic relationship or clonal origin of the isolates in the same geographical region. The Asian reference strains, regardless of their biotypes and serogroups (classical O1, El Tor O1, O139, or O151), showed a genetic resemblance, but had different patterns from the strains collected during the two outbreaks in Thailand. Of 200 Ogawa strains collected during the first outbreak in Thailand, two patterns (clones)—PF-I and PF-II—predominated, while other isolates caused sporadic cases and were grouped together as pattern PF-III. PF-II also predominated during the second outbreak, but none of the 40 isolates (39 Inaba and 1 Ogawa) of the second outbreak had the pattern PF-I; a minority showed a new pattern—PF-IV, and others caused single cases, but were not groupable. In summary, this study documented the sustained appearance of the pathogenic V. cholerae O1 clone PF-II, the disappearance of clones PF-I and PF-III, and the emergence of new pathogenic clones during the two outbreaks of cholera. Data of the study on molecular characteristics of indigenous V. cholerae clinical isolates have public-health implications, not only for epidemic tracing of existing strains but also for the

  1. Response characteristics of a viscoelastic gel under the co-action of sound waves and an electric field

    NASA Astrophysics Data System (ADS)

    Tang, Hong; Zhao, Xiaopeng; Wang, Baoxiang; Zhao, Yan

    2006-02-01

    We design a flexible sound tunable sandwiched panel structure, which is composed of a nanoelectrorheological gel layer and two conductive rubber sheets, and experimentally investigate the tunable behaviors of the sound transmitted through the panel. For the frequency range of 380-500 Hz the transmitted sound pressure level (SPL) decreases with the electric field strength Ee, while at about 550-650 Hz the SPL increases with Ee. Within 500-550 Hz a hump appears and the hump apex shifts in the high frequency direction with increase of Ee. Besides this, the phase angle of the transmitted sound wave changes with Ee within these frequency ranges. The weight fraction of particles in the electrorheological gels also influences these observed tunable characteristics. The theoretical calculation based on a vibration-radiation model agrees with the experimental results, qualitatively. It is revealed that the electric field induced viscoelasticity change in the electrorheological gel and hence the vibration-radiation variation on the sandwiched panel is the origin of the phenomenon. The flexible composite electrorheological panel could be used in sound sensitive artificial skins or sound tunable actuators and has potential for use in robots and intelligent structures and systems.

  2. Comparison between pulsed-field and constant-field gel electrophoresis for measurement of DNA double-strand breaks in irradiated Chinese hamster ovary cells.

    PubMed

    Wlodek, D; Banáth, J; Olive, P L

    1991-11-01

    Pulsed-field gel electrophoresis (PFGE) is one of the most sensitive methods for detecting DNA double-strand breaks in mammalian cells. However, it has been observed that constant-field gel electrophoresis (CFGE), when optimized, can detect breaks with equal efficiency. The migration of DNA from the well and the separation of DNA molecules according to size appear to be different processes; only the latter requires the application of PFGE. CFGE is very sensitive and can detect DNA damage produced by less than 5 Gy of radiation. Low voltage (ca. 0.6 V/cm) during electrophoresis appears to be essential for the migration of the largest fraction of DNA from the agarose plug containing the cells; the electrophoresis run time, cell density in the plug, agarose concentration, nature of detergent and extent of radiolabelling are less important. It is concluded that CFGE is equally sensitive but more rapid and economical than PFGE for the measurement of DNA damage.

  3. Untangling Slab Dynamics Using 3-D Numerical and Analytical Models

    NASA Astrophysics Data System (ADS)

    Holt, A. F.; Royden, L.; Becker, T. W.

    2016-12-01

    Increasingly sophisticated numerical models have enabled us to make significant strides in identifying the key controls on how subducting slabs deform. For example, 3-D models have demonstrated that subducting plate width, and the related strength of toroidal flow around the plate edge, exerts a strong control on both the curvature and the rate of migration of the trench. However, the results of numerical subduction models can be difficult to interpret, and many first order dynamics issues remain at least partially unresolved. Such issues include the dominant controls on trench migration, the interdependence of asthenospheric pressure and slab dynamics, and how nearby slabs influence each other's dynamics. We augment 3-D, dynamically evolving finite element models with simple, analytical force-balance models to distill the physics associated with subduction into more manageable parts. We demonstrate that for single, isolated subducting slabs much of the complexity of our fully numerical models can be encapsulated by simple analytical expressions. Rates of subduction and slab dip correlate strongly with the asthenospheric pressure difference across the subducting slab. For double subduction, an additional slab gives rise to more complex mantle pressure and flow fields, and significantly extends the range of plate kinematics (e.g., convergence rate, trench migration rate) beyond those present in single slab models. Despite these additional complexities, we show that much of the dynamics of such multi-slab systems can be understood using the physics illuminated by our single slab study, and that a force-balance method can be used to relate intra-plate stress to viscous pressure in the asthenosphere and coupling forces at plate boundaries. This method has promise for rapid modeling of large systems of subduction zones on a global scale.

  4. Tunneling field effect transistor integrated with black phosphorus-MoS2 junction and ion gel dielectric

    NASA Astrophysics Data System (ADS)

    Xu, Jiao; Jia, Jingyuan; Lai, Shen; Ju, Jaehyuk; Lee, Sungjoo

    2017-01-01

    We report an interband tunneling field effect transistor (TFET) integrated with a Black Phosphorus (BP)-MoS2 junction and ion gel as a top gate dielectric. The operation of the BP-MOS2 TFET is based on the modulation of the energy band alignment of the BP-MoS2 junction with electrostatic gating control on the MoS2 channel from the top gate through the ion gel dielectric and the supply of tunneling carriers from the BP source, which is degenerately doped with ion gel. The obtained subthreshold swing of the BP-MoS2 TFET reached 65 mV/dec at room temperature and 51 mV/dec at 160 K, maintaining low SS values in more than 2 orders of drain current range. The demonstrated interband TFET based on the BP-MoS2 junction shows significant promise for further application to a new class of two-dimensional functional devices.

  5. SUB-SLAB PROBE INSTALLATION

    EPA Science Inventory

    Sub-slab sampling has become an integral part of vapor intrusion investigations. It is now recommended in guidance documents developed by EPA and most states. A method for sub-slab probe installation was devised in 2002, presented at conferences through 2005, and finally docume...

  6. Transmission of Citrobacter koseri from mother to infant documented by ribotyping and pulsed-field gel electrophoresis.

    PubMed

    Papasian, C J; Kinney, J; Coffman, S; Hollis, R J; Pfaller, M A

    1996-10-01

    We describe a case in which Citrobacter koseri (formerly C. diversus) was transmitted from a pregnant mother with chorioamnionitis and bacteremia to her infant who was bacteremic at birth and in apparent septic shock. Two highly discriminating molecular methods, ribotyping and pulsed field gel electrophoresis, were used to examine restriction fragment length polymorphisms within the genomic DNA of maternal and infant isolates. Both techniques identified the maternal and infant isolates as the same strain, distinct from epidemiologically unrelated controls, thus confirming their common origin.

  7. The association of serotype and pulsed-field gel electrophoresis genotype in isolates of Streptococcus pneumoniae isolated in Israel.

    PubMed

    Bar-Meir, M; Naaman, G; Assous, M; Korenman, Z; Valinsky, L; Picard, E

    2015-05-01

    The relationship between Streptococcus pneumoniae isolates causing invasive infections in children admitted to a single center in central Israel was examined by pulsed-field gel electrophoresis (PFGE) and serotyping. Although there was a close correlation between serotype and PFGE clone, the genetic diversity varied by serotype, with some genotypes comprising multiple serotypes. Additionally, clones C and D were associated with higher penicillin minimum inhibitory concentrations. Serotyping alone may be insufficient for epidemiological mapping of pneumococcal isolates in the era of pneumococcal conjugate polysaccharide vaccines.

  8. DNA fingerprinting by pulsed-field gel electrophoresis to investigate a nosocomial pneumonia caused by Legionella bozemanii serogroup 1.

    PubMed Central

    Lück, P C; Helbig, J H; Hagedorn, H J; Ehret, W

    1995-01-01

    We typed 18 isolates of Legionella bozemanii obtained from clinical and environmental sources by pulsed-field gel electrophoresis. Each of the unrelated strains showed individual restriction patterns of the genomic DNA when either the SfiI or NotI restriction enzyme was used. One strain isolated from a patient with nosocomial legionellosis and two strains from the corresponding hospital water supply were indistinguishable, arguing for a transmission of L. bozemanii from the water supply to the patient. In conclusion, macrorestriction analysis is a valuable tool for studies of the molecular epidemiology of L. bozemanii. PMID:7618888

  9. One-day pulsed-field gel electrophoresis protocol for rapid determination of emetic Bacillus cereus isolates.

    PubMed

    Kaminska, Paulina S; Fiedoruk, Krzysztof; Jankowska, Dominika; Mahillon, Jacques; Nowosad, Karol; Drewicka, Ewa; Zambrzycka, Monika; Swiecicka, Izabela

    2015-04-01

    Bacillus cereus, the Gram-positive and spore-forming ubiquitous bacterium, may cause emesis as the result of food intoxication with cereulide, a heat-stable emetic toxin. Rapid determination of cereulide-positive B. cereus isolates is of highest importance due to consequences of this intoxication for human health and life. Here we present a 1-day pulsed-field gel electrophoresis for emetic B. cereus isolates, which allows rapid and efficient determination of their genomic relatedness and helps determining the source of intoxication in case of outbreaks caused by these bacilli.

  10. Seismic moment release during slab rupture beneath the Banda Sea

    NASA Astrophysics Data System (ADS)

    Sandiford, Mike

    2008-08-01

    The highest intermediate depth moment release rates in Indonesia occur in the slab beneath the largely submerged segment of the Banda arc in the Banda Sea to the east of Roma, termed the Damar Zone. The most active, western-part of this zone is characterized by downdip extension, with moment release rates (~1018 Nm yr-1 per 50 km strike length) implying the slab is stretching at ~10-14 s-1 consistent with near complete slab decoupling across the 100-200 km depth range. Differential vertical stretching along the length of the Damar Zone is consistent with a slab rupture front at ~100-200 km depth beneath Roma propagating eastwards at ~100 km Myr-1. Complexities in the slab deformation field are revealed by a narrow zone of anomalous in-plane P-axis trends beneath Damar, where subhorizontal constriction suggests extreme stress concentrations ~100 km ahead of the slab rupture front. Such stress concentrations may explain the anomalously deep ocean gateways in this region, in which case ongoing slab rupture may have played a key role in modulating the Indonesian throughflow in the Banda Sea over the last few million years.

  11. Preparation of α-mannoside hydrogel and electrical detection of saccharide-protein interactions using the smart gel-modified gate field effect transistor

    NASA Astrophysics Data System (ADS)

    Maeda, Yasuhiro; Matsumoto, Akira; Miura, Yoshiko; Miyahara, Yuji

    2012-02-01

    The purpose of this study was to detect saccharide-protein interaction capitalizing on the gel-modified field effect transistor [FET]. A lectin-sensitive polymer gel that undergoes volume changes in response to the formation of molecular complex between 'pendant' carbohydrate and a 'target' lectin concanavalin A [Con A] was synthesized. It was revealed that direction and magnitude of the gel response (swelling or deswelling) could be readily designed depending on composition and network density of the gel. The Con A-sensitive polymer gel has shown the ability to transduce the detection of saccharide-protein interactions into electrical signals for FET. PACS: 87.85.jf, bio-based materials

  12. Leaky unstable modes and electromagnetic radiation amplification by an anisotropic plasma slab

    SciTech Connect

    Vagin, K. Yu. Uryupin, S. A.

    2015-09-15

    The interaction between electromagnetic radiation and a photoionized plasma slab with an anisotropic electron velocity distribution is studied. It is shown that the fields of leaky modes are amplified due to the development of aperiodic instability in the slab, which leads to an increase in both the reflected and transmitted fields. The transmitted field can significantly increase only if the slab thickness does not exceed the ratio of the speed of light to the electron plasma frequency, whereas there is no upper bound on the slab thickness for the reflected signal to be amplified.

  13. Characterization of multidrug-resistant Escherichia coli by antimicrobial resistance profiles, plasmid replicon typing, and pulsed-field gel electrophoresis.

    PubMed

    Lindsey, Rebecca L; Frye, Jonathan G; Thitaram, Sutawee N; Meinersmann, Richard J; Fedorka-Cray, Paula J; Englen, Mark D

    2011-06-01

    The objective of this study was to examine the distribution of multidrug resistance in Escherichia coli in relation to plasmid replicon types, animal sources, and genotypes. E. coli isolates (n = 35) from seven different animal sources were selected and tested for susceptibility to 15 antimicrobials; pulsed-field gel electrophoresis was used to determine genetic relationships among the E. coli isolates. Plasmid types based on their incompatibility (Inc) replicon types were determined, and linkage disequilibrium analysis was performed for antimicrobial resistance profiles, replicon types, and animal source. A high degree of genotypic diversity was observed: 34 different pulsed-field gel electrophoresis types among the 35 isolates examined. Twelve different plasmid Inc types were detected, and all isolates carried at least one replicon type. IncF (n = 25; 71.4%) and IncFIB (n = 19; 54.3%) were the most common replicon types identified. Chloramphenicol resistance was significantly linked with four Inc types (A/C, FIIA, F, and Y), and amoxicillin/clavulanic acid was linked with three Inc types (B/O, P and Y). Resistance to any other antimicrobial was linked to two or fewer replicon types. The isolate source was linked with resistance to seven antimicrobials and IncI1. We conclude that commensal E. coli from animal sources are highly variable genotypically and are reservoirs of a diverse array of plasmids carrying antimicrobial resistance.

  14. Hyper alginate gel microbead formation by molecular diffusion at the hydrogel/droplet interface.

    PubMed

    Hirama, Hirotada; Kambe, Taisuke; Aketagawa, Kyouhei; Ota, Taku; Moriguchi, Hiroyuki; Torii, Toru

    2013-01-15

    We report a simple method for forming monodispersed, uniformly shaped gel microbeads with precisely controlled sizes. The basis of our method is the placement of monodispersed sodium alginate droplets, formed by a microfluidic device, on an agarose slab gel containing a high-osmotic-pressure gelation agent (CaCl(2) aq.): (1) the droplets are cross-linked (gelated) due to the diffusion of the gelation agent from the agarose slab gel to the sodium alginate droplets and (2) the droplets simultaneously shrink to a fraction of their original size (<100 μm in diameter) due to the diffusion of water molecules from the sodium alginate droplets to the agarose slab gel. We verified the mass transfer mechanism between the droplet and the agarose slab gel. This method circumvents the limitations of gel microbead formation, such as the need to prepare microchannels of various sizes, microchannel clogging, and the deformation of the produced gel microbeads.

  15. General eigenstates of Maxwell's equations in a two-constituent composite medium and their application to a calculation of the local electric field in a flat-slab microstructure

    NASA Astrophysics Data System (ADS)

    Farhi, Asaf; Bergman, David J.

    2016-09-01

    An exact calculation of the local electric field E(r) is described for the case of an external current or plane wave source in a setup of an E1, μ1 slab in an E2, μ2 medium. For this purpose we first calculate all the general eigenstates of the full Maxwell equations. These eigenstates are then used to develop an exact expansion for the physical values of E(r) in the system characterized by physical values of E1, E2, μ1, and μ2. Results are compared with those of a previous calculation of the local field where μ = 1 everywhere. Numerical results are shown for the eigenvalues in practically important configurations where attaining an optical image with sub-wavelength resolution has practical significance. We show that the k >> k2 components are enhanced for the TM field when E1/E2 = -1 and for the TE field when μ1/μ2 = -1 where the enhancement of the evanescent waves starts from lower k values as we approach a setup with both E1/E2 = -1 and μ1/μ2 = -1. We also show that the eigenfunctions for the setup where μ = 1 everywhere correspond to configurations of 3D phased arrays.

  16. The history and principles of chemical dosimetry for 3-D radiation fields: gels, polymers and plastics.

    PubMed

    Doran, Simon J

    2009-03-01

    Over recent decades, modern protocols of external beam radiotherapy have been developed that involve very steep dose gradients and are thus extremely sensitive to errors in treatment delivery. A recent credentialling study by the Radiological Physics Center at the MD Anderson Cancer Center (Texas, USA) has noted potentially significant inaccuracies in test treatments at a variety of institutions. 3-D radiation dosimetry (often referred to as "gel dosimetry") may have an important role in commissioning new treatment protocols, to help prevent this type of error. This article discusses the various techniques of 3-D radiation dosimetry, with a focus on the types of radiosensitive samples used and on the optical computed tomography readout technique.

  17. The impact of slab dip variations, gaps and rollback on mantle wedge flow: insights from fluids experiments

    NASA Astrophysics Data System (ADS)

    MacDougall, Julia G.; Kincaid, Chris; Szwaja, Sara; Fischer, Karen M.

    2014-05-01

    Observed seismic anisotropy and geochemical anomalies indicate the presence of 3-D flow around and above subducting slabs. To investigate how slab geometry and velocity affect mantle flow, we conducted a set of experiments using a subduction apparatus in a fluid-filled tank. Our models comprise two independently adjustable, continuous belts to represent discrete sections of subducting slabs that kinematically drive flow in the surrounding glucose syrup that represents the upper mantle. We analyse how slab dip (ranging from 30° to 80°), slab dip difference between slab segments (ranging from 20° to 50°), rates of subduction (4-8 cm yr-1) and slab/trench rollback (0-3 cm yr-1) affect mantle flow. Whiskers were used to approximate mineral alignment induced by the flow, as well as to predict directions of seismic anisotropy. We find that dip variations between slab segments generate 3-D flow in the mantle wedge, where the path lines of trenchward moving mantle material above the slab are deflected towards the slab segment with the shallower dip. The degree of path line deflection increases as the difference in slab dip between the segments increases, and, for a fixed dip difference, as slab dip decreases. In cases of slab rollback and large slab dip differences, we observe intrusion of subslab material through the gap and into the wedge. Flow through the gap remains largely horizontal before eventual downward entrainment. Whisker alignment in the wedge flow is largely trench-normal, except near the lateral edges of the slab where toroidal flow dominates. In addition, whisker azimuths located above the slab gap deviate most strongly from trench-normal orientations when slab rollback does not occur. Such flow field complexities are likely sufficient to affect deep melt production and shallow melt delivery. However, none of the experiments produced flow fields that explain the trench-parallel shear wave splitting fast directions observed over broad arc and backarc

  18. Interaction of electromagnetic fields with chondrocytes in gel culture. Final report, 15 Jan 92-14 Jan 94

    SciTech Connect

    Grodzinsky, A.J.; Buschmann, M.D.; Gluzband, Y.A.

    1992-01-14

    The specific objectives of this research period were: (1) to quantify the effect of applied electric fields on chondrocyte metabolism, using a range of stimulation frequencies and amplitudes; (2) to compare the chondrocyte biosynthetic response to applied fields at early times in agarose gel culture before an extracellular matrix has accumulated and at later times after significant deposition of matrix around and between the cells; and (3) to begin to interpret the biosynthetic response to applied fields in terms of models of physical mechanisms. The results of these studies suggest that electric fields applied to chondrocytes in agarose can modulate the synthesis of proteoglycans and protein constituents. Biosynthesis may be inhibited or stimulated depending on the amplitude of the applied current density. In addition, the presence of extracellular matrix may enhance the ability of normal chondrocytes and cells in intact cartilage to respond to electric fields, although the presence of matrix was not required for the stimulatory response to be observed with Swarm rat chondrosarcoma cells.

  19. New Packaging for Amplifier Slabs

    SciTech Connect

    Riley, M.; Thorsness, C.; Suratwala, T.; Steele, R.; Rogowski, G.

    2015-03-18

    The following memo provides a discussion and detailed procedure for a new finished amplifier slab shipping and storage container. The new package is designed to maintain an environment of <5% RH to minimize weathering.

  20. Optimization of reinforced concrete slabs

    NASA Technical Reports Server (NTRS)

    Ferritto, J. M.

    1979-01-01

    Reinforced concrete cells composed of concrete slabs and used to limit the effects of accidental explosions during hazardous explosives operations are analyzed. An automated design procedure which considers the dynamic nonlinear behavior of the reinforced concrete of arbitrary geometrical and structural configuration subjected to dynamic pressure loading is discussed. The optimum design of the slab is examined using an interior penalty function. The optimization procedure is presented and the results are discussed and compared with finite element analysis.

  1. Optimization of reinforced concrete slabs

    NASA Technical Reports Server (NTRS)

    Ferritto, J. M.

    1979-01-01

    Reinforced concrete cells composed of concrete slabs and used to limit the effects of accidental explosions during hazardous explosives operations are analyzed. An automated design procedure which considers the dynamic nonlinear behavior of the reinforced concrete of arbitrary geometrical and structural configuration subjected to dynamic pressure loading is discussed. The optimum design of the slab is examined using an interior penalty function. The optimization procedure is presented and the results are discussed and compared with finite element analysis.

  2. Efficient Vortex Generation in Subwavelength Epsilon-Near-Zero Slabs.

    PubMed

    Ciattoni, Alessandro; Marini, Andrea; Rizza, Carlo

    2017-03-10

    We show that a homogeneous and isotropic slab, illuminated by a circularly polarized beam with no topological charge, produces vortices of order 2 in the opposite circularly polarized components of the reflected and transmitted fields, as a consequence of the transverse magnetic and transverse electric asymmetric response of the rotationally invariant system. In addition, in the epsilon-near-zero regime, we find that vortex generation is remarkably efficient in subwavelength thick slabs up to the paraxial regime. This physically stems from the fact that a vacuum paraxial field can excite a nonparaxial field inside an epsilon-near-zero slab since it hosts slowly varying fields over physically large portions of the bulk. Our theoretical predictions indicate that epsilon-near-zero media hold great potential as nanophotonic elements for manipulating the angular momentum of the radiation, since they are available without resorting to complicated micro- or nanofabrication processes and can operate even at very small (ultraviolet) wavelengths.

  3. Efficient Vortex Generation in Subwavelength Epsilon-Near-Zero Slabs

    NASA Astrophysics Data System (ADS)

    Ciattoni, Alessandro; Marini, Andrea; Rizza, Carlo

    2017-03-01

    We show that a homogeneous and isotropic slab, illuminated by a circularly polarized beam with no topological charge, produces vortices of order 2 in the opposite circularly polarized components of the reflected and transmitted fields, as a consequence of the transverse magnetic and transverse electric asymmetric response of the rotationally invariant system. In addition, in the epsilon-near-zero regime, we find that vortex generation is remarkably efficient in subwavelength thick slabs up to the paraxial regime. This physically stems from the fact that a vacuum paraxial field can excite a nonparaxial field inside an epsilon-near-zero slab since it hosts slowly varying fields over physically large portions of the bulk. Our theoretical predictions indicate that epsilon-near-zero media hold great potential as nanophotonic elements for manipulating the angular momentum of the radiation, since they are available without resorting to complicated micro- or nanofabrication processes and can operate even at very small (ultraviolet) wavelengths.

  4. Subduction starts by stripping slabs

    NASA Astrophysics Data System (ADS)

    Soret, Mathieu; Agard, Philippe; Dubacq, Benoît; Prigent, Cécile; Plunder, Alexis; Yamato, Philippe; Guillot, Stéphane

    2017-04-01

    Metamorphic soles correspond to tectonic slices welded beneath most large-scale ophiolites. These slivers of oceanic crust metamorphosed up to granulite facies conditions are interpreted as having formed during the first My of intra-oceanic subduction from heat transfer from the incipient mantle wedge towards the top of the subducting plate. Our study reappraises the formation of metamorphic sole through detailed field and petrological work on three classical key sections across the Semail ophiolite (Oman and United Arab Emirates). Geothermobarometry and thermodynamic modelling show that metamorphic soles do not record a continuous temperature gradient, as expected from simple heating by the upper plate or by shear heating and proposed by previous studies. The upper, high-temperature metamorphic sole is subdivided in at least two units, testifying to the stepwise formation, detachment and accretion of successive slices from the downgoing slab to the mylonitic base of the ophiolite. Estimated peak pressure-temperature conditions through the metamorphic sole are, from top to bottom, 850˚C - 1GPa, 725°C - 0.8 GPa and 530°C - 0.5 GPa. These estimates appear constant within each unit but separated by a gap of 100 to 200˚C and 0.2 GPa. Despite being separated by hundreds of kilometres below the Semail ophiolite and having contrasting locations with respect to the ophiolite ridge axis, metamorphic soles show no evidence for significant petrological variations along strike. These constraints allow to refine the tectonic-petrological model for the genesis of metamorphic soles, formed through the stepwise stacking of several homogeneous slivers of oceanic crust and its sedimentary cover. Metamorphic soles do not so much result from downward heat transfer (ironing effect) but rather from progressive metamorphism during strain localization and cooling of the plate interface. The successive thrusts are the result of rheological contrasts between the sole (initially at the

  5. [Molecular typing of Klebsiella pneumonia by pulse-field gel electrophoresis in combination with multilocus sequence typing].

    PubMed

    Gao, Yuan; Zhang, Li; Li, Ma-chao; Huang, Cheng; Ren, Hong-yu; Zhou, Hai-jian; Zhu, Bing-qing; Li, Qian; Wang, Xiao-lei; Shao, Zhu-jun

    2010-07-01

    To type Klebsiella pneumonia through methods including pulse-field gel electrophoresis (PFGE) in combination with multilocus sequence typing. Four selected different EPs, referring to the Standard Operating Procedure of PulseNet China, were used. The single colony of Klebsiella pneumonia was quantified after enriched culture. Embedding organisms in agarose and genome DNA were lysed with Proteinase K and then digested by restriction endonuclease XbaI, to produce agarose gel. Fingerprint was obtained through PFGE and bands were marked with their molecular weights and then analyzed by BioNumerics software. Using MLST to analyze the strains that were highly similar, by PFGE typing By comparing the four results from each EPs, fk3 (switch time from 6s to 36s, total run time is 18.5 hours) seemed to be better than the others. 59 strains of Klebsiella pneumonia were divided into 47 PFGE types and 19 PFGE clusters. The highly similar strains could be typed into ST-340, ST-342, ST-343, ST-344, ST-345 by MLST. Among them, ST-342, ST-343, ST-344, ST-345 types were all new MLST types that were reported in China. Highly similar Klebsiella pneumonias typed by PFGE could also be typed by MLST.

  6. Structural analysis of mitochondrial DNA molecules from fungi and plants using moving pictures and pulsed-field gel electrophoresis.

    PubMed

    Bendich, A J

    1996-02-02

    The size and structure of mitochondrial DNA (mtDNA) molecules was investigated by conventional and pulsed-field gel electrophoresis (PFGE) and by analyzing moving pictures during electrophoresis of individual fluorescently labelled mtDNA molecules. Little or no mtDNA that migrated into the gel was found in circular form for fungi (Schizosaccharomyces pombe, Saccharomyces cerevisiae and Neurospora crassa) or plants (Brassica hirta, tobacco, voodoo lily and maize). Most mtDNA migrated as a smear of linear DNA sizes from about 50 to 100 or 250 kilobases (kb), depending on the species, irrespective of the size of the mitochondrial genome over a range of 0.06 to 570 kb. S. cerevisiae, B. hirta and tobacco also yielded a linear mtDNA fraction containing molecules > 1000 kb in size. About half the mtDNA remained in the well of the gel after PFGE. Moving pictures revealed that this well-bound (wb) mtDNA contained molecules larger than the genome size in linear form for all species (except N. crassa) and in multi-fibered, comet-like forms for most of the wb mtDNA of N. crassa and Sc. pombe. A minor amount of the wb mtDNA with visually interpretable structure was circular: circle sizes were both larger and smaller than the 80-kb genome of S. cerevisiae, larger than the 19-kb genome of Sc. pombe and smaller than the 208-kb and 570-kb genomes of B. hirta and maize, respectively. About 25 to 75% of the wb mtDNA from cultured tobacco cells was found in circles smaller than its genome size. Partial digestion of Sc. pombe mtDNA with restriction endonucleases that cleave once per genome revealed gel bands at about 38 kb and 19 kb with a smear of sizes between the bands and below the 19-kb band, suggesting a head-to-tail genomic concatemer as the most prominent form in extracted mtDNA. A pattern of bands with smears was also found for complete digests (with multiply cleaving enzymes) of mtDNA from Sc. pombe, S. cerevisiae and N. crassa, but bands without smears were found for

  7. Analyzing genetic diversity in conifers...isozyme resolution by starch gel electrophoresis

    Treesearch

    M. Thompson Conkle

    1972-01-01

    Enzymes in forest tree materials can be resolved by starch gel electrophoresis. A gel slab is prepared in a mold assembled from glass and plastic. Wicks containing an aqueous extract of macerated plant material are inserted in the gel and processed. The gel is sliced, stained, examined, and photographed. Isozyme bands produced by differential migration of enzymes...

  8. Continental underplating after slab break-off

    NASA Astrophysics Data System (ADS)

    Magni, V.; Allen, M. B.; van Hunen, J.; Bouilhol, P.

    2017-09-01

    We present three-dimensional numerical models to investigate the dynamics of continental collision, and in particular what happens to the subducted continental lithosphere after oceanic slab break-off. We find that in some scenarios the subducting continental lithosphere underthrusts the overriding plate not immediately after it enters the trench, but after oceanic slab break-off. In this case, the continental plate first subducts with a steep angle and then, after the slab breaks off at depth, it rises back towards the surface and flattens below the overriding plate, forming a thick horizontal layer of continental crust that extends for about 200 km beyond the suture. This type of behaviour depends on the width of the oceanic plate marginal to the collision zone: wide oceanic margins promote continental underplating and marginal back-arc basins; narrow margins do not show such underplating unless a far field force is applied. Our models show that, as the subducted continental lithosphere rises, the mantle wedge progressively migrates away from the suture and the continental crust heats up, reaching temperatures >900 °C. This heating might lead to crustal melting, and resultant magmatism. We observe a sharp peak in the overriding plate rock uplift right after the occurrence of slab break-off. Afterwards, during underplating, the maximum rock uplift is smaller, but the affected area is much wider (up to 350 km). These results can be used to explain the dynamics that led to the present-day crustal configuration of the India-Eurasia collision zone and its consequences for the regional tectonic and magmatic evolution.

  9. Time-based distribution of Staphylococcus saprophyticus pulsed field gel-electrophoresis clusters in community-acquired urinary tract infections.

    PubMed

    Sousa, Viviane Santos de; Rabello, Renata Fernandes; Dias, Rubens Clayton da Silva; Martins, Ianick Souto; Santos, Luisa Barbosa Gomes da Silva dos; Alves, Elisabeth Mendes; Riley, Lee Woodford; Moreira, Beatriz Meurer

    2013-02-01

    The epidemiology of urinary tract infections (UTI) by Staphylococcus saprophyticus has not been fully characterised and strain typing methods have not been validated for this agent. To evaluate whether epidemiological relationships exist between clusters of pulsed field gel-electrophoresis (PFGE) genotypes of S. saprophyticus from community-acquired UTI, a cross-sectional surveillance study was conducted in the city of Rio de Janeiro, Brazil. In total, 32 (16%) female patients attending two walk-in clinics were culture-positive for S. saprophyticus. Five PFGE clusters were defined and evaluated against epidemiological data. The PFGE clusters were grouped in time, suggesting the existence of community point sources of S. saprophyticus. From these point sources, S. saprophyticus strains may spread among individuals.

  10. DNA polymorphism in Mycobacterium paratuberculosis, "wood pigeon mycobacteria," and related mycobacteria analyzed by field inversion gel electrophoresis.

    PubMed Central

    Lévy-Frébault, V V; Thorel, M F; Varnerot, A; Gicquel, B

    1989-01-01

    Mycobacterium paratuberculosis strains, mycobacteria from patients suffering from Crohn's disease, "wood pigeon mycobacteria," and representatives of Mycobacterium avium-Mycobacterium intracellulare were compared by restriction endonuclease DraI digestion and field inversion gel electrophoresis. Characteristic profiles were seen for M. paratuberculosis, including isolates from patients suffering from Crohn's disease, for wood pigeon mycobacteria, and for M. avium-M. intracellulare serotypes 2, 16, 18, and 19. Two M. paratuberculosis strains used for vaccine production (St 18 and 316 F) presented patterns different from those of the other M. paratuberculosis strains. Strains St 18 yielded a pattern identical to that of the M. avium type strain serotype 2, whereas 316 F gave a unique pattern. The method developed in this study represents a useful taxonomic tool for the identification and classification of mycobacteria. Images PMID:2574186

  11. Diagnosis of an outbreak of Salmonella typhimurium in chinchillas (Chinchilla lanigera) by pulsed-field gel electrophoresis.

    PubMed

    Gornatti Churria, Carlos D; Vigo, Germán B; Origlia, Javier; Campos, Josefina; Caffer, María; Píscopo, Miguel; Herrero Loyola, Miguel; Petruccelli, Miguel; Pichel, Mariana

    2014-01-01

    Adult chinchillas (Chinchilla lanigera) that had suddenly died in a commercial farm located in La Plata City, Buenos Aires Province, Argentina, in July 2012 were macroscopically, histopathologically, and microbiologically examined. Salmonella enterica serovar Typhimurium (S. Typhimurium) was isolated from the liver, spleen, heart, lungs, kidneys and intestines from each of the five animals evaluated. The five strains were susceptible to ampicillin, cephalotin, cefotaxime, nalidixic acid, gentamicin, streptomycin, chloramphenicol, fosfomycin, nitrofurantoin and trimethoprim-sulfamethoxazole, and resistant to tetracycline. Each of the five S. Typhimurium isolates was analyzed by XbaI- pulsed-field gel electrophoresis (PFGE), showing an identical electrophoretic profile with 15 defined bands, which was found to be identical to pattern ARJPXX01.0220 of the PulseNet Argentine National database of Salmonella PFGE patterns. This is the first work describing the postmortem diagnosis of an outbreak of salmonellosis in chinchillas by using molecular methods such as PFGE.

  12. Development of a multispecies identification field test by modified agar-gel immunodiffusion.

    PubMed

    Cutufelli, M E; Mageau, R P; Schwab, B; Johnston, R W

    1993-01-01

    A multispecies identification field test (MULTI-SIFT) was developed for detection of beef, poultry, pork, sheep, horse, and deer in a wide variety of raw meat products. The test is an adaptation of previously developed field screening immunodiffusion tests for detection of single species. MULTI-SIFT was demonstrated to be specific, relatively sensitive, and accurate in the complete speciation of 100 meat samples.

  13. Analysis of Genomic Diversity among Helicobacter pylori Strains Isolated from Iranian Children by Pulsed Field Gel Electrophoresis

    PubMed Central

    Falsafi, Tahereh; Sotoudeh, Nazli; Feizabadi, Mohammad-Mehdi; Mahjoub, Fatemeh

    2014-01-01

    Objective: Presence of genomic diversity among Helicobacter pylori (H. pylori) strains have been suggested by numerous investigators. Little is known about diversity of H. pylori strains isolated from Iranian children and their association with virulence of the strains. Our purpose was to assess the degree of genomic diversity among H. pylori strains isolated from Iranian-children, on the basis of vacA genotype, cagA status of the strains, sex, age as well as the pathological status of the patients. Methods: Genomic DNA from 44 unrelated H. pylori strains isolated during 1997–2009, was examined by pulse-field gel electrophoresis (PFGE). Pathological status of the patients was performed according to the modified Sydney-system and genotype/status of vacA/cagA genes was determined by PCR. PFGE was performed using XbaI restriction-endonuclease and the field inversion-gel electrophoresis system. Findings: No significant relationship was observed between the patterns of PFGE and the cagA/vacA status/genotype. Also no relationship was observed between age, sex, and pathological status of the children and the PFGE patterns of their isolates. Similar conclusion was obtained by Total Lab software. However, more relationship was observed between the strains isolated in the close period (1997–2009, 2001–2003, 2005–2007, and 2007–2009) and more difference was observed among those obtained in the distant periods (1997 and 2009). Conclusion: H. pylori strains isolated from children in Iran are extremely diverse and this diversity is not related to their virulence characteristics. Occurrence of this extreme diversity may be related to adaptation of H. pylori strains to variable living conditions during transmission between various host individuals. PMID:26019775

  14. The use of pulsed-field gel electrophoresis to investigate the epidemiology of Mycoplasma bovis in French calf feedlots.

    PubMed

    Arcangioli, Marie-Anne; Aslan, Hamidé; Tardy, Florence; Poumarat, François; Le Grand, Dominique

    2012-04-01

    Mycoplasma bovis is a major cause of respiratory outbreaks in cattle feedlots. In this study pulsed-field gel electrophoresis (PFGE) was used to trace field strains and provide information on M. bovis patterns of spread in calf feedlots. The suitability of KpnI, MluI and SmaI restriction enzymes was assessed on different sets of strains. The discriminative power of the first two enzymes was first assessed using 28 epidemiologically unrelated strains; stability was 100% on multiple isolates from in vivo experimental infection. Thirty-nine field isolates from six feedlots were then evaluated. In contrast to the unique fingerprints displayed by the unrelated strains, the isolates from the feedlots showed identical patterns at the time of the outbreak of respiratory disease and 4 weeks later. The PFGE typing results suggest that M. bovis strains follow a clonal epidemic spread pattern at the herd level and that the same strain persists in calves of the herd after the clinical signs have disappeared.

  15. Segmentation of the Farallon slab

    NASA Astrophysics Data System (ADS)

    Liu, L.; Stegman, D. R.

    2011-12-01

    Recent tomography images reveal a complex 3D mantle structure beneath western United States, with feature morphology varying rapidly with depth. By assimilating plate motion history, paleo-age of sea floor, and paleo-geography of plate boundaries in a 3-D numerical model, we simulate the Farallon-Juan de Fuca subduction during the past 40 Ma. We find that the highly segmented upper mantle structure of western U.S. is a direct result of the Farallon subduction. We show that the tilted 'horseshoe'-shaped fast seismic anomaly beneath Nevada and Utah at 300-600 km depth range is in fact a segment of curled slab subducted since 15 Ma, and the shallower linear slab beneath the Cascades is younger than 5 Ma. The distinct morphology between these two parts of the subduction system indicates the strong influence of the fast trench rollback since 20 Ma, the northward migrating JF-PA-NA triple-junction, and the toroidal flow around slab edges. The observed mantle structures are used to constrain the rheology of the upper mantle through matching the shape, depth, and location of modeled subducted slab segments. The inferred viscosity for the asthenosphere is 5×10^19 Pa s and that for the transition zone is 1.5×10^21 Pa s. The slab is found to be about 2 orders of magnitude stronger than the ambient mantle above 410 km depth, but of similar order of magnitude viscosity in the transition zone.

  16. Rheological evolution of subducting slabs

    NASA Astrophysics Data System (ADS)

    Hirth, G.

    2016-12-01

    The mechanical behavior of subducting lithosphere depends on both the rheological evolution of the slab and how the slab is modified prior to subduction. Geophysical data demonstrate that the combination of thermal evolution and deformation lead to alteration of the slab at both mid-ocean ridges and the outer rise of subduction zones. In addition, the locations of earthquakes in these locations are generally consistent with both extrapolation of laboratory data that constrain the depth to the brittle-plastic transition, and deformation mechanisms inferred from microstructural analysis of mantle rocks recovered from the oceanic lithosphere. However, the frictional properties of both mantle aggregates and their alteration products suggest that linking the location of lithospheric earthquakes to regions that become hydrothermally altered is not straightforward. Furthermore, the inferred link between the location of intermediate-depth seismicity and the conditions of dehydration reactions is challenged by laboratory studies on dehydration embrittlement. In this presentation, I will introduce these apparent discrepancies; provide some possible resolutions for them based on scaling of laboratory data and discuss the implications for how an integrated understanding of slab rheology informs our understanding of the mechanical and geochemical evolution of the slab.

  17. Modeling radon entry into Florida slab-on-grade houses.

    PubMed

    Revzan, K L; Fisk, W J; Sextro, R G

    1993-10-01

    Radon entry into a Florida house whose concrete slab is supported by a permeable concrete-block stem wall and a concrete footer is modeled. The slab rests on backfill material; the same material is used to fill the footer trench. A region of undisturbed soil is assumed to extend 10 m beyond and below the footer. The soil is assumed homogeneous and isotropic except for certain simulations in which soil layers of high permeability or radium content are introduced. Depressurization of the house induces a pressure field in the soil and backfill. The Laplace equation, resulting from Darcy's law and the continuity equation, is solved using a steady-state finite-difference model to determine this field. The mass-transport equation is then solved to obtain the diffusive and advective radon entry rates through the slab; the permeable stem wall; gaps at the intersections of the slab, stem wall, and footer; and gaps in the slab. These rates are determined for variable soil, backfill, and stem-wall permeability and radium content, slab-opening width and position, slab and stem-wall diffusivity, and water table depth. The variations in soil permeability and radium content include cases of horizontally stratified soil. We also consider the effect of a gap between the edge of the slab and the stem wall that restricts the passage of soil gas from the stem wall into the house. Calculations indicate that the total radon entry rate is relatively low unless the soil or backfill permeability or radium content is high. Variations in most of the factors, other than the soil permeability and radium content, have only a small effect on the total radon entry rate. However, for a fixed soil permeability, the total radon entry rate may be reduced by a factor of 2 or more by decreasing the backfill permeability, by making the stem wall impermeable and gap-free, (possibly by constructing a one-piece slab/stem-wall/footer), or by increasing the pressure in the interior of the stem wall (by

  18. Photonic crystal slab quantum cascade detector

    SciTech Connect

    Reininger, Peter Schwarz, Benedikt; Harrer, Andreas; Zederbauer, Tobias; Detz, Hermann; Maxwell Andrews, Aaron; Gansch, Roman; Schrenk, Werner; Strasser, Gottfried

    2013-12-09

    In this Letter, we demonstrate the design, fabrication, and characterization of a photonic crystal slab quantum cascade detector (PCS-QCD). By employing a specifically designed resonant cavity, the performance of the photodetector is improved in three distinct ways. The PCS makes the QCD sensitive to surface normal incident light. It resonantly enhances the photon lifetime inside the active zone, thus increasing the photocurrent significantly. And, the construction form of the device inherently decreases the noise. Finally, we compare the characteristics of the PCS-QCD to a PCS - quantum well infrared photodetector and outline the advantages for certain fields of applications.

  19. Photonic crystal slab quantum cascade detector

    NASA Astrophysics Data System (ADS)

    Reininger, Peter; Schwarz, Benedikt; Harrer, Andreas; Zederbauer, Tobias; Detz, Hermann; Maxwell Andrews, Aaron; Gansch, Roman; Schrenk, Werner; Strasser, Gottfried

    2013-12-01

    In this Letter, we demonstrate the design, fabrication, and characterization of a photonic crystal slab quantum cascade detector (PCS-QCD). By employing a specifically designed resonant cavity, the performance of the photodetector is improved in three distinct ways. The PCS makes the QCD sensitive to surface normal incident light. It resonantly enhances the photon lifetime inside the active zone, thus increasing the photocurrent significantly. And, the construction form of the device inherently decreases the noise. Finally, we compare the characteristics of the PCS-QCD to a PCS - quantum well infrared photodetector and outline the advantages for certain fields of applications.

  20. Molecular typing of Japanese field isolates and live commercial vaccine strain of Mycoplasma synoviae using improved pulsed-field gel electrophoresis and vlhA gene sequencing.

    PubMed

    Harada, Kazuki; Kijima-Tanaka, Mayumi; Uchiyama, Mariko; Yamamoto, Tomoko; Oishi, Koji; Arao, Megumi; Takahashi, Toshio

    2009-12-01

    In the present study, pulsed-field gel electrophoresis (PFGE) and vlhA gene sequence analysis were applied and verified for typing the Mycoplasma synoviae live vaccine MS-H strain and field isolates from diseased chickens in Japan. The previously published PFGE protocol using SmaI digestion could not allow the discrimination of two of the 11 M. synoviae field isolates from the vaccine strain and had relatively low discrimination power (D = 0.885). On the other hand, our new PFGE protocols using BlnI and BamHI digestions as well as the vlhA sequence analysis allowed the discrimination of all 11 M. synoviae field isolates from the vaccine strain. In addition, these PFGE protocols using BlnI and BamHI digestions generated unique fragment patterns in epidemiologically unrelated isolates, including those with identical SmaI-digested patterns or vlhA gene sequences (D = 0.987 and 1.000, respectively), and generated indistinguishable or closely related patterns in epidemiologically related isolates. Therefore, we believe that they would be useful tools to determine whether M. synoviae clinical isolates from diseased chickens are derived from the vaccine strain or wild-type strain and to further elucidate the epidemiology of M. synoviae infection.

  1. Genotypes, antibiogram, and pulsed-field gel electrophoresis profiles of Escherichia coli strains from piglets in Korea.

    PubMed

    Lee, Su In; Rayamahji, Nabin; Lee, Won Jung; Cha, Seung Bin; Shin, Min Kyung; Roh, Yu Mi; Yoo, Han Sang

    2009-07-01

    Adherence factors and enterotoxins are major virulence factors of enterotoxigenic Escherichia coli (ETEC). Antibiotics have been used frequently for the treatment and prevention of ETEC infection in piggeries worldwide, including Korea. Therefore, data on both virulence profiles and antibiotic resistance patterns are useful in the epidemiological study of ETEC. A total number of 198 E. coli field isolates were examined. The most prevalent pathotype was F1, followed by a combination of F1 and EAST1. All of the 71 isolates were resistant to more than 2 antibiotics used in a disk diffusion test, and 87.94% of the isolates were found to be resistant to more than 4 antibiotics. Investigations were also conducted to correlate the virulence gene profiles with antibiogram and pulsed-field gel electrophoresis (PFGE). Although a high degree of polymorphism was noted among strains having the same virulence patterns, the highest similarity pattern was observed carrying the same virulence profiles and similar antibiogram. Thus, investigation of both virulence profiles and antibiogram is essential to the epidemiological study of ETEC. Moreover, the PFGE method might be applicable as a tool to reveal genetic relatedness among E. coli strains from piggeries in Korea.

  2. The Dynamics of Double Slab Subduction

    NASA Astrophysics Data System (ADS)

    Holt, A. F.; Royden, L. H.; Becker, T. W.

    2017-01-01

    We use numerical models to investigate the dynamics of two interacting slabs with parallel trenches. Cases considered are: a single slab reference, outward dipping slabs (out-dip), inward dipping slabs (in-dip), and slabs dipping in the same direction (same-dip). Where trenches converge over time (same-dip and out-dip systems), large positive dynamic pressures in the asthenosphere are generated beneath the middle plate, and large trench-normal extensional forces are transmitted through the middle plate. This results in slabs that dip away from the middle plate at depth, independent of trench geometry. The single slab, the front slab in the same-dip case, and both out-dip slabs undergo trench retreat and exhibit stable subduction. However, slabs within the other double subduction systems tend to completely overturn at the base of the upper mantle, and exhibit either trench advance (rear slab in same-dip), or near-stationary trenches (in-dip). For all slabs, the net slab-normal dynamic pressure at 330 km depth is nearly equal to the slab normal force induced by slab buoyancy. For double subduction, the net outward force on the slabs due to dynamic pressure from the asthenosphere is effectively counterbalanced by the net extensional force transmitted through the middle plate. Thus, dynamic pressure at depth, inter-plate coupling, and lithospheric stresses are closely linked and their effects cannot be isolated. Our results provide insights into both the temporal evolution of double slab systems on Earth and, more generally, how the various components of subduction systems, from mantle flow/pressure to inter-plate coupling, are dynamically linked.

  3. Design and experimental testing of air slab caps which convert commercial electron diodes into dual purpose, correction-free diodes for small field dosimetry

    SciTech Connect

    Charles, P. H.; Cranmer-Sargison, G.; Thwaites, D. I.; Kairn, T.; Crowe, S. B.; Langton, C. M.; Trapp, J. V.; Pedrazzini, G.; Aland, T.; Kenny, J.

    2014-10-15

    Purpose: Two diodes which do not require correction factors for small field relative output measurements are designed and validated using experimental methodology. This was achieved by adding an air layer above the active volume of the diode detectors, which canceled out the increase in response of the diodes in small fields relative to standard field sizes. Methods: Due to the increased density of silicon and other components within a diode, additional electrons are created. In very small fields, a very small air gap acts as an effective filter of electrons with a high angle of incidence. The aim was to design a diode that balanced these perturbations to give a response similar to a water-only geometry. Three thicknesses of air were placed at the proximal end of a PTW 60017 electron diode (PTWe) using an adjustable “air cap”. A set of output ratios (OR{sub Det}{sup f{sub c}{sub l}{sub i}{sub n}}) for square field sizes of side length down to 5 mm was measured using each air thickness and compared to OR{sub Det}{sup f{sub c}{sub l}{sub i}{sub n}} measured using an IBA stereotactic field diode (SFD). k{sub Q{sub c{sub l{sub i{sub n,Q{sub m{sub s{sub r}{sup f{sub c}{sub l}{sub i}{sub n},f{sub m}{sub s}{sub r}}}}}}}}} was transferred from the SFD to the PTWe diode and plotted as a function of air gap thickness for each field size. This enabled the optimal air gap thickness to be obtained by observing which thickness of air was required such that k{sub Q{sub c{sub l{sub i{sub n,Q{sub m{sub s{sub r}{sup f{sub c}{sub l}{sub i}{sub n},f{sub m}{sub s}{sub r}}}}}}}}} was equal to 1.00 at all field sizes. A similar procedure was used to find the optimal air thickness required to make a modified Sun Nuclear EDGE detector (EDGEe) which is “correction-free” in small field relative dosimetry. In addition, the feasibility of experimentally transferring k{sub Q{sub c{sub l{sub i{sub n,Q{sub m{sub s{sub r}{sup f{sub c}{sub l}{sub i}{sub n},f{sub m}{sub s}{sub r

  4. Pseudomonas aeruginosa Endophthalmitis after Penetrating Keratoplasty Transmitted from the Same Donor to Two Recipients Confirmed by Pulsed-Field Gel Electrophoresis ▿

    PubMed Central

    Oguido, Ana Paula Miyagusko Taba; Casella, Antonio Marcelo Barbante; Hofling-Lima, Ana Luisa; Pacheco, Sergio Arruda; Bispo, Paulo José Martins; Marques, Fernanda

    2011-01-01

    Two devastating cases of multidrug-resistant Pseudomonas aeruginosa endophthalmitis after keratoplasty as the result of transmission from the same donor were confirmed by pulsed-field gel electrophoresis. Strategies for preventing donor-to-host transmission, such as the use of antimicrobial agents of greater efficacy and better methods for detecting microorganisms in preservation medium, could minimize this type of transmission. PMID:21775545

  5. A comparison of non-typhoidal Salmonella from humans and food animals using pulsed-field gel electrophoresis and antimicrobial susceptibility patterns

    USDA-ARS?s Scientific Manuscript database

    Salmonellosis is one of the most important foodborne diseases affecting humans. To characterize the relationship between Salmonella causing human infections and their food animal reservoirs, we compared pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility patterns of non-typhoida...

  6. A comparison of BOX-PCR and pulsed-field gel electrophoresis to determine genetic relatedness of enterococci from different environments

    USDA-ARS?s Scientific Manuscript database

    Aims: The genetic relatedness of enterococci from poultry litter to enterococci from nearby surface water and groundwater in the Lower Fraser Valley regions of British Columbia, Canada was determined. Methods and Results: BOX-PCR and Pulsed-Field Gel Electrophoresis (PFGE) were used to subtype en...

  7. Acupuncture injection for field amplified sample stacking and glass microchip-based capillary gel electrophoresis.

    PubMed

    Ha, Ji Won; Hahn, Jong Hoon

    2017-02-01

    Acupuncture sample injection is a simple method to deliver well-defined nanoliter-scale sample plugs in PDMS microfluidic channels. This acupuncture injection method in microchip CE has several advantages, including minimization of sample consumption, the capability of serial injections of different sample solutions into the same microchannel, and the capability of injecting sample plugs into any desired position of a microchannel. Herein, we demonstrate that the simple and cost-effective acupuncture sample injection method can be used for PDMS microchip-based field amplified sample stacking in the most simplified straight channel by applying a single potential. We achieved the increase in electropherogram signals for the case of sample stacking. Furthermore, we present that microchip CGE of ΦX174 DNA-HaeⅢ digest can be performed with the acupuncture injection method on a glass microchip while minimizing sample loss and voltage control hardware.

  8. How mantle slabs drive plate tectonics.

    PubMed

    Conrad, Clinton P; Lithgow-Bertelloni, Carolina

    2002-10-04

    The gravitational pull of subducted slabs is thought to drive the motions of Earth's tectonic plates, but the coupling between slabs and plates is not well established. If a slab is mechanically attached to a subducting plate, it can exert a direct pull on the plate. Alternatively, a detached slab may drive a plate by exciting flow in the mantle that exerts a shear traction on the base of the plate. From the geologic history of subduction, we estimated the relative importance of "pull" versus "suction" for the present-day plates. Observed plate motions are best predicted if slabs in the upper mantle are attached to plates and generate slab pull forces that account for about half of the total driving force on plates. Slabs in the lower mantle are supported by viscous mantle forces and drive plates through slab suction.

  9. Transient slab flattening beneath Colombia

    NASA Astrophysics Data System (ADS)

    Wagner, L. S.; Jaramillo, J. S.; Ramírez-Hoyos, L. F.; Monsalve, G.; Cardona, A.; Becker, T. W.

    2017-07-01

    Subduction of the Nazca and Caribbean Plates beneath northwestern Colombia is seen in two distinct Wadati Benioff Zones, one associated with a flat slab to the north and one associated with normal subduction south of 5.5°N. The normal subduction region is characterized by an active arc, whereas the flat slab region has no known Holocene volcanism. We analyze volcanic patterns over the past 14 Ma to show that in the mid-Miocene a continuous arc extended up to 7°N, indicating normal subduction of the Nazca Plate all along Colombia's Pacific margin. However, by 6 Ma, we find a complete cessation of this arc north of 3°N, indicating the presence of a far more laterally extensive flat slab than at present. Volcanism did not resume between 3°N and 6°N until after 4 Ma, consistent with lateral tearing and resteepening of the southern portion of the Colombian flat slab at that time.

  10. Modeling radon entry into Florida slab-on-grade houses

    SciTech Connect

    Revzan, K.L.; Fisk, W.J.; Sextro, R.G. )

    1993-10-01

    Radon entry into a Florida house whose concrete slab is supported by a permeable concrete-block stem wall and a concrete footer is modeled. The slab rests on backfill material; the same material is used to fill the footer trench. A region of undisturbed soil is assumed to extend 10 m beyond and below the footer. The soil is assumed homogeneous and isotropic except for certain simulations in which soil layers of high permeability or radium content are introduced. Depressurization of the house induces a pressure field in the soil and backfill. The Laplace equation, resulting from Darcy's law and the continuity equation, is solved using a steady-state finite-difference model to determine this field. The mass-transport equation is then solved to obtain the diffusive and advective radon entry rates through the slab; the permeable stem wall; gaps at the intersections of the slab, stem wall, and footer; and gaps in the slab. These rates are determined for variable soil, backfill, and stem-wall permeability and radium content, slab-opening width and position, slab and stem-wall diffusivity, and water table depth. The variations in soil permeability and radium content include cases of horizontally stratified soil. We also consider the effect of a gap between the edge of the slab and the stem wall that restricts the passage of soil gas from the stem wall into the house. Calculations indicate that the total radon entry rate is relatively low unless the soil or backfill permeability or radium content is high. Variations in most of the factors, other than the soil permeability and radium content, have only a small effect on the total radon entry rate. However, for a fixed soil permeability, the total radon entry rate may be reduced by a factor of 2 or more by decreasing the backfill permeability, by making the stem wall impermeable and gap-free, (possibly by constructing a one-piece slab/stem-wall/footer), or by increasing the pressure in the interior of the stem wall.

  11. A charge-coupled-device camera image analysis system for quantifying DNA distributions in agarose gels after pulsed-field gel electrophoresis

    SciTech Connect

    Dewey, W.C.; Thompson, L.L.; Trinh, M.L.; Latz, D.L. |; Ward, J.F.

    1994-10-01

    A charge-coupled-device camera system was coupled to a personal computer and, with uniformity in illumination and detection (within 4-8%) along each lane, was used for quantifying the distribution of DNA molecules that migrate from the PFGE well (plug) into the lane at distances varying from 1 to 50 mm (with 0.5 mm/pixel). By using a specially designed transmission filter for transmitting 470-725 nm fluorescence from ethidium bromide-stained DNA while eliminating most of the fluorescence (<400 nm) from the agarose gel, and by using neutral density filters to prevent saturation of the camera, the fluorescence intensity is linearly related to the amount of DNA varying from {approximately} 0.03 {mu}g in a 3-mm-diameter cylindrical plug 5 mm long (equal to background) to {approximately} 4 {mu}g (where ethidium bromide staining saturates). The percentage DNA released from the plug and distribution in the lane (with 1-2 mm resolution) obtained by quantifying DNA fluorescence were not significantly different from the same data obtained by analysis of radioactivity of the same DNA labeled with [{sup 3}H]dThd. However, scattering of fluorescence from one lane into an adjacent lane 3 mm away and as far as 10 mm from the plug into the lane presented a problem. This problem was overcome by using a form with slots to cover every other lane when the images were obtained and either (1) cutting the lane from the plug and moving it 15 mm away or (2) imaging the intact gel and applying a correction for {approximately} 7% of the fluorescence from the plug tailing out {approximately} 10 mm beyond the first 1 mm in the lane. In addition, the following were required: (1) carefully controlled staining and destaining procedures, and (2) a low background that is obtained as an average uniform background in each lane 5 mm beyond where DNA migration stops. 31 refs., 7 figs.

  12. The dynamics of double slab subduction from numerical and semi-analytic models

    NASA Astrophysics Data System (ADS)

    Holt, A.; Royden, L.; Becker, T. W.

    2015-12-01

    Regional interactions between multiple subducting slabs have been proposed to explain enigmatic slab kinematics in a number of subduction zones, a pertinent example being the rapid pre-collisional plate convergence of India and Eurasia. However, dynamically consistent 3-D numerical models of double subduction have yet to be explored, and so the physics of such double slab systems remain poorly understood. Here we build on the comparison of a fully numerical finite element model (CitcomCU) and a time-dependent semi-analytic subduction models (FAST) presented for single subduction systems (Royden et. al., 2015 AGU Fall Abstract) to explore how subducting slab kinematics, particularly trench and plate motions, can be affected by the presence of an additional slab, with all of the possible slab dip direction permutations. A second subducting slab gives rise to a more complex dynamic pressure and mantle flow fields, and an additional slab pull force that is transmitted across the subduction zone interface. While the general relationships among plate velocity, trench velocity, asthenospheric pressure drop, and plate coupling modes are similar to those observed for the single slab case, we find that multiple subducting slabs can interact with each other and indeed induce slab kinematics that deviate significantly from those observed for the equivalent single slab models. References Jagoutz, O., Royden, L. H., Holt, A. F. & Becker, T. W., 2015, Nature Geo., 8, 10.1038/NGEO2418. Moresi, L. N. & Gurnis, M., 1996, Earth Planet. Sci. Lett., 138, 15-28. Royden, L. H. & Husson, L., 2006, Geophys. J. Int. 167, 881-905. Zhong, S., 2006, J. Geophys. Res., 111, doi: 10.1029/2005JB003972.

  13. Segmentation of the Farallon slab

    NASA Astrophysics Data System (ADS)

    Liu, Lijun; Stegman, Dave R.

    2011-11-01

    Recent tomography images reveal a complex 3D mantle structure beneath western United States, with feature morphology varying rapidly with depth. By assimilating plate motion history, paleo-age of sea floor, and paleo-geography of plate boundaries in a 3-D numerical model, we simulate the Farallon-Juan de Fuca subduction during the past 40 Ma. We find that the highly segmented upper mantle structure of western U.S. is a direct result of the Farallon subduction. We show that the tilted 'horseshoe'-shaped fast seismic anomaly beneath Nevada and Utah at 300-600 km depth range is in fact a segment of curled slab subducted since 15 Ma, and the shallower linear slab beneath the Cascades is younger than 5 Ma. The distinct morphology between these two parts of the subduction system indicates the strong influence of the fast trench rollback since 20 Ma, the northward migrating JF-PA-NA triple-junction, and the toroidal flow around slab edges. The observed mantle structures are used to constrain the rheology of the upper mantle through matching the shape, depth, and location of modeled subducted slab segments. The inferred viscosity for the asthenosphere is 5 × 10 19 Pa s and those for the transition zone and lower mantle are 1.5 × 10 21 Pa s and 2 × 10 22 Pa s, respectively. The slab is found to be about 2 orders of magnitude stronger than the ambient mantle above 410 km depth, but of similar order of magnitude viscosity in the transition zone.

  14. A generalized slab-wise framework for parallel transmit multiband RF pulse design

    PubMed Central

    Wu, Xiaoping; Schmitter, Sebastian; Auerbach, Edward J.; Uğurbil, Kâmil; de Moortele, Pierre-François Van

    2015-01-01

    Purpose We propose a new slab-wise framework to design parallel transmit multi-band pulses for volumetric simultaneous multi-slice imaging with a large field of view along the slice direction (FOVs). Theory and Methods The slab-wise framework divides FOVs into a few contiguous slabs and optimizes pulses for each slab. Effects of relevant design parameters including slab number and transmit B1 (B1+) mapping slice placement were investigated for human brain imaging by designing pulses with global or local SAR control based on electromagnetic simulations of a 7T head RF array. Pulse design using in-vivo B1+ maps was demonstrated and evaluated with Bloch simulations. Results RF performance with respect to SAR reduction or B1+ homogenization across the entire human brain improved with increasing slabs; however, this improvement was non-linear and leveled off at ~12 slabs when the slab thickness reduced to ~12 mm. The impact of using different slice placements for B1+ mapping was small. Conclusion Compared to slice-wise approaches where each of the many imaging slices requires both B1+ mapping and pulse optimization, the proposed slab-wise design framework is shown to attain comparable RF performance while drastically reducing the number of required pulses; therefore, it can be used to increase time efficiency for B1+ mapping, pulse calculation and sequence preparation. PMID:25994797

  15. Calculation and comparison of thermal effect in laser diode pumped slab lasers with different pumping structures

    NASA Astrophysics Data System (ADS)

    Huang, Feng; Jiang, Nan; Wang, Yuefeng; Dong, Wei; Niu, Yanxiong

    2008-03-01

    Laser diode (LD) pumped slab laser, as an important high average power solid-state laser, is a promising laser source in military and industrial fields. The different laser diode pumping structures lead to different thermal effect in the slab gain medium. The thermal and stress analysis of slab laser with different pumping structure are performed by finite element analysis (FEA) with the software program ANSYS. The calculation results show that the face pumped and cooled laser results in a near one-dimension temperature distribution and eliminates thermal stress induced depolarization. But the structure is low pump efficiency due to the small thickness of slabs and the requirement to cool and pump through the same faces. End-pumped slab laser is high pump efficiency and excellent mode match, but its pumping arrangement is fairly complicated. The edge-pumped face-cooling slab laser's pump efficiency is better than face-pumping, and its pumping structure is simpler than end-pumped laser, but the tensile stress on surfaces may initiate failure of the gain medium so it is important to design so that the stress is well below the stress fracture limit. The comparison of the thermal effects with different pumping structure shows that, the edge-pumped slab laser has engineering advantages in high power slab laser's application. Furthermore, the end-pumped slab laser tends to get the best beam quality, so it is fit for the application which has a special requirement on laser beam quality.

  16. Diversity of pulsed-field gel electrophoresis patterns of cereulide-producing isolates of Bacillus cereus and Bacillus weihenstephanensis.

    PubMed

    Castiaux, Virginie; N'guessan, Elise; Swiecicka, Izabela; Delbrassinne, Laurence; Dierick, Katelijne; Mahillon, Jacques

    2014-04-01

    Bacillus cereus is an important foodborne pathogen causing diarrhoea, emesis and in, rare cases, lethal poisonings. The emetic syndrome is caused by cereulide, a heat-stable toxin. Originally considered as a rather homogenous group, the emetic strains have since been shown to display some diversity, including the existence of two clusters of mesophilic B. cereus and psychrotolerant B. weihenstephanensis. Using pulsed-field gel electrophoresis (PFGE) analysis, this research aimed to better understand the diversity and spatio-temporal occurrence of emetic strains originating from environmental or food niches vs. those isolated from foodborne cases. The diversity was evaluated using a set of 52 B. cereus and B. weihenstephanensis strains isolated between 2000 and 2011 in ten countries. PFGE analysis could discriminate 17 distinct profiles (pulsotypes). The most striking observations were as follows: (1) more than one emetic pulsotype can be observed in a single outbreak; (2) the number of distinct isolates involved in emetic intoxications is limited, and these potentially clonal strains frequently occurred in successive and independent food poisoning cases; (3) isolates from different countries displayed identical profiles; and (4) the cereulide-producing psychrotolerant B. weihenstephanensis were, so far, only isolated from environmental niches. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  17. Genotyping of Yersinia enterocolitica biotype 1A strains from clinical and nonclinical origins by pulsed-field gel electrophoresis.

    PubMed

    Campioni, Fábio; Falcão, Juliana P

    2014-06-01

    Yersinia enterocolitica biotype 1A (B1A) strains are considered mainly nonpathogenic. However, some studies considered strains of this biotype to be the causal agents of infections in humans and animals. In South America, there are no studies that have compared clinical and nonclinical strains of B1A typed by pulsed-field gel electrophoresis (PFGE) and none that have compared the capability of different enzymes on typing these strains. This study typed 51 Y. enterocolitica B1A strains isolated in Brazil and Chile by PFGE, testing the enzymes XbaI, NotI, and XhoI. The resulting dendrograms discriminated the strains in 47, 40, and 49 pulsotypes generated by the cleavage with the enzymes XbaI, NotI, and XhoI, respectively. The majority of the strains were grouped independently of their clinical or nonclinical origins. The high discriminatory power of PFGE confirmed the heterogeneity of B1A strains but could not divide the strains studied into clusters that differed in the frequency of some virulence genes as observed in studies using other methodologies.

  18. Frequencies of virulence genes and pulse field gel electrophoresis fingerprints in Escherichia coli isolates from canine pyometra.

    PubMed

    Maluta, Renato P; Borges, Clarissa A; Beraldo, Lívia G; Cardozo, Marita V; Voorwald, Fabiana A; Santana, André M; Rigobelo, Everlon C; Toniollo, Gilson H; Avila, Fernando A

    2014-11-01

    Escherichia coli is the most common bacterial agent isolated from canine pyometra. The frequencies of 24 virulence genes and pulsed field gel electrophoresis (PFGE) profiles were determined for 23 E. coli isolates from cases of canine pyometra in Brazil. The frequencies of virulence genes were 91.3% fimH, 91.3% irp-2, 82.6% fyuA, 56.5% iroN, 47.8% traT, 39.1% usp, 34.8% sfaD/E, 34.8% tsh, 30.4% papC, 30.4% hlyA, 26.1% papGIII, 26.1% cnf-1, 21.7% papE/F, 21.7% iss, 17.4% iutA, 17.4% ompT, 17.4% cvaC, 17.4% hlyF, 17.4% iucD, 13.0% iucC, 13.0% astA, 4.3% papGII, 0% afaB/C and 0% papGI. The high frequency of yersiniabactin (fyuA and irp2) and salmochelin (iroN) genes suggests that iron uptake systems might be important in the pathogenesis of canine pyometra. PFGE profiles of 19 isolates were heterogeneous, confirming that E. coli isolates from canine pyometra are unlikely to be epidemic clones.

  19. Arcobacter species and their pulsed-field gel electrophoresis genotypes in Finnish raw milk during summer 2011.

    PubMed

    Revez, Joana; Huuskonen, Marianne; Ruusunen, Marjo; Lindström, Miia; Hänninen, Marja-Liisa

    2013-09-01

    The aim of this study was to investigate the occurrence of Arcobacter species in raw milk in Finland. A total of 177 raw milk samples, each from a separate farm, were examined from June to August 2011. Arcobacter species were isolated using an enrichment and selective detection procedure. Overall, 26 (15 % ) of the 177 samples yielded Arcobacter spp. Samples from 25 farms were positive for Arcobacter butzleri and from 1 farm for Arcobacter cryaerophilus. Moreover, both Arcobacter butzleri and A. cryaerophilus were recovered from 1 positive sample. To evaluate a possible genetic variability, one strain of A. butzleri from each farm and the A. cryaerophilus sample were analyzed by pulsed-field gel electrophoresis. Genotyping revealed that Arcobacter spp. populations are heterogeneous, and no dominant clone has spread in the investigated samples. Our study is the first report on the isolation of both A. butzleri and A. cryaerophilus in raw milk in Finland. Based on our findings, the presence of Arcobacter species in raw milk may pose a potential hazard for human health, in particular for consumers who prefer drinking unpasteurized milk.

  20. Temporal and spatial distribution of Cronobacter isolates in a milk powder processing plant determined by pulsed-field gel electrophoresis.

    PubMed

    Hein, Ingeborg; Gadzov, Boris; Schoder, Dagmar; Foissy, Helmut; Malorny, Burkhard; Wagner, Martin

    2009-03-01

    A milk powder processing line was sampled for the presence of Enterobacteriaceae and the opportunistic neonatal pathogen Cronobacter at six different sampling sites during an 11-month period. The highest number of Enterobacteriaceae-positive samples was recovered from the raw milk concentrate before pasteurization (78.2%) and from nonproduct samples of the processing line (86.5%), which included swabs from the drying tower and screw conveyers, swabs from the explosion chamber, waste water after the automated cleaning-in-place procedure, air filter cut-outs, and floor samples underneath the outlet of the packaging machine. The prepackaged and packaged final product was contaminated at a rate of 6.6% and 7.1%, respectively. The prevalence of Cronobacter in the prefinal product and the prepackaged and packaged final product was 14.3%, 3.8%, and 2.1%, respectively. Pulsed-field gel electrophoresis (PFGE) analysis of 133 Cronobacter isolates yielded 40 different PFGE profiles. Long-term persistence in the processing line of some of these PFGE profiles was observed. Comparison of the PFGE profiles recovered at different sampling sites revealed the supply air as a potential source for extrinsic Cronobacter contamination. In addition, recovery of the same PFGE profiles before and after CIP events followed by heat treatment indicated the inefficiency of these hygiene measures to completely eliminate Cronobacter from all areas of the processing line. This information provides an essential basis for developing control and prevention strategies concerning this opportunistic pathogen.

  1. Pulsed-Field Gel Electrophoresis Genotyping of Taylorella equigenitalis Isolates Collected in the United States from 1978 to 2010▿

    PubMed Central

    Aalsburg, Alan M.; Erdman, Matthew M.

    2011-01-01

    Taylorella equigenitalis is the etiologic agent of contagious equine metritis (CEM), a venereal disease of horses. A total of 82 strains of T. equigenitalis isolated in the United States were analyzed by pulsed-field gel electrophoresis (PFGE) after digestion of genomic DNA with restriction enzyme ApaI. Twenty-eight of those strains isolated from horses in the 2009 U.S. outbreak (CEM09) were further analyzed with NotI and NaeI enzymes. When ApaI alone was used for analysis, the 82 isolates clustered into 15 different genotypes that clearly defined groups of horses with known epidemiological connections. The PFGE profiles of the CEM09 isolates were indistinguishable after digestion with ApaI, NotI, and NaeI and did not match those of isolates from previous U.S. outbreaks in 1978 and 2006 or of any other isolate from the National Veterinary Services Laboratories (NVSL) culture library. Coupled with the fact that the CEM09 isolates are epidemiologically related, these results suggest a common source for the outbreak not linked to previous occurrences of CEM in the United States. PMID:21191049

  2. Genotyping of Staphylococcus aureus isolated from various sites on farms with dairy sheep using pulsed-field gel electrophoresis.

    PubMed

    Vautor, E; Abadie, G; Guibert, J-M; Huard, C; Pépin, M

    2003-10-08

    We investigated the genetic diversity of 179 Staphylococcus aureus isolates recovered from various sites in 10 farms producing cheeses manufactured with raw ewe's milk. Isolates were collected from handcrafted cheeses, bulk tank milk, milk from half-udders, skin abscesses on the udder if present, hands and anterior nares of farmers, and air of the milking area. The isolates were typed using pulsed-field gel electrophoresis (PFGE) of DNA SmaI digests and compared to other isolates of S. aureus isolated in different hosts or in different locations. The results showed that nine farms were contaminated by S. aureus isolates with identical banding patterns (named OV) or by genetically related isolates (named OV'). These dominant banding patterns were found in a variable proportion of the samples from each farm (range: 11-100%). Most of the strains isolated from nasal carriage or strains isolated from other regions or from other animal species had different PFGE patterns to OV or OV', except for three strains. These results show that a single clone of S. aureus is widely distributed both in infected mammary glands and in cheese produced from raw milk. This study confirms that infected mammary glands are the main source of the contamination of dairy products in sheep.

  3. Differences between two clinical Staphylococcus capitis subspecies as revealed by biofilm, antibiotic resistance, and pulsed-field gel electrophoresis profiling.

    PubMed

    Cui, Bintao; Smooker, Peter M; Rouch, Duncan A; Daley, Andrew J; Deighton, Margaret A

    2013-01-01

    Coagulase-negative staphylococci have been identified as major causes of late-onset neonatal bacteremia in neonatal intensive care units. Sixty isolates of Staphylococcus capitis obtained from blood cultures of neonates between 2000 and 2005 were examined in this study. Biochemical analysis confirmed that 52 of these isolates belonged to the subsp. urealyticus, and the remaining 8 belonged to the subsp. capitis. Isolates of the predominant subsp. urealyticus clones were characterized by their resistance to penicillin, erythromycin, and oxacillin and their biofilm formation ability, whereas subsp. capitis isolates were generally antibiotic susceptible and biofilm negative. Pulsed-field gel electrophoresis (PFGE) after SacII digestion separated the 60 isolates into five major clusters. Sequence analysis showed that, in S. capitis, the ica operon plus the negative regulator icaR was 4,160 bp in length. PCRs demonstrated the presence of the ica operon in all isolates. Further analysis of five isolates (two biofilm-positive subsp. urealyticus, one biofilm-negative subsp. urealyticus, and two biofilm-negative subsp. capitis) revealed that the ica operons were identical in all of the biofilm-positive subsp. urealyticus strains; however, the biofilm-negative isolates showed variations. The distinctive phenotypic and genotypic characteristics revealed by this study may affect the epidemiology of the two subspecies of S. capitis in the clinical setting. These results may provide a better understanding of the contribution of these two species to bloodstream infections in neonates.

  4. Comparison of pulsed-field gel electrophoresis and enterobacterial repetitive intergenic consensus PCR and biochemical tests to characterize Lactococcus garvieae.

    PubMed

    Ture, M; Altinok, I; Capkin, E

    2015-01-01

    Biochemical test, pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) were used to compare 42 strains of Lactococcus garvieae isolated from different regions of Turkey, Italy, France and Spain. Twenty biotypes of L. garvieae were formed based on 54 biochemical tests. ERIC-PCR of genomic DNA from different L. garvieae strains resulted in amplification of multiple fragments of DNA in sizes ranging between 200 and 5000 bp with various band intensities. After cutting DNA with ApaI restriction enzyme and running on the PFGE, 11–22 resolvable bands ranging from 2 to 194 kb were observed. Turkish isolates were grouped into two clusters, and only A58 (Italy) strain was connected with Turkish isolates. Similarities between Turkish, Spanish, Italian and French isolates were <50% except 216-6 Rize strain. In Turkey, first lactococcosis occurred in Mugla, and then, it has been spread all over the country. Based on ERIC-PCR, Spanish and Italian strains of L. garvieae were related to Mugla strains. Therefore, after comparing PFGE profiles, ERIC-PCR profiles and phenotypic characteristics of 42 strains of L. garvieae, there were no relationships found between these three typing methods. PFGE method was more discriminative than the other methods. © 2014 John Wiley & Sons Ltd.

  5. Pulsed-field gel electrophoretic analysis and some characteristics of Staphylococcus aureus isolated from retail foods and human hands.

    PubMed

    Shimamura, Yuko; Murata, Masatsune

    2011-01-01

    This study investigates whether there is a predominant Staphylococcus aureus strain in retail foods and healthy human hands, and examines the relationship between pulsed-field gel electrophoresis (PFGE) banding patterns and the S. aureus characteristics of staphylococcal enterotoxin (SE) type, coagulase type, and β-lactamase activity. Ninety-four strains of S. aureus isolated from retail foods and healthy human hands were analyzed by PFGE. Several strains isolated from the same shop or a chain store showed identical patterns, indicating that the origins of these strains were identical. After excluding these strains showing identical patterns, 54 strains were used for the PFGE analysis. No spread of a particular clone in the environment surrounding the food was apparent. The PFGE analysis of these 54 strains was classified in 6 lineages (L1-L6). There was no relationship between the PFGE banding pattern and coagulase type or SE type. Eleven (84.6%) of the 13 isolates in PFGE banding pattern L5 did not produce β-lactamase, suggesting that the production of β-lactamase influenced a specific PFGE banding pattern.

  6. Incidence and molecular epidemiology of Pseudomonas aeruginosa bacteremias in patients with acute leukemia: analysis by pulsed-field gel electrophoresis.

    PubMed

    Fanci, R; Paci, C; Anichini, P; Pecile, P; Marra, G; Casini, C; Nicoletti, P

    2003-10-01

    The incidence and molecular epidemiology of P. aeruginosa bacteremias, were monitored in patients with acute leukemia to define mechanisms of possible nosocomial transmission. From September 1997 to March 2001 febrile episodes were examined and blood isolates of P. aeruginosa were studied employing Pulsed-Field gel Electrophoresis (PFGE). Evaluation of DNA correlation was performed according to Tenover criteria. A total of 309 febrile episodes occurred in 187 patients. Of 139 organisms isolated in 116 bacteremias, 48% were gram negative bacilli (GNB); P. aeruginosa bacteremias were recorded in 34 (51%) of GNB sepsis. Evaluation of DNA correlation showed 2 related in 1997, 7 related in 1998, 10 related in 1999, 6 related in 2000-2001 (mainly closely and possibly related); therefore isolates closely related among themselves were also possibly related with other strains. About 60% of patients with related strains were hospitalized in the same room or in different rooms but became infected in the same period. Our data suggest a horizontal spread among the patients even if other sources were possible. The study assessed the usefulness of PFGE in bacteriological epidemiology.

  7. A pulsed-field gel electrophoresis (PFGE) map of twelve loci on chromosome 11q11-q13

    SciTech Connect

    Petty, E.M.; Bale, A.E. ); Arnold, A. ); Marx, S.J. )

    1993-02-01

    We report a pulsed-field gel electrophoresis map of 12 loci on proximal human chromosome 11q. Linkage studies have shown that this region of chromosome 11 contains the genes for familial atopic disease (APY) and multiple endocrine neoplasia type I (MEN1) (4). A physical map containing polymorphic loci will aid in the isolation of these disease genes. The map reported here has two noncontiguous groups of loci accounting for 8 of the 12 loci evaluated. One group spans a maximum distance of 1600 kb and included D11S146, BCL1, PRAD1, INT2, and HSTF1. The other group includes FTY1, C1NH, and COX8. TCN1, PGA, and PYGM did not yield any comigrating fragments and could not be physically linked on this PFGE map. These data enhance previously published physical maps of proximal 11q by refining the localization of and distances between markers in the BCL1 region. Additionally, new information about the locations and physical relationships between FTH1, C1NH, and COX 8 is presented. 14 refs., 3 figs.

  8. Pulsed-field gel electrophoresis typing, antibiotic resistance, and plasmid profiles of Escherichia coli strains isolated from foods.

    PubMed

    Uysal, Ahmet; Durak, Yusuf

    2012-11-01

    Bacterial contamination in foods and antimicrobial resistance levels of common pathogenic strains causing food-borne disease are important in human health. Thus, typing technologies are important tools to determine primary sources of bacterial contamination. In this study, 40 Escherichia coli strains isolated from 85 food samples were evaluated in terms of genetic diversity, susceptibility to certain antibiotics, and plasmid profiles. Pulsed-field gel electrophoresis was used to identify the genetic relations of E. coli isolates. It was determined that the 40 E. coli strains revealed 32 different pulsotypes represented by 6 subtypes. Antibiotic susceptibility tests conducted by using a disc diffusion method against 15 antibiotics showed that although the isolates revealed 14 different types of resistance profiles, the strains showed the greatest resistance to ampicillin (77.5%), followed by ticarcillin-clavulanic acid (30%), tetracycline (22.5%), and cephalothin (14.5%). Plasmid isolations studies of the strains conducted by the method of alkaline lysis revealed that 18 (45%) of 40 E. coli strains contain 31 different plasmid bands ranging between 64.4 and 1 kb. The results showed that PFGE was a powerful method in tracking sources of food contamination and that the antibiotic resistance levels of food isolates were high and should be monitored.

  9. Studies on the genomic heterogeneity of Micrococcus luteus strains by macro-restriction analysis using pulsed-field gel electrophoresis.

    PubMed

    Murayama, O; Matsuda, M; Moore, J E

    2003-01-01

    Macro-restriction analysis by means of double digestion using DraI and VspI demonstrated that they cleaved the genomic DNAs from Micrococcus luteus JCM1464(T), JCM3347, and JCM3348 into four to five fragments in a distinguishable manner by pulsed-field gel electrophoresis (PFGE). Separate digestion with DraI and VspI cleaved the genomic DNA from M. luteus ATCC9341 into a relatively limited number of restriction fragments (six pieces). SspI and XbaI cleaved the genomic DNA from each of the four strains into restriction fragments in a distinctly different and distinguishable manner.Thus, PFGE profiles after digestion with these four restriction enzymes that recognize six specific base sequences demonstrated the heterogeneity at the whole genomic DNA level among the four strains of M. luteus. The size of the genomic DNA of M. luteus ATCC9341 was estimated to be approximately 2.3 Mb by the summing the lengths of the restriction fragments generated by each three restriction enzymes (DraI, SspI, and VspI) and averaging the results.

  10. Genetic Diversity of Streptococcus suis Strains Isolated from Pigs and Humans as Revealed by Pulsed-Field Gel Electrophoresis

    PubMed Central

    Berthelot-Hérault, Florence; Marois, Corinne; Gottschalk, Marcelo; Kobisch, Marylène

    2002-01-01

    The genetic diversity of 123 Streptococcus suis strains of capsular types 2, 1/2, 3, 7, and 9, isolated from pigs in France and from humans in different countries, was evaluated by pulsed-field gel electrophoresis (PFGE) of DNA restricted with SmaI. The method was highly discriminative (D = 0.98), results were reproducible, and the PFGE analysis was easy to interpret. Among all S. suis strains, 74 PFGE patterns were shown. At 60% homology, three groups (A, B, and C) were identified, and at 69% homology, eight subgroups (a to h) were observed. Strains isolated from diseased pigs or from humans were statistically clustered in group B, especially in subgroup d. By contrast, S. suis strains isolated from clinically healthy pigs were preferentially included in subgroup b of group A. Relationships could be established between capsular types 1/2, 3, and 9 and groups A, e, and B, respectively. S. suis strains isolated from humans were homogeneous, and a very high level of association between these strains and four DNA patterns was observed. The PFGE used in this study is a very useful tool for evaluating the genetic diversity of S. suis strains, and it would be used for epidemiological investigations. PMID:11825980

  11. Genetic diversity of Streptococcus suis strains isolated from pigs and humans as revealed by pulsed-field gel electrophoresis.

    PubMed

    Berthelot-Hérault, Florence; Marois, Corinne; Gottschalk, Marcelo; Kobisch, Marylène

    2002-02-01

    The genetic diversity of 123 Streptococcus suis strains of capsular types 2, 1/2, 3, 7, and 9, isolated from pigs in France and from humans in different countries, was evaluated by pulsed-field gel electrophoresis (PFGE) of DNA restricted with SmaI. The method was highly discriminative (D = 0.98), results were reproducible, and the PFGE analysis was easy to interpret. Among all S. suis strains, 74 PFGE patterns were shown. At 60% homology, three groups (A, B, and C) were identified, and at 69% homology, eight subgroups (a to h) were observed. Strains isolated from diseased pigs or from humans were statistically clustered in group B, especially in subgroup d. By contrast, S. suis strains isolated from clinically healthy pigs were preferentially included in subgroup b of group A. Relationships could be established between capsular types 1/2, 3, and 9 and groups A, e, and B, respectively. S. suis strains isolated from humans were homogeneous, and a very high level of association between these strains and four DNA patterns was observed. The PFGE used in this study is a very useful tool for evaluating the genetic diversity of S. suis strains, and it would be used for epidemiological investigations.

  12. Pulsed field gel electrophoresis: a review of application and interpretation in the molecular epidemiology of infectious disease.

    PubMed

    Goering, Richard V

    2010-10-01

    Over the years, approaches to the epidemiological analysis of infectious disease have undergone a remarkable evolutionary transition moving from phenotypic to molecular in nature. As discussed here, the quest for a clearer comparison of genomic relatedness between bacterial clinical isolates has involved four generations of molecular iteration. First generation plasmid analysis gave way to a second generation use of restriction enzymes and probes. This was followed by third generation pulsed field gel electrophoresis (PFGE) and PCR-based methods with movement now to fourth-generation DNA sequence-based approaches. Remarkably, despite (or perhaps because of) its more than 20-year history as a typing method, PFGE has demonstrated exceptional staying power. The reasons for this endurance as well as the pros and cons of PFGE use are examined in this review. In broad context the history and technology behind PFGE are considered. Issues commonly influencing the quality of PFGE data and its analysis are discussed. Specifics regarding the mechanics of DNA preparation, restriction-enzyme digestion, and proper conditions for electrophoresis are detailed and, most importantly for any approach to epidemiological assessment, issues regarding the analysis and interpretation of PFGE data are explored. Copyright 2010 Elsevier B.V. All rights reserved.

  13. Evaluation of the discriminatory power of pulsed-field gel electrophoresis and PCR fingerprinting for epidemiologic typing of Candida species.

    PubMed

    Voss, Andreas; Pfaller, Michael A.; Hollis, Richard J.; Melchers, Willem J.G.; Meis, Jacques F.G.M.

    1998-02-01

    OBJECTIVE: To evaluate the discriminatory power of genotyping methods (PCR fingerprinting and pulsed-field gel electrophoresis) validated for Candida albicans in other Candida species. METHODS: Molecular typing methods are increasingly being applied for studies where the interpretation of data essentially relies on the typing results rather than epidemiologic data. In this situation, the discriminatory power (ability to identify differences among epidemiologically unrelated strains) of the typing method is important in allowing one to draw valid conclusions. By applying PCR fingerprinting, electrophoretic karyotyping, and restriction fragment endonuclease analysis using standard restriction enzymes and primers proven to be useful in previous studies, we evaluated whether the use of multiple genotyping methods is sufficient to delineate known unrelated strains among seven Candida species. RESULTS: All three methods identified individual genotypes for each of the seven Candida species studied. However, optimal strain delineation required the combined use of all three typing methods and was observed only within the small number of C. albicans and C. tropicalis isolates tested in this study. CONCLUSION: Typing assays that are able to delineate a certain Candida species may not be used blindly for other species of that genus. Regarding the limited number of strains tested, further validation of the discriminative power of genotyping methods (including in C. tropicalis) should be done.

  14. In vivo conformation of mitochondrial DNA revealed by pulsed-field gel electrophoresis in the true slime mold, Physarum polycephalum.

    PubMed

    Sakurai, R; Sasaki, N; Takano, H; Abe, T; Kawano, S

    2000-04-28

    Pulsed-field gel electrophoresis (PFGE) was used to examine the in vivo and in vitro conformations of Physarum polycephalum mitochondrial DNA (mtDNA). We used plugs containing isolated mitochondria, isolated mitochondrial nucleoids (mt-nuclei), and isolated mtDNA, in addition to whole cells. The mtDNA contained in the myxamoebae, plasmodia, isolated mitochondria, and isolated mt-nuclei was circular, but most of the isolated mtDNA had been site-specifically fragmented and linearized during DNA preparation and storage under low ionic strength conditions. Restriction mapping of Physarum mtDNA by the direct digestion of the isolated mt-nuclei from two different strains, DP89 x AI16 and KM88 x AI16, resulted in the circular form. A linear mitochondrial plasmid, mF, is known to promote mitochondrial fusion and integration of itself into the mtDNA in Physarum. Linearization of mtDNA by the integration of the mF plasmid was demonstrated when we used PFGE to analyze isolated mitochondria from the plasmodial strain DP89 x NG7 carrying the mF plasmid (mF+). The PFGE system can be used not only to determine whether the form of mtDNA is linear or circular but also to analyze the dynamic conformational changes of mtDNA.

  15. Development and validation of a PulseNet standardized pulsed-field gel electrophoresis protocol for subtyping of Vibrio cholerae.

    PubMed

    Cooper, K L F; Luey, C K Y; Bird, M; Terajima, J; Nair, G B; Kam, K M; Arakawa, E; Safa, A; Cheung, D T; Law, C P; Watanabe, H; Kubota, K; Swaminathan, B; Ribot, E M

    2006-01-01

    PulseNet is a network that utilizes standardized pulsed-field gel electrophoresis (PFGE) protocols with the purpose of conducting laboratory-based surveillance of foodborne pathogens. PulseNet standardized PFGE protocols are subject to rigorous testing during the developmental phase and careful evaluation during a validation process assessing its robustness and reproducibility in different laboratories. Here we describe the development and validation of a rapid PFGE protocol for subtyping Vibrio cholerae for use in PulseNet International activities. While the protocol was derived from the existing PulseNet protocol for Escherichia coli O157, various aspects of this protocol were optimized for use with V. cholerae, most notably a change of the primary and secondary restriction enzyme to SfiI and NotI, respectively, and the use of a two-block electrophoresis program. External validation of this protocol was undertaken through a collaboration between three PulseNet Asia Pacific laboratories (Public Health Laboratory Centre, Hong Kong, National Institute of Infectious Diseases, Japan, and International Center for Diarrhoeal Diseases Research-Bangladesh) and PulseNet USA. Comparison of PFGE patterns generated by each of the participating laboratories demonstrated that the protocol is robust and reproducible.

  16. Comparison of ribotyping, arbitrarily primed PCR, and pulsed-field gel electrophoresis for molecular typing of Listeria monocytogenes.

    PubMed Central

    Louie, M; Jayaratne, P; Luchsinger, I; Devenish, J; Yao, J; Schlech, W; Simor, A

    1996-01-01

    Fifty-one clinical isolates of Listeria monocytogenes (15 isolates from two outbreaks and 36 epidemiologically unrelated isolates) were typed by conventional serotyping, ribotyping (RT), pulsed-field gel electrophoresis (PFGE), and arbitrarily primed PCR (AP-PCR). Serotyping was unable to distinguish between related and unrelated strains of L. monocytogenes. Each of the three molecular methods showed excellent typeability and reproducibility. Restriction with EcoRI and PvuII gave 16 and 23 RT patterns, respectively. Restriction with ApaI or SmaI generated 22 and 26 PFGE profiles, respectively. ApaI profiles were easier to interpret, with 10 to 15 bands each, while SmaI profiles had 15 to 20 bands each. AP-PCR with two different primers yielded 29 and 31 randomly amplified polymorphic DNA patterns, respectively. Strains from the same outbreak shared concordant patterns by each of the three methods. Of the three techniques evaluated, RT was the least discriminating and could not distinguish between strains from the two outbreaks. The abilities of AP-PCR and PFGE to differentiate between strains were comparable. However, AP-PCR was more rapid and easier to perform. We conclude that the DNA profiles generated by either AP-PCR or PFGE can be used to differentiate outbreak strains from epidemiologically unrelated strains and to clearly identify unrelated strains as being distinct from one another. We recommend that at least two independent primers be used for AP-PCR typing in order to improve its discriminatory power. PMID:8748263

  17. Casimir force in presence of multi layer magnetodielectric slabs

    SciTech Connect

    Kheirandish, Fardin; Soltani, Morteza; Sarabadani, Jalal

    2011-03-15

    Research Highlights: > The Casimir force has been obtained in the presence of some dielectrics. > The approach is based on a Lagrangian. > It can be generalized to include the rough surfaces. > Finite temperature correction can be easily obtained. - Abstract: By using the path-integral formalism, electromagnetic field in the presence of some linear, isotropic magnetodielectric slabs is quantized and related correlation functions are found. In the framework of path-integral techniques, Casimir force between two infinitely large, parallel and ideal conductors, with a different number of magnetodielectric slabs in between, is obtained by calculating the Green's function corresponding to each geometry.

  18. Instantaneous mantle flow induced by subduction of a freely sinking slab

    NASA Astrophysics Data System (ADS)

    Piromallo, C.; Becker, T. W.; Funiciello, F.; Faccenna, C.

    2007-05-01

    We conduct three-dimensional (3-D) subduction experiments by a finite element approach to study flow around slabs which are prescribed based on a transient subduction stage from a laboratory model. Instantaneous velocity fields are examined for a slab that sinks freely into the mantle, focusing on the toroidal vs. poloidal components as a function of boundary conditions (BCs), plate width, and viscosity contrast between slab and mantle. Results show that the toroidal flow is important for the circulation geometries in the vertical plane. In particular, the material resumed at surface in the back-arc wedge by the return flow cell below the slab tip is minimal with respect to 2-D models, in agreement with laboratory models. Furthermore, we find that circulation is characterized by an upward flow component close to slab sides that could be important for local tectonic structures at slab edges. We show that BCs affect the magnitude and pattern of velocities. In particular, in proximity of the slab the flow field is similar for no- and free-slip BCs, while strong variations exist elsewhere. Moreover, the characteristic spatial length-scale is given by the box height. By modeling different viscosity contrasts between slab and mantle (η'), we find that significant return flow around edges can only be obtained for stiff slabs and that the strength of the toroidal/poloidal Ratio increases with η', nearly independent of slab width. For η' ≥ 103, the toroidal is ~60-70% of the poloidal component, while we estimate about 40-50% for lower viscosity contrasts. In our models, the toroidal term peaks for slab/mantle viscosity ratios η'max~ 102. This trend is found not only for transient but also for steady-state, rollback subduction. Estimates for effective viscosity contrasts in nature are comparable to, or somewhat higher than ηmax.

  19. Erysipelothrix rhusiopathiae: genetic characterization of midwest US isolates and live commercial vaccines using pulsed-field gel electrophoresis.

    PubMed

    Opriessnig, T; Hoffman, L J; Harris, D L; Gaul, S B; Halbur, P G

    2004-03-01

    This is the first report of molecular characterization of US erysipelas field isolates and vaccine strains of Erysipelothrix rhusiopathiae by pulsed-field gel electrophoresis (PFGE). Erysipelas in pigs is mainly caused by E. rhusiopathiae serotypes 1a, 1b, and 2. In 2001, erysipelas reemerged as a clinical problem in pigs in the midwestern United States. In this work 90 erysipelas isolates (58 recent and 28 archived field isolates as well as 4 live-vaccine strains) were genetically characterized. Because of the limited availability of antiserum, 74/90 isolates (44/58 recent isolates) were serotyped. The serotype of the majority (79.6%) of the 44 recent isolates tested was determined to be 1a, 13.6% were serotype 1b, and 6.8% of recent isolates were serologically untypeable. Among all 90 isolates, 23 different PFGE patterns were identified. There were 43 isolates identified as serotype 1a with 4 genetic patterns: 38/43, 1A(I); 3/43, 1A(III); 1/43, 1B(V); and 1/43, 3B. Sixteen serotype 1b isolates had 11 unique genetic patterns: 4/16 were genotype 1B(III), 2/16 were genotype 3A(I), and 1/16 was in genotype groups 1A(V), 1A(VI), 1A(VII), 1B(I), 1B(IV), 1B(VII), 2, 4, and 5. Six genetic patterns were distinguished among the 10 serotype 2 isolates: 1A(IV) (1/10), 1A(V) (1/10), 1B(VI) (1/10), 2 (4/10), 7 (1/10), and 8 (2/8). Erysipelas vaccine strains (modified live) were similar to each other but different from current field strains, sharing 78.6% identity with the most prevalent genotype 1A(I) based on the PFGE-SmaI pattern. Compared with serotyping, PFGE genotyping is a more distinguishing technique, easy to perform and not dependent on the limited availability of antiserum.

  20. Pulsed-Field Gel Electrophoresis characterization of Listeria monocytogenes isolates from cheese manufacturing plants in São Paulo, Brazil.

    PubMed

    Barancelli, Giovana V; Camargo, Tarsila M; Gagliardi, Natália G; Porto, Ernani; Souza, Roberto A; Campioni, Fabio; Falcão, Juliana P; Hofer, Ernesto; Cruz, Adriano G; Oliveira, Carlos A F

    2014-03-03

    This study aimed to evaluate the occurrence of Listeria monocytogenes in cheese and in the environment of three small-scale dairy plants (A, B, C) located in the Northern region state of São Paulo, Brazil, and to characterize the isolates using conventional serotyping and PFGE. A total of 393 samples were collected and analyzed from October 2008 to September 2009. From these, 136 came from dairy plant A, where only L. seeligeri was isolated. In dairy plant B, 136 samples were analyzed, and L. innocua, L. seeligeri and L. welshimeri were isolated together with L. monocytogenes. In dairy plant C, 121 samples were analyzed, and L. monocytogenes and L. innocua were isolated. Cheese from dairy plants B and C were contaminated with Listeria spp, with L. innocua being found in Minas frescal cheese from both dairy plants, and L. innocua and L. monocytogenes in Prato cheese from dairy plant C. A total of 85 L. monocytogenes isolates were classified in 3 serotypes: 1/2b, 1/2c, and 4b, with predominance of serotype 4b in both dairy plants. The 85 isolates found in the dairy plants were characterized by genomic macrorestriction using ApaI and AscI with Pulsed Field Gel Electrophoresis (PFGE). Macrorestriction yielded 30 different pulsotypes. The presence of indistinguishable profiles repeatedly isolated during a 12-month period indicated the persistence of L. monocytogenes in dairy plants B and C, which were more than 100 km away from each other. Brine used in dairy plant C contained more than one L. monocytogenes lineage. The routes of contamination were identified in plants B and C, and highlighted the importance of using molecular techniques and serotyping to track L. monocytogenes sources of contamination, distribution, and routes of contamination in dairy plants, and to develop improved control strategies for L. monocytogenes in dairy plants and dairy products.

  1. A pulsed field gel electrophoresis (PFGE) study that suggests a major world-wide clone of Salmonella enterica serovar Enteritidis.

    PubMed

    Pang, Jen-Chieh; Chiu, Tsai-Hsin; Helmuth, Reiner; Schroeter, Andreas; Guerra, Beatriz; Tsen, Hau-Yang

    2007-05-30

    Since human infections by Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) have been increasing world-wide over the past years and epidemiological studies have implicated the consumption of meat, poultry, eggs and egg products, elucidation of the predominant subtypes for this Salmonella spp. is important. In this study, 107 poultry and food isolates of Salmonella Enteritidis obtained from Germany were analyzed by pulsed field gel electrophoresis (PFGE), and the subtypes were compared with those of the 124 human isolates obtained in Taiwan. Results showed that for these 107 poultry and food isolates, when XbaI, SpeI and NotI were used for chromosomal DNA digestion followed by PFGE analysis, a total of 19, 20 and 19 PFGE patterns, respectively, were identified. Of them, 51 (47.7%), 52 (48.6%) and 42 (39.3%) strains belong to a single pattern of X3, S3 and N3, respectively, and 34 strains belong to a pattern combination of X3S3N3, which was the major subtype. When PFGE patterns of these 107 German isolates were compared with those of the 124 human isolates obtained in Taiwan, pattern combination of X3S3N3 was found as the most common pattern shared by isolates from both areas. PT4 is a major phage type for German and Taiwan isolates. Although most of the X3S3N3 strains are of this phage type, some strains of other PFGE patterns are also of this phage type. Since strains used in this study were unrelated, i.e., they were isolated from different origins in areas geographically far apart from each other, the PFGE study suggests a major world-wide clone of S. enterica serovar Enteritidis.

  2. Analysis of Genetic Diversity of Streptococcus suis Clinical Isolates from Pigs in Spain by Pulsed-Field Gel Electrophoresis

    PubMed Central

    Vela, Ana I.; Goyache, Joaquin; Tarradas, Carmen; Luque, Inmaculada; Mateos, Ana; Moreno, Miguel A.; Borge, Carmen; Perea, J. Anselmo; Domínguez, Lucas; Fernández-Garayzábal, José F.

    2003-01-01

    Pulsed-field gel electrophoresis (PFGE) was used to investigate the diversity of Streptococcus suis isolates of various serotypes recovered from swine clinical samples in Spain. Capsular types 9 (64.9%) and 2 (14.8%) were the most frequently isolated serotypes followed by serotype 7 (5.9%) and serotype 8 (4.3%). The PFGE results of this study with 60 different pulsotypes indicate a great genetic diversity among the S. suis isolates, which is consistent with the broad distribution of S. suis in the swine population. Forty-five percent of the pulsotypes corresponded to single isolates, no pulsotype was common to all farms, and at least 3 different pulsotypes were isolated in 56% of herds in which more than 3 clinical isolates were analyzed. These results reveal a great diversity both between and within herds throughout the strains of S. suis studied, demonstrating that different strains of S. suis are associated with infection in pigs. Some pulsotypes were more frequently isolated and exhibited a wider distribution over herds than others, and were the unique or predominant strains in several herds, suggesting the existence of a prevalent or a few prevalent clones responsible for a large proportion of clinical cases. Overall, the great genetic heterogeneity of the clinical strains of S. suis, the isolation of different strains within the same herd, and the predominance of particular strains in some herds are evidence that infection by S. suis is a dynamic process and reinforce the idea that the epidemiology of S. suis infection is very complex. PMID:12791872

  3. Diversity of Campylobacter isolates from retail poultry carcasses and from humans as demonstrated by pulsed-field gel electrophoresis.

    PubMed

    Dickins, M Avery; Franklin, Sharon; Stefanova, Rossina; Schutze, Gordon E; Eisenach, Kathleen D; Wesley, Irene; Cave, M Donald

    2002-06-01

    Campylobacter spp. are a major contaminant of poultry. Eating undercooked chicken and handling raw poultry have been identified as risk factors for campylobacteriosis in humans. Previous studies have found Campylobacter spp. on 90% of poultry carcasses. In the present study, pulsed-field gel electrophoresis (PFGE) was used to assess the genetic diversity of strains on retail poultry carcasses. PFGE patterns of isolates from campylobacteriosis cases were compared to those from the poultry isolates. Over a 1-year study period (March 2000 through February 2001), whole fresh young chickens (n = 72) were obtained from three retail outlets in an urban community in the south-central United States. Campylobacter spp. were isolated from 82% of these carcasses. Strains (n = 70) were defined on the basis of their PFGE pattern. Sixty-seven percent of the carcasses from which Campylobacter spp. were isolated were contaminated with more than one PFGE-distinguishable strain. During the 1-year study period, most of the PFGE patterns (59%) were limited to isolates obtained from a single carcass. Forty-one percent of the PFGE-distinguishable strains were recovered from more than one carcass. Ninety-seven percent of the carcasses contaminated with the same strain were purchased at the same time from the same store. To examine the degree of genetic stability, four strains were followed in vitro over an estimated 1,000 doublings. The PFGE pattern of one of these isolates underwent minor changes during in vitro growth. The data indicate extensive variability in the PFGE patterns of Campylobacter spp. isolated from humans and from poultry carcasses. In spite of difficulties caused by such diversity and the fact that some carcasses are contaminated with more than one strain, the pattern variation provides a useful method for linking a particular strain to its source.

  4. Use of pulsed-field gel electrophoresis to determine genomic diversity in strains of Helicobacter hepaticus from geographically distant locations.

    PubMed Central

    Saunders, K E; McGovern, K J; Fox, J G

    1997-01-01

    In 1992 a helical microorganism associated with chronic active hepatitis and a high incidence of hepatocellular tumors was identified in the hepatic parenchyma of A/JCr mice. By using biochemical tests, phenotypic characterization, and 16S rRNA gene sequence analysis, the organism was classified as a novel Helicobacter species and named Helicobacter hepaticus. Recent surveys completed in our laboratory indicate that H. hepaticus is widespread in academic and commercial mouse colonies. The aim of this study was to examine the H. hepaticus genome by pulsed-field gel electrophoresis (PFGE) to determine the degree of genomic variation and genomic size. This technique has been used to identify significant genomic diversity among strains of Helicobacter pylori and to demonstrate only slight genomic diversity among strains of Helicobacter mustelae. Genomic DNAs from 11 isolates of H. hepaticus from the United States, Germany, France, and The Netherlands were subjected to PFGE after digestion with SmaI. Isolates from three independent sources within the United States had very similar PFGE patterns, suggesting that the genomic DNAs of these isolates are conserved. Genomic DNA isolated from a fourth source within the United States had a PFGE pattern different from those of the other U.S. isolates. Isolates obtained from Germany, France, and The Netherlands had PFGE patterns that differed markedly from those of the U.S. isolates and from one another. The use of DNA fingerprinting may be useful in subsequent epidemiological studies of H. hepaticus when the source and method of spread of this murine pathogen need to be ascertained. By PFGE, the genomic size of H. hepaticus is estimated to be roughly 1.3 Mb, which compares to 1.67 Mb for H. pylori and 1.7 Mb for H. mustelae. PMID:9350747

  5. Comparison of multilocus sequence typing and pulsed-field gel electrophoresis for Salmonella spp. identification in surface water

    NASA Astrophysics Data System (ADS)

    Kuo, Chun Wei; Hao Huang, Kuan; Hsu, Bing Mu; Tsai, Hsien Lung; Tseng, Shao Feng; Kao, Po Min; Shen, Shu Min; Chou Chiu, Yi; Chen, Jung Sheng

    2013-04-01

    Salmonella is one of the most important pathogens of waterborne diseases with outbreaks from contaminated water reported worldwide. In addition, Salmonella spp. can survive for long periods in aquatic environments. To realize genotypes and serovars of Salmonella in aquatic environments, we isolated the Salmonella strains by selective culture plates to identify the serovars of Salmonella by serological assay, and identify the genotypes by Multilocus sequence typing (MLST) based on the sequence data from University College Cork (UCC), respectively. The results show that 36 stream water samples (30.1%) and 18 drinking water samples (23.3%) were confirmed the existence of Salmonella using culture method combined PCR specific invA gene amplification. In this study, 24 cultured isolates of Salmonella from water samples were classified to fifteen Salmonella enterica serovars. In addition, we construct phylogenetic analysis using phylogenetic tree and Minimum spanning tree (MST) method to analyze the relationship of clinical, environmental, and geographical data. Phylogenetic tree showed that four main clusters and our strains can be distributed in all. The genotypes of isolates from stream water are more biodiversity while comparing the Salmonella strains genotypes from drinking water sources. According to MST data, we can found the positive correlation between serovars and genotypes of Salmonella. Previous studies revealed that the result of Pulsed field gel electrophoresis (PFGE) method can predict the serovars of Salmonella strain. Hence, we used the MLST data combined phylogenetic analysis to identify the serovars of Salmonella strain and achieved effectiveness. While using the geographical data combined phylogenetic analysis, the result showed that the dominant strains were existed in whole stream area in rainy season. Keywords: Salmonella spp., MLST, phylogenetic analysis, PFGE

  6. Epidemiologic analysis of sporadic Salmonella typhi isolates and those from outbreaks by pulsed-field gel electrophoresis.

    PubMed Central

    Thong, K L; Cheong, Y M; Puthucheary, S; Koh, C L; Pang, T

    1994-01-01

    Pulsed-field gel electrophoresis (PFGE) was used to compare and analyze 158 isolates of Salmonella typhi from five well-defined outbreaks of typhoid fever in Malaysia and also isolates involved in sporadic cases of typhoid fever occurring during the same period. Digestion of chromosomal DNAs from these S. typhi isolates with the restriction endonucleases XbaI (5'-TCTAGA-3'), SpeI (5'-ACTAGT-3'), and AvrII (5'-CCTAGG-3') and then PFGE produced restriction endonuclease analysis (REA) patterns consisting of 11 to 24 DNA fragments ranging in size from 20 to 630 kbp. Analysis of the REA patterns generated by PFGE after digestion with XbaI and SpeI indicated that the S. typhi isolates obtained from sporadic cases of infection were much more heterogeneous (at least 13 different REA patterns were detected; Dice coefficient, between 0.73 and 1.0) than those obtained during outbreaks of typhoid fever. The clonal nature and the close genetic identities of isolates from outbreaks in Alor Setar, Penang, Kota Kinabalu, Johor Bahru, and Kota Bahru were suggested by the fact that only a limited number of REA patterns, which mostly differed by only a single band, were detected (one to four patterns; Dice coefficient, between 0.82 and 1.0), although a different pattern was associated with each of these outbreaks. Comparison of REA patterns with ribotyping for 18 S. typhi isolates involved in sporadic cases of infection showed a good correlation, in that 72% of the isolates were in the same group. There was no clear correlation of phage types with a specific REA pattern. We conclude that PFGE of s. typhi chromosomal DNA digested with infrequently cutting restriction endonucleases is a useful method for comparing and differentiating S. typhi isolates for epidemiological purposes. Images PMID:7914202

  7. Pulsed-Field Gel Electrophoresis Analysis of Bordetella pertussis Isolates Circulating in Europe from 1998 to 2009

    PubMed Central

    Advani, Abdolreza; Hallander, Hans O.; Dalby, Tine; Krogfelt, Karen Angeliki; Guiso, Nicole; Njamkepo, Elisabeth; von Könnig, Carl Heinz Wirsing; Riffelmann, Marion; Mooi, Frits R.; Sandven, Per; Lutyńska, Anna; Fry, Norman K.; Mertsola, Jussi

    2013-01-01

    Between 1998 and 2009, Bordetella pertussis clinical isolates were collected during three periods, i.e., 1998 to 2001 (n = 102), 2004 to 2005 (n = 154), and 2007 to 2009 (n = 140), from nine countries with distinct vaccination programs, i.e., Denmark, Finland, France, Germany, The Netherlands, Norway, Poland, Sweden, and the United Kingdom. Pulsed-field gel electrophoresis (PFGE) analysis was performed according to standardized recommendations for epidemiological typing of B. pertussis. There were 81 different PFGE profiles, five of which (BpSR3, BpSR5, BpSR10, BpSR11, and BpSR12) were observed in 61% of the 396 isolates and shown to be predominant in almost all countries. The major profile, BpSR11, showed a decreasing trend from 25% to 30% in 1998 to 2005 to 13% in 2007 to 2009, and there were increases in BpSR3 and BpSR10 from 0% and 8% to 21% and 22%, respectively. One difference between these profiles is that BpSR11 contains isolates harboring the fim3-2 allele and BpSR3 and BpSR10 contain isolates harboring the fim3-1 allele. The total proportion of the five predominant profiles increased from 44% in 1998 to 2001 to 63% in 2004 to 2005 to 70% in 2007 to 2009. In conclusion, common PFGE profiles were identified in B. pertussis populations circulating in European countries with different vaccination programs and different vaccine coverages. These prevalent isolates contain the novel pertussis toxin promoter ptxP3 allele. However, there is evidence for diversifying selection between ptxP3 strains characterized by distinct PFGE profiles. This work shows that, even within a relatively short time span of 10 years, successful isolates which spread through Europe and cause large shifts in B. pertussis populations may emerge. PMID:23175253

  8. Analysis of genetic diversity of Streptococcus suis clinical isolates from pigs in Spain by pulsed-field gel electrophoresis.

    PubMed

    Vela, Ana I; Goyache, Joaquin; Tarradas, Carmen; Luque, Inmaculada; Mateos, Ana; Moreno, Miguel A; Borge, Carmen; Perea, J Anselmo; Domínguez, Lucas; Fernández-Garayzábal, José F

    2003-06-01

    Pulsed-field gel electrophoresis (PFGE) was used to investigate the diversity of Streptococcus suis isolates of various serotypes recovered from swine clinical samples in Spain. Capsular types 9 (64.9%) and 2 (14.8%) were the most frequently isolated serotypes followed by serotype 7 (5.9%) and serotype 8 (4.3%). The PFGE results of this study with 60 different pulsotypes indicate a great genetic diversity among the S. suis isolates, which is consistent with the broad distribution of S. suis in the swine population. Forty-five percent of the pulsotypes corresponded to single isolates, no pulsotype was common to all farms, and at least 3 different pulsotypes were isolated in 56% of herds in which more than 3 clinical isolates were analyzed. These results reveal a great diversity both between and within herds throughout the strains of S. suis studied, demonstrating that different strains of S. suis are associated with infection in pigs. Some pulsotypes were more frequently isolated and exhibited a wider distribution over herds than others, and were the unique or predominant strains in several herds, suggesting the existence of a prevalent or a few prevalent clones responsible for a large proportion of clinical cases. Overall, the great genetic heterogeneity of the clinical strains of S. suis, the isolation of different strains within the same herd, and the predominance of particular strains in some herds are evidence that infection by S. suis is a dynamic process and reinforce the idea that the epidemiology of S. suis infection is very complex.

  9. Genomic Diversity within the Genus Pediococcus as Revealed by Randomly Amplified Polymorphic DNA PCR and Pulsed-Field Gel Electrophoresis

    PubMed Central

    Simpson, P. J.; Stanton, C.; Fitzgerald, G. F.; Ross, R. P.

    2002-01-01

    The genomic diversity of 33 previously assigned strains from six species within the genus Pediococcus was assessed by randomly amplified polymorphic DNA (RAPD) PCR and pulsed-field-gel electrophoresis (PFGE). The RAPD PCR patterns produced by two separate random primers, termed P1 (ACGCGCCCT) and P2 (ATGTAACGCC), were compared by the Pearson correlation coefficient and the unweighted pair group method with arithmetic averages clustering algorithm. Pattern variations between repeat samples set a strain discrimination threshold of less than 70% similarity. P1 and P2 primers alone and in combination produced 14, 21, and 28 distinct patterns, respectively. When each strain was assigned with a type strain with which it shared the highest level of similarity, both primers grouped 17 of the 27 strains to their proposed species. PFGE following genomic digestion with the restriction enzymes ApaI, NotI, and AscI produced 30, 32, and 28 distinct macrorestriction patterns, respectively. Specific DNA fragments within the NotI and AscI macrorestriction patterns for each strain were observed that allowed 27 of the 33 strains to be assigned to their proposed species. For example, following digestion with AscI, all Pediococcus parvulus strains were characterized by two DNA fragments, one of approximately 220 kb and another between 700 and 800 kb. The exceptions correlated with those observed with both RAPD PCR primers and included three P. damnosus and two P. pentosaceus strains that grew at temperatures regarded as nonpermissive for their proposed species but not for those with which they grouped. PMID:11823217

  10. Performance Assessment of DNA Fragment Sizing by High-Sensitivity Flow Cytometry and Pulsed-Field Gel Electrophoresis

    PubMed Central

    Ferris, Matthew M.; Yan, Xiaomei; Habbersett, Robbert C.; Shou, Yulin; Lemanski, Cheryl L.; Jett, James H.; Yoshida, Thomas M.; Marrone, Babetta L.

    2004-01-01

    The sizing of restriction fragments is the chief analytical technique utilized in the production of DNA fingerprints. Few techniques have been able to compete with pulsed-field gel electrophoresis (PFGE), which is capable of discriminating among bacteria at species and strain levels by resolving restriction fragments. However, an ultrasensitive flow cytometer (FCM) developed in our lab has also demonstrated the ability to discriminate bacteria at species and strain levels. The abilities of FCM warrant a quantitative parallel comparison with PFGE to assess and evaluate the accuracy and precision of DNA fragment sizing by both techniques. Replicate samples of Staphylococcus aureus Mu50 were analyzed along with two clinical S. aureus isolates. The absolute fragment sizing accuracy was determined for PFGE (5% ± 2%) and FCM (4% ± 4%), with sequence-predicted Mu50 SmaI fragment sizes used as a reference. Precision was determined by simple arithmetic methods (relative standard deviation for PFGE [RSDPFGE ] = 3% ± 2% and RSDFCM = 1.2% ± 0.8%) as well as by the use of dendrograms derived from Dice coefficient-unweighted pair group method with arithmetic averages (UPGMA) and Pearson-UPGMA analyses. All quantitative measures of PFGE and FCM precision were equivalent, within error. The precision of both methods was not limited by any single sample preparation or analysis step that was tracked in this study. Additionally, we determined that the curve-based clustering of fingerprint data provided a more informative and useful assessment than did traditional band-based methods. PMID:15131156

  11. Analysis of Molecular Epidemiology of Chilean Salmonella enterica Serotype Enteritidis Isolates by Pulsed-Field Gel Electrophoresis and Bacteriophage Typing

    PubMed Central

    Fernandez, Jorge; Fica, Alberto; Ebensperger, German; Calfullan, Hector; Prat, Soledad; Fernandez, Alda; Alexandre, Marcela; Heitmann, Ingrid

    2003-01-01

    Human Salmonella enterica serotype Enteritidis infections emerged in Chile in 1994. S. enterica serotype Enteritidis phage type 1 isolates predominated in the north, and phage type 4 isolates predominated in the central and southern regions. A study was planned to characterize this epidemic using the best discriminatory typing technique. Research involved 441 S. enterica serotype Enteritidis isolates, including clinical preepidemic samples (n = 74; 1975 to 1993) and epidemic (n = 199), food (n = 72), poultry (n = 57), and some Latin American (n = 39) isolates. The best method was selected based on a sample of preepidemic isolates, analyzing the discriminatory power (DP) obtained by phage typing and randomly amplified polymorphic DNA and pulsed-field gel electophoresis (PFGE) analysis. The highest DP was associated with BlnI PFGE-bacteriophage typing analysis (0.993). A total of 38 BlnI patterns (B patterns) were identified before the epidemic period, 19 since 1994, and only 4 in both periods. Two major clusters were identified by phylogenetic analysis, and the predominant B patterns clustered in the same branch. Combined analysis revealed that specific B pattern-phage type combinations (subtypes) disappeared before 1994, that different genotypes associated with S. enterica serotype Enteritidis phage type 4 had been observed since 1988, and that strain diversity increased before the expansion of S. enterica serotype Enteritidis in 1994. Predominant subtype B3-phage type 4 was associated with the central and southern regions, and subtype B38-phage type 1 was associated with the north (P < 0.0001). Food and poultry isolates matched the predominant S. enterica serotype Enteritidis subtypes, but isolates identified in neighboring countries (Peru and Bolivia) did not match S. enterica serotype Enteritidis subtypes identified in the north of Chile. The results of this work demonstrate that genetic diversity, replacement, and expansion of specific S. enterica serotype

  12. Epidemiological Typing of Campylobacter Isolates from Meat Processing Plants by Pulsed-Field Gel Electrophoresis, Fatty Acid Profile Typing, Serotyping, and Biotyping

    PubMed Central

    Steele, M.; McNab, B.; Fruhner, L.; DeGrandis, S.; Woodward, D.; Odumeru, J. A.

    1998-01-01

    Campylobacter spp. are a leading cause of bacterial gastroenteritis. Foods of animal origin, particularly undercooked poultry, are common sources of Campylobacter species associated with disease in humans. A collection of 110 Campylobacter jejuni and 31 C. coli human and environmental isolates from different Ontario, Canada, abattoirs were analyzed by pulsed-field gel electrophoresis, fatty acid profile typing, and biotyping. Previously collected serotyping data for the same isolates were also analyzed in this study. Pulsed-field gel electrophoresis was found to be the most discriminatory of the typing methods, followed by serotyping, fatty acid profile typing, and biotyping. A wide variety of typing profiles were observed within the isolates, suggesting that several different Campylobacter sp. strains were present within the abattoirs. PMID:9647797

  13. Epidemiological typing of Campylobacter isolates from meat processing plants by pulsed-field gel electrophoresis, fatty acid profile typing, serotyping, and biotyping.

    PubMed

    Steele, M; McNab, B; Fruhner, L; DeGrandis, S; Woodward, D; Odumeru, J A

    1998-07-01

    Campylobacter spp. are a leading cause of bacterial gastroenteritis. Foods of animal origin, particularly under-cooked poultry, are common sources of Campylobacter species associated with disease in humans. A collection of 110 Campylobacter jejuni and 31 C. coli human and environmental isolates from different Ontario, Canada, abattoirs were analyzed by pulsed-field gel electrophoresis, fatty acid profile typing, and biotyping. Previously collected serotyping data for the same isolates were also analyzed in this study. Pulsed-field gel electrophoresis was found to be the most discriminatory of the typing methods, followed by serotyping, fatty acid profile typing, and biotyping. A wide variety of typing profiles were observed within the isolates, suggesting that several different Campylobacter sp. strains were present within the abattoirs.

  14. Out-of-plane resonances in terahertz photonic crystal slabs modulated by optical pumping.

    PubMed

    Shi, Yulei; Zhou, Qing-Li; Liu, Wei; Zhang, Cunlin

    2011-10-10

    This paper describes detailed optical-pump-terahertz-probe studies of two-dimensional photonic crystal slabs for propagation perpendicular to the slabs. When the slabs are excited by an 800 nm pump pulse and the effect of shielding by photocarriers is removed, we find that the decaying tail in the transmitted terahertz radiation is strikingly enhanced. The photocarriers weaken guided resonances, but they also greatly enhance the excitation efficiency of guided resonances and the ability of the guided resonances to transfer energy back to the radiation field. This increases the resonance-assisted contribution to transmitted field. The photoinduced resonant extremes agree well with the Fano model.

  15. Pulsed-field gel electrophoresis analysis of more than one clinical isolate of Campylobacter spp. from each of 49 patients in New Zealand.

    PubMed

    Gilpin, Brent; Robson, Beth; Lin, Susan; Scholes, Paula; On, Stephen

    2012-02-01

    Pulsed-field gel electrophoresis (PFGE) analysis demonstrated that while 76% of patients had only one genotype of campylobacter, 10% carried two different but related genotypes (Dice coefficients > 0.78), and 14% carried at least two unrelated genotypes (Dice coefficients < 0.65). This supports the clustering of Campylobacter isolates with similar PFGE patterns, highlights the need to analyze multiple isolates from both sources and patients, and confirms that caution should be exercised before epidemiological links between patients or sources are dismissed.

  16. What really causes flat slab subduction?

    NASA Astrophysics Data System (ADS)

    Manea, V. C.; Perez-Gussinye, M.; Manea, M.

    2014-12-01

    How flat slab geometries are generated has been long debated. It has been suggested thattrenchward motion of thick cratons in some areas of South America and Cenozoic NorthAmerica progressively closed the asthenospheric wedge and induced flat subduction. Here wedevelop time-dependent numerical experiments to explore how trenchward motion of thickcratons may result in flat subduction. We find that as the craton approaches the trench andthe wedge closes, two opposite phenomena control slab geometry: the suction between oceanand continent increases, favoring slab flattening, while the mantle confined within the closingwedge dynamically pushes the slab backward and steepens it. When the slab retreats, as inthe Peru and Chile flat slabs, the wedge closure rate and dynamic push are small and suctionforces generate, in some cases, flat subduction. We model the past 30 m.y. of subduction in theChilean flat slab area and demonstrate that trenchward motion of thick lithosphere, 200-300km, currently ~700-800 km away from the Peru-Chile Trench, reproduces a slab geometrythat fits the stress pattern, seismicity distribution, and temporal and spatial evolution ofdeformation and volcanism in the region. We also suggest that varying trench kinematics mayexplain some differing slab geometries along South America. When the trench is stationaryor advances, the mantle flow within the closing wedge strongly pushes the slab backward andsteepens it, possibly explaining the absence of flat subduction in the Bolivian orocline.

  17. The influence of particle size and static magnetic fields on the uptake of magnetic nanoparticles into three dimensional cell-seeded collagen gel cultures.

    PubMed

    Lewis, Emily E L; Child, Hannah W; Hursthouse, Andrew; Stirling, David; McCully, Mark; Paterson, David; Mullin, Margaret; Berry, Catherine C

    2015-08-01

    Over recent decades there has been and continues to be major advances in the imaging, diagnosis and potential treatment of medical conditions, by the use of magnetic nanoparticles. However, to date the majority of cell delivery studies employ a traditional 2D monolayer culture. This article aims to determine the ability of various sized magnetic nanoparticles to penetrate and travel through a cell seeded collagen gel model, in the presence or absence of a magnetic field. Three different sized (100, 200, and 500 nm) nanoparticles were employed in the study. The results showed cell viability was unaffected by the presence of nanoparticles over a 24-h test period. The initial uptake of the 100 nm nanoparticle into the collagen gel structure was superior compared to the larger sized nanoparticles under the influence of a magnetic field and incubated for 24 h. Interestingly, it was the 200 nm nanoparticles, which proved to penetrate the gel furthest, under the influence of a magnetic field, during the initial culture stage after 1-h incubation.

  18. Role of Hydrogen in stagnant slabs and big mantle wedge

    NASA Astrophysics Data System (ADS)

    Ohtani, E.; Zhao, D.

    2008-12-01

    Eastern China, Europe, and United State (e.g., [7]). According to the BMW model by Zhao [2], the intra-plate volcanisms in Northeast China including Mt. Changbai are different from the hot plumes and they might be generated due to some processes related to the deep-seated dehydration from the stagnant slab. Recent geochemical studies on volcanic rocks and associated mantle xenoliths in Northeast China (e.g., [8]) indicated that there is no geochemical evidence for involvement of subducting slab in most basalts, i.e., no depletion of high field strength elements and no enrichment of large ion lithophile elements. There is no clear evidence for a high-3He/4He mantle plume component in these rocks, i.e., 3He/4He ratios are significantly below the high 3He/4He ratios of mantle plumes such as those beneath Hawaii and Iceland. The geochemical signatures of the deep dehydration should be different from those in the conventional mantle wedge, since the fluids generated at such depths are completely different from those at the shallow depths. Further studies including the element partitioning between fluids and mantle under the deep upper mantle and the transition zone conditions are necessary to clarify the possible role of the Big Mantle Wedge on the intra-plate volcanism. [1] Fukao, et al., J. G. R. 108, doi:10.1029/2001JB000989, 2003. [2] Zhao et al., Chin. Sci. Bulletin 49, 1401, 2004, [3] Ohtani, Elements, 1, 25, 2005. [4] Richard et al., EPSL, 251, 156, 2006. [5] Hae et al., EPSL, 243, 141, 2006. [6] Litasov and Ohtani, PEPI, 134, 105, 2002. [7] Song et al., Nature, 427, 530, 2004. [8] Chen et al., Lithos, 96, 108, 2007

  19. Slab Driven Mantle Deformation and Plate-Mantle Decoupling

    NASA Astrophysics Data System (ADS)

    Jadamec, M. A.; MacDougall, J.; Fischer, K. M.

    2015-12-01

    Observations of shear wave splitting derived from local sources in subduction zones suggest viscous flow in the mantle wedge is commonly non-parallel to both the subducting plate velocity vector and the motion of the overriding plate. However, far from the subduction zone trench, observations indicate the fast axis of shear wave splitting tends to align with the velocity vector of the surface plates. Similarly, previous 3D geodynamic models show the slab can drive local decoupling of the mantle and surface plates, in both direction and speed. This suggests that there is some distance from the trench over which there is significant decoupling of the mantle flow from surface plate motion, and that this decoupling zone then decays with continued distance from the trench, resulting in far-field plate-mantle coupling. Here we present results from geodynamic models of subduction coupled with calculations of olivine fabric deformation and synthetic splitting to 1) examine the influence of slab strength, slab dip, and non-Newtonian viscosity on the deformation fabric in the mantle wedge and subslab mantle and 2) quantify the spatial extent and intensity of this slab driven decoupling zone. We compare the deformation fabric in a 2D corner flow solution with varying dip to that of a 2D free subduction model with varying initial dip and slab strength. The results show that using an experimentally derived flow law to define viscosity (both diffusion creep and dislocation creep deformation mechanisms) has a first order effect on the viscosity structure and flow velocity in the upper mantle. The free subduction models using the composite viscosity formulation produce a zone of subduction induced mantle weakening that results in reduced viscous support of the slab and lateral variability in coupling of the mantle to the base of the surface plates. The maximum yield stress, which places an upper bound on the slab strength, can also have a significant impact on the viscosity

  20. Laboratory and field evaluation of a combined fluid-loss-control additive and gel breaker for fracturing fluids

    SciTech Connect

    Cantu, L.A.; Boyd, P.A. )

    1990-08-01

    More than 200% increase in fracture conductivity and permeability was obtained when a new degradable fluid-loss-control additive was used in place of silica flour (SF) in 40-lbm crosslinked hydroxypropyl-guar (HPG) fracturing-fluid systems. The new additive, and organic acid particulate (OAP), slowly degraded into water-soluble monomeric units at temperatures {ge}150{degrees}F after fracture stimulation experiments. The high-acid-content degradation product then acted as an excellent HPG gel breaker and effectively cleaned the proppant packs. As a fluid-loss-control additive, the measured wall-building coefficients were as good as, or better than, those of SF in crosslinked-gel, linear-gel, and N{sub 2}-foam systems. This paper summarizes a 2-year study of the evaluation and application of this new product in fracturing-fluid systems.

  1. Laser applications in machining slab materials

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoping

    1990-10-01

    Since the invention of the laser back in 1960, laser technology has been extensively applied in many fields of science and technology. These has been a history of nearly two decades of using lasers as an energy source in machining materials, such as cutting, welding, ruling and boring, among other operations. With the development of flexible automation in production, the advantages of laser machining have has grown more and more obvious. The combination of laser technology and computer science further promotes the enhancement and upgrading of laser machining and related equipment. At present, many countries are building high quality laser equipment for machining slab materials, such as the Coherent and Spectra Physics corporations in the United States, the Trumpf Corporation in West Germany, the Amada Corporation in Japan, and the Bystronic Corporation in Switzerland, among other companies.

  2. Higher order modes in photonic crystal slabs.

    PubMed

    Gansch, Roman; Kalchmair, Stefan; Detz, Hermann; Andrews, Aaron M; Klang, Pavel; Schrenk, Werner; Strasser, Gottfried

    2011-08-15

    We present a detailed investigation of higher order modes in photonic crystal slabs. In such structures the resonances exhibit a blue-shift compared to an ideal two-dimensional photonic crystal, which depends on the order of the slab mode and the polarization. By fabricating a series of photonic crystal slab photo detecting devices, with varying ratios of slab thickness to photonic crystal lattice constant, we are able to distinguish between 0th and 1st order slab modes as well as the polarization from the shift of resonances in the photocurrent spectra. This method complements the photonic band structure mapping technique for characterization of photonic crystal slabs. © 2011 Optical Society of America

  3. The transition from stress softening to stress hardening under cyclic loading induced by magnetic field for magneto-sensitive polymer gels

    NASA Astrophysics Data System (ADS)

    Xu, Yangguang; Liao, Guojiang; Zhang, Canyang; Wan, Qiang; Liu, Taixiang

    2016-04-01

    Magneto-sensitive polymer gel (MSPG) is a kind of ferromagnetic particle filled smart polymer composite, whose magneto-mechanical coupling mechanism has attracted increasing attention in recent years. In this work, the magneto-induced rheological response of MSPG under cyclic shear loading was investigated. It was found that magnetic field is the critical reason for the transition from stress softening to stress hardening under cyclic loading. Besides, the particle concentration and temperature are the controlling factors in the structure optimization of MSPG in the presence of magnetic field. The magneto-induced hardening mechanism was further proposed based on the related experimental results.

  4. Molecular typing of haemorrhagic septicaemia-associated Pasteurella multocida isolates from Pakistan and Thailand using multilocus sequence typing and pulsed-field gel electrophoresis.

    PubMed

    Moustafa, Ahmed M; Bennett, Mark D; Edwards, John; Azim, Kamran; Mesaik, Muhammed A; Choudhary, M Iqbal; Pathanasophon, Pornpen; Worarach, Apasara; Ali, Qurban; Abubakar, Muhammad; Anjum, Rehana

    2013-12-01

    A comparative genetic study of 23 field isolates and vaccine strains of Pasteurella multocida associated with haemorrhagic septicaemia cases from Pakistan and Thailand was done using pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The MLST sequence type (ST) for all 20 of the 23 isolates tested was 122. The PFGE results showed one band difference between the Pakistani and the Thai isolates. Sequence type 122 is the dominant associated profile with haemorrhagic septicaemia (HS) cases in South Asia. The study supports the concept of using PFGE for short-term epidemiology and MLST for long-term epidemiology. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Slab melting versus slab dehydration in subduction-zone magmatism

    PubMed Central

    Mibe, Kenji; Kawamoto, Tatsuhiko; Matsukage, Kyoko N.; Fei, Yingwei; Ono, Shigeaki

    2011-01-01

    The second critical endpoint in the basalt-H2O system was directly determined by a high-pressure and high-temperature X-ray radiography technique. We found that the second critical endpoint occurs at around 3.4 GPa and 770 °C (corresponding to a depth of approximately 100 km in a subducting slab), which is much shallower than the previously estimated conditions. Our results indicate that the melting temperature of the subducting oceanic crust can no longer be defined beyond this critical condition and that the fluid released from subducting oceanic crust at depths greater than 100 km under volcanic arcs is supercritical fluid rather than aqueous fluid and/or hydrous melts. The position of the second critical endpoint explains why there is a limitation to the slab depth at which adakitic magmas are produced, as well as the origin of across-arc geochemical variations of trace elements in volcanic rocks in subduction zones. PMID:21536910

  6. Slab melting versus slab dehydration in subduction-zone magmatism.

    PubMed

    Mibe, Kenji; Kawamoto, Tatsuhiko; Matsukage, Kyoko N; Fei, Yingwei; Ono, Shigeaki

    2011-05-17

    The second critical endpoint in the basalt-H(2)O system was directly determined by a high-pressure and high-temperature X-ray radiography technique. We found that the second critical endpoint occurs at around 3.4 GPa and 770 °C (corresponding to a depth of approximately 100 km in a subducting slab), which is much shallower than the previously estimated conditions. Our results indicate that the melting temperature of the subducting oceanic crust can no longer be defined beyond this critical condition and that the fluid released from subducting oceanic crust at depths greater than 100 km under volcanic arcs is supercritical fluid rather than aqueous fluid and/or hydrous melts. The position of the second critical endpoint explains why there is a limitation to the slab depth at which adakitic magmas are produced, as well as the origin of across-arc geochemical variations of trace elements in volcanic rocks in subduction zones.

  7. Use of pulsed-field gel electrophoresis to monitor a five-strain mixture of Listeria monocytogenes in frankfurter packages.

    PubMed

    Porto, Anna C S; Wonderling, Laura; Call, Jeffrey E; Luchansky, John B

    2003-08-01

    In a previous study, the viability of a five-strain mixture of Listeria monocytogenes (including Scott A [serotype 4b, clinical isolate], 101M [serotype 4b, beef-pork sausage isolate], F6854 [serotype 1/2a, turkey frankfurter isolate], H7776 [serotype 4b, frankfurter isolate], and MFS-2 [serotype 1/2a, pork plant isolate]) was monitored during refrigerated storage of frankfurters prepared with and without 3.0% added potassium lactate. Throughout a 90-day period of storage at 4 degrees C, the initial inoculum level of 20 CFU per package remained relatively constant in packages containing frankfurters prepared with potassium lactate, but pathogen counts increased to 4.6 log10 CFU in packages containing frankfurters prepared without added potassium lactate. To determine which of the five strains persisted under these conditions, randomly selected colonies obtained after 28 and 90 days of refrigerated storage of frankfurters were analyzed by pulsed-field gel electrophoresis (PFGE) with the restriction enzyme SmaI to generate distinct banding patterns for each of the five strains. Then, with the use of PFGE as a tool for identification, the percentages of the strains on days 28 and 90 of the growth study were compared. In the absence of any added potassium lactate in the product, 43% of the 58 isolates recovered on day 28 were identified as strain Scott A, 12% were identified as strain 101M, 22% were identified as strain F6854, 10% were identified as strain H7776, and 12% were identified as strain MFS-2. However, by day 90, an appreciable number (83%) of the 60 isolates analyzed were identified as strain MFS-2. In packages containing frankfurters formulated with 3.0% potassium lactate, all five strains were present at frequencies of 5 to 36% among the 19 isolates tested on day 28; however, by day 90, strain MFS-2 made up the statistical majority (63%) of the 27 isolates tested. The results of this study indicate that strain MFS-2, a serotype 1/2a isolate recovered from

  8. Population Genetic Structure of Listeria monocytogenes Strains as Determined by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing

    PubMed Central

    Henri, Clémentine; Félix, Benjamin; Guillier, Laurent; Leekitcharoenphon, Pimlapas; Michelon, Damien; Mariet, Jean-François; Aarestrup, Frank M.; Mistou, Michel-Yves; Hendriksen, René S.

    2016-01-01

    ABSTRACT Listeria monocytogenes is a ubiquitous bacterium that may cause the foodborne illness listeriosis. Only a small amount of data about the population genetic structure of strains isolated from food is available. This study aimed to provide an accurate view of the L. monocytogenes food strain population in France. From 1999 to 2014, 1,894 L. monocytogenes strains were isolated from food at the French National Reference Laboratory for L. monocytogenes and classified according to the five risk food matrices defined by the European Food Safety Authority (EFSA). A total of 396 strains were selected on the basis of different pulsed-field gel electrophoresis (PFGE) clusters, serotypes, and strain origins and typed by multilocus sequence typing (MLST), and the MLST results were supplemented with MLST data available from Institut Pasteur, representing human and additional food strains from France. The distribution of sequence types (STs) was compared between food and clinical strains on a panel of 675 strains. High congruence between PFGE and MLST was found. Out of 73 PFGE clusters, the two most prevalent corresponded to ST9 and ST121. Using original statistical analysis, we demonstrated that (i) there was not a clear association between ST9 and ST121 and the food matrices, (ii) serotype IIc, ST8, and ST4 were associated with meat products, and (iii) ST13 was associated with dairy products. Of the two major STs, ST121 was the ST that included the fewest clinical strains, which might indicate lower virulence. This observation may be directly relevant for refining risk analysis models for the better management of food safety. IMPORTANCE This study showed a very useful backward compatibility between PFGE and MLST for surveillance. The results enabled better understanding of the population structure of L. monocytogenes strains isolated from food and management of the health risks associated with L. monocytogenes food strains. Moreover, this work provided an accurate view

  9. Population Genetic Structure of Listeria monocytogenes Strains as Determined by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing.

    PubMed

    Henri, Clémentine; Félix, Benjamin; Guillier, Laurent; Leekitcharoenphon, Pimlapas; Michelon, Damien; Mariet, Jean-François; Aarestrup, Frank M; Mistou, Michel-Yves; Hendriksen, René S; Roussel, Sophie

    2016-09-15

    Listeria monocytogenes is a ubiquitous bacterium that may cause the foodborne illness listeriosis. Only a small amount of data about the population genetic structure of strains isolated from food is available. This study aimed to provide an accurate view of the L. monocytogenes food strain population in France. From 1999 to 2014, 1,894 L. monocytogenes strains were isolated from food at the French National Reference Laboratory for L. monocytogenes and classified according to the five risk food matrices defined by the European Food Safety Authority (EFSA). A total of 396 strains were selected on the basis of different pulsed-field gel electrophoresis (PFGE) clusters, serotypes, and strain origins and typed by multilocus sequence typing (MLST), and the MLST results were supplemented with MLST data available from Institut Pasteur, representing human and additional food strains from France. The distribution of sequence types (STs) was compared between food and clinical strains on a panel of 675 strains. High congruence between PFGE and MLST was found. Out of 73 PFGE clusters, the two most prevalent corresponded to ST9 and ST121. Using original statistical analysis, we demonstrated that (i) there was not a clear association between ST9 and ST121 and the food matrices, (ii) serotype IIc, ST8, and ST4 were associated with meat products, and (iii) ST13 was associated with dairy products. Of the two major STs, ST121 was the ST that included the fewest clinical strains, which might indicate lower virulence. This observation may be directly relevant for refining risk analysis models for the better management of food safety. This study showed a very useful backward compatibility between PFGE and MLST for surveillance. The results enabled better understanding of the population structure of L. monocytogenes strains isolated from food and management of the health risks associated with L. monocytogenes food strains. Moreover, this work provided an accurate view of L. monocytogenes

  10. The impact of two-dimensional pulsed-field gel electrophoresis techniques for the consistent and complete mapping of bacterial genomes: refined physical map of Pseudomonas aeruginosa PAO.

    PubMed Central

    Römling, U; Tümmler, B

    1991-01-01

    The SpeI/DpnI map of the 5.9 Mb Pseudomonas aeruginosa PAO (DSM 1707) genome was refined by two-dimensional (2D) pulsed-field gel electrophoresis techniques (PFGE) which allow the complete and consistent physical mapping of any bacterial genome of interest. Single restriction digests were repetitively separated by PFGE employing different pulse times and ramps in order to detect all bands with optimum resolution. Fragment order was evaluated from the pattern of 2D PFGE gels: 1. Partial-complete digestion. A partial restriction digest was separated in the first dimension, redigested to completion, and subsequently perpendicularly resolved in the second dimension. 2D-gel comparisons of the ethidium bromide stain of all fragments and of the autoradiogram of end-labeled partial digestion fragments was nearly sufficient for the construction of the macrorestriction map. 2. Reciprocal gels. A complete restriction digest with enzyme A was run in the first dimension, redigested with enzyme B, and separated in the second orthogonal direction. The order of restriction digests was reverse on the second gel. In case of two rare-cutters, fragments were visualized by ethidium bromide staining or hybridization with genomic DNA. If a frequent and a rare cutter were employed, linking fragments were identified by end-labeling of the first digest. 3. A few small fragments were isolated by preparative PFGE and used as a probe for Southern analysis.--38 SpeI and 15 DpnI fragments were positioned on the map. The zero point was relocated to the 'origin of replication'. The anonymous mapping techniques described herein are unbiased by repetitive DNA, unclonable genomic regions, unfavourable location of restriction sites, or cloning artifacts as frequently encountered in other top-down or bottom-up approaches. Images PMID:1905802

  11. Efficacy, safety and tolerability of field treatment of actinic keratosis with ingenol mebutate 0.015 % gel: a single center case series.

    PubMed

    Bobyr, Ivan; Campanati, Anna; Consales, Veronica; Giuliodori, Katia; Scalise, Alessandro; Offidani, Annamaria

    2016-01-01

    Actinic keratosis (AK) is a cutaneous intraepithelial neoplasm appearing within areas referred as 'fields of cancerization'. AK can progress to invasive squamous cell carcinoma. Treatments that target both clinically visible and subclinical AKs in cancerization fields are able to reduce the risk of malignant progression. Ingenol mebutate gel is a new effective topical therapy for AK, used once daily for 2 or 3 days depending on the location of lesions. Three elderly patients with multiple non-hypertrophic AKs within a contiguous 25-cm(2) treatment area on the face or scalp were treated with ingenol mebutate 0.015 % gel once daily for three consecutive days and followed up over a period of 57 days. Although individual local responses to treatment varied, all patients had total clearance of AK lesions without any sign of recurrence. In addition, all patients said that they were satisfied with the effectiveness of ingenol mebutate treatment and the aesthetic outcome, and would be prepared to use this agent again to treat AK in the future, if necessary. These three cases demonstrate that ingenol mebutate 0.015 % gel is effective and well tolerated in a clinical setting, with effective clearance of AK lesions present on the face and scalp, and good patient acceptability.

  12. High-resolution separation and accurate size determination in pulsed-field gel electrophoresis of DNA. 1. DNA size standards and the effect of agarose and temperature

    SciTech Connect

    Mathew, M.K.; Smith, C.L.; Cantor, C.R. )

    1988-12-27

    Pulsed-field gel electrophoresis (PGF) subjects DNA alternately to two electrical fields to resolve DNA ranging from 10,000 base pairs (10 kb) to 10,000 kb in size. The separations are quite sensitive to a variety of experimental variables. This makes it critical to have a wide range of reliable size standards. A technique is described for preparing mixtures of bacteriophage DNA oligomers that span a size range from monomer to more than 30-mer. The relationship between size and mobility of oligomers of different bacteriophage DNA monomers is generally self-consistent. Thus, these samples can serve as primary length standards for DNAs ranging from 10 kb to more than 1,500 kb. They have been used to estimate the size of the chromosomal DNAs from various Saccharomyces cerevisiae strains and to test the effect of gel concentration and temperature on PFG. DNA resolution during PFG is slightly improved in agarose gels with small pore sizes, in contrast to continuous electrophoresis where the opposite is observed. PFG mobility is surprisingly sensitive to changes in the running temperature.

  13. Electromagnetic fluctuation-induced interactions in randomly charged slabs.

    PubMed

    Rezvani, Vahid; Sarabadani, Jalal; Naji, Ali; Podgornik, Rudolf

    2012-09-21

    Randomly charged net-neutral dielectric slabs are shown to interact across a featureless dielectric continuum with long-range electrostatic forces that scale with the statistical variance of their quenched random charge distribution and inversely with the distance between their bounding surfaces. By accounting for the whole spectrum of electromagnetic field fluctuations, we show that this long-range disorder-generated interaction extends well into the retarded regime where higher order (non-zero) Matsubara frequencies contribute significantly. This occurs even for highly clean samples with only a trace amount of charge disorder and shows that disorder effects can be important down to the nanoscale. As a result, the previously predicted non-monotonic behavior for the total force between dissimilar slabs as a function of their separation distance is substantially modified by higher order contributions, and in almost all cases of interest, we find that the equilibrium inter-surface separation is shifted to substantially larger values compared to predictions based solely on the zero-frequency component. This suggests that the ensuing non-monotonic interaction is more easily amenable to experimental detection. The presence of charge disorder in the intervening dielectric medium between the two slabs is shown to lead to an additional force that can be repulsive or attractive depending on the system parameters and can, for instance, wash out the non-monotonic behavior of the total force when the intervening slab contains a sufficiently large amount of disorder charges.

  14. Electromagnetic fluctuation-induced interactions in randomly charged slabs

    NASA Astrophysics Data System (ADS)

    Rezvani, Vahid; Sarabadani, Jalal; Naji, Ali; Podgornik, Rudolf

    2012-09-01

    Randomly charged net-neutral dielectric slabs are shown to interact across a featureless dielectric continuum with long-range electrostatic forces that scale with the statistical variance of their quenched random charge distribution and inversely with the distance between their bounding surfaces. By accounting for the whole spectrum of electromagnetic field fluctuations, we show that this long-range disorder-generated interaction extends well into the retarded regime where higher order (non-zero) Matsubara frequencies contribute significantly. This occurs even for highly clean samples with only a trace amount of charge disorder and shows that disorder effects can be important down to the nanoscale. As a result, the previously predicted non-monotonic behavior for the total force between dissimilar slabs as a function of their separation distance is substantially modified by higher order contributions, and in almost all cases of interest, we find that the equilibrium inter-surface separation is shifted to substantially larger values compared to predictions based solely on the zero-frequency component. This suggests that the ensuing non-monotonic interaction is more easily amenable to experimental detection. The presence of charge disorder in the intervening dielectric medium between the two slabs is shown to lead to an additional force that can be repulsive or attractive depending on the system parameters and can, for instance, wash out the non-monotonic behavior of the total force when the intervening slab contains a sufficiently large amount of disorder charges.

  15. Evaluation of the thermal bridging effects on the thermal performance of slab-on-grade floor foundation

    SciTech Connect

    Al-Anzi, A.A.; Krarti, M.

    1997-12-31

    A steady-state solution is developed to determine the thermal interaction between a slab-on-grade floor and above-grade walls. In particular, the thermal bridging effects at the slab/wall joints are evaluated for various insulation configurations. Using a finite-difference numerical technique (FDM), the temperature field within the building envelope and the soil, the heat flux profiles along the foundation surfaces, and the total slab and wall heat losses are determined and analyzed for both interior and exterior insulation configurations. It was found that a significant thermal interaction exists between the slab-on-grade floor and the above-grade walls. In particular, it was found that adding thermal insulation to the slab or to the walls affects the thermal performance of both the slab and the walls.

  16. GPS-derived surface imprint of toroidal flow at the Calabrian slab edges

    NASA Astrophysics Data System (ADS)

    Palano, Mimmo; Piromallo, Claudia; Chiarabba, Claudio

    2017-04-01

    Tearing of the lithosphere and toroidal upper mantle circulation have been modeled and proposed at slab edges of several retreating subduction zones. While tear faults laterally decouple the subducting lithosphere during retreat and promote strike-slip motion in the overriding plate, toroidal flow around slab edges accommodates the displacement, from beneath the stiff slab, of less viscous mantle material towards the mantle wedge. Edge processes jointly contribute to surface crustal deformation, which can be revealed both by geodetic and geological observations. We document this effect in the Calabrian subduction system, where the Ionian slab rollback has been taking place since 30 Ma, following a step-wise process accompanied by migration of lithospheric tearing. We observe GPS velocities with symmetric toroidal patterns around the slab hinges: a counterclockwise rotation rate of 1.29 °/Ma around a pole located in the Sibari Gulf for the northern slab edge and a clockwise rotation rate of 1.74 °/Ma around a pole close to the NE Sicily coastal area at the southern slab edge. These small-scale, opposite rotations occur at complex sets of active faults representing the lithospheric tears currently accommodating the SE-ward migration of the subduction system. At depth, the mantle flow field imaged by seismic anisotropy reveals instead an asymmetry: a toroidal pattern of sub-slab return flow appears only at the southern slab edge, while at the northern end SKS-splitting fast directions are trench parallel. A possible cause for this asymmetric coupling of the upper plate deformation with underlying mantle flow is the immature stage of the northern slab tear.

  17. Insights on slab-driven mantle flow from advances in three-dimensional modelling

    NASA Astrophysics Data System (ADS)

    Jadamec, Margarete A.

    2016-10-01

    The wealth of seismic observations collected over the past 20 years has raised intriguing questions about the three-dimensional (3D) nature of the mantle flow field close to subduction zones and provided a valuable constraint for how the plate geometry may influence mantle flow proximal to the slab. In geodynamics, there has been a new direction of subduction zone modelling that has explored the 3D nature of slab-driven mantle flow, motivated in part by the observations from shear wave splitting, but also by the observed variations in slab geometries worldwide. Advances in high-performance computing are now allowing for an unprecedented level of detail to be incorporated into numerical models of subduction. This paper summarizes recent advances from 3D geodynamic models that reveal the complex nature of slab-driven mantle flow, including trench parallel flow, toroidal flow around slab edges, mantle upwelling at lateral slab edges, and small scale convection within the mantle wedge. This implies slab-driven mantle deformation zones occur in the asthenosphere proximal to the slab, wherein the mantle may commonly flow in a different direction and rate than the surface plates, implying laterally variable plate-mantle coupling. The 3D slab-driven mantle flow can explain, in part, the lateral transport of geochemical signatures in subduction zones. In addition, high-resolution geographically referenced models can inform the interpretation of slab structure, where seismic data are lacking. The incorporation of complex plate boundaries into high-resolution, 3D numerical models opens the door to a new avenue of research in model construction, data assimilation, and modelling workflows, and gives 3D immersive visualization a new role in scientific discovery.

  18. Electrophoretic extraction of proteins from two-dimensional electrophoresis gel spots

    DOEpatents

    Zhang, Jian-Shi; Giometti, C.S.; Tollaksen, S.L.

    1987-09-04

    After two-dimensional electrophoresis of proteins or the like, resulting in a polyacrylamide gel slab having a pattern of protein gel spots thereon, an individual protein gel spot is cored out from the slab, to form a gel spot core which is placed in an extraction tube, with a dialysis membrane across the lower end of the tube. Replicate gel spots can be cored out from replicate gel slabs and placed in the extraction tube. Molten agarose gel is poured into the extraction tube where the agarose gel hardens to form an immobilizing gel, covering the gel spot cores. The upper end portion of the extraction tube is filled with a volume of buffer solution, and the upper end is closed by another dialysis membrane. Upper and lower bodies of a buffer solution are brought into contact with the upper and lower membranes and are provided with electrodes connected to the positive and negative terminals of a dc power supply, thereby producing an electrical current which flows through the upper membrane, the volume of buffer solution, the agarose, the gel spot cores and the lower membrane. The current causes the proteins to be extracted electrophoretically from the gel spot cores, so that the extracted proteins accumulate and are contained in the space between the agarose gel and the upper membrane. 8 figs.

  19. A slab expression in the Gibraltar arc?

    NASA Astrophysics Data System (ADS)

    Nijholt, Nicolai; Govers, Rob; Wortel, Rinus

    2017-04-01

    The present-day geodynamic setting of the Gibraltar arc region results from several Myrs of subduction rollback in the overall (oblique) convergence of Africa and Iberia. As for most rollback settings in a convergence zone, the interaction of these two components is complex and distinctly non-stationary. Gibraltar slab rollback is considered to have stalled, or at least diminished largely in magnitude, since the late Miocene/early Pliocene, suggesting that the effect of the slab on present-day surface motions is negligible. However, GPS measurements indicate that the Gibraltar arc region has an anomalous motion with respect to both Iberia and Africa, i.e., the Gibraltar arc region does not move as part of the rigid Iberian, or the rigid African plate. A key question is whether this surface motion is an expression of the Gibraltar slab. Seismic activity in the Gibraltar region is diffuse and considerable in magnitude, making it a region of high seismic risk. Unlike the North African margin to the east, where thrust earthquakes dominate the focal mechanism tables, a complex pattern is observed with thrust, normal and strike-slip earthquakes in a region stretching between the northern Moroccan Atlas across the Gibraltar arc and Alboran Sea (with the Trans-Alboran Shear Zone) to the Betics of southern Spain. Even though no large mega-thrust earthquakes have been observed in recent history, slab rollback may not have completely ceased. However, since no activity has been observed in the accretionary wedge, probably since the Pliocene, it is likely that the subduction interface is locked. In this study, we perform a series of numerical models in which we combine the relative plate convergence, variable magnitude of friction on fault segments, regional variations in gravitational potential energy and slab pull of the Gibraltar slab. We seek to reproduce the GPS velocities and slip sense on regional faults and thereby determine whether the Gibraltar slab has an effect on

  20. Subducting slabs: Jellyfishes in the Earth's mantle

    NASA Astrophysics Data System (ADS)

    Loiselet, Christelle; Braun, Jean; Husson, Laurent; Le Carlier de Veslud, Christian; Thieulot, Cedric; Yamato, Philippe; Grujic, Djordje

    2010-08-01

    The constantly improving resolution of geophysical data, seismic tomography and seismicity in particular, shows that the lithosphere does not subduct as a slab of uniform thickness but is rather thinned in the upper mantle and thickened around the transition zone between the upper and lower mantle. This observation has traditionally been interpreted as evidence for the buckling and piling of slabs at the boundary between the upper and lower mantle, where a strong contrast in viscosity may exist and cause resistance to the penetration of slabs into the lower mantle. The distribution and character of seismicity reveal, however, that slabs undergo vertical extension in the upper mantle and compression near the transition zone. In this paper, we demonstrate that during the subduction process, the shape of low viscosity slabs (1 to 100 times more viscous than the surrounding mantle) evolves toward an inverted plume shape that we coin jellyfish. Results of a 3D numerical model show that the leading tip of slabs deform toward a rounded head skirted by lateral tentacles that emerge from the sides of the jellyfish head. The head is linked to the body of the subducting slab by a thin tail. A complete parametric study reveals that subducting slabs may achieve a variety of shapes, in good agreement with the diversity of natural slab shapes evidenced by seismic tomography. Our work also suggests that the slab to mantle viscosity ratio in the Earth is most likely to be lower than 100. However, the sensitivity of slab shapes to upper and lower mantle viscosities and densities, which remain poorly constrained by independent evidence, precludes any systematic deciphering of the observations.

  1. Subducting Slabs: Jellyfishes in the Earth's Mantle

    NASA Astrophysics Data System (ADS)

    Loiselet, C.; Braun, J.; Husson, L.; Le Carlier de Veslud, C.; Thieulot, C.; Yamato, P.; Grujic, D.

    2010-12-01

    The constantly improving resolution of geophysical data, seismic tomography and seismicity in particular, shows that the lithosphere does not subduct as a slab of uniform thickness but is rather thinned in the upper mantle and thickened around the transition zone between the upper and lower mantle. This observation has traditionally been interpreted as evidence for the buckling and piling of slabs at the boundary between the upper and lower mantle, where a strong contrast in viscosity may exist and cause resistance to the penetration of slabs into the lower mantle. The distribution and character of seismicity reveal, however, that slabs undergo vertical extension in the upper mantle and compression near the transition zone. In this paper, we demonstrate that during the subduction process, the shape of low viscosity slabs (1 to 100 times more viscous than the surrounding mantle) evolves toward an inverted plume shape that we coin jellyfish. Results of a 3D numerical model show that the leading tip of slabs deform toward a rounded head skirted by lateral tentacles that emerge from the sides of the jellyfish head. The head is linked to the body of the subducting slab by a thin tail. A complete parametric study reveals that subducting slabs may achieve a variety of shapes, in good agreement with the diversity of natural slab shapes evidenced by seismic tomography. Our work also suggests that the slab to mantle viscosity ratio in the Earth is most likely to be lower than 100. However, the sensitivity of slab shapes to upper and lower mantle viscosities and densities, which remain poorly constrained by independent evidence, precludes any systematic deciphering of the observations.

  2. Slab Stagnation: How, When, and Where?

    NASA Astrophysics Data System (ADS)

    King, S. D.; Frost, D. J.; Rubie, D. C.

    2015-12-01

    Many slabs appear to stagnate in the transition zone although some slabs appear to stagnate at a depth of 1000 km and others appear to descend into the lower mantle relatively unaltered or, perhaps buckling as they descend. Because tomographic images provide a modern day snapshot of a time-dependent process, it is unclear whether the diversity of subducted slab geometries are a manifestation of the same process captured at different times in the lifetime of the subducting system or whether different subduction zones are subject to different conditions that control their evolution. At one time, stagnation of the slab at the base of the transition zone was thought to be due to the transformation of ringwoodite to bridgmanite plus ferropericlase, although subsequent experimental work showed that this transformation does not produce sufficient buoyancy to stall slab descent. In addition to phase transformations in the olivine system, rheology (specifically a ``viscosity hill'' in the upper part of the lower mantle), trench migration, depth-dependent thermodynamic parameters, and composition have all been investigated as potential slab stagnation mechanisms. The transformation of pyroxene to majoritic garnet occurs by extremely slow diffusion and thus pyroxene unlikely to transform at equilibrium pressures. We have shown that the presence of metastable pyroxene in the cold cores of subducted slabs is sufficient to cause flat-slab subduction. Given the diversity of slab structures, it is quite likely that a combination of mechanisms control slab dynamics. We will investigate slabs stagnation using numerical experiments in 2D and 3D with dislocation/diffusion creep rheology, phase transformations, and plate reconstructions to control the evolution of the plate system.

  3. Microchip capillary gel electrophoresis using programmed field strength gradients for the ultra-fast analysis of genetically modified organisms in soybeans.

    PubMed

    Kim, Yun-Jeong; Chae, Joon-Seok; Chang, Jun Keun; Kang, Seong Ho

    2005-08-12

    We have developed a novel method for the ultra-fast analysis of genetically modified organisms (GMOs) in soybeans by microchip capillary gel electrophoresis (MCGE) using programmed field strength gradients (PFSG) in a conventional glass double-T microchip. Under the programmed electric field strength and 0.3% poly(ethylene oxide) sieving matrix, the GMO in soybeans was analyzed within only 11 s of the microchip. The MCGE-PFSG method was a program that changes the electric field strength during GMO analysis, and was also applied to the ultra-fast analysis of PCR products. Compared to MCGE using a conventional and constantly applied electric field, the MCGE-PFSG analysis generated faster results without the loss of resolving power and reproducibility for specific DNA fragments (100- and 250-bp DNA) of GM-soybeans. The MCGE-PFSG technique may prove to be a new tool in the GMO analysis due to its speed, simplicity, and high efficiency.

  4. INDEPENDENT VERIFICATION OF THE BUILDING 3550 SLAB AT OAK RIDGE NATIONAL LABORATORY OAK RIDGE, TENNESSEE

    SciTech Connect

    Weaver, Phyllis C.

    2012-05-08

    The Oak Ridge Institute for Science and Education (ORISE) has completed the independent verification survey of the Building 3550 Slab. The results of this effort are provided. The objective of this verification survey is to provide independent review and field assessment of remediation actions conducted by Safety and Ecology Corporation (SEC) to document that the final radiological condition of the slab meets the release guidelines. Verification survey activities on the Building 3550 Slab that included scans, measurements, and the collection of smears. Scans for alpha, alpha plus beta, and gamma activity identified several areas that were investigated.

  5. Applying MHD technology to the continuous casting of steel slab

    NASA Astrophysics Data System (ADS)

    Takeuchi, Eiichi

    1995-05-01

    The application of magnetohydrodynamics (MHD) in the continuous casting process started with the electromagnetic stirring of the stand pool with a traveling magnetic field. It has now advanced to the electromagnetic stirring of molten steel in the mold and the control of molten steel flow by an in-mold direct current magnetic field brake. These applied MHD techniques are designed to further improve the continuous casting process capability. They improve the surface quality of cast steel by homogenizing the meniscus temperature, stabilizing initial solidification, and cleaning the surface layer. They also improve the internal quality of cast steel by preventing inclusions from penetrating deep into the pool and promoting the flotation of argon bubbles. Applied MHD technology is still advancing in scope and methods in addition to the improvement of conventional continuously cast slab qualities. The continuous casting of bimetallic slab by suppressing mixing in the pool is one example of this progress.

  6. Bolometric detection of ferromagnetic resonance in YIG slab

    NASA Astrophysics Data System (ADS)

    Tu, Sa; Białek, Marcin; Zhang, Youguang; Zhao, Weisheng; Yu, Haiming; Ansermet, Jean-Philippe

    2017-10-01

    The resistance of the Pt bar deposited on the YIG slab was monitored while the magnetic field was ramped through the ferromagnetic resonance with the YIG slab facing a coplanar waveguide resonator excited at 4.3 GHz excitation. The resistance change provides detection of the ferromagnetic resonance with a high signal-to-noise ratio. It is ascribed to a change in the temperature of the Pt bars. The thermal origin of the signal is confirmed by the observation that the signal vanishes when field modulation is applied at frequencies above 6 Hz. The spin pumping effect was vanishingly small, and the anisotropic magnetoresistance of the Pt bar, though quite easily observed, would imply a rectification voltage that is much smaller than the bolometric effect.

  7. The slab geometry laser. I - Theory

    NASA Technical Reports Server (NTRS)

    Eggleston, J. M.; Kane, T. J.; Kuhn, K.; Byer, R. L.; Unternahrer, J.

    1984-01-01

    Slab geometry solid-state lasers offer significant performance improvements over conventional rod-geometry lasers. A detailed theoretical description of the thermal, stress, and beam-propagation characteristics of a slab laser is presented. The analysis includes consideration of the effects of the zig-zag optical path, which eliminates thermal and stress focusing and reduces residual birefringence.

  8. Slab Houses: Reflections of the Past.

    ERIC Educational Resources Information Center

    Cappetta, Ann

    1990-01-01

    Describes how students, influenced by Victorian architecture, created ceramic slab houses. Students devised a solution to depict the reflective nature of Victorian bay windows. Project incorporates art history, handbuilding, and surface ornamentation. Outlines and illustrates steps involved in making slab houses that can be adapted for use by…

  9. The slab geometry laser. I - Theory

    NASA Technical Reports Server (NTRS)

    Eggleston, J. M.; Kane, T. J.; Kuhn, K.; Byer, R. L.; Unternahrer, J.

    1984-01-01

    Slab geometry solid-state lasers offer significant performance improvements over conventional rod-geometry lasers. A detailed theoretical description of the thermal, stress, and beam-propagation characteristics of a slab laser is presented. The analysis includes consideration of the effects of the zig-zag optical path, which eliminates thermal and stress focusing and reduces residual birefringence.

  10. Application of mirror reflection principle for numerical modeling of uniform slab brightness coefficients by using linear singular integral equations

    NASA Astrophysics Data System (ADS)

    Smokty, Oleg I.

    2017-02-01

    The mirror reflection principle and radiation field photometrical invariants given by the author have been applied to find uniform slab brightness coefficients by using modified linear singular integral equations. On this basis, certain mathematical aspects of the numerical realization of the angular discretization method to solve the linear singular integral equations for brightness coefficients photometrical invariants of an arbitrary optical thickness homogeneous slab.

  11. A comparison of microseismicity induced by gel-proppant-and water-injected hydraulic fractures, Carthage Cotton Valley gas field, East Texas

    SciTech Connect

    Rutledge, J. T.; Phillips, W. S.

    2002-01-01

    In May and July, 1997, a consortia of operators and service companies conducted a series of hydraulic fracture imaging tests in the Carthage Cotton Valley gas field of East Texas (Walker, 1997). Microseismic data were collected and processed for six hydraulic fracture treatments in two wells (3 completion intervals per well) (Mayerhofer et al., 2000). One well was completed with gel-proppant treatments in which a viscous crosslink gel was injected to entrain high concentrations of sand proppant into formation. The second well was completed using treated water and very low proppant concentrations (waterfracs). Waterfracs have been shown to be just as effective as the conventional gel-proppant treatments in Cotton Valley reservoirs, but at greatly reduced cost. Mayerhofer and Meehan (1998) suggest two possible reasons why waterfracs are successful: (1) Induced shear displacement along natural and hydraulic fractures results in self-propping (shear dilation enhanced by fracture branching, proppant and spalled rock fragments), and (2) Fracture extension and cleanup is easier to achieve with low-viscosity fluids. With improved source location precision and focal mechanism determination (fracture plane orientation and sense of slip), we have reexamined the Cotton Valley data, comparing the seismicity induced by water and gel-proppant treatments at common depth intervals. We have improved the location precision and computed focal mechanism of microearthquakes induced during a series of hydraulic fracture completions within the Cotton Valley formation of East Texas. Conventional gel-proppant treatments and treatments using treated water and very low proppant concentrations (waterfracs) were monitored. Waterfracs have been shown to be just as effective as the conventional gel-proppant treatments in Cotton Valley reservoirs, but at greatly reduced cost (Mayerhofer and Meehan, 1998). Comparison of the seismicity induced by the two treatment types show similar distributions of

  12. Equilibrium Slab Models of Lyman-Alpha Clouds

    NASA Technical Reports Server (NTRS)

    Charlton, Jane C.; Salpeter, Edwin E.; Hogan, Craig J.

    1993-01-01

    We model the L(sub y(alpha)) clouds as slabs of hydrogen with an ionizing extragalactic radiation field incident from both sides. In general, the equilibrium configuration of a slab at redshift z approx. less than 5 is determined by a balance of the gas pressure, gravity (including the effects of a dark matter halo), and the pressure exerted by the inter-galactic medium, P(sub ext). These models have been used to make predictions of the number of slabs as a function of the neutral hydrogen column density, N(sub H). A break in the curve is predicted at the transition between regimes where gravity and pressure are the dominant confining forces, with a less rapid decrease at larger N(sub H). The transition from optically thin to optically thick slabs leads to a gap in the distribution, whose location is governed largely by the spectrum of ionizing radiation. There are certain parallels between lines of sight through the outer HI disk of spiral galaxy with increasing radius, and the progression from damped, to Lyman limit, to forest clouds. We discuss briefly the possibility that at least some of the observed low z forest clouds may be a separate population, associated with galaxies, as suggested by the observations of Bahcall et al. This population could dominate the forest at present if the dark matter attached to galaxies should lead to gravity confinement for this disk population, while the isolated clouds remain pressure confined. The formalism developed in this paper will allow a more detailed study. We also discuss a more general parameter study of the equilibrium configuration of slabs, including mock gravity and L(sub y(alpha)) photon trapping.

  13. Beam splitting by a plane-parallel absorptive slab.

    PubMed

    Halevi, P

    1982-10-01

    A study of the transmission of inhomogeneous electromagnetic waves through an interface between a transparent and an absorbing medium leads to the prediction of a novel effect. A beam of unpolarized light passing through a dissipative plane-parallel slab splits into two parallel beams. The electric field in one beam is perpendicular to the plane of incidence, whereas in the other beam it is parallel to this plane.

  14. Reflection and transmission of Gaussian beam by a chiral slab

    NASA Astrophysics Data System (ADS)

    Yan, Bing; Zhang, Huayong; Zhang, Jianyong

    2016-06-01

    Based on the generalized Lorenz-Mie theory framework, the reflection and transmission of an incident Gaussian beam by a chiral slab were investigated, by expanding the incident Gaussian beam, reflected beam, internal beam as well as transmitted beam in terms of cylindrical vector wave functions. The unknown expansion coefficients were determined by virtue of the boundary conditions. For a localized beam model, numerical results of the normalized field intensity distributions are presented, and the propagation characteristics are discussed concisely in this paper.

  15. Diode-side-pumped Alexandrite slab lasers.

    PubMed

    Damzen, M J; Thomas, G M; Minassian, A

    2017-05-15

    We present the investigation of diode-side-pumping of Alexandrite slab lasers in a range of designs using linear cavity and grazing-incidence bounce cavity configurations. An Alexandrite slab laser cavity with double-pass side pumping produces 23.4 mJ free-running energy at 100 Hz rate with slope efficiency ~40% with respect to absorbed pump energy. In a slab laser with single-bounce geometry output power of 12.2 W is produced, and in a double-bounce configuration 6.5 W multimode and 4.5 W output in TEM00 mode is produced. These first results of slab laser and amplifier designs in this paper highlight some of the potential strategies for power and energy scaling of Alexandrite using diode-side-pumped Alexandrite slab architectures with future availability of higher power red diode pumping.

  16. Magnetoelectric sensor excitations in hexaferrite slabs

    NASA Astrophysics Data System (ADS)

    Zare, Saba; Izadkhah, Hessam; Somu, Sivasubramanian; Vittoria, Carmine

    2015-06-01

    We developed techniques for H- and E-field sensors utilizing single phase magnetoelectric (ME) hexaferrite slabs in the frequency range of 100 Hz to 10 MHz. Novel circuit designs incorporating both spiral and solenoid coils and single and multi-capacitor banks were developed to probe the physics and properties of ME hexaferrites and explore ME effects for sensor detections. Fundamental measurements of the anisotropic tensor elements of the magneto-electric coupling parameter were performed using these novel techniques. In addition, for H-field sensing experiments we measured sensitivity of about 3000 Vm-1/G using solenoid coils and 8000 Vm-1/G using spiral coils. For E-field, sensing the sensitivity was 10-4 G/Vm-1 and using single capacitor detector. Sensitivity for multi-capacitor detectors was measured to be in the order of 10-3 G/Vm-1 and frequency dependent exhibiting a maximum value at ˜1 MHz. Tunability of 0.1%-90% was achieved for tunable inductor applications using both single and multi-capacitors excitation. We believe that significant (˜106) improvements in sensitivity and tunability are feasible with simple modifications of the fabrication process.

  17. Slab stagnation and detachment under northeast China

    NASA Astrophysics Data System (ADS)

    Honda, Satoru

    2016-03-01

    Results of tomography models around the Japanese Islands show the existence of a gap between the horizontally lying (stagnant) slab extending under northeastern China and the fast seismic velocity anomaly in the lower mantle. A simple conversion from the fast velocity anomaly to the low-temperature anomaly shows a similar feature. This feature appears to be inconsistent with the results of numerical simulations on the interaction between the slab and phase transitions with temperature-dependent viscosity. Such numerical models predict a continuous slab throughout the mantle. I extend previous analyses of the tomography model and model calculations to infer the origins of the gap beneath northeastern China. Results of numerical simulations that take the geologic history of the subduction zone into account suggest two possible origins for the gap: (1) the opening of the Japan Sea led to a breaking off of the otherwise continuous subducting slab, or (2) the western edge of the stagnant slab is the previous subducted ridge, which was the plate boundary between the extinct Izanagi and the Pacific plates. Origin (2) suggesting the present horizontally lying slab has accumulated since the ridge subduction, is preferable for explaining the present length of the horizontally lying slab in the upper mantle. Numerical models of origin (1) predict a stagnant slab in the upper mantle that is too short, and a narrow or non-existent gap. Preferred models require rather stronger flow resistance of the 660-km phase change than expected from current estimates of the phase transition property. Future detailed estimates of the amount of the subducted Izanagi plate and the present stagnant slab would be useful to constrain models. A systematic along-arc variation of the slab morphology from the northeast Japan to Kurile arcs is also recognized, and its understanding may constrain the 3D mantle flow there.

  18. Three-dimensional Numerical Models of Slab Edges: Implications for Mantle Upwelling and Anomalous Volcanism

    NASA Astrophysics Data System (ADS)

    Jadamec, M.; Moresi, L. N.; Durance-Sie, P. M.; Mclean, K. A.

    2013-05-01

    addition, higher temperatures in the mantle wedge in regions of active back arc spreading and young oceanic lithosphere in the upper plate can enhance slab melting and lead to increased mantle flow velocities due to the reduction in the temperature-dependent viscosity. Models of this kind can provide a framework for interpreting how the 3D solid state flow field may influence melt migration patterns in subduction zones with slab edges.

  19. An improved protocol for the preparation and restriction enzyme digestion of pulsed-field gel electrophoresis agarose plugs for the analysis of Legionella isolates.

    PubMed

    Chang, Bin; Amemura-Maekawa, Junko; Watanabe, Haruo

    2009-01-01

    Pulsed-field gel electrophoresis (PFGE), which determines the genomic relatedness of isolates, is currently used for the epidemiological investigation of infectious agents such as bacteria. In particular, this method has been used for the epidemiological investigation of Legionella outbreaks. However, it takes 4 days to complete a Legionella-PFGE analysis. Due to partial digestion and DNA damage, the reproducibility of the obtained fragment digestion patterns is poor for this pathogen. In this study, we report an improved protocol that takes only 2 days to complete and that allows clear discrimination of the restriction profile with higher reproducibility than that previously achieved.

  20. Emergence of a mutL Mutation Causing Multilocus Sequence Typing–Pulsed-Field Gel Electrophoresis Discrepancy among Pseudomonas aeruginosa Isolates from a Cystic Fibrosis Patient

    PubMed Central

    García-Castillo, María; Máiz, Luis; Morosini, María-Isabel; Rodríguez-Baños, Mercedes; Suarez, Lucrecia; Fernández-Olmos, Ana; Baquero, Fernando; Cantón, Rafael

    2012-01-01

    A multilocus sequence type (MLST) shift (from ST242 to ST996) was detected in Pseudomonas aeruginosa isolates with a uniform pulsed-field gel electrophoresis (PFGE) pattern obtained from a chronically colonized patient. MLST mutational change involved the mutL gene with the consequent emergence of a hypermutable phenotype. This observation challenges the required neutrality of mutL as an appropriate marker in MLST and alerts researchers to the limitations of MLST-only-based population studies in chronic infections under constant antibiotic selective pressure. PMID:22322352

  1. Emergence of a mutL mutation causing multilocus sequence typing-pulsed-field gel electrophoresis discrepancy among Pseudomonas aeruginosa isolates from a cystic fibrosis patient.

    PubMed

    García-Castillo, María; Máiz, Luis; Morosini, María-Isabel; Rodríguez-Baños, Mercedes; Suarez, Lucrecia; Fernández-Olmos, Ana; Baquero, Fernando; Cantón, Rafael; del Campo, Rosa

    2012-05-01

    A multilocus sequence type (MLST) shift (from ST242 to ST996) was detected in Pseudomonas aeruginosa isolates with a uniform pulsed-field gel electrophoresis (PFGE) pattern obtained from a chronically colonized patient. MLST mutational change involved the mutL gene with the consequent emergence of a hypermutable phenotype. This observation challenges the required neutrality of mutL as an appropriate marker in MLST and alerts researchers to the limitations of MLST-only-based population studies in chronic infections under constant antibiotic selective pressure.

  2. A numerical model for calculating vibration due to a harmonic moving load on a floating-slab track with discontinuous slabs in an underground railway tunnel

    NASA Astrophysics Data System (ADS)

    Hussein, M. F. M.; Hunt, H. E. M.

    2009-03-01

    This paper presents a new method for modelling floating-slab tracks with discontinuous slabs in underground railway tunnels. The track is subjected to a harmonic load moving with a constant velocity. The model consists of two sub-models. The first is an infinite track with periodic double-beam unit formulated as a periodic infinite structure. The second is modelled with a new version of the Pipe-in-Pipe (PiP) model that accounts for a tunnel wall embedded in a half-space. The two sub-models are coupled by writing the force transmitted from the track to the tunnel as a continuous function using Fourier series representation and satisfying the compatibility condition. The displacements at the free surface are calculated for a track with discontinuous slab and compared with those of a track with continuous slab. The results show that the far-field vibration can be significantly increased due to resonance frequencies of slabs for tracks with discontinuous slabs.

  3. Tunable structures comprising two photonic crystal slabs--optical study in view of multi-analyte enhanced detection.

    PubMed

    Shi, Lina; Pottier, Pierre; Skorobogatiy, Maksim; Peter, Yves-Alain

    2009-06-22

    Using finite-difference time-domain method, we characterize the normal-incidence transmission properties of a two slab photonic crystal device in a view of its applications in fluorescence enhancement and multi-analyte detection. Individual slabs consist of a square or a triangular lattice of air holes embedded into a silicon nitride slab. The geometrical parameters are chosen so that the individual slabs operate in a guided resonance regime where strong reflectivity under the normal incidence angle is observed in a broad spectral range. When placed in the close proximity of each other, the two photonic crystal slab system exhibits a narrow Fabry-Perot type transmission peak corresponding to the excitation of a resonant mode in the cavity formed by the two slabs. We then study the effects of the size of the air gap between the two photonic crystal slabs on the spectral position and bandwidth of a resonance transmission peak. Finally, we investigate the electromagnetic energy distributions at the wavelength of a transmission resonance in the double slab photonic crystals. As a final result we demonstrate that this structure can provide electric field enhancement at the slab surface, which can be used for fluorescence enhancement.

  4. Cretaceous Arctic magmatism: Slab vs. plume? Or slab and plume?

    NASA Astrophysics Data System (ADS)

    Gottlieb, E. S.; Miller, E. L.; Andronikov, A. V.; Brumley, K.; Mayer, L. A.; Mukasa, S. B.

    2010-12-01

    Tectonic models for the Cretaceous paleogeographic evolution of the Arctic Ocean and its adjacent landmasses propose that rifting in the Amerasia Basin (AB) began in Jura-Cretaceous time, accompanied by the development of the High Arctic Large Igneous Province (HALIP). During the same timespan, deformation and slab-related magmatism, followed by intra-arc rifting, took place along the Pacific side of what was to become the Arctic Ocean. A compilation and comparison of the ages, characteristics and space-time variation of circum-Arctic magmatism allows for a better understanding of the role of Pacific margin versus Arctic-Atlantic plate tectonics and the role of plume-related magmatism in the origin of the Arctic Ocean. In Jura-Cretaceous time, an arc built upon older terranes overthrust the Arctic continental margins of North America and Eurasia, shedding debris into foreland basins in the Brooks Range, Alaska, across Chukotka, Russia, to the Lena Delta and New Siberian Islands region of the Russian Arctic. These syn-tectonic sediments have some common sources (e.g., ~250-300 Ma magmatic rocks) as determined by U-Pb detrital zircon geochronology. They are as young as Valanginian-Berriasian (~136 Ma, Gradstein et al., 2004) and place a lower limit on the age of formation of the AB. Subsequent intrusions of granitoid plutons, inferred to be ultimately slab-retreat related, form a belt along the far eastern Russian Arctic continental margin onto Seward Peninsula and have yielded a continuous succession of zircon U-Pb ages from ~137-95 Ma (n=28) and a younger suite ~91-82 Ma (n=16). All plutons dated were intruded in an extensional tectonic setting based on their relations to wall-rock deformation. Regional distribution of ages shows a southward migration of the locus of magmatism during Cretaceous time. Basaltic lavas as old as 130 Ma and as young as 80 Ma (40Ar/39Ar)) erupted across the Canadian Arctic Islands, Svalbard and Franz Josef Land and are associated with

  5. The use of high field strength and parallel imaging techniques for MRI-based gel dosimetry in stereotactic radiosurgery

    NASA Astrophysics Data System (ADS)

    Seimenis, I.; Moutsatsos, A.; Petrokokkinos, L.; Kantemiris, I.; Benekos, O.; Efstathopoulos, E.; Papagiannis, P.; Spevacek, V.; Semnicka, J.; Dvorak, P.

    2009-07-01

    The poor clinical acceptance of polymer gel dosimetry for dose verification in stereotactic radio-surgery applications stems, inter alia, from the increased MRI acquisition times needed to meet the associated spatial resolution demands. To examine whether this could be partly alleviated by the employment of 3 Tesla imagers and parallel imaging techniques, a PolyAcrylamide Gel filled tube was irradiated in a Leksell Gamma Knife unit with two single irradiation shots (4 mm and 8 mm) and underwent four different scanning sessions using an optimised, volume selective, 32 echo CPMG pulse sequence: One performed on a 1.5 T imager with 0.5 × 0.5 mm2 in-plane spatial resolution and 0.75 mm slice thickness (scan A), while the rest three on a 3.0 T imager; one with the same spatial resolution as in scan A (scan B) and two with finer in-plane resolution (scans C and D). In scans B and C the sensitivity encoding (SENSE) parallel imaging technique was employed. Relative dose distributions derived by scan A were benchmarked against Monte Carlo and treatment planning system calculations, and then used as the reference for the comparison of 2D relative dose distributions derived by each scan in terms of dose difference and distance-to-agreement criteria (γ index tool). Findings suggest that careful MRI planning based on a figure of merit accounting for scanning time and precision for a given increase in spatial resolution, could facilitate the introduction of polymer gel dosimetry into the clinical setting as a practical quality assurance tool for complex radio-surgery techniques.

  6. Electrophoretic extraction of proteins from two-dimensional electrophoresis gel spots

    DOEpatents

    Zhang, Jian-Shi; Giometti, Carol S.; Tollaksen, Sandra L.

    1989-01-01

    After two-dimensional electrophoresis of proteins or the like, resulting in a polyacrylamide gel slab having a pattern of protein gel spots thereon, an individual protein gel spot is cored out from the slab, to form a gel spot core which is placed in an extraction tube, with a dialysis membrane across the lower end of the tube. Replicate gel spots can be cored out from replicate gel slabs and placed in the extraction tube. Molten agarose gel is poured into the extraction tube where the agarose gel hardens to form an immobilizing gel, covering the gel spot cores. The upper end portion of the extraction tube is filled with a volume of buffer solution, and the upper end is closed by another dialysis membrane. Upper and lower bodies of a buffer solution are brought into contact with the upper and lower membranes and are provided with electrodes connected to the positive and negative terminals of a DC power supply, thereby producing an electrical current which flows through the upper membrane, the volume of buffer solution, the agarose, the gel spot cores and the lower membrane. The current causes the proteins to be extracted electrophoretically from the gel spot cores, so that the extracted proteins accumulate and are contained in the space between the agarose gel and the upper membrane. A high percentage extraction of proteins is achieved. The extracted proteins can be removed and subjected to partial digestion by trypsin or the like, followed by two-dimensional electrophoresis, resulting in a gel slab having a pattern of peptide gel spots which can be cored out and subjected to electrophoretic extraction to extract individual peptides.

  7. Electrophoretic extraction of proteins from two-dimensional electrophoresis gel spots

    SciTech Connect

    Zhang, J.S.; Giometti, C.S.; Tollaksen, S.L.

    1989-04-25

    After two-dimensional electrophoresis of proteins or the like, resulting in a polyacrylamide gel slab having a pattern of protein gel spots thereon, an individual protein gel spot is cored out from the slab, to form a gel spot core which is placed in an extraction tube, with a dialysis membrane across the lower and of the tube. Replicate gel spots can be cored out from replicate gel slabs and placed in the extraction tube. Molten agarose gel is poured into the extraction tube where the agarose gel hardens to form an immobilizing gel, covering the gel spot cores. The upper end portion of the extraction tube is filled with a volume of buffer solution, and the upper end is closed by another dialysis membrane. Upper and lower bodies of a buffer solution are brought into contact with the upper and lower membranes and are provided with electrodes connected to the positive and negative terminals of a DC power supply, thereby producing an electrical current which flows through the upper membrane, the volume of buffer solution, the agarose, the gel spot cores and the lower membrane. The current causes the proteins to be extracted electrophoretically from the gel spot cores, so that the extracted proteins accumulate and are contained in the space between the agarose gel and the upper membrane. A high percentage extraction of proteins is achieved. The extracted proteins can be removed and subjected to partial digestion by trypsin or the like, followed by two-dimensional electrophoresis, resulting in a gel slab having a pattern of peptide gel spots which can be cored out and subjected to electrophoretic extraction to extract individual peptides.

  8. Detecting slab structure beneath the Mediterranean

    NASA Astrophysics Data System (ADS)

    Miller, Meghan S.; Sun, Daoyuan; Piana Agostinetti, Nicola

    2013-04-01

    The presence of subducted slabs in the Mediterranean has been well documented with seismic tomography, however, these images, which are produced by smoothed, damped inversions, underestimate the sharpness of the structures. The position and extent of the slabs and the presence possible tears or gaps in the subducted lithosphere are still debated, yet the shape and location these structures are important for kinematic reconstructions and evolution of the entire subduction zone system. Extensive distribution of broadband seismic instrumentation in the Mediterranean (Italian National Seismic Network in Italy and the NSF-PICASSO project in Spain and Morocco) has allowed us to use alternative methodologies to detect the position of the slabs and slab tears beneath the Central and Western Mediterranean. Using S receiver functions we are able to identify S-to-p conversions from the bottom of the subducted slab and a lack of these signals where there are gaps or tears in the slab. We also analyze broadband waveforms for changes in P wave coda from deep (> 300 km depth) local earthquakes. The waveform records for stations in southern Italy and around the Betic-Rif show large amplitude, high frequency (f > 5 Hz) late arrivals with long coda after relatively low-frequency onset. High frequency arrivals are the strongest from events whose raypaths travel within the slab to the stations where they are recorded allowing for mapping of where the subducted material is located within the upper mantle. These two methods, along with inferring the slab position from fast P-wave velocity perturbations in tomography and intermediate depth seismicity, provide additional geophysical evidence to aid in interpretation of the complex, segmented slab structure beneath the Mediterranean.

  9. Andean flat subduction maintained by slab tunneling

    NASA Astrophysics Data System (ADS)

    Schepers, Gerben; van Hinsbergen, Douwe; Kosters, Martha; Boschman, Lydian; McQuarrie, Nadine; Spakman, Wim

    2016-04-01

    In two segments below the Andean mountain belt, the Nazca Plate is currently subducting sub-horizontally below South America over a distance of 200-300 km before the plate bends into the mantle. Such flat slab segments have pronounced effects on orogenesis and magmatism and are widely believed to be caused by the downgoing plate resisting subduction due to its local positive buoyancy. In contrast, here we show that flat slabs primarily result from a local resistance against rollback rather than against subduction. From a kinematic reconstruction of the Andean fold-thrust belt we determine up to ~390 km of shortening since ~50 Ma. During this time the South American Plate moved ~1400 km westward relative to the mantle, thus forcing ~1000 km of trench retreat. Importantly, since the 11-12 Ma onset of flat slab formation, ~1000 km of Nazca Plate subduction occurred, much more than the flat slab lengths, which leads to our main finding that the flat slabs, while being initiated by arrival of buoyant material at the trench, are primarily maintained by locally impeded rollback. We suggest that dynamic support of flat subduction comes from the formation of slab tunnels below segments with the most buoyant material. These tunnels trap mantle material until tearing of the tunnel wall provides an escape route. Fast subduction of this tear is followed by a continuous slab and the process can recur during ongoing rollback of the 7000 km wide Nazca slab at segments with the most buoyant subducting material, explaining the regional and transient character of flat slabs. Our study highlights the importance of studying subduction dynamics in absolute plate motion context.

  10. Hydrous manganese oxide doped gel probe sampler for measuring in situ reductive dissolution rates. 2. Field deployment.

    PubMed

    Farnsworth, Claire E; Griffis, Sarah D; Wildman, Richard A; Hering, Janet G

    2010-01-01

    In situ rates of reductive dissolution in submerged shoreline sediments at Lake Tegel (Berlin, Germany) were measured with a novel hydrous manganese (Mn) oxide-doped gel probe sampler in concert with equilibrium gel probe and sequential extraction measurements. Rates were low in the top 8 cm, then showed a peak from 8 to 14 cm, with a maximum at 12 cm depth. This rate corresponded with a peak in dissolved porewater iron (Fe) at 11 cm depth. Below 14 cm, the reductive dissolution rate reached an intermediate steady value. Lower rates at depth corresponded with increases in operationally defined fractions of carbonate-bound and organic- and sulfide-bound Mn and Fe as detected by sequential extraction. Observed rates of reductive dissolution, which reflect a capacity for Mn reduction rather than actual rates under ambient conditions, appear to correlate with porewater chemistry and sequential extraction fractions as expected in early sediment diagenesis, and are consistent with previous measurements of in situ reductive dissolution rates. Significant downward advection in this bank filtration setting depletes the Mn and Fe oxides in the sediments and enhances the transport of dissolved Fe and Mn into the infiltrating water.

  11. Application Improvements of Slab-Coupled Optical Fiber Sensors

    NASA Astrophysics Data System (ADS)

    Chadderdon, Spencer Lee

    This dissertation explores techniques for improving slab-coupled optical fiber sensor (SCOS) technology for use in specific applications and sensing configurations. SCOS are advantageous for their small size and all-dielectric composition which permit non-intrusive measurement of electric fields within compact environments; however, their small size also limits their sensitivity. This work performs a thorough analysis of the factors contributing to the performance of SCOS and demonstrates methods which improve SCOS, while maintaining its small dimensions and high level of directional sensitivity. These improvements include increasing the sensitivity by 9x, improving the frequency response to include sub 300 kHz frequencies, and developing a method to tune the resonances. The analysis shows that the best material for the slab waveguide is an electro-optic polymer because of its low RF permittivity combined with high electro-optic coefficient. Additional improvements are based on changing the crystal orientation to a transverse configuration, which enhances the sensitivity due to a combined increase in the effective electro-optic coefficient and electric field penetration into the slab. The transverse SCOS configuration not only improves the overall sensitivity but increases the directional sensitivity of the SCOS. Lithium niobate and electro-optic polymer are both experimentally shown to exhibit minimal frequency dependent sensitivity making them suitable for broad frequency applications. Simultaneous interrogation of multiple SCOS with a single tunable laser is achieved by tuning the resonant wavelengths of KTP SCOS so their resonances overlap.

  12. Nonlocal microscopic theory of quantum friction between parallel metallic slabs

    SciTech Connect

    Despoja, Vito

    2011-05-15

    We present a new derivation of the friction force between two metallic slabs moving with constant relative parallel velocity, based on T=0 quantum-field theory formalism. By including a fully nonlocal description of dynamically screened electron fluctuations in the slab, and avoiding the usual matching-condition procedure, we generalize previous expressions for the friction force, to which our results reduce in the local limit. Analyzing the friction force calculated in the two local models and in the nonlocal theory, we show that for physically relevant velocities local theories using the plasmon and Drude models of dielectric response are inappropriate to describe friction, which is due to excitation of low-energy electron-hole pairs, which are properly included in nonlocal theory. We also show that inclusion of dissipation in the nonlocal electronic response has negligible influence on friction.

  13. Differential single nucleotide polymorphism-based analysis of an outbreak caused by Salmonella enterica serovar Manhattan reveals epidemiological details missed by standard pulsed-field gel electrophoresis.

    PubMed

    Scaltriti, Erika; Sassera, Davide; Comandatore, Francesco; Morganti, Marina; Mandalari, Carmen; Gaiarsa, Stefano; Bandi, Claudio; Zehender, Gianguglielmo; Bolzoni, Luca; Casadei, Gabriele; Pongolini, Stefano

    2015-04-01

    We retrospectively analyzed a rare Salmonella enterica serovar Manhattan outbreak that occurred in Italy in 2009 to evaluate the potential of new genomic tools based on differential single nucleotide polymorphism (SNP) analysis in comparison with the gold standard genotyping method, pulsed-field gel electrophoresis. A total of 39 isolates were analyzed from patients (n=15) and food, feed, animal, and environmental sources (n=24), resulting in five different pulsed-field gel electrophoresis (PFGE) profiles. Isolates epidemiologically related to the outbreak clustered within the same pulsotype, SXB_BS.0003, without any further differentiation. Thirty-three isolates were considered for genomic analysis based on different sets of SNPs, core, synonymous, nonsynonymous, as well as SNPs in different codon positions, by Bayesian and maximum likelihood algorithms. Trees generated from core and nonsynonymous SNPs, as well as SNPs at the second and first plus second codon positions detailed four distinct groups of isolates within the outbreak pulsotype, discriminating outbreak-related isolates of human and food origins. Conversely, the trees derived from synonymous and third-codon-position SNPs clustered food and human isolates together, indicating that all outbreak-related isolates constituted a single clone, which was in line with the epidemiological evidence. Further experiments are in place to extend this approach within our regional enteropathogen surveillance system. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  14. Differential Single Nucleotide Polymorphism-Based Analysis of an Outbreak Caused by Salmonella enterica Serovar Manhattan Reveals Epidemiological Details Missed by Standard Pulsed-Field Gel Electrophoresis

    PubMed Central

    Scaltriti, Erika; Sassera, Davide; Comandatore, Francesco; Morganti, Marina; Mandalari, Carmen; Gaiarsa, Stefano; Bandi, Claudio; Zehender, Gianguglielmo; Bolzoni, Luca; Casadei, Gabriele

    2015-01-01

    We retrospectively analyzed a rare Salmonella enterica serovar Manhattan outbreak that occurred in Italy in 2009 to evaluate the potential of new genomic tools based on differential single nucleotide polymorphism (SNP) analysis in comparison with the gold standard genotyping method, pulsed-field gel electrophoresis. A total of 39 isolates were analyzed from patients (n = 15) and food, feed, animal, and environmental sources (n = 24), resulting in five different pulsed-field gel electrophoresis (PFGE) profiles. Isolates epidemiologically related to the outbreak clustered within the same pulsotype, SXB_BS.0003, without any further differentiation. Thirty-three isolates were considered for genomic analysis based on different sets of SNPs, core, synonymous, nonsynonymous, as well as SNPs in different codon positions, by Bayesian and maximum likelihood algorithms. Trees generated from core and nonsynonymous SNPs, as well as SNPs at the second and first plus second codon positions detailed four distinct groups of isolates within the outbreak pulsotype, discriminating outbreak-related isolates of human and food origins. Conversely, the trees derived from synonymous and third-codon-position SNPs clustered food and human isolates together, indicating that all outbreak-related isolates constituted a single clone, which was in line with the epidemiological evidence. Further experiments are in place to extend this approach within our regional enteropathogen surveillance system. PMID:25653407

  15. Associated risk factors and pulsed field gel electrophoresis of nasal isolates of Staphylococcus aureus from medical students in a tertiary hospital in Lagos, Nigeria.

    PubMed

    Adesida, Solayide A; Abioye, Olusegun A; Bamiro, Babajide S; Brai, Bartholomew I C; Smith, Stella I; Amisu, Kehinde O; Ehichioya, Deborah U; Ogunsola, Folasade T; Coker, Akitoye O

    2007-02-01

    Staphylococcus aureus infections are growing problems worldwide with important implications in hospitals. The organism is normally present in the nasal vestibule of about 35% of apparently healthy individuals and its carriage varies between different ethnic and age groups. Staphylococcal nasal carriage among health workers is particularly important to establish new clones and track origin of infections during outbreak situations. To determine the carriage rate and compare the pulsed field gel patterns of the strains, nasal swabs were collected from 185 medical students in a teaching hospital in Lagos, Nigeria. Isolates of S. aureus were tested for heamolysin production, methicillin sensitivity and Pulsed Field Gel Electrophoresis (PFGE) was performed. The results showed S.aureus nasal carrier rate of 14% with significant rate among males compared to females. All the isolates produced heamolysin. Antibiotic susceptibility pattern revealed that majority of the isolates was susceptible. Five strains (19%) harboured resistant determinants to penicillin and tetracycline. None of the strains was resistant to methicillin. 44% of the isolates typed by PFGE had type B, the most predominant pulsotype. PFGE A clone exhibited a single resistance phenotype suggesting a strong clonal relationship that could punctual an outbreak in the hospital. The results speculate that nasal carriage among medical personnel could be a function of various risk factors. Personal hygiene and behaviour may however be the means to reducing colonization and spread of S.aureus in our hospitals.

  16. The Implementation of Slab Geometry for Membrane-Channel Molecular Dynamics Simulations

    PubMed Central

    Bostick, David; Berkowitz, Max L.

    2003-01-01

    Slab geometric boundary conditions are applied in the molecular dynamics simulation of a simple membrane-channel system. The results of the simulation were compared to those of an analogous system using normal three-dimensional periodic boundary conditions. Analysis of the dynamics and electrostatics of the system show that slab geometric periodicity eliminates the artificial bulk water orientational polarization that is present while using normal three-dimensional periodicity. Furthermore, even though the water occupancy and volume of our simple channel is the same when using either method, the electrostatic properties are considerably different when using slab geometry. In particular, the orientational polarization of water is seen to be different in the interior of the channel. This gives rise to a markedly different electric field within the channel. We discuss the implications of slab geometry for the future simulation of this type of system and for the study of channel transport properties. PMID:12829468

  17. Geodetic constraint on the motion of a slab window: Implication for the Mendocino Crustal Conveyor model

    NASA Astrophysics Data System (ADS)

    Peng, Y.; Dong, D.; Yan, J.; Chen, W.

    2017-07-01

    The migration of the slab window in the Northern California Coast Ranges provides a unique setting to study the viscous coupling between crust and asthenosphere flow. The mechanisms of these dynamic processes are explained by the Mendocino Crustal Conveyor model, which predicts a 2-D "double-humped" surface uplift rate pattern on a 400 km long profile. To evaluate the Mendocino Crustal Conveyor (MCC) model using accurate geodetic measurements, we derive the vertical velocity field from 43 continuous GPS (CGPS) stations in the Coast Ranges region and project it onto the profile along three possible orientations of the slab window. The CGPS measured uplift rates are in good agreement with the MCC prediction, when the slab window orientation is parallel to the symmetry axis of the region of thickened crust. Thus, the CGPS solutions not only provide a complementary means to diagnose the MCC model but also provide an effective way to constrain the orientation of the slab window.

  18. Seismic evidence for rotating mantle flow around subducting slab edge associated with oceanic microplate capture

    NASA Astrophysics Data System (ADS)

    Mosher, Stephen G.; Audet, Pascal; L'Heureux, Ivan

    2014-07-01

    Tectonic plate reorganization at a subduction zone edge is a fundamental process that controls oceanic plate fragmentation and capture. However, the various factors responsible for these processes remain elusive. We characterize seismic anisotropy of the upper mantle in the Explorer region at the northern limit of the Cascadia subduction zone from teleseismic shear wave splitting measurements. Our results show that the mantle flow field beneath the Explorer slab is rotating anticlockwise from the convergence-parallel motion between the Juan de Fuca and the North America plates, re-aligning itself with the transcurrent motion between the Pacific and North America plates. We propose that oceanic microplate fragmentation is driven by slab stretching, thus reorganizing the mantle flow around the slab edge and further contributing to slab weakening and increase in buoyancy, eventually leading to cessation of subduction and microplate capture.

  19. Application of PCR-denaturing-gradient gel electrophoresis (DGGE) method to examine microbial community structure in asparagus fields with growth inhibition due to continuous cropping.

    PubMed

    Urashima, Yasufumi; Sonoda, Takahiro; Fujita, Yuko; Uragami, Atsuko

    2012-01-01

    Growth inhibition due to continuous cropping of asparagus is a major problem; the yield of asparagus in replanted fields is low compared to that in new fields, and missing plants occur among young seedlings. Although soil-borne disease and allelochemicals are considered to be involved in this effect, this is still controversial. We aimed to develop a technique for the biological field diagnosis of growth inhibition due to continuous cropping. Therefore, in this study, fungal community structure and Fusarium community structure in continuously cropped fields of asparagus were analyzed by polymerase chain reaction/denaturing-gradient gel electrophoresis (PCR-DGGE). Soil samples were collected from the Aizu region of Fukushima Prefecture, Japan. Soil samples were taken from both continuously cropped fields of asparagus with growth inhibition and healthy neighboring fields of asparagus. The soil samples were collected from the fields of 5 sets in 2008 and 4 sets in 2009. We were able to distinguish between pathogenic and non-pathogenic Fusarium by using Alfie1 and Alfie2GC as the second PCR primers and PCR-DGGE. Fungal community structure was not greatly involved in the growth inhibition of asparagus due to continuous cropping. By contrast, the band ratios of Fusarium oxysporum f. sp. asparagi in growth-inhibited fields were higher than those in neighboring healthy fields. In addition, there was a positive correlation between the band ratios of Fusarium oxysporum f. sp. asparagi and the ratios of missing asparagus plants. We showed the potential of biological field diagnosis of growth inhibition due to continuous cropping of asparagus using PCR-DGGE.

  20. Application of PCR-Denaturing-Gradient Gel Electrophoresis (DGGE) Method to Examine Microbial Community Structure in Asparagus Fields with Growth Inhibition due to Continuous Cropping

    PubMed Central

    Urashima, Yasufumi; Sonoda, Takahiro; Fujita, Yuko; Uragami, Atsuko

    2012-01-01

    Growth inhibition due to continuous cropping of asparagus is a major problem; the yield of asparagus in replanted fields is low compared to that in new fields, and missing plants occur among young seedlings. Although soil-borne disease and allelochemicals are considered to be involved in this effect, this is still controversial. We aimed to develop a technique for the biological field diagnosis of growth inhibition due to continuous cropping. Therefore, in this study, fungal community structure and Fusarium community structure in continuously cropped fields of asparagus were analyzed by polymerase chain reaction/denaturing-gradient gel electrophoresis (PCR-DGGE). Soil samples were collected from the Aizu region of Fukushima Prefecture, Japan. Soil samples were taken from both continuously cropped fields of asparagus with growth inhibition and healthy neighboring fields of asparagus. The soil samples were collected from the fields of 5 sets in 2008 and 4 sets in 2009. We were able to distinguish between pathogenic and non-pathogenic Fusarium by using Alfie1 and Alfie2GC as the second PCR primers and PCR-DGGE. Fungal community structure was not greatly involved in the growth inhibition of asparagus due to continuous cropping. By contrast, the band ratios of Fusarium oxysporum f. sp. asparagi in growth-inhibited fields were higher than those in neighboring healthy fields. In addition, there was a positive correlation between the band ratios of Fusarium oxysporum f. sp. asparagi and the ratios of missing asparagus plants. We showed the potential of biological field diagnosis of growth inhibition due to continuous cropping of asparagus using PCR-DGGE. PMID:22200640

  1. Three-dimensional Numerical Models of Mantle Flow Through the Cocos-Nazca Slab Gap

    NASA Astrophysics Data System (ADS)

    Jadamec, M.; Fischer, K. M.

    2013-05-01

    , seafloor ages, and geologic history are used to construct the variable thickness of the overriding Caribbean and South American plates (Feng et al., 2007; Muller et al., 2008; Rychert et al., 2008; Abt et al., 2010b; Lekic and Romanowicz, 2011; Yuan et al., 2011). The predicted motion of the Cocos and Nazca plates are compared to observed plate motions (DeMets and Dixon, 1999) and the predicted mantle flow fields are compared to local S wave and teleseismic SK(K)S observations of seismic anisotropy (Abt et al., 2009, 2010a). The direction of Cocos and Nazca surface plate motion is reasonably well reproduced regardless of whether the Cocos and Nazca slabs are a continuous slab at depth or separated by a gap. However, the inclusion of a gap between the Cocos and Nazca slabs has a significant effect on the mantle flow field, reversing the direction of the slab entrained flow beneath the Caribbean plate and resulting in counterclockwise toroidal flow around the southern Cocos slab edge and clockwise toroidal flow around the northern Nazca slab edge. The results have implications for the initiation slab tears and indicate complexity in the coupling between the lithosphere and mantle in subduction zones.

  2. Slab Geometry and Stress State of the Southwestern Colombia Subduction Zone

    NASA Astrophysics Data System (ADS)

    Chang, Ying

    A high rate of intermediate-depth earthquakes is concentrates in the Cauca cluster (3.5°N-5.5°N) and isolated from nearby seismicity in the southwestern Colombia subduction zone. Previously-studied nests of intermediate-depth earthquakes show that a high seismicity rate is often associated with a slab tear, detachment, or contortion. The cause of the less-studied Cauca cluster is unknown. To investigate the cause, we image the slab geometry using precise relative locations of intermediate-depth earthquakes. We use the earthquake catalog produced and seismic waveforms recorded by the Colombian National Seismic Network from January 2010 to March 2014. We calculate the focal mechanisms to examine whether the earthquakes reactivate pre-existing faults or form new fractures. The focal mechanisms are inverted for the intraslab stress field to check the stress guide hypothesis and to evaluate the stress orientations with regard to the change in the slab geometry. The earthquake relocations indicate that the Cauca segment has a continuous 20 km thick seismic zone and increases in dip angle from north to south. Two 40-km-tall fingers of earthquakes extend out of the slab and into the mantle wedge. Different from the previously-studied nests, the Cauca cluster does not correspond to slab contortions or tearing. The cluster may be associated with a high amount of dehydrated fluid. The determined focal mechanisms of 69 earthquakes have various types and variably-oriented nodal planes, corresponding to the reactivation of pre-existing faults and the formation of new fractures. The results of stress inversion show that the extensional axis in the northern Cauca segment is in the plane of the slab and 25° from the downdip direction, and the southern part has along-strike extension. The compression is subnormal to the plane of the slab. The stress field supports the stress guide hypothesis and shows a consistent rotation with increase in slab dip angle.

  3. SU-D-213-06: Dosimetry of Modulated Electron Radiation Therapy Using Fricke Gel Dosimeter

    SciTech Connect

    Gawad, M Abdel; Elgohary, M; Hassaan, M; Emam, M; Desouky, O; Eldib, A; Ma, C

    2015-06-15

    Purpose: Modulated electron radiation therapy (MERT) has been proposed as an effective modality for treatment of superficial targets. MERT utilizes multiple beams of different energies which are intensity modulated to deliver optimized dose distribution. Energy independent dosimeters are thus needed for quantitative evaluations of MERT dose distributions and measurements of absolute doses delivered to patients. Thus in the current work we study the feasibility of Fricke gel dosimeters in MERT dosimetry. Methods: Batches of radiation sensitive Fricke gel is fabricated and poured into polymethyl methacrylate cuvettes. The samples were irradiated in solid water phantom and a thick layer of bolus was used as a buildup. A spectrophotometer system was used for measuring the color changes (the absorbance) before and after irradiation and then we calculate net absorbance. We constructed calibration curves to relate the measured absorbance in terms of absorbed dose for all available electron energies. Dosimetric measurements were performed for mixed electron beam delivery and we also performed measurement for segmented field delivery with the dosimeter placed at the junction of two adjacent electron beams of different energies. Dose measured by our gel dosimetry is compared to that calculation from our precise treatment planning system. We also initiated a Monte Carlo study to evaluate the water equivalence of our dosimeters. MCBEAM and MCSIM codes were used for treatment head simulation and phantom dose calculation. PDDs and profiles were calculated for electron beams incident on a phantom designed with 1cm slab of Fricke gel. Results: The calibration curves showed no observed energy dependence with all studied electron beam energies. Good agreement was obtained between dose calculated and that obtained by gel dosimetry. Monte Carlo results illustrated the tissue equivalency of our Gel dosimeters. Conclusion: Fricke Gel dosimeters represent a good option for the dosimetric

  4. Radiation pressure of active dispersive chiral slabs.

    PubMed

    Wang, Maoyan; Li, Hailong; Gao, Dongliang; Gao, Lei; Xu, Jun; Qiu, Cheng-Wei

    2015-06-29

    We report a mechanism to obtain optical pulling or pushing forces exerted on the active dispersive chiral media. Electromagnetic wave equations for the pure chiral media using constitutive relations containing dispersive Drude models are numerically solved by means of Auxiliary Differential Equation Finite Difference Time Domain (ADE-FDTD) method. This method allows us to access the time averaged Lorentz force densities exerted on the magnetoelectric coupling chiral slabs via the derivation of bound electric and magnetic charge densities, as well as bound electric and magnetic current densities. Due to the continuously coupled cross-polarized electromagnetic waves, we find that the pressure gradient force is engendered on the active chiral slabs under a plane wave incidence. By changing the material parameters of the slabs, the total radiation pressure exerted on a single slab can be directed either along the propagation direction or in the opposite direction. This finding provides a promising avenue for detecting the chirality of materials by optical forces.

  5. Embedded ceria nanoparticles in gel improve electrophoretic separation: a preliminary demonstration.

    PubMed

    Zarei, Mohammad; Ahmadzadeh, Hossein; Goharshadi, Elaheh K

    2015-07-07

    Slab gel electrophoresis is still the gold standard method for the separation of biomolecules such as proteins and DNA with advantages such as simplicity, affordability, and high throughput, but it suffers from inadequate separation speed and resolution. Single capillary gel electrophoresis, on the other hand, offers faster separation time and improved resolution at the expense of higher cost and loss of high throughput capability. The high surface to volume ratio of the capillary causes improved heat dissipation leading to a reduced Joule heating and a higher resolution. Here, for the first time, we show the use of dispersed ceria nanoparticles (NPs) to improve the resolution and speed of protein separation in slab gel electrophoresis. We measured the rheological parameters of separation medium in order to find a meaningful relationship between viscosity changes, Joule heating, and band broadening. The results showed that ceria NPs decrease the viscosity of polyacrylamide gel. By loading 0.03% (w/v) ceria NPs into polyacrylamide gel at 25 °C, the viscosity decreased 22% and the thermal conductivity increased to 81%, which resulted in 35% reduction in Joule heating and 47% increase in resolution. This work is a cross disciplinary of theoretical physical chemistry for thermal conductivity and rheological measurements of PA and ceria suspensions and application in slab gel electrophoresis. We report here, for the first time, that embedded NPs in PA gel could potentially interface high throughput capability of slab gel electrophoresis with high separation speed of single capillary electrophoresis.

  6. Crystallization from Gels

    NASA Astrophysics Data System (ADS)

    Narayana Kalkura, S.; Natarajan, Subramanian

    Among the various crystallization techniques, crystallization in gels has found wide applications in the fields of biomineralization and macromolecular crystallization in addition to crystallizing materials having nonlinear optical, ferroelectric, ferromagnetic, and other properties. Furthermore, by using this method it is possible to grow single crystals with very high perfection that are difficult to grow by other techniques. The gel method of crystallization provides an ideal technique to study crystal deposition diseases, which could lead to better understanding of their etiology. This chapter focuses on crystallization in gels of compounds that are responsible for crystal deposition diseases. The introduction is followed by a description of the various gels used, the mechanism of gelling, and the fascinating phenomenon of Liesegang ring formation, along with various gel growth techniques. The importance and scope of study on crystal deposition diseases and the need for crystal growth experiments using gel media are stressed. The various crystal deposition diseases, viz. (1) urolithiasis, (2) gout or arthritis, (3) cholelithiasis and atherosclerosis, and (4) pancreatitis and details regarding the constituents of the crystal deposits responsible for the pathological mineralization are discussed. Brief accounts of the theories of the formation of urinary stones and gallstones and the role of trace elements in urinary stone formation are also given. The crystallization in gels of (1) the urinary stone constituents, viz. calcium oxalate, calcium phosphates, uric acid, cystine, etc., (2) the constituents of the gallstones, viz. cholesterol, calcium carbonate, etc., (3) the major constituent of the pancreatic calculi, viz., calcium carbonate, and (4) cholic acid, a steroidal hormone are presented. The effect of various organic and inorganic ions, trace elements, and extracts from cereals, herbs, and fruits on the crystallization of major urinary stone and gallstone

  7. A simple analytical solution for slab detachment

    NASA Astrophysics Data System (ADS)

    Schmalholz, Stefan M.

    2011-04-01

    An analytical solution is presented for the nonlinear dynamics of high amplitude necking in a free layer of power-law fluid extended in layer-parallel direction due to buoyancy stress. The solution is one-dimensional (1-D) and contains three dimensionless parameters: the thinning factor (i.e. ratio of current to initial layer thickness), the power-law stress exponent, n, and the ratio of time to the characteristic deformation time of a viscous layer under buoyancy stress, t/ tc. tc is the ratio of the layer's effective viscosity to the applied buoyancy stress. The value of tc/ n specifies the time for detachment, i.e. the time it takes until the layer thickness has thinned to zero. The first-order accuracy of the 1-D solution is confirmed with 2-D finite element simulations of buoyancy-driven necking in a layer of power-law fluid embedded in a linear or power-law viscous medium. The analytical solution is accurate within a factor about 2 if the effective viscosity ratio between the layer and the medium is larger than about 100 and if the medium is a power-law fluid. The analytical solution is applied to slab detachment using dislocation creep laws for dry and wet olivine. Results show that one of the most important parameters controlling the dynamics of slab detachment is the strength of the slab which strongly depends on temperature and rheological parameters. The fundamental conclusions concerning slab detachment resulting from both the analytical solution and from earlier published thermo-mechanical numerical simulations agree well, indicating the usefulness of the highly simplified analytical solution for better understanding slab detachment. Slab detachment resulting from viscous necking is a combination of inhomogeneous thinning due to varying buoyancy stress within the slab and a necking instability due to the power-law viscous rheology ( n > 1). Application of the analytical solution to the Hindu Kush slab provides no "order-of-magnitude argument" against

  8. Photocatalytic, highly hydrophilic porcelain stoneware slabs

    NASA Astrophysics Data System (ADS)

    Raimondo, M.; Guarini, G.; Zanelli, C.; Marani, F.; Fossa, L.; Dondi, M.

    2011-10-01

    Photocatalytic, highly hydrophilic industrial porcelain stoneware large slabs were realized by deposition of nanostructured TiO2 coatings. Different surface finishing and experimental conditions were considered in order to assess the industrial feasibility. Photocatalytic and wetting behaviour of functionalized slabs mainly depends on surface phase composition in terms of anatase/rutile ratio, this involving - as a key issue - the deposition of TiO2 on industrially sintered products with an additional annealing step to strengthen coatings' performances and durability.

  9. Behavior of Partially Restrained Reinforced Concrete Slabs.

    DTIC Science & Technology

    1986-09-01

    Experimental Deflections and Coupling Forces. ........ 72 3.4 Method of Approximating Support Rotations . . . 76 3.5 Free-Body Diagram Used in Computing...common types of structural elements. Slabs are found in practically every type of structural system, ’ whether steel or concrete, single -story or...Because of the nature of reinforced concrete slabs, accurate evaluations of stresses, strains, and deflections are difficult to make by elasticity

  10. Subwavelength electromagnetic dynamics in stacked complementary plasmonic crystal slabs.

    PubMed

    Iwanaga, Masanobu

    2010-07-19

    Resonant electromagnetic fields in stacked complementary plasmonic crystal slabs (sc-PlCSs) are numerically explored in subwavelength dimensions. It is found that the local plasmon resonances in the sc-PlCSs are composite states of locally enhanced electric and magnetic fields. Two sc-PlCSs are analyzed in this paper and it is shown that each sc-PlCS realizes a resonant electromagnetic state suggested by one of Maxwell equations. It is moreover clarified that the local plasmons open efficient paths of Poynting flux, those result in high-contrast polarized transmission.

  11. Ultra-low field T1 vs. T1rho at 3T and 7T: study of rotationally immobilized protein gels and animal brain tissues

    NASA Astrophysics Data System (ADS)

    Dong, Hui; Inglis, Ben; Barr, Ian; Clarke, John

    2015-03-01

    Clinical magnetic resonance imaging (MRI) machines operating in static fields of typically 1.5 T or 3 T can capture information on slow molecular dynamics utilizing the so-called T1rho technique. This technique, in which a radiofrequency (RF) spin-lock field is applied with microtesla amplitude, has been used, for example, to determine the onset time of stroke in studies on rats. The long RF pulse, however, may exceed the specific absorption rate (SAR) limit, putting subjects at risk. Ultra-low-field (ULF) MRI, based on Superconducting Quantum Interference Devices (SQUIDs), directly detects proton signals at a static magnetic field of typically 50-250 μT. Using our ULF MRI system with adjustable static field of typically 55 to 240 μT, we systematically measured the T1 and T2 dispersion profiles of rotationally immobilized protein gels (bovine serum albumin), ex vivo pig brains, and ex vivo rat brains with induced stroke. Comparing the ULF results with T1rho dispersion obtained at 3 T and 7 T, we find that the degree of protein immobilization determines the frequency-dependence of both T1 and T1rho. Furthermore, T1rho and ULF T1 show similar results for stroke, suggesting that ULF MRI may be used to image traumatic brain injury with negligible SAR. This research was supported by the Henry H. Wheeler, Jr. Brain Imaging Center and the Donaldson Trust.

  12. Standing sausage modes in curved coronal slabs

    NASA Astrophysics Data System (ADS)

    Pascoe, D. J.; Nakariakov, V. M.

    2016-09-01

    Context. Magnetohydrodynamic waveguides such as dense coronal loops can support standing modes. The ratios of the periods of oscillations for different longitudinal harmonics depend on the dispersive nature of the waveguide and so may be used as a seismological tool to determine coronal parameters. Aims: We extend models of standing sausage modes in low β coronal loops to include the effects of loop curvature. The behaviour of standing sausage modes in this geometry is used to explain the properties of observed oscillations that cannot be accounted for using straight loop models. Methods: We perform 2D numerical simulations of an oscillating coronal loop, modelled as a dense slab embedded in a potential magnetic field. The loop is field-aligned and so experiences expansion with height in addition to being curved. Standing sausage modes are excited by compressive perturbations of the loop and their properties are studied. Results: The spatial profiles of standing sausage modes are found to be modified by the expanding loop geometry typical for flaring loops and modelled by a potential magnetic field in our simulations. Longitudinal harmonics of order n > 1 have anti-nodes that are shifted towards the loop apex and the amplitude of anti-nodes near the loop apex is smaller than those near the loop footpoints. Conclusions: We find that the observation of standing sausage modes by the Nobeyama Radioheliograph in a flaring coronal loop on 12 January 2000 is consistent with interpretation in terms of the global mode (n = 1) and third harmonic (n = 3). This interpretation accounts for the period ratio and spatial structure of the observed oscillations.

  13. Numerical analysis of the shifting slabs applied in a wireless power transfer system to enhance magnetic coupling

    NASA Astrophysics Data System (ADS)

    Dong, Yayun; Yang, Xijun; Jin, Nan; Li, Wenwen; Yao, Chen; Tang, Houjun

    2017-05-01

    Shifting medium is a kind of metamaterial, which can optically shift a space or an object a certain distance away from its original position. Based on the shifting medium, we propose a concise pair of shifting slabs covering the transmitting or receiving coil in a two-coil wireless power transfer system to decrease the equivalent distance between the coils. The electromagnetic parameters of the shifting slabs are calculated by transformation optics. Numerical simulations validate that the shifting slabs can approximately shift the electromagnetic fields generated by the covered coil; thus, the magnetic coupling and the efficiency of the system are enhanced while remaining the physical transmission distance unchanged. We also verify the advantages of the shifting slabs over the magnetic superlens. Finally, we provide two methods to fabricate shifting slabs based on split-ring resonators.

  14. Use of a ring chromosome and pulsed-field gels to study interhomolog recombination, double-strand DNA breaks and sister-chromatid exchange in yeast

    SciTech Connect

    Game, J.C. ); Sitney, K.C.; Cook, V.E.; Mortimer, R.K. )

    1989-12-01

    The authors describe a system that uses pulsed-field gels for the physical detection of recombinant DNA molecules, double-strand DNA breaks (DSB) and sister-chromatid exchange in the yeast Saccharomyces cerevisiae. The system makes use of a circular variant of chromosome II (Chr. III). Meiotic recombination between this ring chromosome and a linear homolog produces new molecules of sizes distinguishable on gels from either parental molecule. They demonstrate that these recombinant molecules are not present either in strains with two linear Chr. III molecules or in rad50 mutants, which are defective in meiotic recombination. In conjunction with the molecular endpoints. They present data on the timing of commitment to meiotic recombination scored genetically. They have used x-rays to linearize circular Chr. III, both to develop a sensitive method for measuring frequency of DSB and as a means of detecting double-size circles originating in part from sister-chromatid exchange, which they find to be frequent during meiosis.

  15. Evaluation and comparison of random amplification of polymorphic DNA, pulsed-field gel electrophoresis and ADSRRS-fingerprinting for typing Serratia marcescens outbreaks.

    PubMed

    Krawczyk, Beata; Naumiuk, Lukasz; Lewandowski, Krzysztof; Baraniak, Anna; Gniadkowski, Marek; Samet, Alfred; Kur, Józef

    2003-10-15

    Amplification of DNA fragments surrounding rare restriction sites (ADSRRS-fingerprinting) is a novel assay based on suppression of polymerase chain reaction (PCR). This phenomenon allows the amplification of only a limited subset of DNA fragments, since only those with two different oligonucleotides ligated at the ends of complementary DNA strands are amplified in the PCR. The DNA fragments can be easily analyzed on polyacrylamide gels, stained with ethidium bromide. We have implemented this method using a set of clinical Serratia marcescens isolates from three outbreaks ongoing in the Public Hospital in Gdańsk (Poland). Clustering of ADSRRS-fingerprinting data matched epidemiological, microbiological, random amplification of polymorphic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE) data. Based on this study, we found that there is at least a similar power of discrimination between the present 'gold-standard' PFGE and the novel method, ADSRRS-fingerprinting. Although the ADSRRS-fingerprinting method may appear to be more complex than the RAPD technique, we found it fast and reproducible.

  16. High transparent shape memory gel

    NASA Astrophysics Data System (ADS)

    Gong, Jin; Arai, Masanori; Kabir, M. H.; Makino, Masato; Furukawa, Hidemitsu

    2014-03-01

    Gels are a new material having three-dimensional network structures of macromolecules. They possess excellent properties as swellability, high permeability and biocompatibility, and have been applied in various fields of daily life, food, medicine, architecture, and chemistry. In this study, we tried to prepare new multi-functional and high-strength gels by using Meso-Decoration (Meso-Deco), one new method of structure design at intermediate mesoscale. High-performance rigid-rod aromatic polymorphic crystals, and the functional groups of thermoreversible Diels-Alder reaction were introduced into soft gels as crosslinkable pendent chains. The functionalization and strengthening of gels can be realized by meso-decorating the gels' structure using high-performance polymorphic crystals and thermoreversible pendent chains. New gels with good mechanical properties, novel optical properties and thermal properties are expected to be developed.

  17. Was there a Laramide "flat slab"?

    NASA Astrophysics Data System (ADS)

    Jones, C. H.

    2014-12-01

    Slab-continent interactions drive most non-collisional orogenies; this has led us to usually anticipate that temporal changes or spatial variations in orogenic style are related to changes in the slab, most especially in the slab's dip. This is most dramatically evident for orogenies in the foreland, well away from the trench, such as the Laramide orogeny. However, the physical means of connecting slab geometry to crustal deformation remain obscure. Dickinson and Snyder (1978) and Bird (1984) laid out a conceptually elegant means of creating foreland deformation from shear between a slab and overriding continental lithosphere, but such strong shear removed all of the continental lithosphere in the western U.S. when included in a numerical simulation of flat slab subduction (Bird, 1988), a removal in conflict with observations of volcanic rocks and xenoliths in many locations. Relying on an increase in edge normal stresses results, for the Laramide, in requiring the little-deformed Colorado Plateau to either be unusually strong or to have risen rapidly enough and high enough to balance edge stresses with body forces. Early deformation in the Plateau rules out unusual strength, and the accumulation and preservation of Late Cretaceous near-sea level sedimentary rocks makes profound uplift unlikely (though not impossible). Relying on comparisons with the Sierras Pampeanas is also fraught with problems: the Sierras are not separated from the Andean fold-and-thrust belt by several hundred kilometers of little-deformed crust, nor were they buried under kilometers of marine muds as were large parts of the Laramide foreland. We have instead suggested that some unusual interactions of an obliquely subducting plate with a thick Archean continental root might provide a better explanation than a truly flat slab (Jones et al., 2011). From this, and given that several flat-slab segments today are not associated with foreland orogenesis and noting that direct evidence for truly

  18. Influence of weak layer heterogeneity on slab avalanche release. Application to the evaluation of avalanche release depths.

    NASA Astrophysics Data System (ADS)

    Gaume, J.; Chambon, G.; Eckert, N.; Naaim, M.

    2012-04-01

    Slab avalanches are generally caused by the collapse of a weak layer underlying a cohesive slab. The two key ingredients for the mechanical description of such slab avalanche releases are the heterogeneity of the weak layer and the redistribution of stresses via the elasticity of the slab. The finite element code Cast3M is used to build a complete full-scale mechanical model of the slab-weak layer system including inertial effects. The weak layer is modeled as a cohesive Mohr-Coulomb interface with cohesion softening which accounts for shear-induced collapse. The overlying slab is represented by an elastic layer. The system is loaded by increasing the slope angle until rupture. We first study the influence of a single weak spot in the weak layer in order to validate the model against analytical solutions. The interaction between two weak spots is also analyzed. The case of heterogeneous weak layers represented through Gaussian stochastic distributions of the cohesion with a spherical spatial covariance is then studied. Several simulations for different realizations of the heterogeneity of the weak layer are carried out and the influence of slab depth and heterogeneity correlation length on avalanche release angle distributions is examined. In particular a heterogeneity smoothing effect caused by slab elasticity and characterized by a typical length scale of the system is evidenced. Finally the model is coupled with extreme snowfall distributions belonging to the GEV class, which allows to recover with very good accuracy release depth distributions obtained from field data.

  19. Calculation of spin and orbital magnetizations in Fe slab systems at finite temperature.

    PubMed

    Garibay-Alonso, R; Reyes-Reyes, M; Urrutia-Bañuelos, Efraín; López-Sandoval, R

    2010-02-10

    The temperature dependence of spin and orbital local magnetizations is theoretically determined for the non-bulk atomic region of (001) and (110) Fe slab systems. A d band Hamiltonian, including spin-orbit coupling terms, was used to model the slabs, which were emulated by using Fe films of sufficient thickness to reach a bulk behavior at their most inner atomic layers. The temperature effects were considered within the static approximation and a simple mean field theory was used to integrate the local magnetic moment and charge thermal fluctuations. The results reflect a clear interplay between electronic itinerancy and the local atomic environment and they can be physically interpreted from the local small charge transfers occurring in the superficial region of the slabs. For recovering the experimental behavior on the results for the (001) slab system, the geometrical relaxations at its non-bulk atomic layers and a d band filling variation are required. A study on the magnetic anisotropy aspects in the superficial region of the slabs is additionally performed by analyzing the results for the orbital local magnetization calculated along two different magnetization directions in both slab systems.

  20. The zone of influence of the subducting slab in the asthenospheric mantle

    NASA Astrophysics Data System (ADS)

    MacDougall, Julia G.; Jadamec, Margarete A.; Fischer, Karen M.

    2017-08-01

    Due to the multidisciplinary nature of combined geodynamics and shear wave splitting studies, there is still much to be understood in terms of isolating the contributions from mantle dynamics to the shear wave splitting signal, even in a two-dimensional (2-D) mantle flow framework. This paper investigates the viscous flow, lattice preferred orientation (LPO) development, and predicted shear wave splitting for a suite of buoyancy-driven subduction models using a non-linear rheology to shed light on the nature of the slab-driven asthenospheric flow and plate-mantle coupling. The slab-driven zone of influence in the mantle, LPO fabric, and resulting synthetic splitting are sensitive to slab strength and slab initial slab dip. The non-linear viscosity formulations leads to dynamic reductions in asthenospheric viscosity extending over 600 km into the mantle wedge and over 300 km behind the trench, with peak flow velocities occurring in models with a weaker slab and moderate slab dip. The olivine LPO fabric in the asthenosphere generally increases in alignment strength with increased proximity to the slab but can be transient and spatially variable on small length scales. The results suggest that LPO formed during initial subduction may persist into the steady state subduction regime. Vertical flow fields in the asthenosphere can produce shear wave splitting variations with back azimuth that deviate from the predictions of uniform trench-normal anisotropy, a result that bears on the interpretation of complexity in shear wave splitting observed in real subduction zones. Furthermore, the models demonstrate the corner flow paradigm should not be equated with a 2-D subduction framework.

  1. Pulsed-field gel electrophoresis (PFGE) typing of Listeria strains isolated from a meat processing plant over a 2-year period.

    PubMed

    Senczek, D; Stephan, R; Untermann, F

    2000-12-05

    As part of a hygiene monitoring program in a meat processing plant a total of 131 Listeria isolates were detected by sampling different processing areas and meat products within a 2-year period. The isolates were differentiated by means of phenotypic characteristics. Furthermore, the genomic ApaI and SmaI fragment patterns of all isolates were examined by pulsed-field gel electrophoresis (PFGE). PFGE using SmaI and ApaI yielded 15 (Listeria monocytogenes), 20 (Listeria innocua) and six (Listeria welshimeri) pulsotypes. Of the environmental Listeria monocytogenes isolates the predominating PFGE-type B was clearly associated with processing area A whereas PFGE-type E predominated in the meat products. Moreover, the study showed the persistence of closely related Listeria strains over a 2-year period in the environment of this meat processing plant.

  2. Comparison of Campylobacter isolates from poultry and humans: association between in vitro virulence properties, biotypes, and pulsed-field gel electrophoresis clusters.

    PubMed

    Nadeau, Eric; Messier, Serge; Quessy, Sylvain

    2003-10-01

    The in vitro virulence properties of 197 temporally and geographically related Campylobacter isolates from chicken broilers and humans were compared. Comparisons of the virulence properties associated with genotypes and biotypes were made. All isolates adhered to, and 63% invaded, INT-407 cells, whereas 13% were cytotoxic for CHO cells. CHO cell-cytotoxic extracts were also cytotoxic for INT-407 cells, but the sensitivity for Vero cells was variable. The proportion of isolates demonstrating a high invasiveness potential (>1,000 CFU ml(-1)) or Vero cell cytotoxicity was significantly higher for human than for poultry isolates. Invasiveness was associated with Campylobacter jejuni isolates of biotypes 1 and 2, whereas CHO and INT-407 cell cytotoxicity was associated with C. jejuni isolates of biotypes 3 and 4. Cytotoxic isolates were also clustered according to pulsed-field gel electrophoresis profiles.

  3. Assessment of Strain Relatedness among Salmonella Serotypes Salinatis, Duisburg, and Sandiego by Biotyping, Ribotyping, IS200 Fingerprinting, and Pulsed-Field Gel Electrophoresis

    PubMed Central

    Old, David C.; Rankin, Shelley C.; Crichton, Pamela B.

    1999-01-01

    Salinatis (antigenic formula, 4,12:d:eh:enz15) is a rare Salmonella serotype currently designated a triphasic variant of the diphasic serotype Duisburg (1,4,12,27:d:enz15) (underlining indicates that the O antigen is determined by phage lysogenization). Salinatis could also be related to serotype Sandiego (4,[5],12:eh:enz15), from which it might have been derived by loss of H-d flagellin genes. Nineteen Salmonella strains of serotypes Salinatis, Duisburg, and Sandiego were examined by biotyping, PvuII and SmaI ribotyping, IS200 fingerprinting, and pulsed-field gel electrophoretic profiling. Results from these methods, used alone or together, indicate that serotype Salinatis is more likely to be related to serotype Sandiego than to serotype Duisburg. For future lists of serotype names, it is recommended that Salinatis be considered a variant of Sandiego. PMID:10325308

  4. Characterization of nosocomial Serratia marcescens isolates: comparison of Fourier-transform infrared spectroscopy with pulsed-field gel electrophoresis of genomic DNA fragments and multilocus enzyme electrophoresis.

    PubMed

    Irmscher, H M; Fischer, R; Beer, W; Seltmann, G

    1999-07-01

    A total of 66 Serratia marcescens isolates from 46 patients was investigated by macrorestriction using XbaI followed by pulsed-field gel electrophoresis. 7 restriction fragment patterns attributable to more than one patient and 9 individual patterns were identified. The isolates were additionally characterized by multilocus enzyme electrophoresis and Fourier-transform infrared spectroscopy. The macrorestriction patterns and the multilocus enzyme electrophoresis patterns corresponded fairly well while the classifications derived from these methods were not completely congruent. The grouping achieved by Fourier-transform infrared spectroscopy on the basis of high (> 1000) and moderately high heterogeneity values (300) was consistent with the macrorestriction results. Grouping on a lower heterogeneity level did not contribute to further discrimination. In general, Fourier-transform infrared spectroscopy was less discriminatory than the two other methods, but easier to perform. Therefore, laboratories equipped with the necessary devices may use it to rapidly select bacterial isolates for macrorestriction or other well established characterization procedures.

  5. Molecular epidemiology of Salmonella spp. isolates from gulls, fish-meal factories, feed factories, animals and humans in Norway based on pulsed-field gel electrophoresis.

    PubMed Central

    Nesse, L. L.; Refsum, T.; Heir, E.; Nordby, K.; Vardund, T.; Holstad, G.

    2005-01-01

    The molecular epidemiology of 98 isolates of Salmonella serovar Agona (n = 27), S. Montevideo (n = 42) and S. Senftenberg (n = 29) from wild-living gulls, fish-meal factories, feed factories, humans and domestic animals was investigated using pulsed-field gel electrophoresis (PFGE) and computerized numerical analysis. Two of the S. Agona profiles were identified both in gulls and in two of the factories. In addition, one of these profiles was detected in two infected poultry farms. Two of the S. Montevideo profiles were also identified both in gulls and in two of the factories, and one of these profiles was observed in a human isolate. Four factories shared an identical S. Senftenberg profile. The S. Senftenberg profile found in gulls was not identified in any other source investigated. The presence of isolates with identical PFGE profiles indicates potential epidemiological links between different factories, as well as between gulls and factories. PMID:15724711

  6. Analysis of the genome of the gram-negative moderate halophiles Halomonas and Chromohalobacter by using pulsed-field gel electrophoresis.

    PubMed

    Mellado, E; García, M T; Roldán, E; Nieto, J J; Ventosa, A

    1998-11-01

    The genomes of 11 moderately halophilic bacteria belonging to the genera Halomonas and Chromohalobacter have been analyzed by restriction endonuclease digestion and pulsed-field gel electrophoresis (PFGE). By using the infrequently cutting restriction endonucleases SpeI and SwaI, highly characteristic fingerprintings were obtained for each of the isolates studied. On the basis of the lengths of the SpeI and SwaI fragments, separated by PFGE, the genome size of the 11 strains studied was estimated. The genome size for 8 Halomonas strains ranged from 1450 to 2830 kb, whereas for the 3 Chromohalobacter strains studied it ranged from 1770 to 2295 kb. Finally, we show that macrorestriction fingerprints could be a useful tool to elucidate the taxonomic position of bacteria belonging to the Halomonas-Deleya complex.

  7. Controllable optical bistability and multistability in a slab defected with monolayer graphene nanostructure

    NASA Astrophysics Data System (ADS)

    Solookinejad, Gh.

    2016-05-01

    In this paper, the optical bistability (OB) and optical multistability (OM) properties of weak probe light in a defect dielectric medium doped by four-level graphene nanostructure is theoretically discussed. The double dark resonance can arise by linear polarized control laser fields which consist of linear left and right circularly polarized light. We show that by adjusting the Rabi-frequencies of control fields, frequency detuning of bichromatic electric fields, the intensity threshold and hysteric curves of OB and OM can be manipulated. Moreover, the thickness of the slab is considered as a controllable parameter which can impact the OB and OM behaviors of weak probe light in a defect slab. We find that the transition from OB to OM or vice versa can be possible by adjusting the thickness of the slab. Our results may provide some new application on Nano-scale devices in future all-optical communication and quantum information technologies.

  8. Numerical study on the curling and warping of hardened rigid pavement slabs

    NASA Astrophysics Data System (ADS)

    Qin, Yinghong

    In-service hardened concrete pavement suffers from environmental loadings caused by curling and warping of the slab. Traditionally, these loadings are computed on the basis of treating the slab as an elastic material, and of evaluating separately the curling and warping components. This dissertation simulates temperature distribution and moisture distribution through the slabs by use of a developed numerical model that couples the heat transfer and moisture transport. The computation of environmental loadings treats the slab as an elastic-viscous material, which considers the relaxation behavior and Pickett effect of the concrete. The heat transfer model considers the impacts of solar radiation, wind speed, air temperature, pavement slab albedo, etc. on the pavement temperature distribution. This dissertation assesses the difference between documented models that aim to predict pavement temperature, highlighting their pros and cons. The moisture transport model is unique for the documented models; it mimics the wetting and drying events occurring at the slab surface. These events are estimated by a proposed statistical algorithm, which is verified by field rainfall data. Analysis of the predicted results examines on the roles of the local air RH (relative humidity), wind speed, rainy pattern in the moisture distribution through the slab. The findings reveal that seasonal air RH plays a decisive role on the slab's moisture distribution; but wind speed and its daily variation, daily RH variation, and seasonal rainfall pattern plays only a secondary role. This dissertation sheds light on the computation of environmental loadings that in-service pavement slabs suffer from. Analysis of the computed stresses centers on the stress relaxation near the surface, stress evolution after the curing ends, and the impact of construction season on the stress's magnitude. An unexpected finding is that the total environmental loadings at the cyclically-stable state divert from the

  9. Cracking behavior of structural slab bridge decks

    NASA Astrophysics Data System (ADS)

    Baah, Prince

    Bridge deck cracking is a common problem throughout the United States, and it affects the durability and service life of concrete bridges. Several departments of transportation (DOTs) in the United States prefer using continuous three-span solid structural slab bridges without stringers over typical four-lane highways. Recent inspections of such bridges in Ohio revealed cracks as wide as 0.125 in. These measured crack widths are more than ten times the maximum limit recommended in ACI 224R-01 for bridge decks exposed to de-icing salts. Measurements using digital image correlation revealed that the cracks widened under truck loading, and in some cases, the cracks did not fully close after unloading. This dissertation includes details of an experimental investigation of the cracking behavior of structural concrete. Prism tests revealed that the concrete with epoxy-coated bars (ECB) develops the first crack at smaller loads, and develops larger crack widths compared to the corresponding specimens with uncoated (black) bars. Slab tests revealed that the slabs with longitudinal ECB developed first crack at smaller loads, exhibited wider cracks and a larger number of cracks, and failed at smaller ultimate loads compared to the corresponding test slabs with black bars. To develop a preventive measure, slabs with basalt and polypropylene fiber reinforced concrete were also included in the test program. These test slabs exhibited higher cracking loads, smaller crack widths, and higher ultimate loads at failure compared to the corresponding slab specimens without fibers. Merely satisfying the reinforcement spacing requirements given in AASHTO or ACI 318-11 is not adequate to limit cracking below the ACI 224R-01 recommended maximum limit, even though all the relevant design requirements are otherwise met. Addition of fiber to concrete without changing any steel reinforcing details is expected to reduce the severity and extent of cracking in reinforced concrete bridge decks.

  10. 46. 84INCH STRIP MILL. SLABS ROLLED AT THE PLANT'S SLABBING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    46. 84-INCH STRIP MILL. SLABS ROLLED AT THE PLANT'S SLABBING MILL ARE REHEATED IN ONE OF TWO CONTINUOUS FURNACES, THEN PUSHED OUT ONTO A CONVEYOR THAT CARRIES THEM TO THE ROUGHING AND FINISHING STANDS. - Corrigan, McKinney Steel Company, 3100 East Forty-fifth Street, Cleveland, Cuyahoga County, OH

  11. Polyclonal infections due to Mycobacterium avium complex in patients with AIDS detected by pulsed-field gel electrophoresis of sequential clinical isolates.

    PubMed Central

    Slutsky, A M; Arbeit, R D; Barber, T W; Rich, J; von Reyn, C F; Pieciak, W; Barlow, M A; Maslow, J N

    1994-01-01

    Invasive infection with organisms of the Mycobacterium avium complex (MAC) is common among patients with advanced human immunodeficiency virus infection. In previous studies, we analyzed multiple individual colonies of MAC isolated from specimens obtained at the same time and observed that 14 to 20% of patients are simultaneously infected with more than one strain. In this study, we examined sequential isolates from 12 patients with AIDS who had two or more MAC isolates available from clinical specimens collected more than 1 week apart; the intervals between the first and last specimens ranged from 8 to 192 (median, 46) days. For each isolate, restriction digests of genomic DNA were analyzed by pulsed-field gel electrophoresis; DNA was prepared by using a protocol, described here in detail, which had been optimized for conditions of bacterial growth and lysis. The pulsed-field gel electrophoresis analysis identified four patients (33%) infected with two different MAC strains. Both M. avium and M. intracellulare were cultured from blood specimens from two patients. In each of the four patients, the second strain was identified from a culture taken within 14 days of the initial study isolate, and in three of these patients, the first strain was detected again in a subsequent culture. These observations suggest that the presence of two different strains among isolates from sequential cultures may reflect ongoing polyclonal infection. We conclude that polyclonal infection with MAC is common among patients with AIDS. The identification of such infections may be critical in the development of effective treatments. Images PMID:7929773

  12. Tracing outbreaks of Streptococcus equi infection (strangles) in horses using sequence variation in the seM gene and pulsed-field gel electrophoresis.

    PubMed

    Lindahl, Susanne; Söderlund, Robert; Frosth, Sara; Pringle, John; Båverud, Viveca; Aspán, Anna

    2011-11-21

    Strangles is a serious respiratory disease in horses caused by Streptococcus equi subspecies equi (S. equi). Transmission of the disease occurs by direct contact with an infected horse or contaminated equipment. Genetically, S. equi strains are highly homogenous and differentiation of strains has proven difficult. However, the S. equi M-protein SeM contains a variable N-terminal region and has been proposed as a target gene to distinguish between different strains of S. equi and determine the source of an outbreak. In this study, strains of S. equi (n=60) from 32 strangles outbreaks in Sweden during 1998-2003 and 2008-2009 were genetically characterized by sequencing the SeM protein gene (seM), and by pulsed-field gel electrophoresis (PFGE). Swedish strains belonged to 10 different seM types, of which five have not previously been described. Most were identical or highly similar to allele types from strangles outbreaks in the UK. Outbreaks in 2008/2009 sharing the same seM type were associated by geographic location and/or type of usage of the horses (racing stables). Sequencing of the seM gene generally agreed with pulsed-field gel electrophoresis profiles. Our data suggest that seM sequencing as a epidemiological tool is supported by the agreement between seM and PFGE and that sequencing of the SeM protein gene is more sensitive than PFGE in discriminating strains of S. equi. Copyright © 2011 Elsevier B.V. All rights reserved.

  13. Goos-Hänchen shifts of the reflected waves from a cold, inhomogeneous, and magnetized plasma slab.

    PubMed

    Xu, Guoding; Zang, Taocheng; Pan, Tao

    2010-01-01

    We discuss theoretically the Goos-Hänchen (GH) shifts of the reflected waves from a cold, inhomogeneous, and magnetized plasma slab by using the invariant imbedding approach. Aiming at the linear and parabolic electron-density profiles, we demonstrate numerically the dependences of the co- and cross-polarized GH shifts on the angle of incidence, external static magnetic field, and the thickness of the plasma slab. The results show that the different electron-density profiles of plasma can result in the very different dependences of the GH shifts on the angle of incidence, external magnetic field, and the slab's thickness; the GH shifts can be switched between the considerably large positive and negative values under certain conditions. Particularly, without altering the structure of the plasma slab, the GH shifts can be manipulated by modifying the angle of incident or the external static magnetic field.

  14. Field emission of silicon emitter arrays coated with sol-gel (Ba0.65Sr0.35)1-xLaxTiO3 thin films

    NASA Astrophysics Data System (ADS)

    Lu, H.; Pan, J. S.; Chen, X. F.; Zhu, W. G.

    2007-07-01

    (Ba0.65Sr0.35)1-xLaxTiO3 (BSLT) thin films with different La concentrations have been deposited on Si field emitter arrays (FEAs) using sol-gel technology for field electron emission applications. The films exhibit the perovskite structure at low La substitution level (x ≤0.5) and the pyrochlore phase at high La concentration (x ≥0.75). The 30-nm-thick BSLT (x =0.25) thin film has higher crystallinity of perovskite structure in the surface region. An x-ray photoelectron spectroscopy study indicates that the oxygen vacancy concentration decreases with La substitution. With respect to the undoped Ba0.65Sr0.35TiO3 thin film, the Fermi level shifts down for the BSLT sample with x =0.1 ascribed to the decreasing oxygen vacancy concentration, and then shifts up for the BSLT sample with x =0.25 attributed to the increasing La substitution level. In highly doped films with an x value over 0.5, it shifts down again associated with the second pyrochlore phase formation. The best enhancement in field emission is found for the BSLT-coated (x =0.25) Si FEAs due to the improved perovskite structure in the surface region and up-moved Fermi level of the coating.

  15. Accidents due to falls from roof slabs.

    PubMed

    Rudelli, Bruno Alves; Silva, Marcelo Valerio Alabarce da; Akkari, Miguel; Santili, Claudio

    2013-01-01

    CONTEXT AND OBJECTIVE Falls from the roof slabs of houses are accidents of high potential severity that occur in large Brazilian cities and often affect children and adolescents. The aims of this study were to characterize the factors that predispose towards this type of fall involving children and adolescents, quantify the severity of associated lesions and suggest preventive measures. DESIGN AND SETTING Descriptive observational prospective longitudinal study in two hospitals in the metropolitan region of São Paulo. METHODS Data were collected from 29 cases of falls from roof slabs involving children and adolescents between October 2008 and October 2009. RESULTS Cases involving males were more prevalent, accounting for 84%. The predominant age group was schoolchildren (7 to 12 years old; 44%). Leisure activities were most frequently being practiced on the roof slab at the time of the fall (86%), and flying a kite was the most prevalent game (37.9%). In 72% of the cases, the children were unaccompanied by an adult responsible for them. Severe conditions such as multiple trauma and traumatic brain injuries resulted from 79% of the accidents. CONCLUSION Falls from roof slabs are accidents of high potential severity, and preventive measures aimed towards informing parents and guardians about the dangers and risk factors associated with this type of accident are needed, along with physical protective measures, such as low walls around the slab and gates with locks to restrict free access to these places.

  16. Characterization of anisotropic acoustic metamaterial slabs

    NASA Astrophysics Data System (ADS)

    Park, Jun Hyeong; Lee, Hyung Jin; Kim, Yoon Young

    2016-01-01

    In an anisotropic acoustic metamaterial, the off-diagonal components of its effective mass density tensor should be considered in order to describe the anisotropic behavior produced by arbitrarily shaped inclusions. However, few studies have been carried out to characterize anisotropic acoustic metamaterials. In this paper, we propose a method that uses the non-diagonal effective mass density tensor to determine the behavior of anisotropic acoustic metamaterials. Our method accurately evaluates the effective properties of anisotropic acoustic metamaterials by separately dealing with slabs made of single and multiple unit cells along the thickness direction. To determine the effective properties, the reflection and transmission coefficients of an acoustic metamaterial slab are calculated, and then the wave vectors inside of the slab are determined using these coefficients. The effective material properties are finally determined by utilizing the spatial dispersion relation of the anisotropic acoustic metamaterial. Since the dispersion relation of an anisotropic acoustic metamaterial is explicitly used, its effective properties can be easily determined by only using a limited number of normal and oblique plane wave incidences into a metamaterial slab, unlike existing approaches requiring a large number of wave incidences. The validity of the proposed method is verified by conducting wave simulations for anisotropic acoustic metamaterial slabs with Z-shaped elastic inclusions of tilted principal material axes.

  17. Two-dimensional agarose gel electrophoresis of DNA topoisomers.

    PubMed

    Roca, Joaquim

    2009-01-01

    The electrophoretic velocity of a duplex DNA ring is mainly determined by its overall shape. Consequently, DNA topoisomers of opposite supercoiling handedness can have identical gel velocity, and topoisomers highly supercoiled cannot be separated beyond some point. These problems are overcome by two-dimensional agarose gel electrophoresis, which involves two successive electrophoresis steps in one gel slab. The first and second electrophoresis steps are conducted in orthogonal directions with different concentrations of DNA intercalating agents. These compounds alter the overall shape of the DNA and, thereby, change the relative mobility of individual DNA topoisomers.

  18. Electromagnetic radiation from a plasma slab during the development of Weibel instability

    SciTech Connect

    Vagin, K. Yu.; Romanov, A. Yu.; Uryupin, S. A.

    2012-01-15

    Electromagnetic radiation from an anisotropic plasma slab formed by ionization of matter in the field of a high-power femtosecond pulse is studied. It is shown that the growth of initial field perturbations in the course of Weibel instability is accompanied by the generation of nonmonochromatic radiation with a characteristic frequency on the order of the instability growth rate. It is found that perturbations with characteristic scale lengths less than or on the order of the ratio of the speed of light to the Langmuir frequency are excited and radiated most efficiently, provided that the slab is thicker than this ratio.

  19. Exact image theory for the problem of dielectric/magnetic slab

    NASA Technical Reports Server (NTRS)

    Lindell, I. V.

    1987-01-01

    Exact image method, recently introduced for the exact solution of electromagnetic field problems involving homogeneous half spaces and microstrip-like geometries, is developed for the problem of homogeneous slab of dielectric and/or magnetic material in free space. Expressions for image sources, creating the exact reflected and transmitted fields, are given and their numerical evaluation is demonstrated. Nonradiating modes, guided by the slab and responsible for the loss of convergence of the image functions, are considered and extracted. The theory allows, for example, an analysis of finite ground planes in microstrip antenna structures.

  20. Design of energy efficient building with radiant slab cooling

    NASA Astrophysics Data System (ADS)

    Tian, Zhen

    2007-12-01

    Air-conditioning comprises a substantial fraction of commercial building energy use because of compressor-driven refrigeration and fan-driven air circulation. Core regions of large buildings require year-round cooling due to heat gains from people, lights and equipment. Negative environmental impacts include CO2 emissions from electric generation and leakage of ozone-depleting refrigerants. Some argue that radiant cooling simultaneously improves building efficiency and occupant thermal comfort, and that current thermal comfort models fail to reflect occupant experience with radiant thermal control systems. There is little field evidence to test these claims. The University of Calgary's Information and Communications Technology (ICT) Building, is a pioneering radiant slab cooling installation in North America. Thermal comfort and energy performance were evaluated. Measurements included: (1) heating and cooling energy use, (2) electrical energy use for lighting and equipment, and (3) indoor temperatures. Accuracy of a whole building energy simulation model was evaluated with these data. Simulation was then used to compare the radiant slab design with a conventional (variable air volume) system. The radiant system energy performance was found to be poorer mainly due to: (1) simultaneous cooling by the slab and heating by other systems, (2) omission of low-exergy (e.g., groundwater) cooling possible with the high cooling water temperatures possible with radiant slabs and (3) excessive solar gain and conductive heat loss due to the wall and fenestration design. Occupant thermal comfort was evaluated through questionnaires and concurrent measurement of workstation comfort parameters. Analysis of 116 sets of data from 82 occupants showed that occupant assessment was consistent with estimates based on current thermal comfort models. The main thermal comfort improvements were reductions in (1) local discomfort from draft and (2) vertical air temperature stratification. The

  1. Detecting lower-mantle slabs beneath Asia and the Aleutians

    NASA Astrophysics Data System (ADS)

    Schumacher, L.; Thomas, C.

    2016-06-01

    To investigate the descend of subducted slabs we search for and analyse seismic arrivals that reflected off the surface of the slab. In order to distinguish between such arrivals and other seismic phases, we search for waves that reach a seismic array with a backazimuth deviating from the theoretical backazimuth of the earthquake. Source-receiver combinations are chosen in a way that their great circle paths do not intersect the slab region, hence the direct arrivals can serve as reference. We focus on the North and Northwest Pacific region by using earthquakes from Japan, the Philippines and the Hindu Kush area recorded at North American networks (e.g. USArray, Alaska and Canada). Using seismic array techniques for analysing the data and record information on slowness, backazimuth and traveltime of the observed out-of-plane arrivals we use these measurements to trace the wave back through a 1-D velocity model to its scattering/reflection location. We find a number of out-of-plane reflections. Assuming only single scattering, most out-of-plane signals have to travel as P-to-P phases and only a few as S-to-P phases, due to the length of the seismograms we processed. The located reflection points present a view of the 3-D structures within the mantle. In the upper mantle and the transition zone they correlate well with the edges of fast velocity regions in tomographic images. We also find reflection points in the mid- and lower mantle and their locations generally agree with fast velocities mapped by seismic tomography models suggesting that in the subduction regions we map, slabs enter the lower mantle. To validate our approach, we calculate and process synthetic seismograms for 3-D wave field propagation through a model containing a slab-like heterogeneity. We show, that depending on the source-receiver geometry relative to the reflection plane, it is indeed possible to observe and back-trace out-of-plane signals.

  2. Biological Effects of Ingenol Mebutate Gel in Moderate to Severe Actinic Fields Assessed by Reflectance Confocal Microscopy: A Phase I Study.

    PubMed

    Ulrich, Martina; Lange-Asschenfeldt, Susanne; Skak, Kresten; Skov, Torsten; Østerdal, Marie Louise; Röwert-Huber, Hans-Joachim; Zibert, John Robert; Stockfleth, Eggert

    2016-10-01

    Ingenol mebutate represents a topical treatment for fields with actinic keratosis (AK). The biological effects of ingenol mebutate in AK, subclinical (SC)-AK, and reference-skin were assessed and graded by in vivo reflectance confocal microscopy (RCM) and histology. Patients with AK and SC-AK lesions in one 25 cm2 field on hands or forearms, and with an area of reference skin on the inner upper arm, were included. The two fields were each treated with ingenol mebutate 0.05% gel (n=16), or vehicle (n=8), on 2 consecutive days; clinical and RCM assessments were performed on days 1, 2, 3, 8, and 57, and biopsies on day 3. Local skin responses were more pronounced in AK fields (6.1 (mean) ± 2.6 (SD)) compared with reference skin (3.5 ± 1.5). The clinical AK lesion reduction was 43.8% and 6.3% with ingenol mebutate and vehicle, respectively. RCM and histology evaluations showed that ingenol mebutate induced a significant pronounced cell death and immune response in AK and SC-AK lesions, compared with reference skin. Ingenol mebutate induced RCM-measured reduction in (investigator-1/investigator-2): AK lesions (34/28%), SC-AK lesions (72/56%), and solar elastosis in AK fields (mean, -0.22/-0.25). In conclusion, ingenol mebutate showed selective pronounced biological responses in AK and SC-AK as compared with reference skin.

    J Drugs Dermatol. 2016;15(10):1181-1189.

  3. Effect of Rotation in an Orthotropic Elastic Slab

    NASA Astrophysics Data System (ADS)

    Santra, S.; Lahiri, A.; Das, N. C.

    2017-02-01

    The fundamental equations of the two dimensional generalized thermoelasticity (L-S model) with one relaxation time parameter in orthotropic elastic slab has been considered under effect of rotation. The normal mode analysis is used to the basic equations of motion and heat conduction equation. Finally, the resulting equations are written in the form of a vector-matrix differential equation which is then solved by the eigenvalue approach. The field variables in the space time domain are obtained numerically. The results corresponding to the cases of conventional thermoelasticity CTE), extended thermoelasticity (ETE) and temperature rate dependent thermoelasticity (TRDTE) are compared by means of graphs.

  4. Stability of Alfven oscillations in a plane plasma slab

    SciTech Connect

    Patudin, V.M.; Sagalakov, A.M.

    1983-05-01

    The stability of the natural Alfven oscillations of a plane slab of a collisional, slightly nonequilibrium plasma in a uniform magnetic field is studied. An effective numerical method, a special version of the differential sweepout method, is proposed. A calculation procedure has been developed. The small-oscillation spectrum is analyzed for parabolic plasma density profiles, and neutral curves are plotted. The growth rates and critical parameters are determined. At a high plasma conductivity, both strongly and weakly localized perturbations near the axis can go unstable. For a density profile with an inflection point, weakly damped oscillations are observed near the inflection point. These oscillations can also be excited by an ion beam.

  5. Slab dragging and the recent geodynamic evolution of the western Mediterranean plate boundary region

    NASA Astrophysics Data System (ADS)

    Spakman, Wim; Chertova, Maria V.; van den Berg, Arie P.; Thieulot, Cedric; van Hinsbergen, Douwe J. J.

    2016-04-01

    and African lithosphere, both plates are dragging the slab by their shared ~NNE component of absolute plate motion, which in fact is invisible in the relative plate convergence frame that is usually adopted. Slab dragging induces mantle resistance that, we demonstrate by numerical modelling, leads in the region to differential lateral motion between the slab and African plate driving indentation of the Africa continental lithosphere leading to crustal shortening explaining the closure of Moroccan seaways and the thickening of the Rif crust. The differential motion also explains the TASZ and the transition from western Betics shortening to eastern Betics extension, both still active today. During Miocene westward slab rollback mantle-resisted slab dragging also provided the driving force of edge delamination of African lithosphere, we propose. These explanations of geological features are fully corroborates by an analysis of the GPS motion field in terms of the strain- and rotation rate fields using the method of Spakman and Nyst (2002), and the predicted crustal flow field. In particular, we derive from the GPS and geological data that the direction of African absolute motion is ~NNE and that the slab experiences at present negligible rollback.

  6. Slab tears and intermediate-depth seismicity

    USGS Publications Warehouse

    Meighan, Hallie E.; Ten Brink, Uri; Pulliam, Jay

    2013-01-01

    Active tectonic regions where plate boundaries transition from subduction to strike slip can take several forms, such as triple junctions, acute, and obtuse corners. Well-documented slab tears that are associated with high rates of intermediate-depth seismicity are considered here: Gibraltar arc, the southern and northern ends of the Lesser Antilles arc, and the northern end of Tonga trench. Seismicity at each of these locations occurs, at times, in the form of swarms or clusters, and various authors have proposed that each marks an active locus of tear propagation. The swarms and clusters start at the top of the slab below the asthenospheric wedge and extend 30–60 km vertically downward within the slab. We propose that these swarms and clusters are generated by fluid-related embrittlement of mantle rocks. Focal mechanisms of these swarms generally fit the shear motion that is thought to be associated with the tearing process.

  7. Aerosol gels

    NASA Technical Reports Server (NTRS)

    Sorensen, Christopher M. (Inventor); Chakrabarti, Amitabha (Inventor); Dhaubhadel, Rajan (Inventor); Gerving, Corey (Inventor)

    2010-01-01

    An improved process for the production of ultralow density, high specific surface area gel products is provided which comprises providing, in an enclosed chamber, a mixture made up of small particles of material suspended in gas; the particles are then caused to aggregate in the chamber to form ramified fractal aggregate gels. The particles should have a radius (a) of up to about 50 nm and the aerosol should have a volume fraction (f.sub.v) of at least 10.sup.-4. In preferred practice, the mixture is created by a spark-induced explosion of a precursor material (e.g., a hydrocarbon) and oxygen within the chamber. New compositions of matter are disclosed having densities below 3.0 mg/cc.

  8. Effect of acidulated phosphate fluoride gel application time on enamel demineralization of deciduous and permanent teeth.

    PubMed

    Calvo, A F B; Tabchoury, C P M; Del Bel Cury, A A; Tenuta, L M A; da Silva, W J; Cury, J A

    2012-01-01

    Although the effect of acidulated phosphate fluoride gel (APF gel) on caries reduction in permanent teeth is based on evidence, the relevance of the clinical application time is still under debate. Also, the effect of 4- versus 1-min application has not been evaluated in deciduous enamel. In a blind, crossover, in situ study of 14 days, 16 adult volunteers wore palatal appliances containing slabs of human permanent and deciduous enamel. At the beginning of each phase, the slabs were submitted to one of the following treatments: no APF application (negative control); APF gel (1.23% F) application for 1 or 4 min. Biofilm accumulation on the slab surface was allowed and the slabs were subjected eight times a day to 20% sucrose, simulating a high cariogenic challenge condition. On the 15th day of each phase, fluoride retained as CaF(2) and fluorapatite (FAp) was determined on the enamel of the slabs and demineralization was assessed by cross-sectional microhardness. Fluoride as CaF(2) and FAp, formed by APF gel application on the enamel slabs not subjected to the cariogenic challenge, was also determined. APF gel reduced demineralization in both enamel types (p < 0.05), but the difference between 1 and 4 min was not statistically significant (p > 0.05). CaF(2) and FAp formed and retained on deciduous and permanent enamel was significantly higher in APF gel groups (p < 0.05), but no significant difference was found between 1 and 4 min (p > 0.05). The findings suggest that 1 min of APF gel application provides a similar effect on inhibition of demineralization as 4 min, for both permanent and deciduous enamel. Copyright © 2012 S. Karger AG, Basel.

  9. Optical bistability in a defect slab with a negative refractive quantum dot nanostructure

    NASA Astrophysics Data System (ADS)

    Jamshidnejad, M.; Asadi Amirabadi, E.; Miraboutalebi, S.; Asadpour, S. H.

    2016-11-01

    We demonstrate optical bistability (OB) in a defect slab doped V-type four-level InGaN/GaN quantum dot nanostructure in the negative refraction frequency band. It has been shown that the OB behavior of such a quantum dot nanostructure system can be controlled by the amplitude of the driving fields and a new parameter for controlling the OB behavior as thickness of the slab medium in the negative refraction band. Meanwhile, we show that the negative refraction frequency band can be controlled by tuning electric permittivity and magnetic permeability by the amplitude of the driving fields and electron concentration in the defect slab doped. Under the numerical simulations, due to the effect of quantum coherence and interference, it is possible to switch bistability by adjusting the optimal conditions in the negative refraction frequency band, which is more practical in all-optical switching or coding elements, and technology based nanoscale devices.

  10. Optical bistability in a defect slab with negative refractive quantum dot nanostructure

    NASA Astrophysics Data System (ADS)

    Jamshidnejad, M.; Asadi Amirabadi, E.; Miraboutalebi, S.; Asadpour, S. H.

    2016-11-01

    We demonstrate optical bistability (OB) in a defect slab doped V-type four-level InGaN/GaN quantum dot nanostructure in the negative refraction frequency band. In this article, will be shown that the OB behavior of such a quantum dot nanostructure system can be controlled by the amplitude of the driving fields and a new parameter for controlling the OB behavior as thickness of the slab medium in the negative refraction band. Meanwhile, we show that the negative refraction frequency band can be controlled by tuning electric permittivity and magnetic permeability by the amplitude of the driving fields and electron concentration in the defect slab doped. Under the numerical simulations, due to the effect of quantum coherence and interference it is possible to switch bistability by adjusting the optimal conditions in the negative refraction frequency band which is more practical in all-optical switching or coding elements and technology based nanoscale devices.

  11. Low-damping epsilon-near-zero slabs: Nonlinear and nonlocal optical properties

    NASA Astrophysics Data System (ADS)

    de Ceglia, Domenico; Campione, Salvatore; Vincenti, Maria Antonietta; Capolino, Filippo; Scalora, Michael

    2013-04-01

    We investigate second-harmonic generation, low-threshold multistability, all-optical switching, and inherently nonlocal effects due to the free-electron gas pressure in an epsilon-near-zero (ENZ) metamaterial slab made of cylindrical, plasmonic nanoshells illuminated by TM-polarized light. Damping compensation in the ENZ frequency region, achieved by using gain medium inside the nanoshells’ dielectric cores, enhances the nonlinear properties. Reflection is inhibited, and the electric field component normal to the slab interface is enhanced near the effective pseudo-Brewster angle, where the effective ɛ≈0 condition triggers a nonresonant, impedance-matching phenomenon. We show that the slab displays a strong effective, spatial nonlocality associated with leaky modes that are mediated by the compensation of damping. The presence of these leaky modes then induces further spectral and angular conditions, where the local fields are enhanced, thus opening new windows of opportunity for the enhancement of nonlinear optical processes.

  12. Reflection and transmission of Gaussian beam from a uniaxial crystal slab

    NASA Astrophysics Data System (ADS)

    Wang, Yan; Yu, Ke; Zha, Xuejun; Xu, Jiwei; Yan, Jinkui

    2006-08-01

    We investigate the characteristics of Gaussian beams reflected and transmitted from a uniaxial crystal slab with an arbitrary orientation of its optical axis. The formulas of the total electric and magnetic fields inside and outside the slab are derived by use of Maxwell's equations and by matching the boundary conditions at the interfaces. Numerical simulations are presented and the field values as well as the power densities are computed. Negative refractions are demonstrated when the beam is transmitted through a uniaxial crystal slab. Beam splitting of the reflected beam is observed and is explained by the resonant transmission for plane waves. Dependences of the lateral shift on the incident angle and beam width are discussed. Negative and positive lateral shifts are observed due to the spatial anisotropic properties.

  13. Extensive decarbonation of continuously hydrated subducting slabs

    NASA Astrophysics Data System (ADS)

    Arzilli, F.; Burton, M. R.; La Spina, G.; Macpherson, C.

    2016-12-01

    CO2 release from subducting slabs is a key element of Earth's carbon cycle, consigning slab carbon either to mantle burial or recycling to the surface through arc volcanism, however, what controls subducted carbon's fate is poorly understood. Fluids mobilized by devolatilization of subducting slabs play a fundamental role in the melting of mantle wedges and in global geochemical cycles [1]. The effect of such fluids on decarbonation in subducting lithologies has been investigated recently [2-5] but mechanisms of carbon transfer from the slab to wedge are poorly understood [2-6]. Several thermodynamic models [2-3], and experimental studies [6] suggest that carbon-bearing phases are stable at sub-arc depths (80-140 km; 2.6-4.5 GPa), implying that this carbon can be subducted to mantle depths of >140 km. This is inconsistent with observations of voluminous CO2 release from arc volcanoes [7-10], located above slabs that are at 2.6-4.5 GPa pressure. Here, we show that continuous hydrated of sediment veneers on subducting slabs by H2O released from oceanic crust and serpentinised mantle lithosphere [11-13], produces extensive slab decarbonation over a narrow, sub-arc pressure range, even for low temperature subduction pathways. This explains the location of CO2-rich volcanism, quantitatively links the sedimentary composition of slab material to the degree of decarbonation and greatly increases estimates for the magnitude of carbon flux through the arc in subduction zones. [1] Hilton, D.R. et al. (2002) Rev. Mineral. Geochem. 47, 319-370. [2] Gorman, P.J. et al. (2006) Geochem. Geophys. Geosyst. 7. [3] Kerrick, D.M. and Connolly, J.A.D. (2001) Nature 411, 293-296. [4] Cook-Kollars, J. et al. (2014) Chem. Geol. 386, 31-48. [5] Collins, N.C. et al. (2015) Chem. Geol. 412, 132-150. [6] Poli, S. et al. (2009) Earth Planet. Sci. Lett. 278, 350-360. [7] Sano, Y. and Williams, S.N. (1996) Geophys. Res. Lett. 23, 2749-2752. [8] Marty, B. and Tolstikhin, I.N. (1998) Chem. Geol

  14. Geomorphic Response to Flat Slab Subduction along the Eastern Foothills of the Colombian Andes

    NASA Astrophysics Data System (ADS)

    Veloza, G.; Taylor, M. H.; Gosse, J. C.; Mora, A.; Becker, T. W.

    2013-12-01

    It is thought that in northwest South America flat slab subduction plays a key role in the recent development of the eastern Colombian Andes. Here we show that the geomorphic response to flat slab subduction is presently occurring >500 km inboard of the subduction zone plate boundary. The Llanos basin located along the eastern edge of the Colombian Andes is experiencing active uplift along the seismically active Cusiana, Yopal, Paz de Ariporo and Tame thrust faults, which we refer to as the Llanos Foothills thrust system (LFTS). The LFTS is comprised of east-directed thrust faults that are listric in geometry with shallowly west-dipping decollements. Locally, actively growing north-south plunging folds are cored by blind thrust faults, and are being incised by antecedent east-flowing streams. Using a combination of field-based observations on the geometry of faulted and folded fluvial terraces, and geochronology from terrestrial cosmogenic nuclides, we show that the fluvial terraces have been uplifted, and locally, incised >200 meters at incision rates exceeding 3 mm/yr. The field observations in combination with earthquakes and geodynamic simulations can be reconciled by flat slab subduction, but it is presently unknown whether the flat slab has a Caribbean or Nazca plate affinity. Different geodynamic scenarios can be tested to understand how the leading edge of the flat slab interacts with the South American craton, and how that interaction controls upper crustal deformation.

  15. Deep ultraviolet laser direct write for patterning sol-gel InGaZnO semiconducting micro/nanowires and improving field-effect mobility

    PubMed Central

    Lin, Hung-Cheng; Stehlin, Fabrice; Soppera, Olivier; Zan, Hsiao-Wen; Li, Chang-Hung; Wieder, Fernand; Ponche, Arnaud; Berling, Dominique; Yeh, Bo-Hung; Wang, Kuan-Hsun

    2015-01-01

    Deep-UV (DUV) laser was used to directly write indium-gallium-zinc-oxide (IGZO) precursor solution and form micro and nanoscale patterns. The directional DUV laser beam avoids the substrate heating and suppresses the diffraction effect. A IGZO precursor solution was also developed to fulfill the requirements for direct photopatterning and for achieving semi-conducting properties with thermal annealing at moderate temperature. The DUV-induced crosslinking of the starting material allows direct write of semi-conducting channels in thin-film transistors but also it improves the field-effect mobility and surface roughness. Material analysis has been carried out by XPS, FTIR, spectroscopic ellipsometry and AFM and the effect of DUV on the final material structure is discussed. The DUV irradiation step results in photolysis and a partial condensation of the inorganic network that freezes the sol-gel layer in a homogeneous distribution, lowering possibilities of thermally induced reorganization at the atomic scale. Laser irradiation allows high-resolution photopatterning and high-enough field-effect mobility, which enables the easy fabrication of oxide nanowires for applications in solar cell, display, flexible electronics, and biomedical sensors. PMID:26014902

  16. The slab geometry laser. II - Thermal effects in a finite slab

    NASA Technical Reports Server (NTRS)

    Kane, T. J.; Byer, R. L.; Eggleston, J. M.

    1985-01-01

    This paper presents two methods for calculating the thermally induced stress, focusing, and depolarization in a pumped zigzag-slab solid-state laser. A computer program capable of detailed calculations of thermal effects in the general case is described. An approximate analysis of slab thermal effects in many cases allows calculation of these effects without use of the computer model directly. The analysis predicts that slabs of square cross section can be designed to have low depolarization and thermal focusing compared to Nd:YAG laser rods.

  17. Prevalence and molecular characterization of Escherichia coli O157:H7 by multiple locus variable number tandem repeat analysis and pulsed field gel electrophoresis in three sheep farming operations in California.

    USDA-ARS?s Scientific Manuscript database

    A yearlong study was conducted to determine the fecal prevalence of Escherichia coli O157:H7 in three sheep ranches. Strain diversity and persistence was compared using multiple locus variable number tandem repeat analysis and pulsed field gel electrophoresis. Ranch C, a feedlot, consisted of young ...

  18. Longitudinal prevalence and molecular typing of Escherichia coli O157:H7 using multiple-locus variable-number tandem-repeats analysis and pulsed field gel electrophoresis in a range cattle herd in California

    USDA-ARS?s Scientific Manuscript database

    Objectives –(1) Identify the seasonal pattern and risk factors for Escherichia coli O157:H7 in feces in range cattle in California, (2) Determine strain diversity and transition over time using Multi-Locus Variable-Number Tandem Repeat Analysis (MLVA) and Pulsed Field Gel Electrophoresis (PFGE) Samp...

  19. Effect of a papain-based gel for chemomechanical caries removal on dentin shear bond strength.

    PubMed

    Lopes, Michelle Cristina; Mascarini, Raphaella Capitoni; da Silva, Bruna Maria Covre Garcia; Flório, Flávia Martão; Basting, Roberta Tarkany

    2007-01-01

    The aim of this study was to assess the shear bond strength of an adhesive restorative system on sound and demineralized dentin after the use of a papain-based agent. Forty human dentin slabs were randomly distributed into 4 groups: (1) sound dentin slabs that received an application of papain-based gel (N=10); (2) sound dentin slabs that did not receive a papain-based gel application (N=10); (3) demineralized slabs that received an application of the agent (N=10); and (4) demineralized slabs that did not receive an application of the agent (N=10). After manual excavation and use of the chemomechanical agent, the slabs were restored with a total etch adhesive system and microhybrid resin composite. The test specimens were individually stored in a damp environment for 7 days, and the shear bond strength test was performed using a universal test machine at a speed of 0.5 mm/min. The fragments were observed under a stereoscopic microscope to assess the fracture mode. Fracture mode assessment showed adhesive and cohesive type fractures in resin for all the groups. The analysis of variance and the Tukey test showed that there were no differences in the shear bond strength means among the groups (P>.05). The use of a papain-based gel to remove dental caries did not interfere in the bond strength of restorative materials to dentin.

  20. Mantle circulation and the lateral migration of subducted slabs

    NASA Technical Reports Server (NTRS)

    Garfunkel, Z.; Anderson, C. A.; Schubert, G.

    1986-01-01

    The geometry of transverse migration of subducted lithospheric slabs is examined, and the way in which this influences the flow in the mantle is studied. The migration of subducted slabs generally appears to be retrograde (at rates of 10-25 mm/yr), so that the descent of material is actually steeper than the slab dip. Retrograde slab migration is probably caused by the tendence of negatively buoyant slabs to sink in the surrounding mantle. The properties of the flow driven by such retrograde slab migration are explored in simple two-dimensional models. The results are used as a guide to infer the contribution of retrograde slab motion to the more complex mantle flow and to examine some consequences of the additional component of mantle flow. It is shown that slab migration is an important factor that causes mantle flow to be geometrically complex and time dependent.

  1. Anomalous transmission of electromagnetic energy through a plasma slab

    NASA Astrophysics Data System (ADS)

    Gradov, O. M.; Stenflo, L.

    1982-05-01

    An electromagnetic wave, incident on a plasma slab, is considered. It is pointed out that the transmitted energy can be larger than the incident energy during restricted time intervals, if the slab density varies properly in time.

  2. Oceanic slab melting and mantle metasomatism.

    PubMed

    Scaillet, B; Prouteau, G

    2001-01-01

    Modern plate tectonic brings down oceanic crust along subduction zones where it either dehydrates or melts. Those hydrous fluids or melts migrate into the overlying mantle wedge trigerring its melting which produces arc magmas and thus additional continental crust. Nowadays, melting seems to be restricted to cases of young (< 50 Ma) subducted plates. Slab melts are silicic and strongly sodic (trondhjemitic). They are produced at low temperatures (< 1000 degrees C) and under water excess conditions. Their interaction with mantle peridotite produces hydrous metasomatic phases such as amphibole and phlogopite that can be more or less sodium rich. Upon interaction the slab melt becomes less silicic (dacitic to andesitic), and Mg, Ni and Cr richer. Virtually all exposed slab melts display geochemical evidence of ingestion of mantle material. Modern slab melts are thus unlike Archean Trondhjemite-Tonalite-Granodiorite rocks (TTG), which suggests that both types of magmas were generated via different petrogenetic pathways which may imply an Archean tectonic model of crust production different from that of the present-day, subduction-related, one.

  3. Effects of Edge Restraint on Slab Behavior

    DTIC Science & Technology

    1986-02-01

    manufactured limestone sand fine aggregate. Two batches were prepared, one for each of the different thickness slab groups. A total of thirty-eight 4...Building Code Require- ments" 1983; Detroit, Mich. 4. T. Takehira, A. T. Derecho , and M. Iqbal; "Design Criteria for De- flection Capacity of

  4. Slab Ice Characterization on Martian Richardson Crater

    NASA Astrophysics Data System (ADS)

    Schmidt, F.; Andrieu, F.; Douté, S.

    2016-09-01

    We compare two models: granular and slab in order to study the ice properties in the Richardson crater using spectroscopy. Thanks to radiative transfer modeling, we determine compactness of CO2 ice, grain size, and abundances of water ice and dust.

  5. INDEPENDENT VERIFICATION OF THE CENTRAL CAMPUS AND SOUTHEAST LABORATORY COMPLEX BUILDING SLABS AT OAK RIDGE NATIONAL LABORATORY, OAK RIDGE, TENNESSEE

    SciTech Connect

    Weaver, Phyllis C.

    2012-07-24

    Oak Ridge Associated Universities/Oak Ridge Institute for Science and Education (ORAU/ORISE) has completed the independent verification survey of the Central Campus and Southeast Lab Complex Building Slabs. The results of this effort are provided. The objective of this verification survey was to provide independent review and field assessment of remediation actions conducted by SEC, and to independently assess whether the final radiological condition of the slabs met the release guidelines.

  6. Lateral displacement of a Gaussian beam transmitted through a one-dimensional left-handed meta-material slab

    NASA Astrophysics Data System (ADS)

    Zhong, Yu; Ran, Lixin; Cheng, Xiangxiang; Kong, Jin Au

    2006-02-01

    In this paper, the transmission of a Gaussian beam passing through a slab made of a one-dimensional left-handed meta-material (1D LHM) is studied. The analytical solution of the electric and the magnetic fields inside and outside the slab are given. The calculation of the power flow of the beam predicts that in the negative pass band of the 1D LHM, there exist different directions of lateral displacements. Such phenomenon is further verified by experiment.

  7. Relations between plate kinematics, slab geometry and overriding plate deformation in subduction zones: insights from statistical observations and laboratory modelling

    NASA Astrophysics Data System (ADS)

    Heuret, A.; Funiciello, F.; Faccenna, C.; Lallemand, S.

    2005-12-01

    3-D laboratory models have been performed in order to investigate the way plates kinematics (subducting and overriding plate absolute motions and the resulting plate convergence rate) influences the geometry of the slab and the overriding plate deformation in subduction zones. In the experiments a viscous plate of silicone (subducting plate) is pushed beneath another plate, which is itself pushed toward or pulled away from the trench (overriding plate), and sinks into a viscous layer of glucose syrup (upper mantle). The subducting and overriding plate velocities explored the variability field of natural subduction plates kinematics. The overriding plate motion exerts a primary role in the control of slab geometries and overriding plate deformation rates. The experiments have revealed two different subduction behaviours: (Style I) the overriding plate moves toward the trench and shortens at high rates, the slab is flat and deflected when reaching the bottom of the box in a forward direction; (Style II) the overriding plates moves away from the trench and shortens at low rates the slab is steep and deflected on the box bottom in a backward direction. To a lesser extent, increasing subducting plate motion is associated to increasing slab dips and overriding plate shortening. Slab geometry and overriding plate deformation are less sensitive to the overall plate convergence rate. These laboratory models behaviours are consistent with statistical analysis performed on natural subduction zones, and enlighten the first order control exerted by the overriding plate absolute motion, on the geometry adopted by the slab and the way the overriding plate deforms.

  8. Accuracy of two-color peak-height-encoded DNA sequencing by capillary gel electrophoresis and laser-induced fluorescence

    NASA Astrophysics Data System (ADS)

    Bay, Sue; Starke, Heather; Elliott, John; Dovichi, Norman J.

    1993-06-01

    The two-color peak-height encoded DNA sequencing technique was evaluated with six clones taken from the malaria genome. This technique produced a sequencing accuracy of at least 97.5%. Capillary gel electrophoresis, using a modest voltage of 200 V/cm, showed a three- fold increase in speed and higher efficiency compared to conventional slab gel technique.

  9. Dexmedetomidine infusion as an anesthetic adjuvant to general anesthesia for appropriate surgical field visibility during modified radical mastectomy with i-gel®: a randomized control study

    PubMed Central

    Rastogi, Bhawana; Gupta, Prashant K; Singh, Ivesh; Singh, Vijendra Pal; Jain, Manish

    2016-01-01

    Background Modified radical mastectomy is associated with appreciable blood loss, while endotracheal intubation leads to elevated hemodynamic responses. The present study aimed to evaluate the clinical efficacy of dexmedetomidine infusion as an anesthetic adjuvant to general anesthesia during modified radical mastectomy with I-Gel. Methods Sixty adult consenting female patients, of American Society of Anesthesiologists physical status 1 to 2 and aged 4,065 years, were blindly randomized into two groups of 30 patients each. The patients in Group I received intravenous dexmedetomidine at a loading dose of 1 µg/kg over 10 min, followed by maintenance infusion of 0.4 to 0.7 µg/kg/h, while patients in Group II were administered an identical amount of saline infusion until 15 min prior to the end of surgery. The primary end point was bleeding at the surgical field and hemodynamic changes; requirement of isoflurane, intraoperative fentanyl consumption and recovery time were assessed as secondary outcomes. Results The patients receiving dexmedetomidine infusion showed significantly less bleeding at the surgical field (P < 0.05). A statistically significant reduction was also observed in the percentage of isoflurane required (0.82 ± 0.80%) to maintain the systolic blood pressure between 100 and 110 mmHg in patients receiving dexmedetomidine infusion compared with the Group II (1.50 ± 0.90%). The mean intraoperative fentanyl consumption in patients in the Group I was also significantly lower compared with that of the Group II (38.43 ± 5.40 µg vs. 75.12 ± 4.60 µg). The mean recovery time from anesthesia did not show any clinically significant difference between the groups. Conclusions Dexmedetomidine infusion can be used safely to decrease the bleeding at the surgical field with smooth recovery from anesthesia. PMID:27924197

  10. Multiple stationary solutions of an irradiated slab

    NASA Astrophysics Data System (ADS)

    Taylor, P. D.; Feltham, D. L.

    2005-04-01

    A mathematical model describing the heat budget of an irradiated medium is introduced. The one-dimensional form of the equations and boundary conditions are presented and analysed. Heat transport at one face of the slab occurs by absorption (and reflection) of an incoming beam of short-wave radiation with a fraction of this radiation penetrating into the body of the slab, a diffusive heat flux in the slab and a prescribed incoming heat flux term. The other face of the slab is immersed in its own melt and is considered to be a free surface. Here, temperature continuity is prescribed and evolution of the surface is determined by a Stefan condition. These boundary conditions are flexible enough to describe a range of situations such as a laser shining on an opaque medium, or the natural environment of polar sea ice or lake ice. A two-stream radiation model is used which replaces the simple Beer's law of radiation attenuation frequently used for semi-infinite domains. The stationary solutions of the governing equations are sought and it is found that there exists two possible stationary solutions for a given set of boundary conditions and a range of parameter choices. It is found that the existence of two stationary solutions is a direct result of the model of radiation absorption, due to its effect on the albedo of the medium. A linear stability analysis and numerical calculations indicate that where two stationary solutions exist, the solution corresponding to a larger thickness is always stable and the solution corresponding to a smaller thickness is unstable. Numerical simulations reveal that when there are two solutions, if the slab is thinner than the smaller stationary thickness it will melt completely, whereas if the slab is thicker than the smaller stationary thickness it will evolve toward the larger stationary thickness. These results indicate that other mechanisms (e.g. wave-induced agglomeration of crystals) are necessary to grow a slab from zero initial

  11. Magnetohydrodynamic stability of natural convection in a vertical porous slab

    NASA Astrophysics Data System (ADS)

    Shankar, B. M.; Kumar, Jai; Shivakumara, I. S.

    2017-01-01

    The stability of the conduction regime of natural convection in an electrically conducting fluid saturated porous vertical slab is investigated in the presence of a uniform external transverse magnetic field. The flow in the porous medium is described by modified Brinkman-extended Darcy equation with fluid viscosity different from effective viscosity. The boundaries of the vertical porous slab are assumed to be rigid-isothermal and electrically non-conducting. The resulting stability equations are solved numerically using Galerkin method. The critical Grashof number Gc, the critical wave number αc and the critical wave speed cc are computed for a wide range of porous parameter σp, the ratio of effective viscosity to the fluid viscosity Λ, the Prandtl number Pr and the Hartmann number M. Based on these parameters, the stability characteristics of the system are discussed in detail. The presence of advective inertia is to instill instability on the flow in a porous medium and found that the magnetic field, porous parameter and ratio of viscosities have a stabilizing effect on both stationary and oscillatory wave instabilities. Besides, the value of Pr at which transition occurs from stationary to oscillatory mode of instability decreases with increasing M ,σp and Λ .

  12. Slab waveguide photobioreactors for microalgae based biofuel production.

    PubMed

    Jung, Erica Eunjung; Kalontarov, Michael; Doud, Devin F R; Ooms, Matthew D; Angenent, Largus T; Sinton, David; Erickson, David

    2012-10-07

    Microalgae are a promising feedstock for sustainable biofuel production. At present, however, there are a number of challenges that limit the economic viability of the process. Two of the major challenges are the non-uniform distribution of light in photobioreactors and the inefficiencies associated with traditional biomass processing. To address the latter limitation, a number of studies have demonstrated organisms that directly secrete fuels without requiring organism harvesting. In this paper, we demonstrate a novel optofluidic photobioreactor that can help address the light distribution challenge while being compatible with these chemical secreting organisms. Our approach is based on light delivery to surface bound photosynthetic organisms through the evanescent field of an optically excited slab waveguide. In addition to characterizing organism growth-rates in the system, we also show here, for the first time, that the photon usage efficiency of evanescent field illumination is comparable to the direct illumination used in traditional photobioreactors. We also show that the stackable nature of the slab waveguide approach could yield a 12-fold improvement in the volumetric productivity.

  13. Method for preparing hydrous zirconium oxide gels and spherules

    DOEpatents

    Collins, Jack L.

    2003-08-05

    Methods for preparing hydrous zirconium oxide spherules, hydrous zirconium oxide gels such as gel slabs, films, capillary and electrophoresis gels, zirconium monohydrogen phosphate spherules, hydrous zirconium oxide spherules having suspendable particles homogeneously embedded within to form a composite sorbent, zirconium monohydrogen phosphate spherules having suspendable particles of at least one different sorbent homogeneously embedded within to form a composite sorbent having a desired crystallinity, zirconium oxide spherules having suspendable particles homogeneously embedded within to form a composite, hydrous zirconium oxide fiber materials, zirconium oxide fiber materials, hydrous zirconium oxide fiber materials having suspendable particles homogeneously embedded within to form a composite, zirconium oxide fiber materials having suspendable particles homogeneously embedded within to form a composite and spherules of barium zirconate. The hydrous zirconium oxide spherules and gel forms prepared by the gel-sphere, internal gelation process are useful as inorganic ion exchangers, catalysts, getters and ceramics.

  14. Necessity of the Ridge for the Flat Slab Subduction: Insights from the Peruvian Flat Slab

    NASA Astrophysics Data System (ADS)

    Knezevic Antonijevic, S.; Wagner, L. S.; Beck, S. L.; Long, M. D.; Zandt, G.; Tavera, H.

    2014-12-01

    Flattening of the subducting plate has been linked to the formation of various geological features, including basement-cored uplifts, the cessation of arc volcanism, ignimbrite flare-ups, and the formation of high plateaus and ore deposits [Humphreys et al., 2003; Gutscher et al., 2000; Rosenbaum et al., 2005]. However, the mechanism responsible for the slab flattening is still poorly understood. Here we focus on the Peruvian flat slab, where the Nazca plate starts to bend at ~80 km depth and travels horizontally for several hundred kilometers, at which point steep subduction resumes. Based on a 1500 km long volcanic gap and intermediate depth seismicity patterns, the Peruvian flat slab appears to have the greatest along-strike extent and, therefore, has been suggested as a modern analogue to the putative flat slab during the Laramide orogeny in the western United States (~80-55 Ma). Combining 3D shear wave velocity structure and Rayleigh wave phase anisotropy between ~10° and 18° S, we find that the subducting Nazca plate is not uniformly flat along the entire region, but fails to the north of the subducting Nazca Ridge. Our results show that, in combination with trench retreat, rapid overriding plate motion, and/or presence of a thick cratonic root, the subduction of buoyant overthickened oceanic crust, such as the Nazca Ridge, is necessary for the formation and sustainability of flat slabs. This finding has important implications for the formation of flat slabs both past and present.

  15. Lamb wave band gaps in one-dimensional radial phononic crystal slabs

    NASA Astrophysics Data System (ADS)

    Li, Yinggang; Chen, Tianning; Wang, Xiaopeng

    2015-10-01

    In this paper, we theoretically investigate the band structures of Lamb wave in one-dimensional radial phononic crystal (PC) slabs composed of a series of alternating strips of epoxy and aluminum. The dispersion relations, the power transmission spectra and the displacement fields of the eigenmodes are calculated by using the finite element method based on two-dimensional axial symmetry models in cylindrical coordinates. The axial symmetry model is validated by three-dimensional finite element model in Cartesian coordinates. Numerical results show that the proposed radial PC slabs can yield several complete band gaps with a variable bandwidth exist for elastic waves. Furthermore, the effects of the filling fraction and the slab thickness on the band gaps are further explored numerically. It is worth observing that, with the increase of the filling fraction, both the lower and upper edges of the band gaps are simultaneously shifted to higher frequency, which results from the enhancement interaction between the rigid resonance of the scatterer and the matrix. The slab thickness is the key parameter for the existence and the width of complete band gaps in the radial PC slabs. These properties of Lamb waves in the radial PC plates can potentially be applied to optimize band gaps, generate filters and design acoustic devices in the rotary machines and structures.

  16. Pseudo-Fourier modal analysis on dielectric slabs with arbitrary longitudinal permittivity and permeability profiles.

    PubMed

    Kim, Hwi; Kim, Seyoon; Lee, Il-Min; Lee, Byoungho

    2006-09-01

    A pseudo-Fourier modal analysis method for analyzing finite-sized dielectric slabs with arbitrary longitudinal permittivity and permeability profiles is proposed. In the proposed method, the permittivity and permeability profiles are represented by the Fourier expansion without using the conventional staircase approximation. The total electromagnetic field distribution inside a dielectric slab is a linear superposition of extracted pseudo-Fourier eigenmodes with specific coupling coefficients selected to satisfy given boundary conditions. The proposed pseudo-Fourier modal analysis method shows excellent agreement with the conventional rigorous coupled-wave analysis with the S-matrix method.

  17. Enhanced detection limit by dark mode perturbation in 2D photonic crystal slab refractive index sensors.

    PubMed

    Nicolaou, Costa; Lau, Wah Tung; Gad, Raanan; Akhavan, Hooman; Schilling, Ryan; Levi, Ofer

    2013-12-16

    We demonstrate for the first time a 300nm thick, 300μm × 300μm 2D dielectric photonic crystal slab membrane with a quality factor of 10,600 by coupling light to slightly perturbed dark modes through alternating nano-hole sizes. The newly created fundamental guided resonances greatly reduce nano-fabrication accuracy requirements. Moreover, we created a new layer architecture resulting in electric field enhancement at the interface between the slab and sensing regions, and spectral sensitivity of >800 nm/RIU, that is, >0.8 of the single-mode theoretical upper limit of spectral sensitivity.

  18. Molecular characterisation of Mycoplasma hyorhinis isolated from pigs using pulsed-field gel electrophoresis and 16S rRNA sequencing

    PubMed Central

    Yamaguti, Maurício; Oliveira, Rosângela C; Marques, Lucas M; Buzinhani, Melissa; Buim, Marcos R; Neto, Renata L; Guimarães, Ana Márcia S; Timenetsky, Jorge

    2015-01-01

    Economic loss in pig breeding is common due to respiratory disorders, and Mycoplasma hyopneumoniae and Mycoplasma hyorhinis, namely, are the most common infectious agents. The aim of this study is to recover these mollicutes and detect their genotypic variations by pulsed-field gel electrophoresis (PFGE) and sequencing the 16 s rRNA gene. One hundred and twenty-six swabs from tonsil and nasal mucus of pigs with respiratory disorders were analysed. A total of 78 lungs were sampled, as well as two trachea and two tonsils obtained from animals with respiratory disorder. A total of 59 isolates were obtained: 1 (1.70 per cent) of M hyopneumoniae, 2 (3.40 per cent) of Mycoplasma flocculare and 56 (94.90 per cent) of M hyorhinis. The PFGE for M hyorhinis showed 10 profiles with enzyme AvaI and 9 profiles with XhoI. A low polymorphism of the 16sRNS gene was detected in M hyorhinis isolates compared with the type strain in the GenBank. M hyorhinis isolates of different herds showed a large heterogenicity with enzymes AvaI and XhoI. The sequencing of the 16S rRNA gene allowed for analysing the interspecific and intraspecific variations of isolated mycoplasmas. PMID:26688737

  19. High genetic diversity of Enterococcus faecium and Enterococcus faecalis clinical isolates by pulsed-field gel electrophoresis and multilocus sequence typing from a hospital in Malaysia.

    PubMed

    Weng, Poh Leng; Ramli, Ramliza; Shamsudin, Mariana Nor; Cheah, Yoke-Kqueen; Hamat, Rukman Awang

    2013-01-01

    Little is known on the genetic relatedness and potential dissemination of particular enterococcal clones in Malaysia. We studied the antibiotic susceptibility profiles of Enterococcus faecium and Enterococcus faecalis and subjected them to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). E. faecium and E. faecalis displayed 27 and 30 pulsotypes, respectively, and 10 representative E. faecium and E. faecalis isolates (five each) yielded few different sequence types (STs): ST17 (2 isolates), ST78, ST203, and ST601 for E. faecium, and ST6, ST16, ST28, ST179, and ST399 for E. faecalis. Resistance to tazobactam-piperacillin and ampicillin amongst E. faecium isolates was highly observed as compared to E. faecalis isolates. All of the isolates were sensitive to vancomycin and teicoplanin. The presence of epidemic and nosocomial strains of selected E. faecium STs: 17, 78, and 203 and E. faecalis ST6 as well as high rates of resistance to multiple antibiotics amongst E. faecium isolates is of a particular concern.

  20. An outbreak of Pseudomonas aeruginosa because of inadequate disinfection procedures in a urology unit: a pulsed-field gel electrophoresis-based epidemiologic study.

    PubMed

    Kayabas, Uner; Bayraktar, Mehmet; Otlu, Baris; Ugras, Murat; Ersoy, Yasemin; Bayindir, Yasar; Durmaz, Riza

    2008-02-01

    Pseudomonas aeruginosa is an opportunistic pathogen causing nosocomial infections in many hospitals. We aimed to investigate the source of urinary tract infections by determining clonal relationship of Pseudomonas aeruginosa strains with pulsed-field gel electrophoresis (PFGE). During a 2-month period, all postoperative infections because of P aeruginosa were investigated in the Urology Department. Patient data were collected from medical records. Surveillance samples were obtained from various places in urological operating rooms. PFGE typing was performed for all P aeruginosa isolates. A total of 14 P aeruginosa strains (12 from patients and 2 from environmental samples) were isolated. PFGE typing of these 14 strains yielded 2 possibly related clones, which differed from each other by 4 major bands. Ten of the patient isolates were clonally identical with the strains of 2 forceps. Typing results confirmed that inadequately disinfected surgical devices can be the source of outbreak. After institution of infection control measures and education, no further clusters of P aeruginosa infection were detected in the Urology Department.

  1. Variable number of tandem repeats and pulsed-field gel electrophoresis cluster analysis of enterohemorrhagic Escherichia coli serovar O157 strains.

    PubMed

    Yokoyama, Eiji; Uchimura, Masako

    2007-11-01

    Ninety-five enterohemorrhagic Escherichia coli serovar O157 strains, including 30 strains isolated from 13 intrafamily outbreaks and 14 strains isolated from 3 mass outbreaks, were studied by pulsed-field gel electrophoresis (PFGE) and variable number of tandem repeats (VNTR) typing, and the resulting data were subjected to cluster analysis. Cluster analysis of the VNTR typing data revealed that 57 (60.0%) of 95 strains, including all epidemiologically linked strains, formed clusters with at least 95% similarity. Cluster analysis of the PFGE patterns revealed that 67 (70.5%) of 95 strains, including all but 1 of the epidemiologically linked strains, formed clusters with 90% similarity. The number of epidemiologically unlinked strains forming clusters was significantly less by VNTR cluster analysis than by PFGE cluster analysis. The congruence value between PFGE and VNTR cluster analysis was low and did not show an obvious correlation. With two-step cluster analysis, the number of clustered epidemiologically unlinked strains by PFGE cluster analysis that were divided by subsequent VNTR cluster analysis was significantly higher than the number by VNTR cluster analysis that were divided by subsequent PFGE cluster analysis. These results indicate that VNTR cluster analysis is more efficient than PFGE cluster analysis as an epidemiological tool to trace the transmission of enterohemorrhagic E. coli O157.

  2. Use of pulsed-field gel electrophoresis typing to study an outbreak of infection due to Serratia marcescens in a neonatal intensive care unit.

    PubMed Central

    Miranda, G; Kelly, C; Solorzano, F; Leanos, B; Coria, R; Patterson, J E

    1996-01-01

    Serratia marcescens is a well-known cause of nosocomial infections and outbreaks, particularly in critically ill neonates and immunocompromised patients. Numerous methods have been proposed for typing. We used pulsed-field gel electrophoresis (PFGE) typing to analyze an outbreak in a neonatal intensive care unit (NICU). We included 23 patient isolates from an outbreak (March to July 1995), and 10 patient isolates from different wards during the same time period. PFGE of whole-cell DNA digested by SpeI was used as a marker of strain identity. The most common presentation of the infection was sepsis in 18 of 23 (78%) neonates. Only four different biotypes were identified; biotype A8d accounted for 84% of the strains. PFGE typing revealed two clones responsible for two different clonal strain dissemination outbreaks from March to July, with 24 patient isolates being pattern A and 4 patient isolates being pattern E. PFGE typing suggests cross transmission between patients in the NICU and other wards. The isolates from 5 other patients showed distinct PFGE patterns. Extensive investigation and cultures failed to identify any environmental or staff reservoir of S. marcescens. This is one of the first reports applying PFGE to the study of S. marcescens, and this method was a useful marker of strain identity. PFGE typing distinguished strains which appeared to be the same by biotyping. PMID:8940460

  3. Genomic DNA fingerprinting by pulsed-field gel electrophoresis as an epidemiological marker for study of nosocomial infections caused by methicillin-resistant Staphylococcus aureus.

    PubMed Central

    Ichiyama, S; Ohta, M; Shimokata, K; Kato, N; Takeuchi, J

    1991-01-01

    In this study, we have compared genomic DNA fingerprintings among isolates of methicillin-resistant Staphylococcus aureus (MRSA) by using pulsed-field gel electrophoresis (PFGE). Chromosomal fragments digested with SmaI were most suitable for the PFGE separation. SmaI cut genomic DNA into 15 to 20 fragments whose sizes ranged from about 30 to 1,500 kb. Thirty-one distinctive fragment patterns were identified in 111 infecting and colonizing MRSA isolates from six different hospitals in Japan. On the basis of the genomic typing by PFGE, we performed an epidemiological investigation of an outbreak of nosocomial MRSA infections among inpatients in Nagoya University Hospital. Ten types of chromosomal digestion were identified in the 20 strains isolated from 18 infected patients and 1 from colonized hospital personnel. According to the restriction patterns, we found that four types of these strains had caused epidemic infections among 13 patients in the outbreak. Two types (types 1 and 4) of the strains were involved in the death of five patients. The other infections were sporadic. The clarity and polymorphism of the chromosomal digestion patterns enabled us to discriminate between isolates which could not be differentiated by antibiogram or plasmid analysis. Classification of the genomic DNA fingerprinting patterns by PFGE is therefore proposed as a useful method for investigating the source, transmission, and spread of nosocomial MRSA infections. Images PMID:1757534

  4. Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Isolates Determined by Pulsed-Field Gel Electrophoresis: Comparison of Isolates from Avian Wildlife, Domestic Animals, and the Environment in Norway

    PubMed Central

    Refsum, Thorbjørn; Heir, Even; Kapperud, Georg; Vardund, Traute; Holstad, Gudmund

    2002-01-01

    The molecular epidemiology of 142 isolates of Salmonella enterica serovar Typhimurium from avian wildlife, domestic animals, and the environment in Norway was investigated using pulsed-field gel electrophoresis (PFGE) and computerized numerical analysis of the data. The bacterial isolates comprised 79 isolates from wild-living birds, including 46 small passerines and 26 gulls, and 63 isolates of nonavian origin, including 50 domestic animals and 13 environmental samples. Thirteen main clusters were discernible at the 90% similarity level. Most of the isolates (83%) were grouped into three main clusters. These were further divided into 20 subclusters at the 95% similarity level. Isolates from passerines, gulls, and pigeons dominated within five subclusters, whereas isolates from domestic animals and the environment belonged to many different subclusters with no predominance. The results support earlier results that passerines constitute an important source of infection to humans in Norway, whereas it is suggested that gulls and pigeons, based on PFGE analysis, represent only a minor source of human serovar Typhimurium infections. Passerines, gulls, and pigeons may also constitute a source of infection of domestic animals and feed plants or vice versa. Three isolates from cattle and a grain source, of which two were multiresistant, were confirmed as serovar Typhimurium phage type DT 104. These represent the first reported phage type DT 104 isolates from other sources than humans in Norway. PMID:12406755

  5. Prevalence of Clostridium botulinum in Finnish Trout Farms: Pulsed-Field Gel Electrophoresis Typing Reveals Extensive Genetic Diversity among Type E Isolates

    PubMed Central

    Hielm, Sebastian; Björkroth, Johanna; Hyytiä, Eija; Korkeala, Hannu

    1998-01-01

    The distribution of Clostridium botulinum serotypes A, B, E, and F in Finnish trout farms was examined. A total of 333 samples were tested with a neurotoxin-specific PCR assay. C. botulinum type E was found in 68% of the farm sediment samples, in 15% of the fish intestinal samples, and in 5% of the fish skin samples. No other serotypes were found. The spore counts determined by the most-probable-number method were considerably higher for the sediments than for the fish intestines and skin; the average values were 2,020, 166, and 310 C. botulinum type E spores kg−1, respectively. The contamination rates in traditional freshwater ponds and marine net cages were high, but in concrete ponds equipped with sediment suction devices the contamination rates were significantly lower. Pulsed-field gel electrophoresis (PFGE) typing of 42 isolates obtained in this survey and 12 North American reference strains generated 28 pulsotypes upon visual inspection, suggesting that there was extensive genetic diversity and that the discriminatory power of PFGE typing in C. botulinum type E was high. A numerical analysis of SmaI-XmaI macrorestriction profiles confirmed these findings, as it divided the 54 isolates into 15 clusters at a similarity level of 76%. For this material, this level of similarity corresponded to a three-band difference in the macrorestriction profiles, which indicated that there is no genotypic proof of a close epidemiological relationship among the clusters. PMID:9797260

  6. Persistence of a Salmonella enterica serotype typhimurium clone in Danish pig production units and farmhouse environment studied by pulsed field gel electrophoresis (PFGE)

    PubMed

    Sandvang, D; Jensen, L B; Baggesen, D L; Baloda, S B

    2000-06-01

    The clonal relationship among Salmonella enterica serotype Typhimurium isolates from selected pig production units in Denmark was investigated by the pulsed field gel electrophoresis (PFGE) typing method to determine environmental survival and spread of Salmonella in different herds. Thirty-four Typhimurium isolated during 1996-1998 from porcine faeces and environmental samples from three pig farms designated 1, 3 and 5 were characterised by PFGE using two restriction enzymes. Farm 5 supplied piglets to farm 1 and the herds were located close to each other. Results of PFGE analysis showed both intra- and inter-relationships, i.e. identical PFGE patterns among the faecal and environmental isolates from farm 1 and farm 5. All the isolates from farm 3 irrespective of the source showed identical PFGE patterns, but were different from samples from farms 1 and 5. This study indicates spread between farms and survival of a farm-specific clone. Furthermore, identical PFGE patterns of isolates from piglet supplier and finisher herds indicate that the farrow-to-grower herd of farm 5 was sub-clinically infected prior to delivery to farm 1 and thereby caused the transmission of Salmonella.

  7. High Genetic Diversity of Enterococcus faecium and Enterococcus faecalis Clinical Isolates by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing from a Hospital in Malaysia

    PubMed Central

    Weng, Poh Leng; Ramli, Ramliza; Shamsudin, Mariana Nor; Cheah, Yoke-Kqueen; Hamat, Rukman Awang

    2013-01-01

    Little is known on the genetic relatedness and potential dissemination of particular enterococcal clones in Malaysia. We studied the antibiotic susceptibility profiles of Enterococcus faecium and Enterococcus faecalis and subjected them to pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). E. faecium and E. faecalis displayed 27 and 30 pulsotypes, respectively, and 10 representative E. faecium and E. faecalis isolates (five each) yielded few different sequence types (STs): ST17 (2 isolates), ST78, ST203, and ST601 for E. faecium, and ST6, ST16, ST28, ST179, and ST399 for E. faecalis. Resistance to tazobactam-piperacillin and ampicillin amongst E. faecium isolates was highly observed as compared to E. faecalis isolates. All of the isolates were sensitive to vancomycin and teicoplanin. The presence of epidemic and nosocomial strains of selected E. faecium STs: 17, 78, and 203 and E. faecalis ST6 as well as high rates of resistance to multiple antibiotics amongst E. faecium isolates is of a particular concern. PMID:23819125

  8. Induction and repair of DNA double-strand breaks using constant-field gel electrophoresis and apoptosis as predictive markers for sensitivity of cancer cells to cisplatin.

    PubMed

    Saleh, Ekram M; El-Awady, Raafat A; Anis, Noha; El-Sharkawy, Nahla

    2012-10-01

    This study was designed to evaluate some parameters that may play a role in the prediction of cancer cells sensitivity to cisplatin (CIS). Sensitivity, induction and repair of DNA double-strand breaks (DSB), cell cycle regulation and induction of apoptosis were measured in four cancer cell lines with different sensitivities to CIS. Using a sulphorhodamine-B assay, the cervical carcinoma cells (HeLa) were found to be the most sensitive to CIS followed by breast carcinoma cells (MCF-7) and liver carcinoma cells (HepG2). Colon carcinoma HCT116 cells were the most resistant. As measured by constant-field gel electrophoresis (CFGE), DSB induction, but not residual DSB exhibited a significant correlation with the sensitivity of cells to CIS. Flow cytometric DNA ploidy analysis revealed that 67% of HeLa cells and 10% of MCF-7 cells shift to sub-G1 phase after incubation with CIS. Additionally, CIS induced the arrest of MCF-7 cells in S-phase and the arrest of HepG2 and HCT116 cells in both S phase and G2/M phase. Determination of the Fas-L level and Caspase-9 activity indicated that CIS-induced apoptosis results from the mitochondrial (intrinsic) pathway. These results, if confirmed using clinical samples, indicate that the induction of DNA DSB as measured by CFGE and the induction of apoptosis should be considered, along with other predictive markers, in future clinical trials to develop predictive assays for platinum -based therapy.

  9. Virulence patterns and long-range genetic mapping of extraintestinal Escherichia coli K1, K5, and K100 isolates: use of pulsed-field gel electrophoresis.

    PubMed Central

    Ott, M; Bender, L; Blum, G; Schmittroth, M; Achtman, M; Tschäpe, H; Hacker, J

    1991-01-01

    A total of 127 extraintestinal Escherichia coli strains of the capsule serotypes K1, K5, and K100 from human and animal sources were analyzed for DNA sequences specific for the genes for various adhesins (P fimbriae [pap] and P-related sequences [prs], S fimbriae [sfa]/F1C fimbriae [foc], and type I fimbriae [fim]), aerobactin (aer), and hemolysin (hly). The expression of corresponding virulence factors was also tested. Twenty-four selected strains were analyzed by long-range DNA mapping to evaluate their genetic relationships. DNA sequences for the adhesins were often found in strains not expressing them, while strains with hemolysin and aerobactin genes usually did express them. Different isolates of the same serotype often expressed different virulence patterns. The use of virulence-associated gene probes for Southern hybridization with genomic DNA fragments separated by pulsed-field gel electrophoresis revealed that a highly heterogeneous restriction fragment length and hybridization pattern existed even within strains of the same serotype. Long-range DNA mapping is therefore useful for the evaluation of genetic relatedness among individual isolates and facilitates the performance of precise molecular epidemiology. Images PMID:1677349

  10. Molecular Subtyping of Vibrio cholerae O1 and O139 by Pulsed-Field Gel Electrophoresis in Hong Kong: Correlation with Epidemiological Events from 1994 to 2002

    PubMed Central

    Kam, Kai Man; Luey, Cindy Kit Yee; Tsang, Yee Man; Law, Choi Ping; Chu, Man Yu; Cheung, Tze Leung; Chiu, Agatha Wai Huen

    2003-01-01

    Two hundred twenty isolates of Vibrio cholerae O1 and O139 collected from 1994 to 2002 in Hong Kong were analyzed by pulsed-field gel electrophoresis (PFGE). Chromosomal DNAs from all V. cholerae isolates in agarose plugs were digested with the restriction enzyme NotI, resulting in 20 to 27 bands. Sixty distinctive PFGE patterns in the range of 10 to 300 kb were noted among 213 isolates typeable by PFGE. By comparing the common PFGE patterns obtained from four well-defined outbreaks of V. cholerae O1 and O139 with those obtained from other, epidemiologically unrelated isolates during the study period, indistinguishable and similar PFGE patterns were identified, indicating their close relatedness, in agreement with the results of epidemiological investigations. Heterogeneous PFGE patterns (with four to six banding differences), however, were identified among strains that were imported from other parts of Asia, including Indonesia, India, and Pakistan. Correlations with epidemiological information further support the usefulness of PFGE as an epidemiological tool in laboratory investigations of suspected outbreaks. Standardization of PFGE methodology will allow international comparison of fingerprint patterns and will form the basis of a laboratory network for tracking V. cholerae. PMID:14532174

  11. Isolation and pulsed-field gel electrophoresis typing of Listeria monocytogenes from modified atmosphere packaged fresh-cut vegetables collected in Ireland.

    PubMed

    Francis, Gillian A; O'Beirne, David

    2006-10-01

    The incidence of Listeria monocytogenes in modified atmosphere packaged fresh-cut fruits and vegetables from chill cabinets of a supermarket in Ireland was investigated over a 2-year period. Overall, 9.58% of fresh-cut produce was contaminated with Listeria spp. Various species of Listeria were isolated from samples, including L. monocytogenes, L. seeligeri, L. innocua, L. welshimeri, and L. ivanovii. No fruit samples contained detectable L. monocytogenes. Overall, a total of 21 L. monocytogenes isolates (2.9% of samples) were recovered from a range of products, including dry coleslaw mix (80% shredded cabbage and 20% shredded carrot), bean sprouts, and leafy vegetables such iceberg, romaine, and radicchio lettuce and mixed salad leaves (curly endive, escarole, and radicchio leaves). Dry coleslaw mix appeared to have the highest incidence of Listeria contamination (20%) compared with other products. Listeria contamination was more frequent (P < 0.05) during the summer and autumn months than during the winter and spring months. The 21 L. monocytogenes isolates were subsequently subtyped by genomic macrorestriction techniques using ApaI with pulsed-field gel electrophoresis (PFGE). PFGE of digested DNA produced bands of 79 to 518 kb. Four PFGE profiles were identified, and approximately 50% of the isolates were associated with profile 1. This study indicates that fresh-cut vegetables packaged under a modified atmosphere can support growth of numerous species of Listeria, including L. monocytogenes.

  12. Real-time imaging of the reorientation mechanisms of YOYO-labelled DNA molecules during 90 degrees and 120 degrees pulsed field gel electrophoresis.

    PubMed Central

    Gurrieri, S; Smith, S B; Wells, K S; Johnson, I D; Bustamante, C

    1996-01-01

    Pulsed field gel electrophoresis (PFGE) techniques have been developed to overcome the limitations of conventional electrophoresis and to increase the separation to DNA chromosomes of few megabase pairs in size. Despite of the large success of these techniques, the various separation protocols employed for PFGE experiments have been determined empirically. However, a deep understanding of the molecular mechanisms of motion responsible for DNA separation becomes necessary for the rational optimization of these techniques. This paper shows the first clear observations of individual molecules of DNA during the reorientation process in 90 degrees PFGE and 120 degrees PFGE. Real-time visualization of the DNA dynamics during PFGE was possible with the use of an epi-illumination fluorescence microscope specifically equipped to run these experiments and by staining the DNA with YOYO-1 (1,1'-(4,4,7,7-tetramethyl-4,7-diazaundecamethylene)-bis-4-[3-meth yl -2,3-dihydro-(benzo-1,3-oxazole)-2-methyl-idene]-quinolinium tetraiodide). This dye forms a very stable, highly fluorescent complex with double-stranded DNA and dramatically improves the quality of the DNA images. The results of computer simulations used to reproduce the molecular mechanisms of motion as well as the DNA separation features are also discussed. PMID:8972863

  13. Genetic Characterization of Atypical Enteropathogenic Escherichia coli Isolates from Ewes' Milk, Sheep Farm Environments, and Humans by Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis

    PubMed Central

    Otero, Verónica; Rodríguez-Calleja, José-María; Otero, Andrés; García-López, María-Luisa

    2013-01-01

    A collection of 81 isolates of enteropathogenic Escherichia coli (EPEC) was obtained from samples of bulk tank sheep milk (62 isolates), ovine feces (4 isolates), sheep farm environment (water, 4 isolates; air, 1 isolate), and human stool samples (9 isolates). The strains were considered atypical EPEC organisms, carrying the eae gene without harboring the pEAF plasmid. Multilocus sequence typing (MLST) was carried out with seven housekeeping genes and 19 sequence types (ST) were detected, with none of them having been previously reported for atypical EPEC. The most frequent ST included 41 strains isolated from milk and human stool samples. Genetic typing by pulsed-field gel electrophoresis (PFGE) resulted in 57 patterns which grouped in 24 clusters. Comparison of strains isolated from the different samples showed phylogenetic relationships between milk and human isolates and also between milk and water isolates. The results obtained show a possible risk for humans due to the presence of atypical EPEC in ewes' milk and suggest a transmission route for this emerging pathogen through contaminated water. PMID:23872571

  14. Genetic characterization of atypical enteropathogenic Escherichia coli isolates from ewes' milk, sheep farm environments, and humans by multilocus sequence typing and pulsed-field gel electrophoresis.

    PubMed

    Otero, Verónica; Rodríguez-Calleja, José-María; Otero, Andrés; García-López, María-Luisa; Santos, Jesús A

    2013-10-01

    A collection of 81 isolates of enteropathogenic Escherichia coli (EPEC) was obtained from samples of bulk tank sheep milk (62 isolates), ovine feces (4 isolates), sheep farm environment (water, 4 isolates; air, 1 isolate), and human stool samples (9 isolates). The strains were considered atypical EPEC organisms, carrying the eae gene without harboring the pEAF plasmid. Multilocus sequence typing (MLST) was carried out with seven housekeeping genes and 19 sequence types (ST) were detected, with none of them having been previously reported for atypical EPEC. The most frequent ST included 41 strains isolated from milk and human stool samples. Genetic typing by pulsed-field gel electrophoresis (PFGE) resulted in 57 patterns which grouped in 24 clusters. Comparison of strains isolated from the different samples showed phylogenetic relationships between milk and human isolates and also between milk and water isolates. The results obtained show a possible risk for humans due to the presence of atypical EPEC in ewes' milk and suggest a transmission route for this emerging pathogen through contaminated water.

  15. Pulsed-field gel electrophoresis analysis of the genome of Rhodococcus fascians: genome size and linear and circular replicon composition in virulent and avirulent strains.

    PubMed

    Pisabarro, A; Correia, A; Martín, J F

    1998-05-01

    Total DNA of virulent and avirulent strains of Rhodococcus fascians was resolved by pulsed-field gel electrophoresis (PFGE) into a discrete number of fragments by digestion with the endonucleases AseI and DraI. Restriction endonucleases PacI, PmeI, and SwaI yielded no fragments upon digestion of R. fascians genome, and all the other tested endonucleases recognizing 6 bp released too many fragments. The genome size was 5.6 megabases for the type strain R. fascians DSM 20669, and 5.8 megabases for the virulent R. fascians D188 strain. However the genome size of R. fascians CECT 3001 (NRRL B15096) was 8.0 megabases. No linear chromosome in the megabase range was observed under pulse conditions in which Saccharomyces cerevisiae and Schizosaccharomyces pombe chromosomes were perfectly resolved, suggesting that the R. fascians chromosome is circular. A new linear plasmid pIRN640 of 640 kb was found in the avirulent R. fascians CECT 3001 that did not hybridize with a probe internal to the fas region of pFiD188 known to be involved in plant pathogenicity in the virulent strain R. fascians D188. Virulence was correlated in all strains tested with the presence of the fas region. The AseI and DraI bands corresponding to the extrachromosomal elements were identified providing the basis for a physical map of this organism.

  16. Comparison of pulsed-field gel electrophoresis & repetitive sequence-based PCR methods for molecular epidemiological studies of Escherichia coli clinical isolates

    PubMed Central

    Bae, Il Kwon; Kim, Juwon; Sun, Je Young Hannah; Jeong, Seok Hoon; Kim, Yong-Rok; Wang, Kang-Kyun; Lee, Kyungwon

    2014-01-01

    Background & objectives: PFGE, rep-PCR, and MLST are widely used to identify related bacterial isolates and determine epidemiologic associations during outbreaks. This study was performed to compare the ability of repetitive sequence-based PCR (rep-PCR) and pulsed-field gel electrophoresis (PFGE) to determine the genetic relationships among Escherichia coli isolates assigned to various sequence types (STs) by two multilocus sequence typing (MLST) schemes. Methods: A total of 41 extended-spectrum β-lactamase- (ESBL-) and/or AmpC β-lactamase-producing E. coli clinical isolates were included in this study. MLST experiments were performed following the Achtman's MLST scheme and the Whittam's MLST scheme, respectively. Rep-PCR experiments were performed using the DiversiLab system. PFGE experiments were also performed. Results: A comparison of the two MLST methods demonstrated that these two schemes yielded compatible results. PFGE correctly segregated E. coli isolates belonging to different STs as different types, but did not group E. coli isolates belonging to the same ST in the same group. Rep-PCR accurately grouped E. coli isolates belonging to the same ST together, but this method demonstrated limited ability to discriminate between E. coli isolates belonging to different STs. Interpretation & conclusions: These results suggest that PFGE would be more effective when investigating outbreaks in a limited space, such as a specialty hospital or an intensive care unit, whereas rep-PCR should be used for nationwide or worldwide epidemiology studies. PMID:25579152

  17. Epidemiological Characteristics and Clinical Treatment Outcome of Typhoid Fever in Ningbo, China, 2005-2014: Pulsed-Field Gel Electorophoresis Results Revealing Great Proportion of Common Transmission Sources.

    PubMed

    Song, Qifa; Yang, Yuanbin; Lin, Wenping; Yi, Bo; Xu, Guozhang

    2017-09-25

    We aimed to describe the molecular epidemiological characteristics and clinical treatment outcome of typhoid fever in Ningbo, China during 2005-2014. Eighty-eight Salmonella Typhi isolates were obtained from 307 hospitalized patients. Three prevalent pulsed-field gel electrophoresis (PFGE) patterns of 54 isolates from 3 outbreaks were identified. Overall, there were 64 (72.7%) isolates from clustered cases and 24 (27.3%) isolates from sporadic cases. Resistance to nalidixic acid (NAL) (n = 47; 53.4%) and ampicillin (AMP) (n = 40; 45.4%) and rare resistance to tetracycline (TET) (n = 2; 2.3%) and gentamicin (GEN) (n = 2; 2.3%) were observed. No isolates resistant to cefotaxime (CTX), chloramphenicol (CL), ciprofloxacin (CIP), and trimethoprim-sulfamethoxazole (SXT) were found. The occurrence of reduced sensitivity to CIP was 52.3% (n = 46). The medians of fever clearance time in cases with and without complications were 7 (interquartile range (IQR): 4-10) and 5 (IQR: 3-7) days (P = 0.001), respectively, when patients were treated with CIP or levofloxacin (LEV) and/or third-generation cephalosporins (CEP). Rates of serious complications were at low levels: peritonitis (2.3%), intestinal hemorrhage (6.8%), and intestinal perforation (1.1%). The present study revealed a long-term clustering trend with respect to PFGE patterns, occasional outbreaks, and the rapid spread of AMP resistance and decreased CIP susceptibility among S. Typhi isolates in recent years.

  18. Comparative typing of Pseudomonas aeruginosa by random amplification of polymorphic DNA or pulsed-field gel electrophoresis of DNA macrorestriction fragments.

    PubMed Central

    Renders, N; Römling, Y; Verbrugh, H; van Belkum, A

    1996-01-01

    Eighty-seven strains of Pseudomonas aeruginosa were typed by random amplification of polymorphic DNA (RAPD) and pulsed-field gel electrophoresis (PFGE) of macrorestriction fragments. Stains were clustered on the basis of interpretative criteria as presented previously for the PFGE analysis. Clusters of strains were also defined on the basis of epidemiological data and subsequently reanalyzed by RAPD. It was found that in an RAPD assay employing the enterobacterial repetitive intergenic consensus sequence ERIC2 as a primer, single band differences can be ignored; in this case, clonally related strains could be grouped as effectively and reliably as with PFGE. These data could be corroborated by the use of other primer species. However, some primers either showed reduced resolution or, in contrast, identified DNA polymorphisms beyond epidemiologically and PFGE-defined limits. Apparently, different primers define different windows of genetic variation. It is suggested that criteria for interpretation of the ERIC2 PCR fingerprints can be simple and straightforward: when single band differences are ignored, RAPD-determined grouping of P. aeruginosa is congruent with that obtained by PFGE. Consequently, this implies that RAPD can be used with trust as a first screen in epidemiological characterization of P. aeruginosa. The ability to measure the rate of molecular evolution of the P. aeruginosa genome clearly depends on the choice of restriction enzyme or primer when RAPD or PFGE, respectively, is applied for the detection of DNA polymorphisms. PMID:8940470

  19. Multilocus sequence typing versus pulsed-field gel electrophoresis for characterization of extended-spectrum beta-lactamase-producing Escherichia coli isolates.

    PubMed

    Nemoy, Lucia L; Kotetishvili, Mamuka; Tigno, Justine; Keefer-Norris, Ananda; Harris, Anthony D; Perencevich, Eli N; Johnson, Judith A; Torpey, Dave; Sulakvelidze, Alexander; Morris, J Glenn; Stine, O Colin

    2005-04-01

    Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains are emerging pathogens. Molecular typing of ESBL-producing E. coli is useful for surveillance purposes, to monitor outbreaks and track nosocomial spread. Although pulsed-field gel electrophoresis (PFGE) is the current "gold standard" for bacterial molecular typing, multilocus sequence typing (MLST) may offer advantages. Forty ESBL-producing E. coli isolates were selected at random from a cohort of intensive care unit patients who had active surveillance perirectal cultures done. PFGE identified 19 unique PFGE types (PT) among the 40 isolates; MLST identified 22 unique sequence types. MLST had greater discriminatory ability than PFGE for ESBL-producing E. coli. Simpson's indices of diversity for PFGE and MLST were 0.895 and 0.956, respectively. There were five clonal complexes (CCs) (isolates with differences of no more than two loci) that each contained multiple PT, but each PT was found in only one CC, indicating genetic consistency within a CC. MLST has clear utility in studies of ESBL-producing E. coli, based on a greater discriminatory ability and reproducibility than PFGE and the ability to a priori define genetically related bacterial strains.

  20. Role of real-time molecular typing in the surveillance of Campylobacter enteritis and comparison of pulsed-field gel electrophoresis profiles from chicken and human isolates.

    PubMed

    Michaud, Sophie; Ménard, Suzanne; Arbeit, Robert D

    2005-03-01

    The goal of the present study was to assess the contribution of real-time molecular typing, used alone or with clinical surveillance, to the prompt identification of clusters of Campylobacter enteritis. Potential poultry sources were sought by comparing the pulsed-field gel electrophoresis genotypes of human and fresh whole retail chicken isolates collected during the same study period. Among 183 human isolates, 82 (45%) had unique genotypes, 72 (39%) represented 26 clusters of 2 to 7 isolates each, and 29 (16%) represented three clusters of 8 to 11 isolates each. Molecular typing was useful for the confirmation of outbreaks suspected on the basis of epidemiological surveillance, but for most small clusters, no epidemiological link could be established. Thus, the added value of real-time molecular typing is questionable, since the numerous small clusters identified were of unclear public health significance. Among 177 chickens, 41 (23%) yielded campylobacter isolates; of these, 19 (46%) had genotypes similar to those of 41 (22%) human isolates. However, a temporal association was demonstrated in only a minority of cases, and most genotypes were present only in a single species, suggesting that sources other than chickens are important in human campylobacteriosis. Further investigation with samples from water and other possible environmental sources is needed to define the most efficient strategy for the application of molecular typing and identification of the source(s) of sporadic cases of campylobacteriosis.

  1. Genomic fingerprinting of shigatoxin-producing Escherichia coli (STEC) strains: comparison of pulsed-field gel electrophoresis (PFGE) and fluorescent amplified-fragment-length polymorphism (FAFLP).

    PubMed

    Heir, E; Lindstedt, B A; Vardund, T; Wasteson, Y; Kapperud, G

    2000-12-01

    For epidemiological studies of shigatoxin-producing Escherichia coli (STEC) infections, rapid, reproducible and highly discriminative methods are required. In this study, we examined the performance of the fluorescent amplified-fragment-length polymorphism (FAFLP) technique for epidemiological fingerprinting of STEC isolates and compared it to the acknowledged fingerprinting method pulsed-field gel electrophoresis (PFGE). A total of 88 STEC isolates, including 82 of serotype O157:H7 or O157:H-, were subjected to fingerprinting by both PFGE and FAFLP. The isolates included sporadic and epidemiologically related strains of both animal and human origin from widespread geographical locations. The FAFLP fingerprint patterns confirmed the clonal nature of STEC O157 strains. Among the 82 O157:H7/H- isolates belonging to 49 distinct groups of epidemiological unrelated isolates, 24 FAFLP profiles and 51 PFGE patterns were obtained. Thus, PFGE had a higher discriminatory power than FAFLP and overall correlated better to available epidemiological data. Consequently, the PFGE technique remains the method of choice in epidemiological investigations of STEC infections.

  2. Multilocus sequence typing reveals a lack of diversity among Escherichia coli O157:H7 isolates that are distinct by pulsed-field gel electrophoresis.

    PubMed

    Noller, Anna C; McEllistrem, M Catherine; Stine, O Colin; Morris, J Glenn; Boxrud, David J; Dixon, Bruce; Harrison, Lee H

    2003-02-01

    Escherichia coli O157:H7 is a major cause of foodborne illness in the United States. Pulsed-field gel electrophoresis (PFGE) is the molecular epidemiologic method mostly commonly used to identify food-borne outbreaks. Although PFGE is a powerful epidemiologic tool, it has disadvantages that make a DNA sequence-based approach potentially attractive. Multilocus sequence typing (MLST) analyzes the internal fragments of housekeeping genes to establish genetic relatedness between isolates. We sequenced selected portions of seven housekeeping genes and two membrane protein genes (ompA and espA) of 77 isolates that were diverse by PFGE to determine whether there was sufficient sequence variation to be useful as an epidemiologic tool. There was no DNA sequence diversity in the sequenced portions of the seven housekeeping genes and espA. For ompA, all but five isolates had sequence identical to that of the reference strains. E. coli O157:H7 has a striking lack of genetic diversity in the genes we explored, even among isolates that are clearly distinct by PFGE. Other approaches to identify improved molecular subtyping methods for E. coli 0157:H7 are needed.

  3. The use of caspase inhibitors in pulsed-field gel electrophoresis may improve the estimation of radiation-induced DNA repair and apoptosis.

    PubMed

    Balart, Josep; Pueyo, Gemma; de Llobet, Lara I; Baro, Marta; Sole, Xavi; Marin, Susanna; Casanovas, Oriol; Mesia, Ricard; Capella, Gabriel

    2011-01-15

    Radiation-induced DNA double-strand break (DSB) repair can be tested by using pulsed-field gel electrophoresis (PFGE) in agarose-encapsulated cells. However, previous studies have reported that this assay is impaired by the spontaneous DNA breakage in this medium. We investigated the mechanisms of this fragmentation with the principal aim of eliminating it in order to improve the estimation of radiation-induced DNA repair. Samples from cancer cell cultures or xenografted tumours were encapsulated in agarose plugs. The cell plugs were then irradiated, incubated to allow them to repair, and evaluated by PFGE, caspase-3, and histone H2AX activation (γH2AX). In addition, apoptosis inhibition was evaluated through chemical caspase inhibitors. We confirmed that spontaneous DNA fragmentation was associated with the process of encapsulation, regardless of whether cells were irradiated or not. This DNA fragmentation was also correlated to apoptosis activation in a fraction of the cells encapsulated in agarose, while non-apoptotic cell fraction could rejoin DNA fragments as was measured by γH2AX decrease and PFGE data. We were able to eliminate interference of apoptosis by applying specific caspase inhibitors, and improve the estimation of DNA repair, and apoptosis itself. The estimation of radiation-induced DNA repair by PFGE may be improved by the use of apoptosis inhibitors. The ability to simultaneously determine DNA repair and apoptosis, which are involved in cell fate, provides new insights for using the PFGE methodology as functional assay.

  4. Characteristics of Clusters of Salmonella and Escherichia coli O157 Detected by Pulsed-Field Gel Electrophoresis that Predict Identification of Outbreaks.

    PubMed

    Jones, Timothy F; Sashti, Nupur; Ingram, Amanda; Phan, Quyen; Booth, Hillary; Rounds, Joshua; Nicholson, Cyndy S; Cosgrove, Shaun; Crocker, Kia; Gould, L Hannah

    2016-12-01

    Molecular subtyping of pathogens is critical for foodborne disease outbreak detection and investigation. Many clusters initially identified by pulsed-field gel electrophoresis (PFGE) are not confirmed as point-source outbreaks. We evaluated characteristics of clusters that can help prioritize investigations to maximize effective use of limited resources. A multiagency collaboration (FoodNet) collected data on Salmonella and Escherichia coli O157 clusters for 3 years. Cluster size, timing, extent, and nature of epidemiologic investigations were analyzed to determine associations with whether the cluster was identified as a confirmed outbreak. During the 3-year study period, 948 PFGE clusters were identified; 849 (90%) were Salmonella and 99 (10%) were E. coli O157. Of those, 192 (20%) were ultimately identified as outbreaks (154 [18%] of Salmonella and 38 [38%] of E. coli O157 clusters). Successful investigation was significantly associated with larger cluster size, more rapid submission of isolates (e.g., for Salmonella, 6 days for outbreaks vs. 8 days for nonoutbreaks) and PFGE result reporting to investigators (16 days vs. 29 days, respectively), and performance of analytic studies (completed in 33% of Salmonella outbreaks vs. 1% of nonoutbreaks) and environmental investigations (40% and 1%, respectively). Intervals between first and second cases in a cluster did not differ significantly between outbreaks and nonoutbreaks. Molecular subtyping of pathogens is a rapidly advancing technology, and successfully identifying outbreaks will vary by pathogen and methods used. Understanding criteria for successfully investigating outbreaks is critical for efficiently using limited resources.

  5. Rapid and high-resolution distinction of community-acquired and nosocomial Staphylococcus aureus isolates with identical pulsed-field gel electrophoresis patterns and spa types.

    PubMed

    Glasner, Corinna; Sabat, Artur J; Dreisbach, Annette; Larsen, Anders R; Friedrich, Alexander W; Skov, Robert L; van Dijl, Jan Maarten

    2013-03-01

    Methicillin-resistant Staphylococcus aureus (MRSA) represent a serious threat for public health worldwide. Of particular concern is the emergence of community-acquired MRSA, which is often difficult to distinguish from nosocomial MRSA due to a lack of suitable typing methods for early detection. For example, the USA300 pulsed-field gel electrophoresis (PFGE) pattern includes both the 'classical' community-acquired USA300 clone with spa type t008 and an epidemiologically unrelated nosocomial clone with spa type t024. Likewise, spa typing cannot distinguish the classic USA300 from nosocomial MRSA with the spa type t008. Since the fast and high-resolution distinction of these S. aureus types is important for infection prevention and surveillance, we investigated whether multiple-locus variable number tandem repeat fingerprinting (MLVF) can be applied to overcome these limitations. Indeed, MLVF correctly grouped 91 MRSA isolates belonging to the classic USA300 lineage, nosocomial MRSA isolates with the USA300 PFGE profile and spa type t024, and nosocomial MRSA isolates with spa type t008 into 3 distinct clusters. Importantly, several sub-clusters were also identified, reflecting epidemiological relationships between the respective isolates. We conclude that MLVF has the discriminatory power needed to rapidly distinguish very similar community-acquired and nosocomial MRSA isolates and that MLVF-based sub-clustering of isolates is highly useful for epidemiological investigations, outbreak prevention, and control. Copyright © 2012 Elsevier GmbH. All rights reserved.

  6. Cost-Effectiveness and Efficacy of spa, SCCmec, and PVL Genotyping of Methicillin-Resistant Staphylococcus aureus as Compared to Pulsed-Field Gel Electrophoresis

    PubMed Central

    Li, Vincent; Chui, Linda; Louie, Lisa; Simor, Andrew; Golding, George R.; Louie, Marie

    2013-01-01

    Pulsed-field gel electrophoresis (PFGE) is a valuable molecular typing assay used for methicillin-resistant Staphylococcus aureus (MRSA) surveillance and genotyping. However, there are several limitations associated with PFGE. In Alberta, Canada, the significant increase in the number of MRSA isolates submitted to the Provincial Laboratory for Public Health (ProvLab) for PFGE typing led to the need for an alternative genotyping method. In this study, we describe the transition from PFGE to Staphylococcus protein A (spa), Staphylococcal cassette chromosome (SCCmec), and Panton-Valentine leukocidin (PVL) typing. A total of 1915 clinical MRSA isolates collected from 2005 to 2009 were used to develop and validate an algorithm for assigning PFGE epidemic types using spa, SCCmec, and PVL typing and the resulting data was used to populate a new Alberta MRSA typing database. An additional 12620 clinical MRSA isolates collected from 2010 to 2012 as part of ongoing routine molecular testing at ProvLab were characterized using the new typing algorithm and the Alberta MRSA typing database. Switching to spa, SCCmec, and PVL from PFGE typing substantially reduced hands-on and turn-around times while maintaining historical PFGE epidemic type designations. This led to an approximate $77,000 reduction in costs from 2010 to 2012. PFGE typing is still required for a small subset of MRSA isolates that have spa types that are rare, novel, or associated with more than one PFGE epidemic type. PMID:24244440

  7. Molecular characterization of Salmonella paratyphi B dT+ and Salmonella Heidelberg from poultry and retail chicken meat in Colombia by pulsed-field gel electrophoresis.

    PubMed

    Donado-Godoy, Pilar; Byrne, Barbara A; Hume, Michael; León, Maribel; Pérez-Gutiérrez, Enriqué; Vives Flores, Martha J; Clavijo, Viviana; Holguin, Ángela; Romero-Zuñiga, Juan J; Castellanos, Ricardo; Tafur, McAllister; Smith, Woutrina A

    2015-04-01

    Salmonella Paratyphi B dT+ variant (also termed Salmonella Java) and Salmonella Heidelberg are pathogens of public health importance that are frequently isolated from poultry. As a step toward implementing the Colombian Integrated Program for Antimicrobial Resistant Surveillance, this study characterized molecular patterns of Salmonella Paratyphi B dT+ and Salmonella Heidelberg isolated from poultry farms, fecal samples, and retail chicken meat using pulsed-field gel electrophoresis (PFGE). The objective of this study was to determine the genetic relationship among isolates and to determine potential geographically predominant genotypes. Based on PFGE analysis, both serovars exhibited high heterogeneity: the chromosomal DNA fingerprints of 82 Salmonella Paratyphi B dT+ isolates revealed 42 PFGE patterns, whereas the 21 isolates of Salmonella Heidelberg revealed 10 patterns. Similar genotypes of both serovars were demonstrated to be present on farms and in retail outlets. For Salmonella Paratyphi B dT+, closely genetically related strains were found among isolates coming from different farms and different integrated poultry companies within two departments (Santander and Cundinamarca) and also from farms located in the two geographically distant departments. For Salmonella Heidelberg, there were fewer farms with genetically related isolates than for Salmonella Paratyphi B dT+. A possible dissemination of similar genotypes of both serovars along the poultry production chain is hypothesized, and some facilitating factors existing in Colombia are reviewed.

  8. Molecular Typing of Fluoroquinolone-Resistant Campylobacter jejuni Isolated from Broilers in Japan Using Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis.

    PubMed

    Ozawa, Manao; Hiki, Mototaka; Kawanishi, Michiko; Abo, Hitoshi; Kojima, Akemi; Asai, Tetsuo; Hamamoto, Shuichi

    2016-01-01

    Fluoroquinolone-resistant Campylobacter jejuni isolates from broilers in Japan were characterized using multilocus sequence typing and pulsed-field gel electrophoresis (PFGE) in order to elucidate the genetic relationship between these strains. Forty-three of the isolates were classified into 20 sequence types and were clustered into 21 PFGE types with 70% similarity. The most dominant clonal complex (CC) was CC-21 (41.9%). Diverse PFGE patterns were observed within the same CC, but the combined analysis of PFGE type and CC revealed that the strains with the same combination were isolated from the same district or neighboring districts. On the other hand, strains with the same combination pattern were also isolated from geographically distant districts. Our results elucidate two possible reasons for the prevalence of fluoroquinolone-resistant C. jejuni among broiler farms: (1) the resistant C. jejuni is clonally disseminated within the limited area, and (2) susceptible C. jejuni acquired fluoroquinolone resistance during the use of fluoroquinolone on the farms.

  9. Effect of bromodeoxyuridine on radiation-induced DNA damage and repair based on DNA fragment size using pulsed-field gel electrophoresis

    SciTech Connect

    Lawrence, T.S.; Davis, M.A.; Normolle, D.P.

    1995-12-01

    We have used biphasic linear ramping pulsed-field gel electrophoresis (PFGE) to understand the effect of incorporation of bromodeoxyuridine (BrdUrd) on radiation-induced DNA damage and repair. This technique permits a determination of the fragment size distribution produced immediately after irradiation as well as during the repair period. We found that incorporation of BrdUrd increased the induction and decreased the repair of radiation damage. The fragment size distribution was consistent with a random breakage model. When we found that significantly more damage was detected after irradiation of deproteinized DNA compared to intact cells, we studied the effects of BrdUrd incorporation on the radiation response of cells or DNA at various phases of preparation for electrophoresis: cells adherent to the culture dish (A), trypsinized cells (B), agarose-embedded cells (C) and deproteinized DNA (D). Although there was a general tendency to detect more damage when irradiation was performed later in the preparation process, steps B and C were the only successive steps which were significantly different. These findings demonstrate that incorporation of BrdUrd randomly increases the induction of radiation damage and decreases its repair at the level of 200 kbp to 5 Mbp fragments. Furthermore, they confirm that the amount of damage detected depends upon the conditions of the cells or DNA at the time of irradiation. 34 refs., 5 figs., 2 tabs.

  10. [Study on the application of pulsed-field gel electrophoresis regarding infection sources identification during an outbreak of Vibrio cholerae in Jiangxi Province].

    PubMed

    Yang, Meng; Diao, Bao-Wei; Cheng, Hui-Jian; Ding, Sheng; Cui, Zhi-Gang; Chen, Fu-Hui; Xu, Xiao-Qian; Kan, Biao; Yuan, Hui

    2007-09-01

    To study the correlation between Vibrio cholerae strains isolated from natural enviroment and fishery products and the source of infection during V. cholerae outbreaks. Cholera toxin gene was detected by polymerase chain reaction (PCR) amplification. Pulsed-field gel electrophoresis (PFGE) was used to subtype the isolates. Results of PFGE were analyzed and clustered by BioNumerics software (Version 4.0). During the outbreaks, a total number of thirty O139 V. cholerae related serogroups were collected from patients, carriers, sewage and fishery products were identified and proved to be toxigenic. They could be clustered into four PFGE patterns when digested by Not I. These two V. cholerae outbreaks were caused by the same source of infection because of the following reasons: (1) PFGE patterns of the predominant strains isolated from two outbreaks were identical; (2) they were identical to the PFGE patterns of the strains isolated from the green turtle and rana catesbiana which were bought from the same wholesale store. Green turtle and rana catesbiana that were contaminated by toxigenic O139 V. cholerae strains seemed to be the source of infection causing the O139 V. cholerae outbreaks in Jiangxi province. Rapid laboratory surveillance and epidemiologic investigation were important in identifying the source of infection during the outbreaks of V. cholera.

  11. Thermally induced phase changes, lateral heterogeneity of the mantle, continental roots, and deep slab anomalies

    NASA Technical Reports Server (NTRS)

    Anderson, Don L.

    1987-01-01

    Factors which influence the lateral heterogeneity in density and seismic velocity with depth in the upper earth mantle are discussed. It is emphasized that most of the increases in density and seismic velocity with depth are caused by pressure-induced solid-solid phase changes in the high-density high-velocity phases of mineral assemblage, due to variations in temperature. In particular, the ilmenite form of MgSiO3 and the gamma-spinel form of Mg2SiO4 have broad stability fields in cold mantle and are not stable in hotter mantle. It is emphasized that the density and velocity anomalies associated with temperature-induced phase changes in mineral assemblage must be taken into account in the thermal models of the slabs; when these effects are accounted for, the geoid and seismic anomalies associated with subducted slabs are consistent with slab confinement to the upper mantle and with layered models of mantle convection.

  12. Synthetic Hydrogen Spectra of Oscillating Prominence Slabs Immersed in the Solar Corona

    NASA Astrophysics Data System (ADS)

    Zapiór, M.; Oliver, R.; Ballester, J. L.; Heinzel, P.

    2016-08-01

    We study the behavior of Hα and Hβ spectral lines and their spectral indicators in an oscillating solar prominence slab surrounded by the solar corona, using an MHD model combined with a 1D radiative transfer code taken in the line of sight perpendicular to the slab. We calculate the time variation of the Doppler shift, half-width, and maximum intensity of the Hα and Hβ spectral lines for different modes of oscillation. We find a non-sinusoidal time dependence of some spectral parameters with time. Because Hα and Hβ spectral indicators have different behavior for different modes, caused by differing optical depths of formation and different plasma parameter variations in time and along the slab, they may be used for prominence seismology, especially to derive the internal velocity field in prominences.

  13. Beam quality active control of a slab MOPA solid state laser with combined deformable mirrors

    NASA Astrophysics Data System (ADS)

    Xiang, Rujian; Xu, Honglai; Li, Guohui; Wu, Jing; Du, Yinglei; Zhang, Kai

    2017-01-01

    A novel phase aberration correcting method based on combined deformable mirrors (DMs) in a slab MOPA (master oscillator and power amplifier) solid state laser system is proposed and validated experimentally. The adaptive optics(AO) system with combined deformable mirrors composed of a one-dimension (1D) DM with 11 actuators and a two-dimension (2D) DM with 67 valid actuators, has been designed to correct the phase aberrations, which doesn't need the high voltage drivers and has an excellent correcting efficiency of the high order phase aberrations. The experimental results show that the wave front of the slab laser beam is compensated well and the residual wave front is less than 0.08 λ rms. The beam quality of the slab laser in the far field is improved to1.67x DL.

  14. Phase-dependent Kerr nonlinearity of a dielectric slab doped by Λ-type atoms

    NASA Astrophysics Data System (ADS)

    Younessi, B.; Sahrai, M.; Aghbulaghi, R.; Poursamad, J. B.

    2017-10-01

    We investigate the linear and nonlinear dispersion and absorption properties of a weak probe field in a dielectric slab doped with Λ -type atoms. The effect of a relative phase between applied fields on linear and nonlinear dispersion, absorption and Kerr nonlinearity is discussed. It is demonstrated that the system is phase sensitive when spontaneously generated coherence and an incoherent pump exist simultaneously. The effect of the coupling field intensity on the Kerr nonlinearity is also presented.

  15. DNA double-strand breaks in mammalian cells exposed to gamma-rays and very heavy ions. Fragment-size distributions determined by pulsed-field gel electrophoresis.

    PubMed

    Kraxenberger, F; Weber, K J; Friedl, A A; Eckardt-Schupp, F; Flentje, M; Quicken, P; Kellerer, A M

    1998-07-01

    The spatial distribution of DNA double-strand breaks (DSB) was assessed after treatment of mammalian cells (V79) with densely ionizing radiation. Cells were exposed to beams of heavy charged particles (calcium ions: 6.9 MeV/u, 2.1.10(3) keV/microm; uranium ions: 9.0 MeV/u, 1.4.10(4) keV/microm) at the linear accelerator UNILAC of GSI, Darmstadt. DNA was isolated in agarose plugs and subjected to pulsed-field gel electrophoresis under conditions that separated DNA fragments of size 50 kbp to 5 Mbp. The measured fragment distributions were compared to those obtained after gamma-irradiation and were analyzed by means of a convolution and a deconvolution technique. In contrast to the finding for gamma-radiation, the distributions produced by heavy ions do not correspond to the random breakage model. Their marked overdispersion and the observed excess of short fragments reflect spatial clustering of DSB that extends over large regions of the DNA, up to several mega base pairs (Mbp). At fluences of 0.75 and 1.5/microm2, calcium ions produce nearly the same shape of fragment spectrum, merely with a difference in the amount of DNA entering the gel; this suggests that the DNA is fragmented by individual calcium ions. At a fluence of 0.8/microm2 uranium ions produce a profile that is shifted to smaller fragment sizes in comparison to the profile obtained at a fluence of 0.4/microm2; this suggests cumulative action of two separate ions in the formation of fragments. These observations are not consistent with the expectation that the uranium ions, with their much larger LET, should be more likely to produce single particle action than the calcium ions. However, a consideration of the greater lateral extension of the tracks of the faster uranium ions explains the observed differences; it suggests that the DNA is closely coiled so that even DNA locations several Mbp apart are usually not separated by less than 0. 1 or 0.2 microm.

  16. Reflection mode two-dimensional photonic-crystal-slab-waveguide-based micropressure sensor

    NASA Astrophysics Data System (ADS)

    Wang, Yi; Bakhtazad, Aref; Sabarinathan, Jayshri

    2011-08-01

    Photonic crystals (PhCs) have recently been the focus for the developing micro- and nano-optical sensors, due to its capability to control and manipulate light on planar devices. This paper presents a novel design of micro-optical pressure sensor based on 2-dimensional PhC slab suspended on Si substrate. A line defect was introduced to the PhC slab to guide and reflect light with frequency in the photonic bandgap in the plane of the slab. The structure, with certain surface treatment, can be used in miro-scale pressure catheters in heart ablation surgeries and other biomedical applications. The working principle of the device is to modify light reflection in the PhC line defect waveguide by moving a substrate vertically in the evanescent field of the PhC waveguide. Evanescent field coupling is the critical step that affects light transmission and reflection. High resolution electron-beam lithography and isotropic wet etching have been used to realize the device on the top layer of a Si-On-Insulator (SOI) wafer. The PhC slab is released by isotropic wet etch of the berried oxide layer. The output reflection spectrum of the device under different pressure conditions is simulated using 3-dimensional finite difference time domain (FDTD) method. The result showed that when the PhC slab is close enough to the substrate (less than 400 nm), the reflected light intensity decreases sharply when the substrate moves towards the PhC slab. Mechanical response of the sensor is also studied.

  17. Slab buckling and its effect on the distributions and focal mechanisms of deep-focus earthquakes

    NASA Astrophysics Data System (ADS)

    Myhill, R.

    2013-02-01

    This integrated study of deep earthquake locations and focal mechanisms investigates the relationship between the shape of subducting slabs and seismic behaviour in Wadati-Benioff zones. High quality earthquake locations are used to map the shapes of subducting slabs which have reached the upper-lower mantle boundary. The resulting slab models reveal the presence of large slab folds in the mantle transition zone. The distributions and focal mechanisms of deep earthquakes are analysed to determine whether these folds have a role in governing Wadati-Benioff zone seismicity. Bands or lineations of dense seismicity are associated with the hinge zones of identified folds. The focal mechanisms of earthquakes within these bands reveal that the mapped fold hinges are commonly perpendicular to the directions of maximum coseismic extension and compression. The hinges plunge at a variety of angles, resulting in systematic deviations from the downdip stress field expected within planar slabs. Slab synforms are typified by earthquake focal mechanisms indicating in-plane compression (e.g. Izu-Bonin, Tonga), while antiforms have earthquake focal mechanisms indicating in-plane extension (e.g. Solomons) or a mixture of in-plane compression and extension (e.g. Tonga). Slab buckling explains both the clustering of earthquakes and the observed focal mechanism orientations within fold hinges. The localization of strain within buckle zones results in several of the peaks observed in regional earthquake depth distributions. During buckling, the directions of maximum shortening and extension are expected to be perpendicular to the fold hinges, in agreement with deep earthquake moment tensors. Displacement of the minimum-strain surface away from the centre of each seismogenic zone can explain the predominance of in-plane compression within synforms and in-plane extension within antiforms. More complex local variation in focal mechanism orientations in the Tonga slab can be explained by a

  18. Causes for the Onset and Stability of Flat Slabs and Associated Overriding Plate Deformation Inferred from Numerical Thermo-Mechanical Models

    NASA Astrophysics Data System (ADS)

    Kanda, R. V. S.; Lowry, A. R.; Buiter, S. J.; Ellis, S. M.

    2015-12-01

    Flat slab subduction comprises only ~10% of the present-day subduction systems. We systematically explore flat-slab subduction and over-riding plate deformation due to previously recognized factors (including a weak mantle wedge, a buoyant oceanic plateau/ridge, slab-age, presence of thick cratonic upper plate), as well as additional factors not considered before (transient plate-velocity variations, and the presence of stagnant slabs at the mantle transition zone). We use a visco-elasto-plastic code, SULEC (Buiter & Ellis, 2012), restrict ourselves to 2D models, and ignore phase transformations. We model a 6000 km by 1500 km domain with 1-10 km variable grid spacing using up-to-date laboratory-derived constitutive laws, and explore the effects of: (a) lateral/vertical structure of the crust and lithosphere (e.g., continental lithosphere with/without a craton; oceanic lithosphere with thickness governed by plate cooling, and a harzburgite layer); (b) a true free upper-surface to predict surface topography; and (c) only far-field (boundary) velocities driving plates, with trench-velocity depending on over-riding plate deformation and slab pull. As in previous studies, we find that positive trench-retreat velocity and weak integrated slab-strength (as measured by differential stress) are necessary, but not sufficient, conditions for flat-slab subduction. While mantle-wedge suction associated with the presence of a craton does promote flat slab subduction, models without a craton also produce flat-slabs when (a) trench-retreat velocities are large and (b) either the slab is positively (structurally or thermally) buoyant or there is an underlying slab at the mantle transition zone. In our models, the duration of flat slab subduction depends on overall slab buoyancy. Younger oceanic lithosphere, esp. if it contains a plateau/ridge, provides a longer-lasting flat-slab (~ 10 Myr or longer, e.g., central Mexico), while older slabs with oceanic ridge/plateau (e.g., Peru

  19. Slab stagnation and buckling in the mantle transition zone: Rheology, phase transition, trench migration, and seismic structure

    NASA Astrophysics Data System (ADS)

    Bina, Craig; Cizkova, Hana

    2014-05-01

    observations better than a flat-lying slab (Zhang et al., 2013). Earthquake hypocentral distributions and focal mechanisms may provide clearer insights into slab buckling, as they appear to vary systematically across regions of slab stagnation (Fukao and Obayashi, 2013). Stress fields computed from our dynamical models may help to illuminate such observations. References: Bina, C.R., and H. Kawakatsu, Buoyancy, bending, and seismic visibility in deep slab stagnation, Phys. Earth Planet. Inter., 183, 330-340, 2010. Čížková, H., and C.R. Bina, Effects of mantle and subduction-interface rheologies on slab stagnation and trench rollback, Earth Planet. Sci. Lett., 379, 95-103, 2013. Fukao, Y., and M. Obayashi, Deepest hypocentral distributions associated with stagnant slabs and penetrated slabs, Fall Meeting Abstracts, AGU, DI14A-01, 2013. Li, Z.-H., and N.M. Ribe, Dynamics of free subduction from 3-D boundary element modeling, J. Geophys. Res., 117, B06408. Matthews, D.C., L. Zheng, and R.G. Gordon, Do trenches advance? Fall Meeting Abstracts, AGU, T43D-2682, 2013. Zhang, Y., Y. Wang, Y. Wu, C. Bina, Z. Jin, and S. Dong, Phase transitions of harzburgite and buckled slab under eastern China, Geochem. Geophys. Geosys., 14, 1182-1199, 2013.

  20. Enhancement of specific absorption rate in lossy dielectric objects using a slab of left-handed material

    NASA Astrophysics Data System (ADS)

    Zhao, Lei; Cui, Tie Jun

    2005-12-01

    An enhancement of the specific absorption rate (SAR) inside a lossy dielectric object has been investigated theoretically based on a slab of left-handed medium (LHM). In order to make an accurate analysis of SAR distribution, a proper Green’s function involved in the LHM slab is proposed, from which an integral equation for the electric field inside the dielectric object is derived. Such an integral equation has been solved accurately and efficiently using the conjugate gradient method and the fast Fourier transform. We have made a lot of numerical experiments on the SAR distributions inside the dielectric object excited by a line source with and without the LHM slab. Numerical experiments show that SAR can be enhanced tremendously when the LHM slab is involved due to the proper usage of strong surface waves, which will be helpful in the potential biomedical applications for hyperthermia. The physical insight for such a phenomenon has also been discussed.

  1. Enhancement of specific absorption rate in lossy dielectric objects using a slab of left-handed material.

    PubMed

    Zhao, Lei; Cui, Tie Jun

    2005-12-01

    An enhancement of the specific absorption rate (SAR) inside a lossy dielectric object has been investigated theoretically based on a slab of left-handed medium (LHM). In order to make an accurate analysis of SAR distribution, a proper Green's function involved in the LHM slab is proposed, from which an integral equation for the electric field inside the dielectric object is derived. Such an integral equation has been solved accurately and efficiently using the conjugate gradient method and the fast Fourier transform. We have made a lot of numerical experiments on the SAR distributions inside the dielectric object excited by a line source with and without the LHM slab. Numerical experiments show that SAR can be enhanced tremendously when the LHM slab is involved due to the proper usage of strong surface waves, which will be helpful in the potential biomedical applications for hyperthermia. The physical insight for such a phenomenon has also been discussed.

  2. Reconciling surface plate motions with rapid three-dimensional mantle flow around a slab edge.

    PubMed

    Jadamec, Margarete A; Billen, Magali I

    2010-05-20

    The direction of tectonic plate motion at the Earth's surface and the flow field of the mantle inferred from seismic anisotropy are well correlated globally, suggesting large-scale coupling between the mantle and the surface plates. The fit is typically poor at subduction zones, however, where regional observations of seismic anisotropy suggest that the direction of mantle flow is not parallel to and may be several times faster than plate motions. Here we present three-dimensional numerical models of buoyancy-driven deformation with realistic slab geometry for the Alaska subduction-transform system and use them to determine the origin of this regional decoupling of flow. We find that near a subduction zone edge, mantle flow velocities can have magnitudes of more than ten times the surface plate motions, whereas surface plate velocities are consistent with plate motions and the complex mantle flow field is consistent with observations from seismic anisotropy. The seismic anisotropy observations constrain the shape of the eastern slab edge and require non-Newtonian mantle rheology. The incorporation of the non-Newtonian viscosity results in mantle viscosities of 10(17) to 10(18) Pa s in regions of high strain rate (10(-12) s(-1)), and this low viscosity enables the mantle flow field to decouple partially from the motion of the surface plates. These results imply local rapid transport of geochemical signatures through subduction zones and that the internal deformation of slabs decreases the slab-pull force available to drive subducting plates.

  3. A small (58-nm) attached sphere perturbs the sieving of 40-80-kilobase DNA in 0.2-2.5% agarose gels: analysis of bacteriophage T7 capsid-DNA complexes by use of pulsed field electrophoresis.

    PubMed

    Serwer, P; Hayes, S J; Moreno, E T; Park, C Y

    1992-09-15

    Although the icosahedral bacteriophage T7 capsid has a diameter (58 nm) that is 234-fold smaller than the length of the linear, double-stranded T7 DNA, binding of a T7 capsid to T7 DNA is found here to have dramatic effects on the migration of the DNA during both pulsed field agarose gel electrophoresis (PFGE; the field inversion mode is used) and constant field agarose gel electrophoresis (CFGE). For these studies, capsid-DNA complexes were obtained by expelling DNA from mature bacteriophage T7; this procedure yields DNA with capsids bound at a variable position on the DNA. When subjected to CFGE at 2-6 V/cm in 0.20-2.5% agarose gels, capsid-DNA complexes arrest at the electrophoretic origin. Progressively lowering the electrical potential gradient to 0.5 V/cm results in migration; most complexes form a single band. The elevated electrical potential gradient (3 V/cm) induced arrest of capsid-DNA complexes is reversed when PFGE is used instead of CFGE. For some conditions of PFGE, the mobility of capsid-DNA complexes is a function of the position of the capsid on the DNA. During either CFGE (0.5 V/cm) or PFGE, capsid-DNA complexes increasingly separate from capsid-free DNA as the percentage of agarose increases. During these studies, capsid-DNA complexes are identified by electron microscopy of enzymatically-digested pieces of agarose gel; this is apparently the first successful electron microscopy of DNA from an agarose gel.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. The effect of subducting slabs in global shear wave tomography

    NASA Astrophysics Data System (ADS)

    Lu, Chang; Grand, Stephen P.

    2016-05-01

    Subducting slabs create strong short wavelength seismic anomalies in the upper mantle where much of Earth's seismicity is located. As such, they have the potential to bias longer wavelength seismic tomography models. To evaluate the effect of subducting slabs in global tomography, we performed a series of inversions using a global synthetic shear wave traveltime data set for a theoretical slab model based on predicted thermal anomalies within slabs. The spectral element method was applied to predict the traveltime anomalies produced by the 3-D slab model for paths corresponding to our current data used in actual tomography models. Inversion tests have been conducted first using the raw traveltime anomalies to check how well the slabs can be imaged in global tomography without the effect of earthquake mislocation. Our results indicate that most of the slabs can be identified in the inversion result but with smoothed and reduced amplitude. The recovery of the total mass anomaly in slab regions is about 88 per cent. We then performed another inversion test to investigate the effect of mislocation caused by subducting slabs. We found that source mislocation largely removes slab signal and significantly degrades the imaging of subducting slabs-potentially reducing the recovery of mass anomalies in slab regions to only 41 per cent. We tested two source relocation procedures-an iterative relocation inversion and joint relocation inversion. Both methods partially recover the true source locations and improve the inversion results, but the joint inversion method worked significantly better than the iterative method. In all of our inversion tests, the amplitudes of artefact structures in the lower mantle caused by the incorrect imaging of slabs (up to ˜0.5 per cent S velocity anomalies) are comparable to some large-scale lower-mantle heterogeneities seen in global tomography studies. Based on our inversion tests, we suggest including a-priori subducting slabs in the

  5. Subduction zone earthquakes and stress in slabs

    NASA Technical Reports Server (NTRS)

    Vassiliou, M. S.; Hager, B. H.

    1988-01-01

    Simple viscous fluid models of subducting slabs are used to explain observations of the distribution of earthquakes as a function of depth and the orientation of stress axes of deep (greater than 300 km) and intermediate (70-300 km) earthquakes. Results suggest the following features in the distribution of earthquakes with depth: (1) an exponential decrease from shallow depths down to 250 to 300 km, (2) a minimum near 250 to 300 km, and (3) a deep peak below 300 km. Many shallow subducting slabs show only the first characteristic, while deeper extending regions tend to show all three features, with the deep peak varying in position and intensity. These data, combined with the results on the stress orientations of various-depth earthquakes, are consistent with the existence of a barrier of some sort at 670-km depth and a uniform viscosity mantle above this barrier.

  6. Slab photonic crystals with dimer colloid bases

    SciTech Connect

    Riley, Erin K.; Liddell Watson, Chekesha M.

    2014-06-14

    The photonic band gap properties for centered rectangular monolayers of asymmetric dimers are reported. Colloids in suspension have been organized into the phase under confinement. The theoretical model is inspired by the range of asymmetric dimers synthesized via seeded emulsion polymerization and explores, in particular, the band structures as a function of degree of lobe symmetry and degree of lobe fusion. These parameters are varied incrementally from spheres to lobe-tangent dimers over morphologies yielding physically realizable particles. The work addresses the relative scarcity of theoretical studies on photonic crystal slabs with vertical variation that is consistent with colloidal self-assembly. Odd, even and polarization independent gaps in the guided modes are determined for direct slab structures. A wide range of lobe symmetry and degree of lobe fusion combinations having Brillouin zones with moderate to high isotropy support gaps between odd mode band indices 3-4 and even mode band indices 1-2 and 2-3.

  7. Subduction zone earthquakes and stress in slabs

    NASA Technical Reports Server (NTRS)

    Vassiliou, M. S.; Hager, B. H.

    1988-01-01

    Simple viscous fluid models of subducting slabs are used to explain observations of the distribution of earthquakes as a function of depth and the orientation of stress axes of deep (greater than 300 km) and intermediate (70-300 km) earthquakes. Results suggest the following features in the distribution of earthquakes with depth: (1) an exponential decrease from shallow depths down to 250 to 300 km, (2) a minimum near 250 to 300 km, and (3) a deep peak below 300 km. Many shallow subducting slabs show only the first characteristic, while deeper extending regions tend to show all three features, with the deep peak varying in position and intensity. These data, combined with the results on the stress orientations of various-depth earthquakes, are consistent with the existence of a barrier of some sort at 670-km depth and a uniform viscosity mantle above this barrier.

  8. Neogene retro-arc basaltic magmatism in southern Patagonia: are there alternatives to teared slabs and slab window models?

    NASA Astrophysics Data System (ADS)

    Roggero, Davide; Müntener, Othmar; Pilet, Sébastien

    2017-04-01

    The Neogene retro-arc magmatism in southern Patagonia (South America) has been associated to the melting of OIB type asthenospheric mantle, related to the opening of a slab window and/or slab tearing beneath South America as a consequence of the subduction of the Chile ridge. This retro-arc magmatism produced alkaline to subalkaline transitional lavas - magmas with geochemical characterictics intermediate between alkaline and calc-alkaline geochemistry - yet the spatial and temporal evolution of the geochemical signatures are largely unconstrained. Here we use detailed field investigations and new geochemical data from the retro-arc lavas of the Sierra Baguales and Cerro del Fraile-Tres Lagos area (southern Patagonia), that are located about 100-150 km east of the active volcanic arc, to test potential relationships between the geochemical signature and the dynamics of the south-Patagonian subduction system in the last 20 million years. New geochemical analysis show that basaltic lavas and mafic rocks from Sierra Baguales are primitive magmas with subalkaline to high-K calc-alkaline signature. Positive Pb and negative Nb anomalies are hallmarks of calc-alkaline magmas, but the enriched incompatible trace element patterns differ from typical arc volcanoes. In contrast, the similar spatially located basaltic lavas from Cerro del Fraile and Tres Lagos have an alkaline and OIB-like signature, suggesting a mantle source without subduction-related component. Studies have demonstrated that melting of amphibole-rich metasomatic veins or cumulates located in the lithospheric mantle are a viable mechanism for the origin of intra-plate alkaline volcanism (e.g. Pilet et al. 2008). Likewise melting amphibole-rich lithologies in the sub-arc mantle might produce the trace element signatures of arc-related transitional to alkaline magmas and are directly related to the metasomatic process induced by mobile components that form the amphibole-rich rocks. Amphibole-rich cumulates

  9. Convection in Slab and Spheroidal Geometries

    NASA Technical Reports Server (NTRS)

    Porter, David H.; Woodward, Paul R.; Jacobs, Michael L.

    2000-01-01

    Three-dimensional numerical simulations of compressible turbulent thermally driven convection, in both slab and spheroidal geometries, are reviewed and analyzed in terms of velocity spectra and mixing-length theory. The same ideal gas model is used in both geometries, and resulting flows are compared. The piecewise-parabolic method (PPM), with either thermal conductivity or photospheric boundary conditions, is used to solve the fluid equations of motion. Fluid motions in both geometries exhibit a Kolmogorov-like k(sup -5/3) range in their velocity spectra. The longest wavelength modes are energetically dominant in both geometries, typically leading to one convection cell dominating the flow. In spheroidal geometry, a dipolar flow dominates the largest scale convective motions. Downflows are intensely turbulent and up drafts are relatively laminar in both geometries. In slab geometry, correlations between temperature and velocity fluctuations, which lead to the enthalpy flux, are fairly independent of depth. In spheroidal geometry this same correlation increases linearly with radius over the inner 70 percent by radius, in which the local pressure scale heights are a sizable fraction of the radius. The effects from the impenetrable boundary conditions in the slab geometry models are confused with the effects from non-local convection. In spheroidal geometry nonlocal effects, due to coherent plumes, are seen as far as several pressure scale heights from the lower boundary and are clearly distinguishable from boundary effects.

  10. Fast Waves in Smooth Coronal Slab

    NASA Astrophysics Data System (ADS)

    Lopin, I.; Nagorny, I.

    2015-03-01

    This work investigates the effect of transverse density structuring in coronal slab-like waveguides on the properties of fast waves. We generalized previous results obtained for the exponential and Epstein profiles to the case of an arbitrary transverse density distribution. The criteria are given to determine the possible (trapped or leaky) wave regime, depending on the type of density profile function. In particular, there are plasma slabs with transverse density structuring that support pure trapped fast waves for all wavelengths. Their phase speed is nearly equal to the external Alfvén speed for the typical parameters of coronal loops. Our findings are obtained on the basis of Kneser’s oscillation theorem. To confirm the results, we analytically solved the wave equation evaluated at the cutoff point and the original wave equation for particular cases of transverse density distribution. We also used the WKB method and obtained approximate solutions of the wave equation at the cutoff point for an arbitrary transverse density profile. The analytic results were supplemented by numerical solutions of the obtained dispersion relations. The observed high-quality quasi-periodic pulsations of flaring loops are interpreted in terms of the trapped fundamental fast-sausage mode in a slab-like coronal waveguide.

  11. Convection in Slab and Spheroidal Geometries

    NASA Technical Reports Server (NTRS)

    Porter, David H.; Woodward, Paul R.; Jacobs, Michael L.

    2000-01-01

    Three-dimensional numerical simulations of compressible turbulent thermally driven convection, in both slab and spheroidal geometries, are reviewed and analyzed in terms of velocity spectra and mixing-length theory. The same ideal gas model is used in both geometries, and resulting flows are compared. The piecewise-parabolic method (PPM), with either thermal conductivity or photospheric boundary conditions, is used to solve the fluid equations of motion. Fluid motions in both geometries exhibit a Kolmogorov-like k(sup -5/3) range in their velocity spectra. The longest wavelength modes are energetically dominant in both geometries, typically leading to one convection cell dominating the flow. In spheroidal geometry, a dipolar flow dominates the largest scale convective motions. Downflows are intensely turbulent and up drafts are relatively laminar in both geometries. In slab geometry, correlations between temperature and velocity fluctuations, which lead to the enthalpy flux, are fairly independent of depth. In spheroidal geometry this same correlation increases linearly with radius over the inner 70 percent by radius, in which the local pressure scale heights are a sizable fraction of the radius. The effects from the impenetrable boundary conditions in the slab geometry models are confused with the effects from non-local convection. In spheroidal geometry nonlocal effects, due to coherent plumes, are seen as far as several pressure scale heights from the lower boundary and are clearly distinguishable from boundary effects.

  12. Implementing slab solar water heating system

    NASA Astrophysics Data System (ADS)

    Raveendran, S. K.; Shen, C. Q.

    2015-08-01

    Water heating contributes a significant part of energy consumption in typical household. One of the most employed technologies today that helps in reducing the energy consumption of water heating would be conventional solar water heating system. However, this system is expensive and less affordable by most family. The main objective of this project is to design and implement an alternative type of solar water heating system that utilize only passive solar energy which is known as slab solar water heating system. Slab solar water heating system is a system that heat up cold water using the solar radiance from the sun. The unique part of this system is that it does not require any form of electricity in order to operate. Solar radiance is converted into heat energy through convection method and cold water will be heated up by using conduction method [1]. The design of this system is governed by the criteria of low implementation cost and energy saving. Selection of material in the construction of a slab solar water heating system is important as it will directly affect the efficiency and performance of the system. A prototype has been built to realize the idea and it had been proven that this system was able to provide sufficient hot water supply for typical household usage at any given time.

  13. Temporal evolution of crack propagation propensity in snow in relation to slab and weak layer properties

    NASA Astrophysics Data System (ADS)

    Schweizer, Jürg; Reuter, Benjamin; van Herwijnen, Alec; Richter, Bettina; Gaume, Johan

    2016-11-01

    If a weak snow layer below a cohesive slab is present in the snow cover, unstable snow conditions can prevail for days or even weeks. We monitored the temporal evolution of a weak layer of faceted crystals as well as the overlaying slab layers at the location of an automatic weather station in the Steintälli field site above Davos (Eastern Swiss Alps). We focussed on the crack propagation propensity and performed propagation saw tests (PSTs) on 7 sampling days during a 2-month period from early January to early March 2015. Based on video images taken during the tests we determined the mechanical properties of the slab and the weak layer and compared them to the results derived from concurrently performed measurements of penetration resistance using the snow micro-penetrometer (SMP). The critical cut length, observed in PSTs, increased overall during the measurement period. The increase was not steady and the lowest values of critical cut length were observed around the middle of the measurement period. The relevant mechanical properties, the slab effective elastic modulus and the weak layer specific fracture, overall increased as well. However, the changes with time differed, suggesting that the critical cut length cannot be assessed by simply monitoring a single mechanical property such as slab load, slab modulus or weak layer specific fracture energy. Instead, crack propagation propensity is the result of a complex interplay between the mechanical properties of the slab and the weak layer. We then compared our field observations to newly developed metrics of snow instability related to either failure initiation or crack propagation propensity. The metrics were either derived from the SMP signal or calculated from simulated snow stratigraphy (SNOWPACK). They partially reproduced the observed temporal evolution of critical cut length and instability test scores. Whereas our unique dataset of quantitative measures of snow instability provides new insights into the

  14. A two- and three-dimensional numerical modelling benchmark of slab detachment

    NASA Astrophysics Data System (ADS)

    Thieulot, Cedric; Glerum, Anne; Hillebrand, Bram; Schmalholz, Stefan; Spakman, Wim; Torsvik, Trond

    2014-05-01

    Subduction is likely to be the most studied phenomenon in Numerical Geodynamics. Over the past 20 years, hundreds of publications have focused on its various aspects (influence of the rheology and thermal state of the plates, slab-mantle coupling, roll-back, mantle wedge evolution, buoyancy changes due to phase change, ...) and results were obtained with a variety of codes. Slab detachment has recently received some attention (e.g. Duretz, 2012) but remains a field worth exploring due to its profound influence on dynamic topography, mantle flow and subsequent stress state of the plates, and is believed to have occured in the Zagros, Carpathians and beneath eastern Anatolia, to name only a few regions. Following the work of Schmalholz (2011), we propose a two- and three-dimensional numerical benchmark of slab detachment. The geometry is simple: a power-law T-shaped plate including an already subducted slab overlies the mantle whose viscosity is either linear or power-law. Boundary conditions are free-slip on the top and the bottom of the domain, and no-slip on the sides. When the system evolves in time, the slab stretches out vertically and shows buoyancy-driven necking, until it finally detaches. The benchmark is subdivided into several sub-experiments with gradually increase in complexity (free surface, coupling of the rheology with temperature, ...). An array of objective measurements is recorded throughout the simulation such as the width of the necked slab over time and the exact time of detachment. The experiments will be run in two-dimensions and repeated in three-dimensional, the latter case being designed so as to allow both poloidal and toroidal flow. We show results obtained with a multitude of Finite Element and Finite Difference codes, using either compositional fields, level sets or tracers to track the compositions. A good agreement is found for most of the measurements in the two-dimensional case, and preliminary three-dimensional measurements will

  15. Pulsed-field gel electrophoresis and multi locus sequence typing for characterizing genotype variability of Yersinia ruckeri isolated from farmed fish in France.

    PubMed

    Calvez, Ségolène; Fournel, Catherine; Douet, Diane-Gaëlle; Daniel, Patrick

    2015-06-23

    Yersinia ruckeri is a pathogen that has an impact on aquaculture worldwide. The disease caused by this bacterial species, yersiniosis or redmouth disease, generates substantial economic losses due to the associated mortality and veterinary costs. For predicting outbreaks and improving control strategies, it is important to characterize the population structure of the bacteria. The phenotypic and genetic homogeneities described previously indicate a clonal population structure as observed in other fish bacteria. In this study, the pulsed-field gel electrophoresis (PFGE) and multi locus sequence typing (MLST) methods were used to describe a population of isolates from outbreaks on French fish farms. For the PFGE analysis, two enzymes (NotI and AscI) were used separately and together. Results from combining the enzymes showed the great homogeneity of the outbreak population with a similarity > 80.0% but a high variability within the cluster (cut-off value = 80.0%) with a total of 43 pulsotypes described and an index of diversity = 0.93. The dominant pulsotypes described with NotI (PtN4 and PtN7) have already been described in other European countries (Finland, Germany, Denmark, Spain and Italy). The MLST approach showed two dominant sequence types (ST31 and ST36), an epidemic structure of the French Y. ruckeri population and a preferentially clonal evolution for rainbow trout isolates. Our results point to multiple types of selection pressure on the Y. ruckeri population attributable to geographical origin, ecological niche specialization and movements of farmed fish.

  16. Diversity of pulsed-field gel electrophoresis pulsotypes, serovars, and antibiotic resistance among Salmonella isolates from wild amphibians and reptiles in the California Central Coast.

    PubMed

    Gorski, Lisa; Jay-Russell, Michele T; Liang, Anita S; Walker, Samarpita; Bengson, Yingjia; Govoni, Jessica; Mandrell, Robert E

    2013-06-01

    A survey of cold-blooded vertebrates and associated surface waters in a produce-growing region on the Central California Coast was done between May and September 2011 to determine the diversity of Salmonella. Samples from 460 amphibians and reptiles and 119 water samples were collected and cultured for Salmonella. Animals sampled were frogs (n=331), lizards (n=59), newts (n=5), salamanders (n=6), snakes (n=39), and toads (n=20). Salmonella was isolated from 37 individual animals, including frogs, lizards, snakes, and toads. Snakes were the most likely to contain Salmonella, with 59% testing positive followed by 15.3% of lizards, 5% of toads, and 1.2% of frogs. Fifteen water samples (12.6%) were positive. Twenty-two different serovars were identified, and the majority of isolates were S. enterica subsp. IIIb, with subsp. I, II, and IIIa also found. The serovar isolated most frequently was S. enterica subsp. IIIb 16:z₁₀:e,n,x,z₁₅, from snakes and frogs in five different locations. S. enterica subsp. I serovar Typhimurium and the monophasic I 6,8:d:- were isolated from water, and subspecies I Duisburg and its variants were found in animals and water. Some samples contained more than one type of Salmonella. Analysis of pulsed-field gel electrophoresis pulsotypes indicated that some strains persisted in animals and water collected from the same location. Sixty-six isolates displayed antibiotic resistance, with 27 isolates resistant to more than one antibiotic, including a subspecies IIIb isolate from snake having resistance to five different antibiotics. Twenty-three isolates were resistant to more than one class of antibiotic, and six isolates were resistant to three classes. While these subspecies of IIIa and IIIb cause fewer instances of human illness, they may serve as reservoirs of antibiotic resistance, determinants in the environment, and be sources of contamination of leafy greens associated with product recalls.

  17. Pulsed-field gel electrophoresis, conventional, and molecular serotyping of Listeria monocytogenes from food proficiency testing trials toward an harmonization of subtyping at European level.

    PubMed

    Félix, Benjamin; Dao, Trinh Tam; Grout, Joël; Lombard, Bertrand; Asséré, Adrien; Brisabois, Anne; Roussel, Sophie

    2012-08-01

    The European Union Reference Laboratory for Listeria monocytogenes (EURL for L. monocytogenes) coordinates a European network of 29 National Reference Laboratories (NRLs). Depending on a national decision, NRLs undertake food, environmental, and veterinary L. monocytogenes strain surveillance in their respective countries. In the framework of the PulseNet Europe network, two pulsed-field gel electrophoresis (PFGE) subtyping proficiency testing (PT) trials were carried out in 2003 and 2006. The obtained data showed that PFGE profiles can be compared and exchanged between laboratories. However, no further PT trial had been performed since 2006. In this context, two PT trials were organized by the EURL to evaluate the ability of NRLs to perform conventional serotyping, molecular serotyping and PFGE subtyping. Eleven well-characterized isolates of L. monocytogenes were used: six and nine isolates were tested in 2009 and 2010, respectively. Three isolates were repeated between the two studies. In the 2010 panel, a strain was tested in duplicate, and two strains were related to the same epidemiological group. The strains were analyzed blind in different laboratories (17 in 2009 and 25 in 2010) using (1) their own in-house method for serotyping methods and (2) standardized protocols based on the PulseNet protocol for PFGE. For conventional serotyping, 86.0% in 2009 and 91.0% in 2010 of the serotypes obtained were in agreement with the EURL data. For molecular serotyping, 93.5% of the results in 2009 and 95.2% in 2010 matched the EURL data. For PFGE, 68.9% in 2009 and 81.7% of the combined AscI/ApaI profiles were indistinguishable from the EURL reference profiles. The variations observed could be attributed to slight standardization defaults or, in a few cases, to a failure in DNA extraction. These PT trials provided a valuable opportunity to improve the subtyping ability of NRLs and facilitate exchanges of subtyping data in the future.

  18. Genetic Diversity of Clostridium sporogenes PA 3679 Isolates Obtained from Different Sources as Resolved by Pulsed-Field Gel Electrophoresis and High-Throughput Sequencing.

    PubMed

    Schill, Kristin M; Wang, Yun; Butler, Robert R; Pombert, Jean-François; Reddy, N Rukma; Skinner, Guy E; Larkin, John W

    2015-10-30

    Clostridium sporogenes PA 3679 is a nonpathogenic, nontoxic model organism for proteolytic Clostridium botulinum used in the validation of conventional thermal food processes due to its ability to produce highly heat-resistant endospores. Because of its public safety importance, the uncertain taxonomic classification and genetic diversity of PA 3679 are concerns. Therefore, isolates of C. sporogenes PA 3679 were obtained from various sources and characterized using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. The phylogenetic relatedness and genetic variability were assessed based on 16S rRNA gene sequencing and whole-genome single nucleotide polymorphism (SNP) analysis. All C. sporogenes PA 3679 isolates were categorized into two clades (clade I containing ATCC 7955 NCA3679 isolates 1961-2, 1990, and 2007 and clade II containing PA 3679 isolates NFL, UW, FDA, and Campbell and ATCC 7955 NCA3679 isolate 1961-4). The 16S maximum likelihood (ML) tree clustered both clades within proteolytic C. botulinum strains, with clade I forming a distinct cluster with other C. sporogenes non-PA 3679 strains. SNP analysis revealed that clade I isolates were more similar to the genomic reference PA 3679 (NCTC8594) genome (GenBank accession number AGAH00000000.1) than clade II isolates were. The genomic reference C. sporogenes PA 3679 (NCTC8594) genome and clade I C. sporogenes isolates were genetically distinct from those obtained from other sources (University of Wisconsin, National Food Laboratory, U.S. Food and Drug Administration, and Campbell's Soup Company). Thermal destruction studies revealed that clade I isolates were more sensitive to high temperature than clade II isolates were. Considering the widespread use of C. sporogenes PA 3679 and its genetic information in numerous studies, the accurate identification and genetic characterization of C. sporogenes PA 3679 are of critical importance.

  19. Genetic Diversity of Clostridium sporogenes PA 3679 Isolates Obtained from Different Sources as Resolved by Pulsed-Field Gel Electrophoresis and High-Throughput Sequencing

    PubMed Central

    Wang, Yun; Butler, Robert R.; Reddy, N. Rukma; Skinner, Guy E.; Larkin, John W.

    2015-01-01

    Clostridium sporogenes PA 3679 is a nonpathogenic, nontoxic model organism for proteolytic Clostridium botulinum used in the validation of conventional thermal food processes due to its ability to produce highly heat-resistant endospores. Because of its public safety importance, the uncertain taxonomic classification and genetic diversity of PA 3679 are concerns. Therefore, isolates of C. sporogenes PA 3679 were obtained from various sources and characterized using pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. The phylogenetic relatedness and genetic variability were assessed based on 16S rRNA gene sequencing and whole-genome single nucleotide polymorphism (SNP) analysis. All C. sporogenes PA 3679 isolates were categorized into two clades (clade I containing ATCC 7955 NCA3679 isolates 1961-2, 1990, and 2007 and clade II containing PA 3679 isolates NFL, UW, FDA, and Campbell and ATCC 7955 NCA3679 isolate 1961-4). The 16S maximum likelihood (ML) tree clustered both clades within proteolytic C. botulinum strains, with clade I forming a distinct cluster with other C. sporogenes non-PA 3679 strains. SNP analysis revealed that clade I isolates were more similar to the genomic reference PA 3679 (NCTC8594) genome (GenBank accession number AGAH00000000.1) than clade II isolates were. The genomic reference C. sporogenes PA 3679 (NCTC8594) genome and clade I C. sporogenes isolates were genetically distinct from those obtained from other sources (University of Wisconsin, National Food Laboratory, U.S. Food and Drug Administration, and Campbell's Soup Company). Thermal destruction studies revealed that clade I isolates were more sensitive to high temperature than clade II isolates were. Considering the widespread use of C. sporogenes PA 3679 and its genetic information in numerous studies, the accurate identification and genetic characterization of C. sporogenes PA 3679 are of critical importance. PMID:26519392

  20. High-resolution hydrodynamic chromatographic separation of large DNA using narrow, bare open capillaries: a rapid and economical alternative technology to pulsed-field gel electrophoresis?

    PubMed

    Liu, Lei; Veerappan, Vijaykumar; Pu, Qiaosheng; Cheng, Chang; Wang, Xiayan; Lu, Liping; Allen, Randy D; Guo, Guangsheng

    2014-01-07

    A high-resolution, rapid, and economical hydrodynamic chromatographic (HDC) method for large DNA separations in free solution was developed using narrow (5 μm diameter), bare open capillaries. Size-based separation was achieved in a chromatographic format with larger DNA molecules being eluting faster than smaller ones. Lambda DNA Mono Cut Mix was baseline-separated with the percentage resolutions generally less than 9.0% for all DNA fragments (1.5 to 48.5 kbp) tested in this work. High efficiencies were achieved for large DNA from this chromatographic technique, and the number of theoretical plates reached 3.6 × 10(5) plates for the longest (48.5 kbp) and 3.7 × 10(5) plates for the shortest (1.5 kbp) fragments. HDC parameters and performances were also discussed. The method was further applied for fractionating large DNA fragments from real-world samples (SacII digested Arabidopsis plant bacterial artificial chromosome (BAC) DNA and PmeI digested Rice BAC DNA) to demonstrate its feasibility for BAC DNA finger printing. Rapid separation of PmeI digested Rice BAC DNA covering from 0.44 to 119.041 kbp was achieved in less than 26 min. All DNA fragments of these samples were baseline separated in narrow bare open capillaries, while the smallest fragment (0.44 kbp) was missing in pulsed-field gel electrophoresis (PFGE) separation mode. It is demonstrated that narrow bare open capillary chromatography can realize a rapid separation for a wide size range of DNA mixtures that contain both small and large DNA fragments in a single run.

  1. Analysis of ventilator-associated pneumonia infection route by genome macrorestriction-pulsed-field gel electrophoresis and its prevention with combined nursing strategies.

    PubMed

    Wang, Xiaodong; Wang, Junping; Li, Jing; Wang, Jing

    2014-12-01

    The aim of the present study was to explore the infection route of ventilator-associated pneumonia (VAP) and assess the effectiveness of a combined nursing strategy to prevent VAP in intensive care units. Bacteria from the gastric juice and drainage from the hypolarynx and lower respiratory tracts of patients with VAP were analyzed using genome macrorestriction-pulsed-field gel electrophoresis (GM-PFGE). A total of 124 patients with tracheal intubation were placed in the intervention group and were treated with a combined nursing strategy, comprising mosapride (gastric motility stimulant) administration and semi-reclining positioning. A total of 112 intubated patients were placed in the control group and received routine nursing care. The incidence rate of VAP, days of ventilation and mortality rate of patients were compared between the two groups. The GM-PFGE fingerprinting results of three strains of Pseudomonas aeruginosa from the gastric juice, subglottic secretion drainage and drainage of the lower respiratory tract in patients with VAP were similar across groups. The number of days spent on a ventilator by patients in the intervention group (7.37±5.32 days) was lower compared with that by patients in the control group (12.34±4.98 days) (P<0.05). The incidence rate of VAP was reduced from 40.81 to 21.25% following intervention with the combined nursing strategy (P<0.05); furthermore, the mortality rate of intubated patients in the intervention group was 29.46%, a significant reduction compared with the 41.94% mortality rate observed in the control group (P<0.05). Gastroesophageal reflux (GER) was confirmed as one of the infection routes for VAP. The combined nursing strategy of gastric motility stimulant administration and the adoption of a semi-reclining position was effective in preventing VAP by reducing the occurrence of GER.

  2. Speciation and strain-typing of Staphylococcus agnetis and Staphylococcus hyicus isolated from bovine milk using a novel multiplex PCR and pulsed-field gel electrophoresis.

    PubMed

    Adkins, P R F; Middleton, J R; Calcutt, M J; Stewart, G C; Fox, L K

    2017-03-22

    Staphylococcus hyicus and Staphylococcus agnetis are two coagulase variable staphylococcal species that can be isolated from bovine milk and are difficult to differentiate. The objectives of this study were to characterize isolates of bovine milk origin from a collection that had previously been characterized as coagulase positive S. hyicus based on phenotypic speciation methods and to develop a PCR-based method for differentiating S. hyicus, S. agnetis, and S. aureus. Isolates (n = 62) were selected from a previous study in which milk samples were collected from cows on 15 dairy herds. Isolates were coagulase tested and speciated using housekeeping gene sequencing. A multiplex PCR to differentiate S. hyicus, S. agnetis, and S. aureus was developed. Pulsed-field gel electrophoresis was conducted to strain type isolates. Based on gene sequencing, 44/62 of the isolates were determined to be either S. agnetis (n = 43) or S. hyicus (n = 1). Overall, 88% (37/42) of coagulase positive S. agnetis isolates were found to be coagulase positive at 4 hours. Herd-level prevalence of coagulase positive S. agnetis ranged from 0 to 2.17%. Strain-typing identified 23 different strains. Six strains were identified more than once and from multiple cows within the herd. Three strains were isolated from cows at more than one time point, with 41-264 days between samplings. These data suggest that S. agnetis is likely more prevalent on dairy farms than S. hyicus Also, some S. agnetis isolates in this study appeared to be contagious and associated with persistent infections.

  3. A comparison of non-typhoidal Salmonella from humans and food animals using pulsed-field gel electrophoresis and antimicrobial susceptibility patterns.

    PubMed

    Sandt, Carol H; Fedorka-Cray, Paula J; Tewari, Deepanker; Ostroff, Stephen; Joyce, Kevin; M'ikanatha, Nkuchia M

    2013-01-01

    Salmonellosis is one of the most important foodborne diseases affecting humans. To characterize the relationship between Salmonella causing human infections and their food animal reservoirs, we compared pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility patterns of non-typhoidal Salmonella isolated from ill humans in Pennsylvania and from food animals before retail. Human clinical isolates were received from 2005 through 2011 during routine public health operations in Pennsylvania. Isolates from cattle, chickens, swine and turkeys were recovered during the same period from federally inspected slaughter and processing facilities in the northeastern United States. We found that subtyping Salmonella isolates by PFGE revealed differences in antimicrobial susceptibility patterns and, for human Salmonella, differences in sources and invasiveness that were not evident from serotyping alone. Sixteen of the 20 most common human Salmonella PFGE patterns were identified in Salmonella recovered from food animals. The most common human Salmonella PFGE pattern, Enteritidis pattern JEGX01.0004 (JEGX01.0003ARS), was associated with more cases of invasive salmonellosis than all other patterns. In food animals, this pattern was almost exclusively (99%) found in Salmonella recovered from chickens and was present in poultry meat in every year of the study. Enteritidis pattern JEGX01.0004 (JEGX01.0003ARS) was associated with susceptibility to all antimicrobial agents tested in 94.7% of human and 97.2% of food animal Salmonella isolates. In contrast, multidrug resistance (resistance to three or more classes of antimicrobial agents) was observed in five PFGE patterns. Typhimurium patterns JPXX01.0003 (JPXX01.0003 ARS) and JPXX01.0018 (JPXX01.0002 ARS), considered together, were associated with resistance to five or more classes of antimicrobial agents: ampicillin, chloramphenicol, streptomycin, sulfonamides and tetracycline (ACSSuT), in 92% of human and 80% of food

  4. Genotyping of Francisella tularensis Strains by Pulsed-Field Gel Electrophoresis, Amplified Fragment Length Polymorphism Fingerprinting, and 16S rRNA Gene Sequencing

    PubMed Central

    García Del Blanco, N.; Dobson, M. E.; Vela, A. I.; De La Puente, V. A.; Gutiérrez, C. B.; Hadfield, T. L.; Kuhnert, P.; Frey, J.; Domínguez, L.; Rodríguez Ferri, E. F.

    2002-01-01

    We evaluated three molecular methods for identification of Francisella strains: pulsed-field gel electrophoresis (PFGE), amplified fragment length polymorphism (AFLP) analysis, and 16S rRNA gene sequencing. The analysis was performed with 54 Francisella tularensis subsp. holarctica, 5 F. tularensis subsp. tularensis, 2 F. tularensis subsp. novicida, and 1 F. philomiragia strains. On the basis of the combination of results obtained by PFGE with the restriction enzymes XhoI and BamHI, PFGE revealed seven pulsotypes, which allowed us to discriminate the strains to the subspecies level and which even allowed us to discriminate among some isolates of F. tularensis subsp. holarctica. The AFLP analysis technique produced some degree of discrimination among F. tularensis subsp. holarctica strains (one primary cluster with three major subclusters and minor variations within subclusters) when EcoRI-C and MseI-A, EcoRI-T and MseI-T, EcoRI-A and MseI-C, and EcoRI-0 and MseI-CA were used as primers. The degree of similarity among the strains was about 94%. The percent similarities of the AFLP profiles of this subspecies compared to those of F. tularensis subsp. tularensis, F. tularensis subsp. novicida, and F. philomiragia were less than 90%, about 72%, and less than 24%, respectively, thus permitting easy differentiation of this subspecies. 16S rRNA gene sequencing revealed 100% similarity for all F. tularensis subsp. holarctica isolates compared in this study. These results suggest that although limited genetic heterogeneity among F. tularensis subsp. holarctica isolates was observed, PFGE and AFLP analysis appear to be promising tools for the diagnosis of infections caused by different subspecies of F. tularensis and suitable techniques for the differentiation of individual strains. PMID:12149360

  5. Pulsed-field gel electrophoresis proficiency testing trials: toward European harmonization of the typing of food and clinical strains of Listeria monocytogenes.

    PubMed

    Félix, Benjamin; Niskanen, Taina; Vingadassalon, Noémie; Dao, Trinh Tam; Asséré, Adrien; Lombard, Bertrand; Brisabois, Anne; Roussel, Sophie

    2013-10-01

    The European Union Reference Laboratory for Listeria monocytogenes (EURL for Lm) coordinates a European network of 35 National Reference Laboratories (NRLs), most of which perform food, environmental, and veterinary Lm strain surveillance in their respective countries. The EURL activities resulted in the recent creation of a database (EURL Lm DB). Typing and related epidemiological data submitted to the EURL Lm DB will be collected and shared by all the NRLs. For a given NRL, the only criterion required in order to submit pulsed-field gel electrophoresis (PFGE) profiles to the database was the successful participation with at least one EURL PFGE and PFGE profile interpretation Proficiency Testing (PT) trial. In this context, the EURL organized a PT trial in 2012 to evaluate the NRL's ability to perform PFGE and profile interpretation. A total of 18 NRLs took part in this study. Upon request from the Food- and Waterborne Diseases and Zoonoses Programme of the European Centre for Disease Prevention and Control, 10 National Public Health Reference Laboratories (NPHLs) also took part in this PT trial. Of the 28 participating laboratories, 16 obtained results classified as "good" or "satisfactory." These 16 laboratories included 10 NRLs (56%) and 6 NPHLs (60%). Of the 22 NRLs and NHPLs that participated in the part of the PT trial related to PFGE profile interpretation, 11 laboratories obtained good results. These 11 laboratories included eight NRLs, which therefore can now submit profiles to the EURL Lm DB. This PT trial provided a valuable opportunity to facilitate and to stimulate the sharing of reproducible PFGE profiles between human and food reference laboratories.

  6. Comparison of automated repetitive-sequence-based polymerase chain reaction and spa typing versus pulsed-field gel electrophoresis for molecular typing of methicillin-resistant Staphylococcus aureus.

    PubMed

    Church, Deirdre L; Chow, Barbara L; Lloyd, Tracie; Gregson, Daniel B

    2011-01-01

    Automated repetitive polymerase chain reaction (PCR) (DiversiLab, bioMérieux, St. Laurent, Quebec, Canada) and single locus sequence typing of the Staphylococcus protein A (spa) gene with spa-type assignment by StaphType RIDOM software were compared to pulsed-field gel electrophoresis (PFGE) as the "gold standard" method for methicillin-resistant Staphylococcus aureus (MRSA) typing. Fifty-four MRSA isolates were typed by all methods: 10 of known PFGE CMRSA type and 44 clinical isolates. Correct assignment of CMRSA type or cluster occurred for 47 of 54 (87%) of the isolates when using a rep-PCR similarity index (SI) of ≥95%. Rep-PCR gave 7 discordant results [CMRSA1 (3), CMRSA2 (1), CMRSA4 (1), and CMRSA10 (2)], and some CMRSA clusters were not distinguished (CMRSA10/5/9, CMRSA 7/8, and CMRSA3/6). Several spa types occurred within a single PFGE or repetitive PCR types among the 19 different spa types found. spa type t037 was shared by CMRSA3 and CMRSA6 strains, and CMRSA9 and most CMRSA10 strains shared spa type t008. Time to results for PFGE, repetitive PCR, and spa typing was 3-4 days, 24 h, and 48 h, respectively. The annual costs of using spa or repetitive PCR were 2.4× and 1.9× higher, respectively, than PFGE but routine use of spa typing would lower annual labor costs by 0.10 full-time equivalents compared to PFGE. Repetitive PCR is a good method for rapid outbreak screening, but MRSA isolates that share the same repetitive PCR or PFGE patterns can be distinguished by spa typing. Copyright © 2011 Elsevier Inc. All rights reserved.

  7. Comparison of the DiversiLab repetitive element PCR system with spa typing and pulsed-field gel electrophoresis for clonal characterization of methicillin-resistant Staphylococcus aureus.

    PubMed

    Babouee, B; Frei, R; Schultheiss, E; Widmer, A F; Goldenberger, D

    2011-04-01

    The emergence of methicillin-resistant Staphylococcus aureus (MRSA) has become an increasing problem worldwide in recent decades. Molecular typing methods have been developed to identify clonality of strains and monitor spread of MRSA. We compared a new commercially available DiversiLab (DL) repetitive element PCR system with spa typing, spa clonal cluster analysis, and pulsed-field gel electrophoresis (PFGE) in terms of discriminatory power and concordance. A collection of 106 well-defined MRSA strains from our hospital was analyzed, isolated between 1994 and 2006. In addition, we analyzed 6 USA300 strains collected in our institution. DL typing separated the 106 MRSA isolates in 10 distinct clusters and 8 singleton patterns. Clustering analysis into spa clonal complexes resulted in 3 clusters: spa-CC 067/548, spa-CC 008, and spa-CC 012. The discriminatory powers (Simpson's index of diversity) were 0.982, 0.950, 0.846, and 0.757 for PFGE, spa typing, DL typing, and spa clonal clustering, respectively. DL typing and spa clonal clustering showed the highest concordance, calculated by adjusted Rand's coefficients. The 6 USA300 isolates grouped homogeneously into distinct PFGE and DL clusters, and all belonged to spa type t008 and spa-CC 008. Among the three methods, DL proved to be rapid and easy to perform. DL typing qualifies for initial screening during outbreak investigation. However, compared to PFGE and spa typing, DL typing has limited discriminatory power and therefore should be complemented by more discriminative methods in isolates that share identical DL patterns.

  8. Comparison of the DiversiLab Repetitive Element PCR System with spa Typing and Pulsed-Field Gel Electrophoresis for Clonal Characterization of Methicillin-Resistant Staphylococcus aureus▿

    PubMed Central

    Babouee, B.; Frei, R.; Schultheiss, E.; Widmer, A. F.; Goldenberger, D.

    2011-01-01

    The emergence of methicillin-resistant Staphylococcus aureus (MRSA) has become an increasing problem worldwide in recent decades. Molecular typing methods have been developed to identify clonality of strains and monitor spread of MRSA. We compared a new commercially available DiversiLab (DL) repetitive element PCR system with spa typing, spa clonal cluster analysis, and pulsed-field gel electrophoresis (PFGE) in terms of discriminatory power and concordance. A collection of 106 well-defined MRSA strains from our hospital was analyzed, isolated between 1994 and 2006. In addition, we analyzed 6 USA300 strains collected in our institution. DL typing separated the 106 MRSA isolates in 10 distinct clusters and 8 singleton patterns. Clustering analysis into spa clonal complexes resulted in 3 clusters: spa-CC 067/548, spa-CC 008, and spa-CC 012. The discriminatory powers (Simpson's index of diversity) were 0.982, 0.950, 0.846, and 0.757 for PFGE, spa typing, DL typing, and spa clonal clustering, respectively. DL typing and spa clonal clustering showed the highest concordance, calculated by adjusted Rand's coefficients. The 6 USA300 isolates grouped homogeneously into distinct PFGE and DL clusters, and all belonged to spa type t008 and spa-CC 008. Among the three methods, DL proved to be rapid and easy to perform. DL typing qualifies for initial screening during outbreak investigation. However, compared to PFGE and spa typing, DL typing has limited discriminatory power and therefore should be complemented by more discriminative methods in isolates that share identical DL patterns. PMID:21307215

  9. A Comparison of Non-Typhoidal Salmonella from Humans and Food Animals Using Pulsed-Field Gel Electrophoresis and Antimicrobial Susceptibility Patterns

    PubMed Central

    Sandt, Carol H.; Fedorka-Cray, Paula J.; Tewari, Deepanker; Ostroff, Stephen; Joyce, Kevin; M’ikanatha, Nkuchia M.

    2013-01-01

    Salmonellosis is one of the most important foodborne diseases affecting humans. To characterize the relationship between Salmonella causing human infections and their food animal reservoirs, we compared pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility patterns of non-typhoidal Salmonella isolated from ill humans in Pennsylvania and from food animals before retail. Human clinical isolates were received from 2005 through 2011 during routine public health operations in Pennsylvania. Isolates from cattle, chickens, swine and turkeys were recovered during the same period from federally inspected slaughter and processing facilities in the northeastern United States. We found that subtyping Salmonella isolates by PFGE revealed differences in antimicrobial susceptibility patterns and, for human Salmonella, differences in sources and invasiveness that were not evident from serotyping alone. Sixteen of the 20 most common human Salmonella PFGE patterns were identified in Salmonella recovered from food animals. The most common human Salmonella PFGE pattern, Enteritidis pattern JEGX01.0004 (JEGX01.0003ARS), was associated with more cases of invasive salmonellosis than all other patterns. In food animals, this pattern was almost exclusively (99%) found in Salmonella recovered from chickens and was present in poultry meat in every year of the study. Enteritidis pattern JEGX01.0004 (JEGX01.0003ARS) was associated with susceptibility to all antimicrobial agents tested in 94.7% of human and 97.2% of food animal Salmonella isolates. In contrast, multidrug resistance (resistance to three or more classes of antimicrobial agents) was observed in five PFGE patterns. Typhimurium patterns JPXX01.0003 (JPXX01.0003 ARS) and JPXX01.0018 (JPXX01.0002 ARS), considered together, were associated with resistance to five or more classes of antimicrobial agents: ampicillin, chloramphenicol, streptomycin, sulfonamides and tetracycline (ACSSuT), in 92% of human and 80% of food

  10. Dynamic buckling of subducting slabs reconciles geological and geophysical observations

    NASA Astrophysics Data System (ADS)

    Lee, Changyeol; King, Scott D.

    2011-12-01

    Ever since the early days of the development of plate tectonic theory, subduction zones have been engrained in geological thinking as the place where steady, linear slabs descend into the mantle at a constant, uniform dip angle beneath volcanic arcs. However, growing evidence from geological and geophysical observations as well as analog and numerical modeling indicates that subducting slabs buckle in a time-dependent manner, in contrast to the steady-state, linear cartoons that dominate the literature. To evaluate the implication of time-dependent slab buckling of geological events, we conduct a series of 2-D numerical dynamic/kinematic subduction experiments by varying the viscosity increase across the 660 km discontinuity and the strength of the subducting slab. Our results show that slab buckling is a universal figure in all the experiments when rate of the trench migration ( Vtrench) is relatively slow ( Vtrench| < 2 cm/a) and viscosity increases across the 660 km discontinuity are greater than a factor of 30. Slab buckling is expressed as alternate shallowing and steepening dip of the subducting slab (from ~ 40 to ~ 100°) which is correlated with increasing and decreasing convergent rate of the incoming oceanic plate toward the trench. Further, the slab buckling in our experiments is consistent with the previously developed scaling laws for slab buckling; using reasonable parameters from subducted slabs the buckling amplitude and period are ~ 400 km and ~ 25 Myr, respectively. The slab buckling behavior in our experiments explains a variety of puzzling geological and geophysical observations. First, the period of slab buckling is consistent with short periodic variations (~ 25 Myr) in the motions of the oceanic plates that are anchored by subduction zones. Second, the scattered distributions of slab dips (from ~ 20 to ~ 90°) in the upper mantle are snapshots of time-dependent slab dip. Third, the current compressional and extensional stress environments in

  11. Mechanical characterization of active polymer gels

    NASA Astrophysics Data System (ADS)

    Marra, Steven P.; Ramesh, Kaliat T.; Douglas, Andrew S.

    2000-06-01

    Ionic polymer gels shrink and swell in response to certain environmental stimuli, such as the application of an electric field or a change in the pH level of the surroundings. This ability to achieve large, reversible deformations with no external mechanical loading has generated much interest in the use of these gels as actuators and artificial muscles. This work focuses on developing a means of characterizing the mechanical properties of such ionic gels and describing how these properties evolve as the gel actuates. A thermodynamically consistent finite elastic constitutive model of an active polymer gel is developed to describe this behavior. The mechanical properties of the gel are characterized by a strain-energy function and the model utilizes an evolving internal variable to describe the actuation state. Applications of the mode to poly(vinyl alcohol)-poly (acrylic acid) gels are presented.

  12. Evolution and diversity of subduction zones controlled by slab width.

    PubMed

    Schellart, W P; Freeman, J; Stegman, D R; Moresi, L; May, D

    2007-03-15

    Subducting slabs provide the main driving force for plate motion and flow in the Earth's mantle, and geodynamic, seismic and geochemical studies offer insight into slab dynamics and subduction-induced flow. Most previous geodynamic studies treat subduction zones as either infinite in trench-parallel extent (that is, two-dimensional) or finite in width but fixed in space. Subduction zones and their associated slabs are, however, limited in lateral extent (250-7,400 km) and their three-dimensional geometry evolves over time. Here we show that slab width controls two first-order features of plate tectonics-the curvature of subduction zones and their tendency to retreat backwards with time. Using three-dimensional numerical simulations of free subduction, we show that trench migration rate is inversely related to slab width and depends on proximity to a lateral slab edge. These results are consistent with retreat velocities observed globally, with maximum velocities (6-16 cm yr(-1)) only observed close to slab edges (<1,200 km), whereas far from edges (>2,000 km) retreat velocities are always slow (<2.0 cm yr(-1)). Models with narrow slabs (< or =1,500 km) retreat fast and develop a curved geometry, concave towards the mantle wedge side. Models with slabs intermediate in width ( approximately 2,000-3,000 km) are sublinear and retreat more slowly. Models with wide slabs (> or =4,000 km) are nearly stationary in the centre and develop a convex geometry, whereas trench retreat increases towards concave-shaped edges. Additionally, we identify periods (5-10 Myr) of slow trench advance at the centre of wide slabs. Such wide-slab behaviour may explain mountain building in the central Andes, as being a consequence of its tectonic setting, far from slab edges.

  13. Viscous Dissipation and Criticality of Subducting Slabs

    NASA Astrophysics Data System (ADS)

    Riedel, Mike; Karato, Shun; Yuen, Dave

    2016-04-01

    Rheology of subducting lithosphere appears to be complicated. In the shallow part, deformation is largely accomodated by brittle failure, whereas at greater depth, at higher confining pressures, ductile creep is expected to control slab strength. The amount of viscous dissipation ΔQ during subduction at greater depth, as constrained by experimental rock mechanics, can be estimated on the basis of a simple bending moment equation [1,2] 2ɛ˙0(z) ∫ +h/2 2 M (z) = h ṡ -h/2 4μ(y,z)y dy , (1) for a complex multi-phase rheology in the mantle transition zone, including the effects of a metastable phase transition as well as the pressure, temperature, grain-size and stress dependency of the relevant creep mechanisms; μ is here the effective viscosity and ɛ˙0(z) is a (reference) strain rate. Numerical analysis shows that the maximum bending moment, Mcrit, that can be sustained by a slab is of the order of 1019 Nm per m according to Mcrit˜=σp ∗h2/4, where σp is the Peierl's stress limit of slab materials and h is the slab thickness. Near Mcrit, the amount of viscous dissipation grows strongly as a consequence of a lattice instability of mantle minerals (dislocation glide in olivine), suggesting that thermo-mechanical instabilities become prone to occur at places where a critical shear-heating rate is exceeded, see figure. This implies that the lithosphere behaves in such cases like a perfectly plastic solid [3]. Recently available detailed data related to deep seismicity [4,5] seems to provide support to our conclusion. It shows, e.g., that thermal shear instabilities, and not transformational faulting, is likely the dominating mechanism for deep-focus earthquakes at the bottom of the transition zone, in accordance with this suggested "deep criticality" model. These new findings are therefore briefly outlined and possible implications are discussed. References [1] Riedel, M. R., Karato, S., Yuen, D. A. Criticality of Subducting Slabs. University of Minnesota

  14. Extensive decarbonation of continuously hydrated subducting slabs

    NASA Astrophysics Data System (ADS)

    Arzilli, Fabio; Burton, Mike; La Spina, Giuseppe; Macpherson,